GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Burkholderia phytofirmans PsJN

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate BPHYT_RS24155 BPHYT_RS24155 5-dehydro-4-deoxyglucarate dehydratase

Query= reanno::BFirm:BPHYT_RS24155
         (305 letters)



>FitnessBrowser__BFirm:BPHYT_RS24155
          Length = 305

 Score =  608 bits (1569), Expect = e-179
 Identities = 305/305 (100%), Positives = 305/305 (100%)

Query: 1   MTTPQELKQIVSEGLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFS 60
           MTTPQELKQIVSEGLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFS
Sbjct: 1   MTTPQELKQIVSEGLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFS 60

Query: 61  LTHNDYSNVVKTATEVCKGKVPILAGAGGPTRVAIAYAQEAERHGANGILLMPHYLTEAC 120
           LTHNDYSNVVKTATEVCKGKVPILAGAGGPTRVAIAYAQEAERHGANGILLMPHYLTEAC
Sbjct: 61  LTHNDYSNVVKTATEVCKGKVPILAGAGGPTRVAIAYAQEAERHGANGILLMPHYLTEAC 120

Query: 121 QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVS 180
           QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVS
Sbjct: 121 QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVS 180

Query: 181 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV 240
           IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV
Sbjct: 181 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV 240

Query: 241 GKLIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMGKLDALIK 300
           GKLIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMGKLDALIK
Sbjct: 241 GKLIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMGKLDALIK 300

Query: 301 TLGPQ 305
           TLGPQ
Sbjct: 301 TLGPQ 305


Lambda     K      H
   0.319    0.136    0.398 

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: 519
Number of extensions: 19
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: 305
Length of database: 305
Length adjustment: 27
Effective length of query: 278
Effective length of database: 278
Effective search space:    77284
Effective search space used:    77284
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate BPHYT_RS24155 BPHYT_RS24155 (5-dehydro-4-deoxyglucarate dehydratase)
to HMM TIGR03249 (kdgD: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))

Software error:

../bin/blast/fastacmd -i /tmp/list.6456.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6456.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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