GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella oneidensis MR-1

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)

Query= uniprot:A1S8Y2
         (425 letters)



>FitnessBrowser__MR1:200454
          Length = 425

 Score =  735 bits (1898), Expect = 0.0
 Identities = 367/423 (86%), Positives = 393/423 (92%)

Query: 1   MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH 60
           MS TNDSLM RR+AAVAGGVGQIHP+FT RAENA+VWDVEGRE+IDFAGGIAVLNTGHLH
Sbjct: 1   MSTTNDSLMARRQAAVAGGVGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLH 60

Query: 61  PKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAI 120
           PKVKAAVA QLE FSHTCFMVLGYESY+ VCEKLNQLVPGDFAKK+ALFTSGSEAVENA+
Sbjct: 61  PKVKAAVAAQLEDFSHTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAV 120

Query: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVS 180
           KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLM ANVFRAEFPCALHGVS
Sbjct: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVS 180

Query: 181 EDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD 240
           +DDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYA +P FM+RLR LCDREGIMLIAD
Sbjct: 181 DDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYG 300
           EVQTGAGRTGTFFAMEQMGV+ADITTFAKSIAGGFPLSGITGRA+VMDAIGPGGLGGTYG
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYG 300

Query: 301 GSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360
           G+PLACAAALAV+EVFEEEKLLER+NAIG  IKSA+  +   +PQIA+VRGLG+M AIEL
Sbjct: 301 GNPLACAAALAVLEVFEEEKLLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIEL 360

Query: 361 MENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420
           ME+GKPAP+YC Q+L EARNRGLILLSCGTYGNVLRILVP+T  D Q+  GL I+   F 
Sbjct: 361 MEDGKPAPQYCAQILAEARNRGLILLSCGTYGNVLRILVPLTVSDTQLDAGLGILKTSFN 420

Query: 421 AVL 423
           AVL
Sbjct: 421 AVL 423


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: 647
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 200454 SO1276 (4-aminobutyrate aminotransferase (NCBI ptt file))
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.28179.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28179.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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