Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate 15892 b1774 predicted oxidoreductase, Zn-dependent and NAD(P)-binding (NCBI)
Query= BRENDA::Q83VI5 (338 letters) >FitnessBrowser__Keio:15892 Length = 347 Score = 154 bits (389), Expect = 3e-42 Identities = 104/346 (30%), Positives = 171/346 (49%), Gaps = 24/346 (6%) Query: 4 LVLTGTKKLEVENIEQPEVKPNEVLIHTAFAGICGTD-HALYAG--LPGSADAVPPIVLG 60 L + GT K + + E P K +EVLI + GICG+D H +G +P D I LG Sbjct: 8 LQVPGTMK--IISAEIPVPKEDEVLIKVEYVGICGSDVHGFESGPFIPPK-DPNQEIGLG 64 Query: 61 HENSGVVAEIGSDVTNVAVGDRVTIDPNIYCGQCKYCRTARPELCENLSAVGVTRN--GG 118 HE +G V +GS V GDRV I+P + CG C+YC + +C ++ + N G Sbjct: 65 HECAGTVVAVGSRVRKFKPGDRVNIEPGVPCGHCRYCLEGKYNICPDVDFMATQPNYRGA 124 Query: 119 FEEYFTAPASVVYQIPDNVSLKSAAVVEPISCAVHGIQLLKVTPYQKALVIGDGFMGELF 178 Y P S Y++PDN+ A+VEP + +H L V P +K +++G G +G + Sbjct: 125 LTHYLCHPESFTYKLPDNMDTMEGALVEPAAVGMHAAMLADVKPGKKIIILGAGCIGLMT 184 Query: 179 VQILQAYGIHQVDLAGIVPEKLAMNKEKFGVKNTYNTKDGDKI-------PEGTYDVVVE 231 +Q + G ++ + ++ ++LAM E+ G N D I + D+V E Sbjct: 185 LQACKCLGATEIAVVDVLEKRLAM-AEQLGATVVINGAKEDTIARCQQFTEDMGADIVFE 243 Query: 232 AVGLPQTQEAAIEASARGAQVLMFGVGGPDAKFQMNTYEVFQKQLTIQGSFINPNAFEDS 291 G T + A RG ++++ G D+ + +++TIQ F N + + Sbjct: 244 TAGSAVTVKQAPYLVMRGGKIMIVGTVPGDSAI---NFLKINREVTIQTVFRYANRYPVT 300 Query: 292 LALLSSGKLDVESLMSHELDY----QTVDDFVNGKLGVVSKAVVKV 333 + +SSG+ DV+S+++H DY Q ++ VN K ++ K V+K+ Sbjct: 301 IEAISSGRFDVKSMVTHIYDYRDVQQAFEESVNNKRDII-KGVIKI 345 Lambda K H 0.316 0.135 0.386 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: 291 Number of extensions: 25 Number of successful extensions: 4 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: 338 Length of database: 347 Length adjustment: 29 Effective length of query: 309 Effective length of database: 318 Effective search space: 98262 Effective search space used: 98262 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: 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