Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_025272949.1 HALAL_RS0104995 cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000527155.1:WP_025272949.1 Length = 381 Score = 399 bits (1024), Expect = e-115 Identities = 210/378 (55%), Positives = 267/378 (70%), Gaps = 7/378 (1%) Query: 18 ATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGE-HQGFEYSRTHNPTRFAYERCVAAL 76 +T AIH G PDP TGAV+PPIYATST+ Q G QG++YSR+ NPTR A E+C+AA+ Sbjct: 8 STRAIHAGSEPDPVTGAVIPPIYATSTFKQDGVGGLRQGYDYSRSGNPTRTALEQCLAAV 67 Query: 77 EGGTRAFAFASGMAATSTVME-LLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVD 135 EGG AFASG+AA ++ LL G H+V DD YGGTFRLF++V +R G+D++ V Sbjct: 68 EGGRHGLAFASGLAAEDAIIRALLKPGDHIVIPDDAYGGTFRLFDKVAKRW-GVDYTPVP 126 Query: 136 LTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQR 195 ++D AA AA T++VW+ETPTNP+L + D+ I +H L VVDNTFA+P LQ+ Sbjct: 127 ISDTAAILAACTDRTRLVWVETPTNPLLTVADLDTIIEQLAQHDLYVVVDNTFATPYLQQ 186 Query: 196 PLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLAL 255 PL GAD+VVHS TKYL GHSD+VGG +V D+ ELA+ +AF QNS+GGV GPFDS+L Sbjct: 187 PLRHGADIVVHSTTKYLGGHSDVVGGGVIVDDD-ELADTLAFHQNSMGGVPGPFDSWLTH 245 Query: 256 RGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSI 315 RGLKTL RM HC+NA +A +L H + +V YPGL HP H +AKRQM FGG+VS Sbjct: 246 RGLKTLAARMDRHCDNAERIASFLNEHSKVSQVYYPGLTDHPSHDVAKRQMRRFGGMVSF 305 Query: 316 VLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRL 375 G +AA C++ ++FTLAESLGGVESL+ HP MTHAS A +L + + LVRL Sbjct: 306 RHADGEEAAVDLCDRAKVFTLAESLGGVESLIEHPGRMTHAS---AEGSELEVPNDLVRL 362 Query: 376 SVGIEDLGDLRGDLERAL 393 SVGIED+ DL GDL++AL Sbjct: 363 SVGIEDVEDLIGDLDQAL 380 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: 548 Number of extensions: 21 Number of successful extensions: 6 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: 381 Length adjustment: 30 Effective length of query: 367 Effective length of database: 351 Effective search space: 128817 Effective search space used: 128817 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