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 6937207 Sama_1377 butyryl-CoA dehydrogenase (RefSeq)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__SB2B:6937207 Length = 385 Score = 295 bits (755), Expect = 1e-84 Identities = 161/379 (42%), Positives = 233/379 (61%), Gaps = 3/379 (0%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60 MDFN EDQ+ D+A +FA L P + D+ H + + +I K GE GFC + PE G Sbjct: 1 MDFNFNEDQRQFADLARQFAADELTPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60 Query: 61 GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120 GMGL L + EELSK T L+ + ++ + +GTE + ++ + G + Sbjct: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIH-NMATWMVTTWGTEAFRAEWSEALTTGAKL 119 Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180 ++ LTEP AG+DA++ T AV +GD+Y++NGSK+FI+ + VV T ++ G G Sbjct: 120 ASYCLTEPGAGSDAASLTTKAVREGDEYVINGSKMFISGAGATELLVVMCRTGEA-GPKG 178 Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240 ISA + G +GK EDKMG + T + FE+ VP +NLLG+EG+GF AM+ LD Sbjct: 179 ISAIAIPADAEGVIYGKAEDKMGWNAQPTRLITFENVRVPVQNLLGEEGQGFTFAMKGLD 238 Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300 GGRI +A ++G A+ AL ++ Y ER+QFG+ ++ FQALQF +ADMAT++ AAR +V Sbjct: 239 GGRINIATCSVGTAQAALERSIAYMNERKQFGKPLAAFQALQFKLADMATELVAARQMVR 298 Query: 301 HAAMLKNEGKPYSEA-AAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKIT 359 AA + P + A AMAK FA+D+ V A+QI GGYGY +YP ER+ R+ ++ Sbjct: 299 LAAFKLDSQDPEATAYCAMAKRFATDIGFAVCDAALQIHGGYGYIREYPLERHFRDVRVH 358 Query: 360 QIYEGTNQVMRIVTSRALL 378 QI EGTN++MR++ SR LL Sbjct: 359 QILEGTNEIMRLIISRRLL 377 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: 356 Number of extensions: 17 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: 383 Length of database: 385 Length adjustment: 30 Effective length of query: 353 Effective length of database: 355 Effective search space: 125315 Effective search space used: 125315 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