Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Echvi_2283 Echvi_2283 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__Cola:Echvi_2283 Length = 391 Score = 276 bits (705), Expect = 9e-79 Identities = 150/367 (40%), Positives = 219/367 (59%), Gaps = 11/367 (2%) Query: 22 SVPIYQTSTYRQDAIGRHK--------GYEYSRSGNPTRFALEELIADLEGGVKGFAFAS 73 S PIY TS++ D+ + G YSR NP L E + +EG G A AS Sbjct: 24 SAPIYMTSSFTFDSAEEARQMFAEEIPGNIYSRYANPNSSDLIEKVCAVEGTEDGIATAS 83 Query: 74 GLAGIH-AVFSLLQSGDHVLLGDDVYGGTFRLFNQVLVKNGLSCTIIDTSDISQIKKAIK 132 G+A + ++ SLL+ GDH+L ++G T +L +V K G++ T D SDI K +K Sbjct: 84 GMAAMFGSMASLLEQGDHILASRSLFGSTHQLLTRVFPKWGITSTYGDISDIENWDKLVK 143 Query: 133 PNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLLLGADIVAHS 192 PNTK L++ETPSNP L++ DL AK H L+ +VDN FATPY Q P GADIVAHS Sbjct: 144 PNTKMLFIETPSNPGLEVIDLEWIGKFAKAHNLILVVDNCFATPYLQQPAKWGADIVAHS 203 Query: 193 GTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGIKTLGLRMEAH 252 TKY+ G V+ GL+ E L +E+ FF G + P ++W+L R ++TL +RME H Sbjct: 204 ATKYIDGQGRVLGGLILGKQE-LIKEVQFFTRHTGPSISPFNAWILSRSMETLAIRMERH 262 Query: 253 QKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKNDSE-AVAFV 311 NAL VA + + + ++E V YP L +HP ++LAKKQM+ G+++ TLK E A F+ Sbjct: 263 CANALAVASYFQDNKELEFVKYPFLKSHPQHDLAKKQMKHGGGIVTLTLKGGIERAQRFI 322 Query: 312 ESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREAAGIRDGLVRLSVGIEHEQDLLED 371 + L++ + +LG S++ PA TH+ + + +R+ GI GL+RLS G+EH D++ D Sbjct: 323 DELQMITVTANLGDTRSIITHPASTTHSKLTEEERQRVGILPGLIRLSAGLEHHDDIIAD 382 Query: 372 LEQAFAK 378 +E+A + Sbjct: 383 IERALER 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: 385 Number of extensions: 22 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: 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 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