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|15644746|ref|NP_206916.1| DNA topoisomerase I (topA)
[Helicobacter pylori 26695]
(736 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|1CY7|A Chain A, Complex Of E.Coli Dna Topoisomerase I W... 412 e-116
pdb|1ECL| Amino Terminal 67kda Domain Of Escherichia Coli... 410 e-115
pdb|1CYY|B Chain B, Crystal Structure Of The 30 Kda Fragmen... 167 4e-42
pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase C... 160 6e-40
pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus 160 6e-40
pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topois... 114 5e-26
pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoi... 112 1e-25
pdb|1DOT| Mol_id: 1; Molecule: Duck Ovotransferrin; Chain... 28 2.8
pdb|1A6D|A Chain A, Thermosome From T. Acidophilum >gi|4699... 28 4.8
pdb|1J7N|B Chain B, Anthrax Toxin Lethal Factor >gi|1697482... 28 4.8
pdb|1MIO|C Chain C, Nitrogenase Molybdenum-Iron Protein 28 4.8
pdb|1MIO|A Chain A, Nitrogenase Molybdenum-Iron Protein 28 4.8
pdb|1TFA|A Chain A, Ovotransferrin, N-Terminal Lobe, Apo Fo... 27 6.2
pdb|1YUA| C-Terminal Domain Of Escherichia Coli Topoisome... 27 6.2
pdb|1QH8|C Chain C, Nitrogenase Mofe Protein From Klebsiell... 27 6.2
pdb|1NNT| Ovotransferrin (Monoferric N-Terminal Half-Mole... 27 6.2
pdb|1ZIN| Adenylate Kinase With Bound Ap5a >gi|2392649|pd... 27 6.2
pdb|1H1L|A Chain A, Nitrogenase Mo-Fe Protein From Klebsiel... 27 6.2
pdb|1IEJ|A Chain A, Ovotransferrin, N-Terminal Lobe, Holo F... 27 6.2
pdb|1PDZ| Mol_id: 1; Molecule: Enolase; Chain: Null; Syno... 27 6.2
pdb|1AIV| Apo Ovotransferrin >gi|1127086|pdb|1OVT| Mol_i... 27 6.2
pdb|1KFV|A Chain A, Crystal Structure Of Lactococcus Lactis... 27 8.1
pdb|1AVQ|A Chain A, Toroidal Structure Of Lambda Exonucleas... 27 8.1
>pdb|1CY7|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'-Thymidine
Monophosphate
pdb|1CY8|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'-Thymidine
Monophosphate And 3'-Thymidine Monophosphate
pdb|1CY6|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3' Thymidine
Monophosphate
pdb|1CY4|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptptp3'
pdb|1CY1|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt
pdb|1CY2|A Chain A, Complex Of E.Coli Dna Topoisomerase I With Tptptp3'
pdb|1CY0|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3'-5'-Adenosine
Diphosphate
Length = 599
Score = 412 bits (1059), Expect = e-116
Identities = 242/589 (41%), Positives = 362/589 (61%), Gaps = 42/589 (7%)
Query: 2 KHLIIVESPAKAKTIKNFLDKNYEVIASKGHVRDL---------------SKFALGIKID 46
K L+IVESPAKAKTI +L +Y V +S GH+RDL +K A K D
Sbjct: 5 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKD 64
Query: 47 ETGFTPN-------------YVVDKDHKELVKQIIELSKKASITYIATDEDREGEAIGYH 93
E G N Y V +++V ++ +L++KA Y+ATD DREGEAI +H
Sbjct: 65 ERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWH 124
Query: 94 VACLIGGKLESYPRIVFHEITQNAILNALKTPRKIDMSKVNAQQARRFLDRIVGFKLSSL 153
+ +IGG Y R+VF+EIT+NAI A P ++++ +VNAQQARRF+DR+VG+ +S L
Sbjct: 125 LREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPL 184
Query: 154 IASKITKGLSAGRVQSAALKLVIDKEREIKAFKPLTYFTLDAYFESHL-EAQLISYKGNK 212
+ KI +GLSAGRVQS A++LV+++EREIKAF P ++ +DA + EA +
Sbjct: 185 LWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQN 244
Query: 213 LKAQELIDEKKAQEIKNELEKESYAISSIVKKSKKSPTPPPFMTSTLQQSASSLLGFSPT 272
K +++++ Q + LEK Y++ K S PF+TSTLQQ+AS+ LGF
Sbjct: 245 DKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVK 304
Query: 273 KTMSIAQKLYEGVATPQGVMGVITYMRTDSLNIAKEALEEARNKILKDYGKDYLPPKAKV 332
KTM +AQ+LYE G ITYMRTDS N++++A+ R I ++GK YLP
Sbjct: 305 KTMMMAQRLYEA--------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQ 356
Query: 333 YSSKNKNAQEAHEAIRPTSIILEPNALKDYLKPEELRLYTLIYKRFLASQMQDALFESQS 392
Y+SK +N+QEAHEAIRP+ + + +LKD ++ + +LY LI+++F+A QM A ++S +
Sbjct: 357 YASK-ENSQEAHEAIRPSDVNVMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDSTT 414
Query: 393 VVVACEKGEFKASGRKLLFDGYYKI---LGNDDKDKLLPNLKENDPIKLEKLESNAHVTE 449
+ V KA GR L FDG+ K+ L D+D++LP + + D + L +L H T+
Sbjct: 415 LTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTK 474
Query: 450 PPARYSEASLIKVLESLGIGRPSTYAPTISLLQNRDYIKVEKKQISALESAFKVIEILEK 509
PPAR+SEASL+K LE GIGRPSTYA IS +Q+R Y++VE ++ A + V + LE+
Sbjct: 475 PPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEE 534
Query: 510 HFEEIVDSKFSASLEEELDNIAQNKADYQQVLKDFYYPFMDKIEAGKKN 558
+F E+++ F+A +E LD +A ++A+++ VL F+ F +++ +K+
Sbjct: 535 NFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKD 583
>pdb|1ECL| Amino Terminal 67kda Domain Of Escherichia Coli Dna Topoisomerase
I (Residues 2-590 Of Mature Protein) Cloning Artifact
Adds Two Residues To The Amino-Terminus Which Were Not
Observed In The Experimental Electron Density (Gly-2,
Ser-1)
Length = 597
Score = 410 bits (1054), Expect = e-115
Identities = 238/589 (40%), Positives = 361/589 (60%), Gaps = 42/589 (7%)
Query: 2 KHLIIVESPAKAKTIKNFLDKNYEVIASKGHVRDLSKFAL-------------------- 41
K L+IVESPAKAKTI +L +Y V +S GH+RDL+ +
Sbjct: 3 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLTSGSAAKKSADSTSTKTAKKPKKPD 62
Query: 42 --GIKIDETGFTP------NYVVDKDHKELVKQIIELSKKASITYIATDEDREGEAIGYH 93
G ++ G P +Y V +++V ++ +L++KA Y+ATD DREGEAI +H
Sbjct: 63 ERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWH 122
Query: 94 VACLIGGKLESYPRIVFHEITQNAILNALKTPRKIDMSKVNAQQARRFLDRIVGFKLSSL 153
+ +IGG Y R+VF+EIT+NAI A P ++++ +VNAQQARRF+DR+VG+ +S L
Sbjct: 123 LREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPL 182
Query: 154 IASKITKGLSAGRVQSAALKLVIDKEREIKAFKPLTYFTLDAYFESHL-EAQLISYKGNK 212
+ KI +GLSAGRVQS A++LV+++EREIKAF P ++ +DA + EA +
Sbjct: 183 LWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQN 242
Query: 213 LKAQELIDEKKAQEIKNELEKESYAISSIVKKSKKSPTPPPFMTSTLQQSASSLLGFSPT 272
K +++++ Q + LEK Y++ K S PF+TSTLQQ+AS+ LGF
Sbjct: 243 DKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVK 302
Query: 273 KTMSIAQKLYEGVATPQGVMGVITYMRTDSLNIAKEALEEARNKILKDYGKDYLPPKAKV 332
KTM +AQ+LYE G ITYMRTDS N++++A+ R I ++GK YLP
Sbjct: 303 KTMMMAQRLYEA--------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQ 354
Query: 333 YSSKNKNAQEAHEAIRPTSIILEPNALKDYLKPEELRLYTLIYKRFLASQMQDALFESQS 392
Y+SK N+QEAHEAIRP+ + + +LKD ++ + +LY LI+++F+A QM A ++S +
Sbjct: 355 YASKG-NSQEAHEAIRPSDVNVMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDSTT 412
Query: 393 VVVACEKGEFKASGRKLLFDGYYKI---LGNDDKDKLLPNLKENDPIKLEKLESNAHVTE 449
+ V KA GR L FDG+ K+ L D+D++LP + + D + L +L H T+
Sbjct: 413 LTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTK 472
Query: 450 PPARYSEASLIKVLESLGIGRPSTYAPTISLLQNRDYIKVEKKQISALESAFKVIEILEK 509
PPAR+SEASL+K LE GIGRPSTYA IS +Q+R Y++VE ++ A + V + LE+
Sbjct: 473 PPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEE 532
Query: 510 HFEEIVDSKFSASLEEELDNIAQNKADYQQVLKDFYYPFMDKIEAGKKN 558
+F E+++ F+A +E LD +A ++A+++ VL F+ F +++ +K+
Sbjct: 533 NFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKD 581
>pdb|1CYY|B Chain B, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna
Topoisomerase I. Hexagonal Form
pdb|1CYY|A Chain A, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna
Topoisomerase I. Hexagonal Form
pdb|1CY9|A Chain A, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna
Topoisomerase I. Monoclinic Form
pdb|1CY9|B Chain B, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna
Topoisomerase I. Monoclinic Form
Length = 264
Score = 167 bits (423), Expect = 4e-42
Identities = 96/239 (40%), Positives = 146/239 (60%), Gaps = 13/239 (5%)
Query: 219 IDEKKAQEIKNELEKESYAISSIVKKSKKSPTPPPFMTSTLQQSASSLLGFSPTKTMSIA 278
+++++ Q + LEK Y++ K S PF+TSTLQQ+AS+ LGF KTM +A
Sbjct: 36 VNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMA 95
Query: 279 QKLYEGVATPQGVMGVITYMRTDSLNIAKEALEEARNKILKDYGKDYLPPKAKVYSSKNK 338
Q+LYE G ITYMRTDS N++++A+ R I ++GK YLP Y+SK +
Sbjct: 96 QRLYEA--------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-E 146
Query: 339 NAQEAHEAIRPTSIILEPNALKDYLKPEELRLYTLIYKRFLASQMQDALFESQSVVVACE 398
N+QEAHEAIRP+ + + +LKD ++ + +LY LI+++F+A QM A ++S ++ V
Sbjct: 147 NSQEAHEAIRPSDVNVMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAG 205
Query: 399 KGEFKASGRKLLFDGYYKI---LGNDDKDKLLPNLKENDPIKLEKLESNAHVTEPPARY 454
KA GR L FDG+ K+ L D+D++LP + + D + L +L H T+PPAR+
Sbjct: 206 DFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARF 264
>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 = 160 bits (404), Expect = 6e-40
Identities = 155/600 (25%), Positives = 262/600 (42%), Gaps = 118/600 (19%)
Query: 4 LIIVESPAKAKTIKNFLDKN----------YE---------VIASKGHVRDL--SKFALG 42
L IVESP KA+ I F K YE V AS GHV DL ++ G
Sbjct: 508 LFIVESPTKARQISRFFGKPSVKVLDGAVVYEIPMQKYVLMVTASIGHVVDLITNRGFHG 567
Query: 43 IKIDETGFTPNYVVDK-------------------------DHKELVKQIIELSKKASIT 77
+ ++ F P Y K + + ++ + +L+ A
Sbjct: 568 VLVNGR-FVPVYASIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLAHDAEFV 626
Query: 78 YIATDEDREGEAIGYHVACLIGGKLESYPRIVFHEITQNAILNALKTPRKIDMSKVNAQQ 137
+ TD D EGE I + + L+ G + R FHE+T+ AIL AL++ R +D + V AQ
Sbjct: 627 IVGTDPDTEGEKIAWDLKNLLSG-CGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQV 685
Query: 138 ARRFLDRIVGFKLSSLIASKIT-KGLSAGRVQSAALKLVIDKEREIKAFKPLTYFTLDAY 196
RR DR +GF LS + + + LSAGR Q+ L +ID+ +E + + +
Sbjct: 686 VRRIEDRWIGFVLSQKLWERFNNRNLSAGRAQTLVLGWIIDRFQESRERRKIAI------ 739
Query: 197 FESHLEAQLISYKGNKLKAQELIDEKKAQEIKNELEKESYAISSIVKKSKKSPTP-PPFM 255
++ +L+ E +E ++ +V++ ++ TP PP+
Sbjct: 740 ----------------VRDFDLVLEHDEEEFDLTIK--------LVEEREELRTPLPPYT 775
Query: 256 TSTLQQSASSLLGFSPTKTMSIAQKLYEGVATPQGVMGVITYMRTDSLNIAKEALEEARN 315
T T+ A+ +L FS +TM IAQ+L+E G+ITY RTDS ++ +
Sbjct: 776 TETMLSDANRILKFSVKQTMQIAQELFEN--------GLITYHRTDSTRVS-----DVGQ 822
Query: 316 KILKDY-GKDYLPPKAKVYSSKNKNAQEAHEAIRPT---------SIILEPNALKDYLKP 365
+I K+Y G D++ + AHE IRPT +I E + + L+
Sbjct: 823 RIAKEYLGDDFV--------GREWGESGAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRW 874
Query: 366 EELRLYTLIYKRFLASQMQDALFESQSVVVACEKGEFKASGRKLLFDGYYKILGNDDKDK 425
E LY LI++RF+ASQ + V +K + G+ + + G +
Sbjct: 875 EHFALYDLIFRRFMASQ-------CRPFKVVVKKYSIEFDGKTAEEERIVRAEGRAYELY 927
Query: 426 LLPNLKENDPIKLEKLESNAHVTEPPARYSEASLIKVLESLGIGRPSTYAPTISLLQNRD 485
+K P ++++ ++++ +I++++ GIGRPSTYA + L R+
Sbjct: 928 RAVWVKNELPTGTFRVKAEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLFMRN 987
Query: 486 YIKVEKKQISALESAFKVIEILEKHFEEIVDSKFSASLEEELDNIAQNKADYQQVLKDFY 545
Y+ + ++ + V L + + + V + LE +D I + + DY + L+D Y
Sbjct: 988 YVVEKYGRMIPTKLGIDVFRFLVRRYAKFVSEDRTRDLESRMDAIERGELDYLKALEDMY 1047
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 160 bits (404), Expect = 6e-40
Identities = 155/600 (25%), Positives = 262/600 (42%), Gaps = 118/600 (19%)
Query: 4 LIIVESPAKAKTIKNFLDKN----------YE---------VIASKGHVRDL--SKFALG 42
L IVESP KA+ I F K YE V AS GHV DL ++ G
Sbjct: 508 LFIVESPTKARQISRFFGKPSVKVLDGAVVYEIPMQKYVLMVTASIGHVVDLITNRGFHG 567
Query: 43 IKIDETGFTPNYVVDK-------------------------DHKELVKQIIELSKKASIT 77
+ ++ F P Y K + + ++ + +L+ A
Sbjct: 568 VLVNGR-FVPVYASIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLAHDAEFV 626
Query: 78 YIATDEDREGEAIGYHVACLIGGKLESYPRIVFHEITQNAILNALKTPRKIDMSKVNAQQ 137
+ TD D EGE I + + L+ G + R FHE+T+ AIL AL++ R +D + V AQ
Sbjct: 627 IVGTDPDTEGEKIAWDLKNLLSG-CGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQV 685
Query: 138 ARRFLDRIVGFKLSSLIASKIT-KGLSAGRVQSAALKLVIDKEREIKAFKPLTYFTLDAY 196
RR DR +GF LS + + + LSAGR Q+ L +ID+ +E + + +
Sbjct: 686 VRRIEDRWIGFVLSQKLWERFNNRNLSAGRAQTLVLGWIIDRFQESRERRKIAI------ 739
Query: 197 FESHLEAQLISYKGNKLKAQELIDEKKAQEIKNELEKESYAISSIVKKSKKSPTP-PPFM 255
++ +L+ E +E ++ +V++ ++ TP PP+
Sbjct: 740 ----------------VRDFDLVLEHDEEEFDLTIK--------LVEEREELRTPLPPYT 775
Query: 256 TSTLQQSASSLLGFSPTKTMSIAQKLYEGVATPQGVMGVITYMRTDSLNIAKEALEEARN 315
T T+ A+ +L FS +TM IAQ+L+E G+ITY RTDS ++ +
Sbjct: 776 TETMLSDANRILKFSVKQTMQIAQELFEN--------GLITYHRTDSTRVS-----DVGQ 822
Query: 316 KILKDY-GKDYLPPKAKVYSSKNKNAQEAHEAIRPT---------SIILEPNALKDYLKP 365
+I K+Y G D++ + AHE IRPT +I E + + L+
Sbjct: 823 RIAKEYLGDDFV--------GREWGESGAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRW 874
Query: 366 EELRLYTLIYKRFLASQMQDALFESQSVVVACEKGEFKASGRKLLFDGYYKILGNDDKDK 425
E LY LI++RF+ASQ + V +K + G+ + + G +
Sbjct: 875 EHFALYDLIFRRFMASQ-------CRPFKVVVKKYSIEFDGKTAEEERIVRAEGRAYELY 927
Query: 426 LLPNLKENDPIKLEKLESNAHVTEPPARYSEASLIKVLESLGIGRPSTYAPTISLLQNRD 485
+K P ++++ ++++ +I++++ GIGRPSTYA + L R+
Sbjct: 928 RAVWVKNELPTGTFRVKAEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLFMRN 987
Query: 486 YIKVEKKQISALESAFKVIEILEKHFEEIVDSKFSASLEEELDNIAQNKADYQQVLKDFY 545
Y+ + ++ + V L + + + V + LE +D I + + DY + L+D Y
Sbjct: 988 YVVEKYGRMIPTKLGIDVFRFLVRRYAKFVSEDRTRDLESRMDAIERGELDYLKALEDMY 1047
>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii
Length = 653
Score = 114 bits (284), Expect = 5e-26
Identities = 129/563 (22%), Positives = 225/563 (39%), Gaps = 76/563 (13%)
Query: 73 KASITYIATDEDREGEAIGYHVAC---LIGGKLESYPRIVFHEITQNAILNALKTPRKID 129
+AS A D DREG+ + V L K + R + +++ A+ R ID
Sbjct: 94 EASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAV------ERAID 147
Query: 130 MSKVNAQQARRFLDRIVGFKLSSLIASKITKG-------------LSAGRVQSAALKLVI 176
+ N++ + + + L +T+ LS GRVQ+ L LV+
Sbjct: 148 RLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVV 207
Query: 177 DKEREIKAFKPLTYFTLDAYFESHLEAQLISYKGNKLKAQELIDEKK-------AQEIKN 229
++ EI+ F +F + A+ + + + + + DE+ A+ + N
Sbjct: 208 RRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVN 267
Query: 230 ELEKESYAISSIVKKSKKSPTPPPFMTSTLQQSASSLLGFSPTKTMSIAQKLYEGVATPQ 289
+ + ++S K + P PF S LQ A+ G S + I QKLYE
Sbjct: 268 RISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYE------ 321
Query: 290 GVMGVITYMRTDSLNIAKE--ALEEARNKILKDYGKDYLPPKAKVYSSKNK----NAQEA 343
+ITY R+D + +E A A + + D LP +N+ +A
Sbjct: 322 -THKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDA 380
Query: 344 HEAIRPTSIILEPNALKDYLKPEELRLYTLIYKRFLASQMQDALFESQSVVVACEKGEFK 403
H AI PT+ N L E ++Y LI +++L DA+F + + KG+F
Sbjct: 381 HHAIIPTARSSAIN-----LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFV 435
Query: 404 ASGRKLLFDGYYKILGNDDKDK-----LLPNLKENDPIKLEKLESNAHVTEPPARYSEAS 458
A R L G+ +LG+ ++D+ LP + + D + EK E T+PP +++A+
Sbjct: 436 AKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDAT 495
Query: 459 LIKVLESL-----------------GIGRPSTYAPTISLLQNRDYIKVEKKQISALESAF 501
L+ + + G+G +T A I LL R ++ + + I + ++
Sbjct: 496 LLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGK 555
Query: 502 KVIEILEKHFEEIVDSKFSASLEEELDNIAQNKADYQQVLKDFYYPFMDKIEAGKKNIIS 561
+ L E +A E L I++ + YQ ++ I+ K+
Sbjct: 556 ALFHSLP---EMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRT--- 609
Query: 562 QKVHEKTGQSCPKCGGELVKKNS 584
V + G P GG KK +
Sbjct: 610 -PVRQFRGIVAPGSGGSADKKKA 631
>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With
An 8-Base Single-Stranded Dna Oligonucleotide
Length = 659
Score = 112 bits (280), Expect = 1e-25
Identities = 128/563 (22%), Positives = 225/563 (39%), Gaps = 76/563 (13%)
Query: 73 KASITYIATDEDREGEAIGYHVAC---LIGGKLESYPRIVFHEITQNAILNALKTPRKID 129
+AS A D DREG+ + V L K + R + +++ A+ R ID
Sbjct: 94 EASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAV------ERAID 147
Query: 130 MSKVNAQQARRFLDRIVGFKLSSLIASKITKG-------------LSAGRVQSAALKLVI 176
+ N++ + + + L +T+ LS GRVQ+ L LV+
Sbjct: 148 RLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVV 207
Query: 177 DKEREIKAFKPLTYFTLDAYFESHLEAQLISYKGNKLKAQELIDEKK-------AQEIKN 229
++ EI+ F +F + A+ + + + + + DE+ A+ + N
Sbjct: 208 RRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVN 267
Query: 230 ELEKESYAISSIVKKSKKSPTPPPFMTSTLQQSASSLLGFSPTKTMSIAQKLYEGVATPQ 289
+ + ++S K + P PF S LQ A+ G S + I QKLYE
Sbjct: 268 RISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYE------ 321
Query: 290 GVMGVITYMRTDSLNIAKE--ALEEARNKILKDYGKDYLPPKAKVYSSKNK----NAQEA 343
+IT+ R+D + +E A A + + D LP +N+ +A
Sbjct: 322 -THKLITFPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDA 380
Query: 344 HEAIRPTSIILEPNALKDYLKPEELRLYTLIYKRFLASQMQDALFESQSVVVACEKGEFK 403
H AI PT+ N L E ++Y LI +++L DA+F + + KG+F
Sbjct: 381 HHAIIPTARSSAIN-----LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFV 435
Query: 404 ASGRKLLFDGYYKILGNDDKDK-----LLPNLKENDPIKLEKLESNAHVTEPPARYSEAS 458
A R L G+ +LG+ ++D+ LP + + D + EK E T+PP +++A+
Sbjct: 436 AKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDAT 495
Query: 459 LIKVLESL-----------------GIGRPSTYAPTISLLQNRDYIKVEKKQISALESAF 501
L+ + + G+G +T A I LL R ++ + + I + ++
Sbjct: 496 LLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGK 555
Query: 502 KVIEILEKHFEEIVDSKFSASLEEELDNIAQNKADYQQVLKDFYYPFMDKIEAGKKNIIS 561
+ L E +A E L I++ + YQ ++ I+ K+
Sbjct: 556 ALFHSLP---EMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRT--- 609
Query: 562 QKVHEKTGQSCPKCGGELVKKNS 584
V + G P GG KK +
Sbjct: 610 -PVRQFRGIVAPGSGGSADKKKA 631
>pdb|1DOT| Mol_id: 1; Molecule: Duck Ovotransferrin; Chain: Null; Synonym:
Dot
pdb|1AOV| Apo Duck Ovotransferrin
Length = 686
Score = 28.5 bits (62), Expect = 2.8
Identities = 16/59 (27%), Positives = 26/59 (43%), Gaps = 11/59 (18%)
Query: 612 DQELCEKCGGEMVQKFSRNGAFLACNNYPEC-----------KNTKSLKNTPNAKETIE 659
+Q+LC +C G+ K RNG + + +C K+T +N P K+ E
Sbjct: 167 EQKLCRQCKGDAKTKCLRNGPYSGYSGAFQCLKDGKGDVAFVKHTTVQENAPEEKDEYE 225
>pdb|1A6D|A Chain A, Thermosome From T. Acidophilum
pdb|1A6E|A Chain A, Thermosome - Mg-Adp-Alf3 Complex
Length = 545
Score = 27.7 bits (60), Expect = 4.8
Identities = 44/188 (23%), Positives = 81/188 (42%), Gaps = 41/188 (21%)
Query: 353 ILEPNALKDYLKPEELRLYTLIYKRFLASQMQDALFESQSVVVACEKGEFKASGRKLLFD 412
I +P+ ++D+L E T +K QM + + +S + VV C+KG + L +
Sbjct: 256 ISDPSKIQDFLNQE-----TNTFK-----QMVEKIKKSGANVVLCQKGIDDVAQHYLAKE 305
Query: 413 GYYKILGNDDKDKLLPNLKENDPIKLEKLESNAHVTE----PPARYSEASLIKVLE---- 464
G Y + +K++D KL K VT+ P+ EA ++ +
Sbjct: 306 GIYAV----------RRVKKSDMEKLAKATGAKIVTDLDDLTPSVLGEAETVEERKIGDD 355
Query: 465 --SLGIGRPSTYAPTISLLQNRDYIKVEKKQISALESAFKVIEILEKHFEEIVDSKF--- 519
+ +G + A +I + D++ E ++ AL A +V+ I ++ D KF
Sbjct: 356 RMTFVMGCKNPKAVSILIRGGTDHVVSEVER--ALNDAIRVVAITKE------DGKFLWG 407
Query: 520 SASLEEEL 527
++E EL
Sbjct: 408 GGAVEAEL 415
>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 = 27.7 bits (60), Expect = 4.8
Identities = 56/275 (20%), Positives = 111/275 (40%), Gaps = 41/275 (14%)
Query: 304 NIAKEALEEARNKILKDYGKDYLPPKAKVYSSKNKNAQEAHEAIRPTSIILEPNALKDYL 363
+I+ EAL E + KI YGKD L + VY A E P +I + +DY+
Sbjct: 91 HISLEALSEDKKKIKDIYGKDALLHEHYVY---------AKEGYEPVLVI---QSSEDYV 138
Query: 364 KPEE--LRLYTLIYK---RFLASQMQDALFESQSVVVACEKGEFKASGRKLLFDGYYKIL 418
+ E L +Y I K R + S++ ++ V+ K + G+ LLF K
Sbjct: 139 ENTEKALNVYYEIGKILSRDILSKINQP-YQKFLDVLNTIKNASDSDGQDLLFTNQLKEH 197
Query: 419 GNDDKDKLLPNLKENDPIKLEKLESNAHVTEPPARYSEASLIKVLESLGIGRPSTYAPTI 478
D + L + ++ ++ ++ A+ EP R + L + P +
Sbjct: 198 PTDFSVEFLE--QNSNEVQEVFAKAFAYYIEPQHR----------DVLQLYAPEAFNYMD 245
Query: 479 SLLQNRDYIKVEKKQISALESAFKVIEILEKHFEEIVDS----------KFSASLEEELD 528
+ + +E+ + + S ++ E +++H++ DS K +E + D
Sbjct: 246 KFNEQEINLSLEELKDQRMLSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKD 305
Query: 529 NIAQN-KADYQQVLKDFYYPFMDKIEAGKKNIISQ 562
+I + + +++LK D + +K + +
Sbjct: 306 DIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKK 340
>pdb|1MIO|C Chain C, Nitrogenase Molybdenum-Iron Protein
Length = 533
Score = 27.7 bits (60), Expect = 4.8
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 55 VVDKDHKELVKQIIELSKKASITYIATDEDREGEAIGYHVACLIGGKLESYPRIVFHEIT 114
++ K +KE K I + + +I A + DR E IGYHV + G +Y ++ +
Sbjct: 196 IIGKGNKEQKKYSINVLGEYNIGGDAWEMDRVLEKIGYHVNATLTGD-ATYEKV---QNA 251
Query: 115 QNAILNALKTPRKID 129
A LN ++ R I+
Sbjct: 252 DKADLNLVQCHRSIN 266
>pdb|1MIO|A Chain A, Nitrogenase Molybdenum-Iron Protein
Length = 525
Score = 27.7 bits (60), Expect = 4.8
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 55 VVDKDHKELVKQIIELSKKASITYIATDEDREGEAIGYHVACLIGGKLESYPRIVFHEIT 114
++ K +KE K I + + +I A + DR E IGYHV + G +Y ++ +
Sbjct: 196 IIGKGNKEQKKYSINVLGEYNIGGDAWEMDRVLEKIGYHVNATLTGD-ATYEKV---QNA 251
Query: 115 QNAILNALKTPRKID 129
A LN ++ R I+
Sbjct: 252 DKADLNLVQCHRSIN 266
>pdb|1TFA|A Chain A, Ovotransferrin, N-Terminal Lobe, Apo Form
pdb|1NFT|A Chain A, Ovotransferrin, N-Terminal Lobe, Iron Loaded Open Form
Length = 329
Score = 27.3 bits (59), Expect = 6.2
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 24/91 (26%)
Query: 612 DQELCEKCGGEMVQKFSRNGAFLACNNYPEC-----------KNTKSLKNTPNAKETIEG 660
+Q+LC +C G+ K +RN + + C K+T +N P+ K+ E
Sbjct: 164 EQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYE- 222
Query: 661 VKCPECGGDIALKRSKKGSFYGCNNYPKCNF 691
+ C + GS +NY CN+
Sbjct: 223 LLCLD------------GSRQPVDNYKTCNW 241
>pdb|1YUA| C-Terminal Domain Of Escherichia Coli Topoisomerase I
Length = 122
Score = 27.3 bits (59), Expect = 6.2
Identities = 11/32 (34%), Positives = 17/32 (52%)
Query: 616 CEKCGGEMVQKFSRNGAFLACNNYPECKNTKS 647
CEK V + G FLA N +P+ + T++
Sbjct: 20 CEKSDAYFVLRDGAAGVFLAANTFPKSRETRA 51
>pdb|1QH8|C Chain C, Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-
Crystallized (Mixed Oxidation) State
pdb|1QH8|A Chain A, Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-
Crystallized (Mixed Oxidation) State
pdb|1QH1|C Chain C, Nitrogenase Mofe Protein From Klebsiella Pneumoniae,
Phenosafranin Oxidized State
pdb|1QGU|C Chain C, Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae,
Dithionite-Reduced State
pdb|1QGU|A Chain A, Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae,
Dithionite-Reduced State
pdb|1QH1|A Chain A, Nitrogenase Mofe Protein From Klebsiella Pneumoniae,
Phenosafranin Oxidized State
Length = 478
Score = 27.3 bits (59), Expect = 6.2
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 400 GEFKASGRKLLFDGYYKILGNDDKDKLLPNLKE 432
G ++ G +++ GY + NDD D+ LP+LKE
Sbjct: 363 GAYEDLGMEIIAAGY-EFAHNDDYDRTLPDLKE 394
>pdb|1NNT| Ovotransferrin (Monoferric N-Terminal Half-Molecule)
Length = 328
Score = 27.3 bits (59), Expect = 6.2
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 24/91 (26%)
Query: 612 DQELCEKCGGEMVQKFSRNGAFLACNNYPEC-----------KNTKSLKNTPNAKETIEG 660
+Q+LC +C G+ K +RN + + C K+T +N P+ K+ E
Sbjct: 163 EQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYE- 221
Query: 661 VKCPECGGDIALKRSKKGSFYGCNNYPKCNF 691
+ C + GS +NY CN+
Sbjct: 222 LLCLD------------GSRQPVDNYKTCNW 240
>pdb|1ZIN| Adenylate Kinase With Bound Ap5a
pdb|1ZIP| Bacillus Stearothermophilus Adenylate Kinase
pdb|1ZIO| Phosphotransferase
Length = 217
Score = 27.3 bits (59), Expect = 6.2
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 615 LCEKCGGEMVQKFSRNGAFLACNNYPECKNTKSL 648
+C+KCGGE+ Q+ N A +A K K L
Sbjct: 149 VCDKCGGELYQRADDNEATVANRLEVNMKQMKPL 182
>pdb|1H1L|A Chain A, Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv
Mutant
pdb|1H1L|C Chain C, Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv
Mutant
Length = 481
Score = 27.3 bits (59), Expect = 6.2
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 400 GEFKASGRKLLFDGYYKILGNDDKDKLLPNLKE 432
G ++ G +++ GY + NDD D+ LP+LKE
Sbjct: 363 GAYEDLGMEIIAAGY-EFAHNDDYDRTLPDLKE 394
>pdb|1IEJ|A Chain A, Ovotransferrin, N-Terminal Lobe, Holo Form, At 1.65 A
Resolution
Length = 332
Score = 27.3 bits (59), Expect = 6.2
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 24/91 (26%)
Query: 612 DQELCEKCGGEMVQKFSRNGAFLACNNYPEC-----------KNTKSLKNTPNAKETIEG 660
+Q+LC +C G+ K +RN + + C K+T +N P+ K+ E
Sbjct: 167 EQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYE- 225
Query: 661 VKCPECGGDIALKRSKKGSFYGCNNYPKCNF 691
+ C + GS +NY CN+
Sbjct: 226 LLCLD------------GSRQPVDNYKTCNW 244
>pdb|1PDZ| Mol_id: 1; Molecule: Enolase; Chain: Null; Synonym:
2-Phospho-D-Glycerate Dehydratase; Ec: 4.2.1.11;
Heterogen: Phosphoglycolate; Heterogen: Mn 2+
pdb|1PDY| Mol_id: 1; Molecule: Enolase; Chain: Null; Synonym:
2-Phospho-D-Glycerate Dehydratase; Ec: 4.2.1.11
Length = 434
Score = 27.3 bits (59), Expect = 6.2
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 7/50 (14%)
Query: 32 HVRDLSKFALGIKI----DETGFTPNYVVDKDHKELVKQIIELSKKASIT 77
H++ + K G+ DE GF PN + +KD +L+++ I KKA T
Sbjct: 191 HLKAVIKARFGLDATAVGDEGGFAPNILNNKDALDLIQEAI---KKAGYT 237
>pdb|1AIV| Apo Ovotransferrin
pdb|1OVT| Mol_id: 1; Molecule: Ovotransferrin; Chain: Null; Synonym:
Conalbumin; Heterogen: Iron (Fe); Heterogen: Bicarbonate
(Co3); Other_details: Diferric Form
Length = 686
Score = 27.3 bits (59), Expect = 6.2
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 24/91 (26%)
Query: 612 DQELCEKCGGEMVQKFSRNGAFLACNNYPEC-----------KNTKSLKNTPNAKETIEG 660
+Q+LC +C G+ K +RN + + C K+T +N P+ K+ E
Sbjct: 167 EQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYE- 225
Query: 661 VKCPECGGDIALKRSKKGSFYGCNNYPKCNF 691
+ C + GS +NY CN+
Sbjct: 226 LLCLD------------GSRQPVDNYKTCNW 244
>pdb|1KFV|A Chain A, Crystal Structure Of Lactococcus Lactis Formamido-
Pyrimidine Dna Glycosylase (Alias Fpg Or Mutm) Non
Covalently Bound To An Ap Site Containing Dna.
pdb|1KFV|B Chain B, Crystal Structure Of Lactococcus Lactis Formamido-
Pyrimidine Dna Glycosylase (Alias Fpg Or Mutm) Non
Covalently Bound To An Ap Site Containing Dna
Length = 271
Score = 26.9 bits (58), Expect = 8.1
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 563 KVHEKTGQSCPKCGGELVK 581
+V+ KTG+ C +CG E+ K
Sbjct: 236 QVYGKTGEKCSRCGAEIQK 254
>pdb|1AVQ|A Chain A, Toroidal Structure Of Lambda Exonuclease Determined At 2.4
Angstroms
pdb|1AVQ|B Chain B, Toroidal Structure Of Lambda Exonuclease Determined At 2.4
Angstroms
pdb|1AVQ|C Chain C, Toroidal Structure Of Lambda Exonuclease Determined At 2.4
Angstroms
Length = 228
Score = 26.9 bits (58), Expect = 8.1
Identities = 18/70 (25%), Positives = 29/70 (40%)
Query: 432 ENDPIKLEKLESNAHVTEPPARYSEASLIKVLESLGIGRPSTYAPTISLLQNRDYIKVEK 491
END L + S +VTE P Y + S+ G+ +RD++K
Sbjct: 87 ENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRL 146
Query: 492 KQISALESAF 501
A++SA+
Sbjct: 147 GGFEAIKSAY 156
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
0.314 0.133 0.371
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,151,069
Number of Sequences: 13198
Number of extensions: 171644
Number of successful extensions: 502
Number of sequences better than 10.0: 23
Number of HSP's better than 10.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 442
Number of HSP's gapped (non-prelim): 43
length of query: 736
length of database: 2,899,336
effective HSP length: 95
effective length of query: 641
effective length of database: 1,645,526
effective search space: 1054782166
effective search space used: 1054782166
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.9 bits)