Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Dsui_1954 Dsui_1954 cysteine synthase B
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__PS:Dsui_1954 Length = 299 Score = 256 bits (653), Expect = 6e-73 Identities = 134/299 (44%), Positives = 196/299 (65%), Gaps = 6/299 (2%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQ----MYAKLEGFNPTGSVKDRIALKMIEQAEAE 57 +Y + + +GNTPLV++ L Q + AKLEG NP GSVKDR AL MI AE Sbjct: 1 MYKTLEDFVGNTPLVQLKRLPGEAIAQRGNVILAKLEGNNPAGSVKDRPALSMISHAEQR 60 Query: 58 GKLHPGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDK 117 G++ PG T+IEATSGNTGI LAM ++GY +I+VM E S+ERR+ ++A+GAE+ILT + Sbjct: 61 GEIRPGDTLIEATSGNTGIALAMAAAMRGYRMILVMPENQSLERRQTMRAYGAELILTPR 120 Query: 118 KLGTDGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAV 177 G + A R VAE + + GK +QF+N N +AH++ T EIW TKG VTHFV+++ Sbjct: 121 DGGMELA-RDVAEKMCDE-GKGIILDQFANPDNPLAHFEGTGPEIWRDTKGQVTHFVSSM 178 Query: 178 GTSGTLMGVGKNLREKNPEIKIIEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIE 237 GT+GT++G + L++KNP I+I+ QP +G I G++ EA +P IY+ ++D + Sbjct: 179 GTTGTIIGTSQFLKKKNPRIQIVGCQPEEGSQIPGIRKWPEAYLPKIYERSRVDRLEYVS 238 Query: 238 SEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLFADRGEKYLSTKLF 296 EA R + +EG+F G+SSG A+ A +LA ++++ IV + DRG++YLST +F Sbjct: 239 QAEAEDMTRRLAREEGLFAGISSGGALAVALRLARELENATIVTIVCDRGDRYLSTGVF 297 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: 303 Number of extensions: 9 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: 299 Length adjustment: 27 Effective length of query: 272 Effective length of database: 272 Effective search space: 73984 Effective search space used: 73984 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