GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Burkholderia phytofirmans PsJN

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate BPHYT_RS21430 BPHYT_RS21430 3-oxoadipate enol-lactonase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__BFirm:BPHYT_RS21430
          Length = 263

 Score =  501 bits (1291), Expect = e-147
 Identities = 246/263 (93%), Positives = 256/263 (97%)

Query: 1   MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60
           MPYAAVNGTELHYRIDG+RHGNAPWIVLSNSLGTDLSMWA QVAALSKHFRVLRYDTRGH
Sbjct: 1   MPYAAVNGTELHYRIDGDRHGNAPWIVLSNSLGTDLSMWASQVAALSKHFRVLRYDTRGH 60

Query: 61  GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120
           GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCG+SMGGLTGVALAARH +R ERV LC
Sbjct: 61  GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGISMGGLTGVALAARHGNRFERVVLC 120

Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180
           NTAARIGSPEVWVPRA KAR+EGM ALADAVLPRWFTADY+EREPVVLA+IRDVFVHTDK
Sbjct: 121 NTAARIGSPEVWVPRAAKARSEGMLALADAVLPRWFTADYIEREPVVLALIRDVFVHTDK 180

Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVELDAS 240
           EGYASNC+AIDAADLRPEAPGIK+PALVISGTHDLAATPAQGRELAQ+I GARYVELDAS
Sbjct: 181 EGYASNCDAIDAADLRPEAPGIKLPALVISGTHDLAATPAQGRELAQSIPGARYVELDAS 240

Query: 241 HISNIERADAFTKTVVDFLTEQK 263
           HISNIE+ADAFTKTVVDFLTEQK
Sbjct: 241 HISNIEKADAFTKTVVDFLTEQK 263


Lambda     K      H
   0.320    0.134    0.402 

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: 364
Number of extensions: 10
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: 263
Length of database: 263
Length adjustment: 25
Effective length of query: 238
Effective length of database: 238
Effective search space:    56644
Effective search space used:    56644
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 BPHYT_RS21430 BPHYT_RS21430 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

Software error:

../bin/blast/fastacmd -i /tmp/list.26163.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26163.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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