Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate WP_092482221.1 BM299_RS04220 electron transfer flavoprotein subunit alpha/FixB family protein
Query= BRENDA::Q18AQ5 (336 letters) >NCBI__GCF_900115975.1:WP_092482221.1 Length = 335 Score = 244 bits (622), Expect = 3e-69 Identities = 134/328 (40%), Positives = 197/328 (60%), Gaps = 7/328 (2%) Query: 4 VLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVIV 63 V+V+ E +N I + ELL +A +S +LGS V GL + + + GAD+V Sbjct: 9 VMVIAELVDNQIHQTTYELLNWGRGLADKLGCDLSCAVLGSDVRGL-NEIIYRGADKVYN 67 Query: 64 VDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTGL 123 V+ +L + +P+T A I P +++ AT+ GR + P +A + TGLTADCT L Sbjct: 68 VNSPSLEKFLAKPFTSALTRLIAEEKPEIIVAAATTTGRTIMPMAAAELGTGLTADCTVL 127 Query: 124 AVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKVE 183 + + K+LL TRPA GGNIMATI RPQM+TVRP ++ D ++ I K E Sbjct: 128 DIDPEEKILLQTRPAIGGNIMATIKTPRHRPQMATVRPRSTRQAGRDSSRRGEIIEKKYE 187 Query: 184 ---FNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVS 240 F+ ++K ++ I + + V I+DA I+V+ G+G+ ++ ++ ELA ++G V Sbjct: 188 PVLFSTSEKFIEF---IIDTTQNVNIQDADIVVAGGKGLKNRDGFKLVEELAGVLGAGVG 244 Query: 241 GSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAP 300 SR +D GW+ Q+G +GKTV P LY+A GISG IQH+AGM+ AEF+VAIN +P+A Sbjct: 245 ASREAVDLGWVSYPHQIGLSGKTVAPKLYVAVGISGKIQHLAGMQTAEFVVAINNDPDAQ 304 Query: 301 IFKYADVGIVGDVHKVLPELISQLSVAK 328 IFK ADVGIVGD +V+PE + + K Sbjct: 305 IFKVADVGIVGDAWEVVPEFVDAIKKIK 332 Lambda K H 0.316 0.135 0.371 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: 319 Number of extensions: 18 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: 336 Length of database: 335 Length adjustment: 28 Effective length of query: 308 Effective length of database: 307 Effective search space: 94556 Effective search space used: 94556 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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