Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_012383630.1 BIND_RS03205 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000019845.1:WP_012383630.1 Length = 307 Score = 133 bits (335), Expect = 5e-36 Identities = 93/315 (29%), Positives = 161/315 (51%), Gaps = 18/315 (5%) Query: 1 MRPKVGVLLKMKREALEELKKYADVEIILYP---SGEELKGVIGRFDGIIVSPTTKITRE 57 M+P++ ++ M L E++ D + +++ G L+ + R GI T + E Sbjct: 1 MKPEILLIEPM----LFEIENRLDHDYVVHRWQGRGTTLEAAL-RIRGIATGGATGVPAE 55 Query: 58 VLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIH 117 ++ + L++I+ + G D +DL EA R I VT GLL+E VA+ +GLI+ +R + Sbjct: 56 LMSSLPNLEIIAINGIGTDAVDLVEAKNRKIGVTTTPGLLTEDVADMALGLILCTLRGLP 115 Query: 118 YADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYWSR 177 AD+F+R +W ++ GK++GILGMG +G+AIA R FG+ + Y Sbjct: 116 EADRFVRDDQWGK-----VSLPLAHTVTGKRLGILGMGRVGRAIAHRAAAFGMDIAYTDV 170 Query: 178 HRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKL-EGKYLVNIGR 236 R +V + A + +L +SD++++A + H++N + L L+N+ R Sbjct: 171 ARFEDVPQRYVA---TLHDLAHESDVLVVAASGGPASRHLVNRTILDALGPHGILINVAR 227 Query: 237 GALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWETVLTPHYAGLALEAQEDV 296 G++VDE+A+ A+++G+L G DVF EP + VL PH A +E + + Sbjct: 228 GSVVDEQALIAALEEGRLGGAGLDVFADEP-HVPSALRLLQNVVLQPHRASATVETRLKM 286 Query: 297 GFRAVENLLKVLRGE 311 G +NL G+ Sbjct: 287 GTLVADNLAAHFAGK 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: 245 Number of extensions: 14 Number of successful extensions: 4 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: 307 Length adjustment: 28 Effective length of query: 305 Effective length of database: 279 Effective search space: 85095 Effective search space used: 85095 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 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