Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_052718021.1 OLEAN_RS12540 hypothetical protein
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000967895.1:WP_052718021.1 Length = 319 Score = 91.3 bits (225), Expect = 3e-23 Identities = 82/283 (28%), Positives = 135/283 (47%), Gaps = 21/283 (7%) Query: 21 KYADVEIILYPSGEELKGVIGRFDGIIVSPTTKITREVLENAERLKVISCHSAGYDNIDL 80 K A +I+++ L + + II T+K E E L ++ +G DNI + Sbjct: 28 KLAGFDIVVWNENVNLNSALVKI-AIIWLETSKFD----EKFENLDLLLVCGSGVDNI-I 81 Query: 81 EEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADK-FIRRGEWESHAKIWTGFK 139 + TK+ Y ++ L+ + + ++ + +H+ K +I K Sbjct: 82 SKLTKKN-YSFQIHRLVDPYLIDRVSNYVVLNVLNVHFNFKNYISNNTTAKWNK------ 134 Query: 140 RIESLYGKK--VGILGMGAIGKAIARRLIPFGVKLYYWSRHR-KVNVEKELKARYMDIDE 196 E + K VGI+G+G IG A +LI K++ W+R++ K ++ + D Sbjct: 135 --ERVRPDKPVVGIMGVGKIGMASMNKLINLNFKVFGWARNKIKHEGLCDIYIGDSEFDR 192 Query: 197 LLEKSDIVILALPLTRDTYHIINEERVKKL-EGKYLVNIGRGALVDEKAVTEAIKQGKLK 255 L + I+I LPLT+ T +IIN + + KL EG Y++NIGRG V + + AIK ++ Sbjct: 193 FLSECSILICCLPLTKKTENIINHDLLYKLNEGSYVINIGRGEHVVDDDLLGAIKDKQIS 252 Query: 256 GYATDVFEKEPVREHELFKYEWETVLTPHYAGLALEAQEDVGF 298 G DVF +EP+ E F + V+TPH AG L A E + Sbjct: 253 GALLDVFREEPLPEIHPFWRDDRIVVTPHVAG-NLNANEQASY 294 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: 273 Number of extensions: 12 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: 319 Length adjustment: 28 Effective length of query: 305 Effective length of database: 291 Effective search space: 88755 Effective search space used: 88755 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