Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_005456495.1 SACCYDRAFT_RS12190 PLP-dependent transferase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000244975.1:WP_005456495.1 Length = 394 Score = 275 bits (702), Expect = 2e-78 Identities = 168/390 (43%), Positives = 232/390 (59%), Gaps = 14/390 (3%) Query: 14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSP--------GEHQGFEYSRTH-NP 64 A L+T ++H G+ D + GAV P+Y ST+A ++ G G Y+R NP Sbjct: 6 AHGLSTRSVHAGELSD-AEGAVHTPLYNHSTFAFATTADLLDVVEGRKAGNLYTRYGLNP 64 Query: 65 TRFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVR 123 T + E +A LEGG +A AF+SGMAA +T + G H++ + ++YGGTF L Sbjct: 65 TIRSTEAKLADLEGGEQALAFSSGMAAEAATFLAHCRTGDHIMCIGEVYGGTFELLGD-N 123 Query: 124 RRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTV 183 G+ +F+ + + T++V+ ETP NP L + DIAAIA AR G LTV Sbjct: 124 LPQVGITTTFLRADEVDRLPEVLTGRTRIVFFETPANPTLTVFDIAAIAAQARTVGALTV 183 Query: 184 VDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIG 243 VDNTFA+P+ Q PL GADLVVHSATKYL GHSD+ G+ + G LA M + +N +G Sbjct: 184 VDNTFATPVNQNPLQHGADLVVHSATKYLGGHSDLTAGV-LTGPAEHLAPVMGWRKN-LG 241 Query: 244 GVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAK 303 V P +FL R +++LP+R+RA + A A+A +LETHP + +V YPGLA+ Q + Sbjct: 242 QVIAPETAFLLARSIRSLPVRVRAQNDTAAAVAAFLETHPRVARVHYPGLATGEQKRIVD 301 Query: 304 RQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARR 363 QM G GG++S VL D ++ +LF +A SLGGVESLV P TH + A R Sbjct: 302 AQMRGGGGMLSAVLDANADQTAAVVDRLQLFAIAPSLGGVESLVTQPITTTHHGLDPAER 361 Query: 364 EQLGISDALVRLSVGIEDLGDLRGDLERAL 393 + GI+D++VRLSVG+ED DL DL +AL Sbjct: 362 AKRGIADSMVRLSVGLEDADDLIADLAQAL 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: 465 Number of extensions: 23 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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