GapMind for catabolism of small carbon sources

 

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

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate 5208938 Shew_1439 maleylacetoacetate isomerase (RefSeq)

Query= reanno::MR1:200836
         (216 letters)



>FitnessBrowser__PV4:5208938
          Length = 214

 Score =  298 bits (764), Expect = 4e-86
 Identities = 145/215 (67%), Positives = 172/215 (80%), Gaps = 2/215 (0%)

Query: 1   MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60
           M L GYWRSSAAYRVRIALNLKG+ AE  SVHLV++GGEQH  +Y ALNPQELVPTL+  
Sbjct: 1   MKLLGYWRSSAAYRVRIALNLKGLDAELESVHLVKNGGEQHLPEYAALNPQELVPTLIEG 60

Query: 61  DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120
           D +    L+QSLAIIEYLDE Y    +LP +   RA VRAMAL+IACE+HPLNNL+VLQY
Sbjct: 61  DNEF--VLSQSLAIIEYLDEQYGGAMMLPTAPKARAEVRAMALSIACEVHPLNNLKVLQY 118

Query: 121 LTQKLTVNEEAKSAWYHHWVATGFTALETQLVRHSGRYCFGDKVTIADLCLVPQVYNAQR 180
           LT  L ++E+AK+AWYHHW+  GF+A E QL +H+G YC+GD+VT+ADLCL+PQVYNA R
Sbjct: 119 LTNTLELDEDAKNAWYHHWIHQGFSAFEKQLEKHAGSYCYGDEVTLADLCLIPQVYNANR 178

Query: 181 FNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215
           F VDL+ YPNI R+W  C+QL AF  AAPERQADA
Sbjct: 179 FKVDLSTYPNIRRIWDNCHQLEAFVLAAPERQADA 213


Lambda     K      H
   0.321    0.134    0.408 

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: 183
Number of extensions: 3
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: 216
Length of database: 214
Length adjustment: 22
Effective length of query: 194
Effective length of database: 192
Effective search space:    37248
Effective search space used:    37248
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 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate 5208938 Shew_1439 (maleylacetoacetate isomerase (RefSeq))
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.5562.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5562.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.