Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate Pf6N2E2_394 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_394 Length = 258 Score = 116 bits (291), Expect = 4e-31 Identities = 88/264 (33%), Positives = 139/264 (52%), Gaps = 20/264 (7%) Query: 5 LNIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHENLLFQKVDVTSREQV 64 L ++GK V+VTG + GIGKA+V+ L+ +V +G +NLL Q D+++RE Sbjct: 4 LGLSGKRVLVTGGTKGIGKAVVELFLAEGAQVLTSARKASGTLSDNLLVQ-ADLSTREGC 62 Query: 65 EASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYE-LDDATFEKITMINQKGLYL 123 +A VAA + G+VD +V+ G P G + LD+ +++ +N Sbjct: 63 DAVVAATRQRLGSVDIIVHVLG--------GSSAPGGGFAALDEEQWQRELNLNLFPAVR 114 Query: 124 VSQAVGRLLVAKKKGVIINMAS-EAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGKYGVR 182 + +A+ ++ +K+GVI+++ S ++ L E +AYA KAA+ +Y++S +KE+ GVR Sbjct: 115 LDRALLPDMLERKEGVILHVTSIQSRLPLPEATTAYAAAKAALSTYSKSLSKEVSPKGVR 174 Query: 183 VVGIAPGIMEATG----LRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVA 238 VV ++PG +E LA E Y GK + G PLGR SEVA Sbjct: 175 VVRVSPGWVETEASVALAERLAQEAGTDYQGGKQIIMQALG-----GIPLGRPSSPSEVA 229 Query: 239 DLVAYYISDRSSYITGITTNVAGG 262 DL+ + S R+S ITG + GG Sbjct: 230 DLIGFLASPRASSITGSEFVIDGG 253 Lambda K H 0.313 0.131 0.361 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: 150 Number of extensions: 9 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: 266 Length of database: 258 Length adjustment: 25 Effective length of query: 241 Effective length of database: 233 Effective search space: 56153 Effective search space used: 56153 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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