Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate 203421 SO4343 aminotransferase, class V (NCBI ptt file)
Query= metacyc::MONOMER-15919 (385 letters) >FitnessBrowser__MR1:203421 Length = 378 Score = 218 bits (554), Expect = 3e-61 Identities = 127/353 (35%), Positives = 199/353 (56%), Gaps = 5/353 (1%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGS 65 +++LM PGP+ V PEVL A A P +GH + +++++ ++ F T+N+ T ++ Sbjct: 15 RRILMGPGPSDVYPEVLAAQARPTVGHLDPLFVSMMDELKSLIQYAFQTKNEMTMAVSAP 74 Query: 66 GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125 G+A M+ N+++ G+KV+ G FGER V+ A+ +D EWG +P AV+ Sbjct: 75 GSAGMETCFVNLVEPGEKVIVCRNGVFGERMRQNVERVGAIAVLVDNEWGTPVDPVAVEA 134 Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185 L + D K + VH ETSTGA + K + + K Y L IVD V+SLGG + VD++ I Sbjct: 135 ALKAHPDAKFLAFVHAETSTGALSDAKTLCALAKQYGCLSIVDAVTSLGGVELRVDEWGI 194 Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLD---LLAYKKYYEEKKQT 241 D +GSQKCL+ PGL+ ++ S A E +K V ++LD ++AY K+ Sbjct: 195 DAIYSGSQKCLSCVPGLSPVSFSPAAVEKLKNRKTPVQSWFLDQSLVMAYWTSAGGKRSY 254 Query: 242 PYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTV 301 +T VN YA++ +L ++ EG+EN KRH+ + RAGLE +G++ E +R + Sbjct: 255 HHTAPVNALYAMHESLRILAAEGLENAWKRHQDMHLVLRAGLEKLGLKFVVAEASRLPQL 314 Query: 302 TSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLA 354 + PEG++D+ R L YN+ + G LAGK +RIG MG +E +A Sbjct: 315 NAIYIPEGVDDAAVRARLLKDYNLEIGAGLGALAGKAWRIGLMGFGARRENVA 367 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: 330 Number of extensions: 14 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: 378 Length adjustment: 30 Effective length of query: 355 Effective length of database: 348 Effective search space: 123540 Effective search space used: 123540 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