Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011158524.1 TX73_RS15190 3-phosphoglycerate dehydrogenase
Query= curated2:O29445 (527 letters) >NCBI__GCF_000195775.1:WP_011158524.1 Length = 329 Score = 201 bits (512), Expect = 3e-56 Identities = 123/320 (38%), Positives = 180/320 (56%), Gaps = 11/320 (3%) Query: 2 KVLVAEPISEEAIDYMRKNG-LE-VEVKTGMSREE----LIREVPKYEAIVVRSQTKVDA 55 K+LV E +S+ + + G +E +E +S E+ L E P + V T+ Sbjct: 7 KLLVTESLSQRGRALIAERGDIEMIEFPNMISAEDFDALLRTEAPVHG--VALGATRFGE 64 Query: 56 EVIQAAKNLKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTISTAEHAIALMLAAARKI 115 + AA+ ++++ R GVG D ID+ A +R + ++ A N+ S AE A+ +ML A++ Sbjct: 65 RELDAAQQMRVVARIGVGYDAIDVPALNKRKVPLMTAGTANSPSVAEQALFMMLTLAKRG 124 Query: 116 PQADRSVKEGKWE-RKKFMGIELRGKTAGVIGLGRVGFEVAKRCKALEMNVLAYDPFVSK 174 + VK G W R + +L GKT ++G GR+G AKRC A+EM VL YDP+V Sbjct: 125 AELHALVKTGAWATRLGLLPFDLFGKTVLIVGFGRIGTRTAKRCLAMEMTVLVYDPYVPA 184 Query: 175 ERAEQIGVKLV-DFDTLLASSDVITVHVPRTKETIGLIGKGQFEKMKDGVIVVNAARGGI 233 E G K V D D L +D +++H P+T ET GL + KMK ++N ARGGI Sbjct: 185 AAIEAAGCKQVSDLDAALPDADFVSLHCPKTAETTGLFDAARLSKMKPTAYLINTARGGI 244 Query: 234 VDEAALYEAIKAGKVAAAALDVYEKEPPSPDNPLLKLDNVVTTPHIAASTREAQLNVGMI 293 V E ALYEA+ AGK+A A LDV+E+EPP + L L NV+ PH+A TREA +G Sbjct: 245 VVEQALYEALLAGKLAGAGLDVFEQEPPPHGHKLFDLPNVIIAPHVAGVTREALDRMGEQ 304 Query: 294 IAEDIVNMAKGLPVR-NAVN 312 A +++++ G P+R N VN Sbjct: 305 TARNMLSVLDGDPIRVNVVN 324 Lambda K H 0.317 0.136 0.376 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: 390 Number of extensions: 18 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: 527 Length of database: 329 Length adjustment: 31 Effective length of query: 496 Effective length of database: 298 Effective search space: 147808 Effective search space used: 147808 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