Align [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized)
to candidate AO356_04305 AO356_04305 cysteine synthase
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_04305 Length = 324 Score = 172 bits (437), Expect = 8e-48 Identities = 111/322 (34%), Positives = 171/322 (53%), Gaps = 26/322 (8%) Query: 10 ALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLR 69 ++GNTPLV + R++PR V + AK+E RNP S+K R MI AE+ G L+ Sbjct: 11 SIGNTPLVQINRIAPRG--------VTILAKIEGRNPGYSVKCRIGANMIWDAESSGKLK 62 Query: 70 PGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGS 129 PG TI+EPTSGNTGI LA A +GY+L+ MP + S+ERR++L+ GA+++ + G Sbjct: 63 PGMTIVEPTSGNTGIGLAFVAAARGYKLMLTMPASMSIERRKVLKALGAELVLTEPAKGM 122 Query: 130 NTAVATAKELAATNPS-WVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLGTTG 187 A+ A E+ A++PS + M Q+ NPAN H TGPE+ D + VAG+GT G Sbjct: 123 KGAIEKAAEILASDPSKYFMPQQFDNPANPAIHEKTTGPEIWNDTDGAVDVLVAGVGTGG 182 Query: 188 TLMGTGRFLREHVAN-VKIVAAEPRYGEGV-------------YALRNMDEGFVPELYDP 233 T+ G R+++ + VA EP + + ++ + GFVP+ D Sbjct: 183 TITGVSRYIKNTCGKPILSVAVEPEVSPVITQAMAGHEIKPSPHKIQGIGAGFVPKNLDL 242 Query: 234 EILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVV 293 I+ V ++ L+ EGI GIS GA + A+ + G+ I +++ Sbjct: 243 SIVDLVERVTDDESKAMALRLMQEEGILCGISCGAAMAVAVRLAEKPEMQGK--TIVVIL 300 Query: 294 ADAGWKYLSTGAYAGSLDDAET 315 D+G +YLS+ ++ + ET Sbjct: 301 PDSGERYLSSMLFSDLFTEQET 322 Lambda K H 0.317 0.134 0.398 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: 294 Number of extensions: 22 Number of successful extensions: 5 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: 323 Length of database: 324 Length adjustment: 28 Effective length of query: 295 Effective length of database: 296 Effective search space: 87320 Effective search space used: 87320 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: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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