Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_011840752.1 RSPH17029_RS05225 glucose 1-dehydrogenase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000015985.1:WP_011840752.1 Length = 254 Score = 240 bits (612), Expect = 2e-68 Identities = 134/249 (53%), Positives = 161/249 (64%), Gaps = 6/249 (2%) Query: 13 LFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFER---L 69 +FRLDG A VTG GIG EI R A +GAR+ + D + AA EL Sbjct: 6 VFRLDGACAAVTGSGSGIGLEICRAFAASGARLILIDRESAALDRAAEELGAAVAARIVA 65 Query: 70 NVTDADAV---ADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCR 126 +VTDA+A+ A A + V +LVN+AGI R A +T D WR V++VN+DG+FW R Sbjct: 66 DVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASR 125 Query: 127 EFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVN 186 FGR M+ARG GAIV+ SMSG I N PQ ++Y ASK AV LTR+LA EWA RGVRVN Sbjct: 126 AFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVN 185 Query: 187 AVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTL 246 A+APGY AT +T + E PE TWL TP+GR EP EIA A L+LAS AAS+VTG L Sbjct: 186 ALAPGYVATEMTLKMRERPELFGTWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAIL 245 Query: 247 VVDGGYTVW 255 VDGGYTVW Sbjct: 246 AVDGGYTVW 254 Lambda K H 0.319 0.134 0.408 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: 228 Number of extensions: 11 Number of successful extensions: 2 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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 Apr 10 2024. 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