Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_011383120.1 AMB_RS03480 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_000009985.1:WP_011383120.1 Length = 389 Score = 243 bits (620), Expect = 7e-69 Identities = 152/379 (40%), Positives = 211/379 (55%), Gaps = 21/379 (5%) Query: 11 TLDMVRD----VATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVL 66 T DM+RD A EIAPRA E+D + FP +GLL + YGG MG L Sbjct: 15 TADMMRDSVAAFAATEIAPRAAEIDRSNEFPNELWPRLGAMGLLGITVDEKYGGAGMGYL 74 Query: 67 TLALILEELGRVCASTALLLIAQTDGML-PIIHGGSPELKERYLRRF-AGESTLLTALAA 124 + +EE+ R AS L A ++ + I G+ K +YL + +GE + ALA Sbjct: 75 EHVVAMEEISRASASVGLSYGAHSNLCVNQIKRNGTEAQKMKYLPKLISGE--YIGALAM 132 Query: 125 TEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFV 184 +EP AGSD+++MK +A ++GD+YV+NG K +ITNG ADVIVVYA TD G +GI+AF+ Sbjct: 133 SEPNAGSDVVSMKLKAEKKGDRYVLNGTKMWITNGPDADVIVVYAKTDVTAGPRGITAFL 192 Query: 185 VEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVF 244 VEK G + K+GMRGS EL F++ EVP EN++GA G G LM L RV Sbjct: 193 VEKTFKGFSVAQKLDKLGMRGSNTGELVFQDCEVPEENVLGAVGKGVNVLMSGLDYERVV 252 Query: 245 CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAEL 304 +GI +D+ V + +R QFG+PI +Q +ADM T A R T A+ Sbjct: 253 LTGGPLGIMAACMDVVVPYVHERTQFGQPIGTFQLMQGKLADMYTTFNACRAYTYAVAKA 312 Query: 305 LDDGDKK------AVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKL 358 D G+ +LYG ++ A + +A+Q LGG+GY+ E R++RDAKL Sbjct: 313 CDRGETSRKDAAGVILYG-------AEKATWMALEAIQTLGGNGYINEYATGRLLRDAKL 365 Query: 359 TQIYTGTNQITRMVTGRAL 377 +I GT++I RM+ GR L Sbjct: 366 YEIGAGTSEIRRMLIGREL 384 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: 364 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 380 Length of database: 389 Length adjustment: 30 Effective length of query: 350 Effective length of database: 359 Effective search space: 125650 Effective search space used: 125650 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