Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate GFF2697 PGA1_c27390 short-chain dehydrogenase/reductase
Query= SwissProt::Q8NK50 (266 letters) >FitnessBrowser__Phaeo:GFF2697 Length = 258 Score = 103 bits (256), Expect = 5e-27 Identities = 79/254 (31%), Positives = 126/254 (49%), Gaps = 10/254 (3%) Query: 15 FSLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVKV 74 F L GK +VTGAS G+G A AE GA + I + R E E E+ + ++ Sbjct: 9 FRLDGKRALVTGASS--GIGRACAVALAEAGAHVTIA-ARRIEPLEALVAEM-QAADMQA 64 Query: 75 KVYKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVVDGSASDWDHVIQVDLSG 134 +V ++ +D +++ ++ G D + +AG +S D + D+D VI +++ G Sbjct: 65 EVMVLDVADIAATRASISERITQNGAFDILVNSAGLARHSPASDTTEGDFDAVIDLNIKG 124 Query: 135 TAYCAKAVGAHFKKQGH-GSLVITASMSGHVANYPQEQTSYNVAKAGCIHLARSLANEW- 192 + +AV G GSL+ +S V ++ Y+ K +S+A EW Sbjct: 125 AYFLTQAVAKGLMAAGKPGSLINISSQMAKVGGL--DRAVYSATKHAVEGFTKSMAIEWG 182 Query: 193 RDFARVNSISPGYIDTGLSDF-IDEKTQELW-RSMIPMGRNGDAKELKGAYVYLVSDASS 250 + RVN+I P +I T L+ D + W S I +GR G+ +++ G VYL SDASS Sbjct: 183 KSGIRVNTICPTFIVTPLTQSTFDRPERRAWIESKIQLGRIGEVEDIMGGVVYLASDASS 242 Query: 251 YTTGADIVIDGGYT 264 TG ++IDGG+T Sbjct: 243 LITGTALMIDGGWT 256 Lambda K H 0.314 0.131 0.379 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: 141 Number of extensions: 5 Number of successful extensions: 2 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: 266 Length of database: 258 Length adjustment: 25 Effective length of query: 241 Effective length of database: 233 Effective search space: 56153 Effective search space used: 56153 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: 42 (22.0 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