Align Cysteine synthase 1; At.OAS.5-8; Beta-substituted Ala synthase 1;1; ARAth-Bsas1;1; CSase A; AtCS-A; Cys-3A; O-acetylserine (thiol)-lyase 1; OAS-TL A; O-acetylserine sulfhydrylase; Protein ONSET OF LEAF DEATH 3; EC 2.5.1.47 (characterized)
to candidate CA265_RS04375 CA265_RS04375 cystathionine beta-synthase
Query= SwissProt::P47998 (322 letters) >FitnessBrowser__Pedo557:CA265_RS04375 Length = 453 Score = 227 bits (578), Expect = 5e-64 Identities = 128/309 (41%), Positives = 183/309 (59%), Gaps = 17/309 (5%) Query: 8 DVTELIGNTPLVYLNNVAEGCVGRVAAKLEMMEPCSSVKDRIGFSMISDAEKKGLIKPGE 67 ++ E IGNTPLV LN + +G G + AK+E P +S+KDR+ MI DAEK G +KPG Sbjct: 5 NILETIGNTPLVKLNTITKGVPGTILAKIETTNPGNSIKDRMAVKMIEDAEKSGKLKPGG 64 Query: 68 SVLIEPTSGNTGVGLAFTAAAKGYKLIITMPASMSTERRIILLAFGVELVLTDP---AKG 124 ++ IE TSGNTG+GLA A KGYK I T S E+ L AFG E+++ + Sbjct: 65 TI-IEGTSGNTGMGLAMAAIIKGYKCIFTTTDKQSKEKVDALRAFGAEVIVCPTNVEPED 123 Query: 125 MKGAIAKAEEILAKTPNGYMLQQFENPANPKIHYETTGPEIWKGTGGKIDGFVSGIGTGG 184 + + + + + PN + Q++N AN + HYE TGPEIW T GKI V G+GTGG Sbjct: 124 PRSYYSVSSRLEREVPNSWKPNQYDNLANSQAHYEQTGPEIWAQTEGKITHLVVGVGTGG 183 Query: 185 TITGAGKYLKEQNANVKLYGVEPV--------ESAILSGGKPGPHKIQGIGAGFIPSVLN 236 TI+G GKYLKE+N N+K++G++ E+ I + P+ +GIG F+P+ +N Sbjct: 184 TISGTGKYLKEKNPNIKVWGIDTYGSVFKKYKETGIFDKDEIYPYITEGIGEDFLPANVN 243 Query: 237 VDLIDEVVQVSSDESIDMARQLALKEGLLVGISSGAAAAAAIKLAQ--RPENAGKLFVAI 294 D+ID +V+ ++ M R +A KEG+ VG S+GAA I+L +PE+ + V I Sbjct: 244 FDVIDLFEKVTDKDAALMTRDIARKEGIFVGNSAGAAIGGLIQLKDKLKPED---VVVVI 300 Query: 295 FPSFGERYL 303 F G RY+ Sbjct: 301 FHDHGSRYM 309 Lambda K H 0.315 0.134 0.374 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: 391 Number of extensions: 21 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: 322 Length of database: 453 Length adjustment: 30 Effective length of query: 292 Effective length of database: 423 Effective search space: 123516 Effective search space used: 123516 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: 42 (22.0 bits) S2: 50 (23.9 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