Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate HSERO_RS05565 HSERO_RS05565 short-chain dehydrogenase
Query= SwissProt::Q8NK50 (266 letters) >FitnessBrowser__HerbieS:HSERO_RS05565 Length = 249 Score = 124 bits (312), Expect = 1e-33 Identities = 83/249 (33%), Positives = 131/249 (52%), Gaps = 9/249 (3%) Query: 17 LKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVKVKV 76 LK KV V+TG +G G+G AR AE GA + + ++ + A A ++ G+ V Sbjct: 3 LKDKVAVITGGAGINGLGYATARLMAEQGARVVVLDLAQADPAAAAARIGSQHLGLVADV 62 Query: 77 YKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVVDGSASDWDHVIQVDLSGTA 136 +D E ++ FG+ID + NAG T ++ + +D+D ++ V L GT Sbjct: 63 -----TDKASCETAAAAILQQFGRIDILVNNAGITQPVKTLEITGADYDRILDVSLRGTL 117 Query: 137 YCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIHLARSLANEW-RDF 195 Y ++AV + Q +GS++ +S+S Y+ AKAG + LAR++A E+ + Sbjct: 118 YMSQAVLPAMRAQQNGSIICISSVSAQRGGGILGGPHYSAAKAGVLGLARAMAREFGPEG 177 Query: 196 ARVNSISPGYIDTGL--SDFIDEKTQELWRSMIPMGRNGDAKELKGAYVYLVSDASSYTT 253 RVNSI+PG I T + +EK E+ IP+ R G A ++ GA V+L SD S Y T Sbjct: 178 IRVNSITPGLIGTDIIKGKLTEEKKAEI-AETIPLARLGRADDIGGACVFLGSDLSQYCT 236 Query: 254 GADIVIDGG 262 G + ++GG Sbjct: 237 GITLDVNGG 245 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: 158 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: 266 Length of database: 249 Length adjustment: 24 Effective length of query: 242 Effective length of database: 225 Effective search space: 54450 Effective search space used: 54450 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