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 RR42_RS21960 RR42_RS21960 cysteine synthase
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Cup4G11:RR42_RS21960 Length = 305 Score = 199 bits (506), Expect = 7e-56 Identities = 124/310 (40%), Positives = 171/310 (55%), Gaps = 19/310 (6%) Query: 5 DSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEA 64 D++LQ +GNTP + +QRL G ++W K E NP GSIKDR A+ M+E AE Sbjct: 4 DNILQTIGNTPHIRVQRLF--------GDTHQVWIKSERANPGGSIKDRIALSMVEAAEQ 55 Query: 65 DGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSA 124 G+L+PG TI+EPTSGNTGI LAM A +KGY+L+ VMP++ SVERR+L+ YGA + Sbjct: 56 SGVLKPGGTIIEPTSGNTGIGLAMVAAVKGYKLVLVMPDSMSVERRRLMLAYGATFDLTP 115 Query: 125 AEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPE-ITHFVAGL 183 E G A+A A+EL A P M Q+ NPAN ++H T E+LAD P+ I V G+ Sbjct: 116 REKGMKGAIARAEELVAATPGAWMPQQFENPANIEAHVNTTALEILADFPQGIDALVTGV 175 Query: 184 GTTGTLMGTGRFLREHVANVKIVAAEPRYGEGV-------YALRNMDEGFVPELYDPEIL 236 GT G + G R L++ +K+ A EP + + ++ + GF+P D +L Sbjct: 176 GTGGHITGCARVLKQKWPALKVYAVEPVASPVISGGAPAPHPIQGIGAGFIPRNLDTALL 235 Query: 237 TARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADA 296 V A A R EG+ GIS+GA L AA+ L AG A + D Sbjct: 236 DGVIQVDAEPAREMARRAAREEGMLVGISSGATL-AAIAQKLPDLPAG--ATVLGFNYDT 292 Query: 297 GWKYLSTGAY 306 G +YL+ + Sbjct: 293 GERYLTVEGF 302 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: 293 Number of extensions: 16 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: 323 Length of database: 305 Length adjustment: 27 Effective length of query: 296 Effective length of database: 278 Effective search space: 82288 Effective search space used: 82288 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