Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_055437324.1 ASC41_RS14275 cysteine synthase family protein
Query= metacyc::MONOMER-20568 (299 letters) >NCBI__GCF_001418085.1:WP_055437324.1 Length = 346 Score = 216 bits (549), Expect = 8e-61 Identities = 122/311 (39%), Positives = 178/311 (57%), Gaps = 20/311 (6%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 ++DN+L+ IGNTP++++ + K AK+E FNP S KDRIAL +IEQAE +G L Sbjct: 7 VFDNVLDLIGNTPMIKLKKMTSEFKGNFLAKVEAFNPGHSSKDRIALYIIEQAEKQGILK 66 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGT 121 PG TIIE TSGNTG +AM+ +KGY+ I+ +S S ++ M+K GA++ + + Sbjct: 67 PGDTIIETTSGNTGFSIAMVSVIKGYDCILAVSSKSSADKIDMLKNMGAKVYVCPANVSA 126 Query: 122 DG--AIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGT 179 D + +VA+ + + NQ+ N+ N AHY +T EIW QT G +TH VA GT Sbjct: 127 DDPRSYYQVAKRLHDEMKGSVYINQYFNQLNIDAHYASTGPEIWNQTNGKITHLVACSGT 186 Query: 180 SGTLMGVGKNLREKNPEIKIIEAQ---------------PTKGHYIQGLKSMEEAIVPAI 224 GT+ G K L+E+NP IKII K Y ++ + + ++P Sbjct: 187 GGTISGTAKYLKEQNPNIKIIGVDAFGSVLKKYHETREFDDKEIYPYRIEGLGKNLIPTA 246 Query: 225 YQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLA---EKIDSGVIVV 281 D IDE + + EE+ AREI EG+F+G +SGAAM A ++L+ E +S IVV Sbjct: 247 TDFDTIDEFVKVTDEESAHTAREIAKTEGLFVGYTSGAAMQAIKQLSASGEFKESDNIVV 306 Query: 282 LFADRGEKYLS 292 +F D G +Y+S Sbjct: 307 IFPDHGSRYMS 317 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: 331 Number of extensions: 21 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: 299 Length of database: 346 Length adjustment: 28 Effective length of query: 271 Effective length of database: 318 Effective search space: 86178 Effective search space used: 86178 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 Jul 26 2024. The underlying query database was built on Jul 25 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