Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_028315684.1 G491_RS0118900 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000429905.1:WP_028315684.1 Length = 326 Score = 236 bits (601), Expect = 1e-66 Identities = 126/323 (39%), Positives = 189/323 (58%), Gaps = 6/323 (1%) Query: 1 MSRMKVLIADSINEKGISELEEVAEVVVNT---TITPEELLDAIKDFDAIVVRSRTKVTR 57 M + KV + +I ++GI L + EV VN +T +EL +AI D D ++ ++ Sbjct: 1 MKKHKVYVTRAIPKEGIELLSQTCEVQVNPHDRPLTQDELFEAIADADGVIGLLSERIDG 60 Query: 58 EVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKI 117 AAP+LK A VG DN+DV+ AT RG+ V N P+ +I AE + L+ ++ R I Sbjct: 61 TFFNAAPKLKGYANYAVGFDNIDVEEATRRGVPVSNTPDVLTIATAEMAWALLFSVCRHI 120 Query: 118 AIADRSVKEGKWE---KNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYI 174 +D+ V+ W+ +F+G E+ GKTLGI+G GRIG + +K F M + + Sbjct: 121 PASDKLVRNDSWKGWSPLQFIGAEVTGKTLGIVGAGRIGRAMAQMSKGFNMKVFYFSRTK 180 Query: 175 SKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGG 234 + + + +L LL +SD +++H PLTPETRH+ + D FK MK+TA+++N ARG Sbjct: 181 KPDFEKALNAKKVELNELLTQSDFISLHTPLTPETRHMFNADSFKKMKNTAYLINTARGP 240 Query: 235 IIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAII 294 ++DE AL ALK GEIAGA LDV+E EP L EL+NVVL H G++T A+ + A++ Sbjct: 241 VVDESALVEALKSGEIAGAGLDVYEFEPKLTPGLRELDNVVLAAHTGSATDTARSNMALL 300 Query: 295 VANEIKTVFQGGAPRNVLNMPVM 317 A + + +GG P LN V+ Sbjct: 301 AAKNLLAMLEGGNPPTCLNPQVL 323 Lambda K H 0.316 0.135 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: 361 Number of extensions: 18 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: 326 Length adjustment: 31 Effective length of query: 494 Effective length of database: 295 Effective search space: 145730 Effective search space used: 145730 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