Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate BWI76_RS20685 BWI76_RS20685 cysteine synthase B
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Koxy:BWI76_RS20685 Length = 303 Score = 251 bits (642), Expect = 1e-71 Identities = 130/296 (43%), Positives = 190/296 (64%), Gaps = 3/296 (1%) Query: 5 NILE-TIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPG 63 N LE TIGNTPLV++ + P+ +++ KLEG NP GSVKDR AL MI +AE G++ PG Sbjct: 2 NTLEYTIGNTPLVKLQRMGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPG 61 Query: 64 STIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDG 123 +IEATSGNTGI LAMI +KGY + ++M + +S ERR ++A+GAE+IL K+ G +G Sbjct: 62 DVLIEATSGNTGIALAMIAALKGYQMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEG 121 Query: 124 AIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTL 183 A + + GK + QF+N N AHY TT EIW QT G +THFV+++GT+GT+ Sbjct: 122 ARDLALAMAQRGEGKLLD--QFNNPDNPYAHYTTTGPEIWRQTDGRITHFVSSMGTTGTI 179 Query: 184 MGVGKNLREKNPEIKIIEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAFA 243 GV + LRE++ + I+ QP +G I G++ +P I+ A +D + I ++A Sbjct: 180 TGVSRFLREQDKAVSIVGLQPEEGSSIPGIRRWPAEYMPGIFNAQLVDVVLDIHQQDAEN 239 Query: 244 KAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLFADRGEKYLSTKLFDTE 299 R + +EGIF G+SSG A++ A ++A + V+V + DRG++YLST +F E Sbjct: 240 TMRMLAVKEGIFCGVSSGGAVVGALRVARENPGAVVVAIVCDRGDRYLSTGVFGEE 295 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: 308 Number of extensions: 18 Number of successful extensions: 2 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: 303 Length adjustment: 27 Effective length of query: 272 Effective length of database: 276 Effective search space: 75072 Effective search space used: 75072 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