Align Serine acetyltransferase, plasmid; SAT; EC 2.3.1.30 (characterized)
to candidate Pf1N1B4_1690 Serine acetyltransferase (EC 2.3.1.30)
Query= SwissProt::Q59967 (319 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1690 Length = 308 Score = 319 bits (818), Expect = 5e-92 Identities = 164/270 (60%), Positives = 198/270 (73%), Gaps = 7/270 (2%) Query: 45 LPSRESLGLILHGLRSVLFPRHFGDPELSVETTHYFIGNTLDKTLNLLNEQIRRELWL-- 102 LPSR ++ IL L LFP G +L E+ +++G+TLD LN L Q R EL Sbjct: 40 LPSRAAMADILEALCGALFPMRLGPVDLREESEDFYVGHTLDVALNALLAQARLELRYAA 99 Query: 103 QHVTQGTPEATPAVLSQHASELTQAFAQALPEIKRLLDSDVNAAYLGDPAAQSISEILFC 162 +H Q E + ++ Q FA ALP ++ LLD+DV AAY GDPAA+S+ E+L C Sbjct: 100 RHSAQADTEVEAKTI-----QIIQDFALALPGLRTLLDTDVLAAYHGDPAARSVDEVLLC 154 Query: 163 YPGITAITFHRLAHRLYQLGLPLLARITAEVSHSETGIDIHPGAAIGGSFFIDHGTGVVI 222 YPGI A+ HRLAH LY+ GLPLLARI+AE++HS TGIDIHPGA IG SFFIDHGTGVVI Sbjct: 155 YPGILAVIHHRLAHHLYRAGLPLLARISAEIAHSATGIDIHPGAQIGRSFFIDHGTGVVI 214 Query: 223 GETCVIGDRVRIYQAVTLGAKSFPRDETGALIKGQARHPVIEDDVVIYAGATLLGRITVG 282 GET +IG+RVRIYQAVTLGAK FP DE G L KG RHP++EDDVVIYAGAT+LGRIT+G Sbjct: 215 GETAIIGERVRIYQAVTLGAKRFPADEDGQLQKGHPRHPIVEDDVVIYAGATILGRITIG 274 Query: 283 RGSTIGGNVWLTRSVPAGSFISQAQIRSDN 312 +GSTIGGNVWLTRSVPAG +SQA ++ D+ Sbjct: 275 KGSTIGGNVWLTRSVPAGCNLSQANLQHDD 304 Lambda K H 0.320 0.137 0.405 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: 335 Number of extensions: 15 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: 319 Length of database: 308 Length adjustment: 27 Effective length of query: 292 Effective length of database: 281 Effective search space: 82052 Effective search space used: 82052 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