GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Shewanella loihica PV-4

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate 5209832 Shew_2285 UDP-glucose 4-epimerase (RefSeq)

Query= metacyc::BSU38860-MONOMER
         (339 letters)



>FitnessBrowser__PV4:5209832
          Length = 351

 Score =  400 bits (1028), Expect = e-116
 Identities = 196/335 (58%), Positives = 243/335 (72%)

Query: 1   MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60
           M+ILVTGGAGYIGSH CVELL++G+++VVLDNLS +  E+L RV++IT   LTF E D+ 
Sbjct: 16  MSILVTGGAGYIGSHACVELLSAGHQLVVLDNLSRAKFESLARVEQITAAKLTFVEGDIR 75

Query: 61  DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120
           D   +D++F+   I+AV+HFAGLKAVGES  +PL+YY NN+ G+  L  AM ++GVK +V
Sbjct: 76  DERTLDALFSHYHIDAVMHFAGLKAVGESTRLPLEYYDNNVVGSMRLLSAMTRHGVKTLV 135

Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180
           FSSSATVYG     PI E  P  +TNPYGQTKL++EQ+  +   A  + SV LLRYFNP 
Sbjct: 136 FSSSATVYGANPPLPIMEAAPRSSTNPYGQTKLVVEQMCAEWANAKQDVSVILLRYFNPV 195

Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240
           GAH SG IGEDP G PNNL+PY+ QVA+G    LSVFG+DY T DGTGVRDYIHV+DL +
Sbjct: 196 GAHESGLIGEDPKGEPNNLLPYITQVAMGHRPYLSVFGSDYATTDGTGVRDYIHVMDLVQ 255

Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300
           GH+ AL ++    G   +NLG+G GYSVLEMV+AFE+ SGK++    A RRPGDIA  +A
Sbjct: 256 GHLAALTRLHGVAGCHTFNLGSGQGYSVLEMVRAFEQASGKDIALHMAPRRPGDIAASYA 315

Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335
            P KA REL W   R L +M  DSWRWQ  N  GY
Sbjct: 316 CPDKAARELDWRVARDLSQMMQDSWRWQCRNPRGY 350


Lambda     K      H
   0.315    0.134    0.395 

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: 423
Number of extensions: 11
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: 339
Length of database: 351
Length adjustment: 29
Effective length of query: 310
Effective length of database: 322
Effective search space:    99820
Effective search space used:    99820
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: 49 (23.5 bits)

Align candidate 5209832 Shew_2285 (UDP-glucose 4-epimerase (RefSeq))
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.24970.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24970.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.