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|15645905|ref|NP_208084.1| ribosomal protein L17
(rpl17) [Helicobacter pylori 26695]
(116 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|1LNR|L Chain L, Crystal Structure Of The Large Ribosoma... 106 8e-25
pdb|1GD8|A Chain A, The Crystal Structure Of Bacteria-Speci... 99 9e-23
pdb|1DCQ|A Chain A, Crystal Structure Of The Arf-Gap Domain... 30 0.090
pdb|1J9M|A Chain A, K38h Mutant Of Streptomyces K15 Dd-Tran... 26 1.00
pdb|1ES3|A Chain A, C98a Mutant Of Streptomyces K15 Dd-Tran... 26 1.00
pdb|1ES2|A Chain A, S96a Mutant Of Streptomyces K15 Dd-Tran... 26 1.00
pdb|1ES4|A Chain A, C98n Mutant Of Streptomyces K15 Dd-Tran... 26 1.00
pdb|1ESI|A Chain A, R248l Mutant Of Streptomyces K15 Dd-Tra... 26 1.00
pdb|1SKF| Crystal Structure Of The Streptomyces K15 Dd-Tr... 26 1.00
pdb|1ES5|A Chain A, S216a Mutant Of Streptomyces K15 Dd-Tra... 26 1.00
pdb|1DAB|A Chain A, The Structure Of Bordetella Pertussis V... 24 5.0
pdb|1IBM|S Chain S, Structure Of The Thermus Thermophilus 3... 24 5.0
pdb|1J5E|S Chain S, Structure Of The Thermus Thermophilus 3... 24 5.0
>pdb|1LNR|L Chain L, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 116
Score = 106 bits (264), Expect = 8e-25
Identities = 56/116 (48%), Positives = 75/116 (64%)
Query: 1 MRHKHGYRKLGRTSSHRKALLKNLAIALIEHNKIETGIYKAKELRSYIEKLTTAARVGDF 60
MRH RKL R SS R AL + A AL+ +I+T + KAKELR ++E+L T A+ GD
Sbjct: 1 MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDL 60
Query: 61 NAHRHVFAYLQNKEATHKLVTEIAPKYAQRNGGYTRIQRTTFRRGDASTLATIEFV 116
++ R V + +K+ K++ E+APKYA+R GGYTRI R RRGD T+A IE V
Sbjct: 61 HSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIELV 116
>pdb|1GD8|A Chain A, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein.
pdb|1GD8|B Chain B, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein.
pdb|1GD8|C Chain C, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein.
pdb|1GD8|D Chain D, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein.
pdb|1GD8|E Chain E, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein.
pdb|1GD8|F Chain F, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein.
pdb|1GD8|G Chain G, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein.
pdb|1GD8|H Chain H, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein.
pdb|1GD8|I Chain I, The Crystal Structure Of Bacteria-Specific L17 Ribosomal
Protein
Length = 118
Score = 99.4 bits (246), Expect = 9e-23
Identities = 55/117 (47%), Positives = 72/117 (61%), Gaps = 1/117 (0%)
Query: 1 MRHKHGYRKLGRTSSHRKALLKNLAIALIEHNKIETGIYKAKELRSYIEKLTTAARVGDF 60
MRH RKL R SSHR AL +N A +L+ H +I T + KAKELR +++ L A+ GD
Sbjct: 1 MRHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDHLIHLAKRGDL 60
Query: 61 NAHRHVFAYLQNKEATHKLVTEIAPKYAQRNGGYTRIQR-TTFRRGDASTLATIEFV 116
+A R V LQ+ + KL EIAP+Y R GGYTR+ + RRGD + LA +E V
Sbjct: 61 HARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKLAERRRGDGAPLALVELV 117
>pdb|1DCQ|A Chain A, Crystal Structure Of The Arf-Gap Domain And Ankyrin
Repeats Of Papbeta
Length = 278
Score = 29.6 bits (65), Expect = 0.090
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 18 KALLKNLAIALIEHNKIETGIYKAKELR-SYIEKLTTAARVGDFNAHRHV 66
K LL+ A I + ET + AK L+ + E+L T A G FN+H HV
Sbjct: 222 KLLLRGKASIEIANESGETPLDIAKRLKHEHCEELLTQALSGRFNSHVHV 271
>pdb|1J9M|A Chain A, K38h Mutant Of Streptomyces K15 Dd-Transpeptidase
Length = 262
Score = 26.2 bits (56), Expect = 1.00
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 32 NKIETGIYKAKELRSYIEKLTTAA-RVGDFNAHRHVFAYLQN--KEATHKLVTEIAPKYA 88
+K +G +A ++S+I K+ TAA +G N H F + N +T + +T+IA A
Sbjct: 106 DKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASS-A 164
Query: 89 QRNGGYTRIQRT 100
+N + + +T
Sbjct: 165 MKNSTFRTVVKT 176
>pdb|1ES3|A Chain A, C98a Mutant Of Streptomyces K15 Dd-Transpeptidase
Length = 262
Score = 26.2 bits (56), Expect = 1.00
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 32 NKIETGIYKAKELRSYIEKLTTAA-RVGDFNAHRHVFAYLQN--KEATHKLVTEIAPKYA 88
+K +G +A ++S+I K+ TAA +G N H F + N +T + +T+IA A
Sbjct: 106 DKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASS-A 164
Query: 89 QRNGGYTRIQRT 100
+N + + +T
Sbjct: 165 MKNSTFRTVVKT 176
>pdb|1ES2|A Chain A, S96a Mutant Of Streptomyces K15 Dd-Transpeptidase
Length = 262
Score = 26.2 bits (56), Expect = 1.00
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 32 NKIETGIYKAKELRSYIEKLTTAA-RVGDFNAHRHVFAYLQN--KEATHKLVTEIAPKYA 88
+K +G +A ++S+I K+ TAA +G N H F + N +T + +T+IA A
Sbjct: 106 DKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASS-A 164
Query: 89 QRNGGYTRIQRT 100
+N + + +T
Sbjct: 165 MKNSTFRTVVKT 176
>pdb|1ES4|A Chain A, C98n Mutant Of Streptomyces K15 Dd-Transpeptidase
Length = 262
Score = 26.2 bits (56), Expect = 1.00
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 32 NKIETGIYKAKELRSYIEKLTTAA-RVGDFNAHRHVFAYLQN--KEATHKLVTEIAPKYA 88
+K +G +A ++S+I K+ TAA +G N H F + N +T + +T+IA A
Sbjct: 106 DKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASS-A 164
Query: 89 QRNGGYTRIQRT 100
+N + + +T
Sbjct: 165 MKNSTFRTVVKT 176
>pdb|1ESI|A Chain A, R248l Mutant Of Streptomyces K15 Dd-Transpeptidase
Length = 262
Score = 26.2 bits (56), Expect = 1.00
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 32 NKIETGIYKAKELRSYIEKLTTAA-RVGDFNAHRHVFAYLQN--KEATHKLVTEIAPKYA 88
+K +G +A ++S+I K+ TAA +G N H F + N +T + +T+IA A
Sbjct: 106 DKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASS-A 164
Query: 89 QRNGGYTRIQRT 100
+N + + +T
Sbjct: 165 MKNSTFRTVVKT 176
>pdb|1SKF| Crystal Structure Of The Streptomyces K15 Dd-Transpeptidase
Length = 262
Score = 26.2 bits (56), Expect = 1.00
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 32 NKIETGIYKAKELRSYIEKLTTAA-RVGDFNAHRHVFAYLQN--KEATHKLVTEIAPKYA 88
+K +G +A ++S+I K+ TAA +G N H F + N +T + +T+IA A
Sbjct: 106 DKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASS-A 164
Query: 89 QRNGGYTRIQRT 100
+N + + +T
Sbjct: 165 MKNSTFRTVVKT 176
>pdb|1ES5|A Chain A, S216a Mutant Of Streptomyces K15 Dd-Transpeptidase
Length = 262
Score = 26.2 bits (56), Expect = 1.00
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 32 NKIETGIYKAKELRSYIEKLTTAA-RVGDFNAHRHVFAYLQN--KEATHKLVTEIAPKYA 88
+K +G +A ++S+I K+ TAA +G N H F + N +T + +T+IA A
Sbjct: 106 DKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASS-A 164
Query: 89 QRNGGYTRIQRT 100
+N + + +T
Sbjct: 165 MKNSTFRTVVKT 176
>pdb|1DAB|A Chain A, The Structure Of Bordetella Pertussis Virulence Factor
P.69 Pertactin
Length = 539
Score = 23.9 bits (50), Expect = 5.0
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 88 AQRNGGYTRIQRTTFRRGDA 107
A G +QR T RRGDA
Sbjct: 210 AAMQGAVVHLQRATIRRGDA 229
>pdb|1IBM|S Chain S, 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|1FJG|S Chain S, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1IBL|S Chain S, 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|1HR0|S Chain S, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNZ|S Chain S, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1HNW|S Chain S, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|S Chain S, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1IBK|S Chain S, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1FKA|S Chain S, Structure Of Functionally Activated Small Ribosomal
Subunit At 3.3 A Resolution
pdb|1JGQ|V Chain V, 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|V Chain V, 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|V Chain V, 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|V Chain V, 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 = 93
Score = 23.9 bits (50), Expect = 5.0
Identities = 18/61 (29%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 33 KIETGIYKAKELRSYIEKLTTAARVGDFNAHRHVFAYLQNKEATHKLVTEIAPKYAQRNG 92
K E + K RS I + +N +HV Y+ HKL E AP R
Sbjct: 25 KGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKL-GEFAPTRTYRGH 83
Query: 93 G 93
G
Sbjct: 84 G 84
>pdb|1J5E|S Chain S, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1QKF|A Chain A, Solution Structure Of The Ribosomal Protein S19 From
Thermus Thermophilus
pdb|1QKH|A Chain A, Solution Structure Of The Ribosomal Protein S19 From
Thermus Thermophilus
pdb|1I94|S Chain S, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|S Chain S, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|S Chain S, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|S Chain S, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 92
Score = 23.9 bits (50), Expect = 5.0
Identities = 18/61 (29%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 33 KIETGIYKAKELRSYIEKLTTAARVGDFNAHRHVFAYLQNKEATHKLVTEIAPKYAQRNG 92
K E + K RS I + +N +HV Y+ HKL E AP R
Sbjct: 24 KGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKL-GEFAPTRTYRGH 82
Query: 93 G 93
G
Sbjct: 83 G 83
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
0.321 0.133 0.374
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 603,521
Number of Sequences: 13198
Number of extensions: 19232
Number of successful extensions: 50
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 46
Number of HSP's gapped (non-prelim): 13
length of query: 116
length of database: 2,899,336
effective HSP length: 76
effective length of query: 40
effective length of database: 1,896,288
effective search space: 75851520
effective search space used: 75851520
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)