GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Sphingomonas koreensis DSMZ 15582

Align Ethylmalonyl-CoA/methylmalonyl-CoA epimerase; EC 5.1.99.-; EC 5.1.99.1 (characterized)
to candidate Ga0059261_3985 Ga0059261_3985 methylmalonyl-CoA epimerase (EC 5.1.99.1)

Query= SwissProt::Q3IZP4
         (134 letters)



>FitnessBrowser__Korea:Ga0059261_3985
          Length = 141

 Score =  150 bits (379), Expect = 7e-42
 Identities = 72/131 (54%), Positives = 93/131 (70%), Gaps = 3/131 (2%)

Query: 2   IGRLNHVAIAVPDLEAAAAQYRNTLGAE-VGAPQDEPDHGVTVIFITLPNTKIELLHPLG 60
           +GRLNH+ +A P +EA+ A YR+ +GA+ + AP D P  GV V F+  PNT+IEL+ PLG
Sbjct: 4   LGRLNHIGVATPSIEASVAFYRDVMGAQTIHAPFDLPAQGVKVCFVDTPNTQIELIEPLG 63

Query: 61  EGSPIAGFLEKNPAGGIHHICYEVEDILAARDRLKEAGARVLGSGEPKIGAHGKPVLFLH 120
             SPI GFL +NPAGG HH+CYEV DI  A+   +  GA+VL  GEP+IGAHG P+ F+H
Sbjct: 64  ADSPIHGFLARNPAGGQHHVCYEVPDIHEAKAWFEAKGAKVL--GEPRIGAHGTPIFFVH 121

Query: 121 PKDFNGCLVEL 131
           PKD  G L E+
Sbjct: 122 PKDMGGVLTEI 132


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: 107
Number of extensions: 9
Number of successful extensions: 4
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: 141
Length adjustment: 15
Effective length of query: 119
Effective length of database: 126
Effective search space:    14994
Effective search space used:    14994
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 Ga0059261_3985 Ga0059261_3985 (methylmalonyl-CoA epimerase (EC 5.1.99.1))
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.6058.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6058.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.