Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate GFF279 Psest_0280 homoserine O-acetyltransferase
Query= SwissProt::A0A0I9RJ56 (370 letters) >FitnessBrowser__psRCH2:GFF279 Length = 379 Score = 240 bits (612), Expect = 5e-68 Identities = 138/359 (38%), Positives = 207/359 (57%), Gaps = 9/359 (2%) Query: 17 PFPFKRGGALHGARVAYETWGTLAADASNAILIVTGLSPDAHAAA----NDANPAAGWWE 72 P G L ++ YET+G L A SNA+LI LS HAA +D P GWW+ Sbjct: 23 PLTLACGRTLADYQLIYETYGELNAARSNAVLICHALSGHHHAAGYHSEDDRKP--GWWD 80 Query: 73 GMVGPGKAIDTDRWFVVCVNSLGSCRGSTGPASLNPATGQPYRLDFPELSIEDGARAAIE 132 +GPGKAIDT+R+FVV +N+LG C GSTGP+S NPA+G+PY DFP +++ED + Sbjct: 81 SCIGPGKAIDTNRFFVVSLNNLGGCNGSTGPSSTNPASGKPYGADFPVVTVEDWVHSQAR 140 Query: 133 VVRAQGIEQLACVVGNSMGGMTALAVLMLHPGIARSHVNISGSAQALPFSIAIRSLQREA 192 + GI Q A VVG S+GGM AL + +P R + I+ + + +IA + R+A Sbjct: 141 LADRLGIAQWAAVVGGSLGGMQALQWTISYPERVRHCLAIASAPKLSAQNIAFNEVARQA 200 Query: 193 IRLDPRWNGGHYDD-DAYPESGMRMARKLGVITYRSALEWDGRFGRVRLDSDQTDDDPFG 251 I DP ++GGH+ + P+ G+ +AR +G ITY S +FGR L S++ + D Sbjct: 201 ILSDPEFHGGHFQEMGVIPKRGLMLARMVGHITYLSDDAMGTKFGR-GLKSEKLNYDFNS 259 Query: 252 LEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEYADGDVLAGLAKIRVEKALAI 311 +EFQVESYL F FD N YL +++++D+FD A A+ D LA ++ + Sbjct: 260 VEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAA-ANDDDLAKTFEVAKADFCVM 318 Query: 312 GANTDILFPVQQQQQVADGLRAGGADARFIGLESPQGHDAFLVDFERFCPAVRGFLDAL 370 TD F ++ +++ D L A + ++ +++PQGHDAFL+ R+ A RG+++ + Sbjct: 319 SFTTDWRFSPERSREIVDALLAARKNVCYLEIDAPQGHDAFLIPNPRYLQAFRGYMNRI 377 Lambda K H 0.322 0.138 0.432 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: 398 Number of extensions: 25 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: 370 Length of database: 379 Length adjustment: 30 Effective length of query: 340 Effective length of database: 349 Effective search space: 118660 Effective search space used: 118660 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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