GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bch in Pseudomonas simiae WCS417

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate GFF2712 PS417_13835 crotonase

Query= reanno::WCS417:GFF2712
         (367 letters)



>lcl|FitnessBrowser__WCS417:GFF2712 PS417_13835 crotonase
          Length = 367

 Score =  738 bits (1904), Expect = 0.0
 Identities = 367/367 (100%), Positives = 367/367 (100%)

Query: 1   MTAQVSSEASHAETLQDEVLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDP 60
           MTAQVSSEASHAETLQDEVLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDP
Sbjct: 1   MTAQVSSEASHAETLQDEVLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDP 60

Query: 61  QVYAVVLRGAGEKAFCAGGDIRSLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALM 120
           QVYAVVLRGAGEKAFCAGGDIRSLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALM
Sbjct: 61  QVYAVVLRGAGEKAFCAGGDIRSLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALM 120

Query: 121 DGFVLGGGMGLVQGADLRVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGELGIYLGVTG 180
           DGFVLGGGMGLVQGADLRVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGELGIYLGVTG
Sbjct: 121 DGFVLGGGMGLVQGADLRVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGELGIYLGVTG 180

Query: 181 VQIRAADALYCGLADWYLESSKLADLDNKLDRLQWHDSPLKDLQGVLAKLAVQQLPDAPL 240
           VQIRAADALYCGLADWYLESSKLADLDNKLDRLQWHDSPLKDLQGVLAKLAVQQLPDAPL
Sbjct: 181 VQIRAADALYCGLADWYLESSKLADLDNKLDRLQWHDSPLKDLQGVLAKLAVQQLPDAPL 240

Query: 241 AVLRPAIDHFFALPDVPSIVEQLQQVTVADSHEWALTTAHLMQTRSPLAMAVTLEMLRRG 300
           AVLRPAIDHFFALPDVPSIVEQLQQVTVADSHEWALTTAHLMQTRSPLAMAVTLEMLRRG
Sbjct: 241 AVLRPAIDHFFALPDVPSIVEQLQQVTVADSHEWALTTAHLMQTRSPLAMAVTLEMLRRG 300

Query: 301 RRLPLEQCFALELHLDRQWFERGDLIEGVRALIIDKDKAPRWNPPTLHGLALSHVESFFH 360
           RRLPLEQCFALELHLDRQWFERGDLIEGVRALIIDKDKAPRWNPPTLHGLALSHVESFFH
Sbjct: 301 RRLPLEQCFALELHLDRQWFERGDLIEGVRALIIDKDKAPRWNPPTLHGLALSHVESFFH 360

Query: 361 NFKKVAN 367
           NFKKVAN
Sbjct: 361 NFKKVAN 367


Lambda     K      H
   0.322    0.138    0.419 

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: 695
Number of extensions: 17
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: 367
Length of database: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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