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_011428126.1 RHE_RS25445 acyl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >NCBI__GCF_000092045.1:WP_011428126.1 Length = 395 Score = 217 bits (552), Expect = 5e-61 Identities = 134/373 (35%), Positives = 194/373 (52%), Gaps = 5/373 (1%) Query: 5 LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGL 64 LT +++M++D A +A++ LAP V + + D + +MGE G G EYGG GL Sbjct: 20 LTNEERMVQDTAHAYAQQKLAPRVLDAFRNEKTDPAIFREMGELGLLGPTISPEYGGAGL 79 Query: 65 DVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFG 124 +Y L E+ +VD G +S SL PI FG+ QKQKYL +A G +G FG Sbjct: 80 GYTAYGLIAREVERVDSGYRSMMSVQSSLVMVPIETFGSAAQKQKYLPKLATGEWIGCFG 139 Query: 125 LTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAF 184 LTEP G+D + T A Y L GSK +I+N AD +VV+A T+ I F Sbjct: 140 LTEPDHGSDPGSMATRAKKVDGGYSLTGSKTWISNAPIADVFVVWAKTEDGL----IRGF 195 Query: 185 ILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRI 244 ILEKG G I K+G SIT E++ + VP+ENLL G K L+ R Sbjct: 196 ILEKGWKGLSAPAIHGKVGLRASITGEVVMDGVFVPEENLL-PGVTGLKGPFTCLNSARF 254 Query: 245 GVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAM 304 G+A ALG AE A A +Y ER+QFGR ++ Q +Q +ADMA +I Sbjct: 255 GIAWGALGAAEDCYARARQYVLERKQFGRPLAANQLIQKKLADMAAEIALGLQGCLRLGR 314 Query: 305 LKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEG 364 +K EG P E ++ K + A+E+ A + GG G + ++ R++ N ++ YEG Sbjct: 315 MKEEGHPPVELTSILKRNSCGKALEMARAARDMLGGNGISDEFGIARHLVNLEVVNTYEG 374 Query: 365 TNQVMRIVTSRAL 377 T+ + ++ R++ Sbjct: 375 THDIHALIIGRSI 387 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: 350 Number of extensions: 15 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: 383 Length of database: 395 Length adjustment: 30 Effective length of query: 353 Effective length of database: 365 Effective search space: 128845 Effective search space used: 128845 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