Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_038017963.1 HA49_RS12580 gluconate 5-dehydrogenase
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >NCBI__GCF_000757425.2:WP_038017963.1 Length = 254 Score = 101 bits (251), Expect = 2e-26 Identities = 74/243 (30%), Positives = 105/243 (43%) Query: 22 LVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCD 81 L R LITG G+G GA V D E EL + + D Sbjct: 7 LTGRRALITGSTQGLGLLMARGLGEHGAEVIINGRDPQRCENAVAELQALGIRASARAFD 66 Query: 82 LTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQ 141 +TD A+ AI ++ GP+ +L+NNA R E E +D I VN + F +Q Sbjct: 67 VTDPVAVTAAIDSIETETGPLDILINNAGIQHRAPFTEFPVEQWDRIIDVNQKSVFLVSQ 126 Query: 142 AVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTL 201 V M G IIN+ S+ L Y SK AV+ LTRG+ +L +NI+VN + Sbjct: 127 QVARKMMVRKRGKIINICSMQSELGRDNITPYAASKGAVKMLTRGMCVELARYNIQVNAI 186 Query: 202 VPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDIVV 261 PG+ +E L D + + +P +L A+FL+A S + + V Sbjct: 187 APGYFDSEMTAALVNDKQFSDWLCQRTPAARWGKPEELMGAAVFLSATASDFVNGHVLFV 246 Query: 262 DGG 264 DGG Sbjct: 247 DGG 249 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: 152 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: 266 Length of database: 254 Length adjustment: 24 Effective length of query: 242 Effective length of database: 230 Effective search space: 55660 Effective search space used: 55660 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