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 Echvi_1473 Echvi_1473 Acyl-CoA dehydrogenases
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__Cola:Echvi_1473 Length = 380 Score = 381 bits (978), Expect = e-110 Identities = 191/379 (50%), Positives = 265/379 (69%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60 M+F LTE+Q MI M +F K + P +E D + L K+GE G G+ P EYG Sbjct: 2 MNFQLTENQSMIAQMIRDFGAKEITPFRKEWDDHQTFPLPLFKKLGELGLMGVLIPSEYG 61 Query: 61 GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120 G G L Y+ A+ EL+K+D G G++++A+ SLC+ I +FG+EEQKQKYL +A + Sbjct: 62 GSGFGYLEYVTAILELAKLDPGIGLSMAAHNSLCSGHIMLFGSEEQKQKYLPKLASCEFL 121 Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180 GA+GLTEP+ G+DA+ +TTA +GD ++LNG+K FIT+G D VV A T + HG Sbjct: 122 GAWGLTEPNTGSDAANMKTTATAEGDYFVLNGAKNFITHGVSGDVAVVIARTGEVGDKHG 181 Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240 ++AF++EKG GFR G+ EDK+G TS TAELIFEDC V K +LG+ GEGF +M+ LD Sbjct: 182 MTAFVVEKGTEGFRGGRKEDKLGMRTSETAELIFEDCRVHKSQILGEVGEGFIQSMKVLD 241 Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300 GGRI +AA +LGIAEGA AA+ YSKER+QF + IS +Q + F +ADMATK+EAA+ L + Sbjct: 242 GGRISIAALSLGIAEGAFEAALSYSKERQQFQKPISAYQGISFKLADMATKLEAAKLLTF 301 Query: 301 HAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQ 360 AA LKN G+ + A+A AK +AS++A+E+ +AVQ++GGYG+T DYP E+Y R+ K+ Sbjct: 302 KAADLKNRGEYVTLASAQAKYYASEIAVELANEAVQVYGGYGFTKDYPVEKYYRDVKLCT 361 Query: 361 IYEGTNQVMRIVTSRALLR 379 I EGT+++ +IV SR LL+ Sbjct: 362 IGEGTSEIQKIVISRELLK 380 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: 393 Number of extensions: 13 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: 380 Length adjustment: 30 Effective length of query: 353 Effective length of database: 350 Effective search space: 123550 Effective search space used: 123550 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