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: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           2,715,099 sequences; 757,237,578 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|NP_622388.1| Transcription antiterminator [Thermoanaerobacte...    57   1e-07
ref|ZP_00061740.1| COG0250: Transcription antiterminator [Clostr...    53   2e-06

>ref|NP_622388.1| Transcription antiterminator [Thermoanaerobacter tengcongensis]
 gb|AAM23992.1| Transcription antiterminator [Thermoanaerobacter tengcongensis]
          Length = 171

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/97 (35%), Positives = 59/97 (60%), Gaps = 6/97 (6%)

Query: 1   VTTVDKEELYFK--KIP----EEEMSIILKLLNQEEEINFSKVYTIESKVYVESGPLKGL 54
           +T+V K+ ++ K  K+P    EEEM +IL L    + I+ S+      +V +  GPL G 
Sbjct: 72  ITSVLKQGVFLKEDKMPASVKEEEMRVILNLTGDSDLIDVSRGVKEGDRVKIIEGPLLGY 131

Query: 55  EGIIKKINKHTRRAKVLVSLMGDQRIIELGIEFIEPV 91
           EG I+K++K  +RAKV+  + G+ + ++LG+E +E +
Sbjct: 132 EGFIQKVDKRKKRAKVIFKVAGEVKSVDLGLEIVEKI 168


>ref|ZP_00061740.1| COG0250: Transcription antiterminator [Clostridium thermocellum
           ATCC 27405]
          Length = 185

 Score = 52.8 bits (125), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 43/80 (53%)

Query: 16  EEEMSIILKLLNQEEEINFSKVYTIESKVYVESGPLKGLEGIIKKINKHTRRAKVLVSLM 75
           E E   +L L N    I  S       K+ +  GPLKG+E ++KKIN+H R A + + +M
Sbjct: 98  ESERQRLLSLCNNNYCIEASYGIIEGDKILIFDGPLKGMESLVKKINRHRREALIEIEIM 157

Query: 76  GDQRIIELGIEFIEPVGSRE 95
           GD R++ + +E +  V   E
Sbjct: 158 GDVRLVTVALEVVRKVSDNE 177


  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Mar 24, 2004  1:53 AM
  Number of letters in database: 757,237,578
  Number of sequences in database:  2,715,099
  
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: 2715099
Number of Hits to DB: 133,270,198
Number of extensions: 4724482
Number of successful extensions: 13730
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 13733
Number of HSP's successfully gapped: 2
Length of query: 98
Length of database: 757,237,578
Length adjustment: 66
Effective length of query: 32
Effective length of database: 578,041,044
Effective search space: 18497313408
Effective search space used: 18497313408
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: 120 (50.8 bits)