GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Phaeobacter inhibens BS107

Align Ethylmalonyl-CoA/methylmalonyl-CoA epimerase; EC 5.1.99.-; EC 5.1.99.1 (characterized)
to candidate GFF2418 PGA1_c24490 methylmalonyl-CoA epimerase

Query= SwissProt::Q3IZP4
         (134 letters)



>FitnessBrowser__Phaeo:GFF2418
          Length = 134

 Score =  258 bits (658), Expect = 3e-74
 Identities = 124/134 (92%), Positives = 130/134 (97%)

Query: 1   MIGRLNHVAIAVPDLEAAAAQYRNTLGAEVGAPQDEPDHGVTVIFITLPNTKIELLHPLG 60
           MIGRLNHVAIAVPDL+AA+AQYRNTLGA+VGAPQDEPDHGVTV+FI LPNTKIELL+PLG
Sbjct: 1   MIGRLNHVAIAVPDLDAASAQYRNTLGAKVGAPQDEPDHGVTVVFIELPNTKIELLYPLG 60

Query: 61  EGSPIAGFLEKNPAGGIHHICYEVEDILAARDRLKEAGARVLGSGEPKIGAHGKPVLFLH 120
           E SPIAGFLEKNPAGGIHHICYEV+DILAARDRLK  GARVLGSGEPKIGAHGKPVLFLH
Sbjct: 61  EASPIAGFLEKNPAGGIHHICYEVDDILAARDRLKAEGARVLGSGEPKIGAHGKPVLFLH 120

Query: 121 PKDFNGCLVELEQV 134
           PKDFNGCLVELEQV
Sbjct: 121 PKDFNGCLVELEQV 134


Lambda     K      H
   0.319    0.141    0.421 

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: 178
Number of extensions: 8
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: 134
Length of database: 134
Length adjustment: 15
Effective length of query: 119
Effective length of database: 119
Effective search space:    14161
Effective search space used:    14161
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: 42 (20.8 bits)

Align candidate GFF2418 PGA1_c24490 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.8789.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8789.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.