GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolM in Pedobacter sp. GW460-11-11-14-LB5

Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate CA265_RS12005 CA265_RS12005 glutathione-dependent formaldehyde dehydrogenase

Query= SwissProt::Q9WYP3
         (395 letters)



>FitnessBrowser__Pedo557:CA265_RS12005
          Length = 385

 Score =  101 bits (252), Expect = 3e-26
 Identities = 78/267 (29%), Positives = 123/267 (46%), Gaps = 30/267 (11%)

Query: 39  EVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVTLGHEFS 98
           ++RV+ VP+P+I  P ++I+KV +  ICGSD+H+      G +        P+ +GHEF 
Sbjct: 11  DIRVDYVPDPKILDPRDVILKVTSTAICGSDLHILS----GAVPQKD----PLIMGHEFM 62

Query: 99  GVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGH-CRPCAE--GFPNHCEN-------- 147
           G+V E G    N +   R  +  P+   +  +C H   P  E   F N+  N        
Sbjct: 63  GIVEEVGASITNLKRGDRVVVPFPISCGKCFFCTHEASPACETSNFKNYGPNGDMMSQKG 122

Query: 148 -----LNELGFNVDGAFAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAV 202
                  +L     G  A+YV+V           E + +   LFL    + PT  +    
Sbjct: 123 AALFGYTDLYGGYSGGQAQYVRVPYADISPRIVPEHLSDEQALFLTD--IFPTGWS---- 176

Query: 203 IVRGGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVID 262
            +    ++ G+ V I G GP+GL A       GAS+VI  +P + R   AK +    +++
Sbjct: 177 AIDWAQLKGGEVVAIFGSGPVGLMAQKAAWINGASRVIAIDPLDYRLEKAKAVNNVDILN 236

Query: 263 PTKENFVEAVLDYTNGLGAKLFLEATG 289
           P K + VEA+ + T G GA L ++A G
Sbjct: 237 PHKVDVVEAIREMTGGRGADLCVDAVG 263


Lambda     K      H
   0.319    0.138    0.418 

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: 370
Number of extensions: 19
Number of successful extensions: 3
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: 395
Length of database: 385
Length adjustment: 31
Effective length of query: 364
Effective length of database: 354
Effective search space:   128856
Effective search space used:   128856
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory