BLASTP 2.2.22 [Sep-27-2009]


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 composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= batch____
         (65 letters)

Database: uniref50.fasta 
           3,077,464 sequences; 1,040,396,356 total letters

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


Results from round 1


                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

UniRef50_P41070 Protein trbD n=32 Tax=root RepID=TRBD_ECOLI           103   2e-21
UniRef50_D0ZHW9 Conjugative transfer protein n=5 Tax=Salmonella ...    84   9e-16

>UniRef50_P41070 Protein trbD n=32 Tax=root RepID=TRBD_ECOLI
          Length = 65

 Score =  103 bits (256), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 65/65 (100%), Positives = 65/65 (100%)

Query: 1  MNMRNINVITVLSVPGKTVSDDFMHAVLSNCATRIVLPAPEKFGSESLPDNFNMTAVGVM 60
          MNMRNINVITVLSVPGKTVSDDFMHAVLSNCATRIVLPAPEKFGSESLPDNFNMTAVGVM
Sbjct: 1  MNMRNINVITVLSVPGKTVSDDFMHAVLSNCATRIVLPAPEKFGSESLPDNFNMTAVGVM 60

Query: 61 KNSEI 65
          KNSEI
Sbjct: 61 KNSEI 65


>UniRef50_D0ZHW9 Conjugative transfer protein n=5 Tax=Salmonella enterica
          RepID=D0ZHW9_SALT1
          Length = 81

 Score = 84.4 bits (207), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 5/57 (8%)

Query: 1  MNMRNINVITVLSVPGKTVSDDFMHAVLSNCATRIVLPAPEKFGSESLPDNFNMTAV 57
          MN+RN     V+SVP ++V DDF+  V+SNC T+I+L    ++       NF++T +
Sbjct: 4  MNIRN-----VISVPDESVQDDFVKYVISNCTTKIILSGRREYNFSRQEYNFSVTGM 55


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


Results from round 2


                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value
Sequences used in model and found again:

UniRef50_P41070 Protein trbD n=32 Tax=root RepID=TRBD_ECOLI           103   2e-21
UniRef50_D0ZHW9 Conjugative transfer protein n=5 Tax=Salmonella ...    84   9e-16

Sequences not found previously or not previously below threshold:


CONVERGED!
>UniRef50_P41070 Protein trbD n=32 Tax=root RepID=TRBD_ECOLI
          Length = 65

 Score =  103 bits (256), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 65/65 (100%), Positives = 65/65 (100%)

Query: 1  MNMRNINVITVLSVPGKTVSDDFMHAVLSNCATRIVLPAPEKFGSESLPDNFNMTAVGVM 60
          MNMRNINVITVLSVPGKTVSDDFMHAVLSNCATRIVLPAPEKFGSESLPDNFNMTAVGVM
Sbjct: 1  MNMRNINVITVLSVPGKTVSDDFMHAVLSNCATRIVLPAPEKFGSESLPDNFNMTAVGVM 60

Query: 61 KNSEI 65
          KNSEI
Sbjct: 61 KNSEI 65


>UniRef50_D0ZHW9 Conjugative transfer protein n=5 Tax=Salmonella enterica
          RepID=D0ZHW9_SALT1
          Length = 81

 Score = 84.4 bits (207), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 5/57 (8%)

Query: 1  MNMRNINVITVLSVPGKTVSDDFMHAVLSNCATRIVLPAPEKFGSESLPDNFNMTAV 57
          MN+RN     V+SVP ++V DDF+  V+SNC T+I+L    ++       NF++T +
Sbjct: 4  MNIRN-----VISVPDESVQDDFVKYVISNCTTKIILSGRREYNFSRQEYNFSVTGM 55


  Database: uniref50.fasta
    Posted date:  Mar 8, 2010 10:38 AM
  Number of letters in database: 1,040,396,356
  Number of sequences in database:  3,077,464
  
Lambda     K      H
   0.312    0.130    0.337 

Lambda     K      H
   0.267   0.0395    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 213,218,352
Number of Sequences: 3077464
Number of extensions: 5601510
Number of successful extensions: 11610
Number of sequences better than 1.0e-01: 2
Number of HSP's better than  0.1 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 11606
Number of HSP's gapped (non-prelim): 4
length of query: 65
length of database: 1,040,396,356
effective HSP length: 37
effective length of query: 28
effective length of database: 926,530,188
effective search space: 25942845264
effective search space used: 25942845264
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.4 bits)
S2: 87 (38.2 bits)
