Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_012818166.1 ADEG_RS00045 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000024605.1:WP_012818166.1 Length = 383 Score = 315 bits (808), Expect = 1e-90 Identities = 167/384 (43%), Positives = 248/384 (64%), Gaps = 6/384 (1%) Query: 1 MDNKQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLT 60 M + L IPGPTPVP V AMA+ IGHR+ DF+++ A L L+ + T+ND+++LT Sbjct: 1 MKKETRLFIPGPTPVPPAVAEAMARPLIGHRTEDFARLYARLEERLRVVLGTKNDIVILT 60 Query: 61 TSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDF 120 +SGTG MEA++ N +SPGD VL GKFG+R+ ++AK +G AVE ++ WGKA+D Sbjct: 61 SSGTGGMEAAVANLVSPGDPVLALVTGKFGERFAELAKVYGGAVEVMEFGWGKAVDLEAV 120 Query: 121 KTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAI 180 + L+A + K ++ TH+ETST V+ND+ + + +G AL++VDAV+S G + + Sbjct: 121 EEKLKA---RRFKVVLATHNETSTTVVNDIRGLGELTRRYG-ALLVVDAVSSAGGMEIRM 176 Query: 181 DDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSP 240 DD G+DV+ + SQK M+PPGL V+ S AW+A E PR+YLDL +KS + ++P Sbjct: 177 DDWGVDVLVTASQKALMVPPGLAIVAASDAAWKAMEENKNPRYYLDLLAARKSKQKYNTP 236 Query: 241 FTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAIT 300 +TP ++L GL +L ++ AEGL+ ++ +H+ A R A++AL L L PD AS +T Sbjct: 237 YTPAVSLFVGLDRALDLILAEGLEKVYRKHRLLARAVRAAIRALGLKLMIPDEYASPVVT 296 Query: 301 AV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEAT 359 V AP G+E +++R + ++ + +AGGQ LKGKIFRI H+G+V DIL +GALE Sbjct: 297 GVWAPEGIEVDRLRKEIASRYGVLLAGGQGPLKGKIFRISHMGYVDAVDILGALGALELG 356 Query: 360 LIELGYEGVTPGSGVAAAAGVLAK 383 L G++ G G+A A VLA+ Sbjct: 357 LYRFGFK-FKLGEGLAQAQAVLAE 379 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: 374 Number of extensions: 17 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: 383 Length adjustment: 30 Effective length of query: 354 Effective length of database: 353 Effective search space: 124962 Effective search space used: 124962 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