Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_012676496.1 PERMA_RS01695 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000021565.1:WP_012676496.1 Length = 381 Score = 280 bits (717), Expect = 4e-80 Identities = 153/379 (40%), Positives = 227/379 (59%), Gaps = 7/379 (1%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 K+ L PGP P+P +V+ A+ + I HR+ +F++I E NL+ L +TE DV+M +SG Sbjct: 4 KERLFTPGPVPLPPQVIKALGQQIIHHRTPEFTQIFLEARENLQKLLKTERDVIMFASSG 63 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTL 123 TGAMEAS+ NF GDRVL+ N GKFG RW ++A + L + + + EWGK D + Sbjct: 64 TGAMEASVANFFRKGDRVLIINAGKFGQRWKELASVYQLKIVDYEIEWGKTYDKERILQI 123 Query: 124 LEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDDL 183 + D IK + + HSETST +D+ + AK L++VD +TS+G V ++L Sbjct: 124 ISEFPD--IKGIFVQHSETSTTTYHDVKYLGDIAKKLDDCLLVVDGITSVGVYQVYPEEL 181 Query: 184 GLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFTP 243 G+DV+ +GSQK M+PPGL + S KA + + +PR+Y D+ K K + + +TP Sbjct: 182 GIDVLVTGSQKALMLPPGLSVLYFSEKAEERASKSDMPRYYFDVLKEAKKQSKGQTAYTP 241 Query: 244 PINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAITAV- 302 INL+ L SL+++ EGLD + RH+ ATR A+K + L L + + SN+ T V Sbjct: 242 AINLIIALNESLKLILGEGLDNLEERHRIMAEATREAVKEIGLKLLS--ESPSNSATGVY 299 Query: 303 APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATLIE 362 +P G++A+++R + K +AGGQDHLKGKIFRI H+G+ D++ I LE L Sbjct: 300 SPAGIDADQLRKEL-LKLGFRVAGGQDHLKGKIFRIAHMGYFDFMDVVQVIAGLEMALKR 358 Query: 363 LGYEGVTPGSGVAAAAGVL 381 +GYE + G GV A V+ Sbjct: 359 IGYE-IEIGKGVRKAQEVI 376 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: 341 Number of extensions: 7 Number of successful extensions: 3 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: 381 Length adjustment: 30 Effective length of query: 354 Effective length of database: 351 Effective search space: 124254 Effective search space used: 124254 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