Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate 201541 SO2397 oxidoreductase, short-chain dehydrogenase/reductase family (NCBI ptt file)
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__MR1:201541 Length = 275 Score = 89.7 bits (221), Expect = 6e-23 Identities = 75/255 (29%), Positives = 125/255 (49%), Gaps = 15/255 (5%) Query: 29 FSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRS--KA 86 F+ +GK + G +SGI A+A AFA AGA+VA+ S+ + A K Sbjct: 7 FNYQGKNVVVVGGTSGINLAIAIAFAHAGANVAVASRSQDKVDAAVLQLKQAHPEGIHLG 66 Query: 87 YKCAVTNAKQVETTIQTIEKDFGKIDIFIANAG--IPWTAGPMIDVPNNEEWDKVVDLDL 144 V + VE + I +FG ID+ ++ A P TA + + V+D+DL Sbjct: 67 VSFDVRDLVAVEQGFEAIASEFGFIDVLVSGAAGNFPATAAKL----TANGFKAVMDIDL 122 Query: 145 NGAYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEW 204 G++ K A + ++ G+ I ++ I Q C AAK V L+R+LA+EW Sbjct: 123 LGSFQVLKTAYPLLRRP-QGNIIQISAPQASIAMPMQAHVC--AAKAGVDMLTRTLAIEW 179 Query: 205 AGFA-RCNTVSPGYMA-TEISDFIPRDT--KEKWWQLIPMGREGDPSELAGAYIYLASDA 260 R N++ PG + TE + + +++ Q +P+ R G+ ++A A ++L S+ Sbjct: 180 GCEGIRINSIIPGPITGTEGFNRLAPSVVLQQQVAQSVPLKRNGEGQDIANAALFLGSEL 239 Query: 261 STYTTGADILVDGGY 275 ++Y TG + VDGG+ Sbjct: 240 ASYITGVVLPVDGGW 254 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: 145 Number of extensions: 10 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: 275 Length adjustment: 25 Effective length of query: 253 Effective length of database: 250 Effective search space: 63250 Effective search space used: 63250 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