Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_010530299.1 ON01_RS06955 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000224785.1:WP_010530299.1 Length = 405 Score = 232 bits (591), Expect = 2e-65 Identities = 131/379 (34%), Positives = 210/379 (55%), Gaps = 17/379 (4%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 + +M PGP P VL A++ P+IG ++ ++ +T+ L+ F T N F + G+ Sbjct: 11 RTIMTPGPVEADPRVLRALSTPIIGQFDTEFLRIMNETMALLRYSFQTNNRWAFPVDGTS 70 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 A ++ + +II+ GDK+L + G FG I + + EWG++ +PE VK Sbjct: 71 RAGIEAVLCSIIEPGDKILIPIFGRFGYLLTEIASRCGADIYTMGKEWGEVFDPEEVKAE 130 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 + K + K V +VH ETSTG P+KEIG+ ++ DAL++VD V++LGG D++ ID Sbjct: 131 MKKVNP-KVVAMVHGETSTGKMQPLKEIGQFCREQDALFVVDAVATLGGVEFKTDEWCID 189 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVI-KKNDDKVGF-------------YLDLLAYK 232 + G+QKCLA P G+A +T +++ ++I ++ D + G Y DL + Sbjct: 190 AAIAGTQKCLAVPSGMAPLTYNDRVEKLIMERKDIERGLADDSDNERRIQSNYFDLSQIQ 249 Query: 233 KYYEEKKQTPYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFA 292 Y+ + +T + ++ YAL L L+ EEGIE R++RH+ +A AGLEAMG+ELF Sbjct: 250 DYWSPDRLNHHTEATSMLYALREGLRLIQEEGIEQRLERHQLHGEALVAGLEAMGLELFG 309 Query: 293 KERARSVTVTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGI-CGEKE 351 + VT K PEGI++++ R L N++ I +AG L G ++RIG MG C + Sbjct: 310 DGENKMPVVTVIKVPEGIDEAQVRQTLINEFGIEIAGAFGPLKGNVWRIGSMGYSCRKNN 369 Query: 352 VLATLACVELALKELGFEV 370 +L L +E L G ++ Sbjct: 370 ILQVLGALEATLLYHGADI 388 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: 13 Number of successful extensions: 4 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: 405 Length adjustment: 31 Effective length of query: 354 Effective length of database: 374 Effective search space: 132396 Effective search space used: 132396 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 26 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