Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_010442787.1 G7G_RS0117695 isovaleryl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_000192475.1:WP_010442787.1 Length = 387 Score = 258 bits (658), Expect = 3e-73 Identities = 151/377 (40%), Positives = 213/377 (56%), Gaps = 3/377 (0%) Query: 36 ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95 +L E+ L EMV A + P A EID +++FP DLGLL VP EYGG G Sbjct: 9 DLGEDVNALREMVHRWAQERVKPMAAEIDASNAFPNELWKEMGDLGLLGVTVPEEYGGAG 68 Query: 96 MDITTFAMVLEEIGKVCASTALMLLAQADGMLSII-LDGSPALKEKYLPRFGEKSTLMTA 154 M + +EE+ + AS +L A ++ ++ I L+G+ K+KYLPR + A Sbjct: 69 MSYLAHTIAVEEVARASASVSLSYGAHSNLCVNQIKLNGTDEQKQKYLPRL-ISGDHVGA 127 Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214 A +E AGSD+++MK RA K+ D Y +NG K +ITNG AD L V+A TDP G+KG++ Sbjct: 128 LAMSESSAGSDVVSMKLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPEAGSKGIT 187 Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274 F++E+ G + K+GMRG +EL FED+EVP EN++GEEG+G A LM L Sbjct: 188 AFLIEKEMKGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVAVLMSGLDYE 247 Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334 RV A GI L+ M + ER+QFGKPI +Q IADM T + +AR V + Sbjct: 248 RVVLAGIGTGIMAACLDEVMPYLAERKQFGKPIGSFQLMQGKIADMYTAMNSARAYVYEV 307 Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 D D +AS+ AM AVQ +GG+G++ + V R+ R+AKL +I Sbjct: 308 AKACDRGDVTRQDAAACC-LYASEQAMVQAHQAVQALGGAGFLSDSPVSRIFRDAKLMEI 366 Query: 395 YTGTNQITRMVTGRSLL 411 GT++I RM+ GR ++ Sbjct: 367 GAGTSEIRRMLIGREMM 383 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: 11 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: 387 Length adjustment: 31 Effective length of query: 383 Effective length of database: 356 Effective search space: 136348 Effective search space used: 136348 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