Align carbamate kinase (EC 2.7.2.2) (characterized)
to candidate WP_110207096.1 DNK54_RS11255 carbamate kinase
Query= BRENDA::P95474 (314 letters) >NCBI__GCF_003194585.1:WP_110207096.1 Length = 318 Score = 234 bits (598), Expect = 2e-66 Identities = 128/318 (40%), Positives = 202/318 (63%), Gaps = 11/318 (3%) Query: 1 MGKRVVIALGGNALQQRGQKGSYEEMMDNVRKTARQIAEIIARGYEVVITHGNGPQVGSL 60 M + V+A+GGNAL + + G+ E++ N A+ IA + A G+ VV+ HGNGPQVG+L Sbjct: 1 MSRIAVVAVGGNALTREHEIGTSEQIEANAHAMAQGIARLHADGWRVVVVHGNGPQVGNL 60 Query: 61 LLHMDAGQATYGIPAQPMDVAGAMSQGWIGYMIQQALKNELRKRGMEKKVVTIITQTIVD 120 + + +P QP+ AM+QG +G ++ +AL + L G V +++ +VD Sbjct: 61 SIQQEESVGL--VPPQPLASVNAMTQGQLGSVLVRAL-DALLGAGT---AVAVVSHMVVD 114 Query: 121 KNDPAFQNPTKPVGPFYDEETAKRLAREKGWIVKEDSGRGWRRVVPSPDPKGHVEAETIK 180 +DPAF +PTKP+GPF+ A++LA E+GW+++ED+GRG+RRVV SP P +E+ I+ Sbjct: 115 PDDPAFVDPTKPIGPFFSAGRAEQLAEERGWVMREDAGRGFRRVVASPRPVELLESAAIR 174 Query: 181 KLVERGVIVIASGGGGVPVI--LEDGEIKGVEAVIDKDLAGEKLAEEVNADIFMILTDVN 238 LVER +V+A GGGG+ V+ ++DG GV+AVIDKD A +A + AD +++T V+ Sbjct: 175 TLVERSHVVLACGGGGIGVLGGVDDG-YPGVDAVIDKDAAAASVAISLRADGLILVTGVD 233 Query: 239 GAALYYGTEKEQWLREVKVEELRKYYEEGHFKAGSMGPKVLAAIRFIEWGGERAIIAHLE 298 ++ YGT ++ + E+ V+ +Y +G F GSMGPKV +AI F++ GG A+I E Sbjct: 234 AVSINYGTPEQTVVHELGVDAAIRYLGDGQFPPGSMGPKVRSAIDFVQAGGSAAVITSAE 293 Query: 299 KAVEALEGKT--GTQVLP 314 +A++ T GT+++P Sbjct: 294 HLHDAIDPTTTFGTRIVP 311 Lambda K H 0.315 0.136 0.392 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: 273 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: 314 Length of database: 318 Length adjustment: 27 Effective length of query: 287 Effective length of database: 291 Effective search space: 83517 Effective search space used: 83517 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: 42 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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