Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_028310611.1 H566_RS0105240 3-oxoacyl-ACP reductase FabG
Query= BRENDA::Q4J9F2 (255 letters) >NCBI__GCF_000482785.1:WP_028310611.1 Length = 246 Score = 164 bits (414), Expect = 2e-45 Identities = 100/249 (40%), Positives = 147/249 (59%), Gaps = 5/249 (2%) Query: 6 LKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEVLGVKAD 65 L KV IVTGA +GIG A +KFA +I V +L +++ V L G + G D Sbjct: 3 LNGKVAIVTGAANGIGLATVRKFASEGAICVVADLDPAQVDAAVTGLLRDGAQARGFAVD 62 Query: 66 VSKKKDVEEFVRRTFETYSRIDVLCNNAGIMDGVTPVAEVSDELWERVLAVNLYSAFYSS 125 V+ ++ V+ V +T + + RIDVL NNAGI + +++ E ++RV+ VNL F S Sbjct: 63 VTDRESVDLMVMKTLDAWGRIDVLVNNAGITADAR-LLKMTAEQFDRVIDVNLRGVFNCS 121 Query: 126 RAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRAVA 185 +AV M+ QG+GVI+N +S+ G+ G F Y K G+I ++ A G +G+R A Sbjct: 122 QAVADTMVGQGRGVILNASSVVGLYGNFGQTNYAATKAGVIAFAKTWARELGPKGVRVNA 181 Query: 186 VLPGTVKTNIGLGSSKPSELGMRTLTKLMSLSSRLAEPEDIANVIVFLASDEASFVNGDA 245 V PG V T+I + P+++ + +T + L RLA PE+IANV FLASDEAS+VNG Sbjct: 182 VCPGFVATHI--LDTIPAKV-LEQMTSRVPL-GRLARPEEIANVYAFLASDEASYVNGAV 237 Query: 246 VVVDGGLTV 254 + V GG++V Sbjct: 238 IEVGGGMSV 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: 155 Number of extensions: 9 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: 246 Length adjustment: 24 Effective length of query: 231 Effective length of database: 222 Effective search space: 51282 Effective search space used: 51282 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