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 WP_057509244.1 ABB28_RS14005 acyl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >NCBI__GCF_001431535.1:WP_057509244.1 Length = 387 Score = 211 bits (538), Expect = 2e-59 Identities = 121/373 (32%), Positives = 200/373 (53%), Gaps = 6/373 (1%) Query: 5 LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGL 64 L+++++ ++D A F ++ + P + + + +L+ ++ G G P YGG G+ Sbjct: 15 LSDEERAVQDSVARFVDQRVLPVIGDCFDQARFPAELVPEIAALGLLGATLPPAYGGGGM 74 Query: 65 DVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFG 124 D ++Y L +EL + D G +S SLC PI+ +G+E Q+ ++L +A G +G FG Sbjct: 75 DAVAYGLICQELERGDSGLRSFVSVQSSLCMHPIFAYGSEAQRLRWLPAMARGERIGCFG 134 Query: 125 LTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAF 184 LTE G+D S+ +T AV +GD++ L+GSK++ITN AD +V+A T+ G+ F Sbjct: 135 LTEAHGGSDPSSMKTRAVREGDQWRLDGSKMWITNAPIADLAIVWAQTE-----DGVQGF 189 Query: 185 ILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRI 244 ILE+GM GF +I KM S T L F+ +VP+ N L G K + L+ R Sbjct: 190 ILERGMAGFSVQEIGRKMSLRASSTGALFFDQVQVPEANRLAGV-VGMKGPLGCLNQARF 248 Query: 245 GVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAM 304 G++ +G A L + Y+ +RE FGR ++ Q+ Q +ADMA +I A+ L Sbjct: 249 GISWGPIGAAIACLREVLAYAGQRELFGRPLAATQSAQIKLADMARRITGAQLLALQLGR 308 Query: 305 LKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEG 364 LK G+ + ++AK +A+++ + + G G T ++ A R+ N + YEG Sbjct: 309 LKEAGRLQPQQVSLAKWNNCRMAIDIARECRDLLGAAGITTEHAAIRHALNLESVITYEG 368 Query: 365 TNQVMRIVTSRAL 377 T V ++V R L Sbjct: 369 TETVHQLVIGREL 381 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: 272 Number of extensions: 13 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: 383 Length of database: 387 Length adjustment: 30 Effective length of query: 353 Effective length of database: 357 Effective search space: 126021 Effective search space used: 126021 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 24 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