Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate Synpcc7942_1714 Synpcc7942_1714 hypothetical protein
Query= BRENDA::I1R9N5 (509 letters) >FitnessBrowser__SynE:Synpcc7942_1714 Length = 338 Score = 86.7 bits (213), Expect = 1e-21 Identities = 80/259 (30%), Positives = 115/259 (44%), Gaps = 28/259 (10%) Query: 98 FLLDWGGILPEFNIAYETWGELNADKSNAILLHTGLSASSHAHSTETNPKPGWWEKFIGP 157 F LD G +LPE ++ Y T+GELN D+SNAIL T A HST + IG Sbjct: 11 FELDCGAVLPEASLVYATYGELNRDRSNAILYPTSYGAQ---HST--------IDWLIGG 59 Query: 158 GGPLDTNKYHVICTNVIGGCNGSTGPSSVDPGNGERYATRFPILTMDDMVRAQFKLLDH- 216 LD +++ ++ N G NG + S DP G A + + D V AQ LL Sbjct: 60 DRILDPDRWFIVIVNQFG--NGLSSSPSNDPACG--LAEQGFWFSHWDSVCAQQALLSQV 115 Query: 217 LGIDKLYASVGSSMGGMQSLAAGVQSPSRVGRIVSISGCARSHPYSIAMRHTQRQVLMMD 276 LGI++L G SMG Q+ + P RV RI ++ G A++ ++ + R L+ D Sbjct: 116 LGIEQLALIYGWSMGAQQAYHWAIAFPDRVQRIAALCGTAKTTEHNRLFLESLRAALIAD 175 Query: 277 PNWNRGFYYGKVPPHAGMKLAREIATVTYRSGPEWEQRFGRRRADSSKPPALCPDFLIET 336 P W+ + + P G K I S + R++ SS +E Sbjct: 176 PTWDGQRF--QATPDRGYKAFARIYASWAASQAFYRAGIYRQQGYSS----------LED 223 Query: 337 YLDHAGEKWCLNYDPNSLL 355 YL+ E DP+ LL Sbjct: 224 YLERGWEANYRQRDPHDLL 242 Lambda K H 0.317 0.134 0.413 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: 452 Number of extensions: 22 Number of successful extensions: 2 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: 509 Length of database: 338 Length adjustment: 31 Effective length of query: 478 Effective length of database: 307 Effective search space: 146746 Effective search space used: 146746 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: 50 (23.9 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