Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_027721255.1 H589_RS0106410 cystathionine beta-lyase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000425265.1:WP_027721255.1 Length = 387 Score = 207 bits (526), Expect = 5e-58 Identities = 133/399 (33%), Positives = 214/399 (53%), Gaps = 34/399 (8%) Query: 1 MH-MQTKLIHGGISEDATT---GAVSVPIYQTSTYRQDAI--------GHHKGYEYSRSG 48 MH + TKL++GG DA ++ P+++ ST D+ G +G EY SG Sbjct: 1 MHKISTKLVNGG--NDAAMQQINTINPPLHRASTVLFDSYSDMLKANCGQFEGIEYGTSG 58 Query: 49 NPTRFALEELIADLEGGVKGFAFASGLAGIHAVF-SLLQSGDHVLLGDDVYGGTFRLFNK 107 + A E + +L+G AF SG++ I V + + GDH+L+ D+VYG T + Sbjct: 59 LAAQKAFESAMVELDGSYGCKAFQSGISAIAMVLMAFTRQGDHILICDNVYGPTRHFCDG 118 Query: 108 VLVKNGLSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLT 167 L K G+ + +S + + I+ TK +++E+P + +I D+ S+ ++ G+++ Sbjct: 119 FLSKYGVKTDYLPSSAGADVIDFIRDETKLIFMESPGSNTFEIQDVPAITSICREKGVVS 178 Query: 168 IVDNTFATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNN---EALAQEIAFFQN 224 ++DNT+ATP Y NP LG DI + S TKY+ GHSD++ G V+TN E + F+ Sbjct: 179 VIDNTWATPLYMNPFELGVDISIQSATKYITGHSDILLGTVSTNERYWETFKKCCGLFE- 237 Query: 225 AIGGVLGPQ-DSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNY 283 PQ D + RG++TL +R++ H+ AL VA +L +H V+ V +P L HP + Sbjct: 238 ----AFAPQEDCYQALRGLRTLAVRLKHHELAALDVATWLSEHDMVDAVIHPALANHPQH 293 Query: 284 ELAKKQMRGFSGMLSFTLK---NDSEATPFVESLKLFILGESLGGVESLVGVPAFMTHAC 340 EL K+ +G SG+ FTLK D + + FV++L LF LG S GG +SL+ FM Sbjct: 294 ELWKRDFKGSSGLFGFTLKEEFEDMDHSLFVDNLGLFGLGYSWGGYKSLITGGKFMRTNH 353 Query: 341 IPKTQREAAGIRDGLVRLSVGIEHEQDLLEDLEQAFAKI 379 + + RL++G+E DL +DL ++ K+ Sbjct: 354 FGYEGKT-------IFRLNIGMEDVDDLKQDLSKSLQKL 385 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: 341 Number of extensions: 18 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: 387 Length adjustment: 30 Effective length of query: 350 Effective length of database: 357 Effective search space: 124950 Effective search space used: 124950 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