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|15645909|ref|NP_208088.1| ribosomal protein S13
(rps13) [Helicobacter pylori 26695]
(120 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|1MJ1|P Chain P, Fitting The Ternary Complex Of Ef-TuTRN... 137 3e-34
pdb|1I94|M Chain M, Crystal Structures Of The Small Ribosom... 135 1e-33
pdb|1QM4|A Chain A, Methionine Adenosyltransferase Complexe... 26 1.1
pdb|1KFD| Dna Polymerase I (Klenow Fragment) (E.C.2.7.7.7... 26 1.4
pdb|1KLN|A Chain A, Dna Polymerase I (Klenow Fragment) (E.C... 26 1.4
pdb|2KFN|A Chain A, Klenow Fragment With Bridging-Sulfur Su... 26 1.4
pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna... 26 1.4
pdb|1LWU|C Chain C, Crystal Structure Of Fragment D From La... 25 1.8
pdb|1QQK|A Chain A, The Crystal Structure Of Fibroblast Gro... 25 3.1
pdb|1GOS|A Chain A, Human Monoamine Oxidase B >gi|17942912|... 24 4.0
pdb|1SCU|A Chain A, Succinyl-Coa Synthetase (Succinate-Coa ... 24 5.3
pdb|1CQJ|A Chain A, Crystal Structure Of Dephosphorylated E... 24 5.3
pdb|1QF6|A Chain A, Structure Of E. Coli Threonyl-Trna Synt... 23 6.9
pdb|1CVR|A Chain A, Crystal Structure Of The Arg Specific C... 23 6.9
>pdb|1MJ1|P Chain P, Fitting The Ternary Complex Of Ef-TuTRNAGTP AND BOSOMAL
Proteins Into A 13 A Cryo-Em Map Of The Coli 70s
Ribosome
pdb|1FJG|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1J5E|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1HR0|M Chain M, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNZ|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1IBK|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1HNW|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1IBL|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site And With The Antibiotic Paromomycin
pdb|1IBM|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site
pdb|1JGQ|P Chain P, The Path Of Messenger Rna Through The Ribosome. This File,
1jgq, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1GIX|P Chain P, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1gix, Contains The 30s Ribosome Subunit,
Three Trna, And Mrna Molecules. 50s Ribosome Subunit Is
In The File 1giy
pdb|1JGO|P Chain P, The Path Of Messenger Rna Through The Ribosome. This File,
1jgo, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1JGP|P Chain P, The Path Of Messenger Rna Through The Ribosome. This File,
1jgp, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
Length = 126
Score = 137 bits (345), Expect = 3e-34
Identities = 67/120 (55%), Positives = 91/120 (75%)
Query: 1 MARIAGVDLPKKKRVEYALTYIYGIGLKSSREILEAVGISFDKRVHELSEDEVSSIAKKI 60
MARIAGV++P+ KRV+ ALTYIYGIG ++E LE GI+ RV +L+E EV + + +
Sbjct: 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60
Query: 61 QQSYLVEGDLRKKVQMDIKSLMDLGNYRGIRHRKGLPVRGQTTKNNARTRKGKKKTVGSK 120
+ ++ +EG+LR +V +IK LMD+G YRG+RHR+GLPVRGQ T+ NARTRKG +KTV K
Sbjct: 61 ENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGK 120
>pdb|1I94|M Chain M, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|M Chain M, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|M Chain M, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|M Chain M, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 125
Score = 135 bits (340), Expect = 1e-33
Identities = 66/119 (55%), Positives = 90/119 (75%)
Query: 2 ARIAGVDLPKKKRVEYALTYIYGIGLKSSREILEAVGISFDKRVHELSEDEVSSIAKKIQ 61
ARIAGV++P+ KRV+ ALTYIYGIG ++E LE GI+ RV +L+E EV + + ++
Sbjct: 1 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE 60
Query: 62 QSYLVEGDLRKKVQMDIKSLMDLGNYRGIRHRKGLPVRGQTTKNNARTRKGKKKTVGSK 120
++ +EG+LR +V +IK LMD+G YRG+RHR+GLPVRGQ T+ NARTRKG +KTV K
Sbjct: 61 NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGK 119
>pdb|1QM4|A Chain A, Methionine Adenosyltransferase Complexed With A
L-Methionine Analogous
pdb|1QM4|B Chain B, Methionine Adenosyltransferase Complexed With A
L-Methionine Analogous
Length = 396
Score = 26.2 bits (56), Expect = 1.1
Identities = 11/24 (45%), Positives = 15/24 (61%)
Query: 21 YIYGIGLKSSREILEAVGISFDKR 44
+ YG K+ RE+LE V +FD R
Sbjct: 334 FTYGTSKKTERELLEVVNKNFDLR 357
>pdb|1KFD| Dna Polymerase I (Klenow Fragment) (E.C.2.7.7.7) Complexed With
Dctp
pdb|1DPI| DNA Polymerase I (Klenow Fragment) (E.C.2.7.7.7) - dCMP Complex
Length = 605
Score = 25.8 bits (55), Expect = 1.4
Identities = 15/45 (33%), Positives = 29/45 (64%), Gaps = 6/45 (13%)
Query: 42 DKRVHELSEDEVSSIAKKIQQSYLVEGDLRKKVQMDIKSLMDLGN 86
D+ V E+ +D+V ++AK+I Q L+E R +D+ L+++G+
Sbjct: 559 DELVFEVHKDDVDAVAKQIHQ--LMENCTR----LDVPLLVEVGS 597
>pdb|1KLN|A Chain A, Dna Polymerase I (Klenow Fragment) (E.C.2.7.7.7) Mutant
With Asp 355 Replaced By Ala (D355a) Complexed With Dna
Length = 605
Score = 25.8 bits (55), Expect = 1.4
Identities = 15/45 (33%), Positives = 29/45 (64%), Gaps = 6/45 (13%)
Query: 42 DKRVHELSEDEVSSIAKKIQQSYLVEGDLRKKVQMDIKSLMDLGN 86
D+ V E+ +D+V ++AK+I Q L+E R +D+ L+++G+
Sbjct: 559 DELVFEVHKDDVDAVAKQIHQ--LMENCTR----LDVPLLVEVGS 597
>pdb|2KFN|A Chain A, Klenow Fragment With Bridging-Sulfur Substrate And
Manganese
pdb|2KFZ|A Chain A, Klenow Fragment With Bridging-Sulfur Substrate And Zinc
Only
pdb|1KFS|A Chain A, All-Oxygen Dna Complexed To The 3'-5' Exonuclease Of Dna
Polymerase I From E. Coli
pdb|1D9D|A Chain A, Crystall Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Short Dna Fragment Carrying 2'-0-
Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'
pdb|1KRP|A Chain A, Rp Isomer Phosphorothioate Dna Complexed To The 3'-5'
Exonuclease Of Dna Polymerase I From E. Coli
pdb|1QSL|A Chain A, Klenow Fragment Complexed With Single-Stranded Substrate
And Europium (Iii) Ion
pdb|2KZZ|A Chain A, Klenow Fragment With Normal Substrate And Zinc Only
pdb|1KSP|A Chain A, Sp Isomer Phosphorothioate Dna Complexed To The 3'-5'
Exonuclease Of Dna Polymerase I From E. Coli
pdb|2KZM|A Chain A, Klenow Fragment With Normal Substrate And Zinc And
Manganese
pdb|1D9F|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Dna Tetramer Carrying
2'-O-(3-Aminopropyl)- Rna Modification
5'-D(Tt)-Ap(U)-D(T)-3'
Length = 605
Score = 25.8 bits (55), Expect = 1.4
Identities = 15/45 (33%), Positives = 29/45 (64%), Gaps = 6/45 (13%)
Query: 42 DKRVHELSEDEVSSIAKKIQQSYLVEGDLRKKVQMDIKSLMDLGN 86
D+ V E+ +D+V ++AK+I Q L+E R +D+ L+++G+
Sbjct: 559 DELVFEVHKDDVDAVAKQIHQ--LMENCTR----LDVPLLVEVGS 597
>pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Dna
Length = 605
Score = 25.8 bits (55), Expect = 1.4
Identities = 15/45 (33%), Positives = 29/45 (64%), Gaps = 6/45 (13%)
Query: 42 DKRVHELSEDEVSSIAKKIQQSYLVEGDLRKKVQMDIKSLMDLGN 86
D+ V E+ +D+V ++AK+I Q L+E R +D+ L+++G+
Sbjct: 559 DELVFEVHKDDVDAVAKQIHQ--LMENCTR----LDVPLLVEVGS 597
>pdb|1LWU|C Chain C, Crystal Structure Of Fragment D From Lamprey Fibrinogen
Complexed With The Peptide Gly-His-Arg-Pro-Amide
pdb|1LWU|F Chain F, Crystal Structure Of Fragment D From Lamprey Fibrinogen
Complexed With The Peptide Gly-His-Arg-Pro-Amide
pdb|1LWU|I Chain I, Crystal Structure Of Fragment D From Lamprey Fibrinogen
Complexed With The Peptide Gly-His-Arg-Pro-Amide
pdb|1LWU|L Chain L, Crystal Structure Of Fragment D From Lamprey Fibrinogen
Complexed With The Peptide Gly-His-Arg-Pro-Amide
Length = 323
Score = 25.4 bits (54), Expect = 1.8
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 33 ILEAVGISFDKRVHELSE 50
ILE +G+S D ++ ELSE
Sbjct: 16 ILEQIGVSHDAQIQELSE 33
>pdb|1QQK|A Chain A, The Crystal Structure Of Fibroblast Growth Factor 7
(Keratinocyte Growth Factor)
pdb|1QQK|B Chain B, The Crystal Structure Of Fibroblast Growth Factor 7
(Keratinocyte Growth Factor)
Length = 140
Score = 24.6 bits (52), Expect = 3.1
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 92 HRKGLPVRGQTTKNNART 109
++KGLPV+G+ TK +T
Sbjct: 114 NQKGLPVKGKKTKKEQKT 131
>pdb|1GOS|A Chain A, Human Monoamine Oxidase B
pdb|1GOS|B Chain B, Human Monoamine Oxidase B
Length = 520
Score = 24.3 bits (51), Expect = 4.0
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 26 GLKSSREILEAVGISFDKRVHELSEDEVSSIAKKIQQSYL------VEGDLRKKVQMDIK 79
G +++REIL A+G + + + + V A+ I ++L V G LR I
Sbjct: 443 GERAAREILHAMGKIPEDEIWQSEPESVDVPAQPITTTFLERHLPSVPGLLRLIGLTTIF 502
Query: 80 SLMDLGNYRGIRHRKGLPVR 99
S LG + H++GL VR
Sbjct: 503 SATALG---FLAHKRGLLVR 519
>pdb|1SCU|A Chain A, Succinyl-Coa Synthetase (Succinate-Coa Ligase)
(Adp-Forming) (E.C.6.2.1.5)
pdb|1SCU|D Chain D, Succinyl-Coa Synthetase (Succinate-Coa Ligase)
(Adp-Forming) (E.C.6.2.1.5)
pdb|1JKJ|A Chain A, E. Coli Scs
pdb|1JKJ|D Chain D, E. Coli Scs
pdb|1JLL|A Chain A, Crystal Structure Analysis Of The E197betaa Mutant Of E.
Coli Scs
pdb|1JLL|D Chain D, Crystal Structure Analysis Of The E197betaa Mutant Of E.
Coli Scs
Length = 288
Score = 23.9 bits (50), Expect = 5.3
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 4 IAGVDLPKKKRVEYALTYIYGIGLKSSRE---ILEAVGISFDKRVHELSE 50
IAGV PK KR+ +A I G G ++ E LEA G+ + + ++ E
Sbjct: 233 IAGVTAPKGKRMGHAGAIIAG-GKGTADEKFAALEAAGVKTVRSLADIGE 281
>pdb|1CQJ|A Chain A, Crystal Structure Of Dephosphorylated E. Coli Succinyl-Coa
Synthetase
pdb|1CQJ|D Chain D, Crystal Structure Of Dephosphorylated E. Coli Succinyl-Coa
Synthetase
pdb|1CQI|A Chain A, Crystal Structure Of The Complex Of Adp And Mg2+ With
Dephosphorylated E. Coli Succinyl-Coa Synthetase
pdb|1CQI|D Chain D, Crystal Structure Of The Complex Of Adp And Mg2+ With
Dephosphorylated E. Coli Succinyl-Coa Synthetase
Length = 286
Score = 23.9 bits (50), Expect = 5.3
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 4 IAGVDLPKKKRVEYALTYIYGIGLKSSRE---ILEAVGISFDKRVHELSE 50
IAGV PK KR+ +A I G G ++ E LEA G+ + + ++ E
Sbjct: 233 IAGVTAPKGKRMGHAGAIIAG-GKGTADEKFAALEAAGVKTVRSLADIGE 281
>pdb|1QF6|A Chain A, Structure Of E. Coli Threonyl-Trna Synthetase Complexed
With Its Cognate Trna
Length = 642
Score = 23.5 bits (49), Expect = 6.9
Identities = 9/21 (42%), Positives = 14/21 (65%)
Query: 40 SFDKRVHELSEDEVSSIAKKI 60
+ +KR+HEL+E I KK+
Sbjct: 119 ALEKRMHELAEKNYDVIKKKV 139
>pdb|1CVR|A Chain A, Crystal Structure Of The Arg Specific Cysteine
Proteinase Gingipain R (Rgpb)
Length = 435
Score = 23.5 bits (49), Expect = 6.9
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 72 KKVQMDIKSLMDLGNYRGIR 91
KK + DIK +D N RG+R
Sbjct: 18 KKYEGDIKDFVDWKNQRGLR 37
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
0.315 0.134 0.359
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 600,691
Number of Sequences: 13198
Number of extensions: 20210
Number of successful extensions: 25
Number of sequences better than 10.0: 14
Number of HSP's better than 10.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 14
Number of HSP's gapped (non-prelim): 14
length of query: 120
length of database: 2,899,336
effective HSP length: 77
effective length of query: 43
effective length of database: 1,883,090
effective search space: 80972870
effective search space used: 80972870
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: 48 (23.1 bits)