Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate Synpcc7942_0371 Synpcc7942_0371 homoserine O-succinyltransferase
Query= SwissProt::Q0BX37 (305 letters) >FitnessBrowser__SynE:Synpcc7942_0371 Length = 299 Score = 318 bits (815), Expect = 1e-91 Identities = 155/295 (52%), Positives = 200/295 (67%), Gaps = 1/295 (0%) Query: 1 MPIRIPDTLPARETLLKEGVAVMTETDAVRQDIRPLQIALLNLMPNKIRTETQIARLIGA 60 MPI IP LPAR L E V + + DA RQDIR LQ+ +LNLMP K+ TETQIAR++ Sbjct: 1 MPIIIPQDLPARRILDAESVFTLGDADARRQDIRALQVVVLNLMPTKVTTETQIARVLAN 60 Query: 61 SPLQVELTLVRVGGHTPKNTSQEHLISFYQTWEEIRERKFDGFIITGAPIEQMPFEEVNY 120 +PLQVELTL+ + P +T EHL +FY T+++IR+R+FDG I+TGAP+E +P+ V+Y Sbjct: 61 TPLQVELTLIHTASYQPTHTDPEHLRNFYSTFDQIRDRQFDGLIVTGAPVETLPWLAVDY 120 Query: 121 WEELTQIFDWTQTNVHSPFYICWGAMAAAYHFHGLPKYQLEAKAFGVFRHRNLDLASPYL 180 W ELT I DW++ V S +ICWGA AA HFHG+ K L AK FGVF H D +SP + Sbjct: 121 WSELTTILDWSREAVRSSLFICWGAQAALQHFHGIEKQTLPAKRFGVFWHHLRDRSSPLV 180 Query: 181 SGFSDDFAIPVSRWTEVRRADVLERQSLRLLIDSDDTGPCLLEDRARRSLYMFNHVEYDS 240 G DDF +PVSR TEV A+VL + L++L +S + G LL D + Y+FNH EYD+ Sbjct: 181 RGHDDDFLVPVSRHTEVIAAEVLAQSQLQILAESSEAGLHLLWDADQHRTYLFNHPEYDA 240 Query: 241 FSLKEEFERDREAGKQIQVPFGYYPGDDPARQPLNRWRSHAHLLFGNWIN-QTYQ 294 +L E+ RDRE G IQ+P YYP DDP + P RWRSHA LL+ NW+N + YQ Sbjct: 241 DTLDREYRRDREKGLPIQLPLNYYPNDDPNQVPRVRWRSHAQLLYTNWLNYEVYQ 295 Lambda K H 0.322 0.138 0.427 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: 313 Number of extensions: 12 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: 305 Length of database: 299 Length adjustment: 27 Effective length of query: 278 Effective length of database: 272 Effective search space: 75616 Effective search space used: 75616 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: 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