Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate RR42_RS21960 RR42_RS21960 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Cup4G11:RR42_RS21960 Length = 305 Score = 211 bits (537), Expect = 2e-59 Identities = 123/301 (40%), Positives = 173/301 (57%), Gaps = 10/301 (3%) Query: 4 DNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPG 63 DNIL+TIGNTP +R+ L + Q++ K E NP GS+KDRIAL M+E AE G L PG Sbjct: 4 DNILQTIGNTPHIRVQRLFGDTH-QVWIKSERANPGGSIKDRIALSMVEAAEQSGVLKPG 62 Query: 64 STIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDG 123 TIIE TSGNTGIGLAM+ VKGY +++VM + +S+ERR+++ A+GA LT ++ G G Sbjct: 63 GTIIEPTSGNTGIGLAMVAAVKGYKLVLVMPDSMSVERRRLMLAYGATFDLTPREKGMKG 122 Query: 124 AIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTL 183 AI + ELV PG + P QF N N AH TTA EI A + V VGT G + Sbjct: 123 AIARAEELVAATPGAWM-PQQFENPANIEAHVNTTALEILADFPQGIDALVTGVGTGGHI 181 Query: 184 MGVGKNLREKNPEIKIIEAQPTKGHYIQG-------LKSMEEAIVPAIYQADKIDEHILI 236 G + L++K P +K+ +P I G ++ + +P +D I + Sbjct: 182 TGCARVLKQKWPALKVYAVEPVASPVISGGAPAPHPIQGIGAGFIPRNLDTALLDGVIQV 241 Query: 237 ESEEAFAKAREIVAQEGIFIGMSSGAAMLA-AQKLAEKIDSGVIVVLFADRGEKYLSTKL 295 ++E A AR +EG+ +G+SSGA + A AQKL + ++ D GE+YL+ + Sbjct: 242 DAEPAREMARRAAREEGMLVGISSGATLAAIAQKLPDLPAGATVLGFNYDTGERYLTVEG 301 Query: 296 F 296 F Sbjct: 302 F 302 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: 271 Number of extensions: 15 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: 305 Length adjustment: 27 Effective length of query: 272 Effective length of database: 278 Effective search space: 75616 Effective search space used: 75616 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