Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate HSERO_RS19280 HSERO_RS19280 D-2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >FitnessBrowser__HerbieS:HSERO_RS19280 Length = 316 Score = 147 bits (372), Expect = 3e-40 Identities = 98/307 (31%), Positives = 163/307 (53%), Gaps = 15/307 (4%) Query: 2 RPKVGVLLKMKREALEELKK-YADVEIILYPSGE-ELKGVIGRFDGIIVSPTTKITREVL 59 RP V ++ ++ + L+ L++ Y +IL P E EL + + GI + K++RE + Sbjct: 6 RPHVLIVARLPQHLLDLLQQHYTCHNLILQPHSEAELAAIAPQIRGIAANGEAKVSREFM 65 Query: 60 ENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYA 119 L+++S GYD +D+ A +RGI+VT +L++ VA+ + L++ R + A Sbjct: 66 ARFPALEIVSVFGVGYDGVDVPAARERGIHVTHTPDVLNDDVADLAMALMLATARNVVRA 125 Query: 120 DKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYWSRHR 179 D+F R GEW+ F + G ++GI+G+G IG+AIA+R F +++ Y +R R Sbjct: 126 DRFARSGEWKKGP-----FPFTTKVSGARLGIVGLGRIGQAIAKRAAAFDMQISYHNRSR 180 Query: 180 KVNVEKELKARYMD-IDELLEKSDIVILALPLTRDTYHIINEERVKKLEGK-YLVNIGRG 237 K++ Y+D I L + D +++ P T ++N E ++ L K +L+N+ RG Sbjct: 181 -----KDVPYTYVDSITALAREVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINVARG 235 Query: 238 ALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWETVLTPHYAGLALEAQEDVG 297 ++VDE A+ A+K G + G DVF EP EL + VLTPH A L + + Sbjct: 236 SVVDEAALIAALKTGVIAGAGLDVFADEPNVPAELAALD-NVVLTPHMASGTLVTRTAMA 294 Query: 298 FRAVENL 304 A NL Sbjct: 295 DLAFNNL 301 Lambda K H 0.319 0.139 0.393 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: 238 Number of extensions: 15 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: 333 Length of database: 316 Length adjustment: 28 Effective length of query: 305 Effective length of database: 288 Effective search space: 87840 Effective search space used: 87840 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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