Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_043747187.1 AMB_RS22510 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000009985.1:WP_043747187.1 Length = 390 Score = 216 bits (551), Expect = 7e-61 Identities = 130/363 (35%), Positives = 204/363 (56%), Gaps = 5/363 (1%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 ++LM PGP+ V P VL A A P IGH + ++++ L+ F ++N+ TF ++G G Sbjct: 11 RILMGPGPSDVHPRVLAAQARPTIGHLDPAFVGMMDELKGLLQAAFRSDNEMTFAVSGPG 70 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 +A M+ N+I+ GD V+ V G FG R V+ A+ ++ WG +P V+ Sbjct: 71 SAGMEACFVNLIEPGDTVVVCVNGVFGGRMKENVERCGARAVVVEDAWGTPVDPAKVEAA 130 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 L ++KA+ VH ETSTG + + + + AL IVDTV+SLGG V VD++ D Sbjct: 131 LKANANVKALAFVHAETSTGVESDAGALCALAHAHGALAIVDTVTSLGGIPVLVDQWGAD 190 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYY--EEKKQTPY 243 +GSQKCL+APPGL+ +T S +A + +K KV ++LDL Y+ K+ + Sbjct: 191 AVYSGSQKCLSAPPGLSPVTFSSRAVQALKSRKTKVQSWFLDLTLLTAYWGGGAKRTYHH 250 Query: 244 TPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTS 303 T VN Y L+ +L ++ EEG++ RH + +A +AGLEAMG+ L E++R + + Sbjct: 251 TAPVNALYGLHESLVMLHEEGLDAAWSRHRAMHEALKAGLEAMGLGLLVAEQSRLPQLNA 310 Query: 304 AKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG-ICGEKEVLATLACVELA 362 PEG++++ R L ++ + + G LAGK++RIG MG + V+A L +E Sbjct: 311 VTVPEGVDEAAVRAQLLARFGLEIGAGLGALAGKVWRIGLMGQSATPRHVMACLTALESV 370 Query: 363 LKE 365 L E Sbjct: 371 LGE 373 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: 308 Number of extensions: 8 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: 390 Length adjustment: 30 Effective length of query: 355 Effective length of database: 360 Effective search space: 127800 Effective search space used: 127800 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 09 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