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|15645918|ref|NP_208097.1| ribosomal protein S8 (rps8)
[Helicobacter pylori 26695]
(131 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|1EG0|E Chain E, Fitting Of Components With Known Struct... 103 6e-24
pdb|1AN7|A Chain A, Ribosomal Protein S8 From Thermus Therm... 101 3e-23
pdb|1I94|H Chain H, Crystal Structures Of The Small Ribosom... 100 5e-23
pdb|1SEI|A Chain A, Structure Of 30s Ribosomal Protein S8 >... 95 2e-21
pdb|1I6U|A Chain A, Rna-Protein Interactions: The Crystal S... 41 5e-05
pdb|1QVB|A Chain A, Crystal Structure Of The Beta-Glycosida... 25 2.9
pdb|1KZG|A Chain A, Dbscdc42(Y889f) >gi|20151150|pdb|1KZG|C... 24 5.0
pdb|1LB1|A Chain A, Crystal Structure Of The Dbl And Plecks... 24 5.0
pdb|1KZ7|A Chain A, Crystal Structure Of The DhPH FRAGMENT ... 24 5.0
pdb|1QUK| Phosphate-Binding Protein Mutant With Asp 137 R... 24 5.0
pdb|1K8K|E Chain E, Crystal Structure Of Arp23 COMPLEX 23 8.5
pdb|1J5X|A Chain A, Crystal Structure Of Conserved Hypothet... 23 8.5
pdb|1I3P|A Chain A, The 3.1 Angstrom Resolution Crystal Str... 23 8.5
pdb|1P35|B Chain B, Crystal Structure Of Baculovirus P35 >g... 23 8.5
pdb|1I4E|A Chain A, Crystal Structure Of The Caspase-8P35 C... 23 8.5
>pdb|1EG0|E Chain E, Fitting Of Components With Known Structure Into An 11.5 A
Cryo-Em Map Of The E.Coli 70s Ribosome
pdb|1FJG|H Chain H, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1IBL|H Chain H, 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|H Chain H, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNZ|H Chain H, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1IBM|H Chain H, 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|H Chain H, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1HNW|H Chain H, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|H Chain H, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1FKA|H Chain H, Structure Of Functionally Activated Small Ribosomal
Subunit At 3.3 A Resolution
pdb|1JGQ|K Chain K, 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|K Chain K, 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|K Chain K, 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|K Chain K, 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
pdb|1J5E|H Chain H, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
Length = 138
Score = 103 bits (257), Expect = 6e-24
Identities = 56/138 (40%), Positives = 80/138 (57%), Gaps = 7/138 (5%)
Query: 1 MVNDIIADSLTRLRNASMRRLEFTQLYYAKIVVSILEIFKEKGFIKDFNVKDKDKKQSVY 60
M+ D IAD LTR+RNA+ E T + ++ IL I +GFIK + D D K +
Sbjct: 1 MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR 60
Query: 61 VQLAY-------DEKGHSKISEVKRLSKPGRRVYKQKNELKRFKNGYGVIVVSTSKGVIT 113
V L Y D + I ++R+SKPGRRVY E+ R + G G+ ++STSKGV+T
Sbjct: 61 VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT 120
Query: 114 NEEAYRQNVGGEVLCSIW 131
+ EA + VGGE++C +W
Sbjct: 121 DREARKLGVGGELICEVW 138
>pdb|1AN7|A Chain A, Ribosomal Protein S8 From Thermus Thermophilus
pdb|1AN7|B Chain B, Ribosomal Protein S8 From Thermus Thermophilus
pdb|1QD7|G Chain G, Partial Model For 30s Ribosomal Subunit
pdb|1EMI|A Chain A, Structure Of 16s Rrna In The Region Around Ribosomal
Protein S8
Length = 136
Score = 101 bits (251), Expect = 3e-23
Identities = 55/135 (40%), Positives = 78/135 (57%), Gaps = 7/135 (5%)
Query: 4 DIIADSLTRLRNASMRRLEFTQLYYAKIVVSILEIFKEKGFIKDFNVKDKDKKQSVYVQL 63
D IAD LTR+RNA+ E T + ++ IL I +GFIK + D D K + V L
Sbjct: 2 DPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYL 61
Query: 64 AY-------DEKGHSKISEVKRLSKPGRRVYKQKNELKRFKNGYGVIVVSTSKGVITNEE 116
Y D + I ++R+SKPGRRVY E+ R + G G+ ++STSKGV+T+ E
Sbjct: 62 KYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDRE 121
Query: 117 AYRQNVGGEVLCSIW 131
A + VGGE++C +W
Sbjct: 122 ARKLGVGGELICEVW 136
>pdb|1I94|H Chain H, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|H Chain H, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|H Chain H, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|H Chain H, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 138
Score = 100 bits (249), Expect = 5e-23
Identities = 52/138 (37%), Positives = 81/138 (58%), Gaps = 7/138 (5%)
Query: 1 MVNDIIADSLTRLRNASMRRLEFTQLYYAKIVVSILEIFKEKGFIKDFNVKDKDKKQSVY 60
M+ D IAD LTR+RNA+ E T++ ++ IL+I +GFIK + + D K +
Sbjct: 1 MLTDPIADMLTRIRNATRVYKESTEVPASRFKEEILKILAREGFIKGYERVEVDGKPYLR 60
Query: 61 VQLAY-------DEKGHSKISEVKRLSKPGRRVYKQKNELKRFKNGYGVIVVSTSKGVIT 113
+ L Y D + I ++R+S+PGRRVY E+ R + G G+ ++ST KGV+T
Sbjct: 61 IHLKYGPRRQGPDPRPEQVIKHIRRISRPGRRVYVGVKEIPRVRRGLGIAILSTPKGVLT 120
Query: 114 NEEAYRQNVGGEVLCSIW 131
+ EA + VGGE++C +W
Sbjct: 121 DREARKLGVGGELICEVW 138
>pdb|1SEI|A Chain A, Structure Of 30s Ribosomal Protein S8
pdb|1SEI|B Chain B, Structure Of 30s Ribosomal Protein S8
Length = 130
Score = 95.1 bits (235), Expect = 2e-21
Identities = 51/130 (39%), Positives = 84/130 (64%), Gaps = 1/130 (0%)
Query: 1 MVNDIIADSLTRLRNASMRRLEFTQLYYAKIVVSILEIFKEKGFIKDFNVKDKDKKQSVY 60
++ D IAD LT +RNA+M R E ++ +KI I EI K +GFI+D+ + +K+ +
Sbjct: 1 VMTDPIADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQGILR 60
Query: 61 VQLAYDEKGHSKISEVKRLSKPGRRVYKQKNELKRFKNGYGVIVVSTSKGVITNEEAYRQ 120
+ L Y I+ +KR+SKPG RVY + +E+ R NG G+ ++STS+GV+T++EA ++
Sbjct: 61 IFLKYGPN-ERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQK 119
Query: 121 NVGGEVLCSI 130
GGE++ +
Sbjct: 120 GTGGEIIAYV 129
>pdb|1I6U|A Chain A, Rna-Protein Interactions: The Crystal Structure Of
Ribosomal Protein S8RRNA COMPLEX FROM METHANOCOCCUS
Jannaschii
pdb|1I6U|B Chain B, Rna-Protein Interactions: The Crystal Structure Of
Ribosomal Protein S8RRNA COMPLEX FROM METHANOCOCCUS
Jannaschii
Length = 130
Score = 40.8 bits (94), Expect = 5e-05
Identities = 29/135 (21%), Positives = 67/135 (49%), Gaps = 16/135 (11%)
Query: 4 DIIADSLTRLRNASMRRLEFTQLYYA-KIVVSILEIFKEKGFIKDFNVKDKDKKQSVYVQ 62
D +A++L + N + + A K++ +L++ ++ G+I +F + + V+
Sbjct: 5 DPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVXQDNGYIGEFEFIEDGRAGIFKVE 64
Query: 63 LAYDEKGHSKISEVKRLSKPGRRVYKQKNELKRFKNGY------GVIVVSTSKGVITNEE 116
L I ++ + R +K ++F+ Y G+++VST++GV ++EE
Sbjct: 65 L---------IGKINKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILIVSTTQGVXSHEE 115
Query: 117 AYRQNVGGEVLCSIW 131
A ++ +GG +L ++
Sbjct: 116 AKKRGLGGRLLAYVY 130
>pdb|1QVB|A Chain A, Crystal Structure Of The Beta-Glycosidase From The
Hyperthermophile Thermosphaera Aggregans
pdb|1QVB|B Chain B, Crystal Structure Of The Beta-Glycosidase From The
Hyperthermophile Thermosphaera Aggregans
Length = 481
Score = 25.0 bits (53), Expect = 2.9
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 93 LKRFKNGYGVIVVSTSKGVITNEEAYRQNVGGEVLCSIW 131
LK N YGV ++ T GV + +A R + S+W
Sbjct: 371 LKELYNRYGVDLIVTENGVSDSRDALRPAYLVSHVYSVW 409
>pdb|1KZG|A Chain A, Dbscdc42(Y889f)
pdb|1KZG|C Chain C, Dbscdc42(Y889f)
Length = 353
Score = 24.3 bits (51), Expect = 5.0
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 67 EKGHSKISEVKRLSKPGRRVYKQKNEL----KRFKNGYG 101
+KGH+K+ E+ R R ++ + + KR +NG G
Sbjct: 223 KKGHTKVKELARFKPMQRHLFLHEKAVLFCKKREENGEG 261
>pdb|1LB1|A Chain A, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|C Chain C, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|E Chain E, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|G Chain G, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
Length = 353
Score = 24.3 bits (51), Expect = 5.0
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 67 EKGHSKISEVKRLSKPGRRVYKQKNEL----KRFKNGYG 101
+KGH+K+ E+ R R ++ + + KR +NG G
Sbjct: 223 KKGHTKVKELARFKPMQRHLFLHEKAVLFCKKREENGEG 261
>pdb|1KZ7|A Chain A, Crystal Structure Of The DhPH FRAGMENT OF MURINE DBS IN
Complex With The Placental Isoform Of Human Cdc42
pdb|1KZ7|C Chain C, Crystal Structure Of The DhPH FRAGMENT OF MURINE DBS IN
Complex With The Placental Isoform Of Human Cdc42
Length = 353
Score = 24.3 bits (51), Expect = 5.0
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 67 EKGHSKISEVKRLSKPGRRVYKQKNEL----KRFKNGYG 101
+KGH+K+ E+ R R ++ + + KR +NG G
Sbjct: 223 KKGHTKVKELARFKPXQRHLFLHEKAVLFCKKREENGEG 261
>pdb|1QUK| Phosphate-Binding Protein Mutant With Asp 137 Replaced By Asn
Complex With Phosphate
Length = 321
Score = 24.3 bits (51), Expect = 5.0
Identities = 16/42 (38%), Positives = 21/42 (49%), Gaps = 1/42 (2%)
Query: 82 PGRRVYKQKNELKRFKNGYGVIVVSTSKGVITNEEAYRQNVG 123
PG ++ Q + R NG G V TS NEE ++ NVG
Sbjct: 121 PGLKLPSQNIAVVRRANGSGTSFVFTSYLAKVNEE-WKNNVG 161
>pdb|1K8K|E Chain E, Crystal Structure Of Arp23 COMPLEX
Length = 178
Score = 23.5 bits (49), Expect = 8.5
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 31 IVVSILEIFKEKGFIKDFNVKDKDKKQSVYVQLAYDE 67
IV + FK F K++ +K++ + +Y+ L E
Sbjct: 41 IVDEAIYYFKANVFFKNYEIKNEADRTLIYITLYISE 77
>pdb|1J5X|A Chain A, Crystal Structure Of Conserved Hypothetical Protein
(Tm0813) From Thermotoga Maritima At 1.8 A Resolution
Length = 342
Score = 23.5 bits (49), Expect = 8.5
Identities = 17/48 (35%), Positives = 27/48 (55%), Gaps = 5/48 (10%)
Query: 80 SKPGRRVYKQKNELKRFKNGYGVIVVSTSKGVITNEEAYRQNVGGEVL 127
SK + + QKNELK+F + V++ K I +E ++N+ EVL
Sbjct: 14 SKTLKEITDQKNELKKFFENF---VLNLEKTEIFSE--IQKNLTDEVL 56
>pdb|1I3P|A Chain A, The 3.1 Angstrom Resolution Crystal Structure Of A
Mutated Baculovirus P35 After Caspase Cleavage
Length = 298
Score = 23.5 bits (49), Expect = 8.5
Identities = 16/63 (25%), Positives = 31/63 (48%), Gaps = 1/63 (1%)
Query: 32 VVSILEIFKEKGFIKDFNVKDKDKKQSVYVQLAYDEKGHSKISEVKRLSKPGRRVYKQKN 91
V+ +EI + I+D V DK ++ VY+ + + + + +S P R V ++ N
Sbjct: 2 VIFPVEIDVSQTIIRDCQV-DKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNN 60
Query: 92 ELK 94
L+
Sbjct: 61 NLR 63
>pdb|1P35|B Chain B, Crystal Structure Of Baculovirus P35
pdb|1P35|A Chain A, Crystal Structure Of Baculovirus P35
pdb|1P35|C Chain C, Crystal Structure Of Baculovirus P35
Length = 299
Score = 23.5 bits (49), Expect = 8.5
Identities = 16/63 (25%), Positives = 31/63 (48%), Gaps = 1/63 (1%)
Query: 32 VVSILEIFKEKGFIKDFNVKDKDKKQSVYVQLAYDEKGHSKISEVKRLSKPGRRVYKQKN 91
V+ +EI + I+D V DK ++ VY+ + + + + +S P R V ++ N
Sbjct: 2 VIFPVEIDVSQTIIRDCQV-DKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNN 60
Query: 92 ELK 94
L+
Sbjct: 61 NLR 63
>pdb|1I4E|A Chain A, Crystal Structure Of The Caspase-8P35 COMPLEX
Length = 300
Score = 23.5 bits (49), Expect = 8.5
Identities = 16/63 (25%), Positives = 31/63 (48%), Gaps = 1/63 (1%)
Query: 32 VVSILEIFKEKGFIKDFNVKDKDKKQSVYVQLAYDEKGHSKISEVKRLSKPGRRVYKQKN 91
V+ +EI + I+D V DK ++ VY+ + + + + +S P R V ++ N
Sbjct: 4 VIFPVEIDVSQTIIRDCQV-DKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNN 62
Query: 92 ELK 94
L+
Sbjct: 63 NLR 65
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 0.136 0.373
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 705,850
Number of Sequences: 13198
Number of extensions: 26325
Number of successful extensions: 71
Number of sequences better than 10.0: 15
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 60
Number of HSP's gapped (non-prelim): 15
length of query: 131
length of database: 2,899,336
effective HSP length: 78
effective length of query: 53
effective length of database: 1,869,892
effective search space: 99104276
effective search space used: 99104276
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)