Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012565752.1 RC1_RS02465 PLP-dependent transferase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000016185.1:WP_012565752.1 Length = 383 Score = 195 bits (495), Expect = 2e-54 Identities = 136/381 (35%), Positives = 188/381 (49%), Gaps = 31/381 (8%) Query: 4 HVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRG-IGESTGFDYVRTKNPTRQLVEDAIA 62 H +T LA+ D T V ++ +T + G + G Y R NPT E +A Sbjct: 7 HPDTLLARAQGAHDPATHGVVPAVHPATTFLRAGDLSYPGGHSYARPFNPTFDGAETLLA 66 Query: 63 NLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDD 122 LE A+ L FSSGM+A + + GD +I +Y G + ++GL D Sbjct: 67 TLEGAAQALLFSSGMSAATAVFQALEPGDHVIAPQVMYWGLRNWLKGFAAQWGLGLDLVD 126 Query: 123 FSDEDCLRSKITPN-TKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQ 181 D + + + P T+ ++ ETP NP + D+ A I G L VDNT TP+L Sbjct: 127 MRDPAAVAAAVRPGRTRLIWAETPANPTWEVTDLAACAEIAHRAGARLAVDNTVPTPLLT 186 Query: 182 RPLELGADIVIHSATKYLGGHNDLLAG-LVVVKDERLGEEMFQHQNAIGAVLPPFDSWLL 240 RP+E GADIV+HSATKYL GH+D+L G L + + E + + GA+ PF++WLL Sbjct: 187 RPVEHGADIVMHSATKYLNGHSDVLGGALATARADGFWERIAAIRANQGAIPGPFEAWLL 246 Query: 241 MRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK-----------------GGML 283 +RGM+TL LR+ + A AQ LA ++ VLYPG GGML Sbjct: 247 LRGMRTLGLRVERACATAQRLAEHFAGHPKLEAVLYPGLPTHPGHAVAARQMRGGFGGML 306 Query: 284 SFRLQ-KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNR-L 341 S R++ AL+ A SLGGVES + + + D P C + L Sbjct: 307 SVRVKGGAAGAVAASAALRIWTRATSLGGVESLVEHRGSIEGPDSP---------CPQDL 357 Query: 342 LRFSVGIEHAEDLKEDLKQAL 362 LR S GIEHA+DL DL+QAL Sbjct: 358 LRLSCGIEHADDLIADLEQAL 378 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: 370 Number of extensions: 15 Number of successful extensions: 5 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: 383 Length adjustment: 30 Effective length of query: 343 Effective length of database: 353 Effective search space: 121079 Effective search space used: 121079 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