Align Serine acetyltransferase; SAT; EC 2.3.1.30 (uncharacterized)
to candidate 5211433 Shew_3842 UDP-N-acetylglucosamine pyrophosphorylase (RefSeq)
Query= curated2:Q65PC9 (216 letters) >FitnessBrowser__PV4:5211433 Length = 454 Score = 44.7 bits (104), Expect = 3e-09 Identities = 36/119 (30%), Positives = 58/119 (48%), Gaps = 13/119 (10%) Query: 54 ARAISQIARFFTGIEIHPGAKIGRRFFIDHGMGVVIGETCEIGN-----NVTVFQGVTLG 108 A + AR G E+ A IG F++ V +GE + G+ + V GV +G Sbjct: 320 AASAGPFARLRPGAELKRDAHIGN--FVEMKKAV-LGEGSKAGHLAYIGDAQVGAGVNIG 376 Query: 109 -GT---GKEKGKRHPT-IEDDALISTGAKVLGSITVGRGAKIGAGSVVLHDVPECSTVV 162 GT + +H T IEDD + + +++ +T+G+GA +GAGS + DV V+ Sbjct: 377 AGTITCNYDGANKHLTVIEDDVFVGSDTQLVAPVTIGKGATLGAGSTITRDVAADELVI 435 Score = 28.1 bits (61), Expect = 3e-04 Identities = 12/52 (23%), Positives = 24/52 (46%) Query: 101 VFQGVTLGGTGKEKGKRHPTIEDDALISTGAKVLGSITVGRGAKIGAGSVVL 152 + +G L + + T+ D +I G +T+G IGAG++++ Sbjct: 245 MLEGANLRDPARIDVRGEVTVGMDVMIDVNVVFQGKVTIGNNVTIGAGAILI 296 Score = 24.3 bits (51), Expect = 0.004 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 2/64 (3%) Query: 45 LYKRKRFFIARAISQIARFFTGIEIHPGAKIGRRFFIDHGMGVVIGETCEIGNNVTVFQG 104 L + +R + ARA ++ G + A+I R + GM V+I VT+ Sbjct: 229 LAQLERAYQARAAEKL--MLEGANLRDPARIDVRGEVTVGMDVMIDVNVVFQGKVTIGNN 286 Query: 105 VTLG 108 VT+G Sbjct: 287 VTIG 290 Lambda K H 0.323 0.142 0.416 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: 276 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 216 Length of database: 454 Length adjustment: 27 Effective length of query: 189 Effective length of database: 427 Effective search space: 80703 Effective search space used: 80703 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 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