Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_011321708.1 AVA_RS25680 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000204075.1:WP_011321708.1 Length = 381 Score = 213 bits (541), Expect = 9e-60 Identities = 121/351 (34%), Positives = 202/351 (57%), Gaps = 3/351 (0%) Query: 3 IDAVKKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFL 61 ++ +LL+ PGP+ P VL AM + +GH + L+++ L+ V+ TEN T Sbjct: 18 LEVPSRLLLGPGPSNAHPAVLQAMNVSPVGHLDPAFLALMDEIQSLLRYVWQTENPLTIA 77 Query: 62 ITGSGTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPE 121 ++G+GTAAM+ I+N ++ GD VL V G FG R ++ Y + + WG + E Sbjct: 78 VSGTGTAAMEATIANAVEPGDVVLIGVAGYFGNRLVDMAGRYGADVRTISKPWGQVFSLE 137 Query: 122 AVKEILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVD 181 ++ L+ + + +VH ETSTGAR P++ +GE+ +++ L +VDTV+SLGG + +D Sbjct: 138 ELRTALEN-NRPAILALVHAETSTGARQPLEGVGELCREFGTLLLVDTVTSLGGVPIFLD 196 Query: 182 KFHIDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVG-FYLDLLAYKKYYEEKKQ 240 + +D+ + SQK L PG + T+S +A E +++ KV +YLD+ KY+ ++ Sbjct: 197 GWGVDLAYSCSQKGLGCSPGASPFTMSSRAIEKLQRRRTKVANWYLDMNLLGKYWGSERV 256 Query: 241 TPYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVT 300 +T +NL YAL AL L+ +EG+ N +RH++ + LE +G+ L ++ R T Sbjct: 257 YHHTAPINLYYALREALRLIAQEGLANCWQRHQKNVEYLWERLEDIGLSLHVEKEYRLPT 316 Query: 301 VTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKE 351 +T+ + P+G++ L N++NI V GG LAGK++R+G MG KE Sbjct: 317 LTTVRIPDGVDGKAVARQLLNEHNIEVGGGLGELAGKVWRVGLMGFNSRKE 367 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: 292 Number of extensions: 17 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