Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_026090172.1 C792_RS0101225 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000330705.1:WP_026090172.1 Length = 382 Score = 262 bits (670), Expect = 1e-74 Identities = 147/361 (40%), Positives = 218/361 (60%), Gaps = 5/361 (1%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSG 66 +KLL+ PGPT +PPEV + MA +IGHR+ D++ L+E+ LK + T+N +++ SG Sbjct: 3 QKLLLTPGPTPIPPEVSSRMAEGMIGHRSNDFNKLMENIQPGLKAILGTKNPVAILSSSG 62 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 T+A++ A+ N+++ + ++ IV+G+FG+RF NI K Y E DVEWG A+P KE Sbjct: 63 TSALETAMVNLVRPDESIVIIVSGSFGDRFRNIAKTYPFEVHVYDVEWGQAADPGRFKEF 122 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDY--DALYIVDTVSSLGGDYVNVDKFH 184 LD +++KAV ETST +P+ E+GE VK Y + L+IVD VS +GG ++++ + Sbjct: 123 LDTKENVKAVFSQSCETSTAVIHPLNELGEAVKSYSSETLFIVDGVSIVGGMTFDMEQDN 182 Query: 185 IDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQTPYT 244 ID VTGSQK L PPGLA + +++ A + N D FYLD+ Y K EE TP+T Sbjct: 183 IDCLVTGSQKALMLPPGLAFVAMNDTARQKASDN-DLPRFYLDINRYFKALEE-HSTPFT 240 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 P+V+L L L+ EEGIEN +RH + RAGL A+ + + + S TVT+ Sbjct: 241 PAVSLIQGLEKVLETYREEGIENVFERHRNMRDMLRAGLRALDLTMLVADEHASPTVTAF 300 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVELALK 364 + E E + L +++ I +AGGQK L GKI RIGHMG +++ L +E L Sbjct: 301 QSSED-ELKVIKNKLKSEHQITIAGGQKDLKGKILRIGHMGYMFPHDMIRVLTAIEAILT 359 Query: 365 E 365 + Sbjct: 360 D 360 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: 318 Number of extensions: 12 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: 382 Length adjustment: 30 Effective length of query: 355 Effective length of database: 352 Effective search space: 124960 Effective search space used: 124960 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 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