Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 15814 b1695 putative oxidoreductase (VIMSS)
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Keio:15814 Length = 383 Score = 169 bits (427), Expect = 2e-46 Identities = 123/377 (32%), Positives = 182/377 (48%), Gaps = 6/377 (1%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEI-DENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95 LTEEQ+LL+ +R L D+N ++P AD G+ VP E+GG Sbjct: 5 LTEEQELLLASIRELITTNFPEEYFRTCDQNGTYPREFMRALADNGISMLGVPEEFGGIP 64 Query: 96 MDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAF 155 D T + L E+ K C + A L+ + S+ GS K E A Sbjct: 65 ADYVTQMLALMEVSK-CGAPAF-LITNGQCIHSMRRFGSAEQLRKTAESTLETGDPAYAL 122 Query: 156 AATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYT-DPSKGAKGMS 214 A TEPGAGSD + T +K K INGQK FIT + V A P K + Sbjct: 123 ALTEPGAGSDNNSATTTYTRKNGKVYINGQKTFITGAKEYPYMLVLARDPQPKDPKKAFT 182 Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274 + V+ PG+ K +G E++ +++EV ++VGEEG GF +M + Sbjct: 183 LWWVDSSKPGIKINPLHK-IGWHMLSTCEVYLDNVEVEESDMVGEEGMGFLNVMYNFEME 241 Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334 R+ A+++ G A+ A E A ++ +R FGKPI H IQ +A MA +++ R +V K Sbjct: 242 RLINAARSTGFAECAFEDAARYANQRIAFGKPIGHNQMIQEKLALMAIKIDNMRNMVLKV 301 Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 D + + +AK + + TAM+V DA+Q+MGG GY E +V R R+ + +I Sbjct: 302 AWQAD-QHQSLRTSAALAKLYCARTAMEVIDDAIQIMGGLGYTDEARVSRFWRDVRCERI 360 Query: 395 YTGTNQITRMVTGRSLL 411 GT++I V GR +L Sbjct: 361 GGGTDEIMIYVAGRQIL 377 Lambda K H 0.318 0.133 0.375 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: 339 Number of extensions: 17 Number of successful extensions: 5 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: 414 Length of database: 383 Length adjustment: 31 Effective length of query: 383 Effective length of database: 352 Effective search space: 134816 Effective search space used: 134816 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