Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate BWI76_RS24210 BWI76_RS24210 cystathionine gamma-lyase
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__Koxy:BWI76_RS24210 Length = 381 Score = 379 bits (972), Expect = e-109 Identities = 202/377 (53%), Positives = 262/377 (69%), Gaps = 4/377 (1%) Query: 2 HMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIAD 61 ++ T +H G D GAV PIY TST+ Q A G H GYEYSRSGNPTR ALE IAD Sbjct: 3 NLHTLSVHSGTFTDEH-GAVMPPIYATSTFAQPAPGQHTGYEYSRSGNPTRHALETAIAD 61 Query: 62 LEGGVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKN-GLSCTIID 120 LE G +G+AFASGLA I V LL H++ DDVYGGT+RL V ++ GL + + Sbjct: 62 LESGTRGYAFASGLAAISTVLELLDKDSHLVAVDDVYGGTYRLIENVRRRSAGLRVSWVK 121 Query: 121 TSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQN 180 DL+ I+ AI+P+T+ +++ETP+NPLLK+ DL+ A++A+ H ++++ DNTFA+P Sbjct: 122 PDDLAAIEAAIRPDTRMIWVETPTNPLLKLADLSAIAAIARRHNIISVTDNTFASPAIHR 181 Query: 181 PLLLGADIVVHSGTKYLGGHSDVVAGL-VTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQ 239 PL LG DIVVHS TKYL GHSDVVAGL V +N ALA+++ + QNA+GGVL P S+L Sbjct: 182 PLELGFDIVVHSATKYLNGHSDVVAGLAVVGDNAALAEKLGYLQNAVGGVLDPFSSFLTL 241 Query: 240 RGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSF 299 RGI+TL LRM+ H NAL +AE+LE+ P+VE+V++P L +HP+++LA++QM GM+S Sbjct: 242 RGIRTLALRMERHSSNALLLAEWLEQQPQVEKVWFPWLASHPHHQLARRQMALPGGMISV 301 Query: 300 TLK-NDSEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRL 358 +K +DS A + LKLF L ESLGGVESLV P MTHA IP QR A GI L+RL Sbjct: 302 VVKGDDSYAERIIRKLKLFTLAESLGGVESLVSQPFSMTHASIPLEQRLANGITPQLIRL 361 Query: 359 SVGIEHEQDLLEDLEQA 375 SVGIE QDL+ D A Sbjct: 362 SVGIEDPQDLIADWRHA 378 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: 415 Number of extensions: 14 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: 381 Length adjustment: 30 Effective length of query: 350 Effective length of database: 351 Effective search space: 122850 Effective search space used: 122850 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