Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate Ac3H11_2991 Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2991 Length = 396 Score = 234 bits (597), Expect = 3e-66 Identities = 144/380 (37%), Positives = 211/380 (55%), Gaps = 8/380 (2%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 L E+ D VRD A EIAPRA ++D+ FP LG+L +P YGG M Sbjct: 14 LGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAM 73 Query: 64 GVLTLALILEELGRVCASTALLLIAQTDGMLPIIH-GGSPELKERYLRRF-AGESTLLTA 121 G L + +EE+ R AS L A ++ + I+ G+ K +YL + +GE + A Sbjct: 74 GYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEH--VGA 131 Query: 122 LAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGIS 181 LA +EP AGSD+++MK +A +G Y++NG K +ITNG AD +VVYA T+PE G++G++ Sbjct: 132 LAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVT 191 Query: 182 AFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTN 241 AF++EKG G + K+GMRGS EL F+++EVPAEN++G G LM L Sbjct: 192 AFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYE 251 Query: 242 RVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKA 301 R +GI Q +D + + DR QFG+ I +Q VADM T ++A R Sbjct: 252 RAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTV 311 Query: 302 AELLD----DGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAK 357 A+ LD D ++ + ++ A + + VQ+ GG+GY+ E + R+ RDAK Sbjct: 312 AKNLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAK 371 Query: 358 LTQIYTGTNQITRMVTGRAL 377 L +I GT++I RM+ GR L Sbjct: 372 LYEIGAGTSEIRRMLIGREL 391 Lambda K H 0.319 0.134 0.371 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: 347 Number of extensions: 11 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: 380 Length of database: 396 Length adjustment: 30 Effective length of query: 350 Effective length of database: 366 Effective search space: 128100 Effective search space used: 128100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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