Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_057508383.1 ABB28_RS09425 cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_001431535.1:WP_057508383.1 Length = 392 Score = 679 bits (1752), Expect = 0.0 Identities = 341/393 (86%), Positives = 365/393 (92%), Gaps = 2/393 (0%) Query: 1 MSNRTTHSHDGDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSR 60 MS + +H+ RALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSR Sbjct: 1 MSESSKPAHE--RALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSR 58 Query: 61 THNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFE 120 THNPTRFAYERCVA+LEGG+R FAFASGMAATSTVMELLDAGSHVVAMDD+YGGTFRLFE Sbjct: 59 THNPTRFAYERCVASLEGGSRGFAFASGMAATSTVMELLDAGSHVVAMDDIYGGTFRLFE 118 Query: 121 RVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGL 180 RVRRRTAGLDFSFVDLTD AAF+AAI TKMVWIETPTNPMLK+VDIAA+A IA++HGL Sbjct: 119 RVRRRTAGLDFSFVDLTDLAAFEAAITPATKMVWIETPTNPMLKIVDIAAVAAIAKQHGL 178 Query: 181 LTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQN 240 + VVDNTFASPMLQRPL LGADLV+HSATKYLNGHSDMVGG+ VVGDN LAEQMAFLQN Sbjct: 179 IIVVDNTFASPMLQRPLELGADLVLHSATKYLNGHSDMVGGMVVVGDNTGLAEQMAFLQN 238 Query: 241 SIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHV 300 SIG VQGPFDSFLALRGLKTLPLRM+AHC NALALAQWLET P++EKVIYPGL SHPQH Sbjct: 239 SIGAVQGPFDSFLALRGLKTLPLRMKAHCANALALAQWLETQPSVEKVIYPGLTSHPQHE 298 Query: 301 LAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPV 360 LA RQM+G+GGIVSIVLKGGF+AAKRFCE+TELFTLAESLGGVESLVNHPAVMTHASIPV Sbjct: 299 LATRQMNGYGGIVSIVLKGGFEAAKRFCERTELFTLAESLGGVESLVNHPAVMTHASIPV 358 Query: 361 ARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 RRE LGIS+ LVRLSVG+E+LGDL DLERAL Sbjct: 359 ERRENLGISEGLVRLSVGVEELGDLMVDLERAL 391 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: 645 Number of extensions: 20 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: 397 Length of database: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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 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