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 GFF1378 PGA1_c13950 cysteine synthase CysK
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Phaeo:GFF1378 Length = 344 Score = 120 bits (302), Expect = 4e-32 Identities = 102/318 (32%), Positives = 151/318 (47%), Gaps = 35/318 (11%) Query: 7 LLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADG 66 L A+G+TPL+ L R+S D + K E NP S+KDR A+ +I+ A A G Sbjct: 7 LADAIGHTPLIRLNRVS-------DETGCEILGKAEFMNPGQSVKDRAALYIIKDAIARG 59 Query: 67 LLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAE 126 L+PG TI+E T+GNTGI LA+ G++ + V+PE S E++ +L L GAQ++ A Sbjct: 60 DLKPGGTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGAQLVQVPAA 119 Query: 127 GGSNT------AVATAKELAATNPSW-VMLYQYGNPANTDSHYCGTGPELLADL-PEITH 178 N + AKELA T P+ + Q+ N AN +H T PE+ ++ Sbjct: 120 PYRNPNNFVRYSERLAKELAKTEPNGAIWANQFDNVANRQAHVETTAPEIWEQTGGKVDG 179 Query: 179 FVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDE-----GFVPELYDP 233 FV +G+ GTL G L+ VKI A+P G +Y+ E G + E Sbjct: 180 FVCAVGSGGTLAGVADALQP--KGVKIGLADP-MGAALYSYYTTGEIATEGGSIAEGIGQ 236 Query: 234 EILTAR---------YSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAG 284 +T Y + DA+ +L+H EG+ G S+ + A+ + A G Sbjct: 237 VRITKNLEGFKPDFCYQIEDRDALPYVFDLLHEEGLVLGGSSAINIAGAVRM---AKDMG 293 Query: 285 ERADIALVVADAGWKYLS 302 I V+ D G +Y S Sbjct: 294 PGKTIVTVLCDYGTRYQS 311 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: 314 Number of extensions: 13 Number of successful extensions: 2 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: 344 Length adjustment: 28 Effective length of query: 295 Effective length of database: 316 Effective search space: 93220 Effective search space used: 93220 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: 49 (23.5 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