Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate AZOBR_RS22365 AZOBR_RS22365 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__azobra:AZOBR_RS22365 Length = 379 Score = 318 bits (816), Expect = 1e-91 Identities = 171/373 (45%), Positives = 240/373 (64%), Gaps = 3/373 (0%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 ++EQ D AR FAQ+ + P AA WD FP + + + A LGF G+ V E++GG G Sbjct: 6 SEEQQAFRDTARDFAQQEMAPNAAHWDENSVFPVDTLRQAAALGFAGIYVGEEFGGSGLG 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 L A+ EE++A + + +S+HN + I +FGN +Q+ERFL L + ++ L Sbjct: 66 RLDAALIFEELSAACPSTAAYISIHNMASWM-IDRFGNAEQRERFLPKLTTMEHFASYCL 124 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP AGSDA+SL+TRA GDHYVLNG K FI+ G + V + T G +GIS Sbjct: 125 TEPGAGSDAASLRTRAERVGDHYVLNGSKAFISGGGTSDVYVCMVRTG-EPGPKGISCIA 183 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 V +PG + E KLG + T ++FE+ +VPVANR+GEEGEG++IA+ L+GGR+ Sbjct: 184 VEKGTPGLSFGKQEHKLGWKSQPTSAVIFENCRVPVANRIGEEGEGFRIAMKGLDGGRLN 243 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IA+ SVG AR E A Y ER+ FGKP+ QA+ F+LADMAT++ AR M+H AAA Sbjct: 244 IAACSVGGARFCLEQAVAYTTERKQFGKPLNAFQALQFKLADMATELDAARLMLHRAAAS 303 Query: 304 RDSGKP-ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362 D+G P A +MAK FA++ +V + ALQ GGYGY+ ++P+ERI+RD+RV QI EG Sbjct: 304 LDAGSPEATAHCAMAKRFATDAGFQVVNEALQLHGGYGYIKEYPIERIFRDLRVHQILEG 363 Query: 363 TSDIQRMVISRNL 375 T++I R++I+R+L Sbjct: 364 TNEIMRVIIARHL 376 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: 375 Number of extensions: 12 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: 379 Length adjustment: 30 Effective length of query: 345 Effective length of database: 349 Effective search space: 120405 Effective search space used: 120405 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