Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_041101095.1 SUTH_RS17520 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000828635.1:WP_041101095.1 Length = 414 Score = 218 bits (556), Expect = 2e-61 Identities = 132/375 (35%), Positives = 211/375 (56%), Gaps = 4/375 (1%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 + LM PGP+ + P + A+ PVIG+ + ++E+ + L+ + T+N TF ++G G Sbjct: 18 RTLMGPGPSEMHPRTIAALGQPVIGYLDPIFVGMMEELKDLLRYTYQTKNPLTFPVSGPG 77 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 + M+ N+++RGDKV+ G FG R V+ G + ++ WG+ +P+ + + Sbjct: 78 SVGMETCFVNLVERGDKVIVCRNGVFGGRMIENVERAGGVCVVVEDTWGEPVDPQKLADA 137 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 L + D K V VH ETSTGA++ K + + K AL IVD V+SLGG V D++ D Sbjct: 138 LKAHPDTKIVAFVHAETSTGAQSDAKTLIALAKQAGALSIVDAVTSLGGTPVLTDEWGAD 197 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEEKKQT-PYT 244 + SQKCL+ PGL+ ++ SE A +K KV +++DL Y+ E ++T +T Sbjct: 198 AIYSASQKCLSCTPGLSPVSFSEAAIARVKARKSKVQSWFMDLNLVMAYWGETQRTYHHT 257 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 N YAL+ AL L+ EEG+E+ RH+R A +AGLEAMG++ +E AR + + Sbjct: 258 APGNSLYALHEALLLLREEGLEHAWARHQRHHLAIKAGLEAMGLKFVVREGARLPQMNAV 317 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGI-CGEKEVLATLACVELAL 363 PEGI +++ R L ++N+ + G LAGKI+R G MG C + V+ +L+ + L Sbjct: 318 HVPEGIAEAEVRKRLLAEFNLEIGAGLGPLAGKIWRFGLMGYSCKAENVMLSLSALGSVL 377 Query: 364 KELGFEVKESGVEVA 378 ++G V+ E A Sbjct: 378 SDMGCAVEVGQAEAA 392 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: 325 Number of extensions: 18 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: 414 Length adjustment: 31 Effective length of query: 354 Effective length of database: 383 Effective search space: 135582 Effective search space used: 135582 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