Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_004514089.1 GMET_RS03505 PLP-dependent transferase
Query= BRENDA::A2RM21 (380 letters) >NCBI__GCF_000012925.1:WP_004514089.1 Length = 391 Score = 387 bits (993), Expect = e-112 Identities = 192/379 (50%), Positives = 264/379 (69%), Gaps = 3/379 (0%) Query: 3 SIKTKVIHGGISTDKTTGAVSVPIYQTSTYKQNGLGQPKEYEYSRSGNPTRHALEELIAD 62 +I T+ G+ D TGAV+VPIYQT+T++ GLGQ Y+Y+RSGNPTR ALEE IA Sbjct: 2 NIATQTAQIGLEWDTRTGAVTVPIYQTATFRHPGLGQSTGYDYTRSGNPTRQALEEGIAR 61 Query: 63 LEGGVQGFAFSSGLAGIHAVLSLFSAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDL 122 LEGG +GFA++SG+A I +L LF GDH+++ +D+YGGT RL D++ T+ + + VD Sbjct: 62 LEGGARGFAYASGMAAIANLLLLFKKGDHLVVTEDLYGGTCRLFDQIFTQYELSFTYVDT 121 Query: 123 SNLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQP 182 S++ ++AA + ETKA++ E+ +NPLLKV DI +SA+ + L +VDNTF TPYL +P Sbjct: 122 SDIKAVRAAIRPETKALFVESLTNPLLKVADIAALSALCRERGLLHIVDNTFLTPYLLRP 181 Query: 183 IALGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRG 242 GADI ++SATKYL GH+D V+GLV +LA + FLQNS+GAVLGPQDSWL RG Sbjct: 182 FDHGADITVYSATKYLAGHNDTVSGLVAVKDPQLAERVYFLQNSVGAVLGPQDSWLTIRG 241 Query: 243 IKTLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLN---SHPGHEIAKKQMSAFGGMIS 299 +KTL++R++ NA ++A++L V KVYYPGL+ HPGHE+ +Q FG MI+ Sbjct: 242 MKTLSVRLDRQQENAGRVAQWLSNHPRVRKVYYPGLSGHPGHPGHELLARQARGFGAMIA 301 Query: 300 FELTDENAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRL 359 FE+ + V+ + + AESLGGVE+LI P V THA IP ELR+ +GI D L+RL Sbjct: 302 FEVDEHALVERLLLKTEVISFAESLGGVETLITFPQVQTHADIPPELRQRLGINDVLLRL 361 Query: 360 SVGVEAIEDLLTDIKEALE 378 SVG+E +DL+ D+ +A E Sbjct: 362 SVGIEDADDLIDDLAQAFE 380 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: 414 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: 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 ( 7.3 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 10 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