Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Dsui_2043 Dsui_2043 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__PS:Dsui_2043 Length = 501 Score = 185 bits (469), Expect = 2e-51 Identities = 111/303 (36%), Positives = 170/303 (56%), Gaps = 19/303 (6%) Query: 7 LETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGSTI 66 L+ IG TPLV + H + P +++ KLE NP GS+KDR+A MI+ AE EG + PGST+ Sbjct: 52 LDLIGATPLVEVTHFDTGP-CRLFLKLESQNPGGSIKDRVARSMIDAAEKEGLIKPGSTL 110 Query: 67 IEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILT--DKKLGTDGA 124 +EAT+GNTG+ L ++G +GY V++V+ + +S E+ +KA GA +++T D +G Sbjct: 111 VEATAGNTGLALTLVGAQRGYKVVLVVPDKMSQEKIFALKALGARVVMTRSDVGVGHPEY 170 Query: 125 IRKVAE-LVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTL 183 + +A+ L E PG ++ NQF N N AH T E+W+Q KG + V VG+ GTL Sbjct: 171 YQDMAQRLASEIPGAWY-VNQFGNPNNPKAHETGTGPELWSQLKGRIDAVVCGVGSGGTL 229 Query: 184 MGVGKNLREKNPEIKIIEAQPTKG--------HYIQG-----LKSMEEAIVPAIYQADKI 230 G+ + R+K+P +K++ A P YI+ ++ + E +P I + Sbjct: 230 TGLTRFFRQKSPRVKMVLADPAGSVLADYVAHGYIKEAGSWLVEGIGEDFIPPICDLTGV 289 Query: 231 DEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLF-ADRGEK 289 E + E+FA ARE++ +EGI G S+G + AA + VV F D G + Sbjct: 290 REAYTVPDAESFAAARELLRKEGIMGGSSTGTLLAAALRYCRTRTKPEHVVTFVCDHGNR 349 Query: 290 YLS 292 YLS Sbjct: 350 YLS 352 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: 383 Number of extensions: 23 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: 501 Length adjustment: 30 Effective length of query: 269 Effective length of database: 471 Effective search space: 126699 Effective search space used: 126699 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: 50 (23.9 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