Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_005459142.1 SACCYDRAFT_RS20695 cystathionine gamma-synthase
Query= BRENDA::A2RM21 (380 letters) >NCBI__GCF_000244975.1:WP_005459142.1 Length = 386 Score = 390 bits (1001), Expect = e-113 Identities = 208/378 (55%), Positives = 260/378 (68%), Gaps = 7/378 (1%) Query: 5 KTKVIHGGISTDKTTGAVSVPIYQTSTYKQNGLGQPKE--YEYSRSGNPTRHALEELIAD 62 +T+ IH G D TGAV VPIYQTSTY Q+G+G +E YEYSR+ NPTR ALEE +A Sbjct: 10 ETRAIHAGQEPDPRTGAVIVPIYQTSTYAQDGVGGTREGDYEYSRTANPTRTALEEALAA 69 Query: 63 LEGGVQGFAFSSGLAGIHAVL-SLFSAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVD 121 LEGG AF+SG+A AVL + GDH++L +DVYGGTFRL+DKVLT+ G+ Y + Sbjct: 70 LEGGRHALAFASGMAASDAVLRTTLRPGDHLVLGNDVYGGTFRLIDKVLTEWGVNYSVAS 129 Query: 122 LSNLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQ 181 LS+LD+++ A + ETK ++ E+P+NPLL + DI ++ +A A +VDNTFATPYLQ Sbjct: 130 LSDLDEVREALRPETKLVWCESPTNPLLGIADIAALAELAHVGGAKLVVDNTFATPYLQT 189 Query: 182 PIALGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQR 241 P+ LGADIV+HS TKYLGGHSDVV G V T+S EL + FL+NS GAV G D+WL R Sbjct: 190 PLELGADIVVHSTTKYLGGHSDVVGGAVITDSDELRERLFFLRNSAGAVPGAFDAWLTLR 249 Query: 242 GIKTLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFE 301 G+KTLA+RME H NA+ IAE L V +VYYPGL HPGH +A KQM FGGM+SF Sbjct: 250 GLKTLAVRMERHCGNAELIAEALAVHPKVERVYYPGLAEHPGHSLAAKQMRRFGGMVSFT 309 Query: 302 LTD-ENAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLS 360 D E A + F LAESLGGVESLIE P MTHAS+ L + + L+RLS Sbjct: 310 HVDGEQAALNVAARTKLFILAESLGGVESLIEHPGRMTHASVAGSL---LQVPAELVRLS 366 Query: 361 VGVEAIEDLLTDIKEALE 378 VG+E DLL D++ AL+ Sbjct: 367 VGIEDAHDLLADLRYALD 384 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: 465 Number of extensions: 14 Number of successful extensions: 5 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 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