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 PfGW456L13_2985 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2985 Length = 383 Score = 341 bits (874), Expect = 2e-98 Identities = 173/376 (46%), Positives = 252/376 (67%) Query: 2 DFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGG 61 D L+E+Q MI+DMA +FA +AP + +KA D L+ KMGE G G+ PEE+GG Sbjct: 3 DIELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEWGG 62 Query: 62 MGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVG 121 +D ++Y LAVEE+S D TG +S + S+ P+ +G+EEQKQ +LA +A G +G Sbjct: 63 TYVDYVAYALAVEEISAGDGATGAFMSIHNSVGCGPVLNYGSEEQKQTWLADLASGQVIG 122 Query: 122 AFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGI 181 F LTEP AG++A +T A L+ ++++NG+K F++NGK A +VFA+TD G GI Sbjct: 123 CFCLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGKRAKLAIVFAVTDPDLGKRGI 182 Query: 182 SAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDG 241 SAF++ GF + E KMG S T + +C +P+ NLLG+ G+G IA+ L+G Sbjct: 183 SAFLVPTDTAGFIVDRTEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLEG 242 Query: 242 GRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYH 301 GRIG+AAQALGIA A AA+ YS++R QFG++I++ Q++ ++ADM ++ AAR ++ H Sbjct: 243 GRIGIAAQALGIARAAFEAALAYSRDRVQFGKAINEHQSIANLLADMHMQLNAARLMILH 302 Query: 302 AAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQI 361 AA L+ GKP A+ AK FAS++A +V + A+QI GGYGY DYP E+Y R+A+ITQI Sbjct: 303 AARLRTAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVEKYYRDARITQI 362 Query: 362 YEGTNQVMRIVTSRAL 377 YEG++++ R+V +R L Sbjct: 363 YEGSSEIQRMVIAREL 378 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: 331 Number of extensions: 6 Number of successful extensions: 1 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: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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 Sep 17 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