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 PfGW456L13_2983 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2983 Length = 375 Score = 356 bits (914), Expect = e-103 Identities = 174/371 (46%), Positives = 256/371 (69%) Query: 7 EDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGLDV 66 +DQQ I+DMA +FA++ L P E D+ H + ++ I +M GF G+ PE++GG Sbjct: 5 DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 Query: 67 LSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFGLT 126 L+Y +A+EE++ D +S + S+ PI +GT+EQK+++L P+A G +GAF LT Sbjct: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124 Query: 127 EPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAFIL 186 EP AG+DAS +T A L+GD Y+LNG K FIT+G+ A +VFA+TD S G GISAFI+ Sbjct: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 Query: 187 EKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRIGV 246 PG++ ++EDK+G H S T +++FED +VP N LG+EGEG++IA+ L+GGR+G+ Sbjct: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGI 244 Query: 247 AAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAMLK 306 A+Q++G+A A AA Y++ERE FG+ I + QA+ F +ADMAT+I AR +V++AA L+ Sbjct: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 Query: 307 NEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEGTN 366 + GKP A+MAK FAS++A +V + A+Q GGYGY D+P ER R+ ++ QIYEGT+ Sbjct: 305 DSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTS 364 Query: 367 QVMRIVTSRAL 377 + R+V SR L Sbjct: 365 DIQRMVISRNL 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: 372 Number of extensions: 12 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: 375 Length adjustment: 30 Effective length of query: 353 Effective length of database: 345 Effective search space: 121785 Effective search space used: 121785 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