Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate WP_066921287.1 ACG33_RS11370 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >NCBI__GCF_001579945.1:WP_066921287.1 Length = 387 Score = 217 bits (552), Expect = 5e-61 Identities = 139/379 (36%), Positives = 214/379 (56%), Gaps = 15/379 (3%) Query: 1 MLLTQDQE---MIRDAVRDFAQTEL-WPHAARWDKEHHFPKDAHQGLAALGAYGICVPEE 56 M T + E ++R + F + EL A R D+E F +D+ + L LG G+ V E Sbjct: 1 MYFTNEPEHIGVLRTTIHRFIEAELPRDKARRLDREKTFDRDSFRRLTELGICGLTVSEH 60 Query: 57 FGGANLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILM--RYGNAQQKRDWLTPLAR 114 FGG N D + +V+EE+ GTS A +C L G+ QQK + L L R Sbjct: 61 FGG-NRDLVAAVMVIEELCRR--GTSLAGPFIHCAFYGALNIEHNGSEQQKEELLPRLLR 117 Query: 115 GEMLGAFCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGA 174 GE++ ++ L+EP VG D +++ T A ++GDE VINGVK++ T + + +D A Sbjct: 118 GELMFSYGLSEPDVGGDLASVGTQARREGDEIVINGVKRWCTGARFADYIYCLTRSDPEA 177 Query: 175 GK-KGMSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAE---GEGY 230 + + +S LVPT+ PG VV +E +G ++T + +N R+PA N++G E G+ Sbjct: 178 PRYRNLSFILVPTSAPGIVVTDIEH-IGLRYAETCDVVLENVRVPAANIVGGEVGWNNGW 236 Query: 231 KIALG-ALEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQ 289 + G AL+ +I +AA ++G+A +A + A YS+ER FG AI HQAV LAD T+ Sbjct: 237 GMLAGPALDIEKIEVAACALGIASAALEDAWQYSQERRQFGKAICGHQAVRHSLADLRTK 296 Query: 290 IEAARQLIWHAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVER 349 + A R +++HAA L D+G+ C E +MAKLF +E A A+ + +G YG ++ +ER Sbjct: 297 LHACRLMLYHAAWLADSGRACTVETSMAKLFITETALEAAIASQRIMGAYGCAEEYDMER 356 Query: 350 IYRDVRVCQIYEGTSDVQK 368 RD+ V I G+SD+Q+ Sbjct: 357 HVRDLLVMPIIGGSSDMQR 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: 339 Number of extensions: 17 Number of successful extensions: 4 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: 387 Length adjustment: 30 Effective length of query: 346 Effective length of database: 357 Effective search space: 123522 Effective search space used: 123522 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