Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 201343 SO2191 cystathionine beta-lyase (NCBI ptt file)
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__MR1:201343 Length = 399 Score = 224 bits (570), Expect = 4e-63 Identities = 135/389 (34%), Positives = 213/389 (54%), Gaps = 17/389 (4%) Query: 2 RMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIG--RHKGYE-------YSRSGNPTR 52 ++ T+++ G + T G ++ P+++ ST D + RH Y R G PT Sbjct: 6 QLATQIVSVGRDKKWTKGVINPPVFRASTIVFDTMEDMRHAAKNKTNGEMFYGRRGTPTH 65 Query: 53 FALEELIADLEGGVKGFAFASGLAGIHA-VFSLLQSGDHVLLGDDVYGGTFRLFNQVLVK 111 FA + +++LEGG + SG A I A + S LQ+GDH+L+ D VY T + +L Sbjct: 66 FAFQAAVSELEGGAGTALYPSGAAAISAALLSFLQAGDHLLMVDSVYEPTRDFCSHILAG 125 Query: 112 NGLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDN 171 + T D I+ I+PNTK L+LE+P + +++ D+ +A +HGL+TI+DN Sbjct: 126 FNIETTYYDPLIGEGIRALIRPNTKVLFLESPGSITMEVQDVPTLCRIAHEHGLVTILDN 185 Query: 172 TFATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLG 231 T+A+P P +G D+ + TKY+ GHSDV+ G T N + Q + +G Sbjct: 186 TWASPINSKPFEMGVDVSIQAATKYIVGHSDVMIGTATANEQYWPQ-LRERSYLLGQTTS 244 Query: 232 PQDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMR 291 P D +L RG++TLG+RM H+KNAL VA +L+ P+V+ + +P T P +E K+ Sbjct: 245 PDDVYLATRGLRTLGVRMAQHEKNALKVANWLQTRPEVDHLRHPAFETCPGHEFFKRDFS 304 Query: 292 GFSGMLSFTLK-NDSEAV-AFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREAA 349 +G+ SF LK D EAV A VE+++ F +G S GG ESL+ + F T+ +A+ Sbjct: 305 ASNGLFSFVLKQGDQEAVTALVENMQHFKMGFSWGGYESLI-LGIFGIERIRSATKWDAS 363 Query: 350 GIRDGLVRLSVGIEHEQDLLEDLEQAFAK 378 L+R+ +G+E +DL+ DL F + Sbjct: 364 ---KPLIRVHIGLEDPEDLIADLSAGFER 389 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: 358 Number of extensions: 17 Number of successful extensions: 5 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: 399 Length adjustment: 30 Effective length of query: 350 Effective length of database: 369 Effective search space: 129150 Effective search space used: 129150 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