Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_057509244.1 ABB28_RS14005 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_001431535.1:WP_057509244.1 Length = 387 Score = 217 bits (553), Expect = 4e-61 Identities = 133/374 (35%), Positives = 197/374 (52%), Gaps = 6/374 (1%) Query: 2 LVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSD 61 L++DE++ + D+V F +R+ P RFP E + E+A LGL G +P +GG Sbjct: 14 LLSDEERAVQDSVARFVDQRVLPVIGDCFDQARFPAELVPEIAALGLLGATLPPAYGGGG 73 Query: 62 TGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121 VAY + +E+ GD + +SV +S+ PI +G+E Q+ ++L +A G +G F Sbjct: 74 MDAVAYGLICQELERGDSGLRSFVSVQSSLCMHPIFAYGSEAQRLRWLPAMARGERIGCF 133 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181 LTE GSD SS+KTRA EGD + L+GSK +IT+ A + IV+A T+ G+ Sbjct: 134 GLTEAHGGSDPSSMKTRAVREGDQWRLDGSKMWITNAPIADLAIVWAQTED-----GVQG 188 Query: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241 FI+ G+ V + K+ AS T + FD VQVP ANRL A G K L L R Sbjct: 189 FILERGMAGFSVQEIGRKMSLRASSTGALFFDQVQVPEANRL-AGVVGMKGPLGCLNQAR 247 Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 GI+ +G A A YA +R+ FG+PL Q+ +LADMA +I+ A+ + L Sbjct: 248 FGISWGPIGAAIACLREVLAYAGQRELFGRPLAATQSAQIKLADMARRITGAQLLALQLG 307 Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361 L++AGR + S+AK MA + + LG G ++ R ++ YE Sbjct: 308 RLKEAGRLQPQQVSLAKWNNCRMAIDIARECRDLLGAAGITTEHAAIRHALNLESVITYE 367 Query: 362 GTSDIQRMVIARNL 375 GT + ++VI R L Sbjct: 368 GTETVHQLVIGREL 381 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: 341 Number of extensions: 12 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: 387 Length adjustment: 30 Effective length of query: 345 Effective length of database: 357 Effective search space: 123165 Effective search space used: 123165 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