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_084200594.1 C0029_RS01670 acyl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >NCBI__GCF_002869505.1:WP_084200594.1 Length = 386 Score = 287 bits (734), Expect = 4e-82 Identities = 163/381 (42%), Positives = 229/381 (60%), Gaps = 3/381 (0%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60 MDF+L EDQ D A FAE LAP D+ I+ + + + GE GF G+ PE G Sbjct: 1 MDFSLNEDQVAFADSARAFAEGALAPHAARWDEESIFPKDALAQAGELGFMGMYTPESAG 60 Query: 61 GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120 G+G+ L L VEEL+K T L+ + ++ + I + + + GT + Sbjct: 61 GLGMSRLDASLIVEELAKGCTATAAFLTIH-NMATSMIGKYCNASVIDAWCPELVMGTKL 119 Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180 ++ LTEP AG+DA++ +T+A GD YI+NG+K+FI+ + D VV T G G Sbjct: 120 ASYCLTEPGAGSDAASLRTSAERDGDDYIVNGAKVFISGAGDTDVLVVMLRTG-GPGPKG 178 Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240 ISA ++ G +GK EDKMG + T + F++ VP N LGKEG+GF IAME LD Sbjct: 179 ISALLIPADAEGISYGKKEDKMGWNAQPTRMVTFDNVRVPVANRLGKEGQGFSIAMEGLD 238 Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300 GGRI +A ++G A+ AL AV Y +ER+QF +I++FQA QF +ADM T++ AAR +V Sbjct: 239 GGRINIATCSIGTAQQALEEAVAYVQERKQFDTAIAEFQATQFKLADMLTELVAARQMVR 298 Query: 301 HAA-MLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKIT 359 AA L N+ S AMAK FA+DV V DA+Q+ GGYGY +YP ER++R+ ++ Sbjct: 299 LAASKLDNKDSQASTYCAMAKRFATDVGFNVCNDALQLHGGYGYIKEYPMERHVRDTRVH 358 Query: 360 QIYEGTNQVMRIVTSRALLRD 380 QI EGTN++MR++ SR LL D Sbjct: 359 QILEGTNEIMRVIVSRRLLMD 379 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: 338 Number of extensions: 20 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: 386 Length adjustment: 30 Effective length of query: 353 Effective length of database: 356 Effective search space: 125668 Effective search space used: 125668 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