Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate Synpcc7942_0684 Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__SynE:Synpcc7942_0684 Length = 249 Score = 136 bits (343), Expect = 4e-37 Identities = 97/260 (37%), Positives = 148/260 (56%), Gaps = 22/260 (8%) Query: 2 EQVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGA--GRAYGFK 59 +++A+V G + +G + LA AG VAV N +++ AD + + A G A+ K Sbjct: 8 DRIALVTGASRGIGRAIALELAAAGAKVAV---NYASSAGAADEVVAAIAAAGGEAFAVK 64 Query: 60 VDATDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLC 119 D + E+ VEAL AV E +GR D+LV +AG+ + + + + D+ L +NL G FLC Sbjct: 65 ADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLC 124 Query: 120 SREFSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITV 179 SR +K+M++ GRII I S G++G+ + YSAAK G +GLT+++A +LA GITV Sbjct: 125 SRAAAKIMLKQR-SGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITV 183 Query: 180 HSLMLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYAS 239 +++ G + + M L AEKL ++ +PL R + +V V+ F A+ Sbjct: 184 NAVAPG-FIATDMTSELA---AEKL-----------LEVIPLGRYGEAAEVAGVVRFLAA 228 Query: 240 D-KAAYCTGQSINVTGGQVM 258 D AAY TGQ IN+ GG VM Sbjct: 229 DPAAAYITGQVINIDGGLVM 248 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: 168 Number of extensions: 11 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: 249 Length adjustment: 24 Effective length of query: 235 Effective length of database: 225 Effective search space: 52875 Effective search space used: 52875 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