Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_012991918.1 THAL_RS04470 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000025605.1:WP_012991918.1 Length = 373 Score = 239 bits (611), Expect = 7e-68 Identities = 135/381 (35%), Positives = 219/381 (57%), Gaps = 14/381 (3%) Query: 6 VKKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLI-TG 64 +K+ L PGP +P V + +I HRT+++ + + K++ + +D F+ Sbjct: 1 MKERLFTPGPVELPDRVRTVLQQQIIHHRTEEFQQAFREVRDLFKRLLESPSDNFVFFAS 60 Query: 65 SGTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVK 124 SGT AM+ ++ N GDKVL + G FGER+ + + + I V WG+ A+PE VK Sbjct: 61 SGTGAMEASVLNFFSEGDKVLVVNGGKFGERWLLLAQHWGLSPIEYKVSWGEAADPEYVK 120 Query: 125 EILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFH 184 ++L+++ D + V + +ETSTG +P+KEIG++ K+ D L + D +++LG +N D+++ Sbjct: 121 DLLERHPDCRGVLIQISETSTGVYHPVKEIGQLCKERDVLLVADGITALGVYRINPDEWN 180 Query: 185 IDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQTPYT 244 ID+ V GSQK L PPGL+ + SE+A E ++ FY D + + ++K QT +T Sbjct: 181 IDVLVGGSQKALMLPPGLSMLWFSERAAERLRNR----AFYFD-IKRELSQQQKGQTAWT 235 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 P+++L AL +L ++LEEG+E +RH +A+ TR + MG+ELFAK A SVT Sbjct: 236 PAISLILALRESLSILLEEGMERVERRHAAVAEGTRRAAQVMGLELFAKRPAISVTALYH 295 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVELALK 364 + E I S R Y + AGGQ H GK+ RI HMG+ K+ L + +E+ L Sbjct: 296 EKAEEIRKSLLR------YGVRTAGGQDHWKGKLIRISHMGV-DPKDGLMLVGLLEVVLY 348 Query: 365 ELGFEVK-ESGVEVAKEVLLK 384 ++G+ V+ +V E L++ Sbjct: 349 KMGYSVRLGEATKVYSETLME 369 Lambda K H 0.316 0.135 0.379 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: 317 Number of extensions: 13 Number of successful extensions: 4 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: 385 Length of database: 373 Length adjustment: 30 Effective length of query: 355 Effective length of database: 343 Effective search space: 121765 Effective search space used: 121765 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: 50 (23.9 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