Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate Pf6N2E2_383 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_383 Length = 255 Score = 127 bits (319), Expect = 2e-34 Identities = 83/255 (32%), Positives = 134/255 (52%), Gaps = 15/255 (5%) Query: 2 EQVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVD 61 ++VAV+ GG +GA LA G+HV + D+N + A R A + + A F++D Sbjct: 6 KKVAVITGGAMGIGAEAASALASDGHHVIICDINTTEAERFAQQLRDQGFCADA--FQID 63 Query: 62 ATDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSR 121 ASV A V+ FGR D+LV SAG+AK P +F F+ ++ +N+ G FLC + Sbjct: 64 VGTPASVSAAFEWVEAKFGRCDVLVNSAGIAKTMPFLEFDADVFNRTMLINVTGTFLCCQ 123 Query: 122 EFSKLMIRDGIKGRIIQINSKSG-KVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVH 180 +++M R GRII I S +G + K + Y +K + LT+ +A++L+EYGIT + Sbjct: 124 LAARIM-RKHEFGRIINIASVAGMRAVGKGRTAYGTSKGAVIALTRQMAVELSEYGITAN 182 Query: 181 SLMLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASD 240 ++ G + +PM + L +E Y + +P KR +++ + + ASD Sbjct: 183 AIAPGP-VDTPMTKEL----------HSDEFRKAYSNAIPAKRYGTTREIAGAVSYLASD 231 Query: 241 KAAYCTGQSINVTGG 255 +AY G + V GG Sbjct: 232 VSAYVNGIVLPVDGG 246 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: 164 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: 255 Length adjustment: 24 Effective length of query: 235 Effective length of database: 231 Effective search space: 54285 Effective search space used: 54285 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