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 5208388 Shew_0900 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__PV4:5208388 Length = 391 Score = 225 bits (573), Expect = 2e-63 Identities = 138/375 (36%), Positives = 205/375 (54%), Gaps = 6/375 (1%) Query: 2 DFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGG 61 D L+ED++MI+DM ++A++ L V ++ +DR++++++GE G G PE YG Sbjct: 15 DALLSEDERMIRDMVHDYAQEKLMTRVLMANRNEHFDREIMNELGELGLLGATLPEAYGC 74 Query: 62 MGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVG 121 + +SY L E+ +VD G +S SL PIY +G E+Q+QKYL +A G VG Sbjct: 75 ANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYAYGNEQQRQKYLPKLATGEWVG 134 Query: 122 AFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGI 181 FGLTEP G+D +T A Y LNG+K++ITN AD +VV+A D GV I Sbjct: 135 CFGLTEPDVGSDPGGMKTRAERIDGGYRLNGAKMWITNSPIADVFVVWAKLD---GV--I 189 Query: 182 SAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDG 241 FILEKGM G KIE K SIT E++ ++ EV +E LL EG K L+ Sbjct: 190 RGFILEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEEALL-PNVEGLKGPFGCLNK 248 Query: 242 GRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYH 301 R G+A ALG AE AA +YS +R QF R ++ Q +Q +ADM T+I + Sbjct: 249 ARYGIAWGALGAAEFCWHAARQYSLDRIQFNRPLAATQLIQKKLADMQTEITTGLFACLQ 308 Query: 302 AAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQI 361 A L ++ EA ++ K + A+E+ + + GG G + ++ R++ N + Sbjct: 309 AGRLMDQDALPVEAISLIKRNSCGKALEIARTSRDMHGGNGISDEFHVIRHVMNLEAVNT 368 Query: 362 YEGTNQVMRIVTSRA 376 YEGT+ + ++ RA Sbjct: 369 YEGTHDIHALILGRA 383 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: 305 Number of extensions: 11 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: 391 Length adjustment: 30 Effective length of query: 353 Effective length of database: 361 Effective search space: 127433 Effective search space used: 127433 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