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= 0001.4308.p
         (332 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...    91   2e-19
gi|300310261|ref|YP_003774353.1| nitrilase regulator protein [He...    82   6e-17

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

 Score = 90.5 bits (223), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/331 (25%), Positives = 153/331 (46%), Gaps = 35/331 (10%)

Query: 19  STRSARQPDHLAYWHELVADKIL---PLDFRAACVDTFEAEMTCIELAGINISLIHASPH 75
           ST+S  Q +  +YW E++ +  +   P+      V  F  E++   L+    + + +   
Sbjct: 5   STQSRAQNERFSYWREVLCEAFVSLNPILNEKHTVIDFAGEVSSRSLSTTAQTRVFSKAQ 64

Query: 76  SAIRTADMVTRGGSESLIFNFLLSGREGEAEQDGRRVSFREGAGAFCNAARPYKLNFRET 135
              R  + + R   E    NF L G      QDG+      G  +  ++ RPY L+++  
Sbjct: 65  HIQRRGEEIRRNPVEYCFANFQLEG-SCVVRQDGQESMVLPGDFSIVDSTRPYFLDYQGD 123

Query: 136 FRLMVLQLP-----------YAALS---DGVRGLDGLVAQDYSAGSEVFPLVLTYLSQLS 181
           + ++  ++P           Y A +   DG  G+ GLVA  ++   E   L +    Q  
Sbjct: 124 WHVLSFRIPREQVISRLASPYKATARRVDGKAGM-GLVASRFARSLEQVDLDMGSGVQ-D 181

Query: 182 KRTHQLDSVMAYRIRQNLVDLIAAMLTEASQRMPLQPSECKTAAMIRVKTFIEKNINDPE 241
             +  L+S++A       + L A +  +   R+P+     + A  + V+T+I  ++ +P 
Sbjct: 182 CLSAALNSIIA-------IALGATLEAQERDRLPV-----REAIRLAVETYIRDHLEEPH 229

Query: 242 LSPSVVSSALRLSSRYINQLLEKEGTSLSRLIWRRRLQLIAEDLVDPRLAALSISSIALA 301
           L P +++S  ++S R +  L E+   S+S LI   RLQ  A DL+ P      + ++AL 
Sbjct: 230 LGPDMLASRFKVSRRTLYSLFEEAPLSVSSLIRELRLQRSARDLLSP--GHPGVLAVALR 287

Query: 302 RGFNDLAHFSKAFRLLYEKTPREYRSSFSFK 332
            GF+D +HFS+ F+  +   PRE+ + F+ K
Sbjct: 288 WGFSDASHFSRLFKRRFGVCPREF-ADFTLK 317


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

 Score = 82.0 bits (201), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 76/307 (24%), Positives = 139/307 (45%), Gaps = 12/307 (3%)

Query: 19  STRSARQPDHLAYWHELVADKILPLDFRAACVDTFEAEMTCIELAGINISLIHASPHSAI 78
           +T     P    YW+++V    L  D +      F+  M+   +  ++++++ +  H   
Sbjct: 6   TTEIVEAPRRFEYWNDVVCRHCLQADSKLLGEPVFDGAMSVNSIGMVDMAIMSSPLHHWR 65

Query: 79  RTADMVTRGGSESLIFNFLLSGREGEAEQDGRRVSFREGAGAFCNAARPYKLNFRETFRL 138
           R A  +     + L   F++SG E    QDGR+   + G  A  + ARP++       ++
Sbjct: 66  RDAHHIRSNPDDDLWLAFMVSG-EAYLAQDGRQARLQSGDMALYDGARPFEFALGPE-KI 123

Query: 139 MVLQLPYAALSDGVRGLDGLVAQDYSAGSEVFPLVLTYLSQLSKR-THQL-DSVMAYRIR 196
            + +LP  +L       + L AQ   A     P V+   S L +  T +  D+  A R  
Sbjct: 124 YLTRLPRKSLLSRCPEAEHLTAQLIDARR---PGVMALRSMLEEAGTCEFNDAESAVRYS 180

Query: 197 QNLVDLIAAMLTEASQRMPLQPSECKTAAMIRVKTFIEKNINDPELSPSVVSSALRLSSR 256
             L+D++A  L     R     +  K     RV  ++ +N  DP+L+  V+++A  +S R
Sbjct: 181 AALLDVLALSLAAPGARTT---AAEKNDLYKRVLAYLRENYTDPQLNLHVLAAAHHVSER 237

Query: 257 YINQLLEKEGTSLSRLIWRRRLQLIAEDLVDPRLAALSISSIALARGFNDLAHFSKAFRL 316
            + +   +   +   ++ R RLQ     L +    A ++++ AL  GF+DL+HFS+ FR 
Sbjct: 238 TLTRAFAQHNQTPMDVLRRVRLQASYRALTEGN--AGNVTTAALDAGFSDLSHFSRVFRA 295

Query: 317 LYEKTPR 323
            +  TP+
Sbjct: 296 AFGCTPQ 302


  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
   0.322    0.133    0.377 

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: 830,719
Number of extensions: 29262
Number of successful extensions: 104
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 101
Number of HSP's successfully gapped: 2
Length of query: 332
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 246
Effective length of database: 1,212,660
Effective search space: 298314360
Effective search space used: 298314360
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: 131 (55.1 bits)