Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate WP_012409825.1 NPUN_RS17395 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >NCBI__GCF_000020025.1:WP_012409825.1 Length = 394 Score = 247 bits (631), Expect = 4e-70 Identities = 140/371 (37%), Positives = 219/371 (59%), Gaps = 8/371 (2%) Query: 3 LTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGANL 62 LT Q+ + R+F E+ A ++D++ + P D Q A G +P+EFGG + Sbjct: 5 LTPQQKNAQAEFREFVDAEVVSQANQYDQQEYTPSDLVQKFAQKRYLGAVLPKEFGGEAM 64 Query: 63 DYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGAFC 122 D +T L+ EEI G + ++V +C V+ L ++GN QK DWL LA GE++ AF Sbjct: 65 DMITYGLLNEEIGRGCSSLRSLLTV-HCMVSHALCKWGNKSQKNDWLPKLASGEIIAAFA 123 Query: 123 LTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGKKGMSAF 182 L+EP+VGSDA ++ TTA GD Y++NG K++IT GQ+A V V + GK SAF Sbjct: 124 LSEPNVGSDAKSVETTATLSGDAYILNGHKKWIT---YGQIADVFLVFAQCEGKP--SAF 178 Query: 183 LVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYK-IALGALEGGR 241 LV N+PG + + LG +S A+++ ++CRIP ENL+G G G+ +A AL+ GR Sbjct: 179 LVEKNSPGLSIKPIFGMLGVRASMLAELHLNDCRIPQENLVGRLGFGFSYVASSALDYGR 238 Query: 242 IGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIWHAA 301 +A SVG+A++ A + Y+ +R+ FG + HQ + + + I+AAR L + A Sbjct: 239 YSVAWGSVGIAQACLSACIRYTSDRKQFGVYLKEHQLIRQMITNMIANIKAARLLCYQAG 298 Query: 302 ALRDAGKP-CLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQIY 360 L++ G P + E ++AK F S +A +V S A+Q GG G +++PVER RD ++ +I Sbjct: 299 YLKEIGDPSSIIETSIAKYFTSTIASQVASDAVQIHGGNGCSSEYPVERYLRDAKIMEII 358 Query: 361 EGTSDVQKIII 371 EG++ +Q++ I Sbjct: 359 EGSTQIQQVTI 369 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: 320 Number of extensions: 15 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: 394 Length adjustment: 30 Effective length of query: 346 Effective length of database: 364 Effective search space: 125944 Effective search space used: 125944 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