Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate AO356_00820 AO356_00820 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00820 Length = 346 Score = 91.7 bits (226), Expect = 3e-23 Identities = 67/194 (34%), Positives = 93/194 (47%), Gaps = 15/194 (7%) Query: 40 VRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHEIVGVVTEVGSKVEKVKVGDNVGIGCL 99 V ++VL GVC SD H + P VPGHE+ G+V EVG V + KVGD + + Sbjct: 28 VVVQVLGTGVCRSDWHGWKGHDPDIQLPHVPGHELAGIVAEVGRDVTRWKVGDRITVP-F 86 Query: 100 VGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGG----YSDTMVADEHFILRWPKN 155 VG C +C C + C + F TH G Y AD + ++ P+N Sbjct: 87 VGGCGACPECNSGNQQVCHS--------QFQPGFTHWGSFAEYVGIHKADLN-LVALPEN 137 Query: 156 LPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVIDI 215 + + A L C +T++ + G G + V G GG+G AV +A A GA V IDI Sbjct: 138 MDFATAASLGCRFVTSFRAVVDQGKVTAGQWVAVHGCGGVGLSAVMIAHAIGANVIAIDI 197 Query: 216 SESKRKEALEKLGA 229 + K K A + LGA Sbjct: 198 CDDKLKLA-QSLGA 210 Lambda K H 0.319 0.137 0.415 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: 276 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: 365 Length of database: 346 Length adjustment: 29 Effective length of query: 336 Effective length of database: 317 Effective search space: 106512 Effective search space used: 106512 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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