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= 0001.3520.p
         (331 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310271|ref|YP_003774363.1| AraC family transcription regul...   153   2e-38
gi|300310261|ref|YP_003774353.1| nitrilase regulator protein [He...   119   5e-28
gi|300313268|ref|YP_003777360.1| transcription regulator protein...    55   7e-09

>gi|300310271|ref|YP_003774363.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 350

 Score =  153 bits (386), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 99/313 (31%), Positives = 158/313 (50%), Gaps = 5/313 (1%)

Query: 17  STAALRPHERVDYWREMVCRRFAEVQ---IASRLGGDFYGEMEAHQYAALRLTRVSAKAQ 73
           ST +   +ER  YWRE++C  F  +           DF GE+ +   +    TRV +KAQ
Sbjct: 5   STQSRAQNERFSYWREVLCEAFVSLNPILNEKHTVIDFAGEVSSRSLSTTAQTRVFSKAQ 64

Query: 74  AVTRLGNDAREESQDCYFAVLLLAGSEFLEQDGRQARLLPGDLAIYDAARPHRLIFPEDF 133
            + R G + R    +  FA   L GS  + QDG+++ +LPGD +I D+ RP+ L +  D+
Sbjct: 65  HIQRRGEEIRRNPVEYCFANFQLEGSCVVRQDGQESMVLPGDFSIVDSTRPYFLDYQGDW 124

Query: 134 RKLILQIPRHDMERRIGRMRHVTARVVDARAGAGALAANFVRAVAASPQEPIPGQHSVLA 193
             L  +IPR  +  R+      TAR VD +AG G +A+ F R++     +   G    L+
Sbjct: 125 HVLSFRIPREQVISRLASPYKATARRVDGKAGMGLVASRFARSLEQVDLDMGSGVQDCLS 184

Query: 194 QQIVDLLVLAIGGA-SAPQLCAAGNRAQSLARVKAFIDAHLCDPGLDSALVAASAGLSSR 252
             +  ++ +A+G    A +      R      V+ +I  HL +P L   ++A+   +S R
Sbjct: 185 AALNSIIAIALGATLEAQERDRLPVREAIRLAVETYIRDHLEEPHLGPDMLASRFKVSRR 244

Query: 253 YVNQLFEDEDTSLMRYVLRRRLEHCHDELLHAGRNGRMYDIALRWGFNDPSHFSRAFRKQ 312
            +  LFE+   S+   +   RL+    +LL  G  G +  +ALRWGF+D SHFSR F+++
Sbjct: 245 TLYSLFEEAPLSVSSLIRELRLQRSARDLLSPGHPG-VLAVALRWGFSDASHFSRLFKRR 303

Query: 313 FGGSPRNLRRYEI 325
           FG  PR    + +
Sbjct: 304 FGVCPREFADFTL 316


>gi|300310261|ref|YP_003774353.1| nitrilase regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 307

 Score =  119 bits (297), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 89/298 (29%), Positives = 147/298 (49%), Gaps = 11/298 (3%)

Query: 26  RVDYWREMVCRRFAEVQIASRLGGD--FYGEMEAHQYAALRLTRVSAKAQAVTRLGNDAR 83
           R +YW ++VCR    +Q  S+L G+  F G M  +    + +  +S+      R  +  R
Sbjct: 15  RFEYWNDVVCRHC--LQADSKLLGEPVFDGAMSVNSIGMVDMAIMSSPLHHWRRDAHHIR 72

Query: 84  EESQDCYFAVLLLAGSEFLEQDGRQARLLPGDLAIYDAARPHRLIF-PEDFRKLILQIPR 142
               D  +   +++G  +L QDGRQARL  GD+A+YD ARP      PE  +  + ++PR
Sbjct: 73  SNPDDDLWLAFMVSGEAYLAQDGRQARLQSGDMALYDGARPFEFALGPE--KIYLTRLPR 130

Query: 143 HDMERRIGRMRHVTARVVDARAGAGALAANFVRAVAASPQEPIPGQHSVLAQQIVDLLVL 202
             +  R     H+TA+++DAR   G +A   +   A + +          +  ++D+L L
Sbjct: 131 KSLLSRCPEAEHLTAQLIDARR-PGVMALRSMLEEAGTCEFNDAESAVRYSAALLDVLAL 189

Query: 203 AIGGASAPQLCAAGNRAQSLARVKAFIDAHLCDPGLDSALVAASAGLSSRYVNQLFEDED 262
           ++    A    A  N      RV A++  +  DP L+  ++AA+  +S R + + F   +
Sbjct: 190 SLAAPGARTTAAEKN--DLYKRVLAYLRENYTDPQLNLHVLAAAHHVSERTLTRAFAQHN 247

Query: 263 TSLMRYVLRRRLEHCHDELLHAGRNGRMYDIALRWGFNDPSHFSRAFRKQFGGSPRNL 320
            + M  + R RL+  +  L   G  G +   AL  GF+D SHFSR FR  FG +P++L
Sbjct: 248 QTPMDVLRRVRLQASYRALTE-GNAGNVTTAALDAGFSDLSHFSRVFRAAFGCTPQSL 304


>gi|300313268|ref|YP_003777360.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 288

 Score = 55.1 bits (131), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 39/102 (38%), Positives = 52/102 (50%), Gaps = 3/102 (2%)

Query: 222 LARVKAFIDAHLCDPGLDSALVAASAGLSSRYVNQLFED-EDTSLMRYVLRRRLEHCHDE 280
             RV   I+AHL  P L+   +A  A  S  +  + F D     + RY+L  RL+H   +
Sbjct: 13  FERVLDHIEAHLHAP-LEVEQLANVAHFSRFHFQRQFADFTGVGVARYILLMRLKHASLQ 71

Query: 281 LLHAGRNGRMYDIALRWGFNDPSHFSRAFRKQFGGSPRNLRR 322
           L    +  R+ DIAL  GF +P  F+RAFR  FG SP   RR
Sbjct: 72  LAFQPQR-RIIDIALEAGFENPESFTRAFRSAFGQSPSQFRR 112


  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
   0.324    0.137    0.408 

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: 922,920
Number of extensions: 33703
Number of successful extensions: 163
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 158
Number of HSP's successfully gapped: 3
Length of query: 331
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 245
Effective length of database: 1,212,660
Effective search space: 297101700
Effective search space used: 297101700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 131 (55.1 bits)