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 BPHYT_RS25400 BPHYT_RS25400 butyryl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__BFirm:BPHYT_RS25400 Length = 381 Score = 328 bits (841), Expect = 2e-94 Identities = 165/373 (44%), Positives = 240/373 (64%), Gaps = 1/373 (0%) Query: 5 LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGL 64 LTE Q +I+D A A + +APT ERD W R + + E GF G+ PE+YGG G Sbjct: 9 LTEQQTLIRDTARRVANEIIAPTAAERDLQSAWPRSELKALAELGFLGMLIPEQYGGSGA 68 Query: 65 DVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFG 124 +L + +A E + VD G + + + A I GTE QKQ+YL +A G +GAF Sbjct: 69 GILDFCIAQHEFAAVDAGLATIMHVH-NFTALTIVEHGTETQKQRYLPAMACGESIGAFL 127 Query: 125 LTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAF 184 LTEP AG+D ++ + +A +GD Y+LNG+K FI+NG EA + FA+TDK+ G G S F Sbjct: 128 LTEPHAGSDTASLRASARREGDHYVLNGTKQFISNGSEAGVGIAFAITDKAAGKRGASTF 187 Query: 185 ILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRI 244 I++ PG+ +IE K+G HT+ TA++ E VP ENLLG EG+G++ M + GRI Sbjct: 188 IIDPNAPGYSVTRIESKLGQHTAHTAQIALEGYRVPAENLLGLEGDGYRTVMAGVSDGRI 247 Query: 245 GVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAM 304 G+A + G+A GAL AAVKY++ERE +G ++K QA+ F +ADMA +++ A HAA Sbjct: 248 GIAFISAGVARGALDAAVKYAREREAYGGPLTKLQAVAFDLADMAAQVDVAWQYCLHAAR 307 Query: 305 LKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEG 364 L++ G + A++AK FAS++A +V +DA+QI GGYGY D+P ERY+R+ +I +IYEG Sbjct: 308 LRDAGFDCIKEASIAKLFASEIAEKVCSDALQIHGGYGYLTDFPVERYLRDVRICKIYEG 367 Query: 365 TNQVMRIVTSRAL 377 T+ + +++ SR L Sbjct: 368 TSHIQKLIISRNL 380 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: 360 Number of extensions: 11 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: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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