Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_012675016.1 SULAZ_RS02850 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000021545.1:WP_012675016.1 Length = 379 Score = 277 bits (708), Expect = 4e-79 Identities = 151/376 (40%), Positives = 226/376 (60%), Gaps = 9/376 (2%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 K+ L PGP P+P +V+ A+ + I HR+ +F+ I + L+ L T+ DVLM +SG Sbjct: 3 KERLFTPGPVPLPPQVIKALGQQIIHHRTPEFTNIFLQTREKLQKLFNTDRDVLMFASSG 62 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTL 123 TGAMEASI+NF S D+VLV N GKFG+RW +AKTF L V + + EWG+ D + + Sbjct: 63 TGAMEASIVNFFSENDKVLVINAGKFGERWRDLAKTFRLQVIDYQIEWGRTYDKDKVSEI 122 Query: 124 LEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDDL 183 ++ + D +K +++ HSETST L+DL ++ + + L++VD +TS+G V ++ Sbjct: 123 VKNNPD--LKGILVQHSETSTTTLHDLQFLSQISSSLEDCLLVVDGITSVGVYKVFPQEI 180 Query: 184 GLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFTP 243 G+D++ +GSQK M+PPGL + S KA + E + +P++Y +K K + + +TP Sbjct: 181 GIDILVTGSQKALMLPPGLSILYYSEKAEKRLEKSNLPKYYFSVKAESKKQAKGQTAYTP 240 Query: 244 PINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLF--APDNAASNAITA 301 INL+ L SL ++ EGLD + RH TR AMK + L L +P N+A+ T Sbjct: 241 AINLIIALNESLNLILEEGLDNLEKRHSILAQMTREAMKEIGLKLLSESPSNSATGVFT- 299 Query: 302 VAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATLI 361 P G++A+K R + K I +AGGQDHLKGKI RI H+G+ D++ I A+E L Sbjct: 300 --PEGIDADKFRKDL-LKIGIRVAGGQDHLKGKIIRIAHMGYFDYLDMIEVISAIEIALY 356 Query: 362 ELGYEGVTPGSGVAAA 377 + GY+ V G GV A Sbjct: 357 KNGYK-VDLGKGVKKA 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: 330 Number of extensions: 10 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: 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