Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_051249709.1 H589_RS19615 hypothetical protein
Query= curated2:Q58424 (524 letters) >NCBI__GCF_000425265.1:WP_051249709.1 Length = 326 Score = 233 bits (594), Expect = 8e-66 Identities = 122/309 (39%), Positives = 191/309 (61%), Gaps = 5/309 (1%) Query: 12 EDAIKILEEVGEVEV----ATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAEKLKVI 67 EDA+ L E ++E+ + ++ + ADVL+ + ++ +++++ + LK+I Sbjct: 18 EDALNKLREA-DLEIIDRRGQNIDTPGFMDDLCRADVLLNGNDLQINSELMDQMKSLKMI 76 Query: 68 GRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEW 127 G+ GVG+D +D+ AATE+ I V N+P + +VA+ T+G++L R IPQ + +++G++ Sbjct: 77 GKYGVGLDMVDIPAATERNIAVCNSPGCNCQAVADQTLGMILGLMRMIPQGDSHMRQGKY 136 Query: 128 DRKRFKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVELVDD 187 D FKG EL+ KTLG++G+G IG+ V RA F M I+GYDPY P E+A+++ +E ++ Sbjct: 137 DHTSFKGTELWKKTLGLVGVGAIGRAVAMRANGFKMRILGYDPYWPAELADALNIERIEK 196 Query: 188 INELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEG 247 E+ + D ++LH LT ++G +Q +MKK++I+VN ARG LI+E ALYEALK G Sbjct: 197 WEEMLPKVDVLSLHCNLTKDNAQMLGSDQFKMMKKSSIVVNAARGELINEDALYEALKSG 256 Query: 248 KIRAAALDVFEEEPPKDNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRGELA 307 +I A +D + EPP +PLLTLDNV+ PH A T E+ V +QI RG Sbjct: 257 EIAGAGIDAWTNEPPTGSPLLTLDNVLAMPHSAAFTVESFSNMDMQVTDQIIDFSRGIQP 316 Query: 308 ENVVNMPNI 316 VN NI Sbjct: 317 RPTVNNINI 325 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: 432 Number of extensions: 23 Number of successful extensions: 1 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: 326 Length adjustment: 31 Effective length of query: 493 Effective length of database: 295 Effective search space: 145435 Effective search space used: 145435 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 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