Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate CCNA_02525 CCNA_02525 aspartate carbamoyltransferase
Query= curated2:Q8DJW4 (310 letters) >FitnessBrowser__Caulo:CCNA_02525 Length = 332 Score = 109 bits (273), Expect = 8e-29 Identities = 104/327 (31%), Positives = 159/327 (48%), Gaps = 35/327 (10%) Query: 4 RFVMETLRGR-------DLLSIADLSRAEAEYLLDLA-AQMKIGKVAPQCPKVLGLL--- 52 R +ET+R R LS DL+ +A LLDLA A + + + Q K L +L Sbjct: 10 REAIETIRARVFAFPKRHFLSAGDLNAPQAADLLDLADAFVALNR---QTSKTLDILKGR 66 Query: 53 -----FQKASTRTRVSFTVAMYQLGGQVIDLNPQSTQVGRGEPLTDTARVLDRYL-DAVA 106 F + STRT+ SF +A +LG V+++NP+++ V +GE L DTA L+ D + Sbjct: 67 TLMNLFFENSTRTQSSFELAGKRLGADVVNMNPKTSSVAKGETLIDTAVTLNAMRPDLLV 126 Query: 107 IRTYGQAELQLFADYARIPVINALT-DREHPCQILADLLTLRESFGTLAGLTLCYIGD-- 163 +R L + V+NA EHP Q L D L++R +FG ++GLT+ GD Sbjct: 127 VRHASSGAASLLSQKVSGHVVNAGDGQHEHPTQALLDALSIRRAFGRVSGLTVAICGDVL 186 Query: 164 GNNVAHSLLLGCALLGVNIRVASPPQFAPLADIVAQAKALSGGKSEVAVLTDPQAAAKGA 223 + VA S + LG ++R+ PP P AQA+ + VAV D ++ GA Sbjct: 187 HSRVARSNVALLHTLGASVRLVGPPTLMP-----AQAE-----RWGVAVHHDMKSGLAGA 236 Query: 224 H-ALYTDVWASMGQEAEAGDRQPIFQPYQINDHLLALADPRAIVLHCLPAHRDEEITASV 282 + + Q A + F+ Y ++ L+ A P A V+H P +R EI + V Sbjct: 237 DVVMMLRLQLERMQGAFVPSTREYFRFYGLDREKLSRAAPGAKVMHPGPMNRGVEIDSDV 296 Query: 283 LEGPQ-SRVWEQAENRLHVQKALLASL 308 + P S + +Q E + + A+LASL Sbjct: 297 ADDPAVSLIQDQVEMGVAARMAVLASL 323 Lambda K H 0.321 0.135 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: 231 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: 310 Length of database: 332 Length adjustment: 28 Effective length of query: 282 Effective length of database: 304 Effective search space: 85728 Effective search space used: 85728 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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