Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate PP_4571 PP_4571 cysteine synthase A
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Putida:PP_4571 Length = 324 Score = 224 bits (572), Expect = 2e-63 Identities = 132/314 (42%), Positives = 179/314 (57%), Gaps = 23/314 (7%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 I+ + +IGNTPLV+IN + P V + AK+EG NP SVK RI M+ AE+ GKL Sbjct: 4 IFADNAHSIGNTPLVQINRIAPRG-VTILAKIEGRNPGYSVKCRIGANMVWDAESSGKLK 62 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGT 121 PG TI+E TSGNTGIGLA + +GY +++ M +S+ERRK++KA GAE++LTD G Sbjct: 63 PGMTIVEPTSGNTGIGLAFVAAARGYKLMLTMPASMSLERRKVLKALGAELVLTDPAKGM 122 Query: 122 DGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSG 181 GAI K E+V +P +YF P QF N N H KTT EIW T G + VA VGT G Sbjct: 123 KGAIEKANEIVASDPEQYFLPGQFENPANPAIHEKTTGPEIWNDTDGAIDVLVAGVGTGG 182 Query: 182 TLMGVGKNLRE-KNPEIKIIEAQPTKG----------------HYIQGLKSMEEAIVPAI 224 T+ GV + ++ + I + +P H IQG+ + VP Sbjct: 183 TITGVSRYIKHTQGKAILSVAVEPVASPLISQTLAGEELKPSPHKIQGIGA---GFVPKN 239 Query: 225 YQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEK--IDSGVIVVL 282 +D+ + EE+ A A ++ +EGI G+S GAAM AA +LAEK + IVV+ Sbjct: 240 LDLSIVDQVETVTDEESKAMAIRLMQEEGILCGISCGAAMAAAVRLAEKPEMQGKTIVVI 299 Query: 283 FADRGEKYLSTKLF 296 D GE+YLS+ LF Sbjct: 300 LPDSGERYLSSMLF 313 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: 290 Number of extensions: 12 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: 324 Length adjustment: 27 Effective length of query: 272 Effective length of database: 297 Effective search space: 80784 Effective search space used: 80784 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