Align 3-hydroxy-isobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate BPHYT_RS09560 BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25665 (368 letters) >FitnessBrowser__BFirm:BPHYT_RS09560 Length = 694 Score = 72.8 bits (177), Expect = 3e-17 Identities = 56/170 (32%), Positives = 83/170 (48%), Gaps = 16/170 (9%) Query: 31 LTLNRPAGLNAITLDMVRSLHRQLDAWSKDPHIHAVVLRGAGEKAFCAGGDIRSLYDSFK 90 +TLN P +N + L + ++ DP I A+VL GAG KAF G DI +++ K Sbjct: 14 ITLNNPP-VNGLGLSTRAGIVEGVERAQNDPAIKAIVLTGAG-KAFSGGADITE-FNTPK 70 Query: 91 SGGTLHEDFFVEEYALDLAIHHYR---KPVLALMDGFVLGGGMGLVQGADLRVVTERSRL 147 +G +E L I KPV+A + +GGG+ L GA R+ +++ Sbjct: 71 AG---------QEPTLATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQI 121 Query: 148 AMPEVAIGYFPDVGGSYFLPRIPG-ELGIYLGVSGVQIRAADALYCGLAD 196 A+PEV +G P GG+ LPR G E + + VSG + + GL D Sbjct: 122 ALPEVKLGILPGAGGTQRLPRAIGLEAALNMIVSGAPVMSEKLADSGLFD 171 Lambda K H 0.321 0.138 0.418 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: 530 Number of extensions: 30 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: 368 Length of database: 694 Length adjustment: 34 Effective length of query: 334 Effective length of database: 660 Effective search space: 220440 Effective search space used: 220440 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 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