Align cystathionine γ-lyase (EC 2.5.1.48) (characterized)
to candidate 5210044 Shew_2491 methionine gamma-lyase (RefSeq)
Query= metacyc::HP0106-MONOMER (380 letters) >FitnessBrowser__PV4:5210044 Length = 391 Score = 306 bits (784), Expect = 6e-88 Identities = 169/387 (43%), Positives = 236/387 (60%), Gaps = 11/387 (2%) Query: 2 RMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAI--------GRHKGYEYSRSGNPTRF 53 ++ T++IH G E GA+ P+ Q++T+ + + G +GY Y+R GNPT Sbjct: 6 KLATQVIHAG-HEANQHGALVSPLVQSATFTFETVEQGGDCFAGEQQGYIYTRLGNPTTA 64 Query: 54 ALEELIADLEGGVKGFAFASGLAGIHA-VFSLLQSGDHVLLGDDVYGGTFRLFNQVLVKN 112 LE +A LEG A ASG+A + A + + L GDH++ VYG TF L + + Sbjct: 65 ELERKMAVLEGSEAAAATASGMAAVSAALLTNLSQGDHLVASKAVYGCTFALMTEQFKRF 124 Query: 113 GLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNT 172 G+ T++D +++ I +AI+PNTKAL+ ETP NP L + DLA A++AK H L++IVDNT Sbjct: 125 GIEVTLVDFCEVANIAQAIRPNTKALFCETPVNPHLDVYDLAAIAALAKRHQLVSIVDNT 184 Query: 173 FATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGP 232 F TP Q PL +G D+V HS TKYL GH DV+AG+V E + + IGGV+ P Sbjct: 185 FMTPLLQRPLSMGIDMVIHSATKYLNGHGDVIAGIVCGTEEMITKVKLEVLKDIGGVISP 244 Query: 233 QDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRG 292 D+WL+ RG+KTL +R+ H NA VAE+L++HP+V RVYYPGL H + L KQM Sbjct: 245 HDAWLILRGLKTLDVRLARHCDNAERVAEYLQQHPQVARVYYPGLKGHSGHALLGKQMLR 304 Query: 293 FSGMLSFTLKNDSEAV-AFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREAAGI 351 G+++F LK +A AF LKLF + SLG ESL+ PA MTH+ R AGI Sbjct: 305 AGGVVAFELKGSFDAAKAFANRLKLFKIAVSLGDAESLIQHPASMTHSPYSPEARMDAGI 364 Query: 352 RDGLVRLSVGIEHEQDLLEDLEQAFAK 378 D L+R+S+G+E D++ DL QAF + Sbjct: 365 GDSLLRISLGLEDSDDIIADLAQAFGE 391 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: 377 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: 391 Length adjustment: 30 Effective length of query: 350 Effective length of database: 361 Effective search space: 126350 Effective search space used: 126350 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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