Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate RR42_RS28565 RR42_RS28565 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Cup4G11:RR42_RS28565 Length = 377 Score = 260 bits (664), Expect = 5e-74 Identities = 150/379 (39%), Positives = 223/379 (58%), Gaps = 7/379 (1%) Query: 35 NELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGT 94 +E +E+Q ++ + R A +AP A E D P LGLL +VP E+GGT Sbjct: 3 HEFSEQQTMIRDTARTFASERLAPCAAEWDRAGQLPAEVVAEMGALGLLGMIVPEEWGGT 62 Query: 95 GMDITTFAMVLEEIGKVCASTA-LMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMT 153 D +A+ +EEI CA+ A LM + + G I+ G+ A KE+YLPR ++ Sbjct: 63 YTDYIAYALAIEEIAAGCAACATLMSVHNSVGCGPILHYGTQAQKERYLPRLAS-GEIIG 121 Query: 154 AFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGM 213 AF TEP AGS+ ++TRA + +V++G K F+TNG A + V+A T+P++G +G+ Sbjct: 122 AFCLTEPQAGSEAHNLRTRARATDNGWVLSGSKQFVTNGQRAGVAIVFAATEPAQGKRGL 181 Query: 214 STFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSI 273 S FVV TPG E+KMG+R + +D +VP + L+GE G+G + L Sbjct: 182 SAFVVPTDTPGFSVHTPERKMGIRASDTCAITLDDCQVPHDALLGEPGEGLRIALSNLEG 241 Query: 274 NRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRK 333 R+ A+QA+GIA+ A E A ++ ER QFG+P+ PI M+ADMATE+ AARLLV + Sbjct: 242 GRIGIAAQALGIARSAFEAACRYAAERVQFGRPLREHAPIANMLADMATELNAARLLVHR 301 Query: 334 ATTLLDAKDKRGPLI--GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKL 391 A + A P + AK +AS+ A +V + A+Q+ GG GY+++Y VER R+A++ Sbjct: 302 AAHMRTAGQ---PCLSEASQAKLYASELAERVCSKALQIHGGYGYLEDYPVERHYRDARI 358 Query: 392 TQIYTGTNQITRMVTGRSL 410 TQIY GT++I RM+ R+L Sbjct: 359 TQIYEGTSEIQRMLIARTL 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: 362 Number of extensions: 15 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: 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