Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Ga0059261_3644 Ga0059261_3644 cysteine synthase A
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Korea:Ga0059261_3644 Length = 306 Score = 216 bits (551), Expect = 4e-61 Identities = 127/302 (42%), Positives = 174/302 (57%), Gaps = 12/302 (3%) Query: 4 DNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPG 63 + ILETIGNTP +RI L P +V + K E NP GS+KDRIAL M+E AEA+G L PG Sbjct: 4 NTILETIGNTPHIRIQRLFPGAEV--WVKSERSNPGGSIKDRIALSMVEAAEADGSLKPG 61 Query: 64 STIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDG 123 TI+E TSGNTG+GLAM+ VKGY +I+VM E +SIERR+++ A+GA LT ++ G G Sbjct: 62 GTIVEPTSGNTGVGLAMVAAVKGYKLILVMPESMSIERRRLMLAYGATFDLTPREKGMKG 121 Query: 124 AIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQ-TKGTVTHFVAAVGTSGT 182 AI + E+V+ PG + P QF N N H KTTA+EI V + VGT G Sbjct: 122 AIERAVEIVESTPGAWM-PQQFENPANVDVHVKTTAQEILNDFADAPVDVIITGVGTGGH 180 Query: 183 LMGVGKNLREKNPEIKIIEAQPTKGHYIQG-------LKSMEEAIVPAIYQADKIDEHIL 235 + GV + L++ P +K+ +P I G ++ + VP D ID I Sbjct: 181 ITGVAETLKKSWPNLKVYAVEPELSPVISGGQPGPHPIQGIGAGFVPKNLHTDAIDGAIQ 240 Query: 236 IESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLF-ADRGEKYLSTK 294 +++ A AR +EG+ +G+SSGA + A K + +G V+ F D GE+YLS Sbjct: 241 VDAGNAKDYARRAAREEGLLVGISSGATLAAIAKKLPDLPAGSRVLGFNYDTGERYLSVP 300 Query: 295 LF 296 F Sbjct: 301 DF 302 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: 284 Number of extensions: 19 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: 306 Length adjustment: 27 Effective length of query: 272 Effective length of database: 279 Effective search space: 75888 Effective search space used: 75888 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