Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate H281DRAFT_01159 H281DRAFT_01159 2-deoxy-D-gluconate 3-dehydrogenase
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__Burk376:H281DRAFT_01159 Length = 266 Score = 134 bits (337), Expect = 2e-36 Identities = 92/269 (34%), Positives = 139/269 (51%), Gaps = 24/269 (8%) Query: 18 VPKVSKNIMERFSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLS 77 +P ++++ F L GKVA +TGS++G+G +A A AQAG D+ + D A Sbjct: 8 IPAINRSAANPFDLGGKVAIVTGSNTGLGAGMALALAQAGCDIVGVSRADAGDTPARV-- 65 Query: 78 KTYGVRSKAYKCAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWD 137 + G R + +++ VE ++ + FG+ID+ + NAGI +D ++WD Sbjct: 66 EVTGRRFADVRADLSSTAPVEDIVRAAVEAFGRIDVLVNNAGI-IRRQDALDF-TEDDWD 123 Query: 138 KVVDLDLNGAYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQM--------QACYNAA 189 V+DL+L ++ A+ A + F KQ G G I+NI M A Y A+ Sbjct: 124 AVMDLNLKSLFFLAQAAARQFVKQQSG---------GKIINIASMLSFQGGIRVASYTAS 174 Query: 190 KCAVLHLSRSLAVEWAG-FARCNTVSPGYMATEISDFIPRDTK--EKWWQLIPMGREGDP 246 K VL L+R LA EWA N ++PGYMAT + + D + ++ IP GR G P Sbjct: 175 KSGVLGLTRLLANEWAAKRINVNAIAPGYMATANTAALREDAQRNDEILSRIPAGRWGAP 234 Query: 247 SELAGAYIYLASDASTYTTGADILVDGGY 275 +LAG ++LAS AS Y G + VDGG+ Sbjct: 235 DDLAGPVVFLASSASDYVHGHTLAVDGGW 263 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: 165 Number of extensions: 10 Number of successful extensions: 6 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: 266 Length adjustment: 25 Effective length of query: 253 Effective length of database: 241 Effective search space: 60973 Effective search space used: 60973 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 17 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