Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012282806.1 HM1_RS07790 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000019165.1:WP_012282806.1 Length = 386 Score = 323 bits (829), Expect = 4e-93 Identities = 167/374 (44%), Positives = 232/374 (62%), Gaps = 16/374 (4%) Query: 5 VETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANL 64 + T + G + TG S PIY+++ + R I E +DY R+ NPTR E+AIA L Sbjct: 9 LSTLVVHAGTDRGQWTGAASVPIYMASTFHQRDIDEGQVYDYSRSGNPTRHAAEEAIACL 68 Query: 65 ENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFS 124 E G RG AF+SGMAA+ T +ALF +GD LIV+ D+YGGTYR+ + W ++G+ + D + Sbjct: 69 EGGTRGFAFASGMAAMSTCLALFSAGDHLIVAQDIYGGTYRILDKVWTRFGVETTFVDTT 128 Query: 125 DEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPL 184 D + + + + PNT+ + +E+P+NP + D+ A + +E G L I DNTF +P LQ+PL Sbjct: 129 DLEAVIAAVRPNTRGLILESPSNPTLAVTDLAGCAALARERGWLTIADNTFMSPCLQKPL 188 Query: 185 ELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGM 244 ELG DIV+HSATK+L GH+DL++G VVV DE LG+ + QNA G +L P DSWLL+RGM Sbjct: 189 ELGIDIVVHSATKFLAGHSDLISGCVVVGDEELGKRIGFLQNAFGNILSPHDSWLLLRGM 248 Query: 245 KTLSLRMRQHQANAQELAAFLEEQEEISDVLYP----------------GKGGMLSFRLQ 288 KTL++RM Q A++LAAFL ++S V YP G G +LSF L Sbjct: 249 KTLAVRMAASQQGARQLAAFLNNHPKVSRVYYPGLDNHPGYGIHNRQASGPGAVLSFDLG 308 Query: 289 KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGI 348 V F +K A SLGGVES ++YP T +H + E RI G+ L+R SVG+ Sbjct: 309 SRAAVKQFFSRVKLPIVAVSLGGVESILSYPTTMSHAAMEPEERIRRGIGPGLIRLSVGL 368 Query: 349 EHAEDLKEDLKQAL 362 E +DL+ DL +AL Sbjct: 369 EDPDDLQADLAEAL 382 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: 360 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: 386 Length adjustment: 30 Effective length of query: 343 Effective length of database: 356 Effective search space: 122108 Effective search space used: 122108 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