Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_078428511.1 BK574_RS10070 cystathionine beta-lyase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_002019605.1:WP_078428511.1 Length = 387 Score = 380 bits (975), Expect = e-110 Identities = 188/378 (49%), Positives = 254/378 (67%) Query: 3 MQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIADL 62 +QT+L+H D TGAVSVPI ST+ Q ++Y RSGNPTR ALEE IA+L Sbjct: 7 LQTRLLHNNQKVDKETGAVSVPIQHASTFHQFDFDQFGTFDYGRSGNPTRAALEETIAEL 66 Query: 63 EGGVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIIDTS 122 EGGV+GFAFASG+A I F LL GDHV++ DVYGGTFR +VL + G+ T +D + Sbjct: 67 EGGVRGFAFASGMAAISTAFMLLSKGDHVVVTTDVYGGTFRFVTQVLNRLGIEYTFVDMT 126 Query: 123 DLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPL 182 + +I+ +I+ NTK +Y+ETPSNP +KITDL + ++AK +G LT VDNTF TP Q P+ Sbjct: 127 NNEEIEASIQENTKVIYVETPSNPTMKITDLREVVALAKKYGCLTFVDNTFMTPALQRPI 186 Query: 183 LLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGI 242 LG D+V+HS TK++GGHSDV+AGL +E + ++AF QN+ G VLG QD WL+ RG+ Sbjct: 187 ELGVDVVLHSATKFIGGHSDVIAGLAVVKDEEVGDQLAFLQNSFGSVLGVQDCWLVLRGL 246 Query: 243 KTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLK 302 KTL +RM+ K A +A +L++ P VERVYYPGL H Y + K Q GF +LSF LK Sbjct: 247 KTLHVRMEHSSKAANELALWLKEQPAVERVYYPGLKDHLGYNIQKDQAEGFGAVLSFELK 306 Query: 303 NDSEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRLSVGI 362 + FV +++ + SLG VES++ PA M+HA +P +RE GI DGL+RLSVG+ Sbjct: 307 DKEAVRQFVAQVEVPVFAVSLGAVESILSYPATMSHAAMPSAEREQRGISDGLLRLSVGL 366 Query: 363 EHEQDLLEDLEQAFAKIS 380 E+ +D+ D AF ++ Sbjct: 367 ENVEDIKRDFLNAFESLA 384 Lambda K H 0.318 0.136 0.394 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: 385 Number of extensions: 14 Number of successful extensions: 1 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: 380 Length of database: 387 Length adjustment: 30 Effective length of query: 350 Effective length of database: 357 Effective search space: 124950 Effective search space used: 124950 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 (21.7 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