Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate BPHYT_RS02220 BPHYT_RS02220 butyryl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__BFirm:BPHYT_RS02220 Length = 376 Score = 583 bits (1503), Expect = e-171 Identities = 286/375 (76%), Positives = 327/375 (87%) Query: 1 MLLTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGA 60 M+L QD M+RDA+R F + + PHAA WD+E FPKD H+ LA LGAYG+ VPE +GGA Sbjct: 1 MVLDQDHLMVRDALRTFVREAITPHAAVWDRERTFPKDVHRQLAELGAYGVLVPEAYGGA 60 Query: 61 NLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGA 120 +D L LAL+LEEIAAGDGGTSTAISV NCPV +IL+ YGN QKRDWLTPLARGEMLGA Sbjct: 61 GMDALALALILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKRDWLTPLARGEMLGA 120 Query: 121 FCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGKKGMS 180 FCLTEP GSDASALRTTA + GD YV+NGVKQFITSGKNG VAIV+AVTDK AGK+G+S Sbjct: 121 FCLTEPQAGSDASALRTTATRDGDAYVLNGVKQFITSGKNGNVAIVMAVTDKAAGKRGIS 180 Query: 181 AFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALEGG 240 AF+VPT+ GYVVAR+EDKLGQHSSDTAQI F++CR+PA NLIGAEGEGY+IAL LEGG Sbjct: 181 AFIVPTDTKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLIGAEGEGYRIALSGLEGG 240 Query: 241 RIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIWHA 300 RIGIAAQSVGMAR+AF+AAL+Y+KERESFG +F+HQAV FRLAD ATQ+EAARQLIWHA Sbjct: 241 RIGIAAQSVGMARAAFEAALSYAKERESFGAPLFSHQAVQFRLADMATQLEAARQLIWHA 300 Query: 301 AALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQIY 360 A+L+DAG+PCL EAAMAKLFASE AER+CSAA+Q GGYG ++DFPVERIYRDVRVCQIY Sbjct: 301 ASLKDAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQIY 360 Query: 361 EGTSDVQKIIIQRAL 375 EGTSD+QKI+I R L Sbjct: 361 EGTSDIQKILIARGL 375 Lambda K H 0.319 0.134 0.396 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: 538 Number of extensions: 15 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: 376 Length of database: 376 Length adjustment: 30 Effective length of query: 346 Effective length of database: 346 Effective search space: 119716 Effective search space used: 119716 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