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_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Cup4G11:RR42_RS26240
          Length = 420

 Score =  600 bits (1548), Expect = e-176
 Identities = 293/421 (69%), Positives = 344/421 (81%), Gaps = 1/421 (0%)

Query: 3   MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62
           MKN +L +R+  ATPRGVGVMC+FYA+RAEN+ LWDVEG  Y DFAAGIAVLNTGHRHPR
Sbjct: 1   MKNADLVRRKDAATPRGVGVMCNFYAERAENSELWDVEGNRYIDFAAGIAVLNTGHRHPR 60

Query: 63  VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122
           ++QA+ AQ+ERFTHTAYQIVPY  Y+ LAE+INA  P     KTA FTTGAEAVENAIKI
Sbjct: 61  LVQAMQAQMERFTHTAYQIVPYASYIELAEKINARAPGAFAKKTAFFTTGAEAVENAIKI 120

Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182
           ARA TGRPGVIAFSG FHGRT++GMALTGKV PYK+GFGPFP D++HAP+P  LHGVS +
Sbjct: 121 ARAATGRPGVIAFSGGFHGRTMMGMALTGKVVPYKVGFGPFPGDVFHAPYPYGLHGVSVQ 180

Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242
            ++ AL  LFK D+DP RVAAII EPVQGEGGF  APA+F+R LRA+CD+HGI+L+ADEV
Sbjct: 181 DSINALHQLFKADVDPKRVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEV 240

Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302
           QTGFGRTGK+FAM H+DV PDL TMAKSLAGGMPLSAV GRA IMDAP PGGLGGTYAGN
Sbjct: 241 QTGFGRTGKLFAMEHYDVTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGN 300

Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362
           PLAVA+A AV+DV+E EKL ER A+LGQ+L++ L   +   P + EVRG+G+M+A EF  
Sbjct: 301 PLAVASALAVLDVLESEKLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVEF-R 359

Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422
            A G+P  E  ++VQ RALE GL+LL+CG YGNV+RFL+PLTIP A  D  L +L  AL 
Sbjct: 360 KADGRPDPEFTRQVQDRALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGLGILEAALL 419

Query: 423 E 423
           +
Sbjct: 420 Q 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: 631
Number of extensions: 16
Number of successful extensions: 2
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: 420
Length adjustment: 32
Effective length of query: 391
Effective length of database: 388
Effective search space:   151708
Effective search space used:   151708
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: 50 (23.9 bits)

Align candidate RR42_RS26240 RR42_RS26240 (4-aminobutyrate aminotransferase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.18209.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18209.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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