Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_085772269.1 B1812_RS14765 acyl-CoA dehydrogenase family protein
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_002117405.1:WP_085772269.1 Length = 557 Score = 211 bits (538), Expect = 3e-59 Identities = 132/387 (34%), Positives = 205/387 (52%), Gaps = 21/387 (5%) Query: 5 DEQLQ-ISDAARQFAQERLKPFAAEWDREHRF-PKEAIGEMAELGFFGMLVPEQWGGCDT 62 DE L+ I R+FA + + PFA EW ++ + P E I +AELG FG+ +PE++GG Sbjct: 173 DETLEAIRSEMRKFASDNVTPFAQEWHAKNEYIPLEVISGLAELGVFGLTIPEEFGGSGM 232 Query: 63 GYLAYAMALEEIAA---GDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLG 119 G +A + EE++ G G+ T + + IL G QKE++L +A+G +L Sbjct: 233 GKIAMCVVSEELSRAYIGVGSLGTRSEIAGEL----ILVGGTKAQKEKYLPKIAAGEILP 288 Query: 120 AFALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSA-GKRG 178 TEP GSD + L+TRA GD Y + G K +IT A V+ + T+P G +G Sbjct: 289 TAVFTEPNNGSDLAGLRTRAVREGDVYKVTGNKTWITHPVRADVMTLLVRTNPEEKGYKG 348 Query: 179 ISAFIV---------PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGE-EGE 228 +S + P + G +E LG +I F+ + P N LG EG Sbjct: 349 LSMLLAEKPRGTDENPFPAKGMTGGEIE-VLGYRGMKEFEIGFDGFETPAENLLGGVEGN 407 Query: 229 GYKIALANLEGGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMAT 288 G+K + E R+ A++++G+A+ A + YA+ER FGKP+ + ++ MA Sbjct: 408 GFKQLMETFESARIQTAARALGVAQCALDLGLRYAKERIQFGKPLFSFPRIFDKIVAMAV 467 Query: 289 QIAVARQMVHYAAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLE 348 +I VARQ+ +++A +D GK +EA MAKL + +A ALQ GG G+ ++P+ Sbjct: 468 EIHVARQITYFSARQKDGGKRCDLEAGMAKLLGARVAWAAADNALQIHGGNGFALEYPVS 527 Query: 349 RIYRDVRVCQIYEGTSDIQRMVISRNL 375 R+ D R+ I+EG ++IQ VI+R L Sbjct: 528 RVLCDARILNIFEGAAEIQAQVIARRL 554 Lambda K H 0.319 0.134 0.389 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: 407 Number of extensions: 23 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: 375 Length of database: 557 Length adjustment: 33 Effective length of query: 342 Effective length of database: 524 Effective search space: 179208 Effective search space used: 179208 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 Apr 09 2024. 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