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|15645926|ref|NP_208105.1| ribosomal protein S3 (rps3)
[Helicobacter pylori 26695]
(234 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|C Chain C, Structure Of The Thermus Thermophilus 3... 229 2e-61
pdb|1I94|C Chain C, Crystal Structures Of The Small Ribosom... 227 8e-61
pdb|1AA7|A Chain A, Influenza Virus Matrix Protein Crystal ... 30 0.18
pdb|1EA3|A Chain A, Influenza Virus M1 Protein >gi|14278293... 30 0.18
pdb|1QRQ|A Chain A, Structure Of A Voltage-Dependent K+ Cha... 27 2.0
pdb|1EXB|A Chain A, Structure Of The Cytoplasmic Beta Subun... 27 2.0
pdb|1AX8| Human Obesity Protein, Leptin 27 2.7
pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Pro... 26 4.6
pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Pro... 26 4.6
pdb|1KYI|A Chain A, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfon... 25 5.9
>pdb|1FJG|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1J5E|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1IBL|C Chain C, 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|C Chain C, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNZ|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1IBM|C Chain C, 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|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1HNW|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1JGQ|F Chain F, 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|F Chain F, 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|F Chain F, 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|F Chain F, 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 = 239
Score = 229 bits (584), Expect = 2e-61
Identities = 116/230 (50%), Positives = 157/230 (67%)
Query: 1 MGQKVNPVGLRLGINRNWTSRWFPSARTAPSNIDEDNKIRKFLKKELYYAGVSEIVIERA 60
MG K++P+G RLGI R+W SRW+ + + ED +IR L+KELY AG++ + IERA
Sbjct: 1 MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA 60
Query: 61 AKKLRVTVVAARPGLIIGKKGVDIEKVKDGLKTLIKKEVSINIKEVKHPQADAQLAAENV 120
A + VTV A+PG++IG+ G I +++ L L K V++N++EV++P A L A+ V
Sbjct: 61 ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV 120
Query: 121 ATQLEKRVAFRRAMKKVMQAALKSGAKGIKVCVSGRLAGAEIARTEWYMEGRVPLHTLRA 180
A Q+E+R A RRA+K+ +Q ++SGAKG KV VSGR+ GAE ARTEW +GRVPLHTLRA
Sbjct: 121 AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA 180
Query: 181 KIDYGFAEAMTVYGIIGVKVWIFKGEVLQKGIQFEKKEEAKEEREPRRSR 230
IDYGFA A T YG++GVK +IF GEV+ + E K E PRR R
Sbjct: 181 NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRR 230
>pdb|1I94|C Chain C, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|C Chain C, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|C Chain C, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|C Chain C, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 238
Score = 227 bits (579), Expect = 8e-61
Identities = 115/229 (50%), Positives = 156/229 (67%)
Query: 2 GQKVNPVGLRLGINRNWTSRWFPSARTAPSNIDEDNKIRKFLKKELYYAGVSEIVIERAA 61
G K++P+G RLGI R+W SRW+ + + ED +IR L+KELY AG++ + IERAA
Sbjct: 1 GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAA 60
Query: 62 KKLRVTVVAARPGLIIGKKGVDIEKVKDGLKTLIKKEVSINIKEVKHPQADAQLAAENVA 121
+ VTV A+PG++IG+ G I +++ L L K V++N++EV++P A L A+ VA
Sbjct: 61 DNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVA 120
Query: 122 TQLEKRVAFRRAMKKVMQAALKSGAKGIKVCVSGRLAGAEIARTEWYMEGRVPLHTLRAK 181
Q+E+R A RRA+K+ +Q ++SGAKG KV VSGR+ GAE ARTEW +GRVPLHTLRA
Sbjct: 121 EQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRAN 180
Query: 182 IDYGFAEAMTVYGIIGVKVWIFKGEVLQKGIQFEKKEEAKEEREPRRSR 230
IDYGFA A T YG++GVK +IF GEV+ + E K E PRR R
Sbjct: 181 IDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRR 229
>pdb|1AA7|A Chain A, Influenza Virus Matrix Protein Crystal Structure At Ph 4.0
pdb|1AA7|B Chain B, Influenza Virus Matrix Protein Crystal Structure At Ph 4.0
Length = 158
Score = 30.4 bits (67), Expect = 0.18
Identities = 20/62 (32%), Positives = 33/62 (52%), Gaps = 5/62 (8%)
Query: 30 PSNIDEDNKIRKFLKKELYYAGVSEIVIERAAKKLRVTVVAARPGLIIGKKGVDIEKVKD 89
P+N+D+ K+ + LK+E+ + G EI + +A L A+ GLI + G +V
Sbjct: 90 PNNMDKAVKLYRKLKREITFHGAKEISLSYSAGAL-----ASCMGLIYNRMGAVTTEVAF 144
Query: 90 GL 91
GL
Sbjct: 145 GL 146
>pdb|1EA3|A Chain A, Influenza Virus M1 Protein
pdb|1EA3|B Chain B, Influenza Virus M1 Protein
Length = 164
Score = 30.4 bits (67), Expect = 0.18
Identities = 20/62 (32%), Positives = 33/62 (52%), Gaps = 5/62 (8%)
Query: 30 PSNIDEDNKIRKFLKKELYYAGVSEIVIERAAKKLRVTVVAARPGLIIGKKGVDIEKVKD 89
P+N+D+ K+ + LK+E+ + G EI + +A L A+ GLI + G +V
Sbjct: 90 PNNMDKAVKLYRKLKREITFHGAKEISLSYSAGAL-----ASCMGLIYNRMGAVTTEVAF 144
Query: 90 GL 91
GL
Sbjct: 145 GL 146
>pdb|1QRQ|A Chain A, Structure Of A Voltage-Dependent K+ Channel Beta Subunit
pdb|1QRQ|B Chain B, Structure Of A Voltage-Dependent K+ Channel Beta Subunit
pdb|1QRQ|C Chain C, Structure Of A Voltage-Dependent K+ Channel Beta Subunit
pdb|1QRQ|D Chain D, Structure Of A Voltage-Dependent K+ Channel Beta Subunit
Length = 325
Score = 26.9 bits (58), Expect = 2.0
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 36 DNKIRKFLKKELYYAGVSEIVIERAAKK-------LRVTVVAARPGLIIGKKGVDIEKVK 88
DN I F E+Y AG +E+V+ KK L +T G ++G+ + +
Sbjct: 43 DNGINLFDTAEVYAAGKAEVVLGNIIKKKGWRRSSLVITTKIFWGGKAETERGLSRKHII 102
Query: 89 DGLKTLIKK 97
+GLK +++
Sbjct: 103 EGLKASLER 111
>pdb|1EXB|A Chain A, Structure Of The Cytoplasmic Beta Subunit-T1 Assembly Of
Voltage-Dependent K Channels
Length = 332
Score = 26.9 bits (58), Expect = 2.0
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 36 DNKIRKFLKKELYYAGVSEIVIERAAKK-------LRVTVVAARPGLIIGKKGVDIEKVK 88
DN I F E+Y AG +E+V+ KK L +T G ++G+ + +
Sbjct: 43 DNGINLFDTAEVYAAGKAEVVLGNIIKKKGWRRSSLVITTKIFWGGKAETERGLSRKHII 102
Query: 89 DGLKTLIKK 97
+GLK +++
Sbjct: 103 EGLKASLER 111
>pdb|1AX8| Human Obesity Protein, Leptin
Length = 146
Score = 26.6 bits (57), Expect = 2.7
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 82 VDIEKVKDGLKTLIKKEVSINIKEVKHPQA 111
V I+KV+D KTLIK V+ I ++ H Q+
Sbjct: 1 VPIQKVQDDTKTLIKTIVT-RINDISHTQS 29
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 25.8 bits (55), Expect = 4.6
Identities = 11/27 (40%), Positives = 20/27 (73%)
Query: 114 QLAAENVATQLEKRVAFRRAMKKVMQA 140
+LA +N+ +LE+R+A RA K+++A
Sbjct: 257 RLAIQNIEQELEERLAELRAQGKLLEA 283
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 25.8 bits (55), Expect = 4.6
Identities = 11/27 (40%), Positives = 20/27 (73%)
Query: 114 QLAAENVATQLEKRVAFRRAMKKVMQA 140
+LA +N+ +LE+R+A RA K+++A
Sbjct: 256 RLAIQNIEQELEERLAELRAQGKLLEA 282
>pdb|1KYI|A Chain A, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|B Chain B, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|C Chain C, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|D Chain D, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|E Chain E, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|F Chain F, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|S Chain S, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|T Chain T, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|U Chain U, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|V Chain V, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|W Chain W, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|X Chain X, Hsluv (H. Influenzae)-Nlvs Vinyl Sulfone Inhibitor Complex
pdb|1G41|A Chain A, Crystal Structure Of Hslu Haemophilus Influenzae
pdb|1G3I|T Chain T, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|A Chain A, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|B Chain B, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|U Chain U, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|X Chain X, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|F Chain F, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|C Chain C, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|D Chain D, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|S Chain S, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|E Chain E, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|V Chain V, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|W Chain W, Crystal Structure Of The Hsluv Protease-Chaperone Complex
Length = 444
Score = 25.4 bits (54), Expect = 5.9
Identities = 32/139 (23%), Positives = 60/139 (43%), Gaps = 17/139 (12%)
Query: 32 NIDEDNKIRKFLKKELYYAGVS--EIVIERAAKKLRVTVVAARPGLIIGKKGVDIEKVKD 89
N D + R+ +K+L + EI I+ +A + A PG+ E++ +
Sbjct: 148 NHDSHSSTRQAFRKKLREGQLDDKEIEIDVSAGVSMGVEIMAPPGM---------EEMTN 198
Query: 90 GLKTLIKKEVSINIKEVKHPQADAQLAAENVATQLEKRVAFRRAMKKVMQAALKSGAKGI 149
L++L + S K+ K DA A + + K + +K + A ++G I
Sbjct: 199 QLQSLFQNLGSDKTKKRKMKIKDALKAL--IDDEAAKLINPEELKQKAIDAVEQNGIVFI 256
Query: 150 ----KVCVSGRLAGAEIAR 164
K+C G +GA+++R
Sbjct: 257 DEIDKICKKGEYSGADVSR 275
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 0.381
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,267,215
Number of Sequences: 13198
Number of extensions: 48595
Number of successful extensions: 111
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 105
Number of HSP's gapped (non-prelim): 10
length of query: 234
length of database: 2,899,336
effective HSP length: 85
effective length of query: 149
effective length of database: 1,777,506
effective search space: 264848394
effective search space used: 264848394
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: 53 (25.0 bits)