Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate 6939183 Sama_3277 Serine--pyruvate transaminase (RefSeq)
Query= metacyc::MONOMER-15919 (385 letters) >FitnessBrowser__SB2B:6939183 Length = 376 Score = 212 bits (540), Expect = 1e-59 Identities = 123/352 (34%), Positives = 198/352 (56%), Gaps = 4/352 (1%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGS 65 +++LM PGP+ V PEVL A + P +GH + ++++ L+ F T+N+ T ++ Sbjct: 14 RRILMGPGPSDVYPEVLLAQSRPTVGHLDPLFVAMMDELKALLQYAFQTQNEVTLAVSAP 73 Query: 66 GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125 G+A M+ N+++ G+KV+ G FGER V+ G A+ +D WG +P+ V+ Sbjct: 74 GSAGMETCFVNLVEPGEKVVVCRNGVFGERMRQNVERCGGVAVVVDFPWGAPVDPQVVEG 133 Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185 +L ++ D + VH ETSTGA + K + + ++++ L IVD V+SLGG + VD++ I Sbjct: 134 VLKQHPDASYLAFVHAETSTGALSDAKTLCALAREHNCLSIVDAVTSLGGVELRVDEWGI 193 Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYY--EEKKQTP 242 D +GSQKCL+ PGL+ ++ S +A E +K V ++LD Y+ K+ Sbjct: 194 DAIYSGSQKCLSCVPGLSPVSFSPRAVEKLKSRKTPVQSWFLDQTLVMGYWGGSGKRAYH 253 Query: 243 YTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVT 302 +T VN YAL+ +L L+ EEG+EN RH+ + + +AGLE +G+ E R + Sbjct: 254 HTAPVNALYALHESLRLLAEEGLENAWARHQHMHQLLKAGLEKLGLGFVVDEAYRLPQLN 313 Query: 303 SAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLA 354 + PEG++D+ R L YN+ + G LAGK +RIG MG E +A Sbjct: 314 AVYIPEGVDDAAVRSQLLKGYNLEIGAGLGDLAGKAWRIGLMGYGARAENVA 365 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: 327 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: 376 Length adjustment: 30 Effective length of query: 355 Effective length of database: 346 Effective search space: 122830 Effective search space used: 122830 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