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 Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__Korea:Ga0059261_2164 Length = 394 Score = 234 bits (597), Expect = 3e-66 Identities = 136/377 (36%), Positives = 208/377 (55%), Gaps = 3/377 (0%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60 +D LT++++M++D A +A++ L P V +DR+++ +MG+ G G PE YG Sbjct: 15 LDAQLTDEERMVRDAARAYAQERLLPRVTRAFLDENFDREIMSEMGQLGLLGPTIPETYG 74 Query: 61 GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120 G GL ++Y L E+ VD G +S SL PI +GTEEQK+KYL + G V Sbjct: 75 GAGLGYVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLLSGEWV 134 Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180 G FGLTEP AG+D + +T A Y + GSK++ITN AD +VV+A +D G G Sbjct: 135 GCFGLTEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAHGG--G 192 Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240 I F+LEKGM G KIE K+ SIT E++ + EV ++ LL E +G K L+ Sbjct: 193 IKGFVLEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVSEDALL-PEVQGLKGPFGCLN 251 Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300 R G+A ++G AE AA +Y+ +R+QFGR ++ Q +Q +A+M T+I Sbjct: 252 RARYGIAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGLQAAL 311 Query: 301 HAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQ 360 A + ++G+ EA ++ K A+E+ A + GG G + ++ R+ N + Sbjct: 312 RAGRMFDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINLETVN 371 Query: 361 IYEGTNQVMRIVTSRAL 377 YEGT+ V ++ RA+ Sbjct: 372 TYEGTHDVHGLILGRAI 388 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: 338 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: 394 Length adjustment: 30 Effective length of query: 353 Effective length of database: 364 Effective search space: 128492 Effective search space used: 128492 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