Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_035219688.1 G491_RS0120880 cysteine synthase family protein
Query= metacyc::MONOMER-20568 (299 letters) >NCBI__GCF_000429905.1:WP_035219688.1 Length = 310 Score = 175 bits (444), Expect = 1e-48 Identities = 103/295 (34%), Positives = 169/295 (57%), Gaps = 17/295 (5%) Query: 10 IGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGS--TII 67 + TPL+ + + +++ KLE N G++K R+A +MIE AE G + + T+I Sbjct: 17 LSRTPLLEFIDPSIGNECRIFIKLENQNVLGNMKTRVAYQMIEDAELNGIIDKRTEVTLI 76 Query: 68 EATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDGAIRK 127 E T GNTG GLA+IG +KGY +++V+ + S E+ K+++ GA + L+D G++ I K Sbjct: 77 EPTGGNTGAGLALIGGMKGYRIVLVIPDNFSSEKIKLLRILGANVFLSDSTKGSNSHILK 136 Query: 128 VAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTLMGVG 187 ELVK+NP + NQF NE N +AHY T +EI A + +F+ VG+ G++ G+G Sbjct: 137 TKELVKKNP-SWIYLNQFENESNMLAHYLNTGKEI-ADNLPKIDYFLTGVGSGGSISGIG 194 Query: 188 KNLREKNPEIKIIEAQP---------TKGHYIQGLKSMEEAIVPAIYQADKIDEHILIES 238 K ++E+ K++ QP T H I+G+ +VP I + ID +ES Sbjct: 195 KRIKERWSSAKVVGVQPLGCNILTGTTVNHCIEGI---SVGLVPKILDLEIIDGLHSVES 251 Query: 239 EEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDS-GVIVVLFADRGEKYLS 292 ++ + ++ +G+ +G+SS A +LAA ++++K++S VIV L D G Y S Sbjct: 252 HKSINYLKYLLKYKGLCVGISSAANILAAVEISQKVESESVIVTLAPDTGRNYFS 306 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: 256 Number of extensions: 19 Number of successful extensions: 5 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: 310 Length adjustment: 27 Effective length of query: 272 Effective length of database: 283 Effective search space: 76976 Effective search space used: 76976 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 10 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