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_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Cup4G11:RR42_RS21370
          Length = 420

 Score =  593 bits (1528), Expect = e-174
 Identities = 292/419 (69%), Positives = 341/419 (81%), Gaps = 1/419 (0%)

Query: 3   MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62
           MKN EL +R+  ATPRGVGVMC+F+A+RAEN+ +WDVEG+ Y DFAAGIAVLNTGHRHPR
Sbjct: 1   MKNAELVRRKDAATPRGVGVMCNFFAERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPR 60

Query: 63  VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122
           +++A+  QLERFTHTAYQIVPY  Y+ LAERIN   P +G  KTA FTTGAEAVENAIKI
Sbjct: 61  LVEAMQRQLERFTHTAYQIVPYASYIELAERINQRAPGRGAKKTAFFTTGAEAVENAIKI 120

Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182
           ARA TGRPGVIAFSG FHGRT++GMALTGKV PYK+GFGPFP +++HAP+P ALHGVS E
Sbjct: 121 ARAATGRPGVIAFSGGFHGRTMMGMALTGKVVPYKVGFGPFPGEVFHAPYPCALHGVSVE 180

Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242
            AL+A+E LFK D+DP RVAAII EPVQGEGGF  AP  F++ LRA+CD+HGI+L+ADEV
Sbjct: 181 DALKAMEHLFKADVDPKRVAAIIFEPVQGEGGFNVAPPAFVKALRAICDEHGILLVADEV 240

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

Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362
           PLAVA+A AV+DV+E E+L  R A+LGQ+L   L A +   P +AE+RGLG+MVA EF  
Sbjct: 301 PLAVASALAVLDVLEGEQLIPRGAALGQRLVARLEALKARVPQIAEIRGLGAMVAVEF-R 359

Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421
            A G P AE  + VQ RALE GL+LL+CG YGNVIRFL+PLTI  A  +  L +L   L
Sbjct: 360 RADGAPDAEFTREVQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILADVL 418


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: 615
Number of extensions: 13
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_RS21370 RR42_RS21370 (4-aminobutyrate aminotransferase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.9417.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9417.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.