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 Dsui_1954 Dsui_1954 cysteine synthase B
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__PS:Dsui_1954 Length = 299 Score = 232 bits (592), Expect = 7e-66 Identities = 129/304 (42%), Positives = 184/304 (60%), Gaps = 9/304 (2%) Query: 4 YDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAE 63 Y +L +GNTPLV L+RL R + AKLE NP GS+KDRPA+ MI AE Sbjct: 2 YKTLEDFVGNTPLVQLKRLPGEAIAQRGNV---ILAKLEGNNPAGSVKDRPALSMISHAE 58 Query: 64 ADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFS 123 G +RPG T++E TSGNTGI+LAMAA ++GYR+I VMPEN S+ERRQ + YGA++I + Sbjct: 59 QRGEIRPGDTLIEATSGNTGIALAMAAAMRGYRMILVMPENQSLERRQTMRAYGAELILT 118 Query: 124 AAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAG 182 +GG A A+++ ++L Q+ NP N +H+ GTGPE+ D ++THFV+ Sbjct: 119 PRDGGMELARDVAEKMCDEGKG-IILDQFANPDNPLAHFEGTGPEIWRDTKGQVTHFVSS 177 Query: 183 LGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSV 242 +GTTGT++GT +FL++ ++IV +P G + +R E ++P++Y+ + V Sbjct: 178 MGTTGTIIGTSQFLKKKNPRIQIVGCQPEEGSQIPGIRKWPEAYLPKIYERSRVDRLEYV 237 Query: 243 GAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLS 302 +A TR L EG+FAGIS+G L AL + E A I +V D G +YLS Sbjct: 238 SQAEAEDMTRRLAREEGLFAGISSGGALAVALRLAREL----ENATIVTIVCDRGDRYLS 293 Query: 303 TGAY 306 TG + Sbjct: 294 TGVF 297 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: 307 Number of extensions: 15 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: 299 Length adjustment: 27 Effective length of query: 296 Effective length of database: 272 Effective search space: 80512 Effective search space used: 80512 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