Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_028322395.1 H567_RS0117635 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000422285.1:WP_028322395.1 Length = 385 Score = 297 bits (760), Expect = 4e-85 Identities = 162/382 (42%), Positives = 240/382 (62%), Gaps = 10/382 (2%) Query: 3 VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 + +EQ + + V A+E++ P AE+ D++ +FP + ++ + E LFG PE +GGS+ Sbjct: 5 LTEEQLMLKETVARIAREQVAPGAEKRDEEAQFPWDMVEILKENALFGADFPEVYGGSEM 64 Query: 63 GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122 G +A + +EE+A + + I+ VH +G +PI GN +QK ++L LA G L AF Sbjct: 65 GLLALCVMIEELAKACASTAVILLVHE-LGTMPIFLAGNSEQKSRYLPRLAAGDALIAFG 123 Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEA-GKRGISA 181 LTEP AGSD SSL+TRA EGD Y+LNGSK FI+ A V+ V A TD G +G Sbjct: 124 LTEPNAGSDVSSLRTRAVKEGDGYLLNGSKIFISHADVAEVICVAARTDTTVPGHKGTGV 183 Query: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241 FIV + G + + E K+G AS T ++V ++V+VP AN L E G+ I + L+ R Sbjct: 184 FIVDKGTSGLSIGKREKKMGLRASSTVEVVLEDVRVPAANLLAEENSGFPIIMKTLDITR 243 Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 I +A+QAVG+A+ A + A Y ERQ FGKPL Q + + +ADMAT++ +RQ+ AA Sbjct: 244 IPVAAQAVGIAQGALDYAIQYTKERQQFGKPLFSFQGLQWMMADMATRVEASRQLTYKAA 303 Query: 302 ALRDA--------GRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRD 353 AL +A R + ++MAK+FA++ A +V +DA+Q LGGYGY+ ++P+ER+ RD Sbjct: 304 ALFEAVPKNLDRVSRELIRHSAMAKVFAADTAMQVTTDAVQLLGGYGYVKEYPVERMMRD 363 Query: 354 VRVCQIYEGTSDIQRMVIARNL 375 ++ QIYEGTS IQ++VI+ L Sbjct: 364 AKITQIYEGTSQIQKVVISSTL 385 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: 348 Number of extensions: 14 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: 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 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