Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_041245567.1 GURA_RS19640 PLP-dependent transferase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000016745.1:WP_041245567.1 Length = 377 Score = 364 bits (934), Expect = e-105 Identities = 190/373 (50%), Positives = 252/373 (67%), Gaps = 16/373 (4%) Query: 5 VETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANL 64 + T+ QIG D TG V+ PIY + +RH G+G+STG+DY R+ NPTRQ +ED IA L Sbjct: 3 ISTQAVQIGLDWDTRTGAVTVPIYQTATFRHPGLGQSTGYDYSRSGNPTRQALEDGIARL 62 Query: 65 ENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFS 124 + G RG A++SGMAAI ++ LF+ GD L+V+ DLYGGTYRLFE +++YGL F Y D S Sbjct: 63 DRGCRGFAYASGMAAITNLLLLFQRGDHLVVTEDLYGGTYRLFEQVFQQYGLEFTYVDTS 122 Query: 125 DEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPL 184 D ++ NT+ +FVE+ TNPL++ ADI +A + KE G L IVDNTF TP L RPL Sbjct: 123 DMAAVKGAFKANTRGLFVESLTNPLLKVADIRALAILCKERGALCIVDNTFLTPYLLRPL 182 Query: 185 ELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGM 244 ELGADI ++SA+KYL GHND +AGLVV K +L E+++ QN++GAVL P DSWL++RGM Sbjct: 183 ELGADITVYSASKYLAGHNDTVAGLVVAKAPQLAEKIYFLQNSVGAVLGPQDSWLVIRGM 242 Query: 245 KTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQ 288 KTL++RM + +ANA +AA+L+ ++ V YPG G M++F ++ Sbjct: 243 KTLAIRMDRQEANAGRIAAWLQRHPLVAKVHYPGLSDHPGHALLQSEAAGFGAMIAFEVK 302 Query: 289 KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGI 348 + V L + I FAESLGGVE+ IT+P QTH DI EIR G+ N LLR SVGI Sbjct: 303 EPAQVEQLLMKTQLISFAESLGGVETLITFPEAQTHADIKPEIRKRLGINNVLLRLSVGI 362 Query: 349 EHAEDLKEDLKQA 361 E A+DL DL+QA Sbjct: 363 EDADDLIADLEQA 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: 363 Number of extensions: 10 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: 377 Length adjustment: 30 Effective length of query: 343 Effective length of database: 347 Effective search space: 119021 Effective search space used: 119021 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