Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_012386323.1 BIND_RS17345 aspartate carbamoyltransferase
Query= curated2:Q8DJW4 (310 letters) >NCBI__GCF_000019845.1:WP_012386323.1 Length = 317 Score = 116 bits (291), Expect = 6e-31 Identities = 103/312 (33%), Positives = 152/312 (48%), Gaps = 31/312 (9%) Query: 13 RDLLSIADLSRAEAEYLLDLAAQMKIGKVAPQCPK--------VLGLLFQKASTRTRVSF 64 R LL IA LS + LLDLA + +V+ Q K L LF +ASTRT+ SF Sbjct: 14 RHLLGIAGLSAQDLTILLDLAEEAI--EVSRQVEKKRTSLRGRTLINLFFEASTRTQSSF 71 Query: 65 TVAMYQLGGQVIDLNPQSTQVGRGEPLTDTARVLDRYLDAVAIRTYGQA-ELQLFADYAR 123 +A +LG V++++ ++ V +GE L DTA L+ + + + QA + L A Sbjct: 72 ELAGKRLGADVMNMSVATSSVKKGETLLDTAMTLNAMRPDIIVVRHAQAGAVHLLAREVD 131 Query: 124 IPVINALTD-REHPCQILADLLTLRESFGTLAGLTLCYIGD--GNNVAHSLLLGCALLGV 180 V+NA EHP Q L D LT+R + G + GL + GD + VA S +L + LG Sbjct: 132 CSVVNAGDGAHEHPTQALLDALTIRRNKGRIEGLIVAICGDILHSRVARSNILSLSALGA 191 Query: 181 NIRVASPPQFAPLADIVAQAKALSGGKSEVAVLTDPQAAAKGAHALYTDVWASMGQEAEA 240 +RV P P + V V D + GA + + + +E Sbjct: 192 RVRVIGPSTLLPTGI----------EQMGVEVFRDMREGLVGADIV---MMLRLQRERMD 238 Query: 241 GDRQP----IFQPYQINDHLLALADPRAIVLHCLPAHRDEEITASVLEGPQSRVWEQAEN 296 G P F+ Y +++ LALA P A+V+H P +R EI + V +GPQSR+ EQ E Sbjct: 239 GGFIPSLKEYFRFYGLDEEKLALARPDALVMHPGPMNRGVEIASRVADGPQSRIREQVEM 298 Query: 297 RLHVQKALLASL 308 + V+ A+L +L Sbjct: 299 GVAVRMAVLEAL 310 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: 202 Number of extensions: 14 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: 317 Length adjustment: 27 Effective length of query: 283 Effective length of database: 290 Effective search space: 82070 Effective search space used: 82070 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 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