Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_011883451.1 alanine--glyoxylate aminotransferase
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000016205.1:WP_011883451.1 Length = 403 Score = 157 bits (396), Expect = 7e-43 Identities = 112/351 (31%), Positives = 177/351 (50%), Gaps = 8/351 (2%) Query: 9 LLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFL-ITGSGT 67 L+M GP +P V A + VI H + ++E E + VF T L + G G+ Sbjct: 26 LMMGAGPVPIPAAVAKANTI-VINHLGATMAKIIEQVKEMARYVFQTRTKWVLGVAGPGS 84 Query: 68 AAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEIL 127 AAM+MAISN+ RG +VL+I G F R A + + L+V +A + + + + Sbjct: 85 AAMEMAISNLAWRGTRVLSIRNGFFSARMAEMATRVGADVATLEVADRSVASLDEIADAI 144 Query: 128 DKYDDIKAVTVVHNETSTGARN-PIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 + + + VT+V ETS N ++EI + K AL +VD V +L + +D + ID Sbjct: 145 AR-ERPEIVTIVQGETSNTVWNRDLREIAALAKAAGALVVVDAVCTLSTMPLEMDAWGID 203 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQTPYTPS 246 +TG QK L++ PG++ I S+ AW+ +K+ + + +A + + YT Sbjct: 204 AVITGGQKGLSSIPGVSLIAFSDAAWDRMKQRPEPNAHWCLDMALAENFWHNAGYHYTAP 263 Query: 247 VNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAKY 306 V+ AL+ AL LV E +E+R RH R A +AG+EAMG+EL+ + R +V + Sbjct: 264 VSGVLALHEALRLVCAETLESRFARHLRCTLALQAGIEAMGLELYTPKECRLNSVVGIET 323 Query: 307 PEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG-ICGEKEVLATL 356 P G+ G +S +Y + ++G I RIG MG C E + TL Sbjct: 324 PAGLTPGMVCGHISKQYQVEISGS---FGLPIVRIGQMGEQCREHNLFRTL 371 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: 356 Number of extensions: 24 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: 403 Length adjustment: 31 Effective length of query: 354 Effective length of database: 372 Effective search space: 131688 Effective search space used: 131688 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