Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_012969776.1 ALVIN_RS02730 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000025485.1:WP_012969776.1 Length = 395 Score = 222 bits (566), Expect = 1e-62 Identities = 130/383 (33%), Positives = 208/383 (54%), Gaps = 5/383 (1%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 + LM PGP V P VL A+A P IGH + ++++ + L+ F T+N T ++ G Sbjct: 11 RTLMGPGPADVHPRVLAALARPTIGHLDPAFVGMMDEVKDLLRTAFRTQNALTMPVSAPG 70 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 +A M+ N+++ GD+V+ + G FG R V+ G I + WG +P+ V + Sbjct: 71 SAGMETCFVNLVEPGDEVVVCINGVFGGRMKENVERAGGVPIVVQGTWGRAVDPDQVADT 130 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 L ++ + + + V ETSTGA++ + + E+ + +D L IVD V++LGG + VD + +D Sbjct: 131 LARHPNARLLAFVQAETSTGAQSDARALAEIARRHDCLTIVDAVTALGGSPLEVDAWGLD 190 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYY--EEKKQTPY 243 +GSQKCL+ PGLA +T +E+A + I+ KV ++LDL Y+ E+K+ + Sbjct: 191 AVYSGSQKCLSCVPGLAPVTFNERALDKIRARQTKVQSWFLDLNLVMGYWSGEQKRSYHH 250 Query: 244 TPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTS 303 T VN YAL+ +L ++ EEG+E KRH A RAGLE +G+EL E R + S Sbjct: 251 TAPVNALYALHESLVMLAEEGVEAAWKRHAHHHLALRAGLETLGLELIVPESERLPQLNS 310 Query: 304 AKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGE-KEVLATLACVELA 362 P GI+++ R L ++YN+ + G LAGK++RIG MG +L L + Sbjct: 311 VAVPAGIDEAALRARLLSRYNLELGAGLGDLAGKVWRIGLMGYSSRPANILLCLGAMASE 370 Query: 363 LKELGFEVKESGVEVAKEVLLKE 385 L +G+ A +L + Sbjct: 371 LDTMGYRADAGAAIAAARAVLDQ 393 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: 332 Number of extensions: 10 Number of successful extensions: 3 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: 395 Length adjustment: 31 Effective length of query: 354 Effective length of database: 364 Effective search space: 128856 Effective search space used: 128856 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