Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate 5210419 Shew_2860 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__PV4:5210419 Length = 432 Score = 170 bits (431), Expect = 6e-47 Identities = 128/398 (32%), Positives = 193/398 (48%), Gaps = 37/398 (9%) Query: 8 EMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAAL----------GAYGICVPEEF 57 + +R+ + F ++P+ + W+++ D + A L G + + +P+ + Sbjct: 22 QALRERLLAFMDEHIYPNESLWEQQVE-EGDRWESPAILAELKAKAKDAGLWNLFLPQVY 80 Query: 58 GG-----ANLDYLTLALVLEEIAAGDGGTSTAISVTNCPVN-----AILMRYGNAQQKRD 107 G NL+Y LA ++ G A V NC +L RYGN +Q+ Sbjct: 81 GEFSPGLTNLEYAPLAEIM-------GRVYWASEVFNCSAPDTGNMEVLARYGNKEQQER 133 Query: 108 WLTPLARGEMLGAFCLTEPHVGS-DASALRTTAVKQGDEYVINGVKQFITSGKNG--QVA 164 WL PL GE+ AF +TEP V S DA+ + T+ V+ GDEYVING K +I+ N Q+ Sbjct: 134 WLQPLLNGEIRSAFSMTEPDVASSDATNVETSIVRDGDEYVINGRKWYISGACNNHTQIH 193 Query: 165 IVIAVTDKGAGKKGM--SAFLVPTNNPGYVVARLEDKLGQHSSDT--AQINFDNCRIPAE 220 IV+ TD K + S LVP N PG V R G + A++ +DN R+P Sbjct: 194 IVMGKTDPDNSNKYIQQSMILVPANTPGVKVVRPMKVFGYDDAPEGHAEVIYDNVRVPVS 253 Query: 221 NLIGAEGEGYKIALGALEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVG 280 N++ EG G++IA G L GRI ++VG+A+ A + ++ R +FG + Q+V Sbjct: 254 NMLLGEGRGFEIAQGRLGPGRIHHCMRTVGLAQRALEQMCERAETRIAFGKPLSKQQSVR 313 Query: 281 FRLADCATQIEAARQLIWHAAALRDAG--KPCLKEAAMAKLFASEMAERVCSAAIQTLGG 338 +A A ++E AR L AAA D G K AM K+ A M V AIQ GG Sbjct: 314 EAIAKSACEVEQARLLTLKAAAKMDQGGNKAAKDLIAMIKIVAPNMGCAVIDRAIQLHGG 373 Query: 339 YGVVNDFPVERIYRDVRVCQIYEGTSDVQKIIIQRALA 376 G+ DF + + Y R ++ +G V + + R LA Sbjct: 374 GGLSQDFFLAKAYTITRSIRLADGPDQVHMMQLGRNLA 411 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: 361 Number of extensions: 22 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: 432 Length adjustment: 31 Effective length of query: 345 Effective length of database: 401 Effective search space: 138345 Effective search space used: 138345 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