Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_036261931.1 DL86_RS12460 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000746085.1:WP_036261931.1 Length = 408 Score = 267 bits (683), Expect = 4e-76 Identities = 161/390 (41%), Positives = 228/390 (58%), Gaps = 12/390 (3%) Query: 13 RALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSS--------PGEHQGFEYSRTHNP 64 R L AT +HGG G I+ T + S G+ G+ YSR NP Sbjct: 11 RTLRPATQLVHGGTQRS-QFGETSEAIFLTQGFVYESMERAEARFKGDEPGYVYSRYSNP 69 Query: 65 TRFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVR 123 T +E +A EG A A ASGMAA T+++M L+ AG HVVA L+G + E + Sbjct: 70 TVVMFEERMALFEGAEAARATASGMAAVTASLMSLVKAGDHVVAARALFGACLYVVEDLL 129 Query: 124 RRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTV 183 R G+ + VD D + ++AA+R +TK++++E+PTNP L++ DIAAIA IA +G L V Sbjct: 130 PRF-GVSSTLVDGADLSQWRAAMRPETKVLFLESPTNPCLEVYDIAAIAAIAHDNGSLLV 188 Query: 184 VDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIG 243 VDN FA+P+LQ+PL+LGAD VV+SATK+++GH +GG+ + AFL+ + G Sbjct: 189 VDNVFATPILQKPLALGADCVVYSATKHIDGHGRCLGGVILASQELIDTHIHAFLRQT-G 247 Query: 244 GVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAK 303 V PF++++ L+ L+TLPLR+R ++A +A +L I V YPG + HPQ L K Sbjct: 248 PVLSPFNAWVLLKSLETLPLRVRQQMQSAERIADFLSGCQHIRLVRYPGRSDHPQADLVK 307 Query: 304 RQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARR 363 RQM G G +VS GG AA F + + ++ +LG +SL+ HPA TH + R Sbjct: 308 RQMRGGGTLVSFEFAGGKAAAFAFANQLSIIKISNNLGDAKSLITHPATTTHQRLTPEAR 367 Query: 364 EQLGISDALVRLSVGIEDLGDLRGDLERAL 393 LG++D L+RLSVG+ED DL DL AL Sbjct: 368 AALGVNDGLLRLSVGLEDADDLIDDLGAAL 397 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: 447 Number of extensions: 18 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: 408 Length adjustment: 31 Effective length of query: 366 Effective length of database: 377 Effective search space: 137982 Effective search space used: 137982 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