GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2E2

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373
          Length = 430

 Score =  436 bits (1121), Expect = e-127
 Identities = 220/416 (52%), Positives = 288/416 (69%), Gaps = 1/416 (0%)

Query: 8   LNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAI 67
           L ++R    PRG+        DRA+ + LWDV+G+ Y DF  GI VLN GH HP+V+ A+
Sbjct: 11  LLRQRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAV 70

Query: 68  AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127
            AQL++ +H  +Q+V Y+ Y+ LA+R+  ++  Q   K A FT+GAEAVENA+KIARAHT
Sbjct: 71  QAQLQKISHACFQVVAYKPYLDLAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHT 130

Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187
            R  VIAF G FHGRTLLG  LTG   PYK  FGPF  +++H P+P+A  GV++  ALQA
Sbjct: 131 NRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSAMALQA 190

Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247
           L+ L  T + P RVAAII+EPVQG+GGF +APA+F++GLRA+  +HGIVLI DE+QTGFG
Sbjct: 191 LDELLATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFG 250

Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307
           RTGK F   H  ++PDL+T+AKSLAGG+PLS V G+A IMDAPLPGGLGGTY GN L+ A
Sbjct: 251 RTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCA 310

Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQ 367
           AA AVI+  E+E+L  R   LG++LR+ LL  +   P + +VRG G M+A E       +
Sbjct: 311 AALAVIEAYEQEQLLARGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLAIELIKHDEAR 370

Query: 368 -PSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422
            P A+  +R+   A   GL+++ CG Y NV+RFL PL   +AQ D AL +L  ALA
Sbjct: 371 TPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQILDGALA 426


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: 549
Number of extensions: 22
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: 430
Length adjustment: 32
Effective length of query: 391
Effective length of database: 398
Effective search space:   155618
Effective search space used:   155618
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 Pf6N2E2_373 (Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19))
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.11477.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11477.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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