Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_013460792.1 SULKU_RS09705 aspartate carbamoyltransferase catalytic subunit
Query= BRENDA::Q5SJ15 (301 letters) >NCBI__GCF_000183725.1:WP_013460792.1 Length = 289 Score = 94.4 bits (233), Expect = 3e-24 Identities = 81/270 (30%), Positives = 124/270 (45%), Gaps = 27/270 (10%) Query: 43 LKGKVLALLFEKPSLRTRTTLEVAMVHLGGHAVYLDQKQVGIGEREPVRDVAKNLERFVE 102 LK K++ LF + S RT+++ E+A LG V+LD ++ + E + D A NL+ Sbjct: 34 LKEKIIITLFFENSTRTKSSFEIAAKRLGAEVVHLDVQKSSTQKGESLVDTAANLDAM-- 91 Query: 103 GIAARVFRHE---TVEALARHAKVPVVNALSD-RAHPLQALADLLTLKEVFGGLAGLEVA 158 G A + RH LA H ++NA AHP QAL DL TL+ FG L G ++A Sbjct: 92 GPHAMIVRHAHAGVPNILAEHTHASIINAGDGAHAHPTQALLDLFTLRRHFGELKGKKIA 151 Query: 159 WVGDGNN--VLNSLLEVAPLAGLKVRVATPKGYEPDPGLLKRANAFFTHDPKEAALGAHA 216 VGD N V NS +E+ G+ + + P + PD L TH+ + A Sbjct: 152 IVGDIKNSRVANSNIELLTRFGMDITLVAPPHFLPDSYLK------MTHNLHDVIHNVDA 205 Query: 217 LYTDVWTSMGQEAEREKR-----LRDF-QGFQVNGELLKLLRPEGVFLHCLPAHYGEETT 270 + S+ + ER L+D+ F + EL+ + + LH P H + Sbjct: 206 I-----MSLRTQTERHSHQTYGSLKDYASDFCITKELVG--ERDIILLHPGPVHRNIDID 258 Query: 271 EEAVHGPRSRVFDQAENRLHTAKAVLLTLL 300 + + PR +V +Q N + AVL L+ Sbjct: 259 DMMLKDPRCKVLEQVRNGVAIRMAVLKALI 288 Lambda K H 0.319 0.137 0.396 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: 224 Number of extensions: 15 Number of successful extensions: 3 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: 289 Length adjustment: 26 Effective length of query: 275 Effective length of database: 263 Effective search space: 72325 Effective search space used: 72325 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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