Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_068460957.1 APY04_RS06700 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_001541235.1:WP_068460957.1 Length = 396 Score = 250 bits (638), Expect = 6e-71 Identities = 141/381 (37%), Positives = 212/381 (55%), Gaps = 5/381 (1%) Query: 1 MDNKQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQT-ENDVLML 59 M + + IPGPT +PE + A+ I HRS F +I+ K + +T + + + Sbjct: 1 MSVQNPIFIPGPTNIPEVLRKAVDMPTIDHRSSLFGQILRPAIDGAKKVFKTTDGQLFIF 60 Query: 60 TTSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPND 119 ++GTG E +I N LSPGD+VL NG F RW+ + + L V I+ WG + Sbjct: 61 PSTGTGGWEIAITNVLSPGDKVLATCNGMFSQRWIDMCRRHQLDVTMIQQAWGDGISAER 120 Query: 120 FKTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKA-HGGALMIVDAVTSLGATPV 178 + +L AD I ++ TH+ET+TGV +D+AA+ + A AL+ VD V+S+G+ Sbjct: 121 VEKILAADKHHRISVVLATHNETATGVKSDIAALRRSLNATKHPALLFVDGVSSIGSMDF 180 Query: 179 AIDDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDS 238 +D+ G+DV SGSQKG+M+PPGL V SA+A +A E A +PR + D++ KS + Sbjct: 181 RMDEWGVDVAVSGSQKGFMLPPGLAIVGFSARALEATENARLPRTFFDIRDMAKSNALNG 240 Query: 239 SPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFA--PDNAAS 296 P+TPP+ L+ GL+ S +M+ EGLD +F RH R R A+ A + L A P+ + Sbjct: 241 FPYTPPVGLLNGLKLSTEMLLEEGLDNVFARHHRIAEGVRAAISAWGMQLCALRPELYSD 300 Query: 297 NAITAVAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGAL 356 P G +A KI + + +A G + GK+FRIGHLG + + LS I Sbjct: 301 TVSAICVPDGFDANKIVARALNAYGVAFGTGIGAVAGKVFRIGHLGSLTEAMALSGIATA 360 Query: 357 EATLIELGYEGVTPGSGVAAA 377 E T+++LG +T G+G AAA Sbjct: 361 EMTMVDLGLP-ITLGAGTAAA 380 Lambda K H 0.317 0.134 0.386 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: 334 Number of extensions: 14 Number of successful extensions: 4 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: 384 Length of database: 396 Length adjustment: 31 Effective length of query: 353 Effective length of database: 365 Effective search space: 128845 Effective search space used: 128845 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 (21.7 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