Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_004043481.1 C498_RS11065 aspartate carbamoyltransferase
Query= BRENDA::Q48296 (295 letters) >NCBI__GCF_000337315.1:WP_004043481.1 Length = 304 Score = 129 bits (323), Expect = 1e-34 Identities = 96/305 (31%), Positives = 153/305 (50%), Gaps = 17/305 (5%) Query: 2 EHLVDINDVESEEIEQLLDLAASMKENPGEFSGVMDNKSLVMLFAKPSTRTRLSFETGMT 61 +HL+ + + E+IE +LD AA + +P F K L + F +PSTRTR+SF++ M Sbjct: 4 DHLISASHLSREDIEAVLDRAADIDADPAAFRQRHAGKVLGLCFFEPSTRTRMSFDSAMK 63 Query: 62 QLGGHGIFFEMG---SSQLSRGEPISDVSQVMSRYEDAIMARLFEHDEMMELAENADVPV 118 +LGG + +MG SS + +GE ++D +V+ Y DA++ R AE DVP+ Sbjct: 64 RLGGQTV--DMGPVESSSVKKGETLADTVRVVEGYADALVLRHPSEGAATMAAEFVDVPL 121 Query: 119 VN-GLTDFLHPCQALTDMFTMQEKDRLD--TLAFVGD--GNNVAHSLMQASAKMGVDCRI 173 VN G HP Q L D++T++E LD T+ +GD HSL +A Sbjct: 122 VNAGDGAGQHPSQTLLDLYTIRENAGLDDLTIGIMGDLKYGRTVHSLAEALTNFDASQHF 181 Query: 174 ATPEGMEPDEEIQD--RVSDANVTVTNDPYEAVDGATAVYGDVFVSMGEEEQREEKLAEF 231 +PE + ++ S A V + E + +Y V E E + + Sbjct: 182 ISPESLRLPRNVRYDLHASGAQVREHTELDEVLPELDVLY--VTRIQRERFPDENEYRKV 239 Query: 232 DG-FQIDQDLMDAARDDAIFMHCLPAHRGEEVTAEVADGPQSVIFDQAENRMHVQKAIVH 290 G +QID + +DAA DD MH LP R +E++ ++ D + F+QA N + V+ A++ Sbjct: 240 AGQYQIDSETLDAAADDLTIMHPLP--RVDEISPDIDDTDHATYFEQAHNGIPVRMALLD 297 Query: 291 TLVNQ 295 L++Q Sbjct: 298 ILLSQ 302 Lambda K H 0.316 0.132 0.369 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: 208 Number of extensions: 9 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: 295 Length of database: 304 Length adjustment: 27 Effective length of query: 268 Effective length of database: 277 Effective search space: 74236 Effective search space used: 74236 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 (21.6 bits) S2: 48 (23.1 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