Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate Echvi_4005 Echvi_4005 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__Cola:Echvi_4005 Length = 262 Score = 130 bits (328), Expect = 2e-35 Identities = 91/261 (34%), Positives = 135/261 (51%), Gaps = 26/261 (9%) Query: 27 ERFSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKA 86 E F L GKVA +TG++ G+G A+A+A A++GA + + ++ EKA G+ + Sbjct: 3 ELFDLSGKVALVTGATHGLGMAMAKALAKSGATLIVNGHTPAKMEKALEEYAADGIEAHG 62 Query: 87 YKCAVTNAKQVETTIQTIEKDFGKIDIFIANAG-IPWTAGPMIDVPNNEEWDKVVDLDLN 145 Y VTN K+V+ + IE FG +DI + NAG I T ++V ++ KVV++DL Sbjct: 63 YLFDVTNEKEVDEKLSEIEGKFGTVDILVNNAGMIQRTPAMEMEV---ADFAKVVNMDLV 119 Query: 146 GAYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWA 205 + +K + K++G G I SM + + Y AAK + L+R+LA EWA Sbjct: 120 SPFLMSKRVAKGMKEKGGGKIINICSMMSELGR--NTVSGYAAAKGGLKMLTRNLATEWA 177 Query: 206 GF-ARCNTVSPGYMATE-----------ISDFIPRDTKEKWWQLIPMGREGDPSELAGAY 253 + + N + PGY ATE +DFI T P GR GDP +L G Sbjct: 178 KYNIQVNGIGPGYFATEQTAPIRVDGHPFNDFIINRT--------PAGRWGDPEDLQGTM 229 Query: 254 IYLASDASTYTTGADILVDGG 274 ++LAS AS + G + VDGG Sbjct: 230 VFLASQASNFVNGQIVYVDGG 250 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: 194 Number of extensions: 11 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: 262 Length adjustment: 25 Effective length of query: 253 Effective length of database: 237 Effective search space: 59961 Effective search space used: 59961 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