Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_011654914.1 RL_RS30575 glyoxylate reductase
Query= CharProtDB::CH_004924 (525 letters) >NCBI__GCF_000009265.1:WP_011654914.1 Length = 312 Score = 124 bits (310), Expect = 6e-33 Identities = 95/290 (32%), Positives = 141/290 (48%), Gaps = 14/290 (4%) Query: 18 LIESDFIEIVQ--KNVADAEDELHTFDALLVRSATK-VTEDLFNKMTSLKIVGRAGVGVD 74 L +SD I IV + VA+ + + +L+ SAT+ + +L +K+ +L V G G D Sbjct: 20 LDQSDLIRIVTGPEGVAEVSEADRSAVRVLMTSATRGCSAELADKLPNLGFVVSQGAGSD 79 Query: 75 NIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANISVKSREWNRTAY-VG 133 IDI K GV V T A+ + L R + +A+ + EW R + VG Sbjct: 80 KIDIPGLEKRGVRVRCVGEALTDDVADLAMTLTIMLCRDLVRADAFARGGEWERGRFDVG 139 Query: 134 SELYGKTLGIVGL-GRIGSEIAQRRGAFGMTVHVFDPFLTEERAKKIGVNSRTF---EEV 189 G T+GI GL GRIG IA R A M + +R G+ + + E + Sbjct: 140 DSPVGMTIGIGGLSGRIGQAIAARASASKMKIAGL------QRGSNEGLGASLYDGWEAL 193 Query: 190 LESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALLEALENGHVAG 249 E++D++ + P T + K ++ +A RLIN RG ++D AL+ ALE +AG Sbjct: 194 AEASDVLVLAVPGTADLKHVIGARELAALGPKGRLINVGRGNLVDTEALIVALETKAIAG 253 Query: 250 AALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQF 299 AALDV + EP + +L P VI TPH+G T + A +EVL F Sbjct: 254 AALDVLDTEPVIPPRLAALPNVILTPHIGGQTWGQRSRGARIAEDEVLAF 303 Lambda K H 0.317 0.134 0.374 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: 351 Number of extensions: 13 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: 525 Length of database: 312 Length adjustment: 31 Effective length of query: 494 Effective length of database: 281 Effective search space: 138814 Effective search space used: 138814 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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