Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate WP_011779837.1 MVAN_RS13160 NAD(P)-dependent oxidoreductase
Query= CharProtDB::CH_091827 (259 letters) >NCBI__GCF_000015305.1:WP_011779837.1 Length = 256 Score = 127 bits (318), Expect = 3e-34 Identities = 90/260 (34%), Positives = 133/260 (51%), Gaps = 7/260 (2%) Query: 1 MNQVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEI-NAEYGESMAYGFG 59 M + VV G G +G + + LA +RV V D+ + A+ VA + N G A Sbjct: 1 MTRTVVVTGAGSGIGRAIANTLAQRNWRVVVTDVNAAAASEVAAALPNPPAGHESAQ--- 57 Query: 60 ADATSEQSVLALSRGVDEIFGRVDLLVYSAGIAKAAFISDFQLGDFDRSLQVNLVGYFLC 119 D TS ++ A++ V E G +D V +AGI+ D + +++++ VNL G F+C Sbjct: 58 LDVTSPENAAAVASDVSERLG-LDAWVSNAGISFMHRFLDAPIERYEQTMDVNLKGVFVC 116 Query: 120 AREFSRLMIRDGIQGRIIQINSKSGKVGS-KHNSGYSAAKFGGVGLTQSLALDLAEYGIT 178 + +R M+R GI G I+ S +GK G S Y A+KFG VGLTQ++A +L E+GIT Sbjct: 117 GQAAAREMVRAGIPGMIVNTASMAGKQGRVPFLSDYVASKFGVVGLTQAMAYELGEHGIT 176 Query: 179 VHSLMLGNLLKSPMFQSLLPQYATKLGIKPDQVEQYYIDKVPLKRGCDYQDVLNMLLFYA 238 V+ + G +++PM L A G PD V I PL R DV + F Sbjct: 177 VNCVCPG-FVETPMQSRELQWEAELRGTTPDGVRAMMIADTPLGRLEQADDVARAVAFLL 235 Query: 239 SPKASYCTGQSINVTGGQVM 258 S A + TG+++ V GG M Sbjct: 236 SDDARFITGEALAVNGGAYM 255 Lambda K H 0.320 0.137 0.391 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: 121 Number of extensions: 5 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: 259 Length of database: 256 Length adjustment: 24 Effective length of query: 235 Effective length of database: 232 Effective search space: 54520 Effective search space used: 54520 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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