Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 5209311 Shew_1789 cystathionine beta-lyase (RefSeq)
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__PV4:5209311 Length = 395 Score = 220 bits (561), Expect = 5e-62 Identities = 139/390 (35%), Positives = 213/390 (54%), Gaps = 17/390 (4%) Query: 1 MRMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIG--RHKGYE-------YSRSGNPT 51 M+ +TK++ G + + G ++ P+++ ST D I RH Y R G PT Sbjct: 1 MKKETKIVSVGRDKKWSKGVINPPVFRASTVVFDTIEDMRHATKNRANGAMFYGRRGTPT 60 Query: 52 RFALEELIADLEGGVKGFAFASGLAGIH-AVFSLLQSGDHVLLGDDVYGGTFRLFNQVLV 110 FA + IA+LEGGV + SG A I A+ S L++GDH+L+ D Y T L +++L Sbjct: 61 HFAFQAAIAELEGGVGTALYPSGSAAISGALLSFLKAGDHLLMVDTAYEPTRDLCDKLLK 120 Query: 111 KNGLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVD 170 G+ T D I+ I+PNTK L+LE+P + L++ D+ +++A H L+ ++D Sbjct: 121 GFGIETTYYDPLIGDGIEALIRPNTKVLFLESPGSITLEVQDVPTLSAIAHRHNLVVMLD 180 Query: 171 NTFATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVL 230 NT+A+P P LG DI + TKY+ GHSDV+ G T N+A ++ +G Sbjct: 181 NTWASPINCRPFELGVDISIQAATKYIVGHSDVMLGTATA-NQAHWDQLRENSYLMGQCT 239 Query: 231 GPQDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQM 290 D +L RG++TLG+RM H+KN L VA L P+V+ + +P + P +E K+ Sbjct: 240 SADDIYLASRGLRTLGVRMAQHEKNGLEVANLLATRPEVDHLRHPAFASCPGHEFFKRDF 299 Query: 291 RGFSGMLSFTLK--NDSEAVAFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREA 348 +G+ SF LK N AFVE + F +G S GG ESL+ + F TQ ++ Sbjct: 300 SASNGLFSFVLKRGNIKAITAFVEGMDHFKMGFSWGGYESLI-LGVFGIDKLRTATQWDS 358 Query: 349 AGIRDGLVRLSVGIEHEQDLLEDLEQAFAK 378 + L+RL VG+E+ +DL++DLE FA+ Sbjct: 359 S---KPLIRLHVGLENPEDLIKDLEAGFAR 385 Lambda K H 0.319 0.137 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: 375 Number of extensions: 20 Number of successful extensions: 6 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 ( 7.4 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