Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate WP_073037063.1 BUB04_RS03730 acyl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >NCBI__GCF_900129305.1:WP_073037063.1 Length = 382 Score = 410 bits (1055), Expect = e-119 Identities = 202/379 (53%), Positives = 275/379 (72%), Gaps = 1/379 (0%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60 M F LTE+Q+MI+DMA +FAE+ +AP E D+ H +++ KMGE G GI P EYG Sbjct: 1 MHFELTEEQRMIQDMARKFAEREIAPVAAELDRTHKHPEEIVKKMGELGLMGITIPPEYG 60 Query: 61 GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120 G G+D +SY+LA+ E+SK G+ +S SL P+Y +GTEEQKQ++L P+A G ++ Sbjct: 61 GAGMDYVSYVLAMIEISKACASCGVIMSVCNSLYNFPVYTYGTEEQKQQFLTPVASGEYL 120 Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180 G +GLTE AG+D + +TTAVL G+++++NG K FITNG A V+ A+TDK +G G Sbjct: 121 GCYGLTEAGAGSDPAKMRTTAVLDGNEWVINGEKKFITNGNVARYCVLAAVTDKEKGYKG 180 Query: 181 ISAFILE-KGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETL 239 IS+F+++ PGF+ G++E+K+G + S TAELIFED +PKENLLGKEGEGFK + TL Sbjct: 181 ISSFLVDLHNTPGFKVGRVEEKLGINASGTAELIFEDARIPKENLLGKEGEGFKQMLTTL 240 Query: 240 DGGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLV 299 DGGRIG+A+QA+GI L A++Y+K REQFGR I+ FQA+Q+ +AD+AT+++AA L Sbjct: 241 DGGRIGIASQAIGIGRAVLEEAIEYAKTREQFGRPIASFQAIQWKLADIATQLDAAELLT 300 Query: 300 YHAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKIT 359 AA L+ G+ Y + AAMAK FASD AM + VQI GGYGY +YP ER+MR+AKIT Sbjct: 301 LRAAWLEQNGRGYEKEAAMAKLFASDTAMWAAVEGVQILGGYGYCKEYPMERHMRDAKIT 360 Query: 360 QIYEGTNQVMRIVTSRALL 378 QIYEGTN++MR+V SR +L Sbjct: 361 QIYEGTNEIMRLVISRNIL 379 Lambda K H 0.318 0.134 0.379 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: 427 Number of extensions: 13 Number of successful extensions: 2 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: 383 Length of database: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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