Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109) (characterized)
to candidate BPHYT_RS20825 BPHYT_RS20825 electron transfer flavoprotein subunit beta
Query= BRENDA::D2RIQ2 (263 letters) >FitnessBrowser__BFirm:BPHYT_RS20825 Length = 249 Score = 96.3 bits (238), Expect = 6e-25 Identities = 66/204 (32%), Positives = 107/204 (52%), Gaps = 6/204 (2%) Query: 1 MNIVVCVKQVPD-TAEMKIDPVTNNLVRDGVTNIMNPYDQYALETALQLKDE-LGAHVTV 58 M ++V VK+V D ++++ + V MNP+D+ A+E A++LK+ + V Sbjct: 1 MKVLVAVKRVVDYNVKVRVKSDGTGVDIANVKMSMNPFDEIAVEEAVRLKEAGVATEVIA 60 Query: 59 ITMGPPHAESVLRDCLAVGADEAKLVSDRAFGGADTLATSAAMANTIKHFGVPDLILCGR 118 ++ G ++ LR LA+GAD A L+ LA A + + P L++ G+ Sbjct: 61 VSAGVTQSQETLRTALAIGADRAILIESSQ--ELQPLAV-AKLLKALVDKEQPSLVILGK 117 Query: 119 QAIDGDTAQVGPEIAEHLGLPQVTAALKVQVKDDTVVVDRDNEQMSMTFTMKMPCVVTV- 177 QAID D+ Q G +A GLPQ T A KV V D V R+ + + T ++K+P VVT Sbjct: 118 QAIDDDSNQTGQMLAALAGLPQATFASKVVVADGKATVSREVDGGAETLSLKLPAVVTTD 177 Query: 178 MRSKDLRFASIRGKMKARKAEIPV 201 +R + R+ ++ MKA+K + V Sbjct: 178 LRLNEPRYVTLPNIMKAKKKPLEV 201 Lambda K H 0.318 0.133 0.375 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: 143 Number of extensions: 6 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: 263 Length of database: 249 Length adjustment: 24 Effective length of query: 239 Effective length of database: 225 Effective search space: 53775 Effective search space used: 53775 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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