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= 031333
         (161 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 = 94.4 bits (233), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 55/155 (35%), Positives = 87/155 (56%), Gaps = 5/155 (3%)

Query: 7   VFRGFQDNTDKIQINSDTRSRKIEELKSCPFSEICWYFTESWDQFRINGRVDVIDGSNSD 66
           VFRGF ++T++++  +DTRS K ++++  P++EICWYF  + +QFR  G + +I   +S 
Sbjct: 44  VFRGFLEDTNQLRFITDTRSAKADQIQQQPWAEICWYFPNTREQFRXAGDLTLISSDDSH 103

Query: 67  PEKLQIREKSWFGCSMKARLQYLDPEQGCPSVNEQPKEFSLDP--CAGPVDAFCVLILDP 124
            +    R   W   S  ARLQ+  P  G P + E    F   P     PV  FC+L+LDP
Sbjct: 104 QDLQPARIAXWQELSDAARLQFGWPYPGKPRIKES-GAFEPSPPDPIEPVPNFCLLLLDP 162

Query: 125 DQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTSP 159
            QVD+L L+   + +++   +D  E  W+S   +P
Sbjct: 163 VQVDHLELRGEPQNRWLYHRNDQQE--WSSEAINP 195


>pdb|1NRG|A Chain A, Structure And Properties Of Recombinant Human
           Pyridoxine-5'-Phosphate Oxidase
          Length = 261

 Score = 28.5 bits (62), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 7   VFRGFQDNTDKIQINSDTRSRKIEELKSCPFSEICWYFTESWDQFRINGRV 57
           + +GF    D  +  ++  SRK +EL S PF+ + +Y+     Q R+ G V
Sbjct: 98  LLKGF--GKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPV 146


>pdb|3HY8|A Chain A, Crystal Structure Of Human Pyridoxine 5'-Phosphate Oxidase
           R229w Mutant
          Length = 261

 Score = 28.5 bits (62), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 7   VFRGFQDNTDKIQINSDTRSRKIEELKSCPFSEICWYFTESWDQFRINGRV 57
           + +GF    D  +  ++  SRK +EL S PF+ + +Y+     Q R+ G V
Sbjct: 98  LLKGF--GKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPV 146


>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 = 1.9,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 110 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 158
            AGP D +      P Q+   NL++   +    R    GE+Y+A LK +
Sbjct: 73  LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 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 = 28.5 bits (62), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 110 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 158
            AGP D +      P Q+   NL++   +    R    GE+Y+A LK +
Sbjct: 76  LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 120


>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 = 28.1 bits (61), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 110 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 158
            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 = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 110 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 158
            AGP D +      P Q+   NL++   +    R    GE+Y+A LK +
Sbjct: 95  LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 139


>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 = 2.4,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 110 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 158
            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 = 2.5,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 110 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 158
            AGP D +      P Q+   NL++   +    R    GE+Y+A LK +
Sbjct: 73  LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 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 = 28.1 bits (61), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 110 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 158
            AGP D +      P Q+   NL++   +    R    GE+Y+A LK +
Sbjct: 76  LAGPDDIYV----SPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVN 120


>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 = 2.7,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 110 CAGPVDAFCVLILDPDQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTS 158
            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 = 3.0,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 6/51 (11%)

Query: 114 VDAFCVLILDP---DQVDYLNLKSNQKLKFMSRLSDNGEKYWASLKTSPEC 161
           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 = 27.3 bits (59), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 10/25 (40%), Positives = 17/25 (68%)

Query: 115 DAFCVLILDPDQVDYLNLKSNQKLK 139
           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 = 27.3 bits (59), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 10/25 (40%), Positives = 17/25 (68%)

Query: 115 DAFCVLILDPDQVDYLNLKSNQKLK 139
           D +C +I D   VDY N+++ ++LK
Sbjct: 240 DIYCGIIADGLHVDYANIRNAKRLK 264


  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
   0.320    0.136    0.440 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,258,957
Number of Sequences: 62578
Number of extensions: 211721
Number of successful extensions: 428
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 422
Number of HSP's gapped (non-prelim): 14
length of query: 161
length of database: 14,973,337
effective HSP length: 91
effective length of query: 70
effective length of database: 9,278,739
effective search space: 649511730
effective search space used: 649511730
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: 47 (22.7 bits)