Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_085218338.1 B9N75_RS08140 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_900177405.1:WP_085218338.1 Length = 525 Score = 195 bits (495), Expect = 5e-54 Identities = 124/384 (32%), Positives = 197/384 (51%), Gaps = 11/384 (2%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ + + P EI ++ G V+ +S++EL I + IRS T++T VLE A Sbjct: 4 VLISDQMDPKAAEIFRERGLEVDE-RPGLSKDELKAIIGGYDGLAIRSATKVTADVLEAA 62 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 L VG IG + +D+ KG+ V N PF N+ + E AI+ + L R L + + Sbjct: 63 PNLKVVGRAGIGVDNVDIPAASAKGVVVMNTPFGNSITTAEHAIALMFALARQLPEADVS 122 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412 G W K+ E+ K LG+IG GNIG+ ++ A + M V YD + AL Sbjct: 123 TQAGKWEKNRFMGVELTAKTLGLIGAGNIGSIVADRALGLRMRVIAYDPFLTPERALQLG 182 Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472 + LD+LL D I+LH + + IL+ E + K KKG ++N +RG ++D AL+ Sbjct: 183 IEKVELDDLLARADFITLHTPLTDQTRGILSAENLAKTKKGVRIINCARGGLIDEAALKA 242 Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532 AL+SGH+AGAA+DVF EP +S L G P + TPH+G ST EAQ N+A V + Sbjct: 243 ALDSGHVAGAALDVFVEEPAK-----QSALFGTPGFVATPHLGASTTEAQVNVAIQVAEQ 297 Query: 533 IIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKI-NQVLASYKINIVGQY 591 I +++ +G N++N P++ + + + ++ ++ Q + I + G Sbjct: 298 IADFLTTGGVTNALNVPSLSAEEAPKLRPYMQLAEKLGSLVGQLEGQRMTGVAIEVEGAA 357 Query: 592 LKTNEK--IGYVITDIDKRYSNDV 613 N+K V+ + + YS+ V Sbjct: 358 ASLNQKPITAAVLAGLMQVYSDTV 381 Score = 28.5 bits (62), Expect = 8e-04 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 6/76 (7%) Query: 558 DAHRLIHIHQNAPGVLAKINQVLASYKINI----VGQYLKTNEKIGYVITDIDKRYSNDV 613 D + ++++APG + ++ L +NI +G++ E + V +D Sbjct: 450 DGEMIYIVNEDAPGFIGRLGTALGEAGVNIGTFNLGRHTAGGEAVALV--SVDSHIDGAT 507 Query: 614 IDALKEIEGTIRFRIL 629 + ALK + G R + L Sbjct: 508 VAALKALPGVKRVKPL 523 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: 626 Number of extensions: 26 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: 2 Length of query: 630 Length of database: 525 Length adjustment: 36 Effective length of query: 594 Effective length of database: 489 Effective search space: 290466 Effective search space used: 290466 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 Jul 26 2024. The underlying query database was built on Jul 25 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