GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Marinobacter adhaerens HP15

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Marino:GFF3766
          Length = 425

 Score =  422 bits (1084), Expect = e-122
 Identities = 210/421 (49%), Positives = 277/421 (65%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           SNKEL   + + +  G    +  FAD A N  +WD +G+  +DFAGGI VLN GH HPKV
Sbjct: 2   SNKELQALKERYVAAGAASPNEQFADHATNAELWDADGKRMIDFAGGIGVLNIGHRHPKV 61

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           V AV+AQL KL HTC  V+ YE Y++L E ++  VP     K +L  +G+EA+ENA+KIA
Sbjct: 62  VEAVKAQLDKLMHTCQTVMPYEGYVKLAEKLSGVVPVRGHAKVMLANSGAEALENAMKIA 121

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RAAT ++  I F G YHGRT YT+A+ GK  PY    G MPG VYRA YP P HG+SED+
Sbjct: 122 RAATGKTNVICFDGGYHGRTFYTMAMNGKAAPYQTDFGPMPGTVYRAPYPVPYHGVSEDE 181

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           A+  +    K D+   + AAIVIEPV GEGGFYA+  +F++ +R +CDE+ I++IADEVQ
Sbjct: 182 ALRGLKMAMKADSPAHNTAAIVIEPVLGEGGFYAAPTSFLKEIRKICDENDILMIADEVQ 241

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           SG GRTG +FA+E  GV PDL T AKS+A G P++ + G  + MDA  P  LGGTY G+P
Sbjct: 242 SGFGRTGKMFAIEHSGVEPDLMTMAKSMADGMPISAIVGTDKYMDASGPNSLGGTYTGSP 301

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362
            AC AAL V  VF++E++L K+  LG+KLK       E+   + +VR LG M A EL E 
Sbjct: 302 TACAAALAVFDVFKEEDILGKSQALGEKLKQRFSQWQEQFAHVDNVRNLGPMAAFELVES 361

Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
            +   P  +L A +  +A++KGLILLSCG Y N LR L+P+TIED  + +GL I+ +   
Sbjct: 362 KESRTPKPELAAAVTKKAKEKGLILLSCGMYGNTLRFLMPVTIEDEVLEEGLAIVEESLK 421

Query: 423 E 423
           E
Sbjct: 422 E 422


Lambda     K      H
   0.320    0.137    0.401 

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: 495
Number of extensions: 15
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: 426
Length of database: 425
Length adjustment: 32
Effective length of query: 394
Effective length of database: 393
Effective search space:   154842
Effective search space used:   154842
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 GFF3766 HP15_3708 (4-aminobutyrate aminotransferase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.6867.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6867.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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