Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized)
to candidate WP_099018991.1 CCS90_RS07845 glucose 1-dehydrogenase
Query= SwissProt::P0C0Y5 (267 letters) >NCBI__GCF_002591915.1:WP_099018991.1 Length = 250 Score = 135 bits (339), Expect = 1e-36 Identities = 88/249 (35%), Positives = 133/249 (53%), Gaps = 10/249 (4%) Query: 19 KGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAY 78 + KVV++TGAS +G+G A A GA V ++ SR+Q + V K G KA A Sbjct: 5 ENKVVLITGAS--RGIGEAIAHQFAAQGAQVIVS--SRSQEGIDAVANAIKQNGGKAGAI 60 Query: 79 KCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSG-ILDGSVEAWNHVVQVDLNGTF 137 C S + L+K + +GQ+D I NA A G +LD EA ++V++ G F Sbjct: 61 TCHNGDKASRDGLIKQTIEQYGQLDVMINNAAANPYFGNVLDMGFEAIKKTIEVNIEGYF 120 Query: 138 HCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFA 197 H ++ G +++G G ++ T+S++G +A F Q+ Y+ +KA I M S A E F Sbjct: 121 HMSQLAGQQMRKQGAGVIINTSSVNGRVAGF--NQSLYSASKAAIISMTESFAKECAQFG 178 Query: 198 -RVNSISPGYIDTGLSDFVPKETQQLWHSM--IPMGRDGLAKELKGAYVYFASDASTYTT 254 RVN++ PG DT + + + L + IP+GR +E+ AY++ ASDA+ Y T Sbjct: 179 IRVNAVLPGLTDTKFASALTQNEAMLKMILPQIPLGRIAQPEEIAPAYLFLASDAAKYIT 238 Query: 255 GADLLIDGG 263 G L IDGG Sbjct: 239 GVSLPIDGG 247 Lambda K H 0.316 0.131 0.383 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: 144 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: 267 Length of database: 250 Length adjustment: 24 Effective length of query: 243 Effective length of database: 226 Effective search space: 54918 Effective search space used: 54918 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 (21.6 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