Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate CA265_RS13080 CA265_RS13080 O-succinylhomoserine sulfhydrylase
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__Pedo557:CA265_RS13080 Length = 388 Score = 270 bits (690), Expect = 5e-77 Identities = 146/365 (40%), Positives = 219/365 (60%), Gaps = 11/365 (3%) Query: 23 SVPIYQTSTYKQNGLGQPK-----EYE---YSRSGNPTRHALEELIADLEGGVQGFAFSS 74 S PIY TS+YK + + E E YSR NP E + LEG GFA ++ Sbjct: 24 SSPIYLTSSYKFEDAEEMRALFANEKEGNVYSRYSNPNTSEFIEKMCLLEGAEDGFATAT 83 Query: 75 GLAGIHAVLSLF-SAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDLSNLDDLKAAFK 133 G+A I F GDH++ + V+G T +L+ V + G+ +D DL D +A K Sbjct: 84 GMAAIFTTFGAFLKNGDHLVSSRSVFGSTHQLLTNVFSNWGVTFDYADLDKPQDWEALIK 143 Query: 134 EETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQPIALGADIVLHS 193 TK I+ ETPSNP + ++D++ + +AK H+ L +VDN FATPYLQQPI GA I +HS Sbjct: 144 PNTKMIFVETPSNPGIDIIDLEFLGDLAKKHNVLLVVDNCFATPYLQQPIKFGAHISIHS 203 Query: 194 ATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRGIKTLALRMEAH 253 ATKY+ G V+ G++ + +A IGF ++S G L P ++W++ + ++TLA+RM+ H Sbjct: 204 ATKYIDGQGRVLGGVILGTKELIADVIGFARHS-GPALSPFNAWILSKSLETLAIRMDRH 262 Query: 254 SANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFELTDE-NAVKDFV 312 NA K+AE+LE + V YP L SHP ++IAKKQM GG+++ + +A + F+ Sbjct: 263 CENALKVAEYLEKHPKIKLVKYPFLPSHPQYDIAKKQMKQGGGIVTIVVEGGIDAARKFM 322 Query: 313 ENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVGVEAIEDLLTD 372 + L F+++ +L S+ PA TH+ + +E R E+GI+ G IRLS+G+E I D+L D Sbjct: 323 DGLQMFSISANLADTRSIATHPATSTHSKLTEEQRNEVGIEQGSIRLSIGLEHINDILAD 382 Query: 373 IKEAL 377 I++AL Sbjct: 383 IEQAL 387 Lambda K H 0.315 0.133 0.366 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: 387 Number of extensions: 10 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: 388 Length adjustment: 30 Effective length of query: 350 Effective length of database: 358 Effective search space: 125300 Effective search space used: 125300 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: 42 (22.0 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