Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate WP_086509102.1 BZY95_RS06205 2-deoxy-D-gluconate 3-dehydrogenase
Query= SwissProt::Q6CEE9 (278 letters) >NCBI__GCF_002151265.1:WP_086509102.1 Length = 250 Score = 122 bits (306), Expect = 8e-33 Identities = 88/261 (33%), Positives = 132/261 (50%), Gaps = 25/261 (9%) Query: 26 MERFSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSK 85 M RF L G+VA +TG + G+G +A A A+AGAD+ + N SDE E + + G R Sbjct: 1 MNRFDLHGRVAMVTGCNKGLGQGLALALAEAGADI-VGVNRSNSDETREKV-EALGRRYV 58 Query: 86 AYKCAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLN 145 A + + + +E G++D+ I NAG A + E+W+ VVD++L Sbjct: 59 AVEAELGRDTPEAIVARALEST-GRLDMLINNAGAIRRAPALTFT--EEDWEAVVDVNLK 115 Query: 146 GAYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQA--------CYNAAKCAVLHLS 197 A++ A+ + ++G G IVN+ + + Y A+K +L L+ Sbjct: 116 AAFFLAQAVARHLVERG---------APGRIVNVASVLSFQGGIRVPAYTASKSGLLGLT 166 Query: 198 RSLAVEWAGFA-RCNTVSPGYMATEISDFIPRDTKEKWWQL--IPMGREGDPSELAGAYI 254 R LA EWA N ++PGYMAT+ + + D L IP GR G P +LAGA I Sbjct: 167 RLLANEWAAHGITVNAIAPGYMATDNTQALREDATRSAEILGRIPAGRWGTPEDLAGAVI 226 Query: 255 YLASDASTYTTGADILVDGGY 275 +L SDA+ Y G + VDGG+ Sbjct: 227 FLCSDAAAYVNGHALAVDGGW 247 Lambda K H 0.317 0.132 0.409 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: 157 Number of extensions: 9 Number of successful extensions: 5 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: 278 Length of database: 250 Length adjustment: 25 Effective length of query: 253 Effective length of database: 225 Effective search space: 56925 Effective search space used: 56925 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 (21.7 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