Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate 5210421 Shew_2862 short chain dehydrogenase (RefSeq)
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__PV4:5210421 Length = 255 Score = 141 bits (355), Expect = 2e-38 Identities = 83/249 (33%), Positives = 142/249 (57%), Gaps = 6/249 (2%) Query: 29 FSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYK 88 F L G++A +TG+S GIG A+AE A GA V + + G ++A Sbjct: 7 FDLSGRIALVTGASRGIGAAIAELLAAYGAHVIVASRKAEGCQTVAEQIIDNGGSAEAMA 66 Query: 89 CAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAY 148 C V + + ++ T + I+ G++DI + NA G ++D N ++K ++++L G + Sbjct: 67 CHVGDLEAIQATFEQIQAKHGRLDILVNNAATNPYFGHILDTDLNA-FNKTMEVNLRGYF 125 Query: 149 YCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAGFA 208 + + AG++ ++QG+G + TAS++ + +MQ Y+ +K AV+ ++++ A E A Sbjct: 126 FMSVTAGRMMREQGHGVILNTASVNA--LQPGEMQGIYSISKAAVVSMTKAFAKECAPLG 183 Query: 209 -RCNTVSPGYMATEISDFIPRDTK--EKWWQLIPMGREGDPSELAGAYIYLASDASTYTT 265 RCN + PG+ T+ + + + K ++ IPMGR PSE+AGA +YL SDAS+YTT Sbjct: 184 IRCNALLPGFTKTQFAGALFNNDKIYQQLIARIPMGRHAVPSEMAGAVLYLVSDASSYTT 243 Query: 266 GADILVDGG 274 G ++VDGG Sbjct: 244 GETLVVDGG 252 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: 172 Number of extensions: 8 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: 255 Length adjustment: 25 Effective length of query: 253 Effective length of database: 230 Effective search space: 58190 Effective search space used: 58190 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