Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012471101.1 GLOV_RS15170 PLP-dependent transferase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000020385.1:WP_012471101.1 Length = 378 Score = 376 bits (966), Expect = e-109 Identities = 193/374 (51%), Positives = 252/374 (67%), Gaps = 16/374 (4%) Query: 5 VETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANL 64 + T+ QIG D TG+V+ PIY + +RH G+G+STGFDY R+ NPTRQ +ED IA L Sbjct: 3 ITTQAVQIGLEWDTRTGSVAIPIYQTATFRHPGLGQSTGFDYTRSGNPTRQALEDGIARL 62 Query: 65 ENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFS 124 + G RG A+++GMAAI ++ LFK+GD ++V+ DLYGGT RLF + ++GL+F Y D + Sbjct: 63 DGGVRGFAYATGMAAITGLLMLFKAGDHIVVTEDLYGGTCRLFNQVFNQFGLSFSYVDTT 122 Query: 125 DEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPL 184 D + + I P T+A+FVET TNPL++ AD+ +A +++ GLLLI DNTF TP L RPL Sbjct: 123 DLAAVEAAIRPETRALFVETLTNPLLKFADLPALAELSRRRGLLLIADNTFLTPYLMRPL 182 Query: 185 ELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGM 244 ELGADI ++SATKYL GHND L GLVV L E ++ +QN++GAVL P DSWL++RGM Sbjct: 183 ELGADITVYSATKYLAGHNDTLGGLVVTNRPELAERIYFYQNSVGAVLAPQDSWLIIRGM 242 Query: 245 KTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQ 288 KTL +R+ +HQ NA +A +LE+ IS V YPG G M++F + Sbjct: 243 KTLGVRLDRHQENALRIATWLEQHPRISKVHYPGLPQHPDHALMKRQARGFGAMIAFEVD 302 Query: 289 KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGI 348 K V L I FAESLGGVES IT+P QTH DIP E+R G+ N LLR SVGI Sbjct: 303 KHALVEQVLLKTGLISFAESLGGVESLITFPEVQTHADIPAELRARLGINNVLLRLSVGI 362 Query: 349 EHAEDLKEDLKQAL 362 E A+DL EDL+QAL Sbjct: 363 EDADDLIEDLRQAL 376 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: 400 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: 378 Length adjustment: 30 Effective length of query: 343 Effective length of database: 348 Effective search space: 119364 Effective search space used: 119364 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