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= 033147
(126 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 = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 42/123 (34%), Positives = 62/123 (50%), Gaps = 5/123 (4%)
Query: 4 QICWYFTESWDQFRINGRVDVIDGSNSDPEKLQIREKSWFGCSMKARLQYLDPEQGCPSV 63
+ICWYF + +QFR G + +I +S + R W S ARLQ+ P G P +
Sbjct: 76 EICWYFPNTREQFRXAGDLTLISSDDSHQDLQPARIAXWQELSDAARLQFGWPYPGKPRI 135
Query: 64 NEQPKEFSLDP--CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLK 121
E F P PV FC+L+LDP QVD+L L+ + +++ +D E W+S
Sbjct: 136 KES-GAFEPSPPDPIEPVPNFCLLLLDPVQVDHLELRGEPQNRWLYHRNDQQE--WSSEA 192
Query: 122 TSP 124
+P
Sbjct: 193 INP 195
>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 = 28.9 bits (63), Expect = 0.86, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 76 AGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 123
AGP D + + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 74 AGPDDIY----VSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 117
>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 = 28.9 bits (63), Expect = 0.86, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 76 AGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 123
AGP D + + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 77 AGPDDIY----VSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 120
>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 = 28.9 bits (63), Expect = 0.86, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 76 AGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 123
AGP D + + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 96 AGPDDIY----VSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 139
>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 = 28.9 bits (63), Expect = 0.86, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 76 AGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 123
AGP D + + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 74 AGPDDIY----VSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 117
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 75 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 123
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 76 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 120
>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 = 1.2, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 75 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 123
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 = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 75 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 123
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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 75 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 123
AGP D + P Q+ NL++ + R GE+Y+A LK +
Sbjct: 73 LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 117
>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 = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 6/51 (11%)
Query: 79 VDAFCVLILDP---DQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTSPEC 126
VDAF + + DQV + +KS+Q+ K +S+L + Y SL TSPE
Sbjct: 210 VDAFTLQYYEGFPMDQVAWGEIKSDQQWKVLSKLKNG---YQDSLFTSPEV 257
>pdb|2P53|A Chain A, Crystal Structure Of N-acetyl-d-glucosamine-6-phosphate
Deacetylase D273n Mutant Complexed With N-acetyl
Phosphonamidate-d-glucosamine-6- Phosphate
pdb|2P53|B Chain B, Crystal Structure Of N-acetyl-d-glucosamine-6-phosphate
Deacetylase D273n Mutant Complexed With N-acetyl
Phosphonamidate-d-glucosamine-6- Phosphate
Length = 382
Score = 26.6 bits (57), Expect = 3.8, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 80 DAFCVLILDPDQVDYLNLKSNQKLK 104
D +C +I D VDY N+++ ++LK
Sbjct: 240 DIYCGIIADGLHVDYANIRNAKRLK 264
>pdb|1YMY|A Chain A, Crystal Structure Of The N-Acetylglucosamine-6-Phosphate
Deacetylase From Escherichia Coli K12
pdb|1YMY|B Chain B, Crystal Structure Of The N-Acetylglucosamine-6-Phosphate
Deacetylase From Escherichia Coli K12
pdb|1YRR|A Chain A, Crystal Structure Of The N-Acetylglucosamine-6-Phosphate
Deacetylase From Escherichia Coli K12 At 2.0 A
Resolution
pdb|1YRR|B Chain B, Crystal Structure Of The N-Acetylglucosamine-6-Phosphate
Deacetylase From Escherichia Coli K12 At 2.0 A
Resolution
pdb|2P50|A Chain A, Crystal Structure Of N-Acetyl-D-Glucosamine-6-Phosphate
Deacetylase Liganded With Zn
pdb|2P50|B Chain B, Crystal Structure Of N-Acetyl-D-Glucosamine-6-Phosphate
Deacetylase Liganded With Zn
pdb|2P50|C Chain C, Crystal Structure Of N-Acetyl-D-Glucosamine-6-Phosphate
Deacetylase Liganded With Zn
pdb|2P50|D Chain D, Crystal Structure Of N-Acetyl-D-Glucosamine-6-Phosphate
Deacetylase Liganded With Zn
Length = 382
Score = 26.6 bits (57), Expect = 3.8, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 80 DAFCVLILDPDQVDYLNLKSNQKLK 104
D +C +I D VDY N+++ ++LK
Sbjct: 240 DIYCGIIADGLHVDYANIRNAKRLK 264
>pdb|3L0O|A Chain A, Structure Of Rna-Free Rho Transcription Termination Factor
From Thermotoga Maritima
pdb|3L0O|B Chain B, Structure Of Rna-Free Rho Transcription Termination Factor
From Thermotoga Maritima
Length = 427
Score = 25.4 bits (54), Expect = 8.7, Method: Composition-based stats.
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 85 LILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLK 121
+ + P Q+ NL + + + R GEKY+A +K
Sbjct: 86 IYISPSQIRKFNLNTGDIISGVIRKPKEGEKYFAMIK 122
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
0.319 0.136 0.442
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,216,505
Number of Sequences: 62578
Number of extensions: 162424
Number of successful extensions: 332
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 318
Number of HSP's gapped (non-prelim): 14
length of query: 126
length of database: 14,973,337
effective HSP length: 87
effective length of query: 39
effective length of database: 9,529,051
effective search space: 371632989
effective search space used: 371632989
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)