BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 028990
(200 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2I51|A Chain A, Crystal Structure Of A Pyridoxamine 5'-Phosphate
Oxidase-Related, Fmn Binding Protein (Npun_f5749) From
Nostoc Punctiforme Pcc 73102 At 1.40 A Resolution
pdb|2I51|B Chain B, Crystal Structure Of A Pyridoxamine 5'-Phosphate
Oxidase-Related, Fmn Binding Protein (Npun_f5749) From
Nostoc Punctiforme Pcc 73102 At 1.40 A Resolution
Length = 195
Score = 134 bits (336), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 74/194 (38%), Positives = 112/194 (57%), Gaps = 5/194 (2%)
Query: 7 APWKQLLLQALESQSHLKHSIYFQLATVGTNGRPSNRTVVFRGFQDNTDKIQINSDTRSR 66
APW+ + AL L ++ Y QLATV NGRP+NRT+VFRGF ++T++++ +DTRS
Sbjct: 5 APWRGAIAHALHRNRSLVYARYLQLATVQPNGRPANRTLVFRGFLEDTNQLRFITDTRSA 64
Query: 67 KIEELKSCPFSEICWYFTESWDQFRINGRVDVIDGSNSDPEKLQIREKSWFGCSMKARLQ 126
K ++++ P++EICWYF + +QFR G + +I +S + R W S ARLQ
Sbjct: 65 KADQIQQQPWAEICWYFPNTREQFRXAGDLTLISSDDSHQDLQPARIAXWQELSDAARLQ 124
Query: 127 YLDPEQGCPSVNEQPKEFSLDP--CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLS 184
+ P G P + E F P PV FC+L+LDP QVD+L L+ + +++ +
Sbjct: 125 FGWPYPGKPRIKES-GAFEPSPPDPIEPVPNFCLLLLDPVQVDHLELRGEPQNRWLYHRN 183
Query: 185 DNGEKYWASLKTSP 198
D E W+S +P
Sbjct: 184 DQQE--WSSEAINP 195
>pdb|1NRG|A Chain A, Structure And Properties Of Recombinant Human
Pyridoxine-5'-Phosphate Oxidase
Length = 261
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 31 LATVGTNGRPSNRTVVFRGFQDNTDKIQINSDTRSRKIEELKSCPFSEICWYFTESWDQF 90
LAT +G+PS R ++ +GF D + ++ SRK +EL S PF+ + +Y+ Q
Sbjct: 83 LATCTRDGKPSARMLLLKGF--GKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQV 140
Query: 91 RINGRV 96
R+ G V
Sbjct: 141 RVEGPV 146
>pdb|3HY8|A Chain A, Crystal Structure Of Human Pyridoxine 5'-Phosphate Oxidase
R229w Mutant
Length = 261
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 31 LATVGTNGRPSNRTVVFRGFQDNTDKIQINSDTRSRKIEELKSCPFSEICWYFTESWDQF 90
LAT +G+PS R ++ +GF D + ++ SRK +EL S PF+ + +Y+ Q
Sbjct: 83 LATCTRDGKPSARMLLLKGF--GKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQV 140
Query: 91 RINGRV 96
R+ G V
Sbjct: 141 RVEGPV 146
>pdb|1T9M|A Chain A, X-Ray Crystal Structure Of Phzg From Pseudomonas
Aeruginosa
pdb|1T9M|B Chain B, X-Ray Crystal Structure Of Phzg From Pseudomonas
Aeruginosa
Length = 214
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 2/81 (2%)
Query: 29 FQLATVGTNGRPSNRTVVFRGFQDNTDKIQINSDTRSRKIEELKSCPFSEICWYFTESWD 88
LATV GRPS R VV + ++D S+K EL P++ Y+ ES
Sbjct: 51 LALATVDGQGRPSTRIVVIAELGERGVVFATHAD--SQKGRELAQNPWASGVLYWRESSQ 108
Query: 89 QFRINGRVDVIDGSNSDPEKL 109
Q +NGR + + +D + L
Sbjct: 109 QIILNGRAERLPDERADAQWL 129
>pdb|1TY9|A Chain A, X-Ray Crystal Structure Of Phzg From Pseudomonas
Fluorescens
pdb|1TY9|B Chain B, X-Ray Crystal Structure Of Phzg From Pseudomonas
Fluorescens
Length = 222
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 40/171 (23%), Positives = 69/171 (40%), Gaps = 8/171 (4%)
Query: 29 FQLATVGTNGRPSNRTVVFRGFQDNTDKIQINSDTRSRKIEELKSCPFSEICWYFTESWD 88
LAT + GRPS R VV D + ++ S+K EL P++ Y+ E+
Sbjct: 59 LALATADSQGRPSTRIVVISEISDA--GVVFSTHAGSQKGRELLHNPWASGVLYWRETSQ 116
Query: 89 QFRINGRVDVIDGSNSDPEKLQIREKSWFGCSMKARLQYLDPEQGCPSVNEQPKEFSLDP 148
Q +NG+ + + +D L+ + S+ + + L Q + Q E P
Sbjct: 117 QIILNGQAVRLPNAKADDAWLKRPYATHPMSSVSRQSEELQDVQAMRNAARQLAELQ-GP 175
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLS-DNGEKYWASLKTSP 198
P + +CV L +++ L N + + RL D + W + P
Sbjct: 176 LPRP-EGYCVFEL---RLESLEFWGNGQERLHERLRYDRSDTGWNVRRLQP 222
>pdb|3ICE|A Chain A, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|B Chain B, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|C Chain C, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|D Chain D, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|E Chain E, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|F Chain F, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
Length = 422
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 197
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 76 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 120
>pdb|1PV4|A Chain A, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|B Chain B, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|C Chain C, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|D Chain D, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|E Chain E, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|F Chain F, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
Length = 419
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 197
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 73 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 117
>pdb|1PVO|A Chain A, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|B Chain B, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|C Chain C, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|D Chain D, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|E Chain E, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|F Chain F, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1XPR|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPU|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPO|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
Length = 419
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 197
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 73 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 117
>pdb|2HT1|A Chain A, The Closed Ring Structure Of The Rho Transcription
Termination Factor In Complex With Nucleic Acid In The
Motor Domains
pdb|2HT1|B Chain B, The Closed Ring Structure Of The Rho Transcription
Termination Factor In Complex With Nucleic Acid In The
Motor Domains
Length = 433
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 197
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 95 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 139
>pdb|1A8V|A Chain A, Structure Of The Rna-Binding Domain Of The Rho
Transcription Terminator
pdb|1A8V|B Chain B, Structure Of The Rna-Binding Domain Of The Rho
Transcription Terminator
Length = 121
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 197
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 76 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 120
>pdb|1NT4|A Chain A, Crystal Structure Of Escherichia Coli Periplasmic
Glucose-1- Phosphatase H18a Mutant Complexed With
Glucose-1-Phosphate
pdb|1NT4|B Chain B, Crystal Structure Of Escherichia Coli Periplasmic
Glucose-1- Phosphatase H18a Mutant Complexed With
Glucose-1-Phosphate
Length = 391
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 153 VDAFCVLILDP---DQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTSPEC 200
VDAF + + DQV + +KS+Q+ K +S+L NG Y SL TSPE
Sbjct: 210 VDAFTLQYYEGFPMDQVAWGEIKSDQQWKVLSKLK-NG--YQDSLFTSPEV 257
>pdb|2A8V|A Chain A, Rho Transcription Termination FactorRNA COMPLEX
pdb|2A8V|B Chain B, Rho Transcription Termination FactorRNA COMPLEX
pdb|2A8V|C Chain C, Rho Transcription Termination FactorRNA COMPLEX
Length = 118
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 197
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 73 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 117
>pdb|1A62|A Chain A, Crystal Structure Of The Rna-Binding Domain Of The
Transcriptional Terminator Protein Rho
Length = 130
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 197
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 73 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 117
>pdb|1A63|A Chain A, The Nmr Structure Of The Rna Binding Domain Of E.Coli Rho
Factor Suggests Possible Rna-Protein Interactions, 10
Structures
Length = 130
Score = 27.7 bits (60), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 149 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 197
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 73 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 117
>pdb|3KYN|A Chain A, Crystal Structure Of Hla-G Presenting Kgppaaltl Peptide
Length = 275
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 23 LKHSIYFQLATVGTNGRPSNRTVVFRGFQDNTDKIQINSDTRSRKIE 69
+ HS+ + A V GR R + G+ D+T ++ +SD+ S ++E
Sbjct: 1 MSHSMRYFSAAVSRPGRGEPRFIAM-GYVDDTQFVRFDSDSASPRME 46
>pdb|1W72|A Chain A, Crystal Structure Of Hla-A1:mage-A1 In Complex With Fab-
Hyb3
pdb|1W72|D Chain D, Crystal Structure Of Hla-A1:mage-A1 In Complex With Fab-
Hyb3
pdb|3BO8|A Chain A, The High Resolution Crystal Structure Of Hla-A1
Complexed With The Mage-A1 Peptide
Length = 274
Score = 27.3 bits (59), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 25 HSIYFQLATVGTNGRPSNRTVVFRGFQDNTDKIQINSDTRSRKIE 69
HS+ + +V GR R + G+ D+T ++ +SD S+K+E
Sbjct: 3 HSMRYFFTSVSRPGRGEPRFIAV-GYVDDTQFVRFDSDAASQKME 46
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.134 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,385,371
Number of Sequences: 62578
Number of extensions: 264127
Number of successful extensions: 492
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 488
Number of HSP's gapped (non-prelim): 16
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
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)