Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate Synpcc7942_1714 Synpcc7942_1714 hypothetical protein
Query= SwissProt::K4ICC9 (336 letters) >FitnessBrowser__SynE:Synpcc7942_1714 Length = 338 Score = 115 bits (287), Expect = 2e-30 Identities = 94/310 (30%), Positives = 136/310 (43%), Gaps = 13/310 (4%) Query: 11 FQLENGEVLPELEVSYSTLGKLNKEKSNVIWVCHALTANAQPEDWWRGLIGNEKGIDTEK 70 F+L+ G VLPE + Y+T G+LN+++SN I + A DW LIG ++ +D ++ Sbjct: 11 FELDCGAVLPEASLVYATYGELNRDRSNAILYPTSYGAQHSTIDW---LIGGDRILDPDR 67 Query: 71 YFIVCANIIGSCYGSTNPKSINPETGEVYGLNFPLFSIRDVTKSLELLSEALEIEHIQFL 130 +FIV N G+ G ++ S +P G + F V LLS+ L IE + + Sbjct: 68 WFIVIVNQFGN--GLSSSPSNDPACG-LAEQGFWFSHWDSVCAQQALLSQVLGIEQLALI 124 Query: 131 IGGSMGGMQAMEWAIEKPDKIKNLILLATNAKHSSWGIALNETQRMAIEADSTF----YK 186 G SMG QA WAI PD+++ + L AK + E+ R A+ AD T+ ++ Sbjct: 125 YGWSMGAQQAYHWAIAFPDRVQRIAALCGTAKTTEHNRLFLESLRAALIADPTWDGQRFQ 184 Query: 187 KETNSGKKGLEAARAIALLSYRNYNTYRHTQVDQEHTADHFRASTYQKYQGEKLSKRFNA 246 + G K A S Y + Q D+ Y+ Sbjct: 185 ATPDRGYKAFARIYASWAASQAFYRAGIYRQQGYSSLEDYLERGWEANYRQRDPHDLLAM 244 Query: 247 KCYWYLSKAMDSHNVGRNRGDCKKALAKIKAETLVIAVQSDLLFPVEEQRFLAQYIPKGK 306 W D G GD KAL I A+TLV+ +DL F E+ AQ IPK Sbjct: 245 IDTWLRCDVSDRPAFG---GDLAKALGSITAQTLVMPSTTDLYFTPEDCEAEAQLIPKAH 301 Query: 307 LEIIDSIYGH 316 I SI+GH Sbjct: 302 YCPIPSIWGH 311 Lambda K H 0.317 0.134 0.397 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: 275 Number of extensions: 17 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: 336 Length of database: 338 Length adjustment: 28 Effective length of query: 308 Effective length of database: 310 Effective search space: 95480 Effective search space used: 95480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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