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_011913061.1 PST_RS09700 acyl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >NCBI__GCF_000013785.1:WP_011913061.1 Length = 379 Score = 346 bits (887), Expect = e-100 Identities = 174/371 (46%), Positives = 245/371 (66%) Query: 7 EDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGLDV 66 EDQ I +MA +FA + L P E+ + H + + I +M GF G+ PE++GG Sbjct: 5 EDQCAIAEMARQFARERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTGY 64 Query: 67 LSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFGLT 126 L+Y +A+EE++ D +S + S+ PI FG ++QK+ +L P+A G +GAF LT Sbjct: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNDQQKRDFLGPLARGEQIGAFALT 124 Query: 127 EPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAFIL 186 EP AG+DAS+ +T A GD Y+LNG+K FIT+GK A T +VFA+TD G GISAFI+ Sbjct: 125 EPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKRGISAFIV 184 Query: 187 EKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRIGV 246 PG++ ++EDK+G H S T ++ FED VP N LG+EGEG++IA+ L+GGRIG+ Sbjct: 185 PTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRIGI 244 Query: 247 AAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAMLK 306 AAQA+G+A A AA Y+ ERE FG+ I + QA+ F +ADMAT+I AR +V+HAA L+ Sbjct: 245 AAQAVGMARAAFEAARDYAGERETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAALR 304 Query: 307 NEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEGTN 366 G+P A+MAK FAS++A V + A+Q GGYGY D+P ER R+ ++ QIYEGT+ Sbjct: 305 EAGRPALVEASMAKLFASEMAERVCSAAIQTLGGYGYLSDFPVERIYRDVRVCQIYEGTS 364 Query: 367 QVMRIVTSRAL 377 + R+V SR L Sbjct: 365 DIQRLVISRNL 375 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: 378 Number of extensions: 10 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: 379 Length adjustment: 30 Effective length of query: 353 Effective length of database: 349 Effective search space: 123197 Effective search space used: 123197 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