BLASTP 2.2.18 [Mar-02-2008]


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= 0587.0015.p
         (98 letters)

Database: pfamseq 
           9,421,015 sequences; 3,060,696,203 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

C3GUD5.1 C3GUD5_BACTU Transcription antitermination protein nusG       86   1e-15
C2NS75.1 C2NS75_BACCE Transcription antitermination protein nusG       86   1e-15
C0ZGR2.1 C0ZGR2_BREBN Putative transcription antitermination pro...    85   2e-15
A7Z6E4.1 A7Z6E4_BACA2 Transcription antitermination protein nusG       80   4e-14
A6TKC4.1 A6TKC4_ALKMQ NusG antitermination factor                      69   1e-10

>C3GUD5.1 C3GUD5_BACTU Transcription antitermination protein nusG
          Length = 179

 Score = 85.9 bits (211), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 65/84 (77%)

Query: 5   DKEELYFKKIPEEEMSIILKLLNQEEEINFSKVYTIESKVYVESGPLKGLEGIIKKINKH 64
           D +++YF +IP++E++ I++LLN    I  S+ Y   SKV V+SGPLKG EGII++I+K 
Sbjct: 90  DDDDIYFLEIPDQEITPIIQLLNDRGTIECSEAYFEGSKVIVKSGPLKGREGIIRRIDKR 149

Query: 65  TRRAKVLVSLMGDQRIIELGIEFI 88
            +RAK+L++ +GD ++I++G+EF+
Sbjct: 150 KKRAKLLLNFLGDTKMIDVGVEFL 173


>C2NS75.1 C2NS75_BACCE Transcription antitermination protein nusG
          Length = 179

 Score = 85.9 bits (211), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 65/84 (77%)

Query: 5   DKEELYFKKIPEEEMSIILKLLNQEEEINFSKVYTIESKVYVESGPLKGLEGIIKKINKH 64
           D +++YF +IP++E++ I++LLN    I  S+ Y   SKV V+SGPLKG EGII++I+K 
Sbjct: 90  DDDDIYFLEIPDQEITPIIQLLNDRGTIECSEAYFEGSKVIVKSGPLKGREGIIRRIDKR 149

Query: 65  TRRAKVLVSLMGDQRIIELGIEFI 88
            +RAK+L++ +GD ++I++G+EF+
Sbjct: 150 KKRAKLLLNFLGDTKMIDVGVEFL 173


>C0ZGR2.1 C0ZGR2_BREBN Putative transcription antitermination protein
          Length = 177

 Score = 85.1 bits (209), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 42/82 (51%), Positives = 61/82 (74%)

Query: 7   EELYFKKIPEEEMSIILKLLNQEEEINFSKVYTIESKVYVESGPLKGLEGIIKKINKHTR 66
           E  Y+  I E+E++ IL+L+   E +++SKVY   SKV VESGPLKGLEGIIKK++KH  
Sbjct: 92  EGAYYSSIEEKEITPILQLMGNGEVVDYSKVYLENSKVIVESGPLKGLEGIIKKVDKHKN 151

Query: 67  RAKVLVSLMGDQRIIELGIEFI 88
           RAK+ ++ MG ++ I++GIE +
Sbjct: 152 RAKIFLTFMGVEKTIDVGIEIL 173


>A7Z6E4.1 A7Z6E4_BACA2 Transcription antitermination protein nusG
          Length = 176

 Score = 80.5 bits (197), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 57/77 (74%)

Query: 10  YFKKIPEEEMSIILKLLNQEEEINFSKVYTIESKVYVESGPLKGLEGIIKKINKHTRRAK 69
           YF  I +EE+  I++L+ + + +++SKVY   SKV V SGPLKG+EGIIKKI+K  RRAK
Sbjct: 95  YFTTIKDEEILPIIRLIGEGDTVDYSKVYIENSKVTVASGPLKGMEGIIKKIDKRKRRAK 154

Query: 70  VLVSLMGDQRIIELGIE 86
           + +S MG  +++ +GIE
Sbjct: 155 ICLSFMGLDKMVNVGIE 171


>A6TKC4.1 A6TKC4_ALKMQ NusG antitermination factor
          Length = 162

 Score = 69.3 bits (168), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 40/77 (51%), Positives = 53/77 (68%), Gaps = 1/77 (1%)

Query: 14  IPEEEMSIILKLLNQEEEINFSKVYTIE-SKVYVESGPLKGLEGIIKKINKHTRRAKVLV 72
           IP EEM  +L+L NQ E I  SKV   E +KV V SGPL G+EG I K++K   RAKV +
Sbjct: 83  IPLEEMQRVLRLCNQGELIGLSKVIVKEGNKVQVVSGPLLGMEGHIIKVDKRKGRAKVCL 142

Query: 73  SLMGDQRIIELGIEFIE 89
           S++GD + ++LGIE I+
Sbjct: 143 SVLGDAKTVDLGIEIIK 159


  Database: pfamseq
    Posted date:  Aug 5, 2010  3:22 PM
  Number of letters in database: 3,060,696,203
  Number of sequences in database:  9,421,015
  
Lambda     K      H
   0.316    0.138    0.362 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9421015
Number of Hits to DB: 516,536,842
Number of extensions: 17559692
Number of successful extensions: 43907
Number of sequences better than 1.0e-05: 13
Number of HSP's gapped: 43919
Number of HSP's successfully gapped: 13
Length of query: 98
Length of database: 3,060,696,203
Length adjustment: 67
Effective length of query: 31
Effective length of database: 2,429,488,198
Effective search space: 75314134138
Effective search space used: 75314134138
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 125 (52.8 bits)