GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas simiae WCS417

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate GFF179 PS417_00900 4-aminobutyrate aminotransferase

Query= metacyc::MONOMER-11537
         (425 letters)



>FitnessBrowser__WCS417:GFF179
          Length = 425

 Score =  810 bits (2091), Expect = 0.0
 Identities = 409/425 (96%), Positives = 419/425 (98%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MSKTNASLMKRREAAVPRGVGQIHPIFA+SAKNATVTDVEGREFIDFAGGIAVLNTGHVH
Sbjct: 1   MSKTNASLMKRREAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV
Sbjct: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGG+FRAL+PNELHGVS
Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGVFRALFPNELHGVS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
            DD+IASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPK FMKRLR LCD+HGILLIAD
Sbjct: 181 DDDAIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKSFMKRLRELCDKHGILLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300
           EVQTGAGRTGTFFAMEQMGV ADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360
           GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL
Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           F++GD+HKPNAAAVA VVAKAR+KGLILLSCGTYGNVLRVLVPLTSPD QLDKGLAIIEE
Sbjct: 361 FDDGDTHKPNAAAVASVVAKAREKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEE 420

Query: 421 CFAEL 425
           CF+EL
Sbjct: 421 CFSEL 425


Lambda     K      H
   0.320    0.137    0.394 

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: 820
Number of extensions: 19
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 GFF179 PS417_00900 (4-aminobutyrate aminotransferase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.14266.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14266.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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