Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_041100879.1 SUTH_RS16735 phosphoglycerate dehydrogenase
Query= curated2:Q58424 (524 letters) >NCBI__GCF_000828635.1:WP_041100879.1 Length = 327 Score = 176 bits (446), Expect = 1e-48 Identities = 110/284 (38%), Positives = 170/284 (59%), Gaps = 8/284 (2%) Query: 30 LTKEELLEKIKDADVLVVRSGTK-VTRDVIEKAEKLKVIGRAGVGVDNIDVEAATEKGII 88 L +EEL E + D DVL+ +GT+ +T V+ +A +LK+I R G+G+D++D+ AA +GI Sbjct: 38 LREEELAEMVTDFDVLI--AGTEPITERVMRRASRLKLISRVGIGLDSVDLLAAERRGIQ 95 Query: 89 VVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEWDRKRFKGIELYGKTLGVIGLG 148 V PDA + +VAELT+GLML+ R+I A + GEW R + G + T+GVIG G Sbjct: 96 VSYTPDAPAPAVAELTIGLMLSLLRSIHTVNARMHSGEWHR--YFGRRIAEITIGVIGAG 153 Query: 149 RIGQQVVKRAKAFGMNIIGYDPYIPKEVAE-SMGVELVDDINELCKRADFITLHVPLTPK 207 RIG QV+ FG I + P E +E V ++ + AD ITLHVPLT + Sbjct: 154 RIGGQVLDCLGGFGRPRILVNDLRPNLRPERDTAIEWVGK-EDIYRSADVITLHVPLTAQ 212 Query: 208 TRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALDVFEEEPPKDNPL 267 T+++I REQ+ MK++AII+N +RGG+++E L + L G + AA+DVFE+EP + L Sbjct: 213 TKNMIRREQLLQMKQDAIIINTSRGGIVNEHDLAQVLDTGHLAGAAIDVFEQEPYAGD-L 271 Query: 268 LTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRGELAENVV 311 + D + T H G+ + + + E+ + L G++ + +V Sbjct: 272 VRSDRCLLTSHMGSMSVDCRMRMEIEATEEAIRFLTGQMLQGLV 315 Lambda K H 0.316 0.137 0.372 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: 386 Number of extensions: 17 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: 524 Length of database: 327 Length adjustment: 31 Effective length of query: 493 Effective length of database: 296 Effective search space: 145928 Effective search space used: 145928 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 (21.5 bits) S2: 50 (23.9 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