Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate 3606894 Dshi_0324 acetylglutamate kinase (RefSeq)
Query= BRENDA::Q87EL2 (421 letters) >FitnessBrowser__Dino:3606894 Length = 287 Score = 113 bits (282), Expect = 8e-30 Identities = 83/284 (29%), Positives = 141/284 (49%), Gaps = 18/284 (6%) Query: 1 MASAKEISQ---YLKRFSQLDAKRFAVVKVGGAVLRDDVDALTS---SLSFLQEVGLTPI 54 +A+A+ +S+ +L+R+ V+K GG + D +A+ S + +++VG+ P+ Sbjct: 11 IATARTLSEAVPFLRRYDDA----IVVIKFGGHAM-GDAEAMASFARDIVLMRQVGVNPV 65 Query: 55 VLHGAGPQLDEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARA 113 ++HG GP ++ L + I VNG RVT T+ +V V N ++++A+ R G RA Sbjct: 66 IVHGGGPMINAMLAKLDINSDFVNGKRVTDAATIEVVEMVLSGLVNKRIVQAINREGGRA 125 Query: 114 TSITGGVFEAHYLD--QETYGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQILNI 171 ++G D G VG V + +R+ IPVIA +G G+ NI Sbjct: 126 IGLSGKDANLIVCDPADPALGFVGEPVEVTPDTLLQLVRSEIIPVIAPIGTGREGETFNI 185 Query: 172 NADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGMKLK 231 N D AA + L+ +++ LT G+ DA GK++ + + E++ + GGM K Sbjct: 186 NGDTAAGAIAAALKADRLLLLTDVSGVKDAQGKVVTELTVE-NIEEMTAAGVIAGGMIPK 244 Query: 232 IEQIKHLLDRLPLESSVSI--TRPADLAKELFTHKGSGTLIRRG 273 E + R + ++V + P ELFT G+G++IRRG Sbjct: 245 TETCVTAI-RGGVRAAVILDGRAPNACLLELFTEHGAGSIIRRG 287 Lambda K H 0.320 0.136 0.399 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: 229 Number of extensions: 12 Number of successful extensions: 3 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: 421 Length of database: 287 Length adjustment: 29 Effective length of query: 392 Effective length of database: 258 Effective search space: 101136 Effective search space used: 101136 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: 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