Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_066922644.1 ACG33_RS01245 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_001579945.1:WP_066922644.1 Length = 385 Score = 241 bits (615), Expect = 2e-68 Identities = 133/375 (35%), Positives = 212/375 (56%), Gaps = 1/375 (0%) Query: 1 MLVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGS 60 ++ DE + D+VR F + ++P +W +A + E G M PE +GGS Sbjct: 4 VIFQDEHETFRDSVRRFFKAEIEPQVPRWRSQGYVDAQAFRRLGEQGYLLMWAPEAYGGS 63 Query: 61 DTGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGA 120 + Y ++E A G ++H+ + I G E+Q++++L P G ++ A Sbjct: 64 GNADLRYEQIVQEENARHGDSGFYFNLHSMIVAPYIAMLGTEEQQQRYLPPAVRGDLILA 123 Query: 121 FALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGIS 180 A+TEP AGSD + +K A GDH++LNGSK +I++G AG VIV A T PE+ + G+ Sbjct: 124 IAMTEPAAGSDLAGMKAHAEDCGDHWLLNGSKTYISNGIQAGAVIVAARTIPES-RTGMG 182 Query: 181 AFIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGG 240 FIV D+PG++ +R +KLG A DT ++ FDNV+V +N LG +G++ + L Sbjct: 183 LFIVDADAPGFRRSRRLEKLGLDAQDTAELFFDNVKVSKSNVLGDPTQGFRNMVRFLATE 242 Query: 241 RIGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHA 300 R+ +A +V A+ AF++ D+ ER++FG+P+ Q F+LADM ++ + V Sbjct: 243 RLMVAISSVAHAQVAFDLTLDFVKERRAFGRPIGALQNTRFQLADMRARLDSTQTFVDQC 302 Query: 301 AALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 L +AGR + AS AKL SE+ +V LQ GG GY+ + + R+YRD RV +I+ Sbjct: 303 VLLANAGRLSAEVASEAKLLGSELENEVIDACLQLHGGMGYMEEHRISRMYRDARVTRIF 362 Query: 361 EGTSDIQRMVIARNL 375 G+S+I + +I+R L Sbjct: 363 AGSSEIMKEIISRGL 377 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: 328 Number of extensions: 15 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: 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