Align carbamate kinase (EC 2.7.2.2) (characterized)
to candidate WP_110208549.1 DNK54_RS18790 carbamate kinase
Query= BRENDA::O96432 (314 letters) >NCBI__GCF_003194585.1:WP_110208549.1 Length = 312 Score = 242 bits (618), Expect = 7e-69 Identities = 126/314 (40%), Positives = 191/314 (60%), Gaps = 3/314 (0%) Query: 1 MRIVVALGGNALLQRGMKGTFQDQQAACRLAMSQIVKIVKDGNELVMTHGNGPQCGAIFL 60 MR+++ALGGNA+ + +DQ AA AM+ + +++ +++V+THGNGPQ G + + Sbjct: 1 MRVLMALGGNAMTNAEGRARPEDQIAAAETAMAAVAGLLEHDHDVVVTHGNGPQVGNLLV 60 Query: 61 QNVAGEQEKVPAMPLHVCGAETQGFLGELLQQELDGALRAEGIKKNVVSIVTQSFVDPKD 120 +N Q VP +PL CGA+TQ LG +L LD L + + ++VT++ VD D Sbjct: 61 KNELAAQV-VPPVPLDWCGAQTQATLGLILMDALDAELARRHVSRRTATLVTRARVDAAD 119 Query: 121 PAFQNPTKPIGPFYSKEEAEFLRNERGYNMVEDAGRGYRMIVPSPVPQKFVEKEAIKTLV 180 P F +PTKPIG EEA+ L + G + +G+R +V SP P + ++ A L+ Sbjct: 120 PGFTHPTKPIGRHLPAEEAQVLI-DHGETWQDMGAKGWRRVVASPAPLEIIDAPAALALI 178 Query: 181 NSGFIVVCSGGGGIPVILDEQENRIEGVDAVIDKDLGASVLAAATNADAFMILTDVPEAL 240 +GF+V+ +GGGGIPV+ E + + GV AVIDKDLGA + A AD +I TDVP+A+ Sbjct: 179 EAGFVVIANGGGGIPVVRRE-DGSLTGVPAVIDKDLGAELFARVVGADVLVIATDVPQAV 237 Query: 241 LNYRKENETAIRQATVAEMEKYIEEGHFIKGSMLPKVQACLRFVKSTGKPALITALDCAL 300 L + + + T+++M Y EGHF GSM PKV A RFV++TG+ +IT+L Sbjct: 238 LRFGTPEAEPVGEVTLSQMRAYAAEGHFGSGSMGPKVDAVCRFVEATGQVGIITSLSAIT 297 Query: 301 QALKGERGTKIVPN 314 A+ G+ GT++VP+ Sbjct: 298 DAVHGQAGTRVVPD 311 Lambda K H 0.318 0.136 0.387 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: 244 Number of extensions: 15 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: 312 Length adjustment: 27 Effective length of query: 287 Effective length of database: 285 Effective search space: 81795 Effective search space used: 81795 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: 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