Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_077278461.1 B1C78_RS07080 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_002000365.1:WP_077278461.1 Length = 387 Score = 184 bits (467), Expect = 6e-51 Identities = 128/414 (30%), Positives = 212/414 (51%), Gaps = 49/414 (11%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 +L L N+ G++ ++ Y + SS MS + I +RS K+ + Sbjct: 4 ILTLNNISVKGLDCFPRDHYEI---SSEMSHPDA---------ILVRSHNMRDMKIPDEV 51 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNL---HDK 351 + GA G N I +E E+G+AVFNAP +N +V EL ++ ++ RNL +D Sbjct: 52 KAIGRAGA---GVNNIPVEEMSERGVAVFNAPGANANAVKELVVAGMLIAARNLFGAYDY 108 Query: 352 T---------LKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD 402 T L+ H K G FE+ G+ LG+IG G IG Q++ A +GM+V YD Sbjct: 109 TRTLDTASPDLERHVEAGKKKFVG-FELPGRVLGVIGLGAIGVQVANAARALGMHVIGYD 167 Query: 403 IVERLALGNATKIDS-------LDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAI 455 ++ + A ++ S +DELL D ++ HV ++++N +++ +MK GA+ Sbjct: 168 --PKITVHRAWQLSSDVQHAATVDELLSKADFLTFHVPLVEATRSMINADRLQRMKPGAV 225 Query: 456 LVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIG 515 ++N +R +VD A AL+ G L A V FP+ +L+ P ++ PH+G Sbjct: 226 ILNFARAGIVDDEAACVALDEGRLH-AYVSDFPSP----------QLMAHPRVVVLPHLG 274 Query: 516 GSTLEAQENIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAK 575 ST EA+EN A V ++ EY+ +GN NSVN P++ LP D HR+ +++N P ++ + Sbjct: 275 ASTREAEENCAVIVAEELREYLENGNVRNSVNLPDLFLPRAGD-HRVTVVNRNLPDMVGQ 333 Query: 576 INQVLASYKINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRIL 629 ++ +L +NIV ++ I Y I D++ + D L I+G +R R+L Sbjct: 334 MSHILGKANLNIVHMVNESRGAIAYSIMDVEGEITEDAARELDAIDGVLRVRVL 387 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: 499 Number of extensions: 31 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: 630 Length of database: 387 Length adjustment: 34 Effective length of query: 596 Effective length of database: 353 Effective search space: 210388 Effective search space used: 210388 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: 52 (24.6 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