GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Dinoroseobacter shibae DFL-12

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate 3610487 Dshi_3868 UDP-glucose 4-epimerase (RefSeq)

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



>FitnessBrowser__Dino:3610487
          Length = 359

 Score =  357 bits (917), Expect = e-103
 Identities = 179/325 (55%), Positives = 227/325 (69%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           IL+TGGAGYIGSHT V L  +G+E+V+LD+ SN++ +  +R++ ITG  +  YE  +LDR
Sbjct: 5   ILLTGGAGYIGSHTYVALKAAGFEVVILDDFSNAARDVPDRLELITGAPVRLYEGSVLDR 64

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
             +  +F E  I+AV+HFA  KAVGESVA+PL Y+  N TG   L + ME   V ++VFS
Sbjct: 65  GLLARLFTETRIDAVVHFAARKAVGESVAMPLAYFETNCTGLVGLLQEMEAACVHRLVFS 124

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182
           SSATVYG+P+ +P  E  P    NPYG TK+  E IL  L T+D +W+   LRYFNP GA
Sbjct: 125 SSATVYGIPDVTPTPETAPHRHMNPYGLTKITGELILDALATSDPKWAFGTLRYFNPAGA 184

Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242
           H S  IGEDP+ IPNNLMPY+AQVA+G+   L VFG+DYPT DGTGVRDYIHV DLAEGH
Sbjct: 185 HGSALIGEDPSDIPNNLMPYIAQVAMGQRPHLQVFGDDYPTPDGTGVRDYIHVEDLAEGH 244

Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302
           V +L+ +L +  +   NLGTG GYSVLEMV A+    G+ +PYR  DRRPGD+    A  
Sbjct: 245 VLSLKSLLETGESHLVNLGTGRGYSVLEMVAAYSAACGRALPYRIVDRRPGDVPIYCATV 304

Query: 303 AKAKRELGWEAKRGLEEMCADSWRW 327
            +A+  LG+EAKR L +MCA SW W
Sbjct: 305 ERARALLGFEAKRDLAQMCASSWAW 329


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: 410
Number of extensions: 12
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: 359
Length adjustment: 29
Effective length of query: 310
Effective length of database: 330
Effective search space:   102300
Effective search space used:   102300
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 3610487 Dshi_3868 (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.1714.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1714.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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