Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_011388544.1 RRU_RS04120 PLP-dependent aspartate aminotransferase family protein
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000013085.1:WP_011388544.1 Length = 390 Score = 409 bits (1050), Expect = e-119 Identities = 211/377 (55%), Positives = 263/377 (69%), Gaps = 2/377 (0%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIADLEG 64 T +H G DATTGAV PIY TST+ Q + G H G+EY+RSGNPTR A E +A+LEG Sbjct: 14 TWAVHAGHGADATTGAVMTPIYATSTFAQSSPGKHTGWEYARSGNPTRAAFERAVAELEG 73 Query: 65 GVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKN-GLSCTIIDTSD 123 G G+AFASGLA + LL G H++ GDD+YGG++RLF KV ++ GL+ + +D SD Sbjct: 74 GTNGYAFASGLAAEATILDLLDHGAHIIAGDDLYGGSWRLFEKVRARSAGLTVSYVDPSD 133 Query: 124 LSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLL 183 L + +AI P TK +++ETPSNPLLKI DLA A++AK+HGL T+VD+TFATP+ Q PL Sbjct: 134 LGAVAQAITPQTKLIWIETPSNPLLKIADLAALAALAKEHGLRTVVDSTFATPWIQRPLD 193 Query: 184 LGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGIK 243 LG DIVVHS TKYL GHSDV+AG+V + LA ++ F QNA G VL P ++L RG+K Sbjct: 194 LGIDIVVHSATKYLNGHSDVIAGVVVVKDPDLASQLGFLQNATGAVLDPFAAFLALRGLK 253 Query: 244 TLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKN 303 TL LRM H N L VA LE KV RV YPGL +HP + LA++QMR F GML+ L++ Sbjct: 254 TLALRMDRHSANGLAVAHALEGRAKVRRVLYPGLASHPQHALARQQMRAFGGMLTLDLES 313 Query: 304 DSEAT-PFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRLSVGI 362 D T F+E+LKLF L ESLGGVESL G P M+H IP +R A GI D LVRLSVGI Sbjct: 314 DLAGTVRFLEALKLFTLAESLGGVESLAGHPVTMSHGSIPVERRTALGITDTLVRLSVGI 373 Query: 363 EHEQDLLEDLEQAFAKI 379 E DL+ DL+QA A + Sbjct: 374 EDAGDLIADLDQALAVV 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: 475 Number of extensions: 26 Number of successful extensions: 3 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: 390 Length adjustment: 30 Effective length of query: 350 Effective length of database: 360 Effective search space: 126000 Effective search space used: 126000 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 Jul 25 2024. The underlying query database was built on Jul 25 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