Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012755216.1 RLEG_RS23530 methionine gamma-lyase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000023185.1:WP_012755216.1 Length = 427 Score = 195 bits (495), Expect = 2e-54 Identities = 131/409 (32%), Positives = 200/409 (48%), Gaps = 51/409 (12%) Query: 4 HVETKLAQIGNRSDEVTGTVSAPIYLSTAY------------------RHRGIGESTGFD 45 H ET++ G + G V P++L++ + R G+ G Sbjct: 17 HPETQMLNYGYDPELSEGAVKPPVFLTSTFVFKTAEDGRDFFDYVSGRREPPEGKGAGLV 76 Query: 46 YVRTKNPTRQLVEDAIANLENGARGLAFSSGMAAIQT-IMALFKSGDELIVSSDLYGGTY 104 Y R +P ++VED +A E G+ FSSGMAAI T ++A + GD ++ S LYGGT Sbjct: 77 YSRFNHPNSEIVEDRLAVYERTESGVLFSSGMAAIATTLLAFVRPGDAILHSQPLYGGTE 136 Query: 105 RLFENEWKKYGLTF--HYDDFSDEDCLRSKITPNTKA----VFVETPTNPLMQEADIEHI 158 L + G D S+ ++ K + +ETP NP D+ I Sbjct: 137 TLLAKTFLNLGAAAVGFADGVSEGSVQKAAAEAMAKGRVSVILIETPANPTNGLVDVAMI 196 Query: 159 ARIT------KEHGLLLIVDNTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVV 212 R+ + H +++ DNT PV QRP+E GADI ++S TKY+GGH+DL+AG V+ Sbjct: 197 RRVADMIGARQGHMPIIVCDNTLLGPVFQRPIEHGADISLYSLTKYVGGHSDLIAGAVLG 256 Query: 213 KDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEIS 272 + + +++ + AIG L P W+L R ++TL LRM + +NA+ +A +L + ++ Sbjct: 257 RKAVI-KQIKALRGAIGTQLDPHSCWMLGRSLETLQLRMERANSNARTVADYLRDHPKVE 315 Query: 273 DVLY------------------PGKGGMLSFRLQKEEWVN-PFLKALKTICFAESLGGVE 313 V Y G G SF ++ + + FL AL+ A SLGG E Sbjct: 316 KVHYLPYHDPDSPAGRTFIAQCTGAGSTFSFDIRGGQPASFKFLNALQIFKLAVSLGGTE 375 Query: 314 SFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIEHAEDLKEDLKQAL 362 S ++PA TH +P ++R GV +R S+GIEH +DL DL+ AL Sbjct: 376 SLASHPAAMTHSGVPADVRQRIGVLESTIRLSIGIEHPDDLIADLELAL 424 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: 354 Number of extensions: 16 Number of successful extensions: 7 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: 427 Length adjustment: 31 Effective length of query: 342 Effective length of database: 396 Effective search space: 135432 Effective search space used: 135432 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