Align Homoserine O-succinyltransferase; HST; EC 2.3.1.46; Homoserine transsuccinylase; HTS (uncharacterized)
to candidate WP_086511565.1 BZY95_RS19555 homoserine acetyltransferase
Query= curated2:A0LCI7 (394 letters) >NCBI__GCF_002151265.1:WP_086511565.1 Length = 410 Score = 184 bits (468), Expect = 3e-51 Identities = 128/375 (34%), Positives = 186/375 (49%), Gaps = 27/375 (7%) Query: 1 MTHEPLTASVGIVTPQHVRLFGASTPLQLDGGTLLHSVDVSYETYGTLNQERSNAVLICH 60 +T P TA G+V Q L +T GG + V + +E YGTLN+ER N +LI H Sbjct: 32 LTSMPATAWDGLVEKQVFELDEYTTV----GGDTIAPVRIGWEAYGTLNEERDNVILITH 87 Query: 61 ALSGNAHAAGYHSKDDKRPGWWDHYIGPGKPFDTNRYFVIASNNLGGCD------GTTGP 114 SG +HAAG +++DD PG+WD IGPGKP DT+ Y++I+S+ L + TTGP Sbjct: 88 FFSGTSHAAGRYTEDDAAPGYWDAIIGPGKPLDTDEYYIISSDTLVNLNVHDPNVTTTGP 147 Query: 115 SSIDPATGMPYGLNFPMITIGDIVRVQHALVRQLGIERLMAVVGGSMGGMQALQWALDYP 174 ++ +P TG P+G +FP++TI D V VQ AL+ GIERL AV+G SMG +QA +WA YP Sbjct: 148 ATPNPETGEPWGTDFPLVTIRDFVEVQKALLESQGIERLHAVMGPSMGALQAYEWASTYP 207 Query: 175 HMVPASVII----AAAPRLTAQNIAFNAVARQAIMADPHFNGGDYYTLPGDPTTKARPES 230 V + + A P L A A+ A I D ++N GDYY +P P Sbjct: 208 ERVERLIPVIGGGVADPWLLATLSAWAA----PIRLDANWNEGDYY--DSEP-----PLD 256 Query: 231 GLALARMMAHITYLSEQGLHERFGRRLQDRDA-LSYGFETDFAVESYLSYQGSSFVKRFD 289 GL A + + +E F R D DA + + +A+E L ++ + D Sbjct: 257 GLREALKLVTLNANHWLWANETFDRSWADEDADPTRELDARYAIEQTLDDIAAARAELAD 316 Query: 290 ANSYLYITKAMDYFDPFPDAETTVQRLTGVESHFLVMSFDTDWRFDTSRSKELVRILHRS 349 AN LY+ KA F + + L +E+ L++ + D F ++ ++ Sbjct: 317 ANHLLYLVKANQSFIA-GHGGSLEEGLGRIEAPTLILYSENDLVFAPEGVRQTAELIEDG 375 Query: 350 LKDCTFQEFSSPAGH 364 D GH Sbjct: 376 GADVELVTLEGKRGH 390 Lambda K H 0.320 0.136 0.417 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: 453 Number of extensions: 26 Number of successful extensions: 3 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: 394 Length of database: 410 Length adjustment: 31 Effective length of query: 363 Effective length of database: 379 Effective search space: 137577 Effective search space used: 137577 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 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