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_086510266.1 BZY95_RS12545 cysteine synthase CysM
Query= BRENDA::P9WP53 (323 letters) >NCBI__GCF_002151265.1:WP_086510266.1 Length = 298 Score = 226 bits (576), Expect = 5e-64 Identities = 127/306 (41%), Positives = 182/306 (59%), Gaps = 13/306 (4%) Query: 3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQA 62 ++ ++ +G+TPLV L+R++ G + L AKLE NP GS+KDRPA+ M+EQA Sbjct: 2 QFPTIEDVVGHTPLVRLKRITA-------GRNNTLLAKLEGNNPAGSVKDRPALSMLEQA 54 Query: 63 EADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIF 122 EA G + PG T++E TSGNTGI+LAMAA +KGYR++ +MP++ S ER+Q + YGA++I Sbjct: 55 EARGDITPGDTLIEATSGNTGIALAMAAAIKGYRMVLIMPDSASSERKQAMAAYGARLIT 114 Query: 123 SAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADL-PEITHFVA 181 + EGG A A+ + + L Q+ NP N +HY GTGPEL ITHFV+ Sbjct: 115 VSKEGGMEEARDLAEAMVSRGEG-KPLNQFANPDNPLAHYRGTGPELWEQTGGTITHFVS 173 Query: 182 GLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYS 241 +GTTGT+MG R+L+E V+IV +P G + +R + ++P ++D + Sbjct: 174 SMGTTGTIMGVSRYLKERNPEVQIVGLQPEDGASIAGIRRWPKEYLPSIFDATRVDRVLD 233 Query: 242 VGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYL 301 +G +A R L EGI AG+S+G L AL V E A I +V D G +YL Sbjct: 234 IGQHEAEEHMRRLAREEGILAGVSSGGALAGALRVAEEV----ENAVIVFIVCDRGDRYL 289 Query: 302 STGAYA 307 STG +A Sbjct: 290 STGLFA 295 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: 325 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: 298 Length adjustment: 27 Effective length of query: 296 Effective length of database: 271 Effective search space: 80216 Effective search space used: 80216 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 10 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