Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_013075073.1 BTUS_RS05245 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000092905.1:WP_013075073.1 Length = 394 Score = 269 bits (687), Expect = 1e-76 Identities = 145/372 (38%), Positives = 232/372 (62%), Gaps = 4/372 (1%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGS 65 +++L+ PGP+ PEVL AMA P++GH + + +T+++L++VF T T ++G+ Sbjct: 8 QRILLGPGPSDCHPEVLKAMATPLVGHLDPVFLEQMNETMQRLREVFQTRYPLTLAMSGT 67 Query: 66 GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125 G+A M+ N ++ GD+V+ + G FGER ++ E I++ WG +P ++E Sbjct: 68 GSAGMETVFVNALEPGDRVVIGICGAFGERMVDVASRTGAEVIQVRAPWGRTVDPGQIQE 127 Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185 L + +KAV VVH ETSTG P++EIG + +D+ AL++VD V+SLGG V V++ I Sbjct: 128 ALKNHPGVKAVAVVHAETSTGVLQPLEEIGRLARDHGALFLVDAVTSLGGVPVPVEEAAI 187 Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEEKKQTPYT 244 D C +G+QKCL+APPGL+ T S K E +++ KV +YLDL ++Y+ ++ +T Sbjct: 188 DACYSGTQKCLSAPPGLSPATFSPKFEEALERRKRKVQSWYLDLTMVRQYWGSERFYHHT 247 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 + + YAL+ AL L+LEEG+E+ +RH +A +AGLEAMG++L+A R +TS Sbjct: 248 APITMMYALHEALGLLLEEGLESVFRRHWVNGRALQAGLEAMGLQLYADAGHRLPQLTSV 307 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICG-EKEVLATLACVELAL 363 PEG+ED+ R L N+Y I + GG + G+++RIG +G + VL L+ +E L Sbjct: 308 WIPEGVEDTLVRNRLLNEYGIEIGGGLGEVKGRVWRIGLLGHSSRRRNVLLLLSALEQIL 367 Query: 364 KELGFEVKESGV 375 + +G+ V ESG+ Sbjct: 368 RSVGYSV-ESGI 378 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: 340 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: 394 Length adjustment: 30 Effective length of query: 355 Effective length of database: 364 Effective search space: 129220 Effective search space used: 129220 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