GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Cupriavidus basilensis 4G11

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Cup4G11:RR42_RS26160
          Length = 424

 Score =  719 bits (1856), Expect = 0.0
 Identities = 354/420 (84%), Positives = 383/420 (91%)

Query: 3   MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62
           MKNLELNQRR LATPRGVGVMCDFYADRAENATLWDVEGR YTDFA GIAVLNTGHRHPR
Sbjct: 1   MKNLELNQRRALATPRGVGVMCDFYADRAENATLWDVEGRQYTDFACGIAVLNTGHRHPR 60

Query: 63  VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122
           VMQA+ AQLERFTHTAYQIVPY+ YV LAERINALVPI GL KTALFTTGAEAVENA+KI
Sbjct: 61  VMQAVIAQLERFTHTAYQIVPYESYVALAERINALVPIDGLKKTALFTTGAEAVENAVKI 120

Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182
           ARAHTGRPGVIAFSG FHGRTLLGMALTGKVAPYK+GFGPFPSDIYHAPFP  LHGVSTE
Sbjct: 121 ARAHTGRPGVIAFSGGFHGRTLLGMALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVSTE 180

Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242
           +++QALE LFKTDIDP RVAAII+EPVQGEGGF  AP DFM+ LRA+CD+HGI+LIADEV
Sbjct: 181 QSIQALESLFKTDIDPQRVAAIIIEPVQGEGGFHPAPVDFMQTLRALCDKHGILLIADEV 240

Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302
           QTGFGRTGK+FAMSH+ V PDLITMAKSLAGGMPLSAV GRA+IMDAPLPGGLGGTYAGN
Sbjct: 241 QTGFGRTGKLFAMSHYPVAPDLITMAKSLAGGMPLSAVCGRASIMDAPLPGGLGGTYAGN 300

Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362
           PLAVAAAHAVI+ IE+E+LCER+ +LG+QL+  L    + CP +A++RGLGSMVA EF D
Sbjct: 301 PLAVAAAHAVIETIEQERLCERATALGKQLKAALQQASQTCPGIADIRGLGSMVAVEFHD 360

Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422
           PATGQPSAE AKRVQ RA+EAGL+LLTCGTYGN IRFLYPLTIPQAQFDAAL VLT+ LA
Sbjct: 361 PATGQPSAELAKRVQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQFDAALVVLTKVLA 420


Lambda     K      H
   0.321    0.136    0.400 

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: 718
Number of extensions: 21
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: 423
Length of database: 424
Length adjustment: 32
Effective length of query: 391
Effective length of database: 392
Effective search space:   153272
Effective search space used:   153272
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: 51 (24.3 bits)

Align candidate RR42_RS26160 RR42_RS26160 (4-aminobutyrate aminotransferase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.17593.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17593.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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