GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kynA in Pseudomonas fluorescens FW300-N2E3

Align Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (characterized)
to candidate AO353_05970 AO353_05970 tryptophan 2,3-dioxygenase

Query= reanno::pseudo3_N2E3:AO353_05970
         (288 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05970
          Length = 288

 Score =  589 bits (1519), Expect = e-173
 Identities = 288/288 (100%), Positives = 288/288 (100%)

Query: 1   MSQCPYSSDQSPSNPPEEWHNAELNFSDSMSYGDYLDLGKILSAQHPLSPDHNEMLFIIQ 60
           MSQCPYSSDQSPSNPPEEWHNAELNFSDSMSYGDYLDLGKILSAQHPLSPDHNEMLFIIQ
Sbjct: 1   MSQCPYSSDQSPSNPPEEWHNAELNFSDSMSYGDYLDLGKILSAQHPLSPDHNEMLFIIQ 60

Query: 61  HQTSELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYH 120
           HQTSELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYH
Sbjct: 61  HQTSELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYH 120

Query: 121 AIRPFLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLAELEKAIATPSLYDESIR 180
           AIRPFLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLAELEKAIATPSLYDESIR
Sbjct: 121 AIRPFLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLAELEKAIATPSLYDESIR 180

Query: 181 LMVSAGLAIDPQRFERDPASPTAYDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFR 240
           LMVSAGLAIDPQRFERDPASPTAYDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFR
Sbjct: 181 LMVSAGLAIDPQRFERDPASPTAYDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFR 240

Query: 241 QWRFRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 288
           QWRFRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL
Sbjct: 241 QWRFRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 288


Lambda     K      H
   0.320    0.135    0.414 

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: 486
Number of extensions: 7
Number of successful extensions: 1
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: 288
Length of database: 288
Length adjustment: 26
Effective length of query: 262
Effective length of database: 262
Effective search space:    68644
Effective search space used:    68644
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: 47 (22.7 bits)

Align candidate AO353_05970 AO353_05970 (tryptophan 2,3-dioxygenase)
to HMM TIGR03036 (kynA: tryptophan 2,3-dioxygenase (EC 1.13.11.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.3210.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3210.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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