Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Echvi_1212 Echvi_1212 Acyl-CoA dehydrogenases
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Cola:Echvi_1212 Length = 379 Score = 288 bits (736), Expect = 2e-82 Identities = 163/377 (43%), Positives = 228/377 (60%), Gaps = 5/377 (1%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 LTEE + E R A + P IE D + +FP +LG L +V +Y G GM Sbjct: 5 LTEEHLAVQEAAREFAKSALLPGVIERDTHATFPHEQVKQMGELGFLGMMVAPQYNGGGM 64 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD--GSPALKEKYLPRFGEKSTLMTA 154 D ++ + +EEI K+ AS A+ + + ++ L+ GS KEKYL ++ A Sbjct: 65 DTLSYVLAIEEISKIDASAAVAMSVN-NSLVCWGLEHYGSEQQKEKYLKPLAA-GEILGA 122 Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214 F +EP AGSD + +T A K GD Y++NG K +ITNG A + V A T+P KG+S Sbjct: 123 FCLSEPEAGSDATSQRTMAEKHGDHYLLNGTKNWITNGGTASVYLVMAQTNPELKHKGIS 182 Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274 TF+VE+ G G E K+G+RG L F D++VP EN +GE+G GF Y M +L Sbjct: 183 TFIVEKDMEGFQVGKKEDKLGIRGSDTHSLMFNDVKVPLENRIGEDGFGFTYAMHSLDGG 242 Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334 R+ A+QA+GIA GA E A+ +++ER+ FGKPI+ IQF +ADMATE+EAAR+LV KA Sbjct: 243 RIGIAAQALGIAAGAYELALAYSKERKAFGKPISQHQAIQFKLADMATEIEAARMLVWKA 302 Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 L D + MAK +AS AM T +AVQ+ GG G+++EY VER+MR+AK+TQI Sbjct: 303 AWLKDQGESYAH-ASAMAKLYASKVAMDTTIEAVQIHGGYGFVKEYHVERLMRDAKITQI 361 Query: 395 YTGTNQITRMVTGRSLL 411 Y GT++I ++V R+LL Sbjct: 362 YEGTSEIQKIVISRNLL 378 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: 357 Number of extensions: 13 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: 379 Length adjustment: 31 Effective length of query: 383 Effective length of database: 348 Effective search space: 133284 Effective search space used: 133284 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