Align cysteine synthase (characterized)
to candidate WP_027722880.1 H589_RS0115570 cysteine synthase family protein
Query= CharProtDB::CH_124760 (351 letters) >NCBI__GCF_000425265.1:WP_027722880.1 Length = 312 Score = 231 bits (589), Expect = 2e-65 Identities = 129/309 (41%), Positives = 184/309 (59%), Gaps = 4/309 (1%) Query: 20 AIGRTPLIRLNTLSNETGCNILAKAEFQNPGGSVKDRAAYYVVRDAEKKGKLSRGGTIVE 79 AIG TPLI L L+ + I AK EF NPGGSVKDR Y++ + EK GKL RGG IVE Sbjct: 7 AIGNTPLIELKNLTGISNIRIYAKLEFLNPGGSVKDRMVSYILNEYEKSGKLQRGGVIVE 66 Query: 80 GTAGNTGIGLAHIARARGYKCVIYMPNTQSQAKIDTLKFLGAEVHPVPV-APFSNPLNYN 138 T+GNTG LA +A +GY+ ++ MP+ S+ K +TLK LGAEV P A +P +Y Sbjct: 67 NTSGNTGAALAMLAVPKGYRVILTMPDKVSREKQETLKALGAEVIVCPTSASPGSPEHYV 126 Query: 139 HQARRHAESTPNASWTDQFDNVANLLSHYETTGPEIWDQTKGTVDGFTCSTGTGGTFAGV 198 +AR A +T NA +Q+DN N+ +HY +TGPEIW+ +G +D F + TGGT +GV Sbjct: 127 QKARDIASTTDNAVMLNQYDNRLNVEAHYNSTGPEIWNTLRGNIDYFVAAGSTGGTISGV 186 Query: 199 TKYLKEKSDGRVASFVADPPGSVLYSHIKTKGKHPDNKGSSFTEGIGQGRITGNVQPVYD 258 K+LKE D ++ + DP GS+ Y + T ++ + EGIG+ I + + Sbjct: 187 GKFLKE-MDPKIKVVMPDPIGSIYYEYFNTGTYSQESISTYQVEGIGEDHIAKCMD--FS 243 Query: 259 LIDDAMKIPDEKSINMFFRLLDQEGLFLGGSSCLNVVAAVEMAKILGPGKTVVTILCDSG 318 ++D M+ D+ + + L +EG+F GGSS N+ +E+ L +VTIL DSG Sbjct: 244 IVDSMMQFTDDMAFSATRLLARKEGIFAGGSSGANIWGCLELMNSLEHPANIVTILPDSG 303 Query: 319 HKYATRLFS 327 KY +++FS Sbjct: 304 VKYLSKIFS 312 Lambda K H 0.317 0.135 0.400 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: 323 Number of extensions: 16 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: 351 Length of database: 312 Length adjustment: 28 Effective length of query: 323 Effective length of database: 284 Effective search space: 91732 Effective search space used: 91732 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: 49 (23.5 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