Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate SMc03797 SMc03797 homoserine O-succinyltransferase
Query= SwissProt::Q7CWE8 (308 letters) >FitnessBrowser__Smeli:SMc03797 Length = 331 Score = 550 bits (1416), Expect = e-161 Identities = 255/304 (83%), Positives = 281/304 (92%) Query: 1 MPIKIPDTLPAFETLVHEGVRVMTETAAIRQDIRPLQIGLLNLMPNKIKTEIQMARLVGA 60 MPIKIPDTLPAFETLVHEGVR+MTET AIRQDIRPLQIGLLNLMPNKIKTEIQMARL+GA Sbjct: 24 MPIKIPDTLPAFETLVHEGVRLMTETEAIRQDIRPLQIGLLNLMPNKIKTEIQMARLIGA 83 Query: 61 SPLQVELSLIRIGGHRAKNTPEEHLLSFYQTWEEVRHRKFDGFIITGAPIELLDYEDVTY 120 +PLQVEL+L+R+ GHR KNTPEEHLL+FY+T+EEV RKFDGFIITGAPIE L+YE+VTY Sbjct: 84 TPLQVELTLVRVNGHRPKNTPEEHLLAFYETFEEVEARKFDGFIITGAPIETLEYEEVTY 143 Query: 121 WNEMQQIFEWTQTNVHSTLNVCWGAMAAIYHFHGVPKYELKEKAFGVYRHRNLSPSSIYL 180 W E+Q+IF+WT TNVHSTLNVCWG MAA+YHFHGVPKY LKEKAFGVYRH+NL PSS+YL Sbjct: 144 WKELQRIFDWTTTNVHSTLNVCWGGMAAVYHFHGVPKYPLKEKAFGVYRHQNLQPSSVYL 203 Query: 181 NGFSDDFQVPVSRWTEVRRADIEKHPELEILMESDEMGVCLAHEKAGNRLYMFNHVEYDS 240 NGFSDDF VPVSRWTEVRRADI++ P+LEILMES E+GVCL HEK GNRLYMFNHVEYDS Sbjct: 204 NGFSDDFAVPVSRWTEVRRADIDRVPDLEILMESKEVGVCLVHEKKGNRLYMFNHVEYDS 263 Query: 241 TSLADEYFRDVNSGVPIKLPHDYFPHNDPELAPLNRWRSHAHLFFGNWINEIYQTTPYDP 300 TSL++EYFRDV++GVPIKLPHDYFPHND L P NRWRSHAHLFFGNWINEIYQTTPY+ Sbjct: 264 TSLSEEYFRDVDAGVPIKLPHDYFPHNDSALPPQNRWRSHAHLFFGNWINEIYQTTPYEL 323 Query: 301 QAIG 304 IG Sbjct: 324 AKIG 327 Lambda K H 0.321 0.137 0.429 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: 481 Number of extensions: 14 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: 308 Length of database: 331 Length adjustment: 28 Effective length of query: 280 Effective length of database: 303 Effective search space: 84840 Effective search space used: 84840 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: 48 (23.1 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