Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_018945975.1 B1A74_RS01040 3-phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_001995255.1:WP_018945975.1 Length = 387 Score = 172 bits (436), Expect = 2e-47 Identities = 116/352 (32%), Positives = 181/352 (51%), Gaps = 34/352 (9%) Query: 297 LMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDK----- 351 ++AVG G N I ++ E+G+AVFNAP +N +V EL I+ ++ RNL Sbjct: 51 VLAVGRAGSGVNNIPVQDLTERGVAVFNAPGANANAVKELVIAGLLLGARNLVPAAGYVQ 110 Query: 352 ---------TLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD 402 T + QG K FE+ G++L ++G G IG +++ A +MGM V +D Sbjct: 111 SLDPDDSGFTAAVEQG---KKRFSGFELPGRRLAVLGLGAIGVKVANAARSMGMEVVGFD 167 Query: 403 --IVERLALGNATKID---SLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILV 457 I A A+ I+ S+D LE D +++HV +N++N E+I M GA+++ Sbjct: 168 PKITVESAWQMASDIERARSVDAALEGADAVTVHVPLTENTQNLVNAERIRSMNPGAMVL 227 Query: 458 NLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGS 517 N++R +VD A +AL GHL D FP L+ P I PH+G S Sbjct: 228 NMARDGIVDDAAAGEALNEGHLHAYVTD-FPV----------PGLLDHPRVITLPHLGAS 276 Query: 518 TLEAQENIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKIN 577 T E++EN A + ++ +Y+ +GN NSVN P + L K R+ I++N P +A+I+ Sbjct: 277 TTESEENCAVMIADQMRDYLENGNVVNSVNLPTLVLE-RKGQARIAVINRNLPDRVAQIS 335 Query: 578 QVLASYKINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRIL 629 V+ INI+ + I Y + D+D S +DAL I+G +R R+L Sbjct: 336 HVIGESDINILHLMNDSRGDIAYTMLDVDGHPSPTTLDALYRIDGVLRARVL 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: 522 Number of extensions: 26 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 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