Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate CA265_RS06375 CA265_RS06375 cystathionine gamma-synthase
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__Pedo557:CA265_RS06375 Length = 379 Score = 395 bits (1015), Expect = e-114 Identities = 202/379 (53%), Positives = 259/379 (68%), Gaps = 2/379 (0%) Query: 1 MHMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIA 60 M TK IH G D TTGAV PIYQTSTY Q + G +KGYEYSR NPTR ALE+ +A Sbjct: 1 MKFATKAIHAGQEPDPTTGAVMTPIYQTSTYWQKSPGDNKGYEYSRGTNPTRKALEDCLA 60 Query: 61 DLEGGVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIID 120 LE G AF+SG+ AV LLQ GD V+ G+D+YGG++R+F K+ K G+ +D Sbjct: 61 ALENAKYGLAFSSGMGATDAVLKLLQPGDEVITGNDLYGGSYRIFTKIFTKYGIKFHFLD 120 Query: 121 TSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQN 180 S I I TK +++ETP+NP ++I D+ A + K+ L+ VDNTFA+PY QN Sbjct: 121 LSKPENILPYINDKTKLVWIETPTNPTMQIIDIEGVAKITKEKNLILTVDNTFASPYLQN 180 Query: 181 PLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQR 240 P+ LGADIV+HS TKY+GGHSDVV G + TN+E L +++ F NA G GPQD++L+ R Sbjct: 181 PIDLGADIVMHSVTKYIGGHSDVVMGALVTNDEQLYKDLWFIYNACGATPGPQDAFLVLR 240 Query: 241 GIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFT 300 GIKTL LRM+AH +N +A +L+ HPKV+++Y+PG HPN+++AKKQMRGF GM+S T Sbjct: 241 GIKTLHLRMKAHCENGERIAHYLKTHPKVDKIYWPGFEDHPNHDIAKKQMRGFGGMISIT 300 Query: 301 LKN-DSEATPFVES-LKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRL 358 LK D E T + S K+F L ESLGGVESL+ PA MTH IPK +RE G+ D L+RL Sbjct: 301 LKGADLEETFRISSNFKVFTLAESLGGVESLINHPATMTHGSIPKEEREKVGVTDNLLRL 360 Query: 359 SVGIEHEQDLLEDLEQAFA 377 SVG+E DLLEDL A A Sbjct: 361 SVGVEDIDDLLEDLANALA 379 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: 450 Number of extensions: 17 Number of successful extensions: 2 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: 379 Length adjustment: 30 Effective length of query: 350 Effective length of database: 349 Effective search space: 122150 Effective search space used: 122150 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