GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Methylocystis bryophila S285

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_085772004.1 B1812_RS13170 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::P76082
         (255 letters)



>NCBI__GCF_002117405.1:WP_085772004.1
          Length = 728

 Score = 94.0 bits (232), Expect = 8e-24
 Identities = 62/189 (32%), Positives = 93/189 (49%), Gaps = 22/189 (11%)

Query: 12  VLLLTLNRPA-ARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEMAE 70
           V LLT + P  + N +   ++ +L   +E  A D +I  CVI      F+ GADL+ M +
Sbjct: 15  VALLTWDMPGRSMNVITEEVMSELAQVVEKVAADAAIKGCVIASGKNAFSGGADLS-MLQ 73

Query: 71  KDLAAT----------------LNDTRP--QLWARLQAFNKPLIAAVNGYALGAGCELAL 112
           K  AA                     R   QL+ RL+   KP   A++G  LG   ELAL
Sbjct: 74  KSRAAHGKALGEKGAEEANRLFFESARKLSQLYRRLETCGKPFAIAIHGVCLGGAFELAL 133

Query: 113 LCD--VVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQ 170
            C   V+   +  + GLPE+ +G+ PGAGGTQR+ R +    A + +  GE ++ + A+ 
Sbjct: 134 ACHHRVLADDDKTKVGLPEVKVGLFPGAGGTQRVARIMPTGDALQFLFKGEQLSGKAAKA 193

Query: 171 AGLVSDVFP 179
           AGL  ++ P
Sbjct: 194 AGLAQELAP 202


Lambda     K      H
   0.318    0.130    0.356 

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: 307
Number of extensions: 11
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: 255
Length of database: 728
Length adjustment: 32
Effective length of query: 223
Effective length of database: 696
Effective search space:   155208
Effective search space used:   155208
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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