Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_092482325.1 BM299_RS04760 hydroxyacid dehydrogenase
Query= curated2:Q58424 (524 letters) >NCBI__GCF_900115975.1:WP_092482325.1 Length = 330 Score = 270 bits (691), Expect = 5e-77 Identities = 144/322 (44%), Positives = 214/322 (66%), Gaps = 13/322 (4%) Query: 3 KILVTDPLHEDAIKILEEVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAE 62 K+L+T+ +HE+ + I+ E E+E+A +E +++ I DAD L+VRS +KVT +IE + Sbjct: 4 KVLLTEAIHEEGMNIIREAAELEIAADPGEETVIKAIADADALIVRS-SKVTSAIIEAGK 62 Query: 63 KLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASL 122 KLKVIGR G+G+DNID++AA + G+ VVN PDA+ +SVAE + ML + + + +L Sbjct: 63 KLKVIGRHGMGLDNIDLKAADQYGVAVVNTPDANVLSVAEHVLATMLYLCKRLKEVDNAL 122 Query: 123 KRGEWDRKR----------FKGIELYGKTLGVIGLGRIGQQVVKRA-KAFGMNIIGYDPY 171 + GE+DR + ELYGKTLG++G+G+I +++ + K F M + GYD Y Sbjct: 123 RTGEFDRPGSLPGLVTKLGYTTQELYGKTLGLVGVGKIARRIAEICTKGFDMQVCGYDAY 182 Query: 172 IPKEVAESMGVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCAR 231 + +V + GVE + E+ ++ADFI++HVPLTP TR +IG++Q+ LMK A ++N AR Sbjct: 183 LAPDVIQQAGVEPCGSLEEVFEKADFISVHVPLTPGTRGLIGKKQLDLMKPTAFLINSAR 242 Query: 232 GGLIDEKALYEALKEGKIRAAALDVFEEEPP-KDNPLLTLDNVIGTPHQGASTEEAQKAA 290 GG+++E LY+ALKE I AA+DVF +EPP K++PL TLDNV+ TPH A T+ A Sbjct: 243 GGVVNEDDLYQALKEKSIAGAAVDVFAQEPPGKNHPLFTLDNVVVTPHIAAMTDGALVRM 302 Query: 291 GTIVAEQIKKVLRGELAENVVN 312 VAE + VLRGE + +VN Sbjct: 303 ARDVAEGVVSVLRGERPKYLVN 324 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: 471 Number of extensions: 19 Number of successful extensions: 5 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: 330 Length adjustment: 31 Effective length of query: 493 Effective length of database: 299 Effective search space: 147407 Effective search space used: 147407 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