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= 0001.1086.p
         (329 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...    97   2e-21
gi|300310261|ref|YP_003774353.1| nitrilase regulator protein [He...    81   1e-16

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

 Score = 96.7 bits (239), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/338 (26%), Positives = 148/338 (43%), Gaps = 29/338 (8%)

Query: 3   KQISTTELPTSQRFRFWSEVVDNYFVKLDCRIEPVPTEKAK----DGLVAQLNHAQLGSL 58
           K  ST     ++RF +W EV+   FV L+    P+  EK       G V+  + +     
Sbjct: 2   KLWSTQSRAQNERFSYWREVLCEAFVSLN----PILNEKHTVIDFAGEVSSRSLSTTAQT 57

Query: 59  DLLE----VQAHPQTVVRNPLRGQDEDYFLFHLQTQGDCQIIQDDRKIVIKPGEMAMYDT 114
            +      +Q   + + RNP+     +Y   + Q +G C + QD ++ ++ PG+ ++ D+
Sbjct: 58  RVFSKAQHIQRRGEEIRRNPV-----EYCFANFQLEGSCVVRQDGQESMVLPGDFSIVDS 112

Query: 115 RRPYQVSLREEFRMRTMRIPVELLRLQLPHPERLVASPVLPQGFVGRFLGNTINSLFDEH 174
            RPY +  + ++ + + RIP E +  +L  P +  A  V  +  +G        SL    
Sbjct: 113 TRPYFLDYQGDWHVLSFRIPREQVISRLASPYKATARRVDGKAGMGLVASRFARSLEQVD 172

Query: 175 QDIPQDQGSALAKATVEMVALGLQSVLPADEALSSSRMCQYHLER--IKHCISCHLGNAE 232
            D+       L+ A   ++A+ L + L A E     R+      R  ++  I  HL    
Sbjct: 173 LDMGSGVQDCLSAALNSIIAIALGATLEAQE---RDRLPVREAIRLAVETYIRDHLEEPH 229

Query: 233 LNVEWLALRLRMSVSSIHRAFECESQTVTEYIWNKRLDACKEALANHKLQRRSISDIAYD 292
           L  + LA R ++S  +++  FE    +V+  I   RL      L +       +  +A  
Sbjct: 230 LGPDMLASRFKVSRRTLYSLFEEAPLSVSSLIRELRLQRSARDLLSPG--HPGVLAVALR 287

Query: 293 WGFSSNAHFSRAFKRHTGMSPRDF-----KAGAMQSNG 325
           WGFS  +HFSR FKR  G+ PR+F     K G    NG
Sbjct: 288 WGFSDASHFSRLFKRRFGVCPREFADFTLKGGLDAGNG 325


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

 Score = 81.3 bits (199), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 78/320 (24%), Positives = 144/320 (45%), Gaps = 20/320 (6%)

Query: 1   MRKQISTTELPTSQRFRFWSEVVDNYFVKLDCRI--EPVPTEKAKDGLVAQLNHAQLGSL 58
           M+ Q +T  +   +RF +W++VV  + ++ D ++  EPV      DG ++ +N   +  +
Sbjct: 1   MKAQYTTEIVEAPRRFEYWNDVVCRHCLQADSKLLGEPV-----FDGAMS-VNSIGMVDM 54

Query: 59  DLLEVQAHPQTVVRNPLRGQDEDYFLFHLQTQGDCQIIQDDRKIVIKPGEMAMYDTRRPY 118
            ++    H      + +R   +D         G+  + QD R+  ++ G+MA+YD  RP+
Sbjct: 55  AIMSSPLHHWRRDAHHIRSNPDDDLWLAFMVSGEAYLAQDGRQARLQSGDMALYDGARPF 114

Query: 119 QVSLREEFRMRTMRIPVELLRLQLPHPERLVASPVLPQGFVGRFLG-NTINSLFDEHQDI 177
           + +L  E ++   R+P + L  + P  E L A     Q    R  G   + S+ +E    
Sbjct: 115 EFALGPE-KIYLTRLPRKSLLSRCPEAEHLTA-----QLIDARRPGVMALRSMLEEAGTC 168

Query: 178 P-QDQGSALAKATVEMVALGLQSVLPADEALSSSRMCQYHLERIKHCISCHLGNAELNVE 236
              D  SA+  +   +  L L    P     ++ +   Y  +R+   +  +  + +LN+ 
Sbjct: 169 EFNDAESAVRYSAALLDVLALSLAAPGARTTAAEKNDLY--KRVLAYLRENYTDPQLNLH 226

Query: 237 WLALRLRMSVSSIHRAFECESQTVTEYIWNKRLDACKEALANHKLQRRSISDIAYDWGFS 296
            LA    +S  ++ RAF   +QT  + +   RL A   AL        +++  A D GFS
Sbjct: 227 VLAAAHHVSERTLTRAFAQHNQTPMDVLRRVRLQASYRALTEGNAG--NVTTAALDAGFS 284

Query: 297 SNAHFSRAFKRHTGMSPRDF 316
             +HFSR F+   G +P+  
Sbjct: 285 DLSHFSRVFRAAFGCTPQSL 304


  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    0.134    0.402 

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: 961,899
Number of extensions: 37744
Number of successful extensions: 114
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 111
Number of HSP's successfully gapped: 2
Length of query: 329
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 243
Effective length of database: 1,212,660
Effective search space: 294676380
Effective search space used: 294676380
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)