Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012536420.1 AFE_RS04205 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000021485.1:WP_012536420.1 Length = 527 Score = 197 bits (500), Expect = 1e-54 Identities = 119/320 (37%), Positives = 173/320 (54%), Gaps = 7/320 (2%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ + + VEI + G VEV + + +E LC I + IRS T + VL A Sbjct: 4 VLIADKMSARAVEIFHERGIAVEV-KTGLGKEALCAIIGQYDGLAIRSATNVDADVLAAA 62 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 +RL VG IG + +D+ ++G+ V N P+ NT + E AI+ ++ R + T+ Sbjct: 63 SRLKVVGRAGIGVDNVDIHAASKRGVIVMNTPYGNTVTTAEHAIALMMAAARMIPQATMS 122 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412 + G W KS E+ K LG+IG GNIG+ + A+ +GM V YD + + A Sbjct: 123 LKAGQWEKSRFQGVELYQKTLGVIGTGNIGSLVIARAQGLGMRVIAYDPYLSKIRAADLG 182 Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472 ++ +D LL D +++H +N+ E KMK GAILVN +RG +VD AL D Sbjct: 183 VELVEMDTLLARADFLTVHTPLTDATRNLFRAETFAKMKPGAILVNAARGCIVDEAALYD 242 Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532 AL+SGHL AA+DVF EP + D P L+ N I TPH+G ST EAQ N+A V + Sbjct: 243 ALKSGHLRAAALDVFCKEPVHGDNP----LLELDNFICTPHLGASTEEAQVNVAIQVAEQ 298 Query: 533 IIEYINSGNTFNSVNFPNIQ 552 I Y+ G N+VN P+++ Sbjct: 299 ISAYLLRGVVQNAVNLPSVK 318 Score = 26.2 bits (56), Expect = 0.004 Identities = 17/83 (20%), Positives = 45/83 (54%), Gaps = 6/83 (7%) Query: 550 NIQLPFLKDAHRLIHI-HQNAPGVLAKINQVLASYKINIVGQYLKTNEKIGYVIT--DID 606 ++++P D L++I +++ PG++ +I +L + INI +L + G ++ +D Sbjct: 446 DVEMPLAGD---LLYIQNRDEPGLIGRIGGLLGAAGINIAQFHLGREKPAGAALSFIAVD 502 Query: 607 KRYSNDVIDALKEIEGTIRFRIL 629 + + +++ + + G + R+L Sbjct: 503 QPLTEVLLEQVASLPGVLAARML 525 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: 601 Number of extensions: 31 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: 527 Length adjustment: 36 Effective length of query: 594 Effective length of database: 491 Effective search space: 291654 Effective search space used: 291654 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