Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Synpcc7942_1496 Synpcc7942_1496 acetylglutamate kinase
Query= BRENDA::A0A0H2X8L7 (447 letters) >FitnessBrowser__SynE:Synpcc7942_1496 Length = 301 Score = 133 bits (335), Expect = 7e-36 Identities = 100/286 (34%), Positives = 146/286 (51%), Gaps = 21/286 (7%) Query: 16 VRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDD--LEALTSSLSFLQEVGLT 73 VR+LS E YL++F A R VVK GGA ++ + EA+ + FL VG+ Sbjct: 14 VRILS------EALPYLQQF----AGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMR 63 Query: 74 PIVLHGAGPQLDAELSAAGIEKQTVNGLRVTSPHALAIVRKVFQAS-NLKLVEALQQNGA 132 P+V+HG GP+++A L GIE Q NGLRVT + +V V N +V + G Sbjct: 64 PVVVHGGGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINTTGG 123 Query: 133 RATSITGG---VFEAEYLNRDTYGLVGEVKAVNLAPIEASLQAGSIPVITSLGETPSGQI 189 RA G + A +++ G VGEV +VN IE L+ G IPVI+S+ +GQ Sbjct: 124 RAVGFCGTDGRLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADENGQS 183 Query: 190 LNVNADFAANELVQELQPYKIIFLTGTGGLLDAEGK---LIDSINLSTEYDHLMQQPWIN 246 N+NAD A E+ L K+I LT T G+L+ + LI +N+ + L+ Q + Sbjct: 184 FNINADTVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRE-LIAQGIVG 242 Query: 247 GGMRVKIE-QIKDLLDRLPLESSVSITRPADLAKELFTHKGSGTLV 291 GGM K++ I+ L + + P L E+FT G GT++ Sbjct: 243 GGMIPKVDCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMI 288 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: 285 Number of extensions: 17 Number of successful extensions: 2 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: 301 Length adjustment: 30 Effective length of query: 417 Effective length of database: 271 Effective search space: 113007 Effective search space used: 113007 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 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