Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_075384713.1 BK574_RS09615 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_002019605.1:WP_075384713.1 Length = 394 Score = 279 bits (714), Expect = 9e-80 Identities = 148/382 (38%), Positives = 233/382 (60%), Gaps = 3/382 (0%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGS 65 +++LM PGP+ V P VL AM+ P++GH + ++ +T+E L+KV+ TEN T ++G+ Sbjct: 9 ERVLMGPGPSNVHPHVLRAMSTPLLGHLDPAFLTIMNETMELLRKVYQTENKLTIAMSGT 68 Query: 66 GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125 G+A M+ N+++ GDKV+ V G FG R ++ + I++ WG++ +P+ VKE Sbjct: 69 GSAGMETVFVNLVEPGDKVIVGVNGLFGTRMVDVAERCGATVIQIKAAWGEIIKPQDVKE 128 Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185 L+ + D K V VVH ETSTG R P++EI E+V +AL++ D V+SLGG +DK + Sbjct: 129 TLETHPDAKLVAVVHAETSTGVRQPLEEISEIVHTTNALFVCDMVTSLGGCPTEIDKLKV 188 Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEEKKQTPYT 244 D +G+QKCL+APPGLA +T+S +A EV+ KV +YLDL Y+ E++ +T Sbjct: 189 DAAYSGTQKCLSAPPGLAPVTMSNRAVEVMNNRKSKVQSWYLDLSMIVSYWGEERSYHHT 248 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 + + Y+L +L L++ EG+EN RH +A + GLEAMG++L K+ R +TS Sbjct: 249 APITMAYSLRESLRLIVNEGVENVFARHALYGEALQQGLEAMGLKLLVKKEHRLHQLTSV 308 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGI-CGEKEVLATLACVELAL 363 P+G++D+K R L KY++ V GG L GK++RIG MG + V L+ +E L Sbjct: 309 CIPQGVDDAKVRKRLLEKYDLEVGGGLGELKGKVWRIGLMGYNAKQANVTLMLSALEDIL 368 Query: 364 KELGFEVKESGVEVAKEVLLKE 385 +E G +++ + +LKE Sbjct: 369 QEEGVAIEKGAALLKANEVLKE 390 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: 354 Number of extensions: 9 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: 394 Length adjustment: 30 Effective length of query: 355 Effective length of database: 364 Effective search space: 129220 Effective search space used: 129220 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