Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_092055964.1 BQ4888_RS07650 PLP-dependent transferase
Query= BRENDA::A2RM21 (380 letters) >NCBI__GCF_900111775.1:WP_092055964.1 Length = 380 Score = 361 bits (926), Expect = e-104 Identities = 180/372 (48%), Positives = 262/372 (70%), Gaps = 1/372 (0%) Query: 6 TKVIHGGISTDKTTGAVSVPIYQTSTYKQNGLGQPKEYEYSRSGNPTRHALEELIADLEG 65 T ++H GI D TGA ++PIYQ STY G GQP EY+Y+RSGNP+R +E+ IA LEG Sbjct: 10 TLLVHQGIDRDPATGASAIPIYQASTYHHVG-GQPGEYDYARSGNPSRRQVEDAIALLEG 68 Query: 66 GVQGFAFSSGLAGIHAVLSLFSAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDLSNL 125 GV+GFA+++G+A I + L+L +GDH+I +D+YGG++R + VL + GI VD+++L Sbjct: 69 GVRGFAYATGMAAIGSALALLKSGDHLIAPNDLYGGSWRYLSTVLPEQGITTSFVDITDL 128 Query: 126 DDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQPIAL 185 + ++AA TKAI+ ETPSNPL + DI+ ++A+A+ LTL+DNTF TP LQ+P+ L Sbjct: 129 NRIEAAITPATKAIFLETPSNPLFNITDIRAVTALARQRGLLTLLDNTFMTPLLQRPLEL 188 Query: 186 GADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRGIKT 245 G D+V+HSATK+LGGHSD++AGLVTT +LA + + QN+ GAVL P DS+L+ RGIKT Sbjct: 189 GVDVVIHSATKFLGGHSDLMAGLVTTADPQLAKRLKYFQNAFGAVLAPFDSFLLARGIKT 248 Query: 246 LALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFELTDE 305 L LR+EA +AQ +AE L+ AV++V++PGL G E+ Q S G ++SFEL ++ Sbjct: 249 LKLRLEAAQRSAQDLAERLQDHPAVARVWFPGLVDFAGRELHFSQASGAGAVLSFELKEQ 308 Query: 306 NAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVGVEA 365 V ++ + +A SLGGVE+++ M+HA+IP E + +GI++ L+R+SVG+E Sbjct: 309 ARVAPLLQQIKLPIIAPSLGGVETILTHCWSMSHAAIPAETKLRLGIRETLLRISVGIED 368 Query: 366 IEDLLTDIKEAL 377 +EDL D+ AL Sbjct: 369 VEDLWEDLAAAL 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: 11 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: 380 Length adjustment: 30 Effective length of query: 350 Effective length of database: 350 Effective search space: 122500 Effective search space used: 122500 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