Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_012115794.1 XAUT_RS19355 phosphoglycerate dehydrogenase
Query= BRENDA::C3SVM7 (410 letters) >NCBI__GCF_000017645.1:WP_012115794.1 Length = 429 Score = 466 bits (1200), Expect = e-136 Identities = 240/408 (58%), Positives = 300/408 (73%), Gaps = 1/408 (0%) Query: 4 VSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRT 63 +SL KDKIK LL+EGV+ A+E L AGYTN+ ALD + LKE+I+ H +G+RSRT Sbjct: 18 LSLSKDKIKVLLLEGVNDSAVELLTNAGYTNLTRLPKALDGDALKEAIKGVHILGIRSRT 77 Query: 64 HLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLL 123 +T DV+ AA++L+AIGCF +GTNQVDLDA+ G+PVFNAPFSNTRSVAELVIGE+++L Sbjct: 78 QITPDVLEAADRLIAIGCFSVGTNQVDLDASRISGVPVFNAPFSNTRSVAELVIGEIVML 137 Query: 124 LRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIE 183 LR +P + AH G W+K A S E RGK LGI+GYG+IG+QL ILAE++G+ V FYD Sbjct: 138 LRRIPTRSHAAHEGRWDKSATNSVEVRGKTLGIVGYGNIGSQLSILAEAMGLKVIFYDHT 197 Query: 184 NKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTV 243 +KL G A V L+ LL SD+VSLHVPE +T M+G EI+ MKPG+ LIN SRGTV Sbjct: 198 DKLRHGQAEPVSTLNALLAQSDIVSLHVPETAATHGMIGRAEIATMKPGAYLINNSRGTV 257 Query: 244 VDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQEN 303 VD+ AL +AL + HL GAA+DVFP EP +N++ F SPL DNV+LTPHIGGST+EAQE Sbjct: 258 VDLDALAEALKAGHLRGAAVDVFPVEPGSNAERFVSPLQGLDNVILTPHIGGSTEEAQER 317 Query: 304 IGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLH-GGRRLMHIHENRPGVLTALNKIFAEQG 362 IG EVA KL+ YSD GST+ AVNFPEV LP G R + IH N PG+L LN++ A Sbjct: 318 IGAEVARKLVDYSDTGSTMGAVNFPEVQLPARPTGTRFIQIHRNLPGMLGRLNEVLARHS 377 Query: 363 VNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410 VNIAAQYL+T A +GYVV+D +A ++ L ++ I GTIRARLLY Sbjct: 378 VNIAAQYLETYADVGYVVLDADASTADSQSVLADIREIEGTIRARLLY 425 Lambda K H 0.318 0.135 0.383 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: 450 Number of extensions: 13 Number of successful extensions: 2 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: 410 Length of database: 429 Length adjustment: 32 Effective length of query: 378 Effective length of database: 397 Effective search space: 150066 Effective search space used: 150066 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 (21.7 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