Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_012104121.1 CKL_RS18530 aminotransferase class V-fold PLP-dependent enzyme
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000016505.1:WP_012104121.1 Length = 382 Score = 213 bits (542), Expect = 7e-60 Identities = 132/369 (35%), Positives = 215/369 (58%), Gaps = 15/369 (4%) Query: 10 LMIPGPTMVPPEVLNAMAL----PVIGHRTKD-YSNLLEDTIEKLKKVFITENDTFLITG 64 ++ PGPT + V AM++ P + + D Y N ED LK T+N T ++ G Sbjct: 6 VLTPGPTEIRENVRLAMSMRTTNPDLDVKFYDFYRNACEDIGRLLK----TKNQTIILGG 61 Query: 65 SGTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVK 124 G ++ A +++ + GD+VL I G FGE FA++VK Y G+ + + Sbjct: 62 EGMLGLEAACASLTEEGDRVLVIDNGVFGEGFADLVKLYGGKVEFFKGNRRREIDIIELA 121 Query: 125 EILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFH 184 + LDK + K T+VH +T +G N + +I ++K L +VD+VS++GG+ + VD + Sbjct: 122 KFLDKDSNFKYATIVHCDTPSGVLNDVSKICPLLKKRGVLTLVDSVSAMGGEKLEVDNWD 181 Query: 185 IDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEEKKQTPY 243 IDI + GSQKC++APPGL I++SE+A +K + + FY +LL ++KYY E K PY Sbjct: 182 IDIVIGGSQKCISAPPGLTLISMSEEALLAMKIRKEPIRSFYCNLLIWEKYY-ENKWFPY 240 Query: 244 TPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTS 303 TP ++ L VALD +LE+ +N ++RH +A++ R + G+ L+ E+ S TVT Sbjct: 241 TPPISNIIGLKVALDNILED--KNILERHRIIAESLRKTIIEAGLNLYV-EKGYSNTVTV 297 Query: 304 AKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLA-TLACVELA 362 + P+GIE+ + R + +NI++AG +L K+ RIGHMG K++++ +L ++ A Sbjct: 298 IEVPKGIEEKQLREFMLINFNIMIAGSFGYLKNKVIRIGHMGENARKDLISYSLYALQEA 357 Query: 363 LKELGFEVK 371 LK +GF+ K Sbjct: 358 LKHMGFQCK 366 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: 367 Number of extensions: 16 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: 382 Length adjustment: 30 Effective length of query: 355 Effective length of database: 352 Effective search space: 124960 Effective search space used: 124960 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