Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate 8502096 DvMF_2809 aminotransferase class V (RefSeq)
Query= metacyc::MONOMER-15919 (385 letters) >FitnessBrowser__Miya:8502096 Length = 367 Score = 185 bits (470), Expect = 2e-51 Identities = 124/359 (34%), Positives = 196/359 (54%), Gaps = 17/359 (4%) Query: 11 MIPGPTMVPPEVLNAMALPV-IGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSGTAA 69 M+PGP + P VL AM G DY L +T L ++ T++D L+TG G A Sbjct: 11 MVPGPVTLHPAVLTAMTRDYGSGQIEPDYLKLYAETGRNLAQLMGTQSDMVLMTGEGMLA 70 Query: 70 MDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEILDK 129 + A+ + + GD+VL++ TG FG+ ++ A E +++ + + + + E + Sbjct: 71 LWAALKSCLVPGDRVLSVGTGVFGDGIGDMAAAIGCEVLKVSLPYNETIDDLTGIEDAIR 130 Query: 130 YDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDA-LYIVDTVSSLGGDYVNVDKFHIDIC 188 K +T VH ET +G NP+ ++G + + L+ VD V+S+GG V D +H D+ Sbjct: 131 SFKPKMLTAVHCETPSGTLNPLADLGALKQTCGVPLFYVDAVASVGGAPVQADAWHADLV 190 Query: 189 VTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFY-LDLLAYKKYYEEKKQTPYTPSV 247 + GSQKCL+APP ++ ++VS AWEV+ + VG+ D +A + ++ + PYTP Sbjct: 191 LGGSQKCLSAPPSMSFLSVSPAAWEVV----EAVGYQGYDAIAPFRTVQQDGRCPYTPYW 246 Query: 248 NLTYALNVALDLVLEE--GIENRVKRHERLAKATRAGLEAMGIELFAKERA-RSVTVTSA 304 + T ALN +L E G++ RH +A+ RAGL +GI+L+ E A S TVT+A Sbjct: 247 HGTAALNAGALAILNEKGGMQGCFDRHREVAERCRAGLAKLGIDLWTAEGAVNSPTVTAA 306 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVELAL 363 PEG ++R L + ++V+G +AGK+FR+GHMG AT A V+ AL Sbjct: 307 IVPEGFTWPEWRQGLRER-GLIVSGSFGPMAGKVFRLGHMG------TQATEALVDAAL 358 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: 316 Number of extensions: 14 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: 367 Length adjustment: 30 Effective length of query: 355 Effective length of database: 337 Effective search space: 119635 Effective search space used: 119635 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