Align Mannitol-1-phosphate 5-dehydrogenase; EC 1.1.1.17 (uncharacterized)
to candidate BWI76_RS15490 BWI76_RS15490 mannitol dehydrogenase family protein
Query= curated2:B0KCW3 (388 letters) >FitnessBrowser__Koxy:BWI76_RS15490 Length = 487 Score = 101 bits (251), Expect = 5e-26 Identities = 72/210 (34%), Positives = 113/210 (53%), Gaps = 20/210 (9%) Query: 108 RKANIDKPLNIMACENALFATNILKNSILEKG---DKDFIEYVNQKIGFPNTAVDRIVPN 164 RKA ++M+C+N ++++N I D D E++ + + FP+T VDRIVP Sbjct: 169 RKAAGLPAFSVMSCDNMPENGHVMRNVICAYARAVDADLAEWITRNVTFPSTMVDRIVPA 228 Query: 165 V-----DIKKEL-----PIDVAVEDFYEWDIEKKAIIG--DLNIKGAELVDDLEPYIERK 212 V D +L P VA E F +W IE + G GAELV D+ P+ E K Sbjct: 229 VTADTLDKIAQLTGVRDPAAVACEPFRQWVIEDNFVAGRPQWEKAGAELVSDVLPFEEMK 288 Query: 213 LFLLNGAHATTAYLGYLKGYKYIHEAIQD-DFIRNIVSKMQEEASIALSKKHNIKIDNLR 271 L +LNG+H+ AYLGYL GY++I++ +QD ++ R + M E + LS +K +L Sbjct: 289 LRMLNGSHSFLAYLGYLAGYQHINDCMQDANYRRAAHTLMLAEQAPTLS----VKGVDLA 344 Query: 272 EYSNKVIKRFKNSYLKDEVVRVGREPTRKL 301 Y+ +I+R+ N LK ++ + ++KL Sbjct: 345 RYAGLLIERYSNPALKHRTWQIAMDGSQKL 374 Lambda K H 0.318 0.139 0.387 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: 355 Number of extensions: 19 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: 388 Length of database: 487 Length adjustment: 32 Effective length of query: 356 Effective length of database: 455 Effective search space: 161980 Effective search space used: 161980 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