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 GFF1601 Psest_1638 cysteine synthase B
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__psRCH2:GFF1601 Length = 300 Score = 220 bits (560), Expect = 4e-62 Identities = 122/306 (39%), Positives = 179/306 (58%), Gaps = 13/306 (4%) Query: 2 TRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQ 61 T Y ++ +GNTPLV LQR+ + + + KLE NP GS+KDRPA+ MI + Sbjct: 3 THYPTIADCIGNTPLVRLQRMPGKTSN-------TILVKLEGNNPAGSVKDRPALSMINR 55 Query: 62 AEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQII 121 AE G ++PG T++E TSGNTGI+LAMAA +KGYR+I +MP+N++ ER+ + YGA++I Sbjct: 56 AELRGDIQPGDTLIEATSGNTGIALAMAAAIKGYRMILIMPDNSTAERKAAMTAYGAELI 115 Query: 122 FSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADL-PEITHFV 180 + E G A A ++ A V L Q+ N N ++HY TGPEL ITHF+ Sbjct: 116 LVSKEEGMEGARDLALKMQAEGRGKV-LDQFANGDNPEAHYNSTGPELWRQTHGSITHFI 174 Query: 181 AGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARY 240 + +GTTGT+MG R+L+E V+IV +P G + +R + ++P++Y E + Sbjct: 175 SSMGTTGTIMGVSRYLKEQNPAVQIVGLQPMEGAAIPGIRRWPQEYLPKIYQAERVDRVV 234 Query: 241 SVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKY 300 + +A + R L EGIF G+S+G + AAL + E A I ++ D G +Y Sbjct: 235 DMSQAEAEQVMRRLAREEGIFCGVSSGGAVAAALRLSQEV----ENAVIVAIICDRGDRY 290 Query: 301 LSTGAY 306 LSTG Y Sbjct: 291 LSTGVY 296 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: 13 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: 300 Length adjustment: 27 Effective length of query: 296 Effective length of database: 273 Effective search space: 80808 Effective search space used: 80808 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