Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_111393797.1 CLV31_RS14820 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_003253485.1:WP_111393797.1 Length = 379 Score = 303 bits (777), Expect = 4e-87 Identities = 170/378 (44%), Positives = 234/378 (61%), Gaps = 5/378 (1%) Query: 36 ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95 +LTEE + E R A E+ P I+ D FP DLG L +V +Y G G Sbjct: 4 QLTEEHLAVQEAAREFAQSELLPGVIDRDSEAKFPHEQIKKMGDLGFLGMMVDPKYNGGG 63 Query: 96 MDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD--GSPALKEKYLPRFGEKSTLMT 153 MD ++ + +EE+ K+ AS ++ + + ++ L+ GS K+KYL R ++ Sbjct: 64 MDTISYVIAMEELSKIDASASVSMSVN-NSLVCWGLEKYGSEEQKQKYLTRLAT-GEILG 121 Query: 154 AFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGM 213 AF +EP AGSD + +T A GD YV+NG K +ITNGS A + V A TD SKG KG+ Sbjct: 122 AFCLSEPEAGSDATSQRTSAEWNGDHYVLNGTKNWITNGSTASVYLVIAQTDASKGHKGI 181 Query: 214 STFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSI 273 S F+VE+G G + G E K+G+RG L F D++VPAEN +GEEG GF + M L+ Sbjct: 182 SVFLVEKGWEGFVIGKKEDKLGIRGSDTHSLMFTDVKVPAENRIGEEGFGFTFAMETLNG 241 Query: 274 NRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRK 333 R+ A+QA+GIA GA E A+ +++ER+ FGKPI+ IQF +ADMAT++EAARLLV K Sbjct: 242 GRIGIAAQALGIASGAYELALAYSKERKAFGKPISQHQAIQFKLADMATQIEAARLLVYK 301 Query: 334 ATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQ 393 A L D + MAK +AS+ AM VT +AVQV GG GY++EY VER+MR+AK+TQ Sbjct: 302 AAWLKDQGEDYAH-ASAMAKLYASEVAMNVTVEAVQVHGGYGYVKEYHVERLMRDAKITQ 360 Query: 394 IYTGTNQITRMVTGRSLL 411 IY GT++I R+V R +L Sbjct: 361 IYEGTSEIQRIVISRGIL 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: 364 Number of extensions: 14 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 24 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