Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate PfGW456L13_2285 Isohexenylglutaconyl-CoA hydratase
Query= reanno::WCS417:GFF2712 (367 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2285 Length = 265 Score = 95.1 bits (235), Expect = 2e-24 Identities = 65/198 (32%), Positives = 101/198 (51%), Gaps = 3/198 (1%) Query: 19 VLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDPQVYAVVLRGAGEKAFCAG 78 +L E+ N + H+TLNRP NA++L MV L S L A D P V A+V+ G G FCAG Sbjct: 10 LLLELHNGVLHITLNRPESRNAMSLQMVAELRSVLAAVRDKPGVRALVIGGVGGH-FCAG 68 Query: 79 GDIRSLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLR 138 GDI+ + ++ G T H+D L + H + V+ ++ G VLGGG+GL +D+ Sbjct: 69 GDIKDMANARAQGPTAHRDLNRVFGTLLQEVQHAPQVVITVLQGAVLGGGLGLACVSDIA 128 Query: 139 VVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGELGIYLGVTGVQIRAADALYCGLADWYL 198 + +++ +PE ++G P + + RI L +T + A GL ++ Sbjct: 129 LSDHQAQFGLPETSLGLLPAQIVPFVVQRIGLTQTRRLALTAARFDGHQARRMGLVH-FV 187 Query: 199 ESSKLADLDNKLDRLQWH 216 E A L +LD + H Sbjct: 188 EHDPQA-LAERLDEVLAH 204 Lambda K H 0.322 0.138 0.419 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: 260 Number of extensions: 15 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: 367 Length of database: 265 Length adjustment: 27 Effective length of query: 340 Effective length of database: 238 Effective search space: 80920 Effective search space used: 80920 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 (21.9 bits) S2: 48 (23.1 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