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 PP_4571 PP_4571 cysteine synthase A
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Putida:PP_4571 Length = 324 Score = 170 bits (431), Expect = 4e-47 Identities = 113/322 (35%), Positives = 173/322 (53%), Gaps = 26/322 (8%) Query: 10 ALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLR 69 ++GNTPLV + R++PR V + AK+E RNP S+K R M+ AE+ G L+ Sbjct: 11 SIGNTPLVQINRIAPRG--------VTILAKIEGRNPGYSVKCRIGANMVWDAESSGKLK 62 Query: 70 PGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGS 129 PG TI+EPTSGNTGI LA A +GY+L+ MP + S+ERR++L+ GA+++ + G Sbjct: 63 PGMTIVEPTSGNTGIGLAFVAAARGYKLMLTMPASMSLERRKVLKALGAELVLTDPAKGM 122 Query: 130 NTAVATAKELAATNPSWVML-YQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLGTTG 187 A+ A E+ A++P L Q+ NPAN H TGPE+ D I VAG+GT G Sbjct: 123 KGAIEKANEIVASDPEQYFLPGQFENPANPAIHEKTTGPEIWNDTDGAIDVLVAGVGTGG 182 Query: 188 TLMGTGRFLREHVAN-VKIVAAEP---------RYGEGV----YALRNMDEGFVPELYDP 233 T+ G R+++ + VA EP GE + + ++ + GFVP+ D Sbjct: 183 TITGVSRYIKHTQGKAILSVAVEPVASPLISQTLAGEELKPSPHKIQGIGAGFVPKNLDL 242 Query: 234 EILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVV 293 I+ +V ++ L+ EGI GIS GA + AA+ + G+ I +++ Sbjct: 243 SIVDQVETVTDEESKAMAIRLMQEEGILCGISCGAAMAAAVRLAEKPEMQGK--TIVVIL 300 Query: 294 ADAGWKYLSTGAYAGSLDDAET 315 D+G +YLS+ ++ + ET Sbjct: 301 PDSGERYLSSMLFSDMFSEQET 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: 280 Number of extensions: 16 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 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