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_011651407.1 RL_RS09090 D-threitol dehydrogenase
Query= SwissProt::Q6CEE9 (278 letters) >NCBI__GCF_000009265.1:WP_011651407.1 Length = 256 Score = 141 bits (356), Expect = 1e-38 Identities = 99/259 (38%), Positives = 138/259 (53%), Gaps = 14/259 (5%) Query: 22 SKNIMERFSLKGKVASITGSSSGIGFAVAEAFAQAGADV-AIWYNSKPSDEKAEYLSKTY 80 SK I FSL GKVA +TG +SGIG A+A AFA GA V I N + KA+ L Sbjct: 4 SKQIDLNFSLGGKVALVTGGASGIGDAIASAFAAKGAVVGVIDINETVAKSKADAL---- 59 Query: 81 GVRSKAYKCAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVV 140 G +K++ C V+N + VE I + F IDI + +AG+ A P D+ E WD+ + Sbjct: 60 GNGAKSFVCDVSNPQSVEAVIAAAQAAFAHIDIVVNSAGVAMLA-PAEDL-TLEAWDRTI 117 Query: 141 DLDLNGAYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSL 200 D++L G + ++ G++ K G G I + V I Q Y A+K V+ LS++L Sbjct: 118 DINLKGTFLVSQAVGRVMLKAGKGGRIINIASQAGTVAIDQ-HVAYCASKFGVIGLSKTL 176 Query: 201 AVEWAGFA-RCNTVSPGYMATEISDFI---PRDTKEKWWQLIPMGREGDPSELAGAYIYL 256 A EW NT+SP + TE+ PR + K + IP GR P E+A A ++L Sbjct: 177 AAEWGKHGITVNTISPTVVLTELGRKAWDNPRGEELK--KRIPTGRFAYPEEIAAAAVFL 234 Query: 257 ASDASTYTTGADILVDGGY 275 AS + GAD+LVDGGY Sbjct: 235 ASSGAEMINGADLLVDGGY 253 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: 169 Number of extensions: 8 Number of successful extensions: 4 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: 256 Length adjustment: 25 Effective length of query: 253 Effective length of database: 231 Effective search space: 58443 Effective search space used: 58443 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