Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate Pf1N1B4_4890 Cystathionine gamma-lyase (EC 4.4.1.1)
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4890 Length = 393 Score = 401 bits (1030), Expect = e-116 Identities = 202/378 (53%), Positives = 271/378 (71%), Gaps = 3/378 (0%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIADLEG 64 T++IH G + D +TGA+ PIY STY Q + G HKG++Y RS NPTRFALE +ADLEG Sbjct: 15 TRVIHAGQTPDPSTGALMPPIYANSTYLQQSPGVHKGFDYGRSHNPTRFALERCVADLEG 74 Query: 65 GVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKN-GLSCTIIDTSD 123 G + FAFASGLA I V LL +G H++ G+D+YGGTFRLF+KV ++ G + +D +D Sbjct: 75 GTRAFAFASGLAAIANVLELLDAGAHIVSGNDLYGGTFRLFDKVRRRSAGHRFSFVDLTD 134 Query: 124 LSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLL 183 L+ + A++ +T+ +++ETPSNPLL +TDL A + + G++ + DNTFA+P+ Q PL Sbjct: 135 LAAFEAALEDDTRMVWVETPSNPLLSLTDLDAVARICRQRGIICVADNTFASPWIQRPLE 194 Query: 184 LGADIVVHSGTKYLGGHSDVVAGL-VTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGI 242 LG DIV+HS TKYL GHSDV+ G+ V N LA+ + F QNA+G + GP D++L RG+ Sbjct: 195 LGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELAERLGFLQNAVGAIAGPFDAFLTLRGV 254 Query: 243 KTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLK 302 KTL LRM+ H NAL +A++LE+ P+V RVYYPGLP+HP +ELA++QMRGF GM+S L Sbjct: 255 KTLALRMERHCSNALELAQWLERQPQVARVYYPGLPSHPQHELARRQMRGFGGMISLDLN 314 Query: 303 ND-SEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRLSVG 361 +D + A F+ES+++F L ESLGGVESL+ PA MTHA IP R GI D LVRLSVG Sbjct: 315 SDLAGAKRFLESVRIFALAESLGGVESLIEHPAIMTHASIPVETRAQLGIGDALVRLSVG 374 Query: 362 IEHEQDLLEDLEQAFAKI 379 +E +DL DL QA +I Sbjct: 375 VEDVEDLRADLAQALMRI 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: 449 Number of extensions: 17 Number of successful extensions: 4 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: 393 Length adjustment: 30 Effective length of query: 350 Effective length of database: 363 Effective search space: 127050 Effective search space used: 127050 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