Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Echvi_1734 Echvi_1734 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Cola:Echvi_1734 Length = 369 Score = 298 bits (764), Expect = 1e-85 Identities = 162/378 (42%), Positives = 230/378 (60%), Gaps = 14/378 (3%) Query: 15 LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVA 74 + TLAIHGG+ AV+ PI ++T+ + YSR+ NP R A E +A Sbjct: 1 MKFETLAIHGGEKKSAPHRAVVQPITLSTTFEH----HEESLIYSRSQNPNRMALEELLA 56 Query: 75 ALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFV 134 LE G+ A AF+SG AA V + L GSH+VA D+Y G + + V L+ +F Sbjct: 57 QLEKGSAAAAFSSGNAAGMAVFQALPLGSHIVAPSDMYHGLKK--QLVELFKDKLEVTFT 114 Query: 135 DLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQ 194 DL+DP + AI+ +TK++WIETP+NPMLK+ DI + +A++ + V DNTFA+P+ Q Sbjct: 115 DLSDPENLEKAIQPNTKLLWIETPSNPMLKISDIRRLTKMAKEDDIRVVCDNTFATPVFQ 174 Query: 195 RPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLA 254 PL LGADLV+HSATKY GHSD++GG + + E +Q+ +Q + G V PFD +L Sbjct: 175 NPLELGADLVMHSATKYFGGHSDILGGALITKKSDEFWKQIVNVQQTGGAVLSPFDCYLL 234 Query: 255 LRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVS 314 +R +KTL RMR H E+A +A +L+ HP +E+V YPGL +HP H +AK QM+GFGGI+S Sbjct: 235 VRSIKTLAYRMRGHAEHAGMIATFLDQHPKVERVFYPGLTAHPGHDVAKSQMTGFGGILS 294 Query: 315 IVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVR 374 ++KG + A + + +T A SLGGVESL+ A + + L+R Sbjct: 295 FLVKGKPEDADKLISSLKYYTNATSLGGVESLIERRAAVEGPDTKTPQN--------LIR 346 Query: 375 LSVGIEDLGDLRGDLERA 392 LSVG+E L DL D+E+A Sbjct: 347 LSVGLEHLDDLLEDMEKA 364 Lambda K H 0.320 0.134 0.391 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: 428 Number of extensions: 14 Number of successful extensions: 4 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: 397 Length of database: 369 Length adjustment: 30 Effective length of query: 367 Effective length of database: 339 Effective search space: 124413 Effective search space used: 124413 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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