GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Pedobacter sp. GW460-11-11-14-LB5

Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate CA265_RS10815 CA265_RS10815 methylmalonyl-CoA epimerase

Query= SwissProt::O58010
         (136 letters)



>FitnessBrowser__Pedo557:CA265_RS10815
          Length = 135

 Score =  126 bits (317), Expect = 1e-34
 Identities = 60/128 (46%), Positives = 89/128 (69%), Gaps = 1/128 (0%)

Query: 7   RIDHVGIAVKNLEEAIKIWEGL-GFKVEEIEEVPDQKVKVAVIKVGENRIELLEATTEDS 65
           +I+H+GIAVK+L  +I I++ L      + E+V  + V  A  K GEN++ELL+AT  DS
Sbjct: 3   KIEHIGIAVKDLNSSIAIYQKLLNTDCYKTEQVASEFVNTAFFKTGENKVELLQATAPDS 62

Query: 66  PIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPKSVT 125
            IAKFIEK+GEGIHH+A  V++I +++E L Q+G+ L+ E P+ GA    + F+HPK   
Sbjct: 63  AIAKFIEKKGEGIHHIAFLVDDILAEMERLHQEGFVLLSESPKKGADDKMVCFVHPKDTN 122

Query: 126 GVLLELCE 133
           GVL+E+C+
Sbjct: 123 GVLIEICQ 130


Lambda     K      H
   0.317    0.138    0.389 

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: 87
Number of extensions: 6
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: 136
Length of database: 135
Length adjustment: 15
Effective length of query: 121
Effective length of database: 120
Effective search space:    14520
Effective search space used:    14520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 42 (20.8 bits)

Align candidate CA265_RS10815 CA265_RS10815 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.29789.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29789.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.