Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_110804536.1 C8J30_RS04555 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2391 (364 letters) >NCBI__GCF_003217355.1:WP_110804536.1 Length = 258 Score = 79.7 bits (195), Expect = 8e-20 Identities = 57/177 (32%), Positives = 89/177 (50%), Gaps = 8/177 (4%) Query: 8 VLAAVRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAFCAG 67 ++ + + V + LNRP LNA+ +++ L + L ADP + VL + +KAF AG Sbjct: 6 LIVEIEDGVALIRLNRPEALNALNSQLLGELAEALKTLDADPAVRCFVLTGS-DKAFAAG 64 Query: 68 GDIRSLYD-SFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGASL 126 DI+ + D SF D + FF E I KP++A + G+ LGGG L Sbjct: 65 ADIKEMADKSFT--DMFLQDFFGTE---GDAILRTRKPIIAAVAGYALGGGCELAMMCDF 119 Query: 127 RVVTERVRMGMPEVGIGYFPDVGGSYFLSRLPGELGTY-MGVTGLQIRAADALHVGL 182 + E + G PE+ +G +GG+ L+R G+ + M +TG + AA+A GL Sbjct: 120 ILCAENAKFGQPEINLGVVAGIGGTQRLTRFVGKSKSMEMHLTGRFMDAAEAERSGL 176 Lambda K H 0.321 0.136 0.412 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: 197 Number of extensions: 9 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: 364 Length of database: 258 Length adjustment: 27 Effective length of query: 337 Effective length of database: 231 Effective search space: 77847 Effective search space used: 77847 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 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