Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate PfGW456L13_2434 Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)
Query= reanno::psRCH2:GFF2391 (364 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2434 Length = 257 Score = 94.0 bits (232), Expect = 4e-24 Identities = 62/165 (37%), Positives = 86/165 (52%), Gaps = 7/165 (4%) Query: 19 LTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAFCAGGDIRSLYDSFQ 78 +TL RP LNA+T E++ L +L+ ADP AVVL + KAF AG DI+ + + Sbjct: 17 ITLQRPQALNALTTELLGELAAELNIAQADPDTRAVVLTGS-RKAFAAGADIKEMAERDL 75 Query: 79 RGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGASLRVVTERVRMGMP 138 G + + A Q I + KPL+A ++GF LGGG L A + + E R G P Sbjct: 76 VGILD-----DPRQASWQAITRFSKPLIAAVNGFALGGGCELAMHADIIIAGEDARFGQP 130 Query: 139 EVGIGYFPDVGGSYFLSRLPGE-LGTYMGVTGLQIRAADALHVGL 182 E+ +G P GG+ L R G+ + M +TG I A A VGL Sbjct: 131 EINLGIMPGAGGTQRLLRAVGKSMAMQMVLTGESIDARQAQRVGL 175 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: 223 Number of extensions: 13 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: 257 Length adjustment: 27 Effective length of query: 337 Effective length of database: 230 Effective search space: 77510 Effective search space used: 77510 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