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 WP_037575993.1 BS73_RS24550 cysteine synthase
Query= BRENDA::P9WP53 (323 letters) >NCBI__GCF_000744815.1:WP_037575993.1 Length = 322 Score = 457 bits (1177), Expect = e-133 Identities = 230/322 (71%), Positives = 262/322 (81%), Gaps = 2/322 (0%) Query: 3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQA 62 RY+S LQA+GNTPLVGL R+S D G + VR+WAKLEDRNPTGS+KDRPA+ MIE+A Sbjct: 2 RYESPLQAVGNTPLVGLPRISAEID-GNESGDVRIWAKLEDRNPTGSVKDRPALNMIERA 60 Query: 63 EADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIF 122 EA+G + PG TILEPTSGNTGISLAMAA+LKGYR++CVMPENTS ERR+LL ++GA++I Sbjct: 61 EAEGRISPGDTILEPTSGNTGISLAMAAKLKGYRMVCVMPENTSEERRELLRMWGAEVIP 120 Query: 123 SAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAG 182 S A GGSNTAV AKELA +P WVMLYQYGN N +HY GTGPE+LADLP +THFVAG Sbjct: 121 SPAAGGSNTAVRVAKELAEEHPDWVMLYQYGNADNAGAHYSGTGPEILADLPTVTHFVAG 180 Query: 183 LGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSV 242 LGTTGTLMG GR+LRE V VKIVAAEPRY + VY LRN+DEGFVPELYD E+LT RYSV Sbjct: 181 LGTTGTLMGVGRYLREKVPGVKIVAAEPRYDDLVYGLRNLDEGFVPELYDAEVLTTRYSV 240 Query: 243 GAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLS 302 G+ DAVRRTREL+ EGIFAGISTGA LHAA GV A AGERAD+ VVAD GWKYLS Sbjct: 241 GSADAVRRTRELLQLEGIFAGISTGAALHAACGVARKAATAGERADVVFVVADGGWKYLS 300 Query: 303 TGAY-AGSLDDAETALEGQLWA 323 TG Y A + + A L+GQLWA Sbjct: 301 TGVYTAETTEAAIETLQGQLWA 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: 426 Number of extensions: 13 Number of successful extensions: 3 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: 322 Length adjustment: 28 Effective length of query: 295 Effective length of database: 294 Effective search space: 86730 Effective search space used: 86730 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 Jul 26 2024. The underlying query database was built on Jul 25 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