Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_028488718.1 Q394_RS0107395 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000621325.1:WP_028488718.1 Length = 400 Score = 156 bits (394), Expect = 1e-42 Identities = 105/341 (30%), Positives = 183/341 (53%), Gaps = 10/341 (2%) Query: 9 LLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFL-ITGSGT 67 L+M GP +P +V A ++ VI H + + ++E + + VF T++ + ++G G+ Sbjct: 23 LMMGAGPVPIPQKVAAANSI-VINHLGETMNRVIEQVKDMGRYVFQTDSSHVMGVSGPGS 81 Query: 68 AAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEIL 127 AAM+MA++N++ G++VL I G F R A IV+ + E L++ + A+ V+ L Sbjct: 82 AAMEMAVANLVLPGERVLCITNGYFSLRMAEIVRRVRAEPTILEMPHNESADLALVERAL 141 Query: 128 DKYDDIKAVTVVHNETS-TGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 K AVT+V ETS T + +I ++ K Y L IVD V +L + +D + +D Sbjct: 142 -KQGQFHAVTLVQGETSNTVCNKNLDQIAKLAKRYGCLVIVDAVCTLSTMPLAMDNWQVD 200 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAW--EVIKKNDDKVGFYLDLLAYKKYYEEKKQTPYT 244 +TG QK L++ PG++ + SE AW ++ ++ + + LD K++ +K YT Sbjct: 201 AIITGGQKGLSSIPGVSLLAFSESAWSKKIARREELPFHWCLDAQLADKFWNQKSY-HYT 259 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 V+ AL+ AL LV EE + R +RH R ++A +AG+E MG+++ +++ R +V Sbjct: 260 APVSGILALHEALRLVCEETLPQRFERHLRCSEALQAGIETMGLKMLVEKQHRLNSVVGI 319 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG 345 P+ + R +S + + ++G I RIG MG Sbjct: 320 IVPDHVSADVVRAHMSKVHKVEISGA---FGLNILRIGQMG 357 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: 310 Number of extensions: 18 Number of successful extensions: 2 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: 400 Length adjustment: 31 Effective length of query: 354 Effective length of database: 369 Effective search space: 130626 Effective search space used: 130626 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 10 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