Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate BWI76_RS16730 BWI76_RS16730 cystathionine gamma-lyase
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__Koxy:BWI76_RS16730 Length = 395 Score = 322 bits (825), Expect = 1e-92 Identities = 166/375 (44%), Positives = 237/375 (63%), Gaps = 2/375 (0%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIADLEG 64 T +H G D T A+ PI S++ Q + + YSR NPTR A E +A+LEG Sbjct: 10 TLAVHAGNQSDPVTHAIFTPIVTASSFIQPNLYEGGDFCYSRVSNPTRKAYESALAELEG 69 Query: 65 GVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKN-GLSCTIIDTSD 123 G+ A ASG+A + V LL H++ VYGGT+RLF K+ G++ + ID +D Sbjct: 70 GIYATATASGMAATNIVMELLPKDAHIIAMKGVYGGTWRLFEKLKTHTTGVTISYIDLND 129 Query: 124 LSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLL 183 + I+ NT +++ETP+NPLL++ D+A+ +AK+ + T VDNTFA+ + PL Sbjct: 130 EQSLINTIQENTALIWIETPTNPLLELVDIAKVCRIAKERAITTCVDNTFASAWNHKPLE 189 Query: 184 LGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGIK 243 +GAD+V+ S +KY+GGHSD++ G V TNNEALA + F + +G + P D++L RG+K Sbjct: 190 MGADMVMLSTSKYVGGHSDLIGGAVITNNEALASRLDFIKTTLGSIASPFDAYLALRGMK 249 Query: 244 TLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKN 303 TL LRM NAL VA++LE HP + VYYPGLP+HP ++L ++QMR +++ TLK Sbjct: 250 TLDLRMARQCGNALRVAQYLENHPAIASVYYPGLPSHPQHQLCRQQMRSGGAVVTATLKG 309 Query: 304 DSEATP-FVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRLSVGI 362 D ++ F+ L F+L ESLGGVES++ A M+H + K +REA G+ D +R SVGI Sbjct: 310 DIQSLKRFIGGLHYFVLAESLGGVESMINHSASMSHGAMSKEEREAIGVYDTTLRFSVGI 369 Query: 363 EHEQDLLEDLEQAFA 377 EH DLL+DLE AFA Sbjct: 370 EHIDDLLQDLESAFA 384 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: 396 Number of extensions: 15 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: 395 Length adjustment: 30 Effective length of query: 350 Effective length of database: 365 Effective search space: 127750 Effective search space used: 127750 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