Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate Ac3H11_2996 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2996 Length = 376 Score = 351 bits (901), Expect = e-101 Identities = 176/373 (47%), Positives = 248/373 (66%) Query: 5 LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGL 64 LT+DQ+MI+D +FA+ L P DK H + + + G GIC PEE+GG L Sbjct: 3 LTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGANL 62 Query: 65 DVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFG 124 D L+ L +EE++ D GT +S + +G +QK+ +L P+A G +GAF Sbjct: 63 DYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGAFC 122 Query: 125 LTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAF 184 LTEP G+DASA +TTAV +GD+Y++NG K FIT+GK +V A+TDK G G+SAF Sbjct: 123 LTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGKKGMSAF 182 Query: 185 ILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRI 244 ++ PG+ ++EDK+G H+S TA++ F++C +P ENL+G EGEG+KIA+ L+GGRI Sbjct: 183 LVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALEGGRI 242 Query: 245 GVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAM 304 G+AAQ++G+A A AA+ YSKERE FG +I QA+ F +AD AT+IEAAR L++HAA Sbjct: 243 GIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIWHAAA 302 Query: 305 LKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEG 364 L++ GKP + AAMAK FAS++A V + A+Q GGYG D+P ER R+ ++ QIYEG Sbjct: 303 LRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQIYEG 362 Query: 365 TNQVMRIVTSRAL 377 T+ V +I+ RAL Sbjct: 363 TSDVQKIIIQRAL 375 Lambda K H 0.318 0.134 0.379 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: 384 Number of extensions: 12 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: 383 Length of database: 376 Length adjustment: 30 Effective length of query: 353 Effective length of database: 346 Effective search space: 122138 Effective search space used: 122138 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: 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