Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_046010920.1 OLEAN_RS07250 fatty acid oxidation complex subunit alpha FadB
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2986 (356 letters) >NCBI__GCF_000967895.1:WP_046010920.1 Length = 715 Score = 74.7 bits (182), Expect = 7e-18 Identities = 56/182 (30%), Positives = 91/182 (50%), Gaps = 8/182 (4%) Query: 4 MQNEVLAEVRNHIGHLTLNRPAGLNALTLDMVRNLHRQLDAWAQDSQVHAVVLRGAGEKA 63 M + +AE+ ++ ++N+ N +TL+ NL DA +S V V++ +G+ Sbjct: 12 MIEDGIAELNFNLDGESVNK---FNRVTLE---NLKAATDAIKGNSDVKGVLVT-SGKDC 64 Query: 64 FCAGGDIRSLHDSFKSGDTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQG 123 F G DI ++FK + ++ VE + AI P L ++G LGGG + Sbjct: 65 FIVGADITEFGEAFKLPEEEIVEWIVEGNQIFNAIEDLPVPTLTAINGIALGGGFEMCLA 124 Query: 124 ADLRVVTEKSRLAMPEVGIGYFPDVGGSYFLSRIPG-ELGIYLGVSGVQIRAADALYCGL 182 D RV++EK+++ +PEV +G P GG+ LSR+ G + I G + RA AL G Sbjct: 125 TDFRVMSEKAKVGLPEVKLGLMPGFGGTVRLSRVIGADNAIEWICMGAENRADKALKMGA 184 Query: 183 AD 184 D Sbjct: 185 VD 186 Lambda K H 0.322 0.139 0.419 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: 518 Number of extensions: 30 Number of successful extensions: 1 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: 356 Length of database: 715 Length adjustment: 34 Effective length of query: 322 Effective length of database: 681 Effective search space: 219282 Effective search space used: 219282 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 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