Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_048082250.1 EI99_RS12140 aspartate carbamoyltransferase
Query= curated2:P18186 (319 letters) >NCBI__GCF_000746075.1:WP_048082250.1 Length = 304 Score = 134 bits (338), Expect = 2e-36 Identities = 98/309 (31%), Positives = 157/309 (50%), Gaps = 21/309 (6%) Query: 12 KDLLTLKDLSEEDINALLAEAGEL----KQNKIQPIFHGKTLAMIFEKSSTRTRVSFEAG 67 KD+++++D +DI +L A E+ + K GK L M+F + STRTR+SFEA Sbjct: 6 KDIISIRDFDRKDIEYILKLAEEMEPIARSEKKSDALSGKLLGMLFYEPSTRTRLSFEAA 65 Query: 68 MAQLGGSAL-FLSQKDLQLGRGETVADTAKVLSGYVDAIMIRTFEHEKVEELAKEADIPV 126 M +LGGS + F +GE + DT +++ Y DA++IR +A D+PV Sbjct: 66 MKRLGGSTIGFAEAGTSSATKGENLTDTVRIVGEYSDALVIRHNMEGTARFVANIVDVPV 125 Query: 127 IN-GLTDKYHPCQALADLLTIKEIKGKLKGVKVAYIGD--GNNVAHSLMIGCAKMGCDIS 183 IN G HP Q + DL T+K I G++ +++A +GD HSL AK D+S Sbjct: 126 INAGDGAGQHPTQTMLDLYTMKRILGRIDDLRIALVGDLKYGRTVHSLAYALAKFDVDVS 185 Query: 184 IASPKGYEVLDEAAEAAKTYALQSGSSVTLTDDPIEAVKDADVIYSDVFTSMGQE--AEE 241 SPK ++ E +SG V TD+ E + DV+Y T + +E + Sbjct: 186 FVSPKELKMPREILHDLS----KSGVDVYETDNIHEVLDKTDVLY---VTRIQKERFPDP 238 Query: 242 QERLAVFAPYQVNAALVSHAKPDYTFLHCLPAHREEEVTAEIIDGPNSAVFQQAENRLHV 301 E L + Y + + L+ + D +H LP R +E++ ++ + P F+QA + V Sbjct: 239 AEYLKIKGAYTITSKLLEGS--DAIVMHPLP--RIDEISHDVDNTPQGRYFEQAFYGVPV 294 Query: 302 QKALLKAIL 310 + ALLK+++ Sbjct: 295 RMALLKSVI 303 Lambda K H 0.315 0.131 0.361 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: 214 Number of extensions: 20 Number of successful extensions: 6 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: 319 Length of database: 304 Length adjustment: 27 Effective length of query: 292 Effective length of database: 277 Effective search space: 80884 Effective search space used: 80884 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 (21.5 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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