Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate 203140 SO4056 cystathionine gamma-synthase (NCBI ptt file)
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__MR1:203140 Length = 393 Score = 326 bits (835), Expect = 8e-94 Identities = 172/375 (45%), Positives = 235/375 (62%), Gaps = 1/375 (0%) Query: 4 IKTKVIHGGISTDKTTGAVSVPIYQTSTYKQNGLGQPKEYEYSRSGNPTRHALEELIADL 63 + T + GI +D GAV PIY ++ Y +G P+E++YSRSGNPTR L + +A L Sbjct: 12 LATLAVRQGIESDTQYGAVVPPIYLSTNYAFDGHKNPREFDYSRSGNPTRSILGDALAKL 71 Query: 64 EGGVQGFAFSSGLAGIHAVLSLFSAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDLS 123 E G G +G+A I V +L D +++ D YGG++RL + K +VD + Sbjct: 72 EKGATGVVTCTGMAAITLVTTLLGPDDLLVVPHDCYGGSYRLFTNLAKKGQFKLLVVDQT 131 Query: 124 NLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQPI 183 + L A ++ K ++ ETPSNPLL+V+DI+ I+ + AL +VDNTF +P LQQP+ Sbjct: 132 DNQALAQAIAQQPKMVWIETPSNPLLRVVDIEAIAKASHGVGALVVVDNTFLSPILQQPL 191 Query: 184 ALGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRGI 243 LGADIV+HS TKY+ GHSDVV G V ++ + + N++G DS+ RG+ Sbjct: 192 LLGADIVIHSTTKYINGHSDVVGGAVIAKDPQIGETLHWWSNTLGLTGSAFDSYQTLRGL 251 Query: 244 KTLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFELT 303 +TLA+R+ H NAQ+I E L S VSKVYYPGL HPGH IA KQ FG M+SFEL Sbjct: 252 RTLAVRIREHQRNAQRIVELLSNSPVVSKVYYPGLADHPGHAIAAKQQKGFGAMLSFELK 311 Query: 304 -DENAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVG 362 E V F++ LS F++AESLGGVESL+ VPA MTH ++ + R E GIKD L+RLSVG Sbjct: 312 GGEAEVVAFLDALSLFSVAESLGGVESLVAVPATMTHRAMEPQARFEAGIKDTLLRLSVG 371 Query: 363 VEAIEDLLTDIKEAL 377 +E +DL+ DI+ L Sbjct: 372 IEDADDLVADIQAGL 386 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: 391 Number of extensions: 14 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: 393 Length adjustment: 30 Effective length of query: 350 Effective length of database: 363 Effective search space: 127050 Effective search space used: 127050 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