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 Echvi_0220 Echvi_0220 cysteine synthase B
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Cola:Echvi_0220 Length = 292 Score = 207 bits (528), Expect = 2e-58 Identities = 118/301 (39%), Positives = 179/301 (59%), Gaps = 13/301 (4%) Query: 7 LLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADG 66 L + +GNTPLV L+ + P+V+++ KLE +NP GS+KDR A MI++A G Sbjct: 3 LFELIGNTPLVELEHIPTN-------PNVKIYCKLEGQNPGGSVKDRAAYSMIKRAMDRG 55 Query: 67 LLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAE 126 L+ G ++E TSGNTGI+LAM A++ G + +MP+N++ ER +E YGA++I + A Sbjct: 56 DLKQGDRVVEATSGNTGIALAMIAKVLGVEMTLIMPDNSTRERVVSMEAYGAKVILTPAA 115 Query: 127 GGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADL-PEITHFVAGLGT 185 + A+E+ A N + +L Q+ NP N +HY GTGPE++ D EITHFV+ +GT Sbjct: 116 KTIEYSRTLAEEM-AKNEGYYILNQFANPDNYQAHYEGTGPEIMRDTNGEITHFVSAMGT 174 Query: 186 TGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAV 245 TGT+MG R+L+E V+IV +P G + +R F+P++YD + V Sbjct: 175 TGTIMGVSRYLKEQKPAVQIVGTQPTDGSSIPGIRRWSPEFLPKIYDASRVDQIIDVSQE 234 Query: 246 DAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGA 305 +A TR + EGI AG+S+G LHAA+ + A +L +G I + D G +YLS+ Sbjct: 235 EATEMTRRMAKEEGILAGMSSGGALHAAVKL-AESLDSGV---IVCITCDRGDRYLSSDL 290 Query: 306 Y 306 + Sbjct: 291 F 291 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: 262 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: 292 Length adjustment: 27 Effective length of query: 296 Effective length of database: 265 Effective search space: 78440 Effective search space used: 78440 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