GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Echinicola vietnamensis KMM 6221, DSM 17526

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Echvi_4610 Echvi_4610 3-oxoacyl-(acyl-carrier-protein) reductase

Query= BRENDA::Q4J702
         (264 letters)



>lcl|FitnessBrowser__Cola:Echvi_4610 Echvi_4610
           3-oxoacyl-(acyl-carrier-protein) reductase
          Length = 248

 Score =  128 bits (322), Expect = 1e-34
 Identities = 79/242 (32%), Positives = 123/242 (50%), Gaps = 4/242 (1%)

Query: 11  GMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDIDE-EGLKRLSDSLRSRGHEVNHMKCDI 69
           G  A++ GAS GIG+AIA  +++ G  V  + +   E  + L   L   G +    + D 
Sbjct: 6   GKTALITGASKGIGRAIALKYAQEGANVAFTFLSSVEKGQALEKELAEFGVKAKGFRSDA 65

Query: 70  TDLNQVKKLVNFSLSVYGNVDALYVTPSINVRKSIENYTYEDFEKVINVNLKGNFMVVKE 129
           +D    ++LVN  +  +G +D L     +     +     E ++ V+N+NLK  F  VK 
Sbjct: 66  SDFKAAEELVNEVVKEFGALDVLINNAGVTRDNLLMRMNEEAWDDVMNINLKSCFNTVKA 125

Query: 130 FLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEYGKYNIRVNVI 189
               +   K G S++  +S+ G     GQ+ YA +KAGII   K  A E G   IR N +
Sbjct: 126 ATRTLMKQKAG-SIINITSVVGIKGNAGQANYAASKAGIIGFTKSVALELGSRGIRSNAV 184

Query: 190 APGVVDTPLTRQIKSDPEWFKAYTEKTILKRWATPEEIANVALFLAMPASSYITGTVIYV 249
           APG ++T +T  +  D +  + + +   +KR   PEE+AN  +FL    SSY++G VI V
Sbjct: 185 APGFIETEMTEVL--DEKTVQGWRDAIPMKRGGQPEEVANACVFLGSDMSSYVSGQVIQV 242

Query: 250 DG 251
           DG
Sbjct: 243 DG 244


Lambda     K      H
   0.317    0.134    0.381 

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: 163
Number of extensions: 14
Number of successful extensions: 4
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: 264
Length of database: 248
Length adjustment: 24
Effective length of query: 240
Effective length of database: 224
Effective search space:    53760
Effective search space used:    53760
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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