Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate 17978 b3939 cystathionine gamma-synthase (NCBI)
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__Keio:17978 Length = 386 Score = 319 bits (817), Expect = 9e-92 Identities = 166/371 (44%), Positives = 238/371 (64%), Gaps = 2/371 (0%) Query: 6 TKVIHGGISTDKTTGAVSVPIYQTSTYKQNGLGQPKEYEYSRSGNPTRHALEELIADLEG 65 T + G++ D+ G V PI+ +STY G +P+ ++YSR GNPTR ++ +A+LEG Sbjct: 7 TIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEG 66 Query: 66 GVQGFAFSSGLAGIHAVLSLF-SAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDLSN 124 G ++G++ IH V ++F GD ++ D YGG++RL D + + VD + Sbjct: 67 GAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGD 126 Query: 125 LDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQPIA 184 L+AA E+ K + E+PSNPLL+V+DI +I +A+ A+++VDNTF +P LQ P+A Sbjct: 127 EQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLA 186 Query: 185 LGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRGIK 244 LGAD+VLHS TKYL GHSDVVAG+V ++ +E+ + N+IG G DS+L+ RG++ Sbjct: 187 LGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLR 246 Query: 245 TLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFELT- 303 TL RME NAQ I ++L+T V K+Y+P L + GHEIA +Q FG M+SFEL Sbjct: 247 TLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDG 306 Query: 304 DENAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVGV 363 DE ++ F+ LS FTLAESLGGVESLI A MTHA + E R GI + L+R+S G+ Sbjct: 307 DEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGI 366 Query: 364 EAIEDLLTDIK 374 E EDL+ D++ Sbjct: 367 EDGEDLIADLE 377 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: 395 Number of extensions: 12 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: 386 Length adjustment: 30 Effective length of query: 350 Effective length of database: 356 Effective search space: 124600 Effective search space used: 124600 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