Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate BPHYT_RS20780 BPHYT_RS20780 acyl-CoA dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_26355 (375 letters) >FitnessBrowser__BFirm:BPHYT_RS20780 Length = 381 Score = 296 bits (757), Expect = 8e-85 Identities = 159/372 (42%), Positives = 228/372 (61%), Gaps = 1/372 (0%) Query: 4 TEEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTG 63 ++ QIR+ R+FAQE ++P E DR+ RFP E +M ELG FG+ VPE +GG Sbjct: 4 SDTHQQIRETTRRFAQEVIRPITEELDRDERFPAEIYTQMGELGLFGITVPEAFGGAGLD 63 Query: 64 YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 AYA+ +EE++ G + + + VG + + G D Q+AK++ PL + A+ + Sbjct: 64 VTAYALVMEELSRGYASVADQCGLLELVGTL-LSVHGTDSQRAKYMQPLLRAKLRPAYCI 122 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TE AG+D S ++T A D + L+G K +I + A V V A TDP+AG+RG+S FI Sbjct: 123 TEADAGTDVSGIRTTAMRTPDGWELSGAKLWIHNAPVADVAFVLARTDPAAGRRGMSIFI 182 Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLGEEGEGYKIALANLEGGRVG 243 V G S E K+GQ AS ++ F+ VK+P LG+EG G+ I ++ L+ GRVG Sbjct: 183 VDCALAGVSKGAKEHKMGQRASQVGELHFDRVKLPQDALLGQEGRGFHIMMSVLDKGRVG 242 Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IAA AVG+A+A EAA DYA+ R FG I E Q + + LADMAT I AR +VH AA Sbjct: 243 IAALAVGIAQAGLEAALDYAQTRKQFGSHIAEFQGIQWMLADMATDIQAARLLVHDAAER 302 Query: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363 ++G+ A + SMAK FA + A K + A+Q GG GY+ + +ER+YRD ++ QIYEGT Sbjct: 303 LEAGERASIACSMAKCFAGDTAVKHSANAVQIFGGSGYIRGYEVERLYRDAKITQIYEGT 362 Query: 364 SDIQRMVISRNL 375 + IQR +++R+L Sbjct: 363 NQIQRTIVARDL 374 Lambda K H 0.320 0.134 0.388 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: 358 Number of extensions: 17 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: 381 Length adjustment: 30 Effective length of query: 345 Effective length of database: 351 Effective search space: 121095 Effective search space used: 121095 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 17 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