Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate NP_661596.1 CT0701 trans-sulfuration enzyme family protein
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000006985.1:NP_661596.1 Length = 380 Score = 368 bits (944), Expect = e-106 Identities = 191/375 (50%), Positives = 257/375 (68%), Gaps = 2/375 (0%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEG 78 T+AIH G +P+ TG+V PP+Y TST+A+ S E F YSR NPTR A E +A LE Sbjct: 5 TIAIHDGNTPESCTGSVTPPVYQTSTFARPSLDERGEFFYSRIGNPTRSALESTLALLEN 64 Query: 79 GTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTD 138 G A FASG+AA M++L G HVV+ D+YGG++R+FE++ R G++ S+ Sbjct: 65 GKHATTFASGVAAMMAAMQVLKPGDHVVSSLDVYGGSYRIFEQLMRPW-GVETSYAASEA 123 Query: 139 PAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLS 198 ++ IR +T+M+WIE+P+NP+L++ DI A+A IA + G++ VDNTFASP QRPL Sbjct: 124 TESYIECIRPETRMIWIESPSNPLLQICDIRALAEIANERGIVLAVDNTFASPYFQRPLD 183 Query: 199 LGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGL 258 LGA +VVHS TKYL GHSD++GG AVV + L + Q + G + GP+D +L RG+ Sbjct: 184 LGAHIVVHSTTKYLGGHSDVIGG-AVVASDDNLNLTIRNYQGAAGAIPGPWDCWLISRGI 242 Query: 259 KTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLK 318 KTL +RM H +NAL LA+ LE HPA+ +VIYPGL SHPQH LAKRQMSGFGG+++I LK Sbjct: 243 KTLKIRMEEHQKNALHLARALEKHPAVSRVIYPGLESHPQHELAKRQMSGFGGMLTIALK 302 Query: 319 GGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVG 378 GG A ++ E +LF +A+SLGGVESLV PA MT + A R++ +D LVRLS+G Sbjct: 303 GGLPAVRKMIESLKLFVIADSLGGVESLVASPARMTLGPLSQAERDRRACTDDLVRLSIG 362 Query: 379 IEDLGDLRGDLERAL 393 +E+ DL DL +AL Sbjct: 363 LENAEDLEADLLQAL 377 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: 455 Number of extensions: 19 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: 380 Length adjustment: 30 Effective length of query: 367 Effective length of database: 350 Effective search space: 128450 Effective search space used: 128450 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