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|15644706|ref|NP_206876.1| ribosomal protein S20
(rps20) [Helicobacter pylori 26695]
(89 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|1FJG|T Chain T, Structure Of The Thermus Thermophilus 3... 47 3e-07
pdb|1IBL|T Chain T, Structure Of The Thermus Thermophilus 3... 47 4e-07
pdb|1I94|T Chain T, Crystal Structures Of The Small Ribosom... 47 4e-07
pdb|1L8W|A Chain A, Crystal Structure Of Lyme Disease Varia... 23 4.2
pdb|1B35|B Chain B, Cricket Paralysis Virus (Crpv) 23 5.5
pdb|1JR7|A Chain A, Crystal Structure Of Gab Reveals Oxidor... 23 7.1
pdb|1HWT|D Chain D, Structure Of A Hap1DNA COMPLEX REVEALS ... 23 7.1
pdb|2HAP|D Chain D, Structure Of A Hap1-18DNA COMPLEX REVEA... 23 7.1
>pdb|1FJG|T Chain T, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1J5E|T Chain T, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1HR0|T Chain T, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNZ|T Chain T, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1HNW|T Chain T, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|T Chain T, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1JGQ|W Chain W, 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|W Chain W, 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|W Chain W, 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|W Chain W, 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 = 106
Score = 47.4 bits (111), Expect = 3e-07
Identities = 33/84 (39%), Positives = 47/84 (55%), Gaps = 6/84 (7%)
Query: 6 SAEKRIRQTIKRTERNRFYKTKIKNIIKAVREAVAVNDVAKAQERLKIANKE---LHKFV 62
SA KR RQ++KR RN+ K+ IK + K +AV + KA+E LKI K + K
Sbjct: 11 SALKRHRQSLKRRLRNKAKKSAIKTLSK---KAVQLAQEGKAEEALKIMRKAESLIDKAA 67
Query: 63 SKGILKKNTASRKVSRLNASVKKI 86
L KN A+R+ SRL V+++
Sbjct: 68 KGSTLHKNAAARRKSRLMRKVRQL 91
>pdb|1IBL|T Chain T, 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|T Chain T, 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|T Chain T, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
Length = 106
Score = 47.0 bits (110), Expect = 4e-07
Identities = 32/84 (38%), Positives = 47/84 (55%), Gaps = 6/84 (7%)
Query: 6 SAEKRIRQTIKRTERNRFYKTKIKNIIKAVREAVAVNDVAKAQERLKIANKE---LHKFV 62
SA KR RQ++KR RN+ K+ IK + K +A+ + KA+E LKI K + K
Sbjct: 11 SALKRHRQSLKRRLRNKAKKSAIKTLSK---KAIQLAQEGKAEEALKIMRKAESLIDKAA 67
Query: 63 SKGILKKNTASRKVSRLNASVKKI 86
L KN A+R+ SRL V+++
Sbjct: 68 KGSTLHKNAAARRKSRLMRKVRQL 91
>pdb|1I94|T Chain T, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|T Chain T, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|T Chain T, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|T Chain T, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 105
Score = 47.0 bits (110), Expect = 4e-07
Identities = 32/84 (38%), Positives = 47/84 (55%), Gaps = 6/84 (7%)
Query: 6 SAEKRIRQTIKRTERNRFYKTKIKNIIKAVREAVAVNDVAKAQERLKIANKE---LHKFV 62
SA KR RQ++KR RN+ K+ IK + K +A+ + KA+E LKI K + K
Sbjct: 10 SALKRHRQSLKRRLRNKAKKSAIKTLSK---KAIQLAQEGKAEEALKIMRKAESLIDKAA 66
Query: 63 SKGILKKNTASRKVSRLNASVKKI 86
L KN A+R+ SRL V+++
Sbjct: 67 KGSTLHKNAAARRKSRLMRKVRQL 90
>pdb|1L8W|A Chain A, Crystal Structure Of Lyme Disease Variable Surface Antigen
Vlse Of Borrelia Burgdorferi
pdb|1L8W|B Chain B, Crystal Structure Of Lyme Disease Variable Surface Antigen
Vlse Of Borrelia Burgdorferi
pdb|1L8W|C Chain C, Crystal Structure Of Lyme Disease Variable Surface Antigen
Vlse Of Borrelia Burgdorferi
pdb|1L8W|D Chain D, Crystal Structure Of Lyme Disease Variable Surface Antigen
Vlse Of Borrelia Burgdorferi
Length = 348
Score = 23.5 bits (49), Expect = 4.2
Identities = 16/61 (26%), Positives = 30/61 (48%), Gaps = 7/61 (11%)
Query: 28 IKNIIKAVREA-------VAVNDVAKAQERLKIANKELHKFVSKGILKKNTASRKVSRLN 80
+ ++KAV+ A A+ +V + K+A+K K ++KGI + A+ +L
Sbjct: 118 LDKLVKAVKTAEGASSGTAAIGEVVADADAAKVADKASVKGIAKGIKEIVEAAGGSEKLK 177
Query: 81 A 81
A
Sbjct: 178 A 178
>pdb|1B35|B Chain B, Cricket Paralysis Virus (Crpv)
Length = 255
Score = 23.1 bits (48), Expect = 5.5
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 44 VAKAQERLKIANKELHKFVSKGILKKNTASRKVSRLNAS 82
+ +RL KE+ FVS+G+ TA + L+ +
Sbjct: 5 IENEDKRLTSEQKEIVHFVSEGVTPSTTALPDIVNLSTN 43
>pdb|1JR7|A Chain A, Crystal Structure Of Gab Reveals Oxidoreductase Fold
Length = 311
Score = 22.7 bits (47), Expect = 7.1
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 38 AVAVNDVAKAQERLKIANKELH 59
AV V+DV +A E +K+A H
Sbjct: 85 AVGVDDVKQADEMVKLATAVAH 106
>pdb|1HWT|D Chain D, Structure Of A Hap1DNA COMPLEX REVEALS DRAMATICALLY
Asymmetric Dna Binding By A Homodimeric Protein
pdb|1HWT|H Chain H, Structure Of A Hap1DNA COMPLEX REVEALS DRAMATICALLY
Asymmetric Dna Binding By A Homodimeric Protein
Length = 81
Score = 22.7 bits (47), Expect = 7.1
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 33 KAVREAVAVNDVAKAQERLKIANKELHK 60
+A +E + N+V K +ER+K K L K
Sbjct: 49 EAEKELLKDNEVKKLRERVKSLEKTLSK 76
>pdb|2HAP|D Chain D, Structure Of A Hap1-18DNA COMPLEX REVEALS THAT
PROTEINDNA Interactions Can Have Direct Allosteric
Effects On Transcriptional Activation
Length = 81
Score = 22.7 bits (47), Expect = 7.1
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 33 KAVREAVAVNDVAKAQERLKIANKELHK 60
+A +E + N+V K +ER+K K L K
Sbjct: 49 EAEKELLKDNEVKKLRERVKSLEKTLSK 76
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 0.126 0.313
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 330,636
Number of Sequences: 13198
Number of extensions: 9230
Number of successful extensions: 22
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 14
Number of HSP's gapped (non-prelim): 8
length of query: 89
length of database: 2,899,336
effective HSP length: 65
effective length of query: 24
effective length of database: 2,041,466
effective search space: 48995184
effective search space used: 48995184
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)