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= 0001.0370.p
         (339 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309734|ref|YP_003773826.1| transcription regulator protein...   435   e-123
gi|300311835|ref|YP_003775927.1| AraC family ethanolamine operon...    69   4e-13
gi|300312312|ref|YP_003776404.1| AraC family ethanolamine operon...    64   2e-11
gi|300313240|ref|YP_003777332.1| AraC family transcription regul...    56   4e-09

>gi|300309734|ref|YP_003773826.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 345

 Score =  435 bits (1119), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 208/338 (61%), Positives = 256/338 (75%)

Query: 1   MPLLAFLIDIHLKRQGSATSGQASTEIKLATPNAFDEFFRETGVRVEAPTTEQARASYEG 60
           MPL AFLI+  +K Q S ++  +ST++ L+ P+  D F R TGV++E      A   YEG
Sbjct: 1   MPLSAFLIESRIKNQASFSALGSSTKVDLSDPHHADTFLRTTGVKIENLNAPHATVQYEG 60

Query: 61  EYFPVPVGAAYRSISKTGWQVRHAPEASGYSLHIQRSGETSWTSTKEALHCSSGSAIIQN 120
           EYF +P G  YRS++ +GW +   PEA GYSL+I RSGE  W + +  +HC SGSAI+ +
Sbjct: 61  EYFLLPEGGLYRSMTASGWVMLSIPEAEGYSLYIPRSGELHWRAAEGLIHCRSGSAIMLD 120

Query: 121 LEQVRQLAGSSASSDEGLFFPVQCLTRKLSHLLDAPVHKPIRFHCPLIHDPHVLAPLKSI 180
           L +++QLA   +SS  G FF + C+T  LS LL+APVH+ +RF  PL+HD HVLAPL S+
Sbjct: 121 LARMQQLASLGSSSGTGFFFSMHCMTHNLSQLLEAPVHRQLRFQSPLVHDAHVLAPLASL 180

Query: 181 IDIIAQGLSGKAPLLKAPLALVNLQQAAAYMVLQNLPHNYSHALASHPPAPAPRQIKRAV 240
            ++IA+GL G APL  APLA+ NL QAA+Y++L NLPHN+SHAL   PPAPAPRQIKRAV
Sbjct: 181 GELIAEGLGGSAPLKNAPLAMANLLQAASYLILHNLPHNHSHALTRRPPAPAPRQIKRAV 240

Query: 241 EFIRASLATPISLNDIAEHSAISVRSLQLGFRKYKGMTPMEFLRTQRLGRVREDLLDPSV 300
           EFI A L+ PI+L DIA H+AISVRSLQ GFR+YK MTPMEFLRTQRLGRVREDLLDP+V
Sbjct: 241 EFIMARLSAPITLADIAAHAAISVRSLQSGFRRYKEMTPMEFLRTQRLGRVREDLLDPAV 300

Query: 301 PADVQHIALSWGFTHFYLFVRYYKKLFGESPQTTLTRR 338
           PAD+QHIALSWGFTH YLF+RYYKK FGESPQ TL RR
Sbjct: 301 PADIQHIALSWGFTHLYLFMRYYKKQFGESPQATLARR 338


>gi|300311835|ref|YP_003775927.1| AraC family ethanolamine operon
           transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 332

 Score = 69.3 bits (168), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 50/154 (32%), Positives = 71/154 (46%), Gaps = 5/154 (3%)

Query: 188 LSGKAPLLKAPLALVNLQQAAAYMVLQNLPHNYSHALASHPPAPAPRQIKRAVEFIRASL 247
           ++G+A    A L L   Q+A    +L  L      A A        R +  A EF  A  
Sbjct: 178 MAGQASGAHAALQL--RQEAVLVALLAMLDEGEIEAEAGASFLRRRRIVNDAREFAMAHQ 235

Query: 248 ATPISLNDIAEHSAISVRSLQLGFRKYKGMTPMEFLRTQRLGRVREDLLDPS---VPADV 304
            +P+++  + E   +S R+LQ  F    GM+PM +LR+ RL  VR  L           +
Sbjct: 236 DSPVTVPMLCEAVHVSRRTLQYCFEDVLGMSPMSYLRSLRLNGVRRALCHGDGRQAVGSI 295

Query: 305 QHIALSWGFTHFYLFVRYYKKLFGESPQTTLTRR 338
             IA +WGF +F  F   YKKLFG++P   L  R
Sbjct: 296 GDIAAAWGFANFSQFSCDYKKLFGQTPSAMLQAR 329


>gi|300312312|ref|YP_003776404.1| AraC family ethanolamine operon
           transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 358

 Score = 63.5 bits (153), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 3/105 (2%)

Query: 234 RQIKRAVEFIRASLATPISLNDIAEHSAISVRSLQLGFRKYKGMTPMEFLRTQRLGRVRE 293
           R I +A   +R       ++  +A H  +S R LQ  F    G+  +EF+R +RL +VR+
Sbjct: 234 RLIDQARRLMRGDAPERATMTQVAAHLGVSRRHLQTCFNTSVGIPAIEFVRAERLNQVRK 293

Query: 294 DLLD---PSVPADVQHIALSWGFTHFYLFVRYYKKLFGESPQTTL 335
            L++     +   +  IA  WGF H   F   Y+ +FGE P  TL
Sbjct: 294 ALVEARRAGLEVSIGDIAADWGFWHLSRFAADYRDMFGELPSKTL 338


>gi|300313240|ref|YP_003777332.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 328

 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 45/87 (51%), Gaps = 1/87 (1%)

Query: 252 SLNDIAEHSAISVRSLQLGFRKYKGMTPMEFLRTQRLGRVREDLLDPS-VPADVQHIALS 310
           S+ ++ +   +S R++Q  F+     TP+ +LR  RL  VR +LL  +   A +  IA  
Sbjct: 235 SIFEVCQRLQVSRRTVQNSFQTVAETTPLNYLRCVRLNGVRRELLSTTHQEASIGDIASR 294

Query: 311 WGFTHFYLFVRYYKKLFGESPQTTLTR 337
           WGF H   F   Y+ LFGE P  T  R
Sbjct: 295 WGFFHLSHFAEDYQALFGELPSQTARR 321


  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
   0.320    0.133    0.395 

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: 966,398
Number of extensions: 37703
Number of successful extensions: 136
Number of sequences better than 1.0e-08: 5
Number of HSP's gapped: 137
Number of HSP's successfully gapped: 5
Length of query: 339
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 253
Effective length of database: 1,212,660
Effective search space: 306802980
Effective search space used: 306802980
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 (21.8 bits)
S2: 131 (55.1 bits)