Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate YP_004139648.1 Mesci_0425 acyl-CoA dehydrogenase domain-containing protein
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >NCBI__GCF_000185905.1:YP_004139648.1 Length = 387 Score = 211 bits (537), Expect = 3e-59 Identities = 129/381 (33%), Positives = 203/381 (53%), Gaps = 12/381 (3%) Query: 3 LTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAA----LGAYGICVPEEFG 58 L+++Q++I + R F + EL+PH ++ +D + + G Y +P + G Sbjct: 5 LSEEQKLIVETTRAFVENELYPHEREVERTGVLRRDLIEEIKVKAIEAGLYAANMPADVG 64 Query: 59 GANLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEML 118 GA LD +T L +E+ G + A+ T + ++ G +Q+ +L P RGE Sbjct: 65 GAGLDTVTWLLYEKEL----GRANYALHWTCVARPSNILLAGTPEQREKYLFPCIRGEKW 120 Query: 119 GAFCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVT---DKGAG 175 +TEP GSD ++ TAV+ GD++V+NG K FI+ AIV + D G Sbjct: 121 DCLAMTEPGAGSDLRGMKATAVQDGDDWVLNGTKHFISHADLADFAIVFMASGEEDSPRG 180 Query: 176 K-KGMSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIAL 234 K K ++AF V G+ V + A + FD+CR+P ++G +G+ +A Sbjct: 181 KRKKITAFFVDKGTKGFTVRDGYRNVSHRGYTNAILEFDDCRLPGAQVLGEVHKGFDVAN 240 Query: 235 GALEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAAR 294 L R+ + A +G A A A+ Y+ +R+ FG I Q V F+LAD AT+++AA Sbjct: 241 SWLGATRLQVGATCLGRAERALGHAVEYAAQRQQFGQQIGKFQGVSFKLADMATELKAAD 300 Query: 295 QLIWHAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDV 354 +++ A D G ++ AMAKL A+EM V AIQ GG G+++D P+ERI+RD Sbjct: 301 LMVFEAGWKYDQGTVTDQDMAMAKLKATEMLAYVADEAIQIHGGMGLMDDLPLERIWRDA 360 Query: 355 RVCQIYEGTSDVQKIIIQRAL 375 RV +I+EGTS++Q+ II RAL Sbjct: 361 RVERIWEGTSEIQRHIISRAL 381 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: 356 Number of extensions: 19 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