Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate 5208004 Shew_0520 O-succinylhomoserine (thiol)-lyase (RefSeq)
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__PV4:5208004 Length = 388 Score = 333 bits (855), Expect = 4e-96 Identities = 177/376 (47%), Positives = 238/376 (63%), Gaps = 1/376 (0%) Query: 4 IKTKVIHGGISTDKTTGAVSVPIYQTSTYKQNGLGQPKEYEYSRSGNPTRHALEELIADL 63 + T + GI +D GAV PIY ++ Y G QP+ ++YSRSGNPTR L + IA+L Sbjct: 6 LATAAVRRGIESDTQHGAVVPPIYLSTNYSFEGHQQPRAFDYSRSGNPTRSILGDAIAEL 65 Query: 64 EGGVQGFAFSSGLAGIHAVLSLFSAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDLS 123 E G G +G+A I V SL D +++ D YGG++RL + K +VD + Sbjct: 66 EQGATGVVTCTGMAAITLVTSLLGPEDLLVVPHDCYGGSYRLFTNLAKKGAFKLLVVDQT 125 Query: 124 NLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQPI 183 + L+ A + K ++ ETPSNPLL+V+DI+ I+ + A +VDNTF +P LQQP+ Sbjct: 126 DERALEQALTQSPKMVWLETPSNPLLRVVDIEAIAQASHKVGAQVVVDNTFLSPVLQQPL 185 Query: 184 ALGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRGI 243 LGADIV+HS TKY+ GHSDVV G V E+ + + N++G DS+L RG+ Sbjct: 186 QLGADIVVHSTTKYINGHSDVVGGAVVAKDPEVGELLHWWSNTLGLTGSAFDSYLTLRGL 245 Query: 244 KTLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFELT 303 +TLA+R+ H ANAQK+ L KAV KVYYPGL HPGHEIA +Q FG M+SFEL Sbjct: 246 RTLAVRIREHQANAQKVLALLCDHKAVEKVYYPGLAEHPGHEIAARQQKGFGAMLSFELK 305 Query: 304 -DENAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVG 362 E+A+ F++ L YF++AESLGGVESL+ VPA MTH ++ + R E G+KD LIRLSVG Sbjct: 306 GGESALVAFLDALQYFSVAESLGGVESLVAVPATMTHRAMDPDARREAGVKDTLIRLSVG 365 Query: 363 VEAIEDLLTDIKEALE 378 +E EDL+ DI LE Sbjct: 366 IEDGEDLVADILAGLE 381 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: 408 Number of extensions: 13 Number of successful extensions: 2 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