GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella amazonensis SB2B

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 6938533 Sama_2636 4-aminobutyrate aminotransferase (RefSeq)

Query= uniprot:A1S8Y2
         (425 letters)



>FitnessBrowser__SB2B:6938533
          Length = 425

 Score =  835 bits (2157), Expect = 0.0
 Identities = 425/425 (100%), Positives = 425/425 (100%)

Query: 1   MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH 60
           MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH
Sbjct: 1   MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH 60

Query: 61  PKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAI 120
           PKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAI
Sbjct: 61  PKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAI 120

Query: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVS 180
           KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVS
Sbjct: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVS 180

Query: 181 EDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD 240
           EDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD
Sbjct: 181 EDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYG 300
           EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYG
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYG 300

Query: 301 GSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360
           GSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL
Sbjct: 301 GSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360

Query: 361 MENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420
           MENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE
Sbjct: 361 MENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420

Query: 421 AVLGK 425
           AVLGK
Sbjct: 421 AVLGK 425


Lambda     K      H
   0.319    0.136    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 722
Number of extensions: 6
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
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: 51 (24.3 bits)

Align candidate 6938533 Sama_2636 (4-aminobutyrate aminotransferase (RefSeq))
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.21728.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21728.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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