Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_035237517.1 Q366_RS06780 acyl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000745975.1:WP_035237517.1 Length = 382 Score = 319 bits (818), Expect = 7e-92 Identities = 166/366 (45%), Positives = 232/366 (63%) Query: 10 IRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGYLAYAM 69 +R R+FAE + P AA DRE RFP E I++M L +FG+ VP GG ++YA+ Sbjct: 12 VRKTVREFAENEIGPHAASLDREGRFPTEIIEKMGPLNYFGLQVPPSLGGAGLDTISYAI 71 Query: 70 TLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALTEPQAG 129 +EE++ A +SVHNSVG PIL+FG DEQ A+F+ +A+G +GAF LTE AG Sbjct: 72 VIEELSRVCAALGLCVSVHNSVGLYPILRFGTDEQIARFVPDMAAGKHIGAFCLTEANAG 131 Query: 130 SDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSP 189 SDA ++T A + Y +NG K F+T+G VV+VFAV + + FIV P Sbjct: 132 SDAGGVETTAAKTEEGYTINGTKIFVTNGGVCDVVLVFAVDAGGKEQSRPNVFIVEKTCP 191 Query: 190 GYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVGIAAQAV 249 G+SV +ED G A+ + FED ++P N LG+ G+G KI L L+ GR+GIAAQA+ Sbjct: 192 GFSVGEIEDLCGMRANPVSSLFFEDCRIPETNLLGKPGQGLKIGLTALDTGRIGIAAQAL 251 Query: 250 GMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGQP 309 G+A+AAFEAA YA+ER F P+ + Q + LADMAT I +R +++ AAA +D G Sbjct: 252 GIAQAAFEAALSYAKERQQFNSPLTKFQTIQNYLADMATSIESSRMLLYRAAAAKDKGGD 311 Query: 310 ALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGTSDIQRM 369 +A+MAKL S A V +A+Q GGYGY ++ +ER +R+ +V QIYEGTS++Q+M Sbjct: 312 FGAQAAMAKLSCSATARTVTDLAVQIHGGYGYSREYDVERYFREAKVTQIYEGTSEVQKM 371 Query: 370 VISRNL 375 VI+R+L Sbjct: 372 VIARHL 377 Lambda K H 0.320 0.134 0.388 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: 345 Number of extensions: 13 Number of successful extensions: 1 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: 382 Length adjustment: 30 Effective length of query: 345 Effective length of database: 352 Effective search space: 121440 Effective search space used: 121440 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