Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_011952836.1 SWIT_RS10095 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000016765.1:WP_011952836.1 Length = 390 Score = 258 bits (660), Expect = 1e-73 Identities = 141/374 (37%), Positives = 222/374 (59%), Gaps = 3/374 (0%) Query: 4 NDEQQQIADAVRAFAQERLKPF-AEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 ++E + D+V F P W + ++ E GL G+ VP ++GG+ Sbjct: 14 SEELRMFEDSVSRFLAAHAGPDRTRHWREQGFVDRDTWRAAGEAGLLGLSVPVEYGGAGV 73 Query: 63 GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122 + A+ +E++ A + + +HN+V I+ + NE+QK ++L + TG + A A Sbjct: 74 DFTFDAVIMEQLGRHH-ALNFAIPLHNAVVAPYIVSYANEEQKRRWLPGVVTGETILAVA 132 Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182 ++EP AGSD ++KT AR EGDHYV+NG K FI++G +A ++IV A TDPEAG RG+S F Sbjct: 133 MSEPGAGSDLQAMKTSARREGDHYVINGQKTFISNGAHASLIIVAAKTDPEAGARGLSLF 192 Query: 183 IVPTDS-PGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241 V TD G+ R+ DK+GQ DT ++ F +++VPV NR+G EG G+ + + L R Sbjct: 193 AVETDEVEGFTRGRLLDKIGQEGRDTAELFFSDMRVPVENRIGPEGGGFAMLMEKLPQER 252 Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 + IA QA+ M AA + Y ER++FG+ +++ Q F+LA+ T+ ++AR + H Sbjct: 253 LVIAWQALAMMEAAIDHTIAYTAERRAFGRAVLDFQNSQFKLAECKTQATIARVFLDHCT 312 Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361 AG ASMAK + +E KV + LQ GGYGY++++P+ +Y+D RV +IY Sbjct: 313 QQLLAGTLDAATASMAKYWITEAQGKVIDECLQLFGGYGYMTEYPIAEMYKDARVFRIYG 372 Query: 362 GTSDIQRMVIARNL 375 GTS+I +++IAR+L Sbjct: 373 GTSEIMKLLIARSL 386 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: 344 Number of extensions: 16 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: 390 Length adjustment: 30 Effective length of query: 345 Effective length of database: 360 Effective search space: 124200 Effective search space used: 124200 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 24 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