Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_008486468.1 B3C1_RS17540 3-hydroxybutyrate dehydrogenase
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >NCBI__GCF_000299915.1:WP_008486468.1 Length = 246 Score = 107 bits (266), Expect = 3e-28 Identities = 78/249 (31%), Positives = 120/249 (48%), Gaps = 18/249 (7%) Query: 27 VLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCDLTDID 86 VL+TGGA+GIG EHFA G +V D+D + +A A L ++ L ++ D I Sbjct: 3 VLVTGGASGIGLGIGEHFAKAGHQVILADLDGAKAQAAAATLPGARGVALNVT-DPAQIQ 61 Query: 87 ALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQAVMED 146 AL + LG + VLVNNA + + E + I + + QA + Sbjct: 62 ALAQE-------LGSLDVLVNNAGIQHVARLEDFPPEKWRQLIDIMLVGPALMTQAFLPA 114 Query: 147 MKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTLVPGWV 206 M+ N G IIN+GSI ++ + YV +K + G + LA +L +I VNT+ P +V Sbjct: 115 MREQNFGRIINIGSIHALVASPFKSAYVAAKHGLLGFAKTLALELAEADITVNTICPAYV 174 Query: 207 MTEKQKRLWLDDAGRRSIKEGQCID----------AELEPADLARMALFLAADDSRMITA 256 T ++ D A + E + + A + ++A A FL + +R ITA Sbjct: 175 KTPLVEKQIADQARENGLTEDEVVSTIMLAPMAKKAFIGIDEIAGTAAFLVSPAARNITA 234 Query: 257 QDIVVDGGW 265 Q +V+DGGW Sbjct: 235 QTLVLDGGW 243 Lambda K H 0.320 0.134 0.388 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: 139 Number of extensions: 6 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: 266 Length of database: 246 Length adjustment: 24 Effective length of query: 242 Effective length of database: 222 Effective search space: 53724 Effective search space used: 53724 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 (21.8 bits) S2: 47 (22.7 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