Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate 201539 SO2395 acyl-CoA dehydrogenase family protein (NCBI ptt file)
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__MR1:201539 Length = 585 Score = 123 bits (308), Expect = 1e-32 Identities = 107/358 (29%), Positives = 148/358 (41%), Gaps = 39/358 (10%) Query: 47 GAYGICVPEEFGGANLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKR 106 G G+C EFGG + + L ++++E+A T + +G+ K+ Sbjct: 91 GWVGLCGEPEFGGMGMPKM-LGVLVDEMAYSACNAFTLYGSLTAGAALCINAHGSEVLKQ 149 Query: 107 DWLTPLARGEMLGAFCLTEPHVGSDASALRTTAVKQGD-EYVINGVKQFITSGKNGQVAI 165 +L L GE GA +TEP GSD +RT AV Q D Y I+G K FIT G + Sbjct: 150 AYLPKLYSGEWAGAMDMTEPQAGSDLRNIRTRAVPQEDGSYAISGSKIFITGGDHDLTEN 209 Query: 166 VI-AVTDKGAGKKGMSAFLVPT----------NNPGYVVARLEDKLGQHSSDTAQINFDN 214 VI V K KG+S FLVP G V +E K+G S T +NFD Sbjct: 210 VIHLVLAKLPESKGISLFLVPKITVNKDGCLGGTNGVSVGSIEHKMGLKGSATCVMNFDE 269 Query: 215 CRIPAENLIGAEGEGYKIALGALEGGRIGIAAQSVGMARSAFDAALAYSKERE------- 267 + LIG G + R+ I Q +G A++A+ A Y+KER Sbjct: 270 AK---GYLIGEPNRGLVCMFTMMNYERLAIGIQGLGSAQAAYQMATDYAKERSQGVAAGG 326 Query: 268 ----SFGTAIFNHQAVGFRLADCATQIEAARQLIWHAAALRDAGKPCLKEAA-------- 315 S I H V L EA R L D K + Sbjct: 327 SPTGSDSDPIIVHGDVRRMLLTIRAMTEAGRALSVFTGKQLDLAKYAQDDVKAKAARYVG 386 Query: 316 ----MAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQIYEGTSDVQKI 369 +AK F ++ A Q GG+G + + VE++ RD R+ QIYEGT+ +Q I Sbjct: 387 LLTPVAKAFLTDRGLDATIMAQQVFGGHGYIRETGVEQLVRDTRIAQIYEGTNGIQAI 444 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: 510 Number of extensions: 29 Number of successful extensions: 5 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: 585 Length adjustment: 33 Effective length of query: 343 Effective length of database: 552 Effective search space: 189336 Effective search space used: 189336 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: 51 (24.3 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