Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate PfGW456L13_1007 Homoserine O-acetyltransferase (EC 2.3.1.31)
Query= SwissProt::Q4ZZ78 (379 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 Length = 379 Score = 723 bits (1867), Expect = 0.0 Identities = 348/379 (91%), Positives = 364/379 (96%) Query: 1 MPTVFPHDSVGLVTPQTAHFSEPLALACGRSLPAYDLIYETYGQLNAARSNAVLICHALS 60 MP FP DSVGLVTPQ AHFSEPLALACGRSLPAYDLIYETYG LNA SNAVLICHALS Sbjct: 1 MPAAFPPDSVGLVTPQVAHFSEPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALS 60 Query: 61 GHHHAAGFHSADDRKPGWWDSCIGPGKPIDTTKFFVVSLNNLGGCNGSTGPSSIDPDTGK 120 GHHHAAG+HSADDRKPGWWDSCIGPGKPIDT+KFFVVSLNNLGGCNGSTGPSSI+PDTGK Sbjct: 61 GHHHAAGYHSADDRKPGWWDSCIGPGKPIDTSKFFVVSLNNLGGCNGSTGPSSINPDTGK 120 Query: 121 PFGANFPVVTVEDWVNSQARLADLLGIDTWAAVIGGSLGGMQALQWTISYPNRVRHCLAI 180 PFGA+FPV+TVEDWV+SQARLAD LGI +AAVIGGSLGGMQA+QW+I+YP+R+RHCLAI Sbjct: 121 PFGADFPVLTVEDWVHSQARLADRLGIAQFAAVIGGSLGGMQAMQWSITYPDRIRHCLAI 180 Query: 181 ASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQERGVIPKRGLMLARMVGHITYLSDDSM 240 ASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQE VIPKRGLMLARMVGHITYLSDDSM Sbjct: 181 ASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQEHNVIPKRGLMLARMVGHITYLSDDSM 240 Query: 241 GEKFGRGLKSEKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANF 300 GEKFGRGLKSEKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANF Sbjct: 241 GEKFGRGLKSEKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANF 300 Query: 301 NDDLAKTFANATARFCVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFL 360 +D+LAKTF A A+FCVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFL Sbjct: 301 DDNLAKTFEGAKAKFCVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFL 360 Query: 361 IPIPRYLQAFGNYMNRISL 379 IPIPRYLQAFGNYMNRI+L Sbjct: 361 IPIPRYLQAFGNYMNRITL 379 Lambda K H 0.321 0.137 0.428 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: 587 Number of extensions: 15 Number of successful extensions: 1 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: 379 Length of database: 379 Length adjustment: 30 Effective length of query: 349 Effective length of database: 349 Effective search space: 121801 Effective search space used: 121801 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