GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Pseudomonas simiae WCS417

Align BadK (characterized)
to candidate GFF2524 PS417_12870 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__WCS417:GFF2524
          Length = 270

 Score =  118 bits (296), Expect = 1e-31
 Identities = 83/264 (31%), Positives = 130/264 (49%), Gaps = 18/264 (6%)

Query: 7   LTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGAD 66
           + E  G V  + +NRP+ +NA+N A    +       +  D + A+V++G  + F++G D
Sbjct: 8   VVELIGNVAHVQINRPEKINAMNAAFWTEIIDIFQWIEDTDAVRAVVLSGAGKHFSSGID 67

Query: 67  IASMAAWSYSDVYGSNFITRNWETIRQ--------------IRKPVLAAVAGLAYGGGCE 112
           +  +A  S ++ +G + + RN   +R+               RKPVLAAV G   GG  +
Sbjct: 68  LMMLA--SVANEFGKD-VGRNARLLRRKILELQASFNAVDNCRKPVLAAVQGYCIGGAID 124

Query: 113 LALACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEAD 172
           L  ACD+  A   A+F++ EI +G+    G  QRLPR IG     ++  + R   AEEA 
Sbjct: 125 LISACDMRYAAEGAQFSIKEIDIGMAADVGTLQRLPRIIGDGMLRELAYTGRQFGAEEAR 184

Query: 173 RYGLVSRVV-DDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERREL 231
             GLV+RV  D D L    + +A  IAA S  A+   K  ++   + T+ +G+ +     
Sbjct: 185 SIGLVNRVYPDQDSLLAGVMEIAHEIAAKSPIAVTGTKAMISYMRDHTVNDGLEYVATWN 244

Query: 232 HARFASADAREGIQAFLEKRAPCF 255
            A   S D R  I A + K+ P F
Sbjct: 245 AAMLQSNDLRVAIAAHMSKQKPEF 268


Lambda     K      H
   0.321    0.135    0.389 

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: 100
Number of extensions: 4
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: 258
Length of database: 270
Length adjustment: 25
Effective length of query: 233
Effective length of database: 245
Effective search space:    57085
Effective search space used:    57085
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: 47 (22.7 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