Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012042059.1 BBTA_RS08500 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000015165.1:WP_012042059.1 Length = 529 Score = 198 bits (504), Expect = 4e-55 Identities = 115/324 (35%), Positives = 180/324 (55%), Gaps = 8/324 (2%) Query: 231 SRINVLLLENVHPIGVEIMKQEGYNVEVVSS-AMSEEELCEKIKNVSIIGIRSKTQITKK 289 S+ VL+ + + P V+I K G V+ + +++L + I + + IRS T+ T K Sbjct: 2 SKPKVLISDALSPAAVQIFKDRGVEVDFQPNLGKDKDKLADIIGDYDGLAIRSATKATAK 61 Query: 290 VLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLH 349 ++E A RL +G IG + +++ KGI V N PF N+ + E AI+ ++ L R + Sbjct: 62 IIERAKRLKVIGRAGIGVDNVEIPAATAKGIIVMNTPFGNSITTAEHAITMMLSLAREIP 121 Query: 350 DKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERL 407 G W K+ E+ GK LG+IG GNIG+ + A+ + M V +D + E Sbjct: 122 QADASTQAGKWEKNRFMGVEITGKTLGVIGCGNIGSIVCDRAQGLRMKVIGFDPFLTEER 181 Query: 408 ALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDV 467 A + LDELL+ D I+LH + +NI++ I KMK+G ++N +RG ++D Sbjct: 182 ARDLGVEKVELDELLKRADFITLHTPLTDKTRNIIDAAAIAKMKQGVRIINCARGGLIDE 241 Query: 468 PALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQ 527 AL AL S H+AGAA+DVF EP + + L G P+ I TPH+G ST EAQEN+A Sbjct: 242 QALLAALNSKHVAGAALDVFAEEPATS-----NPLFGHPSVICTPHLGASTTEAQENVAL 296 Query: 528 FVPGKIIEYINSGNTFNSVNFPNI 551 + ++ +Y+ +G N++NFP+I Sbjct: 297 QIAEQMSDYLLTGAISNAINFPSI 320 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: 653 Number of extensions: 34 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 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 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