GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Cupriavidus basilensis 4G11

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate RR42_RS00755 RR42_RS00755 3-oxoadipate enol-lactonase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__Cup4G11:RR42_RS00755
          Length = 280

 Score =  180 bits (457), Expect = 3e-50
 Identities = 99/257 (38%), Positives = 146/257 (56%), Gaps = 6/257 (2%)

Query: 6   VNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGHGHSEA 65
           V    LH RIDG   G+ PW+VL+++LG + ++W      L+  +RVLRYD RGHG S+A
Sbjct: 15  VGDISLHVRIDG---GDGPWVVLAHALGANHTLWDATARHLAPRYRVLRYDLRGHGQSDA 71

Query: 66  PKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALCNTAAR 125
           P G Y++ +L  D   LMD +++  A+F G+S+GG+ G   A RH +R+  + L  T  R
Sbjct: 72  PIGAYSMIRLADDAACLMDVMEVPAAHFVGVSVGGMIGQTAAVRHPERLLSLTLAATVNR 131

Query: 126 --IGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDKEGY 183
             +    +W  R       GM  +AD+ + RWF+A +    P  +A +R++ + T   GY
Sbjct: 132 TPLDVHPMWHERIGHVEAHGMAGVADSTMQRWFSAAFRGAHPQEVARVREMLLATPVHGY 191

Query: 184 ASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVEL-DASHI 242
              C+AI A DL      I  P LV++G  DL A PA  RE+A AI GAR   L  A+H+
Sbjct: 192 VGTCQAIMAFDLAGAISRIHCPTLVVAGEEDLGAPPAMAREIAGAIPGARLEILPHAAHL 251

Query: 243 SNIERADAFTKTVVDFL 259
           ++IE+A+ F   +  FL
Sbjct: 252 AHIEQAERFHAVLDAFL 268


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: 232
Number of extensions: 11
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: 263
Length of database: 280
Length adjustment: 25
Effective length of query: 238
Effective length of database: 255
Effective search space:    60690
Effective search space used:    60690
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 RR42_RS00755 RR42_RS00755 (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.25488.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25488.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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