Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_048061314.1 MTH_RS07670 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000008645.1:WP_048061314.1 Length = 385 Score = 413 bits (1062), Expect = e-120 Identities = 204/371 (54%), Positives = 276/371 (74%), Gaps = 2/371 (0%) Query: 9 LLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSGTA 68 LLMIPGPT V VL AM+ ++ HR+ + +L +T E + VF T N ++L+TGSGTA Sbjct: 5 LLMIPGPTRVAQRVLKAMSENIVNHRSALFGRILTETTEMMSDVFRTSNKSYLLTGSGTA 64 Query: 69 AMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEILD 128 AM+ A++NII+ GDK+LN+V G FG+RFA IV+A+ GE+I +DVEWG P+ + L+ Sbjct: 65 AMEAAVANIIEPGDKILNVVGGKFGQRFAQIVEAFGGESITIDVEWGKAVNPDDIGYTLE 124 Query: 129 KYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHIDIC 188 + DDIKAVTVVHNETSTG NPI+EIG+++ DYDALYIVDTVSSLGGD V+V+ + IDIC Sbjct: 125 ENDDIKAVTVVHNETSTGVANPIREIGKIMDDYDALYIVDTVSSLGGDEVDVESYGIDIC 184 Query: 189 VTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYE-EKKQTPYTPSV 247 VTGSQKCLAAPPG+AAIT+S AW VI+ D+ +YL+L Y+K + E +TPYTP+V Sbjct: 185 VTGSQKCLAAPPGMAAITLSNDAWRVIEAVDNPRTYYLNLKKYRKSGDAEPPETPYTPAV 244 Query: 248 NLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAKYP 307 +L YA++ AL +++EEG+ NR+KRH+ A+ATR ++A+ +ELF E S TVT+ P Sbjct: 245 SLIYAMHEALKVIMEEGLSNRIKRHKIAAEATRNAVKALDLELFPDEAVSSTTVTAVNLP 304 Query: 308 EGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVELALKELG 367 EG+ D + RG + NKY++ +AGGQ HL G+IFRIGHMG +E++ T + +E+ L+ELG Sbjct: 305 EGVTDGELRGTMRNKYHVELAGGQDHLKGRIFRIGHMGNITHRELITTFSALEMTLRELG 364 Query: 368 FEVKESGVEVA 378 FEV E G VA Sbjct: 365 FEV-EMGEAVA 374 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: 437 Number of extensions: 17 Number of successful extensions: 2 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: 385 Length adjustment: 30 Effective length of query: 355 Effective length of database: 355 Effective search space: 126025 Effective search space used: 126025 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 09 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