Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_012676496.1 PERMA_RS01695 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000021565.1:WP_012676496.1 Length = 381 Score = 268 bits (684), Expect = 2e-76 Identities = 146/381 (38%), Positives = 233/381 (61%), Gaps = 7/381 (1%) Query: 6 VKKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGS 65 +K+ L PGP +PP+V+ A+ +I HRT +++ + + E L+K+ TE D + S Sbjct: 3 IKERLFTPGPVPLPPQVIKALGQQIIHHRTPEFTQIFLEARENLQKLLKTERDVIMFASS 62 Query: 66 GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125 GT AM+ +++N ++GD+VL I G FG+R+ + Y+ + + ++EWG + E + + Sbjct: 63 GTGAMEASVANFFRKGDRVLIINAGKFGQRWKELASVYQLKIVDYEIEWGKTYDKERILQ 122 Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDY-DALYIVDTVSSLGGDYVNVDKFH 184 I+ ++ DIK + V H+ETST + +K +G++ K D L +VD ++S+G V ++ Sbjct: 123 IISEFPDIKGIFVQHSETSTTTYHDVKYLGDIAKKLDDCLLVVDGITSVGVYQVYPEELG 182 Query: 185 IDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQTPYT 244 ID+ VTGSQK L PPGL+ + SEKA E K+ D +Y D+L K + K QT YT Sbjct: 183 IDVLVTGSQKALMLPPGLSVLYFSEKAEERASKS-DMPRYYFDVLKEAK-KQSKGQTAYT 240 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 P++NL ALN +L L+L EG++N +RH +A+ATR ++ +G++L ++ + S T Sbjct: 241 PAINLIIALNESLKLILGEGLDNLEERHRIMAEATREAVKEIGLKLLSESPSNS--ATGV 298 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVELALK 364 P GI+ + R L K VAGGQ HL GKIFRI HMG +V+ +A +E+ALK Sbjct: 299 YSPAGIDADQLRKELL-KLGFRVAGGQDHLKGKIFRIAHMGYFDFMDVVQVIAGLEMALK 357 Query: 365 ELGFEVK-ESGVEVAKEVLLK 384 +G+E++ GV A+EV+L+ Sbjct: 358 RIGYEIEIGKGVRKAQEVILE 378 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: 390 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: 381 Length adjustment: 30 Effective length of query: 355 Effective length of database: 351 Effective search space: 124605 Effective search space used: 124605 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