GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2C3

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate AO356_26715 AO356_26715 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26715
          Length = 430

 Score =  434 bits (1117), Expect = e-126
 Identities = 220/415 (53%), Positives = 285/415 (68%), Gaps = 1/415 (0%)

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

Query: 68  AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127
            AQL++ +H  +Q+V Y+ Y+ L +R+  LV  Q   K ALFT+GAEAVENA+KIARAHT
Sbjct: 71  QAQLQKVSHACFQVVAYKPYLDLVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHT 130

Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187
            RP VI+F G FHGRTLLG  LTG   PYK  FGPF  +++H P+P+A  G S+E ALQA
Sbjct: 131 NRPAVISFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSSEMALQA 190

Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247
           L  L  T + P RVAAII+EPVQG+GGF +AP +F++ LR + +QHGIVLI DE+QTGFG
Sbjct: 191 LNELLATQVAPDRVAAIIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFG 250

Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307
           RTGK F   H  ++PDL+T+AKSLAGG+P+S V GRA IMDAPLPGGLGGTY GN L+ A
Sbjct: 251 RTGKWFGFQHAGIQPDLVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCA 310

Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFC-DPATG 366
           AA AVID  E+E+L ER   LG++LR+ LL  +   P + +VRG G M+A E   D    
Sbjct: 311 AALAVIDAYEQEQLLERGQVLGERLRQGLLRLQARHPRIGDVRGTGFMLAIELIKDDEAR 370

Query: 367 QPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421
            P AE  +++  +A    L+++ CG + NV+RFL PL   ++Q D AL +L  AL
Sbjct: 371 SPDAELTQQLIDQARVGRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAAL 425


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: 529
Number of extensions: 21
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 AO356_26715 AO356_26715 (4-aminobutyrate aminotransferase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.5894.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5894.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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