Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate PfGW456L13_1007 Homoserine O-acetyltransferase (EC 2.3.1.31)
Query= SwissProt::S2KHP1 (367 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 Length = 379 Score = 245 bits (626), Expect = 1e-69 Identities = 140/365 (38%), Positives = 205/365 (56%), Gaps = 8/365 (2%) Query: 2 PDARRFIELPGPVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAAS--SM 59 P F E P+ + G LP+ + YET+G L NA+L+ LS HAA S Sbjct: 15 PQVAHFSE---PLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGYHSA 71 Query: 60 ADPSPGWWEYMIGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSV 119 D PGWW+ IGPGKPIDT +FFV+++N+LG C GSTGP+SINP TG+P+ DFP L+V Sbjct: 72 DDRKPGWWDSCIGPGKPIDTSKFFVVSLNNLGGCNGSTGPSSINPDTGKPFGADFPVLTV 131 Query: 120 EDIVAAARGACRALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTI 179 ED V + LGI V G SLGGM A+ +++ YP R ++I++A + I Sbjct: 132 EDWVHSQARLADRLGIAQFAAVIGGSLGGMQAMQWSITYPDRIRHCLAIASAPKLSAQNI 191 Query: 180 ALRSIQREAVRADPAWAGGNYAPGEG-PKDGMRVARQLGILTYRSAEEWLQRFDRERLEG 238 A + R+A+ DP + GG++ PK G+ +AR +G +TY S + ++F R L+ Sbjct: 192 AFNEVARQAILTDPEFHGGSFQEHNVIPKRGLMLARMVGHITYLSDDSMGEKFGR-GLKS 250 Query: 239 SDDSANPFAMAFQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRR 298 + + ++ FQV+SY+ +F+ RFDAN YL +++A+D FD A + D +L Sbjct: 251 EKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDNLAKTFEG 310 Query: 299 IDAKRALVAGVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPM 358 AK V TTDW F + R++ + L A V Y E+ + QGHDAFL+ R+ Sbjct: 311 AKAK-FCVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPIPRYLQA 369 Query: 359 VAEFL 363 ++ Sbjct: 370 FGNYM 374 Lambda K H 0.320 0.135 0.414 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: 386 Number of extensions: 24 Number of successful extensions: 4 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: 367 Length of database: 379 Length adjustment: 30 Effective length of query: 337 Effective length of database: 349 Effective search space: 117613 Effective search space used: 117613 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 (21.8 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