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= 0004.0105.p
         (148 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312385|ref|YP_003776477.1| SorC family transcription regul...   298   2e-82
gi|300309780|ref|YP_003773872.1| transcription regulator [Herbas...    54   7e-09

>gi|300312385|ref|YP_003776477.1| SorC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 326

 Score =  298 bits (762), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 143/148 (96%), Positives = 146/148 (98%)

Query: 1   VPAFFDYPETRTALWREKSIKAIRDLQERASILLFSIGAEATGSYIHTAGYLGEEERQIL 60
           VPAFFDYPETRTALWREKSIKAIRDLQERASILLFSIGAEATGSYIHTAGYLGEEERQIL
Sbjct: 179 VPAFFDYPETRTALWREKSIKAIRDLQERASILLFSIGAEATGSYIHTAGYLGEEERQIL 238

Query: 61  RDEGLVGDIATVFFRADGSWRDVAFNARNSGPDMECFARAAHSLCVVSGTGKLPGLKAAL 120
           RDEGLVGDIATVFFRADGSWRDVAFNARNSGPDM+CF RAAH+LCVVSG GKLPGLKAAL
Sbjct: 239 RDEGLVGDIATVFFRADGSWRDVAFNARNSGPDMDCFTRAAHALCVVSGAGKLPGLKAAL 298

Query: 121 RGGFINELIIDEPSARLLVEQIRSGAAA 148
           RGGFINELIIDEPSARLLVEQIR+GAAA
Sbjct: 299 RGGFINELIIDEPSARLLVEQIRNGAAA 326


>gi|300309780|ref|YP_003773872.1| transcription regulator
           [Herbaspirillum seropedicae SmR1]
          Length = 320

 Score = 53.5 bits (127), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 38/136 (27%), Positives = 63/136 (46%), Gaps = 3/136 (2%)

Query: 2   PAFFDYPETRTALWREKSIKAIRDLQERASILLFSIGAEATGSYIHTAGYLGEEERQILR 61
           P   +    R      ++ K +  L ERA +    IG  A    +H  G++ + E   L+
Sbjct: 182 PRVAESESDRQQWCNHRAYKIVTGLAERADVTFLGIGTIALQGAMHEDGFIDDGEVAELQ 241

Query: 62  DEGLVGDIATVFFRADGSWRDVAFNARNSGPDM-ECFARAAHSLCVVSGTGKLPGLKAAL 120
            +G VG++    F  DG     + +AR + P + +   R   + C   G+ K   ++AAL
Sbjct: 242 RQGAVGEMICHAFDIDGVMLPSSLSARVTTPPLTQRPQRPVIAFC--GGSKKAEAVRAAL 299

Query: 121 RGGFINELIIDEPSAR 136
           RGG++  L+ DE  AR
Sbjct: 300 RGGWLTGLVTDEVCAR 315


  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
   0.321    0.137    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: 490,480
Number of extensions: 19899
Number of successful extensions: 60
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 60
Number of HSP's successfully gapped: 2
Length of query: 148
Length of database: 1,619,870
Length adjustment: 77
Effective length of query: 71
Effective length of database: 1,255,275
Effective search space: 89124525
Effective search space used: 89124525
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 126 (53.1 bits)