GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Shewanella amazonensis SB2B

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate 6938103 Sama_2224 UDP-glucose 4-epimerase (RefSeq)

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



>FitnessBrowser__SB2B:6938103
          Length = 336

 Score =  487 bits (1254), Expect = e-142
 Identities = 230/336 (68%), Positives = 275/336 (81%)

Query: 1   MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60
           M ILVTGGAGYIG+HT V L  +G E++VLDNLSN+  EALNRV++ITG+ + F + D+L
Sbjct: 1   MTILVTGGAGYIGTHTVVALQQAGMEVLVLDNLSNACVEALNRVEQITGQAVPFVQGDIL 60

Query: 61  DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120
           D+  +  +F +N+IEAVIHFAGLKAVGESVA PL+YY NN+TGT +LC+ M ++ VK++V
Sbjct: 61  DKPLLMKIFMDNDIEAVIHFAGLKAVGESVAQPLRYYENNVTGTLVLCQVMAEFNVKQLV 120

Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180
           FSSSATVYG P + PITEDFP GATNPYGQ+KLM+E IL DLH +D  W++A LRYFNP 
Sbjct: 121 FSSSATVYGDPASLPITEDFPTGATNPYGQSKLMVEHILADLHHSDPSWNIARLRYFNPV 180

Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240
           GAH SG IGEDPN IPNNLMP+++QVAVGK E+LS+FGNDYPT DGTGVRDYIHVVDLA+
Sbjct: 181 GAHESGLIGEDPNDIPNNLMPFISQVAVGKREKLSIFGNDYPTHDGTGVRDYIHVVDLAD 240

Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300
           GH+KALEK+    G   YNLGTG GYSVL+MVKAFEK SGK VPY  A RRPGDIA C+A
Sbjct: 241 GHLKALEKLRTQPGLVTYNLGTGQGYSVLDMVKAFEKASGKAVPYEIAPRRPGDIAACYA 300

Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336
           DP KA +ELGW+AK  ++EM A SWRWQS N NGY+
Sbjct: 301 DPGKATKELGWKAKLSVDEMAASSWRWQSGNPNGYR 336


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: 476
Number of extensions: 8
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: 339
Length of database: 336
Length adjustment: 28
Effective length of query: 311
Effective length of database: 308
Effective search space:    95788
Effective search space used:    95788
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 6938103 Sama_2224 (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.818.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.818.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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