Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_011942555.1 BBTA_RS00130 ornithine carbamoyltransferase
Query= BRENDA::P0A5M9 (307 letters) >NCBI__GCF_000015165.1:WP_011942555.1 Length = 287 Score = 95.1 bits (235), Expect = 2e-24 Identities = 91/303 (30%), Positives = 129/303 (42%), Gaps = 26/303 (8%) Query: 3 RHFLRDDDLSPAEQAEVLELAAELKKDPVSRRPLQ--GPRGVAVIFDKNSTRTRFSFELG 60 R L DL A+ +L A EL +R Q R +A++ D R +F+LG Sbjct: 5 RDILALGDLDGADILGMLTRAQELAACWHAREMPQTLAGRRIALVVDDGGWRNTTAFDLG 64 Query: 61 IAQLGGHAVVVDSGSTQLGRDETLQDTAKVLSRYVDAIVWRTFGQERLDAMASVATVPVI 120 +GG V V +L E +D A L + DA+V RT E L A++ A PV+ Sbjct: 65 ARSMGGLCVHVP---IRLNATEAAEDLAAYLDNWFDAVVCRTPELEMLYALSHWAQAPVV 121 Query: 121 NALSDEFHPCQVLADLQTIAERKGALRGLRLSYFGDGANNMAHSLLLGGVTAGIHVTVAA 180 NA + + HPC+ L DL + R GA+ GL+++ AN + + V V V Sbjct: 122 NARTRQNHPCETLGDLAFLWHRHGAIDGLKIAVVAPAANILGSWIEAAQVLPIEVVQVYP 181 Query: 181 PEGFLPDPSVRAAAERRAQDTGASVTVTADAHAAAAGADVLVTDTWTSMGQENDGLDRVK 240 P S R R A D G ADV++TD W +++D D Sbjct: 182 ARWHAPGESPRF---RVATDLG-----------ELQDADVIITDCWP---RDDDAGD--- 221 Query: 241 PFRPFQLNSRLLALADSDAIVLHCLPAHRGDEITDAVMDGPASAVWDEAENRLHAQKALL 300 + +Q+ + LL D L C P RG E++ M A V LHAQ A L Sbjct: 222 -LQDYQITAALLDGLRPDLDFLPCPPVTRGMEVSGDAMLHRACRVVQAKAFLLHAQNAAL 280 Query: 301 VWL 303 W+ Sbjct: 281 EWV 283 Lambda K H 0.319 0.133 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: 192 Number of extensions: 13 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: 307 Length of database: 287 Length adjustment: 26 Effective length of query: 281 Effective length of database: 261 Effective search space: 73341 Effective search space used: 73341 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: 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