Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate Ga0059261_3793 Ga0059261_3793 Acyl-CoA dehydrogenases
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Korea:Ga0059261_3793 Length = 381 Score = 293 bits (749), Expect = 7e-84 Identities = 152/362 (41%), Positives = 220/362 (60%) Query: 12 DAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAMAL 71 D R+F +RL+P +E + P + EM LG FG+ + E++GG L Sbjct: 13 DTVRRFVAQRLRPLESEVEAADAIPDTIVEEMKALGLFGLSIAEEFGGLGLTMLEECRVA 72 Query: 72 EEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAGSD 131 E+ A + + +G ++ G +QK +L +ASG ++ +FALTEP GSD Sbjct: 73 IEMGRTTPAFRSTFGTNVGIGSQGLVMAGTSEQKAAWLPRIASGEIITSFALTEPDVGSD 132 Query: 132 ASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSPGY 191 + ++K RA +GD Y L+G K+FIT+ A + V A T G RG+SAF+VP D PG Sbjct: 133 SGAVKARAVRDGDVYRLSGTKRFITNADKASLFTVMARTGDEPGARGVSAFLVPRDLPGI 192 Query: 192 KVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSVGM 251 + E K+GQ + ++F+DV VP ANRLGEEGEG+KIA+ L+ GR+ I++ SVG+ Sbjct: 193 SIGEPEKKMGQKGAKVADVIFDDVPVPAANRLGEEGEGFKIAMRVLDRGRLHISAVSVGV 252 Query: 252 ARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKPAL 311 A YA ER+ FGKPI EHQ + LAD T+ AR +V AA +D+GK + Sbjct: 253 AERLIADCVAYASERKQFGKPIAEHQLIQAMLADSKTECLAARALVLETAAAKDAGKDVV 312 Query: 312 VEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRMVI 371 +E++ AKLFA+EM +V A+Q LGG GY+ D+ +ER+YRDVR+ +IYEGTS IQ+++I Sbjct: 313 MESAAAKLFATEMVGRVADRAVQILGGAGYIEDYGIERLYRDVRLFRIYEGTSQIQQLII 372 Query: 372 SR 373 +R Sbjct: 373 AR 374 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: 333 Number of extensions: 11 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: 381 Length adjustment: 30 Effective length of query: 345 Effective length of database: 351 Effective search space: 121095 Effective search space used: 121095 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