Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate Dsui_2042 Dsui_2042 cystathionine beta-lyase/cystathionine gamma-synthase
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__PS:Dsui_2042 Length = 392 Score = 405 bits (1042), Expect = e-118 Identities = 215/382 (56%), Positives = 263/382 (68%), Gaps = 11/382 (2%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGY-----EYSRSGNPTRFALEELI 59 T+ IH G D TTGAVS+PIY TSTY Q A+ K Y +Y+RS NPTR ALE I Sbjct: 9 TRAIHAGQEPDPTTGAVSIPIYATSTYVQPALNEPKQYAGATFDYARSANPTRLALERCI 68 Query: 60 ADLEGGV----KGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNG-L 114 ADLEGG GFAFASGLA V LL +G HV+ DD+YGG+ RLFN+V + L Sbjct: 69 ADLEGGAFATATGFAFASGLAASATVLELLPAGSHVVASDDLYGGSVRLFNRVRSNSADL 128 Query: 115 SCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFA 174 T D S I+ AI P TK L++ETPSNPLLK+ DL A++ KD GLLT+ DNTFA Sbjct: 129 KVTYADFSSRESIEAAITPETKLLWVETPSNPLLKLVDLDLVAAIGKDRGLLTVADNTFA 188 Query: 175 TPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQD 234 +P+ Q PL G DIVVHS TKYL GHSDV+AG+ T LA+ +AF QNA G VLGP D Sbjct: 189 SPWIQRPLEHGFDIVVHSATKYLNGHSDVIAGVAVTARADLAERLAFLQNAAGAVLGPFD 248 Query: 235 SWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFS 294 ++L RG+KTL LRM+ H NA +A +LE+HP +E+V+YPGL +HP +ELAK+QMRGF Sbjct: 249 AFLALRGLKTLALRMERHCANAEAIARWLEQHPAIEKVHYPGLASHPQHELAKRQMRGFG 308 Query: 295 GMLSFTLKND-SEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRD 353 GM+S +K A +E+ K+F+L ESLGGVESL+ +PA MTHA +P QR GI D Sbjct: 309 GMVSAVVKGGLPAAKKLLENTKIFVLAESLGGVESLIELPALMTHASVPPEQRRRIGIDD 368 Query: 354 GLVRLSVGIEHEQDLLEDLEQA 375 GLVRLSVG+E +DLL DLEQA Sbjct: 369 GLVRLSVGVEDVEDLLADLEQA 390 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: 462 Number of extensions: 22 Number of successful extensions: 5 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: 392 Length adjustment: 30 Effective length of query: 350 Effective length of database: 362 Effective search space: 126700 Effective search space used: 126700 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