Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_017896025.1 PN53_RS14945 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000816635.1:WP_017896025.1 Length = 392 Score = 232 bits (592), Expect = 1e-65 Identities = 131/366 (35%), Positives = 222/366 (60%), Gaps = 13/366 (3%) Query: 10 LMIPGPTMVPPEVLNAMAL----PVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGS 65 +M PGPT V V A ++ P + ++ D+ ++T +L KV T+N+ ++ G Sbjct: 6 IMTPGPTEVSENVRIARSIRCTNPDLDNKFYDF---YKETCNRLGKVLNTKNEVRVLCGE 62 Query: 66 GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125 G ++ A +++ ++GD+VL I G FGE FA+ ++ Y G+ + + E +KE Sbjct: 63 GILGLEAACASLTEKGDRVLVIDNGIFGEGFADFIRLYCGKVVFFKADRKHAINIEDLKE 122 Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185 LDK +D K TVVH +T +G N I +I ++K Y L +VD+V+++GG+ + VDK++I Sbjct: 123 FLDKDNDFKYATVVHCDTPSGVLNDISKICPLLKKYGILTVVDSVAAMGGENLEVDKWNI 182 Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVG-FYLDLLAYKKYYEEKKQTPYT 244 DI + GSQKC++APPGL +++S+ A+ ++ +G FY +LLA+K YYE+ K PYT Sbjct: 183 DIVIGGSQKCISAPPGLTIVSISKDAFSSMENRKSPIGSFYCNLLAWKNYYED-KWFPYT 241 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 P V+ Y L A+D +L++ + + RH+ +A +TR + G++L+ E S TVT Sbjct: 242 PPVSDIYGLREAVDNILKD--KEILNRHKNIASSTRYAVRKAGLDLYT-EDGYSSTVTVI 298 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGE-KEVLATLACVELAL 363 + P+GI+D+K R + Y++++AG +L G++ RIGHMG +V TL ++ +L Sbjct: 299 QVPDGIQDNKLREYMEENYDVMIAGSFGYLKGEVIRIGHMGENARYDKVSYTLYALQQSL 358 Query: 364 KELGFE 369 ++ GF+ Sbjct: 359 EKFGFK 364 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: 391 Number of extensions: 22 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: 392 Length adjustment: 30 Effective length of query: 355 Effective length of database: 362 Effective search space: 128510 Effective search space used: 128510 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 Jul 25 2024. The underlying query database was built on Jul 25 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