Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate YP_428422.1 Rru_A3341 acetylglutamate kinase
Query= BRENDA::A0A0H2X8L7 (447 letters) >NCBI__GCF_000013085.1:YP_428422.1 Length = 310 Score = 112 bits (280), Expect = 2e-29 Identities = 87/291 (29%), Positives = 149/291 (51%), Gaps = 29/291 (9%) Query: 25 AKEISQ---YLKRFSQLDAKRFAVVKVGGAVLRDDLEALTSS--LSFLQEVGLTPIVLHG 79 AK +S+ Y++RF+ L V+K GG + D A T + + L++VG+ P+V+HG Sbjct: 23 AKTLSEALPYMRRFAGLTI----VIKYGGHAMGDPELAKTFARDVVLLKQVGMNPVVVHG 78 Query: 80 AGPQLDAELSAAGIEKQTVNGLRVTSPHALAIVRKVFQAS-NLKLVEALQQNGARATSIT 138 GPQ+ L I+ ++GLRVT + +V V S N +V + Q G A ++ Sbjct: 79 GGPQIGRMLDTLRIQSTFIDGLRVTDAATVDVVEMVLAGSINKAIVTEINQAGGCAVGLS 138 Query: 139 GG---VFEAEYLNRDTY------------GLVGEVKAVNLAPIEASLQAGSIPVITSLGE 183 G + +A + R + G VGE ++ + + IPVI +G Sbjct: 139 GKDGRLIQARKMVRKRHDPESNIERVLDLGFVGEPVVIDPHVLIQFRDSDIIPVIAPIGI 198 Query: 184 TPSGQILNVNADFAANELVQELQPYKIIFLTGTGGLLDAEGKLIDSINLSTEYDHLMQQP 243 +G+ N+NAD AA L +++ +++ LT G+LD + +LI +++ L Q+ Sbjct: 199 GEAGETFNINADTAAGALAAQMKAARLLMLTDVKGVLDKDKQLIQELSVD-RARLLKQEG 257 Query: 244 WINGGMRVKIEQIKDLLDRLPLESSVSITR--PADLAKELFTHKGSGTLVR 292 I+GGM K+E D ++R +E++V + P + E+FT +G+GTL+R Sbjct: 258 TISGGMIPKVETCIDAVER-GVEAAVIVDGRVPHAVLLEIFTPRGAGTLIR 307 Lambda K H 0.318 0.134 0.383 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: 291 Number of extensions: 11 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: 447 Length of database: 310 Length adjustment: 30 Effective length of query: 417 Effective length of database: 280 Effective search space: 116760 Effective search space used: 116760 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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