Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_073042118.1 BUB04_RS18115 PLP-dependent transferase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_900129305.1:WP_073042118.1 Length = 390 Score = 262 bits (669), Expect = 1e-74 Identities = 158/384 (41%), Positives = 221/384 (57%), Gaps = 24/384 (6%) Query: 2 SQHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRG-IGESTGFDYVRTKN-PTRQLVED 59 S+ T+ GN D +TG V+ PI+ S+AYR G +GE Y R +N PT++ V + Sbjct: 10 SKGFSTRAVHAGNVEDVMTGGVNTPIFPSSAYRVPGPLGEVV---YPRYQNIPTQRAVAE 66 Query: 60 AIANLENGARGLAFSSGMAAIQTIMALFKS-GDELIVSSDLYGGTYRLFENEWKKYGLTF 118 IA LE G L SSGMAAI ++ F + GD +++ DLYGGT+ L E + G+ Sbjct: 67 KIAALEGGESALVVSSGMAAISSVFLAFCAPGDHVVLQRDLYGGTHHLAARELPRLGVET 126 Query: 119 HYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTP 178 + D + + + P T+ +++ETP+NPLM+ D+E +AR+ + G+L +VDNTF TP Sbjct: 127 TWVPSQDPEDFEAALGPATRILYLETPSNPLMKILDLEALARVARRRGVLTVVDNTFATP 186 Query: 179 VLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSW 238 V Q PL LG DIV+HS TKYL GH+DL G +V + + L E ++ A G L P+D + Sbjct: 187 VNQNPLALGIDIVVHSGTKYLNGHSDLCCGAIVTRRD-LMERIYGVVAAYGPSLSPYDCY 245 Query: 239 LLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGM 282 LL RGMKTL++RMRQH N ++AAFL+ + V YPG G M Sbjct: 246 LLERGMKTLAVRMRQHNENGAKIAAFLDGHPRVRQVYYPGLANHPGHHIAALQMRAFGAM 305 Query: 283 LSFRLQKE-EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRL 341 LSF + ++ L+ A SLGGVES +PA +H + E R+A G+ + L Sbjct: 306 LSFEPDCDTATAQVVMERLRFFKPAVSLGGVESLACFPAQTSHAPLSPEERLALGISDSL 365 Query: 342 LRFSVGIEHAEDLKEDLKQALCQV 365 +R SVGIE EDL EDL QAL + Sbjct: 366 IRLSVGIEDPEDLMEDLDQALAAI 389 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: 380 Number of extensions: 18 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: 390 Length adjustment: 30 Effective length of query: 343 Effective length of database: 360 Effective search space: 123480 Effective search space used: 123480 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