GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kynA in Acidovorax sp. GW101-3H11

Align Tryptophan 2,3-dioxygenase; TDO; Tryptamin 2,3-dioxygenase; Tryptophan oxygenase; TO; TRPO; Tryptophan pyrrolase; Tryptophanase; EC 1.13.11.11 (characterized)
to candidate Ac3H11_1156 Tryptophan 2,3-dioxygenase (EC 1.13.11.11)

Query= SwissProt::Q1LK00
         (299 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1156
          Length = 298

 Score =  398 bits (1022), Expect = e-116
 Identities = 198/297 (66%), Positives = 233/297 (78%), Gaps = 4/297 (1%)

Query: 7   CPMGHGAAPQNGDGGDS-GDTGNGWHGAQMDFARDMSYGDYLGLDQILSAQHPLSPDHNE 65
           CP  H  AP N   G +  ++      AQ+DF++ MSYGDYL LD IL+AQ PLSP H+E
Sbjct: 2   CPFSHTPAPANEAPGTALPESIVHEERAQLDFSKSMSYGDYLQLDAILTAQKPLSPAHDE 61

Query: 66  MLFIVQHQTTELWMKLMLHELRAARDGVKSDQL---QPAFKMLARVSRIMDQLVQAWNVL 122
           MLFIVQHQT+ELWMKLMLHELRAA D + +        AFKMLARVSRIM+QLV AW+VL
Sbjct: 62  MLFIVQHQTSELWMKLMLHELRAAIDRIANPDTGTRAEAFKMLARVSRIMEQLVSAWSVL 121

Query: 123 ATMTPPEYSAMRPYLGASSGFQSYQYREIEFILGNKNAAMLRPHAHRPEHLELVETALHT 182
           ATMTPPEY+AMRPYL +SSGFQSYQYR IEF LGNKNAAML+PH HRP+ L  V +A  T
Sbjct: 122 ATMTPPEYTAMRPYLASSSGFQSYQYRAIEFSLGNKNAAMLKPHEHRPDLLAQVRSAYET 181

Query: 183 PSMYDEAIRLMARRGFQIDPEVVERDWTQPTQYNASVEAAWLEVYRNPSAHWELYELGEK 242
           PS+YD +++L+A+ G  I    +ERDWTQP   + +V+ AWL VYR+P  +W+LY+LGEK
Sbjct: 182 PSLYDVSLQLLAKEGLHIPASHLERDWTQPYMESEAVKEAWLAVYRDPQKYWDLYQLGEK 241

Query: 243 FVDLEDAFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRRMLDVVLFPELWKLRTDL 299
             D+EDAFR WRFRHVTTVERVIGFKRGTGGT GVSYLR+MLDVVLFPE+WKLRTDL
Sbjct: 242 LTDIEDAFRLWRFRHVTTVERVIGFKRGTGGTGGVSYLRKMLDVVLFPEIWKLRTDL 298


Lambda     K      H
   0.321    0.136    0.424 

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: 356
Number of extensions: 8
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: 299
Length of database: 298
Length adjustment: 27
Effective length of query: 272
Effective length of database: 271
Effective search space:    73712
Effective search space used:    73712
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: 48 (23.1 bits)

Align candidate Ac3H11_1156 (Tryptophan 2,3-dioxygenase (EC 1.13.11.11))
to HMM TIGR03036 (kynA: tryptophan 2,3-dioxygenase (EC 1.13.11.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.10272.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10272.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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