Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_077244352.1 B1A74_RS08315 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_001995255.1:WP_077244352.1 Length = 400 Score = 229 bits (584), Expect = 1e-64 Identities = 132/366 (36%), Positives = 210/366 (57%), Gaps = 5/366 (1%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGS 65 ++ LM PGP+ V P VL+AM+ P+IGH + ++E+ L+ F TEN T ++ Sbjct: 10 QRTLMGPGPSDVNPRVLSAMSRPIIGHLDPVFVGMMEEMKGLLQYAFQTENALTLPVSAP 69 Query: 66 GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125 G+A M+ N+++ GDKV+ + G FG R V+ G A+ ++ +WG+ P+ V + Sbjct: 70 GSAGMETCFVNLVEPGDKVIVCINGVFGTRMKENVERCGGTAVVVEDDWGNPVSPDKVAD 129 Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185 L D K + VH ETSTGAR+ ++ + + +++D L IVD+V+ L G + VD + + Sbjct: 130 ALKGNPDAKILAFVHAETSTGARSDVETLCRLAREHDCLTIVDSVTGLAGSPLYVDDWGV 189 Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYY--EEKKQTP 242 D +G+QKCL+ PGL+ ++ S++A + I+ KV ++LDL Y+ K+ Sbjct: 190 DAIYSGTQKCLSCTPGLSPVSFSQRAVDRIQARSHKVQSWFLDLNLVMGYWGGGSKRAYH 249 Query: 243 YTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVT 302 +T +N YAL+ +L ++ EEG+EN RH R A RAGLEAMG+E E R + Sbjct: 250 HTAPINALYALHESLVILQEEGLENSWARHCRHHDALRAGLEAMGLEFLVAEEHRLPQLN 309 Query: 303 SAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGI-CGEKEVLATLACVEL 361 S PEG++++ RG L +Y + + G AGK++RIG MG E+ VL L+ +E Sbjct: 310 SVYVPEGVDEAAVRGELLERYGLEIGAGLGPYAGKVWRIGLMGYGANERNVLTCLSALEA 369 Query: 362 ALKELG 367 L + G Sbjct: 370 VLADRG 375 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: 356 Number of extensions: 19 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: 400 Length adjustment: 31 Effective length of query: 354 Effective length of database: 369 Effective search space: 130626 Effective search space used: 130626 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