Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_111393797.1 CLV31_RS14820 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_003253485.1:WP_111393797.1 Length = 379 Score = 368 bits (945), Expect = e-106 Identities = 183/372 (49%), Positives = 263/372 (70%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 T+E L + +AAR+FAQ L P + D E +FP E I +M +LGF GM+V ++ G Sbjct: 6 TEEHLAVQEAAREFAQSELLPGVIDRDSEAKFPHEQIKKMGDLGFLGMMVDPKYNGGGMD 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 ++Y +A+EE++ D + S MSV+NS+ C + K+G+++QK+++L LA+G +LGAF L Sbjct: 66 TISYVIAMEELSKIDASASVSMSVNNSLVCWGLEKYGSEEQKQKYLTRLATGEILGAFCL 125 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 +EP+AGSDA+S +T A NGDHYVLNG K +IT+G A V +V A TD S G +GIS F+ Sbjct: 126 SEPEAGSDATSQRTSAEWNGDHYVLNGTKNWITNGSTASVYLVIAQTDASKGHKGISVFL 185 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 V G+ + + EDKLG SDT ++F DV+VP NR+GEEG G+ A+ L GGR+G Sbjct: 186 VEKGWEGFVIGKKEDKLGIRGSDTHSLMFTDVKVPAENRIGEEGFGFTFAMETLNGGRIG 245 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IA+Q++G+A A+E A Y++ER++FGKPI +HQA+ F+LADMATQI AR +V+ AA L Sbjct: 246 IAAQALGIASGAYELALAYSKERKAFGKPISQHQAIQFKLADMATQIEAARLLVYKAAWL 305 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 +D G+ ++MAKL+ASE+A V A+Q GGYGY+ ++ +ER+ RD ++ QIYEGT Sbjct: 306 KDQGEDYAHASAMAKLYASEVAMNVTVEAVQVHGGYGYVKEYHVERLMRDAKITQIYEGT 365 Query: 364 SDIQRMVISRNL 375 S+IQR+VISR + Sbjct: 366 SEIQRIVISRGI 377 Lambda K H 0.319 0.134 0.389 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: 337 Number of extensions: 11 Number of successful extensions: 1 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: 379 Length adjustment: 30 Effective length of query: 345 Effective length of database: 349 Effective search space: 120405 Effective search space used: 120405 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