GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Magnetospirillum magneticum AMB-1

Align Ethylmalonyl-CoA/methylmalonyl-CoA epimerase; EC 5.1.99.-; EC 5.1.99.1 (characterized)
to candidate WP_011384956.1 AMB_RS12960 methylmalonyl-CoA epimerase

Query= SwissProt::Q3IZP4
         (134 letters)



>NCBI__GCF_000009985.1:WP_011384956.1
          Length = 134

 Score =  228 bits (581), Expect = 2e-65
 Identities = 109/133 (81%), Positives = 119/133 (89%)

Query: 1   MIGRLNHVAIAVPDLEAAAAQYRNTLGAEVGAPQDEPDHGVTVIFITLPNTKIELLHPLG 60
           MIG+LNHVAIAVPDL AA A YR+TLGA+V AP  +P HGVTV+F+ LPNTK+ELLHP+G
Sbjct: 1   MIGKLNHVAIAVPDLAAATALYRDTLGAKVSAPVPQPAHGVTVVFVELPNTKVELLHPMG 60

Query: 61  EGSPIAGFLEKNPAGGIHHICYEVEDILAARDRLKEAGARVLGSGEPKIGAHGKPVLFLH 120
           E SPIAGFLEKNP+GGIHHICYEVEDILAARD+LK  GARVLG GEPKIGAH KPVLFLH
Sbjct: 61  EKSPIAGFLEKNPSGGIHHICYEVEDILAARDKLKATGARVLGDGEPKIGAHDKPVLFLH 120

Query: 121 PKDFNGCLVELEQ 133
           PKDFNG LVELEQ
Sbjct: 121 PKDFNGTLVELEQ 133


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: 159
Number of extensions: 7
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 WP_011384956.1 AMB_RS12960 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.1786.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1786.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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