Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate GFF1011 PGA1_c10280 isovaleryl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Phaeo:GFF1011 Length = 386 Score = 254 bits (649), Expect = 3e-72 Identities = 152/379 (40%), Positives = 212/379 (55%), Gaps = 7/379 (1%) Query: 36 ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95 +L E+ L +MV A + P A EID+ + FP +LGLL VP E+GG G Sbjct: 9 DLGEDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFGGAG 68 Query: 96 MDITTFAMVLEEIGKVCASTALMLLAQADGMLSII-LDGSPALKEKYLPRF--GEKSTLM 152 M + +EEI + AS +L A ++ ++ I L+G+ K KYLPR GE + Sbjct: 69 MSYLAHTVAVEEIARASASVSLSYGAHSNLCVNQIKLNGNAEQKAKYLPRLVSGEH---V 125 Query: 153 TAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKG 212 A A +E GAGSD+++M RA K+ D Y +NG K +ITNG AD L V+A TDP G+KG Sbjct: 126 GALAMSEAGAGSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPDAGSKG 185 Query: 213 MSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALS 272 M+ F++E+ G + K+GMRG +EL FED+EVP EN++GEEGKG LM L Sbjct: 186 MTAFLIEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGLD 245 Query: 273 INRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVR 332 RV A GI ++ M + +ER+QFG+PI + +Q IADM T + AR V Sbjct: 246 YERVVLAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYVY 305 Query: 333 KATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLT 392 + D K +AS+ AM AVQ GG+GY+ + V R+ R+AKL Sbjct: 306 EVAKACD-KGTVTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDAKLM 364 Query: 393 QIYTGTNQITRMVTGRSLL 411 +I GT++I RM+ GR L+ Sbjct: 365 EIGAGTSEIRRMLIGRELM 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: 356 Number of extensions: 10 Number of successful extensions: 6 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: 386 Length adjustment: 31 Effective length of query: 383 Effective length of database: 355 Effective search space: 135965 Effective search space used: 135965 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