Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Synpcc7942_0171 Synpcc7942_0171 cysteine synthase A
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__SynE:Synpcc7942_0171 Length = 372 Score = 187 bits (475), Expect = 3e-52 Identities = 122/314 (38%), Positives = 175/314 (55%), Gaps = 18/314 (5%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 I + ++TIGNTPL+R+N L+ + K E NP GSVKDR AL +IE AE +GKL Sbjct: 47 IRNGFIDTIGNTPLIRLNSLSEATGCNILGKAEFLNPGGSVKDRAALFIIEDAERQGKLR 106 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGT 121 PG T++E T+GNTGIGLA I KGY +IV+ E S E+ +++ GAE+ Sbjct: 107 PGGTVVEGTAGNTGIGLAHICNAKGYRCLIVIPETQSQEKIDLLRTLGAEVRTVPAVPYR 166 Query: 122 D-GAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTS 180 D KV+ + E NQF N N+ AHY TT EIW QT+GTV +VAA GT Sbjct: 167 DPNNYVKVSGRLAEELDNAIWANQFDNLANRQAHYATTGPEIWQQTEGTVDAWVAATGTG 226 Query: 181 GTLMGVGKNLREKNPEIKIIEAQP----------TKGHYIQGLKSMEEAI----VPAIYQ 226 GT GV L+E++ +++ + A P T +++G S+ E I + A Q Sbjct: 227 GTYAGVALYLKEQSSKVRCVVADPMGSGLYSWVKTGEIHLEG-SSVTEGIGNSRITANMQ 285 Query: 227 ADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG-VIVVLFAD 285 ID+ I I EA +++ ++G+F+G S G + AA +LA+++ G IV + D Sbjct: 286 DVPIDDAIQIADPEALEIIYQLLHRDGLFMGGSVGINVAAAYRLAKEMGPGHTIVTVLCD 345 Query: 286 RGEKYLSTKLFDTE 299 G +Y S +LF+ E Sbjct: 346 GGARYQS-RLFNAE 358 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: 324 Number of extensions: 18 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: 372 Length adjustment: 28 Effective length of query: 271 Effective length of database: 344 Effective search space: 93224 Effective search space used: 93224 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: 49 (23.5 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