Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Ga0059261_3452 Ga0059261_3452 Cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Korea:Ga0059261_3452 Length = 330 Score = 184 bits (467), Expect = 2e-51 Identities = 116/307 (37%), Positives = 161/307 (52%), Gaps = 15/307 (4%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 + ++ + IGNTPLVR+ + +Y K E NP SVKDR AL +++ AEA G L Sbjct: 3 VANDTIALIGNTPLVRLKGPSTAAGCDIYGKCEFANPGASVKDRAALFIVQDAEARGLLA 62 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTD-KKLG 120 PG TI+E T+GNTGIGLA++G KGY IIVM E S E+ ++A GAE++L Sbjct: 63 PGGTIVEGTAGNTGIGLALVGNAKGYKTIIVMPETQSREKMDTLRALGAELVLVPAAPYS 122 Query: 121 TDGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTS 180 G + + E NQF N N+ AH TAEEIW Q +G + F A GT Sbjct: 123 NPGHFVHTSRRIAEETPNAIWANQFDNIANRKAHIVGTAEEIWTQMEGRIDGFTCAAGTG 182 Query: 181 GTLMGVGKNLREKNPEIKIIEAQPTKG----HYIQG-LK----SMEEAI----VPAIYQA 227 GT+ GVG L+EK+ + I + P +Y G LK S+ E I + A + Sbjct: 183 GTIAGVGLGLKEKDERVTIALSDPHGAALYEYYAHGELKAEGSSVAEGIGQGRITANLEG 242 Query: 228 DKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGV-IVVLFADR 286 ID I EE ++A+EG+ +G+SSG + A +L ++ G I + D Sbjct: 243 APIDTQFRISDEEGLEWVERLLAEEGLCLGLSSGINVAGAVRLGRELGPGKRIATILCDT 302 Query: 287 GEKYLST 293 G +YLST Sbjct: 303 GFRYLST 309 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: 333 Number of extensions: 23 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: 330 Length adjustment: 27 Effective length of query: 272 Effective length of database: 303 Effective search space: 82416 Effective search space used: 82416 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