Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Dsui_0977 Dsui_0977 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__PS:Dsui_0977 Length = 378 Score = 266 bits (681), Expect = 6e-76 Identities = 151/377 (40%), Positives = 221/377 (58%), Gaps = 7/377 (1%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 LT+EQ+++ + +R A +AP A E D+NH+FP A +LG + VP E+GG GM Sbjct: 3 LTQEQEMIRDSMRAFAQERLAPFAAEWDKNHTFPAEALKELGELGAMGMCVPEEWGGAGM 62 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRF--GEKSTLMT 153 D + + LEEI +T+ ++ Q I G+ KE++L GEK + Sbjct: 63 DYMSLVLTLEEIAAGDGATSTIVSVQNSLACGITQKYGTDQQKEEWLKPLARGEK---LG 119 Query: 154 AFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGM 213 F TEP GSD A+ TRA + GD +V+NG K FIT G A + V+A TD + G KG+ Sbjct: 120 CFCLTEPHTGSDAAAITTRADRDGDHFVLNGVKQFITTGKHAHMAIVFAVTDKAAGKKGI 179 Query: 214 STFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSI 273 S F+V T G I G E+KMG ++ FED VPA L+G+EG+G+ + L Sbjct: 180 SCFLVPTDTKGFIVGRTEEKMGQHASDTVQIIFEDCRVPASALLGKEGEGYKIALSNLEA 239 Query: 274 NRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRK 333 R+ A+Q++G+A+ A E A+++ +ER FG+PI + F +ADM T ++AARL+V + Sbjct: 240 GRIGIAAQSIGMARAAFEAAVRYAKERVTFGQPIIEHQAVNFRLADMNTLLDAARLMVWR 299 Query: 334 ATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQ 393 A L DA K MAK FAS+ A K+ +DA+Q+ GG GY ++ VER+ R+ +++Q Sbjct: 300 AAALKDA-GKPCLKEASMAKMFASEAAEKIASDAIQIHGGVGYTSDFPVERIYRDVRISQ 358 Query: 394 IYTGTNQITRMVTGRSL 410 IY G N I R+V GRS+ Sbjct: 359 IYEGANDIQRLVIGRSI 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: 376 Number of extensions: 15 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: 378 Length adjustment: 31 Effective length of query: 383 Effective length of database: 347 Effective search space: 132901 Effective search space used: 132901 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