Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate AO356_30295 AO356_30295 fatty-acid oxidation protein subunit alpha
Query= reanno::psRCH2:GFF2391 (364 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30295 Length = 703 Score = 78.6 bits (192), Expect = 5e-19 Identities = 63/185 (34%), Positives = 88/185 (47%), Gaps = 13/185 (7%) Query: 12 VRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAFCAGGDIR 71 V V +T+N P +NA+T EM + ++ ADP + A+VL G+ F AG DIR Sbjct: 11 VEGVVAVITVNNPP-VNALTPEMRGSIIDAVTHANADPAVAAIVLMGGGQN-FIAGADIR 68 Query: 72 SLYDSFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGASLRVVTE 131 Q G T ALD A KP +A + G+ LGGG+ R+ Sbjct: 69 ------QFGKARTITTSMSAAALD----ASAKPTVAAIHGYALGGGLEHALACHYRIALP 118 Query: 132 RVRMGMPEVGIGYFPDVGGSYFLSRLPG-ELGTYMGVTGLQIRAADALHVGLADWCVSHD 190 ++G+PEV +G P GG+ L RL G + T + V+ I A +AL +GL V Sbjct: 119 TAKLGLPEVALGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQIVPGT 178 Query: 191 QIAEL 195 Q EL Sbjct: 179 QNQEL 183 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: 577 Number of extensions: 33 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: 703 Length adjustment: 34 Effective length of query: 330 Effective length of database: 669 Effective search space: 220770 Effective search space used: 220770 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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