Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_012333237.1 M446_RS16475 O-succinylhomoserine (thiol)-lyase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000019365.1:WP_012333237.1 Length = 388 Score = 319 bits (818), Expect = 8e-92 Identities = 172/375 (45%), Positives = 233/375 (62%), Gaps = 2/375 (0%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEG 78 T+A G D + GAV PP+Y ++TY + +G++Y+R NPTR +A LEG Sbjct: 10 TIAAANGIGADAAFGAVAPPLYLSTTYTFAEFETPRGYDYARLGNPTRDQLADTIAKLEG 69 Query: 79 GTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTD 138 G RA ASGMAA + L G +VA D YGGT RL +R +FVD TD Sbjct: 70 GARAVVTASGMAALDLALSPLSPGDLLVAPHDCYGGTHRLLS-LRAAKGHYRVAFVDQTD 128 Query: 139 PAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLS 198 AA AA+ +++ ETP+NP++++VD+ A +AR+ G L VVDNTF SP LQ+P++ Sbjct: 129 AAALSAALAERPRILLTETPSNPLMRIVDLGRTAALAREAGALFVVDNTFLSPALQQPIA 188 Query: 199 LGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGL 258 GADLVVHS TK++NGHSD++GG AVV A L E++A N+IG PFD++L LRGL Sbjct: 189 HGADLVVHSTTKFINGHSDVIGG-AVVAAQAALGEELANWANTIGVTGSPFDAYLTLRGL 247 Query: 259 KTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLK 318 +TL R+ ++A +A +L HPA+ +V YPGL HP H +A+ Q GFG ++S L Sbjct: 248 RTLFARLERQQQSAAVVASFLAAHPAVARVHYPGLPDHPGHAVARAQQRGFGAMLSFELA 307 Query: 319 GGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVG 378 GG +A + +FTLAESLGG+ESL+ HP MTHA++ R G+ D L+RLSVG Sbjct: 308 GGREAVRTLVGALRVFTLAESLGGIESLIAHPVSMTHAAMAPEARRAAGVGDGLLRLSVG 367 Query: 379 IEDLGDLRGDLERAL 393 +E DL DL AL Sbjct: 368 LEAESDLLADLAVAL 382 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: 458 Number of extensions: 26 Number of successful extensions: 3 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: 388 Length adjustment: 31 Effective length of query: 366 Effective length of database: 357 Effective search space: 130662 Effective search space used: 130662 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