Align Cysteine synthase 1; CS 1; O-acetylserine (thiol)-lyase 1; OAS-TL 1; O-acetylserine sulfhydrylase 1; O-succinylserine sulfhydrylase; EC 2.5.1.-; EC 2.5.1.47 (characterized)
to candidate Ga0059261_3452 Ga0059261_3452 Cysteine synthase
Query= SwissProt::Q7RYW6 (376 letters) >FitnessBrowser__Korea:Ga0059261_3452 Length = 330 Score = 337 bits (864), Expect = 3e-97 Identities = 176/324 (54%), Positives = 217/324 (66%), Gaps = 5/324 (1%) Query: 38 IAKGLTGAIGNTPLIRLNRLSEETGCEILGKAEFMNPGGSVKDRAALYVVKDAEERGLLR 97 +A IGNTPL+RL S GC+I GK EF NPG SVKDRAAL++V+DAE RGLL Sbjct: 3 VANDTIALIGNTPLVRLKGPSTAAGCDIYGKCEFANPGASVKDRAALFIVQDAEARGLLA 62 Query: 98 PGGTVVEGTAGNTGIGLAHVCRSKGYKLVIYMPNTQSQGKIDLLRLLGAEVYPVPAVAFE 157 PGGT+VEGTAGNTGIGLA V +KGYK +I MP TQS+ K+D LR LGAE+ VPA + Sbjct: 63 PGGTIVEGTAGNTGIGLALVGNAKGYKTIIVMPETQSREKMDTLRALGAELVLVPAAPYS 122 Query: 158 NPENYNHQARRHAERLDNAVWTNQFDNIANRRAHIETTGPEIWAQTGGKVDAFTCATGTG 217 NP ++ H +RR AE NA+W NQFDNIANR+AHI T EIW Q G++D FTCA GTG Sbjct: 123 NPGHFVHTSRRIAEETPNAIWANQFDNIANRKAHIVGTAEEIWTQMEGRIDGFTCAAGTG 182 Query: 218 GTFAGTTRYLKEVSGGRVKAFLADPPGSVLHSYFSSGGKLIERSGSSITEGIGQGRITDN 277 GT AG LKE RV L+DP G+ L+ Y++ G ++ GSS+ EGIGQGRIT N Sbjct: 183 GTIAGVGLGLKE-KDERVTIALSDPHGAALYEYYAHGE--LKAEGSSVAEGIGQGRITAN 239 Query: 278 LKQDVDLVDGSMTISDEKTIEMVYRCLDEEGLYLGASSTLNVVAAKEVAEKLGKGSTVVT 337 L+ +D ISDE+ +E V R L EEGL LG SS +NV A + +LG G + T Sbjct: 240 LEGAP--IDTQFRISDEEGLEWVERLLAEEGLCLGLSSGINVAGAVRLGRELGPGKRIAT 297 Query: 338 MLCDGAYRYADRLFSRKWLEQKNL 361 +LCD +RY L++R WL+ K L Sbjct: 298 ILCDTGFRYLSTLYNRDWLQSKGL 321 Lambda K H 0.316 0.134 0.392 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: 22 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: 376 Length of database: 330 Length adjustment: 29 Effective length of query: 347 Effective length of database: 301 Effective search space: 104447 Effective search space used: 104447 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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