Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate GFF1301 PGA1_c13170 sorbitol dehydrogenase PolS
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__Phaeo:GFF1301 Length = 257 Score = 111 bits (278), Expect = 1e-29 Identities = 77/255 (30%), Positives = 128/255 (50%), Gaps = 8/255 (3%) Query: 5 AVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDATD 64 A++ G + +GA E A G V +AD++ + A A I + A ++D TD Sbjct: 9 ALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQIGAA-----AIAVELDVTD 63 Query: 65 EASVE-ALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSREF 123 +AS++ AL+R V E FG D+L+ +A V AAP+ + + + +N+ G + Sbjct: 64 QASIDRALSRTV-ECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFMMQAA 122 Query: 124 SKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLM 183 ++ MI G G+II + S++G+ G S Y A K + LTQS L+L +GI V+++ Sbjct: 123 AQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNAIA 182 Query: 184 LGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDKAA 243 G ++ + + +A+ G P + + VP R D+ + +F AS+ A Sbjct: 183 PG-VVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFLASEDAD 241 Query: 244 YCTGQSINVTGGQVM 258 Y Q+ NV GGQ M Sbjct: 242 YVVAQTYNVDGGQWM 256 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: 149 Number of extensions: 7 Number of successful extensions: 3 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: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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