Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_084274752.1 B8779_RS01105 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_900176045.1:WP_084274752.1 Length = 369 Score = 204 bits (519), Expect = 3e-57 Identities = 133/381 (34%), Positives = 206/381 (54%), Gaps = 18/381 (4%) Query: 9 LLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSGTA 68 LL PGPT VP + MALP I HRT +++ + ++T E L + + D ++ +GT Sbjct: 2 LLFTPGPTPVPERIRQVMALPTIHHRTPEFTKIFKETRELLLDL-LKMQDAVMLASTGTG 60 Query: 69 AMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEILD 128 AM+ ++N+ + K L + G FGERF I KA+ E + L W A+ + V + L Sbjct: 61 AMEACVTNLCHK--KALVVNAGKFGERFVKIAKAFGKEVVELTYPWDTAAKIDDVVQALK 118 Query: 129 KYDDIKAVTVVHNETSTGARNPIKEIGEVVKDY--DALYIVDTVSSLGGDYVNVDKFHID 186 ++ DI A + E+S G R+P++EI +K + D I D ++++G + +N +ID Sbjct: 119 EHPDIDAFCIQICESSGGLRHPVEEIAAAIKAHNPDVSVIADGITAVGVEPINTT--NID 176 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQTPYTPS 246 +TGSQK L PPGLA I +S A I K + GFY +L + K E T YT + Sbjct: 177 ALITGSQKALMLPPGLAMIGLSLHALGKIGKGE---GFYFNLASELKKQRE-GTTAYTAA 232 Query: 247 VNLTYALNVALDLVLEE-GIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAK 305 L L L ++L+E G++ +R A ATR LEA+G+ ++ ++ A ++T A Sbjct: 233 TTLVIGLREILHILLKEIGLDEVYDHTDRRATATRVALEALGLAIYPQKPANAMT---AI 289 Query: 306 YPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVELALKE 365 Y E ED R +L N+Y + VAGGQ+ L G++FRI HMG+ E + VE A+ + Sbjct: 290 YDEQAED--IRKLLKNRYGVNVAGGQEDLKGRLFRINHMGLIEPNEAAWVVNAVEKAMAD 347 Query: 366 LG-FEVKESGVEVAKEVLLKE 385 LG E + ++ E+ E Sbjct: 348 LGRIEYRGIANKIFNEIYFSE 368 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: 352 Number of extensions: 19 Number of successful extensions: 7 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: 369 Length adjustment: 30 Effective length of query: 355 Effective length of database: 339 Effective search space: 120345 Effective search space used: 120345 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