Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011735719.1 PPRO_RS09115 PLP-dependent transferase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000015045.1:WP_011735719.1 Length = 383 Score = 366 bits (940), Expect = e-106 Identities = 187/374 (50%), Positives = 256/374 (68%), Gaps = 16/374 (4%) Query: 4 HVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIAN 63 +++T+ Q G D TG +S PIY S +RH G+G+STGFDY R+ NPTR +E IA Sbjct: 2 NIDTQAVQTGLEWDTRTGALSIPIYQSATFRHPGLGQSTGFDYSRSGNPTRLALEQGIAR 61 Query: 64 LENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDF 123 ++ G+RG AFSSGMAAI +++ LF+ GD L+V+ DLYGGT RLF+ + ++GL+F Y D Sbjct: 62 MDGGSRGFAFSSGMAAITSLLLLFQEGDHLVVTEDLYGGTCRLFDRIFTRFGLSFSYVDT 121 Query: 124 SDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRP 183 +D + + + ITP+TKA+FVET TNPL++ ADI ++ I E GLLLI DNTF TP L RP Sbjct: 122 TDREEVLAAITPSTKALFVETLTNPLLKFADIPALSTICHERGLLLIADNTFLTPYLLRP 181 Query: 184 LELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRG 243 LE GADI ++SATKYL GHND +AGL VV+D +L E+++ HQN+ GAVL P DSWL++RG Sbjct: 182 LERGADITVYSATKYLSGHNDTVAGLAVVRDPQLAEQVYFHQNSAGAVLGPQDSWLVIRG 241 Query: 244 MKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRL 287 MKTL +R+ + Q NA ++A +L+ +++ V YPG G M++F + Sbjct: 242 MKTLGVRLDRQQENALKIARWLQRHPQVTRVHYPGLEEHPDHDLIRRHARGFGAMIAFEV 301 Query: 288 QKEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVG 347 + V L + I FAESLGGVE+ +T+P QTH DIP E+R G+ + LLR SVG Sbjct: 302 ESHSLVEQLLLRTQLISFAESLGGVETLMTFPEGQTHADIPPELRARLGINDVLLRLSVG 361 Query: 348 IEHAEDLKEDLKQA 361 IE+ +DL +DL QA Sbjct: 362 IENVDDLIDDLNQA 375 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: 406 Number of extensions: 12 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: 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