BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= gi|15645812|ref|NP_207989.1| DNA-directed RNA
polymerase, beta subunit (rpoB) [Helicobacter pylori 26695]
(2890 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-R... 862 0.0
pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus ... 862 0.0
pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase... 704 0.0
pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoen... 702 0.0
pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase... 520 e-148
pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus ... 511 e-145
pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-R... 509 e-144
pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoen... 509 e-144
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.... 220 2e-57
pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex >g... 117 1e-26
pdb|1DBR|A Chain A, Hypoxanthine Guanine Xanthine >gi|27811... 33 0.59
pdb|1FSG|C Chain C, Toxoplasma Gondii Hypoxanthine-Guanine ... 33 0.59
pdb|1QK5|B Chain B, Toxoplasma Gondii Hypoxanthine-Guanine ... 32 1.0
pdb|1J7N|B Chain B, Anthrax Toxin Lethal Factor >gi|1697482... 32 1.3
pdb|1BG3|A Chain A, Rat Brain Hexokinase Type I Complex Wit... 31 1.7
pdb|1GJX|A Chain A, Solution Structure Of The Lipoyl Domain... 31 2.3
pdb|1FDZ|A Chain A, N-Acetylneuraminate Lyase In Complex Wi... 31 2.3
pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v 31 2.3
pdb|1NAL|1 Chain 1, Mol_id: 1; Molecule: N-Acetylneuraminat... 31 2.3
pdb|1XYN| Molecule: Endo-1,4-Beta-Xylanase I; Synonym: Xy... 30 2.9
pdb|1JAD|A Chain A, C-Terminal Domain Of Turkey Plc-Beta >g... 30 2.9
pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant 30 2.9
pdb|1FIY| Three-Dimensional Structure Of Phosphoenolpyruv... 30 3.8
pdb|1DGK|N Chain N, Mutant Monomer Of Recombinant Human Hex... 30 5.0
pdb|1QHA|A Chain A, Human Hexokinase Type I Complexed With ... 30 5.0
pdb|1HKB|A Chain A, Crystal Structure Of Recombinant Human ... 30 5.0
pdb|1CZA|N Chain N, Mutant Monomer Of Recombinant Human Hex... 30 5.0
pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant 30 5.0
pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junct... 29 6.6
pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant 29 6.6
pdb|1DU5|A Chain A, The Crystal Structure Of Zeamatin. >gi|... 29 8.6
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 862 bits (2227), Expect = 0.0
Identities = 476/993 (47%), Positives = 643/993 (63%), Gaps = 88/993 (8%)
Query: 1394 KDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGK 1453
K+ ++ LASPEKI SWSYGEV+KPETINYRTLKPERDGLF +IFGP KDYEC CGK
Sbjct: 3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 1454 YKKPRFKDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMK 1513
YK+ RF + CE+C V +T S VRR+RM HIELATP AHIW+V +PS+I TLL +
Sbjct: 63 YKRQRF-EAKVCERCAVEVTRSIVRRYRMAHIELATPAAHIWFVKDVPSKIATLLDLSAT 121
Query: 1514 DLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFV------- 1566
+LE+VLY+ YIV +P A D V K +L +
Sbjct: 122 ELEQVLYFNKYIVLDPKAAVLD---AVPVEKRQLLTDXXXXXXXXXXXXXXXXXXXXXXX 178
Query: 1567 ---------------AQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLK 1611
A+MG EAI++LL+E+DL L + L EE+K S A++ K KRL+
Sbjct: 179 XXXXXXXXXXXXXIDARMGAEAIQELLKELDLEKLERELLEEMKHP-SRARRAKARKRLE 237
Query: 1612 VVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRL 1671
VV +FL+SGNRPEWM+L +PVLPPDLRP+V +DGG+FA SD+N+LYRR+INRN RLK+L
Sbjct: 238 VVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKL 297
Query: 1672 MELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKG-ANKRPLKSLSEIIKGKQGRFRQN 1730
+ GAPEII+RNEKRMLQEAVD + DNGR + V ++RPL+SL++I+ GKQGRFRQN
Sbjct: 298 LAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQN 357
Query: 1731 LLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMI 1790
LLGKRVD+SGRSVIVVGP LK+ +CGLPK MALELFKP LL K+EE+ +A +K A+RM+
Sbjct: 358 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRML 417
Query: 1791 EQK---SNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFN 1847
E++ +EVW+ L+E+ G VLLNRAPTLH+ IQAF P L++G++IQLHPLVC AFN
Sbjct: 418 ERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFN 477
Query: 1848 ADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKS 1907
ADFDGDQMAVHVPLS A AE ++ MLS+ N+L PASG+ +A PS+D++LGLYY++ +
Sbjct: 478 ADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRK 537
Query: 1908 GVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ------------------------- 1942
KG F++ E + A + E+ ++A I V +
Sbjct: 538 EKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGL 597
Query: 1943 ------------GNIIATSAGRMIIKSILPDFIPTDLWNRPMKKKDI----GVLVDYVHK 1986
G + TS GR++ I+ + + + + + + D+ L D V++
Sbjct: 598 LDLQDTVTTRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQ 657
Query: 1987 VG---GIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQ 2043
G+ TA LD LK GF +T +GI+I ++D + P++KQ+ +E+A ++++I+Q
Sbjct: 658 AFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQA 717
Query: 2044 YDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAQDKEGFNSIYMMADSGARGSAAQIR 2103
Y+ G LTD+ERY+++I WTE +K+++ + ++ FN +Y+MA SGARG+ QIR
Sbjct: 718 YEMGFLTDRERYDQVIQLWTETTEKVTQAVFNNF-EENYPFNPLYVMAQSGARGNPQQIR 776
Query: 2104 QLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTR 2163
QL MRGLM KP G E P+ S+F+EGL VLEYF S+HGARKG ADTAL+TA++GYLTR
Sbjct: 777 QLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTR 836
Query: 2164 KLIDVSQNVKVVSDDCGTHEGIEITDIAVGS-------ELIEPLEERIFGRVLLEDVIDP 2216
KL+DV+ + V DCGT I + + +E ++GRVL +V +
Sbjct: 837 KLVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREV-EA 895
Query: 2217 ITNEIL--LYADTLIDEEGAKKVVEAG-IKSITIRTPVTCKAPKGVCAKCYGLNLGEGKM 2273
+ + Y +L D K EAG ++ + +R+P+TC+ GVC KCYG +L +
Sbjct: 896 LGRRLEEGRYL-SLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARP 954
Query: 2274 SYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTA 2306
GEAVGVVAA+SIGEPGTQLT+RTFH GG A
Sbjct: 955 VSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVA 987
Score = 204 bits (520), Expect = 9e-53
Identities = 111/231 (48%), Positives = 158/231 (68%), Gaps = 4/231 (1%)
Query: 2642 DITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSMDYFVD 2701
DIT GLPRV ELFEAR+PK K A++SE+DG+V + ++ + V S +G S +Y +
Sbjct: 991 DITQGLPRVIELFEARRPKAK--AVISEIDGVVRIEEG-EDRLSVFVES-EGFSKEYKLP 1046
Query: 2702 KGKQILVHADEFVHAGEAMTDGVISSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADK 2761
K ++LV ++V AG+ +T G I H +L G + + +Y+V E+Q+VYR QGV + DK
Sbjct: 1047 KDARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDK 1106
Query: 2762 HIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITR 2821
HIEI+V QML+ V + D GDS+ +EG ++ K + N R+IA P +P+L+G+T+
Sbjct: 1107 HIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTK 1166
Query: 2822 AAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
+A+ + S +SAASFQ TT VLTEA+IA KKD L LKENV+LGR+IP GTG
Sbjct: 1167 SALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1217
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase-
Includes Complete Structure With Side-Chains (Except For
Disordered Regions)-Further Refined From Original
Deposition-Contains Additional Sequence Information
Length = 1265
Score = 862 bits (2227), Expect = 0.0
Identities = 478/994 (48%), Positives = 647/994 (65%), Gaps = 89/994 (8%)
Query: 1394 KDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGK 1453
K+ ++ LASPEKI SWSYGEV+KPETINYRTLKPERDGLF +IFGP KDYEC CGK
Sbjct: 3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 1454 YKKPRFKDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMK 1513
YK+ RF+ CE+CGV +T S VRR+RMGHIELATP AHIW+V +PS+IGTLL +
Sbjct: 63 YKRQRFEG-KVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFAT 121
Query: 1514 DLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFV------- 1566
+LE+VLY+ YIV +P A D V K +L +
Sbjct: 122 ELEQVLYFNKYIVLDPKGAVLDGVP---VEKRQLLTDXXXXXXXXXXXXXXXXXXXXXXX 178
Query: 1567 ---------------AQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLK 1611
A+MG EAI++LL+E+DL L + L EE+K S A++ K KRL+
Sbjct: 179 XXXXXXXXXXXXXIDARMGAEAIQELLKELDLEKLERELLEEMKHP-SRARRAKARKRLE 237
Query: 1612 VVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRL 1671
VV +FL+SGNRPEWM+L +PVLPPDLRP+V +DGG+FA SD+N+LYRR+INRN RLK+L
Sbjct: 238 VVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKL 297
Query: 1672 MELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKG-ANKRPLKSLSEIIKGKQGRFRQN 1730
+ GAPEII+RNEKRMLQEAVD + DNGR + V ++RPL+SL++I+ GKQGRFRQN
Sbjct: 298 LAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQN 357
Query: 1731 LLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMI 1790
LLGKRVD+SGRSVIVVGP LK+ +CGLPK MALELFKP LL K+EE+ +A +K A+RM+
Sbjct: 358 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRML 417
Query: 1791 EQK---SNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFN 1847
E++ +EVW+ L+E+ G VLLNRAPTLH+ IQAF P L++G++IQLHPLVC AFN
Sbjct: 418 ERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFN 477
Query: 1848 ADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKS 1907
ADFDGDQMAVHVPLS A AE ++ MLS+ N+L PASG+ +A PS+D++LGLYY++ +
Sbjct: 478 ADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRK 537
Query: 1908 GVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ------------------------- 1942
KG F++ E + A + E+ ++A I V +
Sbjct: 538 EKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGL 597
Query: 1943 ------------GNIIATSAGRMIIKSILPDFIPTDLWNRPMKKKDI----GVLVDYVHK 1986
G + T+ GR++ I+ + + + + + + D+ L D V++
Sbjct: 598 LDLQDTVTTRYLGRRLETNPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQ 657
Query: 1987 VG---GIGITATFLDNLKTLGFRYATKAGI-SISMEDIITPKDKQKMVEKAKVEVKKIQQ 2042
G+ TA LD LK GF +T +GI +I ++D + P++KQ+ +E+A ++++I+Q
Sbjct: 658 AFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEKQRYLEEADRKLRQIEQ 717
Query: 2043 QYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAQDKEGFNSIYMMADSGARGSAAQI 2102
Y+ G LTD+ERY+++I WTE +K+++ + ++ FN +Y+MA SGARG+ QI
Sbjct: 718 AYEMGFLTDRERYDQVIQLWTETTEKVTQAVFNNF-EENYPFNPLYVMAQSGARGNPQQI 776
Query: 2103 RQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLT 2162
RQL MRGLM KP G E P+ S+F+EGL VLEYF S+HGARKG ADTAL+TA++GYLT
Sbjct: 777 RQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLT 836
Query: 2163 RKLIDVSQNVKVVSDDCGTHEGIEITDIAVGS-------ELIEPLEERIFGRVLLEDVID 2215
RKL+DV+ + V DCGT + I + + +E ++GRVL +V +
Sbjct: 837 RKLVDVAHEIVVREADCGTTKYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREV-E 895
Query: 2216 PITNEIL--LYADTLIDEEGAKKVVEAG-IKSITIRTPVTCKAPKGVCAKCYGLNLGEGK 2272
+ + Y +L D K EAG ++ + +R+P+TC+ GVC KCYG +L +
Sbjct: 896 ALGRRLEEGRYL-SLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMAR 954
Query: 2273 MSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTA 2306
GEAVGVVAA+SIGEPGTQLT+RTFH GG A
Sbjct: 955 PVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVA 988
Score = 203 bits (517), Expect = 2e-52
Identities = 111/231 (48%), Positives = 157/231 (67%), Gaps = 4/231 (1%)
Query: 2642 DITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSMDYFVD 2701
DIT GLPRV ELFEAR+PK K A++SE+DG+V + ++ + V S +G S +Y +
Sbjct: 992 DITQGLPRVIELFEARRPKAK--AVISEIDGVVRIEEG-EDRLSVFVES-EGFSKEYKLP 1047
Query: 2702 KGKQILVHADEFVHAGEAMTDGVISSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADK 2761
K ++LV ++V AG+ +T G I H +L G + + +Y+V E+Q+VYR QGV + DK
Sbjct: 1048 KDARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDK 1107
Query: 2762 HIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITR 2821
HIEI+V QML+ V + D GDS +EG ++ K + N R+IA P +P+L+G+T+
Sbjct: 1108 HIEIVVRQMLKYVEVTDPGDSPLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTK 1167
Query: 2822 AAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
+A+ + S +SAASFQ TT VLTEA+IA KKD L LKENV+LGR+IP GTG
Sbjct: 1168 SALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1218
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
Length = 1524
Score = 704 bits (1818), Expect = 0.0
Identities = 413/934 (44%), Positives = 577/934 (61%), Gaps = 92/934 (9%)
Query: 1529 PGEAAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQ 1588
PG+ D K + Y + + +N+ R E A+MG EAI+ LL+E+DL L +
Sbjct: 417 PGDVLADGGKVKSDV-YGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEK 475
Query: 1589 SLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGK 1648
L EE+K S A++ K KRL+VV +FL+SGNRPEWM+L +PVLPPDLRP+V +DGG+
Sbjct: 476 ELLEEMKHP-SRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGR 534
Query: 1649 FAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKG- 1707
FA SD+N+LYRR+INRN RLK+L+ GAPEII+RNEKRMLQEAVD L DNGR V
Sbjct: 535 FATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNP 594
Query: 1708 ANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFK 1767
+ RPL+SL++I+ GKQGRFRQNLLGKRVD+SGRSVIVVGP LK+ +CGLPK MALELFK
Sbjct: 595 GSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFK 654
Query: 1768 PHLLSKLEERGYATTLKQAKRMIEQK---SNEVWECLQEITEGYPVLLNRAPTLHKQSIQ 1824
P LL K+EE+G A +K A+RM+E++ +EVW+ L+E+ G VLLNRAPTLH+ IQ
Sbjct: 655 PFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQ 714
Query: 1825 AFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPAS 1884
AF P L++G++IQLHPLVC AFNADFDGDQMAVHVPLS A AE ++ MLS+ N+L PAS
Sbjct: 715 AFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPAS 774
Query: 1885 GKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ-- 1942
G+ +A PS+D++LGLYY++ + KG F++ E + A + E+ ++A I+V +
Sbjct: 775 GEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRET 834
Query: 1943 -----------------------------------GNIIATSAGRMIIKSILPDFIPTD- 1966
G + TS GR++ I+ + + +
Sbjct: 835 SVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEK 894
Query: 1967 -LW-----NRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDI 2020
W + P +K + LV G+ TA LD LK GF ++T +GI+I ++D
Sbjct: 895 VAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDA 954
Query: 2021 ITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAQD 2080
+ P++K++ +E+A ++ +I+Q Y+ G LTD+ERY++I+ WTE +K+++ + ++
Sbjct: 955 VIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNF-EE 1013
Query: 2081 KEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNS 2140
FN +Y+MA SGARG+ QIRQL +RGLM KP G E P+ S+F+EGL VLEYF S
Sbjct: 1014 NYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFIS 1073
Query: 2141 THGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEI----TDIAVGSEL 2196
+HGARKG ADTAL+TA++GYLTRKL+DV+ + V DCGT I + D S
Sbjct: 1074 SHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLR 1133
Query: 2197 IE---PLEERIFGRVLLEDV-IDPITNEILLYADTLIDEEGAKKVVEAG-IKSITIRTPV 2251
+ +E ++GRVL +V + + E Y ++ D K EAG I+ + +R+P+
Sbjct: 1134 LRKRADIEAGLYGRVLAREVEVLGVRLEEGRYL-SMDDVHLLIKAAEAGEIQEVPVRSPL 1192
Query: 2252 TCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQD 2311
TC+ GVC KCYG +L + GEAVG+VAAQSIGEPGTQLT+RTFH GG A +
Sbjct: 1193 TCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAAD- 1251
Query: 2312 EREIVASKEGFVRFYNLRTYTNKEGKNIIANRRNASILVVEPKIKAPFDGELRIETVYEE 2371
+G R L + K +I+ DG +RIE E+
Sbjct: 1252 ------ITQGLPRVIELFEARRPKAKAVISE----------------IDGVVRIEETEEK 1289
Query: 2372 VVVSVKNG--------DQEAKFVLRRSDIVKPSE 2397
+ V V++ +EA+ +++ D V+ +
Sbjct: 1290 LSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQ 1323
Score = 205 bits (522), Expect = 5e-53
Identities = 111/231 (48%), Positives = 157/231 (67%), Gaps = 4/231 (1%)
Query: 2642 DITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSMDYFVD 2701
DIT GLPRV ELFEAR+PK K A++SE+DG+V + K + V S +G S +Y +
Sbjct: 1251 DITQGLPRVIELFEARRPKAK--AVISEIDGVVRI-EETEEKLSVFVES-EGFSKEYKLP 1306
Query: 2702 KGKQILVHADEFVHAGEAMTDGVISSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADK 2761
K ++LV ++V AG+ +T G I H +L G + + +Y+V E+Q+VYR QGV + DK
Sbjct: 1307 KEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDK 1366
Query: 2762 HIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITR 2821
HIEI+V QM++ V + D GDS+ +EG ++ K + N R+IA P +P+L+G+T+
Sbjct: 1367 HIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTK 1426
Query: 2822 AAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
+A+ + S +SAASFQ TT VLTEA+IA KKD L LKENV+LGR+IP GTG
Sbjct: 1427 SALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Score = 197 bits (502), Expect = 1e-50
Identities = 96/163 (58%), Positives = 120/163 (72%), Gaps = 4/163 (2%)
Query: 1394 KDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGK 1453
K+ ++ LASPEKI SWSYGEV+KPETINYRTLKPERDGLF +IFGP KDYEC CGK
Sbjct: 3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 1454 YKKPRFKDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMK 1513
YK+ RF+ CE+CGV +T S VRR+RMGHIELATP AHIW+V +PS+IGTLL +
Sbjct: 63 YKRQRFEG-KVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSAT 121
Query: 1514 DLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILNEEQYQNI 1556
+LE+VLY+ YIV +P A + V K +L +E+Y+ +
Sbjct: 122 ELEQVLYFSKYIVLDPKGAILNGVP---VEKRQLLTDEEYREL 161
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1524
Score = 702 bits (1812), Expect = 0.0
Identities = 392/836 (46%), Positives = 545/836 (64%), Gaps = 63/836 (7%)
Query: 1529 PGEAAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQ 1588
PG+ D K + Y + + +N+ R E A+MG EAI++LL+E+DL L +
Sbjct: 417 PGDVLADGGKVKSEI-YGRVEVDLVRNVVRVVESYDIDARMGAEAIQELLKELDLEKLER 475
Query: 1589 SLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGK 1648
L EE+K S A++ K KRL+VV +FL+SGNRPEWM+L +PVLPPDLRP+V +DGG+
Sbjct: 476 ELLEEMKHP-SRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGR 534
Query: 1649 FAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKG- 1707
FA SD+N+LYRR+INRN RLK+L+ GAPEII+RNEKRMLQEAVD + DNGR + V
Sbjct: 535 FATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNP 594
Query: 1708 ANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFK 1767
++RPL+SL++I+ GKQGRFRQNLLGKRVD+SGRSVIVVGP LK+ +CGLPK MALELFK
Sbjct: 595 GSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFK 654
Query: 1768 PHLLSKLEERGYATTLKQAKRMIEQK---SNEVWECLQEITEGYPVLLNRAPTLHKQSIQ 1824
P LL K+EE+ +A +K A+RM+E++ +EVW+ L+E+ G VLLNRAPTLH+ IQ
Sbjct: 655 PFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQ 714
Query: 1825 AFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPAS 1884
AF P L++G++IQLHPLVC AFNADFDGDQMAVHVPLS A AE ++ MLS+ N+L PAS
Sbjct: 715 AFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPAS 774
Query: 1885 GKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ-- 1942
G+ +A PS+D++LGLYY++ + KG F++ E + A + E+ ++A I V +
Sbjct: 775 GEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRET 834
Query: 1943 -----------------------------------GNIIATSAGRMIIKSILPDFIPTDL 1967
G + TS GR++ I+ + + +
Sbjct: 835 SVGRLKFVFANPDEALLAVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEK 894
Query: 1968 WNRPMKKKDI----GVLVDYVHKVG---GIGITATFLDNLKTLGFRYATKAGISISMEDI 2020
+ + + D+ L D V++ G+ TA LD LK GF +T +GI+I ++D
Sbjct: 895 VAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDA 954
Query: 2021 ITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAQD 2080
+ P++KQ+ +E+A ++++I+Q Y+ G LTD+ERY+++I WTE +K+++ + ++
Sbjct: 955 VIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNF-EE 1013
Query: 2081 KEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNS 2140
FN +Y+MA SGARG+ QIRQL MRGLM KP G E P+ S+F+EGL VLEYF S
Sbjct: 1014 NYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFIS 1073
Query: 2141 THGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGS------ 2194
+HGARKG ADTAL+TA++GYLTRKL+DV+ + V DCGT I + +
Sbjct: 1074 SHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLR 1133
Query: 2195 -ELIEPLEERIFGRVLLEDVIDPITNEIL--LYADTLIDEEGAKKVVEAG-IKSITIRTP 2250
+E ++GRVL +V + + + Y +L D K EAG ++ + +R+P
Sbjct: 1134 LRKRSDIESGLYGRVLAREV-EALGRRLEEGRYL-SLEDVHFLIKAAEAGEVREVPVRSP 1191
Query: 2251 VTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTA 2306
+TC+ GVC KCYG +L + GEAVGVVAA+SIGEPGTQLT+RTFH GG A
Sbjct: 1192 LTCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVA 1247
Score = 204 bits (520), Expect = 9e-53
Identities = 111/231 (48%), Positives = 158/231 (68%), Gaps = 4/231 (1%)
Query: 2642 DITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSMDYFVD 2701
DIT GLPRV ELFEAR+PK K A++SE+DG+V + ++ + V S +G S +Y +
Sbjct: 1251 DITQGLPRVIELFEARRPKAK--AVISEIDGVVRIEEG-EDRLSVFVES-EGFSKEYKLP 1306
Query: 2702 KGKQILVHADEFVHAGEAMTDGVISSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADK 2761
K ++LV ++V AG+ +T G I H +L G + + +Y+V E+Q+VYR QGV + DK
Sbjct: 1307 KDARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDK 1366
Query: 2762 HIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITR 2821
HIEI+V QML+ V + D GDS+ +EG ++ K + N R+IA P +P+L+G+T+
Sbjct: 1367 HIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTK 1426
Query: 2822 AAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
+A+ + S +SAASFQ TT VLTEA+IA KKD L LKENV+LGR+IP GTG
Sbjct: 1427 SALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Score = 200 bits (509), Expect = 2e-51
Identities = 97/163 (59%), Positives = 120/163 (73%), Gaps = 4/163 (2%)
Query: 1394 KDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGK 1453
K+ ++ LASPEKI SWSYGEV+KPETINYRTLKPERDGLF +IFGP KDYEC CGK
Sbjct: 3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 1454 YKKPRFKDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMK 1513
YK+ RF+ CE+CGV +T S VRR+RMGHIELATP AHIW+V +PS+IGTLL +
Sbjct: 63 YKRQRFEG-KVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSAT 121
Query: 1514 DLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILNEEQYQNI 1556
+LE+VLY+ YIV +P A D V K +L +E+Y+ +
Sbjct: 122 ELEQVLYFNKYIVLDPKGAVLDGVP---VEKRQLLTDEEYREL 161
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
Length = 1119
Score = 520 bits (1339), Expect = e-148
Identities = 289/613 (47%), Positives = 391/613 (63%), Gaps = 29/613 (4%)
Query: 374 AAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLT 433
A IR+ +++PGDP + A +V L DP RYDL GR K KLG+ + T
Sbjct: 234 ALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGR-TLAR 292
Query: 434 HED-------IITTVKYLMKIKNNQG--KIDDRDHLGNRRIRAVGELLANELHSGLVKMQ 484
ED + T++YL + ++DD DHLGNRRIR VGEL+ ++ GL ++
Sbjct: 293 FEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLA 352
Query: 485 KTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRL 544
+ +++++ + G+ DSL P LVNS+ + + I EFF QLSQF D+TNPLS + HKRR+
Sbjct: 353 RGVRERM--LMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRI 410
Query: 545 SALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAP 604
SALG GGL ++R GF+ RDVH THYGRICP+ETPEG NIGLI +L+ + RV++LGFI P
Sbjct: 411 SALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTP 470
Query: 605 YKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGN-ILGDLIETRVEGEIVLNEKSK 663
Y++VV G V E +Y+TA +ED + IA A+TP+ EGN I + + R +GE V+ +
Sbjct: 471 YRRVVGGVVTDEVVYMTATEEDRYTIAQANTPL--EGNRIAAERVVARRKGEPVIVSPEE 528
Query: 664 VTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIA 723
V MD+S + V +LIPFLEHDDANRALMG+NMQ QAVPL+R+ AP+V TG+E+ +
Sbjct: 529 VEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVV 588
Query: 724 RDSWGAIKANRAGVVEKIDSKNIYILGESKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKV 783
RDS A+ A G V K+D I + E+ + Y L++ R+NQ T+ +Q P V V
Sbjct: 589 RDSLAALYAEEDGEVAKVDGNRIVV---RYEDGRLVEYPLRRFYRSNQGTALDQRPRVVV 645
Query: 784 GDKVGAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSECITKDDIFTSTHI 843
G +V G ++ADGP+ + G LALG+NV VA MP++GYNFEDAIV+SE + K D +TS HI
Sbjct: 646 GQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHI 705
Query: 844 YEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEI 903
E++AR+ K G E T DIP + E AL LDE G+V++G V G ILVG+TS KGE
Sbjct: 706 ERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGES 765
Query: 904 KSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVI--------DVKVFTKKGYEKDARV 955
+ TPEERLLR+IFG+KA V + SL PP G V+ D V K G + RV
Sbjct: 766 EPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRV 825
Query: 956 LSAYEEEKAKLDM 968
Y +K KL +
Sbjct: 826 ---YVAQKRKLQV 835
Score = 301 bits (770), Expect = 9e-82
Identities = 161/301 (53%), Positives = 210/301 (69%), Gaps = 17/301 (5%)
Query: 1070 LPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPL 1129
L GV + V++Y+A KRKL+VGDK+A RHGNKG+V+ I+PV DMP+ DG PVD++LNPL
Sbjct: 815 LKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPL 874
Query: 1130 GVPSRMNIGQILEMHLGLVGKEFGKQIARMLEDKTKD-FAKELRAKMLEIANAINEKDPL 1188
GVPSRMN+GQILE HLGL G G++ + D K+ KEL A+ E+ + +
Sbjct: 875 GVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGF 934
Query: 1189 TIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGR 1248
+ E E+L A+ K+ + +E+ +LF + GK+ LYDGR
Sbjct: 935 GVDKRE----VEVLRRAE------KLGLVTPGKTPEEQLKELF------LQGKVVLYDGR 978
Query: 1249 TGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308
TGE + + VG M+++KL+H+V++K+HARSTGPYSL+T QP+GGKA FGGQRFGEMEVW
Sbjct: 979 TGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVW 1038
Query: 1309 ALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALD 1368
ALEAYGAAHTL+EMLT+KSDDI GR AY AI KGE V E +PE+F VL KELQ+LALD
Sbjct: 1039 ALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALD 1098
Query: 1369 I 1369
+
Sbjct: 1099 V 1099
Score = 108 bits (270), Expect = 8e-24
Identities = 72/212 (33%), Positives = 112/212 (51%), Gaps = 24/212 (11%)
Query: 22 LEVPNLLLLQRDSYDSFLYSKEGKES----GIEKVFKSIFPIQDEHNR---ITLEYAGCE 74
+ +P L +Q +SY L + E GI+ F+ FPI++E + L++
Sbjct: 13 IPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYR 72
Query: 75 FGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMT 134
G+ + E E+ +TY PL +++LI KDT G+ IKE +F+ IPLMT
Sbjct: 73 LGEPPFPQDECREKDLTYQAPLYARLQLI--HKDT------GL--IKEDEVFLGHIPLMT 122
Query: 135 ERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTGQII--PDRGSWLYFEYDS 192
E SFIING +RV+V+Q+HRSPGV F + + Y II P RG W+ E +
Sbjct: 123 EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR----YIASIIPLPKRGPWIDLEVEP 178
Query: 193 KDVLYARINKRRKVPVTILFRAMDYQKQDIIK 224
V+ ++NK RK P+ +L R + Y ++ + +
Sbjct: 179 NGVVSMKVNK-RKFPLVLLLRVLGYDQETLAR 209
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1119
Score = 511 bits (1317), Expect = e-145
Identities = 288/646 (44%), Positives = 408/646 (62%), Gaps = 28/646 (4%)
Query: 341 LGHDA-SIIQSFSADSESLKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKK 399
LG+D ++++ SA + ++ L + A +R+ +++PGDP + A ++
Sbjct: 200 LGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFG 259
Query: 400 LFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHED-------IITTVKYLMKIKNNQG 452
L DP+RYDL GR K KLG+ + T + ED + T++YL +
Sbjct: 260 LLADPKRYDLGEAGRYKAEEKLGVGLSGR-TLVRFEDGEFKDEVFLPTLRYLFALTAGVP 318
Query: 453 --KIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSK 510
++DD DHLGNRRIR VGEL+A++ GL ++ + +++++ + G+ D+L P LVNS+
Sbjct: 319 GHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERM--VMGSPDTLTPAKLVNSR 376
Query: 511 MITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYG 570
+ + + EFF QLSQF D+TNPLS + HKRR+SALG GGL ++R GF+ RDVH THYG
Sbjct: 377 PLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYG 436
Query: 571 RICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHII 630
RICP+ETPEG NIGLI +L+ + RV+ LGFI PY++V +G V E +Y+TA +ED + I
Sbjct: 437 RICPVETPEGANIGLITSLAAYARVDALGFIRTPYRRVKNGVVTEEVVYMTASEEDRYTI 496
Query: 631 APASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDA 690
A A+TP++ + I D + R GE V+ +V MD+S + + +LIPFLEHDDA
Sbjct: 497 AQANTPLEGD-RIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFLEHDDA 555
Query: 691 NRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILG 750
NRALMG+NMQ QAVPL+R+ AP+V TG+E+ + RDS A+ A G V K+D I +
Sbjct: 556 NRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVVKVDGTRIAV-- 613
Query: 751 ESKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVGAGQIIADGPSMDRGELALGKNV 810
E+ + + L++ R+NQ T+F+Q P V+VG +V G ++ADGP+ + G LALG+NV
Sbjct: 614 -RYEDGRLVEHPLRRYARSNQGTAFDQRPRVRVGQRVKKGDLLADGPASEEGFLALGQNV 672
Query: 811 RVAFMPWNGYNFEDAIVVSECITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEE 870
VA MP++GYNFEDAIV+SE + K D +TS HI E++AR+ K G E T DIP + E
Sbjct: 673 LVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEA 732
Query: 871 ALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYC 930
AL LDE GIV++G V G ILVG+TS KGE + +PEERLLR+IFG+KA V + SL
Sbjct: 733 ALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRV 792
Query: 931 PPSLEGTVI--------DVKVFTKKGYEKDARVLSAYEEEKAKLDM 968
PP G V+ D V K G + RV A +K KL +
Sbjct: 793 PPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVA---QKRKLQV 835
Score = 301 bits (770), Expect = 9e-82
Identities = 161/301 (53%), Positives = 213/301 (70%), Gaps = 17/301 (5%)
Query: 1070 LPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPL 1129
L GV + V++++A KRKL+VGDK+A RHGNKG+V+ I+PV DMP+ DG PVD++LNPL
Sbjct: 815 LKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPL 874
Query: 1130 GVPSRMNIGQILEMHLGLVGKEFGKQ-IARMLEDKTKDFAKELRAKMLEIANAINEKDPL 1188
GVPSRMN+GQILE HLGL G G++ I+ + + T+ KEL A+ + + +
Sbjct: 875 GVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGF 934
Query: 1189 TIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGR 1248
+ E +E+L A+ K+ + +E+ +LF+L GK+ LYDGR
Sbjct: 935 GVDKRE----KEVLARAE------KLGLVSPGKSPEEQLKELFDL------GKVVLYDGR 978
Query: 1249 TGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308
TGE + VG M+++KL+H+V++K+HARSTGPYSL+T QP+GGKA FGGQRFGEMEVW
Sbjct: 979 TGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVW 1038
Query: 1309 ALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALD 1368
ALEAYGAAHTL+EMLTIKSDDI GR AY+AI KGE V E +PE+F VL KELQ+LALD
Sbjct: 1039 ALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPESFRVLVKELQALALD 1098
Query: 1369 I 1369
+
Sbjct: 1099 V 1099
Score = 109 bits (272), Expect = 5e-24
Identities = 71/212 (33%), Positives = 113/212 (52%), Gaps = 24/212 (11%)
Query: 22 LEVPNLLLLQRDSYDSFLYSKEGKES----GIEKVFKSIFPIQDEHNR---ITLEYAGCE 74
+ +P L +Q +SY L + E GI+ FK FPI++ + L++
Sbjct: 13 IPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYR 72
Query: 75 FGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMT 134
G ++ E E+ +TY PL +++LI KDT G+ IKE +F+ +PLMT
Sbjct: 73 IGDPPFSQDECREKDLTYQAPLYARLQLI--HKDT------GL--IKEDEVFLGHLPLMT 122
Query: 135 ERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTGQII--PDRGSWLYFEYDS 192
E SFIING +RV+V+Q+HRSPGV F + + Y II P RG W+ E ++
Sbjct: 123 EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR----YIASIIPLPKRGPWIDLEVEA 178
Query: 193 KDVLYARINKRRKVPVTILFRAMDYQKQDIIK 224
V+ ++NK RK P+ +L R + Y ++ +++
Sbjct: 179 SGVVTMKVNK-RKFPLVLLLRVLGYDQETLVR 209
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 509 bits (1311), Expect = e-144
Identities = 288/646 (44%), Positives = 406/646 (62%), Gaps = 29/646 (4%)
Query: 341 LGHDA-SIIQSFSADSESLKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKK 399
LG+D ++++ SA + ++ L + A +R+ +++PGDP + A ++
Sbjct: 200 LGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFG 259
Query: 400 LFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHED-------IITTVKYLMKIKNNQG 452
L DP+RYDL GR K KLG+ + T + ED + T++YL +
Sbjct: 260 LLADPKRYDLGEAGRYKAEEKLGVGLSGR-TLVRFEDGEFKDEVFLPTLRYLFALTAGVP 318
Query: 453 --KIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSK 510
++DD DHLGNRRIR VGEL+A++ GL ++ + +++++ + G+ D+L P LVNS+
Sbjct: 319 GHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERM--VMGSPDTLTPAKLVNSR 376
Query: 511 MITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYG 570
+ + + EFF QLSQF D+TNPLS + HKRR+SALG GGL ++R GF+ RDVH THYG
Sbjct: 377 PLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYG 436
Query: 571 RICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHII 630
RICP+ETPEG NIGLI +L+ + RV+ LGFI PY++V +G V E +Y+TA +ED + I
Sbjct: 437 RICPVETPEGANIGLITSLAAYARVDALGFIRTPYRRVKNGVVTEEVVYMTASEEDRYTI 496
Query: 631 APASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDA 690
A A+TP++ + I D + R GE V+ +V MD+S + + +LIPFLEHDDA
Sbjct: 497 AQANTPLEGD-RIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFLEHDDA 555
Query: 691 NRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILG 750
NRALMG+NMQ QAVPL+R+ AP+V TG+E+ + RDS A+ A G V K+D I +
Sbjct: 556 NRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVVKVDGTRIAVRY 615
Query: 751 ESKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVGAGQIIADGPSMDRGELALGKNV 810
E + L++ R+NQ T+F+Q P V+VG +V G ++ADGP+ + G LALG+NV
Sbjct: 616 EDGRLVH----PLRRYARSNQGTAFDQRPRVRVGQRVKKGDLLADGPASEEGFLALGQNV 671
Query: 811 RVAFMPWNGYNFEDAIVVSECITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEE 870
VA MP++GYNFEDAIV+SE + K D +TS HI E++AR+ K G E T DIP + E
Sbjct: 672 LVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEA 731
Query: 871 ALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYC 930
AL LDE GIV++G V G ILVG+TS KGE + +PEERLLR+IFG+KA V + SL
Sbjct: 732 ALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRV 791
Query: 931 PPSLEGTVI--------DVKVFTKKGYEKDARVLSAYEEEKAKLDM 968
PP G V+ D V K G + RV A +K KL +
Sbjct: 792 PPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVA---QKRKLQV 834
Score = 301 bits (770), Expect = 9e-82
Identities = 161/301 (53%), Positives = 213/301 (70%), Gaps = 17/301 (5%)
Query: 1070 LPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPL 1129
L GV + V++++A KRKL+VGDK+A RHGNKG+V+ I+PV DMP+ DG PVD++LNPL
Sbjct: 814 LKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPL 873
Query: 1130 GVPSRMNIGQILEMHLGLVGKEFGKQ-IARMLEDKTKDFAKELRAKMLEIANAINEKDPL 1188
GVPSRMN+GQILE HLGL G G++ I+ + + T+ KEL A+ + + +
Sbjct: 874 GVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGF 933
Query: 1189 TIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGR 1248
+ E +E+L A+ K+ + +E+ +LF+L GK+ LYDGR
Sbjct: 934 GVDKRE----KEVLARAE------KLGLVSPGKSPEEQLKELFDL------GKVVLYDGR 977
Query: 1249 TGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308
TGE + VG M+++KL+H+V++K+HARSTGPYSL+T QP+GGKA FGGQRFGEMEVW
Sbjct: 978 TGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVW 1037
Query: 1309 ALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALD 1368
ALEAYGAAHTL+EMLTIKSDDI GR AY+AI KGE V E +PE+F VL KELQ+LALD
Sbjct: 1038 ALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPESFRVLVKELQALALD 1097
Query: 1369 I 1369
+
Sbjct: 1098 V 1098
Score = 109 bits (272), Expect = 5e-24
Identities = 71/212 (33%), Positives = 113/212 (52%), Gaps = 24/212 (11%)
Query: 22 LEVPNLLLLQRDSYDSFLYSKEGKES----GIEKVFKSIFPIQDEHNR---ITLEYAGCE 74
+ +P L +Q +SY L + E GI+ FK FPI++ + L++
Sbjct: 13 IPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYR 72
Query: 75 FGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMT 134
G ++ E E+ +TY PL +++LI KDT G+ IKE +F+ +PLMT
Sbjct: 73 IGDPPFSQDECREKDLTYQAPLYARLQLI--HKDT------GL--IKEDEVFLGHLPLMT 122
Query: 135 ERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTGQII--PDRGSWLYFEYDS 192
E SFIING +RV+V+Q+HRSPGV F + + Y II P RG W+ E ++
Sbjct: 123 EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR----YIASIIPLPKRGPWIDLEVEA 178
Query: 193 KDVLYARINKRRKVPVTILFRAMDYQKQDIIK 224
V+ ++NK RK P+ +L R + Y ++ +++
Sbjct: 179 SGVVTMKVNK-RKFPLVLLLRVLGYDQETLVR 209
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1118
Score = 509 bits (1311), Expect = e-144
Identities = 288/646 (44%), Positives = 406/646 (62%), Gaps = 29/646 (4%)
Query: 341 LGHDA-SIIQSFSADSESLKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKK 399
LG+D ++++ SA + ++ L + A +R+ +++PGDP + A ++
Sbjct: 200 LGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFG 259
Query: 400 LFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHED-------IITTVKYLMKIKNNQG 452
L DP+RYDL GR K KLG+ + T + ED + T++YL +
Sbjct: 260 LLADPKRYDLGEAGRYKAEEKLGVGLSGR-TLVRFEDGEFKDEVFLPTLRYLFALTAGVP 318
Query: 453 --KIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSK 510
++DD DHLGNRRIR VGEL+A++ GL ++ + +++++ + G+ D+L P LVNS+
Sbjct: 319 GHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERM--VMGSPDTLTPAKLVNSR 376
Query: 511 MITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYG 570
+ + + EFF QLSQF D+TNPLS + HKRR+SALG GGL ++R GF+ RDVH THYG
Sbjct: 377 PLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYG 436
Query: 571 RICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHII 630
RICP+ETPEG NIGLI +L+ + RV+ LGFI PY++V +G V E +Y+TA +ED + I
Sbjct: 437 RICPVETPEGANIGLITSLAAYARVDALGFIRTPYRRVKNGVVTEEVVYMTASEEDRYTI 496
Query: 631 APASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDA 690
A A+TP++ + I D + R GE V+ +V MD+S + + +LIPFLEHDDA
Sbjct: 497 AQANTPLEGD-RIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFLEHDDA 555
Query: 691 NRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILG 750
NRALMG+NMQ QAVPL+R+ AP+V TG+E+ + RDS A+ A G V K+D I +
Sbjct: 556 NRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVVKVDGTRIAVRY 615
Query: 751 ESKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVGAGQIIADGPSMDRGELALGKNV 810
E + L++ R+NQ T+F+Q P V+VG +V G ++ADGP+ + G LALG+NV
Sbjct: 616 EDGRLVH----PLRRYARSNQGTAFDQRPRVRVGQRVKKGDLLADGPASEEGFLALGQNV 671
Query: 811 RVAFMPWNGYNFEDAIVVSECITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEE 870
VA MP++GYNFEDAIV+SE + K D +TS HI E++AR+ K G E T DIP + E
Sbjct: 672 LVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEA 731
Query: 871 ALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYC 930
AL LDE GIV++G V G ILVG+TS KGE + +PEERLLR+IFG+KA V + SL
Sbjct: 732 ALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRV 791
Query: 931 PPSLEGTVI--------DVKVFTKKGYEKDARVLSAYEEEKAKLDM 968
PP G V+ D V K G + RV A +K KL +
Sbjct: 792 PPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVA---QKRKLQV 834
Score = 301 bits (770), Expect = 9e-82
Identities = 161/301 (53%), Positives = 213/301 (70%), Gaps = 17/301 (5%)
Query: 1070 LPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPL 1129
L GV + V++++A KRKL+VGDK+A RHGNKG+V+ I+PV DMP+ DG PVD++LNPL
Sbjct: 814 LKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPL 873
Query: 1130 GVPSRMNIGQILEMHLGLVGKEFGKQ-IARMLEDKTKDFAKELRAKMLEIANAINEKDPL 1188
GVPSRMN+GQILE HLGL G G++ I+ + + T+ KEL A+ + + +
Sbjct: 874 GVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGF 933
Query: 1189 TIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGR 1248
+ E +E+L A+ K+ + +E+ +LF+L GK+ LYDGR
Sbjct: 934 GVDKRE----KEVLARAE------KLGLVSPGKSPEEQLKELFDL------GKVVLYDGR 977
Query: 1249 TGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308
TGE + VG M+++KL+H+V++K+HARSTGPYSL+T QP+GGKA FGGQRFGEMEVW
Sbjct: 978 TGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVW 1037
Query: 1309 ALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALD 1368
ALEAYGAAHTL+EMLTIKSDDI GR AY+AI KGE V E +PE+F VL KELQ+LALD
Sbjct: 1038 ALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPESFRVLVKELQALALD 1097
Query: 1369 I 1369
+
Sbjct: 1098 V 1098
Score = 109 bits (272), Expect = 5e-24
Identities = 71/212 (33%), Positives = 113/212 (52%), Gaps = 24/212 (11%)
Query: 22 LEVPNLLLLQRDSYDSFLYSKEGKES----GIEKVFKSIFPIQDEHNR---ITLEYAGCE 74
+ +P L +Q +SY L + E GI+ FK FPI++ + L++
Sbjct: 13 IPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYR 72
Query: 75 FGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMT 134
G ++ E E+ +TY PL +++LI KDT G+ IKE +F+ +PLMT
Sbjct: 73 IGDPPFSQDECREKDLTYQAPLYARLQLI--HKDT------GL--IKEDEVFLGHLPLMT 122
Query: 135 ERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTGQII--PDRGSWLYFEYDS 192
E SFIING +RV+V+Q+HRSPGV F + + Y II P RG W+ E ++
Sbjct: 123 EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR----YIASIIPLPKRGPWIDLEVEA 178
Query: 193 KDVLYARINKRRKVPVTILFRAMDYQKQDIIK 224
V+ ++NK RK P+ +L R + Y ++ +++
Sbjct: 179 SGVVTMKVNK-RKFPLVLLLRVLGYDQETLVR 209
>pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
Length = 1733
Score = 220 bits (560), Expect = 2e-57
Identities = 219/890 (24%), Positives = 374/890 (41%), Gaps = 164/890 (18%)
Query: 1400 QLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRF 1459
Q L SPE++ + S +++ PET++ + + GL PR
Sbjct: 18 QFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGL-------------------NDPRL 58
Query: 1460 KDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLL---GVKMKDLE 1516
I KC GHI+LA PV H+ ++ + + G + D
Sbjct: 59 GSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEH 118
Query: 1517 RVLYYEAYIVKEPGE---AAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFVAQMGGEA 1573
L +A +K+ + A + TK+V + D+ +E+ + R GG
Sbjct: 119 NELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSR----------GGCG 168
Query: 1574 IKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKV--------VESFLNSG----- 1620
D + L+ S K++ ++D + +++ ++ V+ F + G
Sbjct: 169 NTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVF 228
Query: 1621 NRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEII 1680
+RPEWM+LT LPV PP +RP ++ + + D+ ++ N L+ L GAP
Sbjct: 229 SRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHA 288
Query: 1681 VRNEKRMLQEAVDVLFDN---GRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVD 1737
+ + +LQ V DN G+ K RP+KS+ +KGK+GR R NL+GKRVD
Sbjct: 289 IEEAESLLQFHVATYMDNDIAGQPQALQKSG--RPVKSIRARLKGKEGRIRGNLMGKRVD 346
Query: 1738 FSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSK-----------------------L 1774
FS R+VI PNL++D+ G+PK++A L P +++ +
Sbjct: 347 FSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVI 406
Query: 1775 EERGYATTLKQAKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGK 1834
+ G L+ +KR + + W+ + I + PVL NR P+LHK S+ A K+I
Sbjct: 407 RDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYS 466
Query: 1835 AIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQD 1894
+L+ V S +NADFDGD+M +HVP S+E AE L + I+ P S K QD
Sbjct: 467 TFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQD 526
Query: 1895 MVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQGNIIATSA---- 1950
+ G+ L+L + F +++++ + V D +I T A
Sbjct: 527 TLCGIRKLTLRDT--------FIELDQVLNML----------YWVPDWDGVIPTPAIIKP 568
Query: 1951 -----GRMIIKSILPDFIPTDLWNR----------------------PMKKKDIGV---- 1979
G+ I+ +P+ I ++ ++KK +G
Sbjct: 569 KPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGG 628
Query: 1980 LVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDII----TPKDKQKMVEKAKV 2035
L+ V + G + A N++ + + G S + D I T ++ + + +AK
Sbjct: 629 LIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKK 688
Query: 2036 EVKKIQQQYDQGLLTDQERY-------NKIIDTWTEVNDKMSKEMMTAIAQDKEGFNSIY 2088
+V + ++ LLT + + ++ E DK + + + N++
Sbjct: 689 KVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGR----LAEVNLKDLNNVK 744
Query: 2089 MMADSGARGSAAQIRQLSAMRGL-------------------MTKPDGSIIETPIISN-F 2128
M +G++GS I Q+SA G +K D S + N +
Sbjct: 745 QMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSY 804
Query: 2129 KEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDD 2178
GL E+F G R+GL DTA+KTA GY+ R+L+ +++ V D+
Sbjct: 805 LRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDN 854
Score = 53.9 bits (128), Expect = 2e-07
Identities = 24/34 (70%), Positives = 28/34 (81%)
Query: 2275 YPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASR 2308
+PGE VGV+AAQSIGEP TQ+TL TFH G AS+
Sbjct: 1059 HPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASK 1092
Score = 44.7 bits (104), Expect = 2e-04
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 2799 NARVIALKGEPAIAEPVLLGITRAAIGSDSI--ISAASFQETTKVLTEASIAMKKDFLED 2856
N R +AL + + L +TR + + SF+ET ++L EA + + D
Sbjct: 1364 NYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRG 1423
Query: 2857 LKENVVLGRMIPVGTGMY 2874
+ ENV+LG+M P+GTG +
Sbjct: 1424 VSENVILGQMAPIGTGAF 1441
>pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
Length = 1224
Score = 117 bits (294), Expect = 1e-26
Identities = 78/257 (30%), Positives = 121/257 (46%), Gaps = 58/257 (22%)
Query: 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSR 1134
+K VK+ + T + ++GDK A RHG KG + DMP+TA+G D+++NP +PSR
Sbjct: 961 LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR 1020
Query: 1135 MNIGQILEMHLGLVGKEFGKQIARMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALE 1194
M + ++E L +K+ ++ + P T +E
Sbjct: 1021 MTVAHLIEC---------------------------LLSKVAALSGNEGDASPFTDITVE 1053
Query: 1195 NCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMR 1254
S +LL S+G ++ +Y+G TG+K+
Sbjct: 1054 GIS--KLLREHGYQSRGFEV-----------------------------MYNGHTGKKLM 1082
Query: 1255 ERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYG 1314
++ G Y +L H+VD+K+HAR+ GP ++T QPV G++ GG RFGEME + A+G
Sbjct: 1083 AQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHG 1142
Query: 1315 AAHTLKEMLTIKSDDIR 1331
AA LKE L SD R
Sbjct: 1143 AASFLKERLMEASDAFR 1159
Score = 64.7 bits (156), Expect = 1e-10
Identities = 49/157 (31%), Positives = 75/157 (47%), Gaps = 21/157 (13%)
Query: 455 DDRDHLGNRRIRAVGELLANELHSGLVKMQKTI-KDKLTTMSGAFDSLMPHDLVNSKMIT 513
DDRDH G +R+ G LLA + K+ K I + T+ A D M +N+K IT
Sbjct: 396 DDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKL-AINAKTIT 454
Query: 514 STIMEFFMGGQ-------------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKDRVGF 559
S + G +SQ +++ S ++H RR + +G G +
Sbjct: 455 SGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLA----- 509
Query: 560 EARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVN 596
+ R +H TH+G +CP ETPEGQ GL+ LS + ++
Sbjct: 510 KPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS 546
Score = 43.5 bits (101), Expect = 3e-04
Identities = 29/104 (27%), Positives = 54/104 (51%), Gaps = 9/104 (8%)
Query: 803 ELALGKNVRVAFMPWNGYNFEDAIVVSECITKDDIFTSTHIYEKEVDARELKHGVE-EFT 861
EL G+N VA ++GYN ED++++++ +F S ++ + +E K+G+ T
Sbjct: 816 ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRS--LFFRSYMDQEKKYGMSITET 873
Query: 862 ADIPD------VKEEALAHLDESGIVKVGTYVSAGMILVGKTSP 899
+ P +K LD+ G++ G VS +++GKT+P
Sbjct: 874 FEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTP 917
Score = 39.7 bits (91), Expect = 0.005
Identities = 27/87 (31%), Positives = 47/87 (53%), Gaps = 1/87 (1%)
Query: 619 YLTAIQEDSHIIAPASTPIDE-EGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGV 677
Y+ A +E+S +IA ++ E N DL + V + + T ++ SM++GV
Sbjct: 692 YIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGV 751
Query: 678 AASLIPFLEHDDANRALMGTNMQRQAV 704
AAS+IPF +H+ + R + M +QA+
Sbjct: 752 AASIIPFPDHNQSPRNTYQSAMGKQAM 778
>pdb|1DBR|A Chain A, Hypoxanthine Guanine Xanthine
pdb|1DBR|B Chain B, Hypoxanthine Guanine Xanthine
pdb|1DBR|D Chain D, Hypoxanthine Guanine Xanthine
pdb|1DBR|C Chain C, Hypoxanthine Guanine Xanthine
Length = 231
Score = 32.7 bits (73), Expect = 0.59
Identities = 31/109 (28%), Positives = 50/109 (45%), Gaps = 14/109 (12%)
Query: 550 GGLVKDRVGFEARDVHPTHYGR----ICPIETPEGQNIGLINTLSTFTRVNDLGFIEAP- 604
GGLVKDRV A D+H T++G IC ++ G LI+ L+T + + P
Sbjct: 49 GGLVKDRVEKLAYDIHRTYFGEELHIICILKGSRGFFNLLIDYLATIQKYSGRESSVPPF 108
Query: 605 ---YKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIET 650
Y ++ + T LT + +D I D+ I+ D+++T
Sbjct: 109 FEHYVRLKSYQNDNSTGQLTVLSDDLSIFR------DKHVLIVEDIVDT 151
>pdb|1FSG|C Chain C, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Complexed With 9-Deazaguanine,
Alpha-D-5-Phosphoribosyl-1-Pyrophosphate (Prpp) And Two
Mg2+ Ions
pdb|1FSG|A Chain A, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Complexed With 9-Deazaguanine,
Alpha-D-5-Phosphoribosyl-1-Pyrophosphate (Prpp) And Two
Mg2+ Ions
pdb|1QK3|B Chain B, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Gmp Complex
pdb|1QK3|A Chain A, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Gmp Complex
pdb|1QK4|A Chain A, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Imp Complex
pdb|1QK3|D Chain D, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Gmp Complex
pdb|1QK4|B Chain B, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Imp Complex
pdb|1QK4|D Chain D, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Imp Complex
pdb|1QK4|C Chain C, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Imp Complex
pdb|1QK3|C Chain C, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase Gmp Complex
Length = 233
Score = 32.7 bits (73), Expect = 0.59
Identities = 31/109 (28%), Positives = 50/109 (45%), Gaps = 14/109 (12%)
Query: 550 GGLVKDRVGFEARDVHPTHYGR----ICPIETPEGQNIGLINTLSTFTRVNDLGFIEAP- 604
GGLVKDRV A D+H T++G IC ++ G LI+ L+T + + P
Sbjct: 52 GGLVKDRVEKLAYDIHRTYFGEELHIICILKGSRGFFNLLIDYLATIQKYSGRESSVPPF 111
Query: 605 ---YKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIET 650
Y ++ + T LT + +D I D+ I+ D+++T
Sbjct: 112 FEHYVRLKSYQNDNSTGQLTVLSDDLSIFR------DKHVLIVEDIVDT 154
>pdb|1QK5|B Chain B, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase With Xmp, Pyrophosphate And
Two Mg2+ Ions
pdb|1QK5|A Chain A, Toxoplasma Gondii Hypoxanthine-Guanine
Phosphoribosyltransferase With Xmp, Pyrophosphate And
Two Mg2+ Ions
Length = 233
Score = 32.0 bits (71), Expect = 1.0
Identities = 20/49 (40%), Positives = 28/49 (56%), Gaps = 4/49 (8%)
Query: 550 GGLVKDRVGFEARDVHPTHYGR----ICPIETPEGQNIGLINTLSTFTR 594
GGLVKDRV A D+H T++G IC ++ G LI+ L+T +
Sbjct: 52 GGLVKDRVEKLAYDIHRTYFGEELHIICILKGSRGFFNLLIDYLATIQK 100
>pdb|1J7N|B Chain B, Anthrax Toxin Lethal Factor
pdb|1J7N|A Chain A, Anthrax Toxin Lethal Factor
pdb|1JKY|A Chain A, Crystal Structure Of The Anthrax Lethal Factor (Lf): Wild-
Type Lf Complexed With The N-Terminal Sequence Of Mapkk2
Length = 776
Score = 31.6 bits (70), Expect = 1.3
Identities = 44/197 (22%), Positives = 92/197 (46%), Gaps = 41/197 (20%)
Query: 218 QKQDIIKMFYPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKVILLAGKKLTSR--K 275
Q +D+++++ P E Y+ F + N +E +LKD +++ SR K
Sbjct: 228 QHRDVLQLYAP------EAFNYMDKFNEQEINLSLE-ELKD----------QRMLSRYEK 270
Query: 276 IKELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVI 335
+++K+++ W + L+E G+ +L + ++ K + IH L +E +
Sbjct: 271 WEKIKQHYQHWSD---------SLSEE---GRGLLKKLQIPIEPKKDDIIHSLSQEEKEL 318
Query: 336 INDLALGHDASIIQSFSADSESLKLLKQTEKIDDENALAAIR---IHKVMKPGDPVTTEV 392
+ + + D+S S + + E LK L+ ID ++L+ ++++ +E
Sbjct: 319 LKRIQI--DSSDFLS-TEEKEFLKKLQ----IDIRDSLSEEEKELLNRIQVDSSNPLSEK 371
Query: 393 AKQFVKKLFFDPERYDL 409
K+F+KKL D + YD+
Sbjct: 372 EKEFLKKLKLDIQPYDI 388
>pdb|1BG3|A Chain A, Rat Brain Hexokinase Type I Complex With Glucose And
Inhibitor Glucose-6-Phosphate
pdb|1BG3|B Chain B, Rat Brain Hexokinase Type I Complex With Glucose And
Inhibitor Glucose-6-Phosphate
Length = 919
Score = 31.2 bits (69), Expect = 1.7
Identities = 49/222 (22%), Positives = 88/222 (39%), Gaps = 47/222 (21%)
Query: 102 LILWEKDTKSG---EKNGIKDIKEQSIFIREIPLMTERTSFI---ING----VERVVVNQ 151
L ++K+ K+G + N +K F+R IP +E+ FI + G + RV VN
Sbjct: 40 LTRFKKEMKNGLSRDYNPTASVKMLPTFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNH 99
Query: 152 LHRSPGVIFKEEESSTSLNKLIYTG--QIIPDRGSWLYFEYDS--KDVLYARINKRRKVP 207
E+ + S+ IY I+ G+ L+ D + + K +K+P
Sbjct: 100 ----------EKNQNVSMESEIYDTPENIVHGSGTQLFDHVADCLGDFMEKKKIKDKKLP 149
Query: 208 V---------------------TILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASL 246
V T F+A + D++K+ +K R + D ++ +
Sbjct: 150 VGFTFSFPCRQSKIDEAVLITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVND 209
Query: 247 DANQRMEFDLKDPQGKVILLAGKKLTSRKIKELKENHLEWVE 288
M D Q +V L+ G + ++EL+ H++ VE
Sbjct: 210 TVGTMMTCGYDDQQCEVGLIIGTGTNACYMEELR--HIDLVE 249
>pdb|1GJX|A Chain A, Solution Structure Of The Lipoyl Domain Of The Chimeric
Dihydrolipoyl Dehydrogenase P64k From Neisseria
Meningitidis
Length = 81
Score = 30.8 bits (68), Expect = 2.3
Identities = 23/75 (30%), Positives = 31/75 (40%), Gaps = 11/75 (14%)
Query: 2422 GGSIADIIQEGWNVPNRIPYASELLVKDNDPIAQDVYAKEKGVIKYYVLEANHLERTHGI 2481
G DII NV + I L+ + D DV A+ GV+K +
Sbjct: 12 GHENVDIIAVEVNVGDTIAVDDTLITLETDKATMDVPAEVAGVVKEV-----------KV 60
Query: 2482 KKGDMVSEKGLFAVI 2496
K GD +SE GL V+
Sbjct: 61 KVGDKISEGGLIVVV 75
>pdb|1FDZ|A Chain A, N-Acetylneuraminate Lyase In Complex With Pyruvate Via
Borohydride Reduction
pdb|1FDZ|D Chain D, N-Acetylneuraminate Lyase In Complex With Pyruvate Via
Borohydride Reduction
pdb|1FDY|A Chain A, N-Acetylneuraminate Lyase In Complex With Hydroxypyruvate
pdb|1FDY|B Chain B, N-Acetylneuraminate Lyase In Complex With Hydroxypyruvate
pdb|1FDY|C Chain C, N-Acetylneuraminate Lyase In Complex With Hydroxypyruvate
pdb|1FDY|D Chain D, N-Acetylneuraminate Lyase In Complex With Hydroxypyruvate
pdb|1FDZ|B Chain B, N-Acetylneuraminate Lyase In Complex With Pyruvate Via
Borohydride Reduction
pdb|1FDZ|C Chain C, N-Acetylneuraminate Lyase In Complex With Pyruvate Via
Borohydride Reduction
Length = 297
Score = 30.8 bits (68), Expect = 2.3
Identities = 29/123 (23%), Positives = 50/123 (40%), Gaps = 4/123 (3%)
Query: 2763 IEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITRA 2822
+++ + Q+ V + G K GDL + + E+ ++ G I LL
Sbjct: 145 VKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADG 204
Query: 2823 AIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMYKNKKIVLR 2882
IGS I +Q K L E I + + N V+ +I TG+++ K VL
Sbjct: 205 GIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTEC--NKVIDLLIK--TGVFRGLKTVLH 260
Query: 2883 ALE 2885
++
Sbjct: 261 YMD 263
>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
Length = 334
Score = 30.8 bits (68), Expect = 2.3
Identities = 51/225 (22%), Positives = 90/225 (39%), Gaps = 34/225 (15%)
Query: 1019 INRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKV 1078
+ + TLA ++ + E+Q + +T L ++ + L+ LE+ D+L I ++
Sbjct: 62 LGKTTLAHII---ASELQTNIHVTSGPVLVKQGDMAAI----LTSLERGDVLFIDEIHRL 114
Query: 1079 KLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIG 1138
+ + D KG + + + P+T G V L L P R G
Sbjct: 115 NKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATVRSGL--LSSPLRSRFG 172
Query: 1139 QILEMHLGLVG--KEFGKQIARMLEDKTKDFAKELRAK------------------MLEI 1178
ILE+ V KE K+ A +++ + +D A E+ AK ML +
Sbjct: 173 IILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTV 232
Query: 1179 ANAINEKDPLTIHALE--NCSDEELLEYAKDWSKGVKMAIPVFEG 1221
A + + +E N DE L E+ + K +K I ++ G
Sbjct: 233 VKADRINTDIVLKTMEVLNIDDEGLDEFDR---KILKTIIEIYRG 274
>pdb|1NAL|1 Chain 1, Mol_id: 1; Molecule: N-Acetylneuraminate Lyase; Chain: 1, 2,
3, 4; Ec: 4.1.3.3
pdb|1NAL|2 Chain 2, Mol_id: 1; Molecule: N-Acetylneuraminate Lyase; Chain: 1, 2,
3, 4; Ec: 4.1.3.3
pdb|1NAL|3 Chain 3, Mol_id: 1; Molecule: N-Acetylneuraminate Lyase; Chain: 1, 2,
3, 4; Ec: 4.1.3.3
pdb|1NAL|4 Chain 4, Mol_id: 1; Molecule: N-Acetylneuraminate Lyase; Chain: 1, 2,
3, 4; Ec: 4.1.3.3
Length = 297
Score = 30.8 bits (68), Expect = 2.3
Identities = 29/123 (23%), Positives = 50/123 (40%), Gaps = 4/123 (3%)
Query: 2763 IEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITRA 2822
+++ + Q+ V + G K GDL + + E+ ++ G I LL
Sbjct: 145 VKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADG 204
Query: 2823 AIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMYKNKKIVLR 2882
IGS I +Q K L E I + + N V+ +I TG+++ K VL
Sbjct: 205 GIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTEC--NKVIDLLIK--TGVFRGLKTVLH 260
Query: 2883 ALE 2885
++
Sbjct: 261 YMD 263
>pdb|1XYN| Molecule: Endo-1,4-Beta-Xylanase I; Synonym: Xyni; Ec: 3.2.1.8
Length = 178
Score = 30.4 bits (67), Expect = 2.9
Identities = 25/141 (17%), Positives = 55/141 (38%), Gaps = 5/141 (3%)
Query: 2402 GGKIEGKVYLPYASGHKVHKGGSIADIIQEGWNVPNRIP--YASELLVKDNDPIAQDVYA 2459
GG++ Y P +G V+ ++ GW + P + V +
Sbjct: 12 GGQVS---YSPSNTGFSVNWNTQDDFVVGVGWTTGSSAPINFGGSFSVNSGTGLLSVYGW 68
Query: 2460 KEKGVIKYYVLEANHLERTHGIKKGDMVSEKGLFAVIADDNGREAARHYIARGSEILIDD 2519
+++YY++E NH G KG + S+ + + + E + A ++ +
Sbjct: 69 STNPLVEYYIMEDNHNYPAQGTVKGTVTSDGATYTIWENTRVNEPSIQGTATFNQYISVR 128
Query: 2520 NSEVSTNSVISKPTTNTFKTI 2540
NS ++ +V + N + ++
Sbjct: 129 NSPRTSGTVTVQNHFNAWASL 149
>pdb|1JAD|A Chain A, C-Terminal Domain Of Turkey Plc-Beta
pdb|1JAD|B Chain B, C-Terminal Domain Of Turkey Plc-Beta
Length = 251
Score = 30.4 bits (67), Expect = 2.9
Identities = 28/119 (23%), Positives = 56/119 (46%), Gaps = 17/119 (14%)
Query: 962 EKAKLDMEHFDRLTMLNREELLRVSSLL-----------SQAI-----LEEPFSHNGKDY 1005
+K + +++ +R REELL+ S+L SQ + LE H G++Y
Sbjct: 35 KKQEKELKELERKGSKRREELLQKYSVLFLEPVYPRGLDSQVVELKERLEXELIHLGEEY 94
Query: 1006 KEGDQIPKEEIASINRFTLASLVK-KYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSI 1063
+G + KE+ A+ + L + K E++ E +++N + KK L + +++ +
Sbjct: 95 HDGIRRRKEQHATEQTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQV 153
>pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant
Length = 334
Score = 30.4 bits (67), Expect = 2.9
Identities = 51/225 (22%), Positives = 89/225 (38%), Gaps = 34/225 (15%)
Query: 1019 INRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKV 1078
+ R TLA ++ + E+Q + +T L ++ + L+ LE+ D+L I ++
Sbjct: 62 LGRTTLAHII---ASELQTNIHVTSGPVLVKQGDMAAI----LTSLERGDVLFIDEIHRL 114
Query: 1079 KLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIG 1138
+ + D KG + + + P+T G L L P R G
Sbjct: 115 NKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGL--LSSPLRSRFG 172
Query: 1139 QILEMHLGLVG--KEFGKQIARMLEDKTKDFAKELRAK------------------MLEI 1178
ILE+ V KE K+ A +++ + +D A E+ AK ML +
Sbjct: 173 IILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTV 232
Query: 1179 ANAINEKDPLTIHALE--NCSDEELLEYAKDWSKGVKMAIPVFEG 1221
A + + +E N DE L E+ + K +K I ++ G
Sbjct: 233 VKADRINTDIVLKTMEVLNIDDEGLDEFDR---KILKTIIEIYRG 274
>pdb|1FIY| Three-Dimensional Structure Of Phosphoenolpyruvate Carboxylase From
Escherichia Coli At 2.8 A Resolution
pdb|1QB4|A Chain A, Crystal Structure Of Mn(2+)-Bound Phosphoenolpyruvate
Carboxylase
Length = 883
Score = 30.0 bits (66), Expect = 3.8
Identities = 21/77 (27%), Positives = 41/77 (52%), Gaps = 4/77 (5%)
Query: 1141 LEMHLGLVGKEFGKQIARMLEDKTKDFAKELR--AKMLEIANAINEKDPLTIHALENCSD 1198
L ++ ++GK G+ I L + + + +R +K N N ++ LT L+N S+
Sbjct: 8 LRSNVSMLGKVLGETIKDALGEHILERVETIRKLSKSSRAGNDANRQELLT--TLQNLSN 65
Query: 1199 EELLEYAKDWSKGVKMA 1215
+ELL A+ +S+ + +A
Sbjct: 66 DELLPVARAFSQFLNLA 82
>pdb|1DGK|N Chain N, Mutant Monomer Of Recombinant Human Hexokinase Type I With
Glucose And Adp In The Active Site
Length = 917
Score = 29.6 bits (65), Expect = 5.0
Identities = 50/218 (22%), Positives = 89/218 (39%), Gaps = 45/218 (20%)
Query: 105 WEKDTKSG---EKNGIKDIKEQSIFIREIPLMTERTSFI---ING----VERVVVNQLHR 154
+ K+ K+G + N +K F+R IP +E+ FI + G + RV VN +
Sbjct: 43 FRKEMKNGLSRDFNPTATVKMLPTFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNH-EK 101
Query: 155 SPGVIFKEEESSTSLNKLIYTGQIIPDRGSWLYFEYDSK---DVLYARINKRRKVPV--- 208
+ V + E T N I+ GS L F++ ++ D + R K +K+PV
Sbjct: 102 NQNVHMESEVYDTPEN-------IVHGSGSQL-FDHVAECLGDFMEKRKIKDKKLPVGFT 153
Query: 209 ------------------TILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASLDANQ 250
T F+A + D++K+ +K R + D ++ +
Sbjct: 154 FSFPCQQSKIDEAILITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVNDTVGT 213
Query: 251 RMEFDLKDPQGKVILLAGKKLTSRKIKELKENHLEWVE 288
M D +V L+ G + ++EL+ H++ VE
Sbjct: 214 MMTCGYDDQHCEVGLIIGTGTNACYMEELR--HIDLVE 249
>pdb|1QHA|A Chain A, Human Hexokinase Type I Complexed With Atp Analogue
Amp-Pnp
pdb|1QHA|B Chain B, Human Hexokinase Type I Complexed With Atp Analogue
Amp-Pnp
pdb|1HKC|A Chain A, Recombinant Human Hexokinase Type I Complexed With Glucose
And Phosphate
Length = 917
Score = 29.6 bits (65), Expect = 5.0
Identities = 50/218 (22%), Positives = 89/218 (39%), Gaps = 45/218 (20%)
Query: 105 WEKDTKSG---EKNGIKDIKEQSIFIREIPLMTERTSFI---ING----VERVVVNQLHR 154
+ K+ K+G + N +K F+R IP +E+ FI + G + RV VN +
Sbjct: 43 FRKEMKNGLSRDFNPTATVKMLPTFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNH-EK 101
Query: 155 SPGVIFKEEESSTSLNKLIYTGQIIPDRGSWLYFEYDSK---DVLYARINKRRKVPV--- 208
+ V + E T N I+ GS L F++ ++ D + R K +K+PV
Sbjct: 102 NQNVHMESEVYDTPEN-------IVHGSGSQL-FDHVAECLGDFMEKRKIKDKKLPVGFT 153
Query: 209 ------------------TILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASLDANQ 250
T F+A + D++K+ +K R + D ++ +
Sbjct: 154 FSFPCQQSKIDEAILITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVNDTVGT 213
Query: 251 RMEFDLKDPQGKVILLAGKKLTSRKIKELKENHLEWVE 288
M D +V L+ G + ++EL+ H++ VE
Sbjct: 214 MMTCGYDDQHCEVGLIIGTGTNACYMEELR--HIDLVE 249
>pdb|1HKB|A Chain A, Crystal Structure Of Recombinant Human Brain Hexokinase
Type I Complexed With Glucose And Glucose-6-Phosphate
pdb|1HKB|B Chain B, Crystal Structure Of Recombinant Human Brain Hexokinase
Type I Complexed With Glucose And Glucose-6-Phosphate
Length = 917
Score = 29.6 bits (65), Expect = 5.0
Identities = 50/218 (22%), Positives = 89/218 (39%), Gaps = 45/218 (20%)
Query: 105 WEKDTKSG---EKNGIKDIKEQSIFIREIPLMTERTSFI---ING----VERVVVNQLHR 154
+ K+ K+G + N +K F+R IP +E+ FI + G + RV VN +
Sbjct: 43 FRKEMKNGLSRDFNPTATVKMLPTFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNH-EK 101
Query: 155 SPGVIFKEEESSTSLNKLIYTGQIIPDRGSWLYFEYDSK---DVLYARINKRRKVPV--- 208
+ V + E T N I+ GS L F++ ++ D + R K +K+PV
Sbjct: 102 NQNVHMESEVYDTPEN-------IVHGSGSQL-FDHVAECLGDFMEKRKIKDKKLPVGFT 153
Query: 209 ------------------TILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASLDANQ 250
T F+A + D++K+ +K R + D ++ +
Sbjct: 154 FSFPCQQSKIDEAILITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVNDTVGT 213
Query: 251 RMEFDLKDPQGKVILLAGKKLTSRKIKELKENHLEWVE 288
M D +V L+ G + ++EL+ H++ VE
Sbjct: 214 MMTCGYDDQHCEVGLIIGTGTNACYMEELR--HIDLVE 249
>pdb|1CZA|N Chain N, Mutant Monomer Of Recombinant Human Hexokinase Type I
Complexed With Glucose, Glucose-6-Phosphate, And Adp
Length = 917
Score = 29.6 bits (65), Expect = 5.0
Identities = 50/218 (22%), Positives = 89/218 (39%), Gaps = 45/218 (20%)
Query: 105 WEKDTKSG---EKNGIKDIKEQSIFIREIPLMTERTSFI---ING----VERVVVNQLHR 154
+ K+ K+G + N +K F+R IP +E+ FI + G + RV VN +
Sbjct: 43 FRKEMKNGLSRDFNPTATVKMLPTFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNH-EK 101
Query: 155 SPGVIFKEEESSTSLNKLIYTGQIIPDRGSWLYFEYDSK---DVLYARINKRRKVPV--- 208
+ V + E T N I+ GS L F++ ++ D + R K +K+PV
Sbjct: 102 NQNVHMESEVYDTPEN-------IVHGSGSQL-FDHVAECLGDFMEKRKIKDKKLPVGFT 153
Query: 209 ------------------TILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASLDANQ 250
T F+A + D++K+ +K R + D ++ +
Sbjct: 154 FSFPCQQSKIDEAILITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVNDTVGT 213
Query: 251 RMEFDLKDPQGKVILLAGKKLTSRKIKELKENHLEWVE 288
M D +V L+ G + ++EL+ H++ VE
Sbjct: 214 MMTCGYDDQHCEVGLIIGTGTNACYMEELR--HIDLVE 249
>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
Length = 334
Score = 29.6 bits (65), Expect = 5.0
Identities = 50/225 (22%), Positives = 89/225 (39%), Gaps = 34/225 (15%)
Query: 1019 INRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKV 1078
+ + TLA ++ + E+Q + +T L ++ + L+ LE+ D+L I ++
Sbjct: 62 LGKTTLAHII---ASELQTNIHVTSGPVLVKQGDMAAI----LTSLERGDVLFIDEIHRL 114
Query: 1079 KLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIG 1138
+ + D KG + + + P+T G L L P R G
Sbjct: 115 NKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGSTTRSGL--LSSPLRSRFG 172
Query: 1139 QILEMHLGLVG--KEFGKQIARMLEDKTKDFAKELRAK------------------MLEI 1178
ILE+ V KE K+ A +++ + +D A E+ AK ML +
Sbjct: 173 IILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTV 232
Query: 1179 ANAINEKDPLTIHALE--NCSDEELLEYAKDWSKGVKMAIPVFEG 1221
A + + +E N DE L E+ + K +K I ++ G
Sbjct: 233 VKADRINTDIVLKTMEVLNIDDEGLDEFDR---KILKTIIEIYRG 274
>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch Migration
Motor
Length = 334
Score = 29.3 bits (64), Expect = 6.6
Identities = 50/225 (22%), Positives = 89/225 (39%), Gaps = 34/225 (15%)
Query: 1019 INRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKV 1078
+ + TLA ++ + E+Q + +T L ++ + L+ LE+ D+L I ++
Sbjct: 62 LGKTTLAHII---ASELQTNIHVTSGPVLVKQGDMAAI----LTSLERGDVLFIDEIHRL 114
Query: 1079 KLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIG 1138
+ + D KG + + + P+T G L L P R G
Sbjct: 115 NKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGL--LSSPLRSRFG 172
Query: 1139 QILEMHLGLVG--KEFGKQIARMLEDKTKDFAKELRAK------------------MLEI 1178
ILE+ V KE K+ A +++ + +D A E+ AK ML +
Sbjct: 173 IILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTV 232
Query: 1179 ANAINEKDPLTIHALE--NCSDEELLEYAKDWSKGVKMAIPVFEG 1221
A + + +E N DE L E+ + K +K I ++ G
Sbjct: 233 VKADRINTDIVLKTMEVLNIDDEGLDEFDR---KILKTIIEIYRG 274
>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant
Length = 334
Score = 29.3 bits (64), Expect = 6.6
Identities = 50/225 (22%), Positives = 89/225 (39%), Gaps = 34/225 (15%)
Query: 1019 INRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKV 1078
+ + TLA ++ + E+Q + +T L ++ + L+ LE+ D+L I ++
Sbjct: 62 LGKTTLAHII---ASELQTNIHVTSGPVLVKQGDMAAI----LTSLERGDVLFIDEIHRL 114
Query: 1079 KLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIG 1138
+ + D KG + + + P+T G L L P R G
Sbjct: 115 NKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGL--LSSPLRSRFG 172
Query: 1139 QILEMHLGLVG--KEFGKQIARMLEDKTKDFAKELRAK------------------MLEI 1178
ILE+ V KE K+ A +++ + +D A E+ AK ML +
Sbjct: 173 IILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTGRIAIRLTKRVRDMLTV 232
Query: 1179 ANAINEKDPLTIHALE--NCSDEELLEYAKDWSKGVKMAIPVFEG 1221
A + + +E N DE L E+ + K +K I ++ G
Sbjct: 233 VKADRINTDIVLKTMEVLNIDDEGLDEFDR---KILKTIIEIYRG 274
>pdb|1DU5|A Chain A, The Crystal Structure Of Zeamatin.
pdb|1DU5|B Chain B, The Crystal Structure Of Zeamatin
Length = 206
Score = 28.9 bits (63), Expect = 8.6
Identities = 14/37 (37%), Positives = 19/37 (50%)
Query: 557 VGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFT 593
VG A D HPT+Y R + P+ + + STFT
Sbjct: 157 VGSAANDCHPTNYSRYFKGQCPDAYSYPKDDATSTFT 193
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.317 0.136 0.381
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,605,649
Number of Sequences: 13198
Number of extensions: 734465
Number of successful extensions: 2217
Number of sequences better than 10.0: 31
Number of HSP's better than 10.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 2076
Number of HSP's gapped (non-prelim): 89
length of query: 2890
length of database: 2,899,336
effective HSP length: 105
effective length of query: 2785
effective length of database: 1,513,546
effective search space: 4215225610
effective search space used: 4215225610
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 63 (28.9 bits)