Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate HSERO_RS14055 HSERO_RS14055 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__HerbieS:HSERO_RS14055 Length = 388 Score = 205 bits (522), Expect = 2e-57 Identities = 115/338 (34%), Positives = 195/338 (57%), Gaps = 9/338 (2%) Query: 29 ELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSRVCGTTGVILSA 88 ++DE +P + V+ + KAG + P+EYGG G + +EE++R G +G Sbjct: 31 KIDEARGYPEQFVDALTKAGWLAALIPQEYGGSGLGLTEASVIMEEINRTGGNSGACHGQ 90 Query: 89 HTSLGSWPIYQYGNEEQKQKFLRPLASGE-KLGAFGLTEPNAGTDASGQQTTAVLDGDEY 147 ++G+ + ++G+ EQK+++L +ASGE +L + +TEP GTD + +T AV GD Y Sbjct: 91 MYNMGT--LLRHGSPEQKERYLPRIASGELRLQSMAVTEPTTGTDTTRIKTVAVKKGDRY 148 Query: 148 ILNGSKIFITNAIAGDIYVVMAMTDK----SKGNKGISAFIVE-KGTPGFSFGVKEKKMG 202 ++NG K++I+ D+ +++A T S+ ++G+S F+V+ K G V+ + Sbjct: 149 VINGQKVWISRVQHSDLMILLARTTPLEQVSRKSEGMSIFLVDLKEAIGHGMEVRPI-LN 207 Query: 203 IRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGALDETVK 262 + T+EL F++ IP ENL+G+EG+GF+ + L+ R IAA+ +G +D+ + Sbjct: 208 MVNHETNELFFDNLEIPAENLIGEEGRGFRYILDGLNAERTLIAAECIGDGYWFIDKATQ 267 Query: 263 YVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVEAAMAKLFA 322 Y +ERV F RP+ Q QF LA+ ++V+AA + YQA D + G +A MAK A Sbjct: 268 YARERVVFDRPIGMNQGVQFPLAEAYIEVEAANLMRYQACALFDAQQSCGAQANMAKYLA 327 Query: 323 AETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEI 360 A+ A E +Q HGG+G+ +Y VER R+ ++ ++ Sbjct: 328 AKAAWEAANVCLQTHGGFGFACEYDVERKFRETRLYQV 365 Lambda K H 0.315 0.133 0.373 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: 343 Number of extensions: 16 Number of successful extensions: 4 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: 378 Length of database: 388 Length adjustment: 30 Effective length of query: 348 Effective length of database: 358 Effective search space: 124584 Effective search space used: 124584 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: 42 (22.0 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