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|15645932|ref|NP_208111.1| ribosomal protein L3 (rpl3)
[Helicobacter pylori 26695]
(191 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|B Chain B, Crystal Structure Of The Large Ribosoma... 110 8e-26
pdb|1K8A|D Chain D, Co-Crystal Structure Of Carbomycin A Bo... 31 0.080
pdb|1GIY|E Chain E, Crystal Structure Of The Ribosome At 5.... 31 0.080
pdb|1FFK|B Chain B, Crystal Structure Of The Large Ribosoma... 31 0.080
pdb|1POW|A Chain A, Pyruvate Oxidase (E.C.1.2.3.3) (Wild Ty... 30 0.14
pdb|1POX|A Chain A, Pyruvate Oxidase (E.C.1.2.3.3) Mutant W... 30 0.14
pdb|1IBD|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Z... 27 1.5
pdb|1IBH|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Z... 27 1.5
pdb|1BZO|A Chain A, Three-Dimensional Structure Of Prokaryo... 27 1.5
pdb|1IBB|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Z... 27 1.5
pdb|1YAI|B Chain B, X-Ray Structure Of A Bacterial Copper,Z... 27 1.5
pdb|1IB5|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Z... 27 1.5
pdb|1IBF|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Z... 27 1.5
pdb|1YFM| Recombinant Yeast Fumarase 26 3.3
pdb|1G0D|A Chain A, Crystal Structure Of Red Sea Bream Tran... 25 5.7
>pdb|1LNR|B Chain B, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 211
Score = 110 bits (276), Expect = 8e-26
Identities = 73/200 (36%), Positives = 117/200 (58%), Gaps = 23/200 (11%)
Query: 7 KIGMSRTI-DANSTPVTLL-----KVLQAKVCQLENGKAL-VAYA--MHKKHNKAIEGQQ 57
KIGM++ + + PVT++ ++Q K Q + +A+ + YA +K NK ++G
Sbjct: 8 KIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHF 67
Query: 58 KKY-----QLSKEFNHFATLKASQQKELGDLDLSALETLKRVKASFKTKGRGFAGVMKRW 112
K ++ +EF FA + +++ +++ A+ +KG+G GVMKRW
Sbjct: 68 AKAGVAPTRILREFRGFAP-------DGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW 120
Query: 113 NFQGGPAAHGSR-FHRRPGSIGNREWPGRVQKGRKMAGHYGNELVTCQN-EVLSFDKESM 170
NF GGPA+HGS+ +HRRPGSIG R+ PGRV KG++MAGH G E VT QN EV+
Sbjct: 121 NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN 180
Query: 171 VLVLKGSVAGFSGAYGRIRA 190
++++KG++ G +G +R+
Sbjct: 181 LILVKGAIPGANGGLVVLRS 200
>pdb|1K8A|D Chain D, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|D Chain D, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|D Chain D, Co-Crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|D Chain D, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|D Chain D, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1JJ2|B Chain B, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|B Chain B, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
Length = 337
Score = 31.2 bits (69), Expect = 0.080
Identities = 20/55 (36%), Positives = 27/55 (48%), Gaps = 4/55 (7%)
Query: 100 TKGRGFAGVMKRWNFQGGPAAHGSR-FHRRPGSIGNREW-PGRVQKGRKMAGHYG 152
TKG+G G +KRW Q H + + RR G++G W P RV+ G G
Sbjct: 206 TKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLG--PWNPSRVRSTVPQQGQTG 258
>pdb|1GIY|E Chain E, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
Length = 338
Score = 31.2 bits (69), Expect = 0.080
Identities = 20/55 (36%), Positives = 27/55 (48%), Gaps = 4/55 (7%)
Query: 100 TKGRGFAGVMKRWNFQGGPAAHGSR-FHRRPGSIGNREW-PGRVQKGRKMAGHYG 152
TKG+G G +KRW Q H + + RR G++G W P RV+ G G
Sbjct: 206 TKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLG--PWNPSRVRSTVPQQGQTG 258
>pdb|1FFK|B Chain B, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
Length = 338
Score = 31.2 bits (69), Expect = 0.080
Identities = 20/55 (36%), Positives = 27/55 (48%), Gaps = 4/55 (7%)
Query: 100 TKGRGFAGVMKRWNFQGGPAAHGSR-FHRRPGSIGNREW-PGRVQKGRKMAGHYG 152
TKG+G G +KRW Q H + + RR G++G W P RV+ G G
Sbjct: 206 TKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLG--PWNPSRVRSTVPQQGQTG 258
>pdb|1POW|A Chain A, Pyruvate Oxidase (E.C.1.2.3.3) (Wild Type)
pdb|1POW|B Chain B, Pyruvate Oxidase (E.C.1.2.3.3) (Wild Type)
Length = 585
Score = 30.4 bits (67), Expect = 0.14
Identities = 24/89 (26%), Positives = 41/89 (45%), Gaps = 12/89 (13%)
Query: 28 QAKVCQLENGKALVAYAMHKKHNKAIEGQQKKYQLSKEFNHFATLKASQQKELGDLDLSA 87
QA + ++N +A +A K+ EG + YQ+ + N A A ++GD++L+A
Sbjct: 339 QANLANVKNWRAYLASLEDKQ-----EGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNA 393
Query: 88 LETLKRVKAS-------FKTKGRGFAGVM 109
LK ++ F T G G G +
Sbjct: 394 NRHLKLTPSNRHITSNLFATMGVGIPGAI 422
>pdb|1POX|A Chain A, Pyruvate Oxidase (E.C.1.2.3.3) Mutant With Pro 178
Replaced By Ser, Ser 188 Replaced By Asn, And Ala 458
Replaced By Val (P178s,S188n,A458v)
pdb|1POX|B Chain B, Pyruvate Oxidase (E.C.1.2.3.3) Mutant With Pro 178
Replaced By Ser, Ser 188 Replaced By Asn, And Ala 458
Replaced By Val (P178s,S188n,A458v)
Length = 585
Score = 30.4 bits (67), Expect = 0.14
Identities = 24/89 (26%), Positives = 41/89 (45%), Gaps = 12/89 (13%)
Query: 28 QAKVCQLENGKALVAYAMHKKHNKAIEGQQKKYQLSKEFNHFATLKASQQKELGDLDLSA 87
QA + ++N +A +A K+ EG + YQ+ + N A A ++GD++L+A
Sbjct: 339 QANLANVKNWRAYLASLEDKQ-----EGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNA 393
Query: 88 LETLKRVKAS-------FKTKGRGFAGVM 109
LK ++ F T G G G +
Sbjct: 394 NRHLKLTPSNRHITSNLFATMGVGIPGAI 422
>pdb|1IBD|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Zn Sod Mutant V29a
Length = 151
Score = 26.9 bits (58), Expect = 1.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 118 PAAHGSRFHRRPGSIGNREWPGRVQKGRKMAGHYGNE 154
P HG H+ GS + E G+V G GHY E
Sbjct: 39 PGMHGFHIHQN-GSCASSEKDGKVVLGGAAGGHYDPE 74
>pdb|1IBH|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Zn Sod Mutant M41i
Length = 151
Score = 26.9 bits (58), Expect = 1.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 118 PAAHGSRFHRRPGSIGNREWPGRVQKGRKMAGHYGNE 154
P HG H+ GS + E G+V G GHY E
Sbjct: 39 PGIHGFHIHQN-GSCASSEKDGKVVLGGAAGGHYDPE 74
>pdb|1BZO|A Chain A, Three-Dimensional Structure Of Prokaryotic Cu,Zn
Superoxide Dismutase From P.Leiognathi, Solved By X-Ray
Crystallography
Length = 151
Score = 26.9 bits (58), Expect = 1.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 118 PAAHGSRFHRRPGSIGNREWPGRVQKGRKMAGHYGNE 154
P HG H+ GS + E G+V G GHY E
Sbjct: 39 PGMHGFHIHQN-GSCASSEKDGKVVLGGAAGGHYDPE 74
>pdb|1IBB|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Zn Sod Mutant W83f
Length = 151
Score = 26.9 bits (58), Expect = 1.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 118 PAAHGSRFHRRPGSIGNREWPGRVQKGRKMAGHYGNE 154
P HG H+ GS + E G+V G GHY E
Sbjct: 39 PGMHGFHIHQN-GSCASSEKDGKVVLGGAAGGHYDPE 74
>pdb|1YAI|B Chain B, X-Ray Structure Of A Bacterial Copper,Zinc Superoxide
Dismutase
pdb|1YAI|A Chain A, X-Ray Structure Of A Bacterial Copper,Zinc Superoxide
Dismutase
pdb|1YAI|C Chain C, X-Ray Structure Of A Bacterial Copper,Zinc Superoxide
Dismutase
Length = 151
Score = 26.9 bits (58), Expect = 1.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 118 PAAHGSRFHRRPGSIGNREWPGRVQKGRKMAGHYGNE 154
P HG H+ GS + E G+V G GHY E
Sbjct: 39 PGMHGFHIHQN-GSCASSEKDGKVVLGGAAGGHYDPE 74
>pdb|1IB5|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Zn Sod Mutant W83y
Length = 151
Score = 26.9 bits (58), Expect = 1.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 118 PAAHGSRFHRRPGSIGNREWPGRVQKGRKMAGHYGNE 154
P HG H+ GS + E G+V G GHY E
Sbjct: 39 PGMHGFHIHQN-GSCASSEKDGKVVLGGAAGGHYDPE 74
>pdb|1IBF|A Chain A, X-Ray 3d Structure Of P.Leiognathi Cu,Zn Sod Mutant V29g
Length = 151
Score = 26.9 bits (58), Expect = 1.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 118 PAAHGSRFHRRPGSIGNREWPGRVQKGRKMAGHYGNE 154
P HG H+ GS + E G+V G GHY E
Sbjct: 39 PGMHGFHIHQN-GSCASSEKDGKVVLGGAAGGHYDPE 74
>pdb|1YFM| Recombinant Yeast Fumarase
Length = 488
Score = 25.8 bits (55), Expect = 3.3
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 5 VQKIGMSRTIDANSTPVTLLKVLQAKVCQLENGKALVAYAM 45
+ KIG + DA TP+TL + V Q+ENG VA+++
Sbjct: 206 IVKIGRTHLQDA--TPLTLGQEFSGYVQQVENGIQRVAHSL 244
>pdb|1G0D|A Chain A, Crystal Structure Of Red Sea Bream Transglutaminase
Length = 695
Score = 25.0 bits (53), Expect = 5.7
Identities = 31/123 (25%), Positives = 50/123 (40%), Gaps = 24/123 (19%)
Query: 3 FLVQKIGMSRTIDANSTPVTLLKVLQAKVCQLENGKALVAYAMHKK----HNKAIEGQQK 58
++VQK G R I + V +N Y H++ H K EG QK
Sbjct: 401 WIVQKDGQRRKITEDHASVG------------KNISTKSVYGNHREDVTLHYKYPEGSQK 448
Query: 59 KYQLSKEFNHFATLKASQQKELGDLDLSALETLKRVKASFKTKGRGFAGVMKRWNFQGGP 118
+ ++ K+ T +++ E G L LS +K + G F +++ N +GG
Sbjct: 449 EREVYKKAGRRVTEPSNEIAEQGRLQLS-------IKHAQPVFGTDFDVIVEVKN-EGGR 500
Query: 119 AAH 121
AH
Sbjct: 501 DAH 503
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 0.133 0.385
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,074,457
Number of Sequences: 13198
Number of extensions: 42575
Number of successful extensions: 91
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: 83
Number of HSP's gapped (non-prelim): 15
length of query: 191
length of database: 2,899,336
effective HSP length: 83
effective length of query: 108
effective length of database: 1,803,902
effective search space: 194821416
effective search space used: 194821416
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: 51 (24.3 bits)