Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate H281DRAFT_01204 H281DRAFT_01204 hypothetical protein
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Burk376:H281DRAFT_01204 Length = 377 Score = 261 bits (668), Expect = 2e-74 Identities = 151/374 (40%), Positives = 217/374 (58%), Gaps = 7/374 (1%) Query: 38 TEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMD 97 TEEQ+++ + R+ A +AP A + D + P DLG L +VP ++GG+ D Sbjct: 6 TEEQRMIRDAARDFATERLAPNAAQWDRDAQLPADVVRQMGDLGFLGMIVPSQWGGSYTD 65 Query: 98 ITTFAMVLEEIGKVCASTA-LMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156 +A+ LEEI CA+ A LM + + G I+ GS A K++YL + AF Sbjct: 66 YVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGSDAQKDRYLHDLATGRRI-GAFC 124 Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216 TEP AGS+ ++TRAV K+++NG K F+TNG+ ADI V+A TDP +G +G+S F Sbjct: 125 LTEPQAGSEANNLRTRAVLCDGKWILNGSKQFVTNGARADIAIVFAVTDPDRGKRGLSAF 184 Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276 +V TPG G E K+G+R + +D VP NL+GE G+G + L R+ Sbjct: 185 IVPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPDANLLGEPGEGLRIALSNLEGGRI 244 Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336 A+QAVGIA+ A + A + ER QFGK + I M+ADMAT + AARLLV A Sbjct: 245 GIAAQAVGIARAAFDAARAYASERMQFGKALKDHQTIANMLADMATRLNAARLLVHHAAR 304 Query: 337 LLDAKDKRGPLI--GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 L A + P + AK FAS+ A +V ++A+Q+ GG GY+++Y VER R+A++TQI Sbjct: 305 LRSAGE---PCLSEASQAKLFASEVAEEVCSNAIQIHGGYGYLEDYAVERHYRDARITQI 361 Query: 395 YTGTNQITRMVTGR 408 Y GT+++ RMV R Sbjct: 362 YEGTSEVQRMVIAR 375 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: 354 Number of extensions: 9 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: 414 Length of database: 377 Length adjustment: 31 Effective length of query: 383 Effective length of database: 346 Effective search space: 132518 Effective search space used: 132518 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