Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate PfGW456L13_2961 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2961 Length = 317 Score = 134 bits (337), Expect = 3e-36 Identities = 86/248 (34%), Positives = 130/248 (52%), Gaps = 7/248 (2%) Query: 56 MLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVV 115 +L +LK L T + D+ GI ++ T D + + ++LI+A+ R +V Sbjct: 66 LLRRLPKLKLLVTGGMRNAALDLKTAAALGIQVSGT-DSYKHAAPELTWALIMAATRNLV 124 Query: 116 ELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSA 175 A ++AG WQ +G D+ GKTL I+GLG IG VA+ + F M+V+ + + Sbjct: 125 VEANALRAGQWQQGLGG-----DLHGKTLAILGLGSIGQRVAQFGQV-FGMRVIAWSENL 178 Query: 176 NPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGA 235 + G RV EL AD + + + L+ ++ L+ A L MK SA+L+N +RG Sbjct: 179 TAERAAQVGVTRVSKQELFEQADVLSVHLVLSERSRGLVDAQALGWMKPSALLVNTARGP 238 Query: 236 TVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMAR 295 VDE ALI+ALQ + GA LDVFE EPLP+ P L NV+A PH+G + + Sbjct: 239 IVDEAALIKALQKQRLAGAALDVFEQEPLPAHHPFRTLDNVLATPHVGYVSQQNYRLFFL 298 Query: 296 NAAENLVA 303 E++ A Sbjct: 299 QMIEDIQA 306 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: 216 Number of extensions: 6 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: 317 Length adjustment: 28 Effective length of query: 293 Effective length of database: 289 Effective search space: 84677 Effective search space used: 84677 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