Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_084276582.1 B8779_RS05635 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_900176045.1:WP_084276582.1 Length = 529 Score = 173 bits (438), Expect = 2e-47 Identities = 121/374 (32%), Positives = 205/374 (54%), Gaps = 25/374 (6%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEE--ELCEKIKNVSIIGIRSKTQITKKVLE 292 +++ +++H EI+ +E ++E V++A + L EKIK+ +I RS T + K++LE Sbjct: 6 IVVCDHLHKKAEEILAKE-QDIEYVNAADVPKGGPLYEKIKDADVIITRSSTPVDKELLE 64 Query: 293 NANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNL---H 349 +A L A+ +G + +D+E C +GI V N P +NT + VEL + ++ MR H Sbjct: 65 HAKNLKAIVRAGVGVDNVDMEECSRRGIIVMNVPTANTIAAVELTFAHMLSCMRAFPYAH 124 Query: 350 DKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERL 407 ++ LK+ + IW + A E++GKKLGIIG+GNIG+++ A M V YD I Sbjct: 125 NQ-LKLER-IWKREAWIGNELKGKKLGIIGFGNIGSRVGKRALAFEMEVITYDPYISPEK 182 Query: 408 ALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDV 467 A K + + CDII++H E N++++E+I KMK G IL+N +RG + + Sbjct: 183 ATNLGVKYTTDFNDILACDIITIHTPKTKETINMIDREEIAKMKDGVILINCARGGLYNE 242 Query: 468 PALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQ 527 AL + L+SG + A +DVF EP +++L+ N +TPH+G +T E+QE IA Sbjct: 243 DALYEGLKSGKIKFAGIDVFAKEPAT-----DNKLLELDNVTVTPHLGANTEESQEKIAI 297 Query: 528 FVPGKIIEYINSGNTFNSVNFP---NIQLPFLKDAHRLIHIHQNAPGVLAKINQ-VLASY 583 + +E + N++N P + PF+K + + Q + A++N+ S Sbjct: 298 GAATQALEAARGISYPNALNLPIKEDEMPPFVKP---YLELTQKMGFLAAQVNKGAYKSI 354 Query: 584 KI---NIVGQYLKT 594 K+ +G+Y+K+ Sbjct: 355 KVIAEGEIGEYIKS 368 Score = 31.6 bits (70), Expect = 9e-05 Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%) Query: 568 NAPGVLAKINQVLASYKINIVGQYL-KTNEKIGYVITDIDKRYSNDVIDALKEIEGTI 624 + PGV+ ++ +LA + INI L + N + + +D S DV+ L +++ + Sbjct: 465 DVPGVIGEVGMILAKHNINIADFRLGRDNHGLALAVIIVDDDVSKDVLKELADLKACL 522 Lambda K H 0.317 0.136 0.377 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: 767 Number of extensions: 44 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 630 Length of database: 529 Length adjustment: 36 Effective length of query: 594 Effective length of database: 493 Effective search space: 292842 Effective search space used: 292842 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: 53 (25.0 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