Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Synpcc7942_1347 Synpcc7942_1347 2-hydroxyacid dehydrogenase-like
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__SynE:Synpcc7942_1347 Length = 331 Score = 107 bits (267), Expect = 4e-28 Identities = 87/274 (31%), Positives = 122/274 (44%), Gaps = 26/274 (9%) Query: 60 ATRLKALSTISV--------GFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASA 111 A L+AL+ + V GF+Q D++ R G+ + P + A+ +LIL Sbjct: 58 AITLEALAELGVEHVALRCAGFNQVDLSAAERLGLRVVRVPAYSPHAVAEHAIALILTLN 117 Query: 112 RRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYT 171 R++ + G++ L G D+ G T+GI+G GRIG AV + GF VL Sbjct: 118 RKIHRAYARTREGNFALD---GLVGFDLNGCTVGIIGTGRIG-AVLTQILRGFGCHVLAH 173 Query: 172 NRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINA 231 + NP A GA +L +L A + L PLTP+T HL+ + M+ +LIN Sbjct: 174 DLVENPDCLAA-GAVYTDLDQLWQEAQIISLHCPLTPQTYHLVNREAIAKMQPGTMLINT 232 Query: 232 SRGATVDEKALIEALQNGTIHGAGLDVFE-----------TEPLPSD--SPLLKLANVVA 278 SRG VD +A+IE L+ I GLDV+E TE + D LL NVV Sbjct: 233 SRGGLVDTQAVIEGLKLKRIGALGLDVYEQEEPLFFQDHSTEIIHDDVFQRLLTFPNVVI 292 Query: 279 LPHIGSATHETRHAMARNAAENLVAALDGTLTSN 312 H T H +A NL G N Sbjct: 293 TGHQAFLTDTALHNIAETTLSNLTDLEQGRACPN 326 Lambda K H 0.317 0.131 0.366 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: 227 Number of extensions: 10 Number of successful extensions: 2 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: 321 Length of database: 331 Length adjustment: 28 Effective length of query: 293 Effective length of database: 303 Effective search space: 88779 Effective search space used: 88779 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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