Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_043920749.1 jaqu_RS19715 SDR family oxidoreductase
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_000877395.1:WP_043920749.1 Length = 250 Score = 103 bits (257), Expect = 3e-27 Identities = 76/243 (31%), Positives = 121/243 (49%), Gaps = 16/243 (6%) Query: 9 IVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADISDEQAAQS 68 +V+GAA G+G AT +++++ G V ++D + A++A A L D AR + D+SD + Sbjct: 7 LVTGAARGIGLATTRLMLDRGWTVAMIDRDGPALDAAADGLRD-ARAFLCDVSDPDQVAA 65 Query: 69 AVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLLRLAAAA 128 +D +AFG + +VN AG+ + G G ++ +V+ NL G F + + A A Sbjct: 66 MIDDVRTAFGRIDAVVNNAGVA----LFGPIEETGFDTWREVMATNLDGPFLVTQAALPA 121 Query: 129 MAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGIRVMT 188 + E RG ++N ASI+ + AY SK A+ LT A E FGIR Sbjct: 122 LKES-------RGSVVNIASISGLRASTLRVAYGTSKAAVIQLTKQQAAEFGEFGIRANC 174 Query: 189 IAPGIFETPM-MAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHII--ENSMLNGEVIR 245 I PG T + MA + E+ + +P R G +E A+ + E S + G+V+ Sbjct: 175 ICPGPVRTKLAMAVHTQEIVDAYHDAIPL-NRYGSEKEIASCIAFLCSDEASYVTGQVLA 233 Query: 246 LDG 248 DG Sbjct: 234 ADG 236 Lambda K H 0.318 0.131 0.358 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: 105 Number of extensions: 7 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: 255 Length of database: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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