Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate CCNA_01493 CCNA_01493 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Caulo:CCNA_01493 Length = 332 Score = 173 bits (438), Expect = 6e-48 Identities = 118/313 (37%), Positives = 160/313 (51%), Gaps = 21/313 (6%) Query: 5 NILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGS 64 ++L+ IGNTPL+R+ + ++ K E NP SVKDR AL +I AEA+G L PG Sbjct: 6 SVLDAIGNTPLIRLARASEATGCEILGKAEFMNPGQSVKDRAALAIIRDAEAKGLLRPGG 65 Query: 65 TIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTD--KKLGTD 122 I+E T+GNTGIGLAM+ GY IV+ S E++ I+ GAE++ D D Sbjct: 66 RIVEGTAGNTGIGLAMVASALGYKTTIVIPRTQSQEKKDAIRLLGAELVEVDAVPYSNPD 125 Query: 123 GAI----RKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVG 178 + R EL + P NQF N N+ AHY TT EI+ QT G V F+ AVG Sbjct: 126 NYVRYSGRLAEELARTEPHGVIWANQFDNTANRDAHYHTTGPEIFDQTSGKVDGFICAVG 185 Query: 179 TSGTLMGVGKNLREKNPEIKIIEAQP----TKGHYIQG-LKSMEEAIVPAIYQAD----- 228 + GTL GV LRE+ P ++I A P Y G LKS +I I Q Sbjct: 186 SGGTLAGVAAALRERKPGVRIGLADPYGAALYAWYKDGELKSEGSSISEGIGQGRITANL 245 Query: 229 ---KIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG-VIVVLFA 284 ID+ + +E ++V EG+ +G S+G + A KLA + G IV + Sbjct: 246 EGLAIDDPFRVSDQEMLEVLYDLVQHEGLCLGGSAGINVAGAIKLATAMGPGHTIVTVLC 305 Query: 285 DRGEKYLSTKLFD 297 D G +Y S KLF+ Sbjct: 306 DHGSRYQS-KLFN 317 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: 285 Number of extensions: 15 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: 332 Length adjustment: 27 Effective length of query: 272 Effective length of database: 305 Effective search space: 82960 Effective search space used: 82960 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