Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate SMa1495 SMa1495 aminotransferase
Query= metacyc::MONOMER-15919 (385 letters) >FitnessBrowser__Smeli:SMa1495 Length = 370 Score = 199 bits (507), Expect = 8e-56 Identities = 122/342 (35%), Positives = 184/342 (53%), Gaps = 4/342 (1%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 +LLM PGP+ V PEVL A A P IGH + L++ ++L+ F T+N TF ++ Sbjct: 9 RLLMGPGPSNVSPEVLAAQARPTIGHLDPSFVGLMDRIKDQLRLAFRTDNRVTFPLSAPA 68 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 + AM+MA+ +++ GD + G FG R A I + E + VEWG +PEAV+ Sbjct: 69 SLAMEMALVTLLEPGDTAIIAQNGVFGGRMAEIAQRAGAEVRLVSVEWGKPVDPEAVRAS 128 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 + + K + VH ETSTG R+ + + ++ L +VDTV+ LGG V+VD++ D Sbjct: 129 ILEAPQAKLLAFVHAETSTGVRSDAASLCALAREAGLLSVVDTVTGLGGIPVSVDEWQAD 188 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEEKKQTPY-- 243 G+QKCL+APPGLA IT S++A +K + ++LDL Y+E + Y Sbjct: 189 AVYAGTQKCLSAPPGLAPITFSDRAVSAVKARKTPIQSWFLDLGLMLGYWEGEGARSYHH 248 Query: 244 TPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTS 303 T VN Y L+ +L +L EG+E RH L+ +GI + R + + Sbjct: 249 TAPVNALYGLHESLSRLLGEGLETAWARHRAAHDRLVERLQGLGIAFVVDKEHRLPQLNT 308 Query: 304 AKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG 345 PEG++D R L +++ I + GG LAG+I+RIG MG Sbjct: 309 VWLPEGVKDVPERRRLLDEFGIEIGGGLGPLAGRIWRIGLMG 350 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: 294 Number of extensions: 19 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: 370 Length adjustment: 30 Effective length of query: 355 Effective length of database: 340 Effective search space: 120700 Effective search space used: 120700 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