Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_012172541.1 AZC_RS20625 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000010525.1:WP_012172541.1 Length = 400 Score = 262 bits (669), Expect = 1e-74 Identities = 155/384 (40%), Positives = 226/384 (58%), Gaps = 12/384 (3%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSP--------GEHQGFEYSRTHNPTRFAYE 70 TL +HGG + P G +Y T + + GE GF YSR NPT +E Sbjct: 17 TLLVHGGTTRSPY-GETSEALYLTQGFVYDNAEACEARFKGEDPGFVYSRYGNPTTAMFE 75 Query: 71 RCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 +A L+G A A ASGMAA + +++ L AG HVVA L+G + E R G+ Sbjct: 76 ERMALLDGAEAARATASGMAAVNASLLCQLKAGDHVVAARALFGSCRWILEDFLPRY-GV 134 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189 + + V+ TD A+KAA R +TK+ ++E+PTNP L+++D+ A+A IA G L +VDN FA Sbjct: 135 ETTLVNGTDLDAWKAAARPNTKIFFLESPTNPTLEIIDVKAVADIAHAQGALLIVDNVFA 194 Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPF 249 +P+LQ+P LGAD+VV+SATK+++G +GG+ + FL+ + G PF Sbjct: 195 TPLLQKPFELGADVVVYSATKHIDGQGRCLGGVVLSSQQFVTDHLQTFLRQT-GPSISPF 253 Query: 250 DSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGF 309 ++++ L+GL+TL LR+ +A LA L P +EKV+YP A HPQ LA+RQM+G Sbjct: 254 NAWVLLKGLETLGLRVERAQSSAATLADALAAEPKVEKVLYPFRADHPQAALARRQMTGG 313 Query: 310 GGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGIS 369 G +V+ V+ GG + A RF ++ ++ +LG +SL+ HPA TH R ++GIS Sbjct: 314 GTLVTFVVGGGKEGAFRFANALKVIRISNNLGDSKSLLTHPATTTHQRFTPEARAEMGIS 373 Query: 370 DALVRLSVGIEDLGDLRGDLERAL 393 D LVRLSVG+E DL D+ +AL Sbjct: 374 DGLVRLSVGLEHPDDLVSDIVQAL 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: 455 Number of extensions: 19 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: 400 Length adjustment: 31 Effective length of query: 366 Effective length of database: 369 Effective search space: 135054 Effective search space used: 135054 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