Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate GFF4128 PS417_21145 oxidoreductase
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__WCS417:GFF4128 Length = 248 Score = 103 bits (256), Expect = 4e-27 Identities = 78/258 (30%), Positives = 131/258 (50%), Gaps = 26/258 (10%) Query: 3 QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNE-SNANRLADTINSRYGAGRAYGFKVD 61 +VA++ GG + +GA + + LA G VA ++ + A L +++ S G+A D Sbjct: 9 KVALIQGGSRGIGAAIVKRLAAQGAAVAFTYVSSVAKAEELQNSVISE--GGKALAIHAD 66 Query: 62 ATDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSR 121 + D ++ A E FGR D+LV +AGV AP+ F+L DFD +L +N+ F+ ++ Sbjct: 67 SADAGAIRNAVNATVEAFGRLDILVNNAGVLAIAPLEDFKLEDFDQTLAINVRSVFIATQ 126 Query: 122 EFSKLMIRDGIKGRIIQINSKSGKVGSKHNSG-YSAAKFGGVGLTQSLALDLAEYGITVH 180 E +K M DG GR+I I S + + G Y+ +K VGLT+ LA DL GIT++ Sbjct: 127 EAAKHM-ADG--GRVINIGSTNAERMPFGGGGPYAMSKAALVGLTKGLARDLGPRGITIN 183 Query: 181 SLMLGNLLKSPMFQSLLP---QYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFY 237 ++ G P+ + P +AE L + + + R +++ + + + Sbjct: 184 NVQPG-----PVDTDMNPANSDFAESL-----------IGLMAVGRYGHVEEIASFVAYL 227 Query: 238 ASDKAAYCTGQSINVTGG 255 A +A Y TG S+ + GG Sbjct: 228 AGPEAGYITGASLTIDGG 245 Lambda K H 0.319 0.136 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: 169 Number of extensions: 10 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: 248 Length adjustment: 24 Effective length of query: 235 Effective length of database: 224 Effective search space: 52640 Effective search space used: 52640 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: 47 (22.7 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