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|15646148|ref|NP_208332.1| transcription-repair
coupling factor (trcF) [Helicobacter pylori 26695]
(999 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|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dn... 272 2e-73
pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Pro... 45 4e-05
pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Pro... 45 4e-05
pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein... 44 7e-05
pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb... 37 0.008
pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide... 37 0.008
pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase C... 33 0.21
pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus 33 0.21
pdb|1F8S|A Chain A, Crystal Structure Of L-Amino Acid Oxida... 30 1.7
pdb|1BG0| Transition State Structure Of Arginine Kinase 27 8.6
pdb|1CNT|1 Chain 1, Ciliary Neurotrophic Factor >gi|2098527... 27 8.6
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 272 bits (695), Expect = 2e-73
Identities = 164/416 (39%), Positives = 252/416 (60%), Gaps = 24/416 (5%)
Query: 445 LLEIASKIIELAAERNLILGKKMDVHLAELEVFKSHAGFEYTSDQEKAIAEISKDLSSHR 504
+L++A + I E++ + KK++ LAE E KS F+ T+ Q++A EI D+ S +
Sbjct: 331 VLQLAFQKIRKEREKHGGIPKKIEGKLAE-EFIKS-LPFKLTNAQKRAHQEIRNDMISEK 388
Query: 505 VMDRLLSGDVGFGKTEVAMHAIFCAFLNGFQSALVVPTTLLAHQHFETLRARFENFGVKV 564
M+RLL GDVG GKT VA AI + GFQ+A +VPT++LA QH+ F F + V
Sbjct: 389 PMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHV 448
Query: 565 ARL--DRYASEKNKLLKAVELGQVDALIGTHAIL--GAKFKNLGLVVVDEEHKFGVKQKE 620
A L SEK K+ + GQ+D +IGTHA++ FKNLGLV++DE+H+FGVKQ+E
Sbjct: 449 ALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRFGVKQRE 508
Query: 621 ALKELSKSVHFLSMSATPIPRTLNMALSQIKGISSLKTPPTDRKPSRTFL--KEKNDELL 678
AL K V L MSATPIPR++ +A ++ + P RK +T L ++ +E+
Sbjct: 509 ALMNKGKMVDTLVMSATPIPRSMALAFYGDLDVTVIDEMPPGRKEVQTMLVPMDRVNEVY 568
Query: 679 KEIIYRELRRNGQIFYIHNHI--ASILKVKTKLE-------DLIPKLKIAILHSQINANE 729
E + +E+ R GQ F ++ I + L VK+ +E ++ P+ K+ ++H +++ E
Sbjct: 569 -EFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEE 627
Query: 730 SEEIMLEFAKGNYQVLLCTSIVESGIHLPNANTIIIDNAQNFGLADLHQLRGRVGRGKKE 789
+ +MLEFA+G Y +L+ T+++E GI +P AN ++I+N + FGLA LHQLRGRVGRG +E
Sbjct: 628 KDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQE 687
Query: 790 GFCYFLIEDQKSLNEQALKRLLALEKNSYLGSGESVAYHDLEIRGGGNLLGQDQSG 845
+C+ ++ D + E+A++RL N+ G +A +DL+ RG G G Q G
Sbjct: 688 AYCFLVVGD---VGEEAMERLRFFTLNT---DGFKIAEYDLKTRGPGEFFGVKQHG 737
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 45.1 bits (105), Expect = 4e-05
Identities = 45/161 (27%), Positives = 72/161 (43%), Gaps = 18/161 (11%)
Query: 634 MSATPIPRTLNMA---LSQIKGISSLKTPPTDRKPSRTFLKEKNDELLKEIIYRELRRNG 690
+SATP P L + + QI + L P D +P+ K + D+L+ EI R R
Sbjct: 392 VSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPT----KGQIDDLIGEIRERVERNER 447
Query: 691 QIFYIHNHIASILKVKTKLEDLIPK--LKIAILHSQINANESEEIMLEFAKGNYQVLLCT 748
+ K+ L D + + +K+A LHS+I E EI+ + G Y VL+
Sbjct: 448 TLV-----TTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGI 502
Query: 749 SIVESGIHLPNANTIIIDNAQNFGL----ADLHQLRGRVGR 785
+++ G+ +P + + I +A G L Q GR R
Sbjct: 503 NLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 543
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 45.1 bits (105), Expect = 4e-05
Identities = 45/161 (27%), Positives = 72/161 (43%), Gaps = 18/161 (11%)
Query: 634 MSATPIPRTLNMA---LSQIKGISSLKTPPTDRKPSRTFLKEKNDELLKEIIYRELRRNG 690
+SATP P L + + QI + L P D +P+ K + D+L+ EI R R
Sbjct: 391 VSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPT----KGQIDDLIGEIRERVERNER 446
Query: 691 QIFYIHNHIASILKVKTKLEDLIPK--LKIAILHSQINANESEEIMLEFAKGNYQVLLCT 748
+ K+ L D + + +K+A LHS+I E EI+ + G Y VL+
Sbjct: 447 TLV-----TTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGI 501
Query: 749 SIVESGIHLPNANTIIIDNAQNFGL----ADLHQLRGRVGR 785
+++ G+ +P + + I +A G L Q GR R
Sbjct: 502 NLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 542
Score = 39.3 bits (90), Expect = 0.002
Identities = 37/139 (26%), Positives = 64/139 (45%), Gaps = 8/139 (5%)
Query: 77 ALENKQETIIIAPISALL---HPLPKKELLESFKITLLEKYNLKDLKDKLFYYGYEILDL 133
AL +++ II+A +S + P +EL+ S ++ + + N L +L Y+ D
Sbjct: 129 ALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRVGMEIERNA--LLRRLVDIQYDRND- 185
Query: 134 VEVEGEASFRGDIVDIYAPNSKAY--RLSFFDTECESIKEFDPITQMSLKEDLLEIEIPP 191
++ G RGD+V+I+ + + R+ FF E E I+E D +T L E P
Sbjct: 186 IDFRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGKVLGEREHVAIFPA 245
Query: 192 TLFSLDESSYKDLKTKVEQ 210
+ F E + +EQ
Sbjct: 246 SHFVTREEKMRLAIQNIEQ 264
>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
pdb|1HV8|B Chain B, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
Length = 367
Score = 44.3 bits (103), Expect = 7e-05
Identities = 62/307 (20%), Positives = 128/307 (41%), Gaps = 47/307 (15%)
Query: 532 NGFQSALVVPTTLLAHQHFETLRARFENFGVKVARLDRYASEKNKLLKAVELGQVDALIG 591
NG ++ ++ PT LA Q + + + N +K+A++ Y KA+ Q+ AL
Sbjct: 73 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKI--YGG------KAI-YPQIKALKN 123
Query: 592 THAILGA-------------KFKNLGLVVVDEEHK-----FGVKQKEALKELSKSVHFLS 633
+ ++G KN+ ++DE + F ++ L +K L
Sbjct: 124 ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKDKRILL 183
Query: 634 MSATPIPRTLNMALSQIKGISSLKTPPTDRKPSRTFLKEKNDELLKEIIYRELRRNGQIF 693
SAT LN+A S +K + +++++ +E + + L +N + +
Sbjct: 184 FSATXPREILNLAKKYXGDYSFIKA-KINANIEQSYVEVNENERFEALC--RLLKNKEFY 240
Query: 694 YIHNHIASILKVKTKLEDLIPKL-----KIAILHSQINANESEEIMLEFAKGNYQVLLCT 748
+ K K ++L L K +H ++ ++ E+++ F + ++L+ T
Sbjct: 241 GL-----VFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIAT 295
Query: 749 SIVESGIHLPNANTIIIDNAQNFGLADLHQLRGRVGRGKKEGFCYFLIEDQKSLNEQALK 808
+ GI + + N +I + + H++ GR GR K+G +I N + K
Sbjct: 296 DVXSRGIDVNDLNCVINYHLPQNPESYXHRI-GRTGRAGKKGKAISII------NRREYK 348
Query: 809 RLLALEK 815
+L +E+
Sbjct: 349 KLRYIER 355
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 37.4 bits (85), Expect = 0.008
Identities = 25/109 (22%), Positives = 56/109 (50%), Gaps = 2/109 (1%)
Query: 76 QALENKQETIIIAPISALLH-PLPKKELLESFKITLLEKYNLKDLKDKLFYYGYEILDLV 134
++L +++ I++A +SA+ P++ + + + Y + L ++L GY+ D+
Sbjct: 125 RSLLTRRDVIVVASVSAIYGLGDPREYRARNLVVERGKPYPREVLLERLLELGYQRNDID 184
Query: 135 EVEGEASFRGDIVDIY-APNSKAYRLSFFDTECESIKEFDPITQMSLKE 182
G +G++++I+ A ++ R+ F E E I + P+T L+E
Sbjct: 185 LSPGRFRAKGEVLEIFPAYETEPIRVELFGDEVERISQVHPVTGERLRE 233
Score = 30.0 bits (66), Expect = 1.3
Identities = 16/77 (20%), Positives = 37/77 (47%), Gaps = 4/77 (5%)
Query: 716 LKIAILHSQINANESEEIMLEFAKGNYQVLLCTSIVESGIHLPNANTIIIDNAQNFGL-- 773
++ LH +++A + + ++ + G+Y L+ +++ G+ +P + + I +A G
Sbjct: 465 IRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLR 524
Query: 774 --ADLHQLRGRVGRGKK 788
L Q GR R +
Sbjct: 525 SERSLIQTIGRAARNAR 541
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 37.4 bits (85), Expect = 0.008
Identities = 25/109 (22%), Positives = 56/109 (50%), Gaps = 2/109 (1%)
Query: 76 QALENKQETIIIAPISALLH-PLPKKELLESFKITLLEKYNLKDLKDKLFYYGYEILDLV 134
++L +++ I++A +SA+ P++ + + + Y + L ++L GY+ D+
Sbjct: 124 RSLLTRRDVIVVASVSAIYGLGDPREYRARNLVVERGKPYPREVLLERLLELGYQRNDID 183
Query: 135 EVEGEASFRGDIVDIY-APNSKAYRLSFFDTECESIKEFDPITQMSLKE 182
G +G++++I+ A ++ R+ F E E I + P+T L+E
Sbjct: 184 LSPGRFRAKGEVLEIFPAYETEPIRVELFGDEVERISQVHPVTGERLRE 232
Score = 30.0 bits (66), Expect = 1.3
Identities = 16/77 (20%), Positives = 37/77 (47%), Gaps = 4/77 (5%)
Query: 716 LKIAILHSQINANESEEIMLEFAKGNYQVLLCTSIVESGIHLPNANTIIIDNAQNFGL-- 773
++ LH +++A + + ++ + G+Y L+ +++ G+ +P + + I +A G
Sbjct: 464 IRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLR 523
Query: 774 --ADLHQLRGRVGRGKK 788
L Q GR R +
Sbjct: 524 SERSLIQTIGRAARNAR 540
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 32.7 bits (73), Expect = 0.21
Identities = 34/127 (26%), Positives = 50/127 (38%), Gaps = 15/127 (11%)
Query: 515 GFGKTEVAMHAIFCAFLNGFQSALVVPTTLLAHQHFETLRARFENFGVKVARLDRY---- 570
G GKT + L G + ++ PT+LL Q ET+R E GV L Y
Sbjct: 81 GVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGR 140
Query: 571 --ASEKNKLLKAVELGQVDALIGTHAILGAKFKNLG---LVVVDEEHKFGVKQKEALKEL 625
EK ++ L +I T L ++ LG + VD+ +A K +
Sbjct: 141 IPKREKENFMQ--NLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVDAI----LKASKNV 194
Query: 626 SKSVHFL 632
K +H L
Sbjct: 195 DKLLHLL 201
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 32.7 bits (73), Expect = 0.21
Identities = 34/127 (26%), Positives = 50/127 (38%), Gaps = 15/127 (11%)
Query: 515 GFGKTEVAMHAIFCAFLNGFQSALVVPTTLLAHQHFETLRARFENFGVKVARLDRY---- 570
G GKT + L G + ++ PT+LL Q ET+R E GV L Y
Sbjct: 81 GVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGR 140
Query: 571 --ASEKNKLLKAVELGQVDALIGTHAILGAKFKNLG---LVVVDEEHKFGVKQKEALKEL 625
EK ++ L +I T L ++ LG + VD+ +A K +
Sbjct: 141 IPKREKENFMQ--NLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVDAI----LKASKNV 194
Query: 626 SKSVHFL 632
K +H L
Sbjct: 195 DKLLHLL 201
>pdb|1F8S|A Chain A, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma, Complexed With Three Molecules
Of O- Aminobenzoate.
pdb|1F8S|B Chain B, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma, Complexed With Three Molecules
Of O- Aminobenzoate.
pdb|1F8S|C Chain C, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma, Complexed With Three Molecules
Of O- Aminobenzoate.
pdb|1F8S|D Chain D, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma, Complexed With Three Molecules
Of O- Aminobenzoate.
pdb|1F8S|E Chain E, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma, Complexed With Three Molecules
Of O- Aminobenzoate.
pdb|1F8S|F Chain F, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma, Complexed With Three Molecules
Of O- Aminobenzoate.
pdb|1F8S|G Chain G, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma, Complexed With Three Molecules
Of O- Aminobenzoate.
pdb|1F8S|H Chain H, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma, Complexed With Three Molecules
Of O- Aminobenzoate.
pdb|1F8R|B Chain B, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma Complexed With Citrate
pdb|1F8R|D Chain D, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma Complexed With Citrate
pdb|1F8R|C Chain C, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma Complexed With Citrate
pdb|1F8R|A Chain A, Crystal Structure Of L-Amino Acid Oxidase From
Calloselasma Rhodostoma Complexed With Citrate
Length = 498
Score = 29.6 bits (65), Expect = 1.7
Identities = 15/49 (30%), Positives = 29/49 (58%)
Query: 68 LGGLREFYQALENKQETIIIAPISALLHPLPKKELLESFKITLLEKYNL 116
+G F+QAL+ K I+ +L+H LPKK++ ++++K++L
Sbjct: 374 IGDDANFFQALDFKDCADIVFNDLSLIHQLPKKDIQSFCYPSVIQKWSL 422
>pdb|1BG0| Transition State Structure Of Arginine Kinase
Length = 356
Score = 27.3 bits (59), Expect = 8.6
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 6/54 (11%)
Query: 109 TLLEKYNLKD----LKDKLFYYGYEILDLVEVEGEASFRGDIVDIYAPNSKAYR 158
+LL+K+ KD +K+K G +LD+++ E G V IYAP++++YR
Sbjct: 24 SLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSG--VGIYAPDAESYR 75
>pdb|1CNT|1 Chain 1, Ciliary Neurotrophic Factor
pdb|1CNT|3 Chain 3, Ciliary Neurotrophic Factor
pdb|1CNT|2 Chain 2, Ciliary Neurotrophic Factor
pdb|1CNT|4 Chain 4, Ciliary Neurotrophic Factor
Length = 187
Score = 27.3 bits (59), Expect = 8.6
Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 18/99 (18%)
Query: 209 EQSPLNSFSKDLTSFGLWFLGEKAQDLLIVYKSIISPRALEEIQELASLNELD------- 261
E SPL +DL S +W + DL + +S + + L + L S + +
Sbjct: 5 EHSPLTPHRRDLCSRSIWLARKIRSDLTALTESYVKHQGLNKNINLDSADGMPVASTDQW 64
Query: 262 CERFKFLKVLENAQGY-----------EDLEIHAHALEG 289
E + ++ EN Q Y ED ++H EG
Sbjct: 65 SELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEG 103
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
0.319 0.137 0.379
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,382,013
Number of Sequences: 13198
Number of extensions: 226503
Number of successful extensions: 624
Number of sequences better than 10.0: 11
Number of HSP's better than 10.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 608
Number of HSP's gapped (non-prelim): 16
length of query: 999
length of database: 2,899,336
effective HSP length: 97
effective length of query: 902
effective length of database: 1,619,130
effective search space: 1460455260
effective search space used: 1460455260
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)