Align Serine O-acetyltransferase; EC 2.3.1.30 (characterized, see rationale)
to candidate Synpcc7942_B2663 Synpcc7942_B2663 putative serine acetyltransferase
Query= uniprot:B8DIT5_DESVM (317 letters) >FitnessBrowser__SynE:Synpcc7942_B2663 Length = 319 Score = 273 bits (698), Expect = 4e-78 Identities = 147/289 (50%), Positives = 188/289 (65%), Gaps = 6/289 (2%) Query: 18 LERIVDEMCAPESYEAVYHRSLHDA--PMPSLEALAEMVSRLRAALLPGFFGAATVHMES 75 L+ IV + + S + + H L D P+PS E+L ++ LR+ L P FG + +E+ Sbjct: 18 LDSIVSAL-SQASTDPLPHHLLSDQFYPLPSRESLGLILHGLRSVLFPRHFGDPELSVET 76 Query: 76 MRYHLAANLDSIYRILSEQIRRGACFT-CADFARECGSCEL--HSRDKAIQFLQRLPEIR 132 Y + LD +L+EQIRR E L H+ + F Q LPEI+ Sbjct: 77 THYFIGNTLDKTLNLLNEQIRRELWLQHVTQGTPEATPAVLSQHASELTQAFAQALPEIK 136 Query: 133 RMLASDVKAAYEGDPAAKSPGETVFCYPSIAAMINHRIAHELYRMEVPLIPRIISEMAHS 192 R+L SDV AAY GDPAA+S E +FCYP I A+ HR+AH LY++ +PL+ RI +E++HS Sbjct: 137 RLLDSDVNAAYLGDPAAQSISEILFCYPGITAITFHRLAHRLYQLGLPLLARITAEVSHS 196 Query: 193 RTGIDIHPGARIDEEFFIDHGTGVVIGETCIIGRGCRIYQGVTLGALSFPKDGDGVLIKG 252 TGIDIHPGA I FFIDHGTGVVIGETC+IG RIYQ VTLGA SFP+D G LIKG Sbjct: 197 ETGIDIHPGAAIGGSFFIDHGTGVVIGETCVIGDRVRIYQAVTLGAKSFPRDETGALIKG 256 Query: 253 NPRHPILEDNVTVYAGATILGRVTIGAGSMIGGNVWVTHDVPPGSKIVQ 301 RHP++ED+V +YAGAT+LGR+T+G GS IGGNVW+T VP GS I Q Sbjct: 257 QARHPVIEDDVVIYAGATLLGRITVGRGSTIGGNVWLTRSVPAGSFISQ 305 Lambda K H 0.322 0.138 0.417 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: 317 Number of extensions: 20 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: 317 Length of database: 319 Length adjustment: 27 Effective length of query: 290 Effective length of database: 292 Effective search space: 84680 Effective search space used: 84680 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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