Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_012116241.1 XAUT_RS21625 isovaleryl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_000017645.1:WP_012116241.1 Length = 390 Score = 255 bits (652), Expect = 1e-72 Identities = 152/386 (39%), Positives = 217/386 (56%), Gaps = 23/386 (5%) Query: 36 ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95 +L E +L + VR+ + EIAPRA EID + FP LGLL EYGG+G Sbjct: 12 DLGETADMLRDTVRSFSDAEIAPRAAEIDRTNQFPRDLWPKLGALGLLGVTAEEEYGGSG 71 Query: 96 MDITTFAMVLEEIGKVCASTALMLLAQADGMLS-IILDGSPALKEKYLPRF--GEKSTLM 152 + + +EEI + AS L A ++ ++ I +G+ K KYLP+ GE + Sbjct: 72 LGYLEHVIAMEEISRASASVGLSYGAHSNLCINQISRNGTAEQKAKYLPKLISGEH---V 128 Query: 153 TAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKG 212 A A +EPGAGSD+++M+TRA KKGD+Y++NG K +ITNG +A+ L V+A TDP+ G KG Sbjct: 129 GALAMSEPGAGSDVVSMRTRADKKGDRYILNGSKMWITNGPIAETLVVYAKTDPAAGPKG 188 Query: 213 MSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALS 272 M+ F+VER PG K+GMRG EL F+D EVP EN++G G+G LM L Sbjct: 189 MTAFLVERDFPGFSTAQKLDKLGMRGSDTGELVFQDCEVPEENVLGAVGRGVNVLMSGLD 248 Query: 273 INRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLV- 331 R A GI Q ++ + + ER+QFG+PI +Q IADM + A + V Sbjct: 249 YERAVLAGGPTGIMQACMDIVLPYVHERKQFGQPIGTFQLMQGKIADMYVTMNATKAYVY 308 Query: 332 -------RKATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVER 384 R ATT DA A +A++ A + +A+Q +GG+GY+ +Y R Sbjct: 309 AVAKACDRGATTREDAAG---------AILYAAEKATWMALEAIQTLGGNGYINDYPTGR 359 Query: 385 MMREAKLTQIYTGTNQITRMVTGRSL 410 ++R+AKL +I GT++I RM+ GR L Sbjct: 360 LLRDAKLYEIGAGTSEIRRMLIGRQL 385 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: 385 Number of extensions: 15 Number of successful extensions: 4 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: 390 Length adjustment: 31 Effective length of query: 383 Effective length of database: 359 Effective search space: 137497 Effective search space used: 137497 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 Apr 09 2024. 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