Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate GFF3930 Psest_4000 amino-acid N-acetyltransferase
Query= curated2:Q2KU83 (300 letters) >FitnessBrowser__psRCH2:GFF3930 Length = 432 Score = 114 bits (286), Expect = 3e-30 Identities = 88/284 (30%), Positives = 140/284 (49%), Gaps = 15/284 (5%) Query: 20 LSEALPYIRRFHGKTIVVKYGGNAMTEERLQRSFAHDVVLLKLVGLNPVVVHGGGPQIDD 79 L ++ PYI +T VV G+ + + HD+VLL +G+ V+V G PQI+ Sbjct: 8 LRDSSPYINSHRDRTFVVMLPGDGLEHANFA-NIVHDLVLLHSLGVRLVLVFGSRPQIEA 66 Query: 80 ALRRLGKQGTFVQGMRVTDAETMEVVEWVLGG-----QVQQDIVMMINEAGGKAVGLTGK 134 L G + F + +RVTDA TME V +G + + + M + G + + G Sbjct: 67 RLAARGIEPRFHRDLRVTDAPTMECVIDAVGQLRIALEARLSMDMAASPMQGARLRVAG- 125 Query: 135 DGMLLQARKKLMADKEKPGELLDIGLVGDVTRVEPAVVKALQDDQFIPVISPIGYGEDGT 194 G + AR + D +D+ G+V R++ + L D++ I ++SP+GY G Sbjct: 126 -GNFVTARPIGVLDG------VDLHHTGEVRRIDRKGIGRLLDERTIVLLSPLGYSPTGE 178 Query: 195 AYNINADVVAGKIAEVLGAEKLLMMTNTPGVLDKSGKLLRSLSAQTIDELFADGTISGGM 254 +N+ + VA + A L A+KL++ PG+LD+SGKL+R L Q I + + S Sbjct: 179 IFNLACEDVATRAAIDLQADKLVLYGAEPGLLDESGKLVRELRPQQI-PAYVERLGSQYQ 237 Query: 255 LPKISSALDAAKNGVPSVHVVDGRVPHCLLLELLTDQGVGTMIS 298 + +A A + GV HVV LL EL T G GT+++ Sbjct: 238 AELLDAAAQACRGGVRRSHVVSYADDGALLNELFTRDGGGTLVT 281 Lambda K H 0.317 0.137 0.386 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: 331 Number of extensions: 17 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: 300 Length of database: 432 Length adjustment: 29 Effective length of query: 271 Effective length of database: 403 Effective search space: 109213 Effective search space used: 109213 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 (21.6 bits) S2: 49 (23.5 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