Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >FitnessBrowser__Smeli:SMc01669 Length = 263 Score = 113 bits (282), Expect = 7e-30 Identities = 75/197 (38%), Positives = 102/197 (51%), Gaps = 2/197 (1%) Query: 21 DEVRFDEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFC 80 D V + GI L+TLNRP +LNAL+Y +I L A L + + AV+L GAG +AF Sbjct: 3 DTVLIEISAGIALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAFS 62 Query: 81 AGGDIRALYDSFHAGT-ALHRQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQAA 139 AGGDI S G A R F QL +RL +PKPV+A ++G+ GGG + +A Sbjct: 63 AGGDIHEFSGSVAKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEVTEAV 122 Query: 140 HLRVLTERSRVAMPETGIGLVPDVGASHFLSKLP-LALALYVGLTGVTLGAADTLLCKLA 198 HL + +ER+R A PE + + P G + L +L AL + LTG L L Sbjct: 123 HLAIASERARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALDMGLV 182 Query: 199 DIAVPAASLEHFEQTLA 215 + VP L + LA Sbjct: 183 NAVVPHEQLIASARALA 199 Lambda K H 0.322 0.137 0.405 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: 221 Number of extensions: 13 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: 384 Length of database: 263 Length adjustment: 27 Effective length of query: 357 Effective length of database: 236 Effective search space: 84252 Effective search space used: 84252 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