Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_012503202.1 CPAR_RS10040 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000020505.1:WP_012503202.1 Length = 379 Score = 273 bits (698), Expect = 6e-78 Identities = 154/376 (40%), Positives = 232/376 (61%), Gaps = 9/376 (2%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 K+ L PGPTPVPE V+L MA I HR+ +F +I+ + +L++L +T V+++T SG Sbjct: 2 KKRLFTPGPTPVPENVMLRMAAPIIHHRNPEFMEILERVHQDLQYLFRTTQPVVVMTCSG 61 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTF-GLAVEEIKAEWGKALDPNDFKT 122 TG MEA+I + + GD+V+ N GKFG+RW ++A+ F G VEE K WG A+ Sbjct: 62 TGGMEAAISSLFTRGDKVITVNGGKFGERWGELARIFTGNCVEE-KVAWGSAITTERMVE 120 Query: 123 LLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDD 182 LL+ + ITHSETSTG +D+ A+ AA H AL++VD +T++GA DD Sbjct: 121 LLK--EHPGAMGVCITHSETSTGTASDVKALCAAIHEHSDALILVDGITAIGAHEFRFDD 178 Query: 183 LGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETAT-IPRFYLDLKKYKKSTDEDSSPF 241 G D+ +GSQKG M+PPGL V++S +A +P++YL LKK KS + +PF Sbjct: 179 WGADICITGSQKGLMMPPGLALVAISERAQDVINNRKGLPQYYLSLKKALKSHAGNDTPF 238 Query: 242 TPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAITA 301 TP ++L+ GL +LQM++AEG++ ++ RH++ A R +AL + LF+ + S A+TA Sbjct: 239 TPAVSLIIGLDEALQMVRAEGIENVWKRHEQLAEACRLGCQALGMELFS--ESPSYAVTA 296 Query: 302 V-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATL 360 V P G + ++ +T++ + I +A GQD KGKIFRI HLG+ + D+L+ +G LE T Sbjct: 297 VWLPEGADWKQFNNTLKIENGITVAAGQDDFKGKIFRISHLGYYDELDMLTMLGGLERTF 356 Query: 361 IELGYEGVTPGSGVAA 376 +G G+G+ A Sbjct: 357 SMMGIP-FEHGAGITA 371 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: 343 Number of extensions: 12 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: 379 Length adjustment: 30 Effective length of query: 354 Effective length of database: 349 Effective search space: 123546 Effective search space used: 123546 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