Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 6936133 Sama_0330 N-acetylglutamate synthase (RefSeq)
Query= BRENDA::Q6V1L5 (301 letters) >FitnessBrowser__SB2B:6936133 Length = 440 Score = 130 bits (327), Expect = 6e-35 Identities = 90/279 (32%), Positives = 150/279 (53%), Gaps = 16/279 (5%) Query: 22 PYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMRPVVVHGGGPEINAWLGRV 81 PY+ G+T VV GG AM Q + + A++ D+ L +G+R V+V+G P+I+A L Sbjct: 15 PYVNAHRGKTFVVMLGGEAMVQPQFR-AIINDVALLHSLGIRIVLVYGARPQIDAALELH 73 Query: 82 GIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSR----INTTGGRAVGFCGTDGRLVL 137 GI P +HNG+R+TD DT++V++ V G + DI +R ++ T + G V+ Sbjct: 74 GIAPAYHNGVRITDEDTLKVIKQV-AGALQFDITARLSMSLSNTPMQGTQLNVVSGNFVI 132 Query: 138 ARPHD-QEGIGFV--GEVNSVNSEVIEPLLERGYIPVISSVAADENGQSFNINADTVAGE 194 A+P ++G+ F G V ++ ++ L+ I ++ +AA G+SFN+ A+ VA + Sbjct: 133 AQPLGVEDGVDFCLSGRVRRIDVNGLKHQLDSRGIVLMGPIAASVTGESFNLTAEEVATQ 192 Query: 195 IAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGIVGG----GMIPKVD 250 +A L A+K+I + GIL+ R +I L ++++ A+ GG G + + Sbjct: 193 VAVKLKADKMIGFSSQNGILD---RNGEVIAELMPNDAQKIFAKMQEGGQACVGTLAFLK 249 Query: 251 CCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIV 289 I + GV H++ ALL E+F+ GIGT IV Sbjct: 250 ASIDACRNGVPRCHLVSYLEDGALLQELFSRDGIGTQIV 288 Lambda K H 0.320 0.139 0.406 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: 323 Number of extensions: 25 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: 301 Length of database: 440 Length adjustment: 29 Effective length of query: 272 Effective length of database: 411 Effective search space: 111792 Effective search space used: 111792 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 Jul 25 2024. The underlying query database was built on Jul 25 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