Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate RR42_RS11250 RR42_RS11250 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Cup4G11:RR42_RS11250 Length = 336 Score = 176 bits (447), Expect = 5e-49 Identities = 115/315 (36%), Positives = 168/315 (53%), Gaps = 18/315 (5%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 + D + TIG+TPL+R+ L+ ++ K E NP GSVKDR AL +I AE G L Sbjct: 3 VKDGFVGTIGHTPLIRLAGLSEETGCEILGKAEFLNPGGSVKDRAALYIIRDAERRGALK 62 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGT 121 PG T++E T+GNTGIGLA + +GY I+V+ + S E+ ++ GAE+ Sbjct: 63 PGGTVVEGTAGNTGIGLAHLCAARGYRCIVVIPDTQSPEKMDRLRLLGAEVRPVPAAPYA 122 Query: 122 D-GAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTS 180 D +KVA + + NQF N N+ AHY+TT EIW T G + FV A GT Sbjct: 123 DPNNYQKVAGRLAQETENAIWANQFDNLANRQAHYETTGPEIWHDTAGKIDAFVCATGTG 182 Query: 181 GTLMGVGKNLREK--NPEIKIIEAQP--------TKGHYIQGL-KSMEEAI----VPAIY 225 GTL GV + L+EK NP ++I+ A P K H ++ S+ E I V A Sbjct: 183 GTLAGVARFLKEKERNPPVRIVLADPHGSGLYHFVKHHEVKAKGNSITEGIGSSRVTANL 242 Query: 226 QADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG-VIVVLFA 284 ID+ + I+ + ++ +EG+++G SSG + AA LA ++ G IV L Sbjct: 243 ADTPIDDAVRIDDQACVDMVYRLLREEGLWVGGSSGINVAAAAWLAREMGPGHTIVTLLC 302 Query: 285 DRGEKYLSTKLFDTE 299 DRG+ Y + +LF+ + Sbjct: 303 DRGDLY-AGRLFNAD 316 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: 328 Number of extensions: 21 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: 299 Length of database: 336 Length adjustment: 27 Effective length of query: 272 Effective length of database: 309 Effective search space: 84048 Effective search space used: 84048 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 09 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