Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_057687361.1 ABB28_RS15950 cysteine synthase A
Query= metacyc::MONOMER-20568 (299 letters) >NCBI__GCF_001431535.1:WP_057687361.1 Length = 319 Score = 235 bits (599), Expect = 1e-66 Identities = 127/304 (41%), Positives = 191/304 (62%), Gaps = 12/304 (3%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 +Y++IL+TIGNTP+V+++ L P V +YAK+E FNP GSVKDR+AL ++ AE G L Sbjct: 3 LYESILDTIGNTPIVKLHRLAP-AHVTLYAKVESFNPGGSVKDRLALAIVLDAEQRGLLK 61 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGT 121 PG TIIEATSGNTG+ LAM+ +GY + M E SIERRK+++A+GA++ILT Sbjct: 62 PGDTIIEATSGNTGVALAMVAAARGYKFVATMVETFSIERRKLMRAYGAKVILTPAAERG 121 Query: 122 DGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKG-TVTHFVAAVGTS 180 G +R+ AEL +E+ +F +QF+N N H TTA EI G + +FV+ GT Sbjct: 122 SGMVRRAAELAQEH--GWFLASQFANPANPAYHRSTTAAEILRDFAGRRLDYFVSGWGTG 179 Query: 181 GTLMGVGKNLREKNPEIKIIEAQPTKGHYIQG-------LKSMEEAIVPAIYQADKIDEH 233 GTL GVG+ L+ P+ +I+ +P ++G ++ VP + + +DE Sbjct: 180 GTLTGVGEVLKVARPQTRIVATEPAGAALLKGDDWKPHKIQGWTPDFVPDVLNRNVVDEL 239 Query: 234 ILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG-VIVVLFADRGEKYLS 292 + +E + A + AR + A+EG+F+G+S+GA + +A +AE+ + G VI+ + D GE+Y S Sbjct: 240 LTVEDDRAISTARRLAAEEGLFVGISAGATLASALDVAERAEPGSVILAMLPDTGERYFS 299 Query: 293 TKLF 296 T LF Sbjct: 300 TPLF 303 Lambda K H 0.315 0.133 0.367 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: 269 Number of extensions: 12 Number of successful extensions: 6 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: 299 Length of database: 319 Length adjustment: 27 Effective length of query: 272 Effective length of database: 292 Effective search space: 79424 Effective search space used: 79424 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: 42 (22.0 bits) S2: 48 (23.1 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