Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Dsui_2521 Dsui_2521 cysteine synthase A
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__PS:Dsui_2521 Length = 328 Score = 205 bits (521), Expect = 1e-57 Identities = 121/308 (39%), Positives = 167/308 (54%), Gaps = 22/308 (7%) Query: 9 TIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGSTIIE 68 +IG TPLVR+N + + AK+EG NP SVK RI M+ AE G L PG ++E Sbjct: 14 SIGRTPLVRLNRVTDGAPATVLAKIEGRNPAYSVKCRIGAAMVWDAEIRGLLGPGKELVE 73 Query: 69 ATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDGAIRKV 128 TSGNTGI LA + V G + + M E +S+ERRK++ A+GA+++LT+ G GAI K Sbjct: 74 PTSGNTGIALAFVAAVYGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGTKGMGGAIAKA 133 Query: 129 AELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTLMGVGK 188 E+ +PGKY QF N N H TT EIW T V FV+ VGT GT+ GV + Sbjct: 134 EEIAASDPGKYVLLQQFKNPANPAIHESTTGPEIWIDTDDKVDIFVSGVGTGGTITGVSR 193 Query: 189 NLREK----------NPEIKIIEAQPTKG-------HYIQGLKSMEEAIVPAIYQADKID 231 ++ P + Q G H IQG+ + VP + ID Sbjct: 194 YFKKTRGAKLWSVAVEPSASPVLTQTRNGEPVKPGPHKIQGIGA---GFVPQVLDLSLID 250 Query: 232 EHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG--VIVVLFADRGEK 289 + +EEA A AR + +EGI G+SSGAA+ A +LA++ ++ IVV+ D GE+ Sbjct: 251 AIEQVSNEEAVAYARRLAREEGIISGISSGAAVAVASRLAQRRENAGKTIVVILPDSGER 310 Query: 290 YLSTKLFD 297 YLS+ LF+ Sbjct: 311 YLSSVLFE 318 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: 306 Number of extensions: 14 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: 328 Length adjustment: 27 Effective length of query: 272 Effective length of database: 301 Effective search space: 81872 Effective search space used: 81872 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