Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate NP_661505.1 CT0605 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_000006985.1:NP_661505.1 Length = 356 Score = 241 bits (614), Expect = 3e-68 Identities = 137/352 (38%), Positives = 198/352 (56%), Gaps = 23/352 (6%) Query: 28 SEPLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFHAETDRKPGWWD 87 +EPL L+ G LP + Y T+G LN E SN +L+CHAL+G+ A+ D WW Sbjct: 20 NEPLQLELGGELPGVRVAYRTWGTLNAEKSNVILVCHALTGN-------ADAD---SWWC 69 Query: 88 SAIGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIVTVKDWVHAQYR 147 G G+ D R F+VC N LG C G+TGP+SV+P SG+ YGPDFP +T++D V+ Q Sbjct: 70 GMFGEGRAFDETRDFIVCSNVLGSCYGTTGPMSVNPLSGRHYGPDFPRITIRDMVNVQRL 129 Query: 148 LMQYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQNIAFNEVARQA 207 L++ LG+ ++G SLGGMQVL+W YP+ + + + R SA IA +E RQA Sbjct: 130 LLRSLGIDRIRLIVGASLGGMQVLEWGAMYPEMAGALMPMGVSGRHSAWCIAQSEAQRQA 189 Query: 208 IITDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFGRELRAGQVQYGFDVE 267 I D E+ G Y D PR+GL ARM+ TY + + +FGR+ R D Sbjct: 190 IAADAEWQDGWY-DPEVQPRKGLAAARMMAMCTYRCFENYQQRFGRKQRE-------DGL 241 Query: 268 FQVESYLRYQGTSFVDRFDANTYLLMTKALDYFDPAQASNDDLVAALAEVKAHFLVVSFT 327 F+ ESY+R+QG V RFDANTY+ +T+A+D D + D AAL +K ++S Sbjct: 242 FEAESYVRHQGDKLVGRFDANTYITLTRAMDMHDLGR-GRDSYEAALGALKMPVEILSID 300 Query: 328 SDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPYYHRVLAGY 379 SD + + E+ R L G ++ + ++ +GHDAFL+ R++ + Sbjct: 301 SDVLYPRQEQEELAR--LIPGSRLLF--LDEPYGHDAFLIDTETVSRMVCEF 348 Lambda K H 0.320 0.135 0.412 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: 396 Number of extensions: 18 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: 403 Length of database: 356 Length adjustment: 30 Effective length of query: 373 Effective length of database: 326 Effective search space: 121598 Effective search space used: 121598 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