Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate 5211062 Shew_3478 N-acetylglutamate synthase (RefSeq)
Query= curated2:B4U7A6 (287 letters) >FitnessBrowser__PV4:5211062 Length = 440 Score = 128 bits (322), Expect = 2e-34 Identities = 87/276 (31%), Positives = 147/276 (53%), Gaps = 11/276 (3%) Query: 17 FIRDFYGKVFVVKYGGAAMEEEELKHSFAKDIALLRYVGIKVVLVHGGGKDITNMLNKLN 76 ++ GK FVV GG A+ + + + S DIALL +GIK+VLVHG I L N Sbjct: 16 YVNAHRGKTFVVMLGGEALAQSQFR-SIINDIALLHSLGIKIVLVHGARPQIDEALAAHN 74 Query: 77 IQTEFINGIRKTDKESLDVARMVLIGKLNKDIVSMLNKEMSN--MHGAIGLSGIDANLLI 134 + E+ NG+R +D+ES V + V +G L DI + L+ +SN M GA ++ + N +I Sbjct: 75 LAPEYYNGVRISDEESFRVIKQV-VGGLQLDITARLSMSLSNTPMQGA-QINVVSGNFVI 132 Query: 135 CTKYYQD-GEDIGYVGKVKTVNTKLIRELIQMDYTPVIAPIGIDPESNQMYNVNADMAAT 193 D G D GKV+ ++ +R + ++ P+ + + +N+ A+ AT Sbjct: 133 AQPLGVDNGVDYCLSGKVRRIDVAGLRRQLDNHGIVLLGPVAAS-VTGECFNLTAEEVAT 191 Query: 194 EIACELGAEKLIFLTDTDGILDKSGKTISSIHKNQ----YKELIEDGTITKGMIPKINSA 249 +IA +L A+K+I + +GILD +G+ I+ + EL ++ G + ++ Sbjct: 192 QIAVKLKADKMIGFSAKEGILDSNGEVIAELMPTDAQRILSELTDEDNWCVGTRAFLQAS 251 Query: 250 IDAILRGVRKVHIINGKIKHSILIEVFTKEGIGTEI 285 IDA GV + H ++ ++L E+F+++GIGT+I Sbjct: 252 IDACRNGVARCHFVSYLDDGALLQELFSRDGIGTQI 287 Lambda K H 0.318 0.139 0.381 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: 279 Number of extensions: 16 Number of successful extensions: 4 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: 287 Length of database: 440 Length adjustment: 29 Effective length of query: 258 Effective length of database: 411 Effective search space: 106038 Effective search space used: 106038 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 (21.7 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