Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_017548686.1 C792_RS0106680 glucose 1-dehydrogenase
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >NCBI__GCF_000330705.1:WP_017548686.1 Length = 243 Score = 145 bits (366), Expect = 8e-40 Identities = 86/240 (35%), Positives = 133/240 (55%), Gaps = 7/240 (2%) Query: 25 RTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCDLTD 84 + V++TGG G+GAS V+ F ++GA+V F D+D AG L DE+G LF+ D+TD Sbjct: 7 KVVIVTGGTGGMGASHVKKFVSEGAQVVFTDLDEGAGRVLQDEMGPQS---LFIKQDVTD 63 Query: 85 IDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQAVM 144 ++ K I + + LGP+ VLVNNA + + +D I VN + F +AV+ Sbjct: 64 SESWNKVIVETEKNLGPVNVLVNNAGVNYSEETEAFPEDEYDRVIEVNQKAVFLGMKAVI 123 Query: 145 EDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTLVPG 204 MK A SGSIIN+ SI + Y SK AV G+T+ A +LG + IRVN++ P Sbjct: 124 PSMKKAASGSIINISSIGGIRGRMESVAYSASKFAVTGMTKVGALELGKYGIRVNSVHPS 183 Query: 205 WVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDIVVDGG 264 V T L+ + G +++ + + L +++ + L+LA+D+S T + V+DGG Sbjct: 184 LVNT----GLFSESTGGKAVASDRPLGRVLTKEEVSALVLYLASDESSYTTGAEHVIDGG 239 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: 145 Number of extensions: 7 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: 243 Length adjustment: 24 Effective length of query: 242 Effective length of database: 219 Effective search space: 52998 Effective search space used: 52998 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