Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_004514090.1 GMET_RS03510 cystathionine gamma-synthase
Query= BRENDA::A2RM21 (380 letters) >NCBI__GCF_000012925.1:WP_004514090.1 Length = 378 Score = 392 bits (1006), Expect = e-113 Identities = 191/368 (51%), Positives = 259/368 (70%) Query: 6 TKVIHGGISTDKTTGAVSVPIYQTSTYKQNGLGQPKEYEYSRSGNPTRHALEELIADLEG 65 T++IH G D TTGAVS+PIYQTST++Q + +Y+Y+RS NPTR ALEE IA LEG Sbjct: 5 TRIIHTGHDIDPTTGAVSIPIYQTSTFRQESVDHFGKYDYARSDNPTREALEETIAQLEG 64 Query: 66 GVQGFAFSSGLAGIHAVLSLFSAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDLSNL 125 G +GFA++SG+A I +VL LFS GDH+++ +DVYGGTFR++ ++ ++ GI VD ++L Sbjct: 65 GTRGFAYASGMAAISSVLLLFSPGDHLVVCEDVYGGTFRVLTQLFSRLGITSTFVDATDL 124 Query: 126 DDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQPIAL 185 D + AAF+ ETK ++ E+PSNPLLK+ D++ + IA+ A+TLVDNTF TPYLQ+P+ + Sbjct: 125 DAIAAAFRPETKGLFLESPSNPLLKITDLEGAARIARERGAITLVDNTFMTPYLQRPLEV 184 Query: 186 GADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRGIKT 245 G DIVLHS TK+L GHSDV+ G EL I F+QN+ GA+LGPQDSWLV RG+KT Sbjct: 185 GCDIVLHSGTKFLNGHSDVICGFAVVKDPELGKRIRFIQNAFGAILGPQDSWLVLRGLKT 244 Query: 246 LALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFELTDE 305 L +RME +A +IA +L K V++V YPGL SHPGH I +Q S G ++SF L Sbjct: 245 LRVRMEESQRSATRIASWLAGEKRVTRVLYPGLPSHPGHAIHARQSSGPGAVLSFALDSL 304 Query: 306 NAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVGVEA 365 + +E + A SLGGVES+I PA M+HA++P E R GI D L+RLSVG+E Sbjct: 305 EVTRRLLEGMKLAAFAVSLGGVESIISYPARMSHAAMPPEERAARGIGDTLVRLSVGLEE 364 Query: 366 IEDLLTDI 373 +DL+ ++ Sbjct: 365 ADDLIAEM 372 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: 397 Number of extensions: 10 Number of successful extensions: 1 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: 378 Length adjustment: 30 Effective length of query: 350 Effective length of database: 348 Effective search space: 121800 Effective search space used: 121800 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