Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_068003992.1 PsAD2_RS06355 SDR family oxidoreductase
Query= SwissProt::O93868 (262 letters) >NCBI__GCF_001623255.1:WP_068003992.1 Length = 263 Score = 112 bits (281), Expect = 6e-30 Identities = 87/254 (34%), Positives = 121/254 (47%), Gaps = 13/254 (5%) Query: 12 KTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVS 71 K IVTGG +GIG A + GA V +I + + A E ++ EFG + CDV Sbjct: 6 KVAIVTGGAQGIGYAIAQRFLEDGAKV-MISDADERAGEAAQEALSEFGHVAFCH-CDVG 63 Query: 72 NTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRAV 131 V + + G I L+ NAGV+ L+ +DF V VN+ G F +AV Sbjct: 64 VRLDVRNMVANTLDEFGDIDVLVNNAGVTAAGDFLTLSEDDFDRVLQVNLKGAFLCSQAV 123 Query: 132 AKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLT---QVFYNSSKAACSNLVKGLAAEWA 188 A+ ++K ++G + IIN SS+N L QV Y SK + L A A Sbjct: 124 ARHMVEKIEEGG------SAGIIINISSVNSVLAIPEQVPYTVSKGGLNQLTNVSAVALA 177 Query: 189 SAGIRVNALSPGYVNTD--QTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHAT 246 GIRVN + PG + TD + D+ + S PL R QP E+ G A L SD A+ Sbjct: 178 KYGIRVNGIGPGSIETDMLKAVVQDESKMNKVLSRTPLGRLGQPSEIAGVASFLASDDAS 237 Query: 247 YMTGGEYFIDGGQL 260 Y++G F DG +L Sbjct: 238 YVSGQTIFADGARL 251 Lambda K H 0.317 0.130 0.372 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: 142 Number of extensions: 7 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: 262 Length of database: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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