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|15645654|ref|NP_207830.1| ribosomal protein S15
(rps15) [Helicobacter pylori 26695]
(90 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|1A32| Ribosomal Protein S15 From Bacillus Stearotherm... 96 5e-22
pdb|1EG0|F Chain F, Fitting Of Components With Known Struct... 94 2e-21
pdb|1QD7|H Chain H, Partial Model For 30s Ribosomal Subunit 94 3e-21
pdb|1AB3| Ribosomal Protein S15 From Thermus Thermophilus... 93 6e-21
pdb|1J5E|O Chain O, Structure Of The Thermus Thermophilus 3... 93 6e-21
pdb|1FKA|O Chain O, Structure Of Functionally Activated Sma... 92 1e-20
pdb|1F7Y|A Chain A, The Crystal Structure Of Two Uucg Loops... 91 2e-20
pdb|1G1X|B Chain B, Structure Of Ribosomal Proteins S15, S6... 90 4e-20
pdb|1DK1|A Chain A, Detailed View Of A Key Element Of The R... 89 1e-19
pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein... 28 0.13
pdb|1I7P|A Chain A, Crystal Structure Of Rat B5r In Complex... 25 1.9
pdb|1PDA| Porphobilinogen Deaminase (E.C.4.3.1.8) 23 5.4
pdb|1EI1|A Chain A, Dimerization Of E. Coli Dna Gyrase B Pr... 23 5.4
pdb|2YPN|A Chain A, Hydroxymethylbilane Synthase 23 5.4
pdb|1YPN| Reduced Form Hydroxymethylbilane Synthase (K59q... 23 5.4
>pdb|1A32| Ribosomal Protein S15 From Bacillus Stearothermophilus
Length = 88
Score = 96.3 bits (238), Expect = 5e-22
Identities = 47/87 (54%), Positives = 64/87 (73%)
Query: 2 ALNLEKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLVA 61
AL E+K+EII+ F ENDTGS EVQ+A+L E+I L EHL+ + KDH SR GLLK+V
Sbjct: 1 ALTQERKREIIEQFKVHENDTGSPEVQIAILTEQINNLNEHLRVHKKDHHSRRGLLKMVG 60
Query: 62 QRRNLLKYIKRTNHARYVVLIEKLGIK 88
+RR LL Y++ + ARY ++EKLG++
Sbjct: 61 KRRRLLAYLRNKDVARYREIVEKLGLR 87
>pdb|1EG0|F Chain F, Fitting Of Components With Known Structure Into An 11.5
A Cryo-Em Map Of The E.Coli 70s Ribosome
pdb|1FJG|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1IBL|O Chain O, 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|O Chain O, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNZ|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1IBM|O Chain O, 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|1IBK|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1HNW|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1JGQ|R Chain R, 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|R Chain R, 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|R Chain R, 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|R Chain R, 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 = 89
Score = 94.4 bits (233), Expect = 2e-21
Identities = 49/88 (55%), Positives = 62/88 (69%)
Query: 1 MALNLEKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLV 60
M + E+KQ++I+ FA DTGS EVQVALL RI L+EHLK + KDH S GLL +V
Sbjct: 1 MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMV 60
Query: 61 AQRRNLLKYIKRTNHARYVVLIEKLGIK 88
QRR LL+Y++R + RY LIEKLGI+
Sbjct: 61 GQRRRLLRYLQREDPERYRALIEKLGIR 88
>pdb|1QD7|H Chain H, Partial Model For 30s Ribosomal Subunit
Length = 85
Score = 94.0 bits (232), Expect = 3e-21
Identities = 46/85 (54%), Positives = 62/85 (72%)
Query: 3 LNLEKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLVAQ 62
L E+K+EII+ F ENDTGS EVQ+A+L E+I L EHL+ + KDH SR GLLK+V +
Sbjct: 1 LTQERKREIIEQFKVHENDTGSPEVQIAILTEQINNLNEHLRVHKKDHHSRRGLLKMVGK 60
Query: 63 RRNLLKYIKRTNHARYVVLIEKLGI 87
RR LL Y++ + ARY ++EKLG+
Sbjct: 61 RRRLLAYLRNKDVARYREIVEKLGL 85
>pdb|1AB3| Ribosomal Protein S15 From Thermus Thermophilus, Nmr, 26
Structures
Length = 88
Score = 92.8 bits (229), Expect = 6e-21
Identities = 48/83 (57%), Positives = 60/83 (71%)
Query: 6 EKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLVAQRRN 65
E+KQ++I+ FA DTGS EVQVALL RI L+EHLK + KDH S GLL +V QRR
Sbjct: 5 EEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRR 64
Query: 66 LLKYIKRTNHARYVVLIEKLGIK 88
LL+Y++R + RY LIEKLGI+
Sbjct: 65 LLRYLQREDPERYRALIEKLGIR 87
>pdb|1J5E|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1I94|O Chain O, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|O Chain O, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|O Chain O, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|O Chain O, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 88
Score = 92.8 bits (229), Expect = 6e-21
Identities = 48/83 (57%), Positives = 60/83 (71%)
Query: 6 EKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLVAQRRN 65
E+KQ++I+ FA DTGS EVQVALL RI L+EHLK + KDH S GLL +V QRR
Sbjct: 5 EEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRR 64
Query: 66 LLKYIKRTNHARYVVLIEKLGIK 88
LL+Y++R + RY LIEKLGI+
Sbjct: 65 LLRYLQREDPERYRALIEKLGIR 87
>pdb|1FKA|O Chain O, Structure Of Functionally Activated Small Ribosomal
Subunit At 3.3 A Resolution
Length = 89
Score = 91.7 bits (226), Expect = 1e-20
Identities = 46/88 (52%), Positives = 62/88 (70%)
Query: 1 MALNLEKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLV 60
M + E+KQ++I+ FA DTGS EVQVALL RI L+EHLK + KDH S GLL +V
Sbjct: 1 MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMV 60
Query: 61 AQRRNLLKYIKRTNHARYVVLIEKLGIK 88
QRR LL+Y++R + RY ++EKLG++
Sbjct: 61 GQRRRLLRYLQREDPERYREIVEKLGLR 88
>pdb|1F7Y|A Chain A, The Crystal Structure Of Two Uucg Loops Highlights The
Role Played By 2'-Hydroxyl Groups In Its Unusual
Stability
Length = 89
Score = 90.9 bits (224), Expect = 2e-20
Identities = 48/88 (54%), Positives = 60/88 (67%)
Query: 1 MALNLEKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLV 60
M + E+KQ++ + FA DTGS EVQVALL RI L+EHLK + KDH S GLL V
Sbjct: 1 MPITKEEKQKVXQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLXXV 60
Query: 61 AQRRNLLKYIKRTNHARYVVLIEKLGIK 88
QRR LL+Y++R + RY LIEKLGI+
Sbjct: 61 GQRRRLLRYLQREDPERYRXLIEKLGIR 88
>pdb|1G1X|B Chain B, Structure Of Ribosomal Proteins S15, S6, S18, And 16s
Ribosomal Rna
pdb|1G1X|G Chain G, Structure Of Ribosomal Proteins S15, S6, S18, And 16s
Ribosomal Rna
Length = 88
Score = 90.1 bits (222), Expect = 4e-20
Identities = 45/83 (54%), Positives = 60/83 (72%)
Query: 6 EKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLVAQRRN 65
E+KQ++I+ FA DTGS EVQVALL RI L+EHLK + KDH S GLL +V QRR
Sbjct: 5 EEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRR 64
Query: 66 LLKYIKRTNHARYVVLIEKLGIK 88
LL+Y++R + RY ++EKLG++
Sbjct: 65 LLRYLQREDPERYREIVEKLGLR 87
>pdb|1DK1|A Chain A, Detailed View Of A Key Element Of The Ribosome Assembly:
Crystal Structure Of The S15-Rrna Complex
Length = 86
Score = 88.6 bits (218), Expect = 1e-19
Identities = 47/82 (57%), Positives = 57/82 (69%)
Query: 6 EKKQEIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLVAQRRN 65
E+KQ++ + FA DTGS EVQVALL RI L+EHLK + KDH S GLL V QRR
Sbjct: 5 EEKQKVXQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLXXVGQRRR 64
Query: 66 LLKYIKRTNHARYVVLIEKLGI 87
LL+Y++R + RY LIEKLGI
Sbjct: 65 LLRYLQREDPERYRXLIEKLGI 86
>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 = 28.5 bits (62), Expect = 0.13
Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 11/94 (11%)
Query: 3 LNLEKKQEIIKAFATKE------NDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGL 56
L+ +++++I+ F K+ D S + V LN ++ HL NP+ + R+G
Sbjct: 272 LSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLN---CVINYHLPQNPESYXHRIGR 328
Query: 57 LKLVAQRRNLLKYIKRTNH--ARYVVLIEKLGIK 88
++ + I R + RY+ KL IK
Sbjct: 329 TGRAGKKGKAISIINRREYKKLRYIERAXKLKIK 362
>pdb|1I7P|A Chain A, Crystal Structure Of Rat B5r In Complex With Fad
pdb|1IB0|A Chain A, Crystal Structure Of Rat B5r In Complex With Fad And Nad
Length = 274
Score = 24.6 bits (52), Expect = 1.9
Identities = 15/47 (31%), Positives = 23/47 (48%)
Query: 10 EIIKAFATKENDTGSCEVQVALLNERIKLLTEHLKANPKDHSSRLGL 56
++I+A ND C + A +E+ LL L+ +HSSR L
Sbjct: 162 QVIRAVLKDPNDHTVCYLLFANQSEKDILLRPELEELRNEHSSRFKL 208
>pdb|1PDA| Porphobilinogen Deaminase (E.C.4.3.1.8)
Length = 296
Score = 23.1 bits (48), Expect = 5.4
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 26 EVQVALLNERIKLLTEHLKANPKDHSSRLGLLKL 59
E++VALL R + +K P + LGL+ +
Sbjct: 54 ELEVALLENRADIAVHSMKDVPVEFPQGLGLVTI 87
>pdb|1EI1|A Chain A, Dimerization Of E. Coli Dna Gyrase B Provides A Structural
Mechanism For Activating The Atpase Catalytic Center
pdb|1EI1|B Chain B, Dimerization Of E. Coli Dna Gyrase B Provides A Structural
Mechanism For Activating The Atpase Catalytic Center
Length = 391
Score = 23.1 bits (48), Expect = 5.4
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 24 SCEVQVALLNERIKLLTEHLKANPKDHSSRLGLLKLVAQRR 64
S EV+ A+ + +LL E+L NP D +G + A+ R
Sbjct: 341 SSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAR 381
>pdb|2YPN|A Chain A, Hydroxymethylbilane Synthase
Length = 313
Score = 23.1 bits (48), Expect = 5.4
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 26 EVQVALLNERIKLLTEHLKANPKDHSSRLGLLKL 59
E++VALL R + +K P + LGL+ +
Sbjct: 65 ELEVALLENRADIAVHSMKDVPVEFPQGLGLVTI 98
>pdb|1YPN| Reduced Form Hydroxymethylbilane Synthase (K59q Mutant) Crystal
Structure After 2 Hours In A Flow Cell Determined By
Time-Resolved Laue Diffraction
Length = 313
Score = 23.1 bits (48), Expect = 5.4
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 26 EVQVALLNERIKLLTEHLKANPKDHSSRLGLLKL 59
E++VALL R + +K P + LGL+ +
Sbjct: 65 ELEVALLENRADIAVHSMKDVPVEFPQGLGLVTI 98
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
0.318 0.135 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: 430,646
Number of Sequences: 13198
Number of extensions: 12505
Number of successful extensions: 36
Number of sequences better than 10.0: 15
Number of HSP's better than 10.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 22
Number of HSP's gapped (non-prelim): 15
length of query: 90
length of database: 2,899,336
effective HSP length: 66
effective length of query: 24
effective length of database: 2,028,268
effective search space: 48678432
effective search space used: 48678432
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: 46 (22.3 bits)