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 352607 BT3080 cysteine synthase A (NCBI ptt file)
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Btheta:352607 Length = 315 Score = 211 bits (538), Expect = 1e-59 Identities = 127/309 (41%), Positives = 174/309 (56%), Gaps = 15/309 (4%) Query: 7 LLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADG 66 L +GNTPL+ L + +G RL K+E NP GS+KDR A+ MIE AE G Sbjct: 8 LTDLVGNTPLLELSNYNKS-----NGLKARLIVKIESFNPAGSVKDRVALAMIEDAEMKG 62 Query: 67 LLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAE 126 +L PGATI+EPTSGNTG+ LA A KGY+LI MP+ SVERR LL+ GA+++ + Sbjct: 63 VLTPGATIIEPTSGNTGVGLAFVAAAKGYKLILTMPDTMSVERRNLLKALGAELVLTPGA 122 Query: 127 GGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLGT 185 G A+A A+EL A P V+L Q+ NPAN H TG E+ D ++ FVAG+GT Sbjct: 123 DGMKGAIAKAEELKAATPGSVILQQFENPANPAMHLRTTGLEIWRDTEGKVDIFVAGVGT 182 Query: 186 TGTLMGTGRFLREHVANVKIVAAEPRYG-------EGVYALRNMDEGFVPELYDPEILTA 238 GT+ G G L+ +VK VA EP G + ++ + GFVP+ Y+ ++ Sbjct: 183 GGTISGVGEALKMRDPSVKAVAVEPADSPVLSGGKPGPHKIQGIGAGFVPKTYNASVVDE 242 Query: 239 RYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGW 298 V DA+R +R L EG+ GIS+GA ++AA + G+ I ++ D G Sbjct: 243 IIQVQNDDAIRTSRALAEEEGLLVGISSGAAVYAATELAKRPENEGKM--IVALLPDTGE 300 Query: 299 KYLSTGAYA 307 +YLST YA Sbjct: 301 RYLSTILYA 309 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: 280 Number of extensions: 13 Number of successful extensions: 4 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: 315 Length adjustment: 28 Effective length of query: 295 Effective length of database: 287 Effective search space: 84665 Effective search space used: 84665 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 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