Align Mannitol-1-phosphate 5-dehydrogenase; EC 1.1.1.17 (uncharacterized)
to candidate 18347 b4323 D-mannonate oxidoreductase, NAD-binding (NCBI)
Query= curated2:O65992 (384 letters) >FitnessBrowser__Keio:18347 Length = 486 Score = 96.3 bits (238), Expect = 2e-24 Identities = 78/257 (30%), Positives = 123/257 (47%), Gaps = 21/257 (8%) Query: 104 LKKRSEINDKPLDIIACENALFASDVLKKAILDGA---DEELKKYLEKSVGFPNCTVDRI 160 L+ R E K +++C+N V K A+L A D +L ++E++V FP VDRI Sbjct: 169 LRLRREKGLKAFTVMSCDNVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRI 228 Query: 161 VPNV------DIEKEL----PIDVAVEDFYEWDIEKNKV--KINNKIIGAEYVEKLDPYL 208 VP +I +L P +A E F +W IE N V + + +GA++V + P+ Sbjct: 229 VPAATPETLQEIADQLGVYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFE 288 Query: 209 ERKLFLLNGAHATIAYLGYLKGYKYIHEAIKDKEINKIIVG-FHSEAVQALSEKHKIDIQ 267 KL +LNG+H+ +AYLGYL GY+ I + + + K E LS D Sbjct: 289 MMKLRMLNGSHSFLAYLGYLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTD-- 346 Query: 268 ILKEYSNKLLKRFENEYLKDDVSRVGRDPMRKLSSNDRLITPLKLCCDLKIDFTNILFGV 327 L Y+ L++RF N L+ ++ D +KL RL+ P++L + ++ GV Sbjct: 347 -LNAYATLLIERFSNPSLRHRTWQIAMDGSQKLP--QRLLDPVRLHLQNGGSWRHLALGV 403 Query: 328 ASGYLFNYKEDEKAQGI 344 A + DE+ I Sbjct: 404 AGWMRYTQGVDEQGNAI 420 Lambda K H 0.316 0.137 0.381 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: 335 Number of extensions: 14 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: 384 Length of database: 486 Length adjustment: 32 Effective length of query: 352 Effective length of database: 454 Effective search space: 159808 Effective search space used: 159808 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 (21.6 bits) S2: 51 (24.3 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