Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate YP_004145060.1 Mesci_6003 acyl-CoA dehydrogenase domain-containing protein
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000185905.1:YP_004145060.1 Length = 390 Score = 259 bits (661), Expect = 1e-73 Identities = 143/373 (38%), Positives = 223/373 (59%), Gaps = 3/373 (0%) Query: 5 DEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGY 64 DE + D F E + P ++++K+ +E+ + GL +PE++GGS G Sbjct: 19 DEVGMLYDMAHRFMSEEIAPRYDEFEKNEMVDRESWLKAGSAGLLCASMPEEYGGSG-GT 77 Query: 65 VAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALT 124 A+ A+ E G + +HNS+ IL +G+E QK+++L LATG ++GA A+T Sbjct: 78 FAHESAIIEAIGHVGVDGFGIGLHNSIVAPYILHYGSEDQKKKWLPKLATGELIGAIAMT 137 Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAFIV 184 EP AGSD +KTRA+ +G+ Y +NGSK FIT+GQ A +IV TDPE G +G S +V Sbjct: 138 EPGAGSDLQGVKTRAQKDGNQYKINGSKTFITNGQLANFIIVVTKTDPEKGAKGTSLIVV 197 Query: 185 PTDS-PGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLG-AEGEGYKIALANLEGGRI 242 TD G+Q R DK+G A+DT ++ F++++VP +N LG EG+G+ + L R+ Sbjct: 198 ETDEVEGFQRGRNLDKIGLKANDTSELFFNDMRVPTSNLLGHEEGQGFVQLMQQLPQERL 257 Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302 I + A+ M A + DY ER++FGK +I+ Q F+LA++ T+ ++ R A Sbjct: 258 QIGTGAIAMIERALALTIDYVKERKAFGKAIIDFQNTQFKLAELKTEATIGRVFYNDCVA 317 Query: 303 LRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362 AG V ASMAK + S++ KV + LQ GGYGY++++P+ R++RD RV +IY G Sbjct: 318 RHIAGGLDPVTASMAKYWLSDLQGKVVDECLQLHGGYGYMNEYPIARMFRDARVQRIYGG 377 Query: 363 TSDIQRMVIARNL 375 T++I +++I R+L Sbjct: 378 TNEIMKLLIGRSL 390 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: 340 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: 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