GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Gracilibacillus halophilus YIM-C55.5

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_003462994.1 J416_RS00905 3-oxoacyl-[acyl-carrier-protein] reductase

Query= BRENDA::Q4J9F2
         (255 letters)



>NCBI__GCF_000359605.1:WP_003462994.1
          Length = 247

 Score =  154 bits (389), Expect = 2e-42
 Identities = 93/250 (37%), Positives = 147/250 (58%), Gaps = 6/250 (2%)

Query: 6   LKNKVVIVTGAGSGIGRAIAKKFALND-SIVVAVELLEDRLNQIVQELRGMGKEVLGVKA 64
           L++KV +VTGA  GIGRAIA + A N  S+ V      D+   +V E+  +G   + ++A
Sbjct: 2   LQDKVALVTGASRGIGRAIALQMAKNGASVAVNYAGSADKAQAVVDEIEEIGGTAIKIQA 61

Query: 65  DVSKKKDVEEFVRRTFETYSRIDVLCNNAGIMDGVTPVAEVSDELWERVLAVNLYSAFYS 124
           +VS +K+V+  V++T +T+ R+DVL NNAGI      +  +S+E ++ V+  NL   F  
Sbjct: 62  NVSNEKEVKAMVKQTIDTFGRLDVLVNNAGITKD-NLLMRMSEEDFDDVIDTNLKGVFVC 120

Query: 125 SRAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRAV 184
           ++AV   M+KQ  G I+N +S+ GI G    A Y  AK G+IGLT+S A     + I   
Sbjct: 121 TKAVTRQMMKQKSGRIINVSSVVGISGNPGQANYVSAKAGVIGLTKSAAQELAAKNILVN 180

Query: 185 AVLPGTVKTNIGLGSSKPSELGMRTLTKLMSLSSRLAEPEDIANVIVFLASDEASFVNGD 244
           AV PG + T++   + + +E     +  L+ L + L E ED+AN  VFLAS+++ ++ G 
Sbjct: 181 AVAPGFIATDM---TDELTEDQKEQILSLIPLKT-LGEAEDVANTAVFLASNQSKYITGQ 236

Query: 245 AVVVDGGLTV 254
            + VDGG+ +
Sbjct: 237 TIQVDGGMVM 246


Lambda     K      H
   0.318    0.135    0.369 

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: 145
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: 255
Length of database: 247
Length adjustment: 24
Effective length of query: 231
Effective length of database: 223
Effective search space:    51513
Effective search space used:    51513
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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