GapMind for catabolism of small carbon sources

 

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

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate CA265_RS09910 CA265_RS09910 short-chain dehydrogenase/reductase

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__Pedo557:CA265_RS09910
          Length = 280

 Score = 93.2 bits (230), Expect = 5e-24
 Identities = 66/204 (32%), Positives = 97/204 (47%), Gaps = 20/204 (9%)

Query: 9   KGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNC--VFAP--AD 64
           K  V  ITG + GLGL+   +L+  G          S    + KK  NN    F P   +
Sbjct: 3   KKKVWFITGASKGLGLSLVHQLLNAGQYVAA----TSRNIGELKKAVNNDGGKFLPLAVN 58

Query: 65  VTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMG 124
           + +E+ V+ A+     KF R+DV +N AG  +      L   +T      +   DVN+ G
Sbjct: 59  LANEQSVEDAIKATIAKFERIDVVINNAGYGIGGSIEELSDAET------RNSFDVNVFG 112

Query: 125 TFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIAR 184
           T NVIR  +  +      +  + G IIN AS+A   G  G A Y+A+K  ++ ++   A 
Sbjct: 113 TLNVIRKASPYL------RAQRAGHIINIASIAGIAGATGWAVYAAAKSAVIALSEVSAE 166

Query: 185 DLAPIGIRVMTIAPGLFGTPLLTS 208
           DL   GI+V  +APG F T  LT+
Sbjct: 167 DLKEFGIKVTVVAPGAFRTSFLTA 190


Lambda     K      H
   0.318    0.135    0.385 

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: 144
Number of extensions: 7
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: 261
Length of database: 280
Length adjustment: 25
Effective length of query: 236
Effective length of database: 255
Effective search space:    60180
Effective search space used:    60180
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 (21.7 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