Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_008486155.1 B3C1_RS16220 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_000299915.1:WP_008486155.1 Length = 249 Score = 108 bits (271), Expect = 8e-29 Identities = 86/249 (34%), Positives = 117/249 (46%), Gaps = 17/249 (6%) Query: 6 KHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVE---AKARELGDNARFAVADISD 62 K +V+GA+ GLG A A L E GA+V+ + AK LG AR AD+ D Sbjct: 7 KRALVTGASRGLGQAMALGLAENGAEVICASSREGGCDDTVAKILALGGKARALAADLGD 66 Query: 63 EQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLL 122 QA Q+ + A++A G + LVN G + E L L +F VI VNL +F L Sbjct: 67 SQAVQALAEQALAA-GPVDVLVNNGGCIYREAALD----FPLDAFDAVIKVNLNAAFQLS 121 Query: 123 RLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARF 182 +L AM + G I+N AS+ +Y G I AY ASK AIA LT A E + Sbjct: 122 QLLGRAMVTKGS------GKIVNIASMLSYSGGIRVPAYTASKHAIAGLTKALANEWGQH 175 Query: 183 GIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPP-RLGRPQEYAALARHIIE--NSML 239 GI+V IAPG F T + D+ S P R G P + + + + Sbjct: 176 GIQVNAIAPGYFRTDNTQALQDDAERSSEIEKRIPAGRWGNPDDLKGAVVFLASKASDYV 235 Query: 240 NGEVIRLDG 248 NG ++ +DG Sbjct: 236 NGHILAVDG 244 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: 123 Number of extensions: 5 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: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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