Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_066920229.1 ACG33_RS08115 O-succinylhomoserine (thiol)-lyase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_001579945.1:WP_066920229.1 Length = 404 Score = 254 bits (649), Expect = 3e-72 Identities = 147/373 (39%), Positives = 204/373 (54%), Gaps = 17/373 (4%) Query: 7 TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLEN 66 T + G +D+ G V P++LS+ + + GE +DY R+ NPTR + A+A+LE Sbjct: 15 TCAVRAGLETDDQHGAVVPPLHLSSTFAFKAFGERRQYDYSRSGNPTRDALATALADLEG 74 Query: 67 GARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDE 126 GA SSGMAA Q L + D LI D YGGTYRL + + L + D +D+ Sbjct: 75 GAGATVTSSGMAAAQLACQLLHADDLLIAPHDCYGGTYRLLSSLAARGALRVVFVDQTDD 134 Query: 127 DCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLEL 186 + + K V+VETP+NPL++ DI AR G LL+VDNTF +PV Q+P L Sbjct: 135 AAFSAALAGGPKLVWVETPSNPLLRIVDIRAAARQVHAAGALLLVDNTFLSPVWQQPFAL 194 Query: 187 GADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKT 246 GAD+V+HS TKYL GH+D++ G +V L E + N IG PFDS+L +RG+++ Sbjct: 195 GADLVLHSTTKYLNGHSDVVGGALVSATAELHERVQWWANCIGVTGAPFDSFLTLRGVRS 254 Query: 247 LSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQKE 290 L RMR H NA ++A L + + +PG G M+SF L Sbjct: 255 LHARMRAHGENALQVAQLLNGHSAVRQIYFPGLPTHPQHDLARTQQSGFGAMMSFELHGG 314 Query: 291 -EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIE 349 V FL L+ AESLGGVES + +PA+ TH + + R A G+ + LLR S+GIE Sbjct: 315 LASVRAFLDGLQCFSLAESLGGVESLVAHPASMTHAAMDAQARQAAGISDSLLRLSIGIE 374 Query: 350 HAEDLKEDLKQAL 362 A+DL DL+ L Sbjct: 375 TAQDLLNDLQAGL 387 Lambda K H 0.319 0.135 0.392 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: 369 Number of extensions: 14 Number of successful extensions: 2 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: 373 Length of database: 404 Length adjustment: 30 Effective length of query: 343 Effective length of database: 374 Effective search space: 128282 Effective search space used: 128282 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 (21.7 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