Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate CCNA_00436 CCNA_00436 acyl-CoA dehydrogenase, short-chain specific
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Caulo:CCNA_00436 Length = 382 Score = 295 bits (754), Expect = 2e-84 Identities = 152/373 (40%), Positives = 232/373 (62%), Gaps = 1/373 (0%) Query: 2 LPTDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCD 61 L + + Q+ D +F ERL+P A+ P + I EM LG FG+ +PE++GG Sbjct: 3 LDLETREQLIDTVARFVAERLRPIEAQVAENDAVPDDVIEEMKGLGLFGLTIPEEFGGLG 62 Query: 62 TGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAF 121 A+ E+ A ++ + +G ++ FGND+QK ++L +ASGA++ +F Sbjct: 63 LTMEEEALVAIELGRASPAFRSVFGTNVGIGSQGLVMFGNDEQKAKWLPGIASGAVITSF 122 Query: 122 ALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSA-GKRGIS 180 ALTEP+AGSD+++++TRA +GD Y+LNG K++IT+ A + V A T+P A G G+S Sbjct: 123 ALTEPEAGSDSAAVQTRATRDGDDYILNGSKRYITNAGKASLFTVMARTNPDAKGGAGVS 182 Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGG 240 AF+VP D PG V + E K+GQ + + F++V+VP NRLG EGEG+K+A+ L+ G Sbjct: 183 AFLVPRDLPGLTVGKPEKKMGQQGAHIHDVTFDNVRVPAWNRLGAEGEGFKVAMQVLDRG 242 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+ IA+ VG+A YA ER+ FG+PI Q + +AD T+ A+ +V Sbjct: 243 RLHIAAVCVGVAERLIADCVAYASERKQFGQPIASFQLIQAMIADSKTEALAAKALVLET 302 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 A RD+G +EA+ +KLFASEM +V A+Q GG GY++D+ +ER+YRDVR+ +IY Sbjct: 303 ARKRDAGVNVTLEAASSKLFASEMVGRVADRAVQVFGGAGYVADYGIERLYRDVRIFRIY 362 Query: 361 EGTSDIQRMVISR 373 EGTS +Q+++I+R Sbjct: 363 EGTSQVQQLIIAR 375 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: 339 Number of extensions: 11 Number of successful extensions: 2 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 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