Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_041099235.1 SUTH_RS10940 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_000828635.1:WP_041099235.1 Length = 248 Score = 88.6 bits (218), Expect = 1e-22 Identities = 73/250 (29%), Positives = 109/250 (43%), Gaps = 16/250 (6%) Query: 9 IVSGAASGLGAATAQMLVEAGAKVM---LVDLNAQAVEAKARELGDNARFAVADISDEQA 65 +V+GA+ GLG A A L GA V+ A ++ G A A+++D A Sbjct: 10 LVTGASRGLGRAIALELGAQGATVVGTATTAAGAAEIQQALDAAGITGWGASANVTDAAA 69 Query: 66 AQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLLRLA 125 ++ + FG + LVN AGI + + + VI NL F L +L Sbjct: 70 CEALIGEIEKKFGPVSVLVNNAGITRDNLAMRMKDD----EWDLVIETNLKAVFRLSKLV 125 Query: 126 AAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGIR 185 M + G IIN S+ G GQA YAA+K +A ++ A+EL I Sbjct: 126 MRGMMK------ARFGRIINITSVVGEAGNPGQANYAAAKAGVAGMSRALAQELGSRNIT 179 Query: 186 VMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIEN--SMLNGEV 243 V +APG +T M + D R +L +P RLG+P E AA + + G Sbjct: 180 VNCVAPGFIDTDMTKALPDAQRDALLGRIPL-GRLGQPDEIAATVAFLASGRAGYITGST 238 Query: 244 IRLDGALRMA 253 + ++G + MA Sbjct: 239 LNVNGGMYMA 248 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: 116 Number of extensions: 6 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: 255 Length of database: 248 Length adjustment: 24 Effective length of query: 231 Effective length of database: 224 Effective search space: 51744 Effective search space used: 51744 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