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= 0001.0493.p
         (70 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309840|ref|YP_003773932.1| cold-shock transcription regula...   140   2e-35
gi|300312332|ref|YP_003776424.1| cold shock-like transcription r...   102   6e-24
gi|300310729|ref|YP_003774821.1| cold-shock DNA-binding domain-c...    93   5e-21

>gi|300309840|ref|YP_003773932.1| cold-shock transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 70

 Score =  140 bits (352), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 68/70 (97%), Positives = 69/70 (98%)

Query: 1  MSTQTGVVKWFNDAKGFGFITPDAGGADVFAHFQDIQSNGFRSLSENQRVSFDRGVGPKG 60
          MS+QTGVVKWFNDAKGFGFITPDAGGADVFAHFQDIQS GFRSLSENQRVSFDRGVGPKG
Sbjct: 1  MSSQTGVVKWFNDAKGFGFITPDAGGADVFAHFQDIQSTGFRSLSENQRVSFDRGVGPKG 60

Query: 61 EKATNIKVIA 70
          EKATNIKVIA
Sbjct: 61 EKATNIKVIA 70


>gi|300312332|ref|YP_003776424.1| cold shock-like transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 68

 Score =  102 bits (254), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 47/62 (75%), Positives = 53/62 (85%)

Query: 5  TGVVKWFNDAKGFGFITPDAGGADVFAHFQDIQSNGFRSLSENQRVSFDRGVGPKGEKAT 64
          TG VKWFNDAKGFGFITPD GG D+FAHF  IQSNGF+SL ENQRVSF+   GPKG++A+
Sbjct: 3  TGTVKWFNDAKGFGFITPDEGGEDLFAHFSAIQSNGFKSLKENQRVSFEVTTGPKGKQAS 62

Query: 65 NI 66
          NI
Sbjct: 63 NI 64


>gi|300310729|ref|YP_003774821.1| cold-shock DNA-binding
          domain-containing protein [Herbaspirillum seropedicae
          SmR1]
          Length = 68

 Score = 92.8 bits (229), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 43/66 (65%), Positives = 52/66 (78%)

Query: 5  TGVVKWFNDAKGFGFITPDAGGADVFAHFQDIQSNGFRSLSENQRVSFDRGVGPKGEKAT 64
          TG VKWFND+KGFGFITPD GG D+FAHF  IQ NGF++L E Q+V FD   GPKG++A+
Sbjct: 3  TGTVKWFNDSKGFGFITPDDGGEDLFAHFSAIQMNGFKTLKEGQKVQFDVTQGPKGKQAS 62

Query: 65 NIKVIA 70
          NI+  A
Sbjct: 63 NIQNAA 68


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.318    0.135    0.404 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 222,946
Number of extensions: 7039
Number of successful extensions: 20
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 20
Number of HSP's successfully gapped: 3
Length of query: 70
Length of database: 1,619,870
Length adjustment: 42
Effective length of query: 28
Effective length of database: 1,421,000
Effective search space: 39788000
Effective search space used: 39788000
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: 41 (21.7 bits)
S2: 123 (52.0 bits)