Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_013683601.1 ARCVE_RS04565 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000194625.1:WP_013683601.1 Length = 375 Score = 287 bits (735), Expect = 3e-82 Identities = 160/385 (41%), Positives = 245/385 (63%), Gaps = 16/385 (4%) Query: 1 MKIDAVKKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTF 60 MK D LLMIPGP + ++ AM+ ++GHR K++S ++ ++ LK++F T++D + Sbjct: 1 MKFDG---LLMIPGPVHLHERIIRAMSRQMMGHRGKEFSEIMRYCVDGLKELFGTKHDVY 57 Query: 61 LITGSGTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEP 120 +I+GSGTA ++ AI++ ++ + G FG+R I Y EA + EWG + Sbjct: 58 IISGSGTAGLEAAIASF-SNVRRITCVDNGKFGDRLGRIASRYT-EADVVRFEWGKSIDL 115 Query: 121 EAVKEILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNV 180 +AV++ L + + A+ VHNETST NP +E+ ++ K Y+AL I+D ++S+GGD V + Sbjct: 116 DAVEKSLAEGSE--ALAFVHNETSTAMLNPAEELAKLAKKYNALVIMDGITSVGGDEVKM 173 Query: 181 DKFHIDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQ 240 DK+ ID+ + GSQKCL APPGLAA+ V+++AW+ ++K FYLDL AY+K + Q Sbjct: 174 DKWGIDVAIVGSQKCLGAPPGLAAVAVNDRAWDYY---NEKCPFYLDLAAYRKKLPD-MQ 229 Query: 241 TPYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERA---R 297 TPYTP+V L +AL AL ++ EEG+ENR++RH +++A R G++LFA+ Sbjct: 230 TPYTPAVPLFFALEEALRIIEEEGLENRIRRHRLMSRAVREWAIEAGLQLFAEPEEPSDY 289 Query: 298 SVTVTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLA 357 S TVT+ + PEG+ D RG L +Y I V+GGQ+HL GKIFRIG MG ++ V+ATLA Sbjct: 290 SNTVTAIRMPEGVTDKDLRGTLQKEYGITVSGGQEHLKGKIFRIGTMGNVCKRHVIATLA 349 Query: 358 CVELALKELGFEVKESGVEVAKEVL 382 V+ L + ++ + + A EVL Sbjct: 350 AVQDIL--MRYDACKPALHAAIEVL 372 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: 372 Number of extensions: 16 Number of successful extensions: 5 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: 375 Length adjustment: 30 Effective length of query: 355 Effective length of database: 345 Effective search space: 122475 Effective search space used: 122475 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