Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate RR42_RS24965 RR42_RS24965 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Cup4G11:RR42_RS24965 Length = 385 Score = 299 bits (766), Expect = 8e-86 Identities = 157/374 (41%), Positives = 236/374 (63%), Gaps = 2/374 (0%) Query: 4 NDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTG 63 ND + + D+VR F +ERL P + P++ + +M ++GLFGM +PE++GG + Sbjct: 5 NDTLEALLDSVRRFVRERLVPAEALVAETDEIPQDIVQDMRDMGLFGMTIPERFGGLELT 64 Query: 64 YVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFAL 123 + E+ A +++ +G IL G +Q+ +L LATG +L +FAL Sbjct: 65 MEEEVRVVMELCQTSPAFRSLLGTTVGIGSQGILMDGTPEQQAAWLPRLATGEILASFAL 124 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEA-GKRGISAF 182 TEP AGSDA SL+T A +GDHYV+NG+K+FIT+ AG+ + A T+P+ G G+SAF Sbjct: 125 TEPDAGSDAGSLRTSAIKDGDHYVVNGTKRFITNAPQAGMFTLMARTNPDIKGSAGVSAF 184 Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGA-EGEGYKIALANLEGGR 241 IV +PG + + K+GQ + TC ++F+NV+VP AN +G EG+G+K A+ L+ GR Sbjct: 185 IVDAKTPGISFGKRDVKMGQKGAHTCDVIFENVRVPAANLIGLKEGQGFKTAMKVLDKGR 244 Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 + IA+ +VG+AR A +YA ER+ FG+P+ E Q + LAD ++ A MV+ AA Sbjct: 245 LHIAAVSVGVARRVLRDALNYALERKQFGQPISEFQLIQAMLADSQAELYAAECMVIDAA 304 Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361 RD GR EAS K+FA+EM +V A+Q LGG GY+S++ +ER YRDVR+ ++YE Sbjct: 305 RRRDEGRNVSTEASCCKMFATEMVGRVADRAVQILGGSGYISEYGIERFYRDVRLFRLYE 364 Query: 362 GTSDIQRMVIARNL 375 GT+ IQ+++IARN+ Sbjct: 365 GTTQIQQIIIARNM 378 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: 355 Number of extensions: 18 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: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 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