Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate WP_057687234.1 ABB28_RS15260 homoserine O-acetyltransferase
Query= SwissProt::A0A0I9RJ56 (370 letters) >NCBI__GCF_001431535.1:WP_057687234.1 Length = 370 Score = 676 bits (1744), Expect = 0.0 Identities = 326/370 (88%), Positives = 347/370 (93%) Query: 1 MTEFIPPGTRFHALPSPFPFKRGGALHGARVAYETWGTLAADASNAILIVTGLSPDAHAA 60 MTEFIPPGT FHALPSPFPFKRGGAL RVAYETWGTL ADA NAILIVTGLSPDAHAA Sbjct: 1 MTEFIPPGTLFHALPSPFPFKRGGALTAGRVAYETWGTLDADAGNAILIVTGLSPDAHAA 60 Query: 61 ANDANPAAGWWEGMVGPGKAIDTDRWFVVCVNSLGSCRGSTGPASLNPATGQPYRLDFPE 120 +N ANPA GWWEGMVGPGK IDTDRWFV+CVNSLGSC+GSTGPAS++ ATG+PYRL FPE Sbjct: 61 SNAANPATGWWEGMVGPGKPIDTDRWFVICVNSLGSCKGSTGPASIDAATGKPYRLSFPE 120 Query: 121 LSIEDGARAAIEVVRAQGIEQLACVVGNSMGGMTALAVLMLHPGIARSHVNISGSAQALP 180 LS+EDGARA++EVVRA GI QLAC+VGNSMGGMTALA+L+LHPGIARSH+NISGSAQALP Sbjct: 121 LSVEDGARASVEVVRALGITQLACLVGNSMGGMTALALLLLHPGIARSHINISGSAQALP 180 Query: 181 FSIAIRSLQREAIRLDPRWNGGHYDDDAYPESGMRMARKLGVITYRSALEWDGRFGRVRL 240 FSIAIRSLQREAIRLDP+WNGG YDD YPESGMRMARKLGVITYRSALEWDGRFGRVRL Sbjct: 181 FSIAIRSLQREAIRLDPQWNGGQYDDANYPESGMRMARKLGVITYRSALEWDGRFGRVRL 240 Query: 241 DSDQTDDDPFGLEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEYADGDVLAGL 300 DSDQ DDDPFGLEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAE+ +GDV+AGL Sbjct: 241 DSDQADDDPFGLEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEHGNGDVMAGL 300 Query: 301 AKIRVEKALAIGANTDILFPVQQQQQVADGLRAGGADARFIGLESPQGHDAFLVDFERFC 360 A I+VEKALAIGANTDILFPVQQQQQ+ADGLRAGGA+A FIGL+SPQGHDAFLVDFERF Sbjct: 301 ATIKVEKALAIGANTDILFPVQQQQQIADGLRAGGAEAHFIGLDSPQGHDAFLVDFERFG 360 Query: 361 PAVRGFLDAL 370 PAVRGFL L Sbjct: 361 PAVRGFLGEL 370 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: 578 Number of extensions: 6 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: 370 Length of database: 370 Length adjustment: 30 Effective length of query: 340 Effective length of database: 340 Effective search space: 115600 Effective search space used: 115600 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: 49 (23.5 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