Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_025764976.1 X939_RS0119550 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_000566685.1:WP_025764976.1 Length = 387 Score = 312 bits (800), Expect = 9e-90 Identities = 159/366 (43%), Positives = 226/366 (61%) Query: 10 ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69 I + R FA + ++P EWD FP E + ELG GMLVPEQ+GG GY Y Sbjct: 20 IQETVRDFALKNIQPHIMEWDESQHFPTEVFHSLGELGLMGMLVPEQYGGAGLGYQEYIT 79 Query: 70 ALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAG 129 A+ ++ D + M+ HNS+ IL FGN+DQK ++L LASG +GA+ LTEP G Sbjct: 80 AIIALSKVDPSIGLSMAAHNSLCTNHILMFGNEDQKNKYLPKLASGEWIGAWGLTEPNTG 139 Query: 130 SDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSP 189 SDA ++KT A +G+ ++LNG K FIT+GQ+ V +V T K G +AFIV + Sbjct: 140 SDAGNMKTTAVRDGEDWILNGAKNFITNGQSGRVAVVITRTGEPGDKHGATAFIVEHGTH 199 Query: 190 GYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSV 249 G+ R E+KLG AS+T ++LFED ++ + RLG+ GEG+ +L L+GGR+ IA+ V Sbjct: 200 GFTSGRKENKLGMRASETVELLFEDCRISDSQRLGQIGEGFIQSLKILDGGRISIAALGV 259 Query: 250 GMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKP 309 G A A+EAA Y++ER FGK I Q +AF+LADM T I + + A +D G+ Sbjct: 260 GTALGAYEAALAYSKERHQFGKAISSFQGIAFKLADMYTDIQASTLLTFQAGKEKDLGQK 319 Query: 310 ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRM 369 + ++AK +SE A +V + A+Q GGYG+ D+P E+ YRD ++C I EGTS+IQ+M Sbjct: 320 VSLSGAVAKYHSSETAVRVATEAVQIYGGYGFTKDYPAEKFYRDSKLCTIGEGTSEIQKM 379 Query: 370 VISRNL 375 VIS+ + Sbjct: 380 VISKEI 385 Lambda K H 0.319 0.134 0.389 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: 367 Number of extensions: 8 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: 375 Length of database: 387 Length adjustment: 30 Effective length of query: 345 Effective length of database: 357 Effective search space: 123165 Effective search space used: 123165 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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