Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate AZOBR_RS09775 AZOBR_RS09775 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2391 (364 letters) >FitnessBrowser__azobra:AZOBR_RS09775 Length = 263 Score = 102 bits (254), Expect = 1e-26 Identities = 62/190 (32%), Positives = 91/190 (47%), Gaps = 7/190 (3%) Query: 7 PVLAAVRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAFCA 66 PVL + LTLNRPA LNA++ + + L A D + A+++ GE+AF A Sbjct: 13 PVLCVTAGGIATLTLNRPAKLNAISTALAAAMLDTLDALEVDAAVRAIIVTGAGERAFSA 72 Query: 67 GGDIRSLYDSFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGASL 126 G DI + +RG F L I ++PKP++A ++G GGG +++ + L Sbjct: 73 GADIAEFTPAVRRGPEAAVRAFRPGQTLCARIESFPKPIIAAVNGICYGGGCEILEASHL 132 Query: 127 RVVTERVRMGMPEVGIGYFPDVGGSYFLSRLPGELGTYMG----VTGLQIRAADALHVGL 182 V +ER E+ +G P GG+ RLP G +TG A AL VGL Sbjct: 133 AVASERASFSKAEIRLGMMPTFGGT---QRLPRNAGRKRALEWLLTGDTFPPAMALAVGL 189 Query: 183 ADWCVSHDQI 192 + V HD + Sbjct: 190 VNQVVPHDAL 199 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: 9 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: 263 Length adjustment: 27 Effective length of query: 337 Effective length of database: 236 Effective search space: 79532 Effective search space used: 79532 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