Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_003944701.1 C1M55_RS12340 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2391 (364 letters) >NCBI__GCF_002893965.1:WP_003944701.1 Length = 259 Score = 73.9 bits (180), Expect = 4e-18 Identities = 55/186 (29%), Positives = 92/186 (49%), Gaps = 6/186 (3%) Query: 8 VLAAVRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAFCAG 67 V V +G + L RP +NA+ ++ L A D + AV++ GEK F AG Sbjct: 5 VTLEVSEGIGTIRLARPP-MNALNRQVQDELAAAAHAATVDKAVKAVIVYG-GEKVFAAG 62 Query: 68 GDIRSLYDSFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGASLR 127 D++ + + G + + L + + PKP +A + G+ LGGG+ + A R Sbjct: 63 ADVKEMAE-MDYGQIR-DAIGGMQAGLGA-VASIPKPTVAAITGYALGGGLEVALSADRR 119 Query: 128 VVTERVRMGMPEVGIGYFPDVGGSYFLSRLPGEL-GTYMGVTGLQIRAADALHVGLADWC 186 +V + ++G+PE+ +G P GG+ L+RL G + TG + A +AL +GL D Sbjct: 120 IVGDNAKLGVPEILLGIIPGGGGTQRLARLIGPAKAKDLVFTGRFVGADEALAIGLVDEV 179 Query: 187 VSHDQI 192 V+ D + Sbjct: 180 VAPDDV 185 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: 194 Number of extensions: 8 Number of successful extensions: 2 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: 259 Length adjustment: 27 Effective length of query: 337 Effective length of database: 232 Effective search space: 78184 Effective search space used: 78184 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