Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate CCNA_00436 CCNA_00436 acyl-CoA dehydrogenase, short-chain specific
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Caulo:CCNA_00436 Length = 382 Score = 310 bits (795), Expect = 3e-89 Identities = 157/370 (42%), Positives = 240/370 (64%), Gaps = 1/370 (0%) Query: 5 DEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGY 64 + ++Q+ D V F ERL+P Q ++ P + I+EM LGLFG+ +PE++GG Sbjct: 6 ETREQLIDTVARFVAERLRPIEAQVAENDAVPDDVIEEMKGLGLFGLTIPEEFGGLGLTM 65 Query: 65 VAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALT 124 A+ E+ A ++ + +G ++ FGN++QK ++L +A+GA++ +FALT Sbjct: 66 EEEALVAIELGRASPAFRSVFGTNVGIGSQGLVMFGNDEQKAKWLPGIASGAVITSFALT 125 Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEA-GKRGISAFI 183 EP+AGSD+++++TRA +GD Y+LNGSK++IT+ A + V A T+P+A G G+SAF+ Sbjct: 126 EPEAGSDSAAVQTRATRDGDDYILNGSKRYITNAGKASLFTVMARTNPDAKGGAGVSAFL 185 Query: 184 VPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRIG 243 VP D PG V + E K+GQ + + FDNV+VP NRLGAEGEG+K+A+ L+ GR+ Sbjct: 186 VPRDLPGLTVGKPEKKMGQQGAHIHDVTFDNVRVPAWNRLGAEGEGFKVAMQVLDRGRLH 245 Query: 244 IASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAAL 303 IA+ VG+A YA+ER+ FG+P+ Q + +AD T+ A+ +VL A Sbjct: 246 IAAVCVGVAERLIADCVAYASERKQFGQPIASFQLIQAMIADSKTEALAAKALVLETARK 305 Query: 304 RDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 RDAG +EA+ +KLFASEM +V A+Q GG GY++D+ +ER+YRDVR+ +IYEGT Sbjct: 306 RDAGVNVTLEAASSKLFASEMVGRVADRAVQVFGGAGYVADYGIERLYRDVRIFRIYEGT 365 Query: 364 SDIQRMVIAR 373 S +Q+++IAR Sbjct: 366 SQVQQLIIAR 375 Lambda K H 0.319 0.134 0.382 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: 372 Number of extensions: 12 Number of successful extensions: 3 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