Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate Ac3H11_2996 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2996 Length = 376 Score = 476 bits (1224), Expect = e-139 Identities = 239/375 (63%), Positives = 291/375 (77%) Query: 1 MLPTDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGC 60 ML T +Q I DA R FAQ L P AA WD+EH FPK+A +A LG +G+ VPE++GG Sbjct: 1 MLLTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGA 60 Query: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGA 120 + YL A+ LEEIAAGDG ST +SV N ++++GN QK +L PLA G MLGA Sbjct: 61 NLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGA 120 Query: 121 FALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS 180 F LTEP GSDAS+L+T A GD YV+NG KQFITSG+N V IV AVTD AGK+G+S Sbjct: 121 FCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGKKGMS 180 Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGG 240 AF+VPT++PGY VAR+EDKLGQH+SDT QI F++ ++P N +G EGEGYKIAL LEGG Sbjct: 181 AFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALEGG 240 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+GIA+QSVGMAR+AF+AA Y++ERESFG I HQAV FRLAD ATQI ARQ++ +A Sbjct: 241 RIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIWHA 300 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 AALRD+GKP L EA+MAKLFASEMAE+VCS A+QTLGGYG ++DFP+ERIYRDVRVCQIY Sbjct: 301 AALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQIY 360 Query: 361 EGTSDIQRMVISRNL 375 EGTSD+Q+++I R L Sbjct: 361 EGTSDVQKIIIQRAL 375 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: 406 Number of extensions: 11 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: 376 Length adjustment: 30 Effective length of query: 345 Effective length of database: 346 Effective search space: 119370 Effective search space used: 119370 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 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