Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate Ga0059261_3986 Ga0059261_3986 Enoyl-CoA hydratase/carnithine racemase
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >FitnessBrowser__Korea:Ga0059261_3986 Length = 259 Score = 80.9 bits (198), Expect = 4e-20 Identities = 69/223 (30%), Positives = 113/223 (50%), Gaps = 11/223 (4%) Query: 19 ADDEVRFDEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKA 78 + + V +D +G+ + LNRP +LNA++ M+ L+ A L A + AV+L G G +A Sbjct: 2 SQETVLYDLTDGVATLRLNRPDRLNAVTGEMLDLIRASLLR-AVDEGARAVLLTGEG-RA 59 Query: 79 FCAGGDIRALYDSFHAGTALHRQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQA 138 FC+G D+ D A + +F + L L P PVV ++G G G+G+A A Sbjct: 60 FCSGADLVGRMDGKPIDPADNLEFHYNP--LAETLSKLPIPVVTAVNGPAAGAGVGIALA 117 Query: 139 AHLRVLTERSRVAMPETGIGLVPDVGASHFLSK-LPLALALYVGLTGVTLGAADT----L 193 + V+ + + + + + IGLVPD GA+ ++K A AL + L G + A D L Sbjct: 118 GDIVVMAKSAYLLLAFSNIGLVPDCGATWLVAKSAGRAKALEMALLGEKVSADDAKDAGL 177 Query: 194 LCKLADIAVPAASLEHFEQTLAA--INRTGDVLADLRAALQAT 234 + ++A+ A+ LAA G + A ++AAL +T Sbjct: 178 VARVAEDDALLATAGGIAAKLAAKPTVALGLIRAQVKAALNST 220 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: 222 Number of extensions: 10 Number of successful extensions: 3 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: 259 Length adjustment: 27 Effective length of query: 357 Effective length of database: 232 Effective search space: 82824 Effective search space used: 82824 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