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.
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:
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