Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate YP_001312755.1 Smed_4014 cystathionine gamma-synthase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000017145.1:YP_001312755.1 Length = 400 Score = 275 bits (704), Expect = 1e-78 Identities = 148/370 (40%), Positives = 219/370 (59%), Gaps = 14/370 (3%) Query: 20 AVSVPIYQTSTYRQDA-------IGHHKGYE-YSRSGNPTRFALEELIADLEGGVKGFAF 71 ++S PIY ++ ++ D G K YSR GNPT + EE IA L GG A Sbjct: 23 SISYPIYMSANFQYDGDIYDQIVAGARKEVNIYSRCGNPTEYKFEEHIAKLTGGTACLAT 82 Query: 72 ASGLAGI-HAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIIDTSDLSQIKKA 130 ASG+A I HA+F +L++GDH++ Y T F+ GL +++D +D+ ++ A Sbjct: 83 ASGMAAISHALFGILKAGDHIVADLTTYSSTHEFFDHRAQDFGLKVSLVDCTDVRAVENA 142 Query: 131 IKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLLLGADIVV 190 + TK LY+E +NP +K+ L +A G++ I DNTFA+P P G D+VV Sbjct: 143 LTEETKVLYVEAIANPTMKVPPLKALVELAHARGIVVICDNTFASPAVCRPHDFGVDVVV 202 Query: 191 HSGTKYLGGHSDVVAGLVTTNNEALA----QEIAFFQ-NAIGGVLGPQDSWLLQRGIKTL 245 S TK++GGH+D V G++T ++ L +++ + N +G L P ++WLL RG +TL Sbjct: 203 ESATKFIGGHNDAVGGVITLKSDILPPDWLEDVRWNTLNKLGAPLSPFNAWLLLRGAQTL 262 Query: 246 GLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKNDS 305 LR++ NAL +A+ LE HP+V RV+YPGLP+HPNY AK+Q+RG MLSF + +++ Sbjct: 263 ALRLEKQCANALALAKHLEAHPRVRRVFYPGLPSHPNYASAKEQLRGGGAMLSFQVDDEA 322 Query: 306 EATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRLSVGIEHE 365 ++ L+L SLGG+ + VPA M IP +REA G+ DGLVR SVGIEH Sbjct: 323 SGVRLLKRLQLCSFAASLGGLRTTTQVPATMAFLDIPSQEREAMGVVDGLVRFSVGIEHI 382 Query: 366 QDLLEDLEQA 375 D++ D++ A Sbjct: 383 DDIIADVDSA 392 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: 407 Number of extensions: 17 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: 400 Length adjustment: 30 Effective length of query: 350 Effective length of database: 370 Effective search space: 129500 Effective search space used: 129500 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 10 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