Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_109967783.1 DK846_RS02360 aspartate carbamoyltransferase
Query= curated2:P18186 (319 letters) >NCBI__GCF_003173355.1:WP_109967783.1 Length = 298 Score = 127 bits (318), Expect = 4e-34 Identities = 101/305 (33%), Positives = 155/305 (50%), Gaps = 21/305 (6%) Query: 15 LTLKDLSEEDINALLAEAGELKQN--KIQPIFHGKTLAMIFEKSSTRTRVSFEAGMAQLG 72 ++++DL I+ L+ A + QP+ K L ++F + STRTR+SFE+ M +LG Sbjct: 5 ISIRDLDRNQIDHLIDRAARIAVYGADAQPLKR-KILGLLFFEPSTRTRMSFESAMLRLG 63 Query: 73 GSALFLSQKDL-QLGRGETVADTAKVLSGYVDAIMIRTFEHEKV--EELAKE-ADIPVIN 128 GS + L ++ + +GET+ADT +V+SGY D I++R H KV LA E AD+PVIN Sbjct: 64 GSCMNLGGVEVSSMAKGETLADTIRVVSGYADTIVLR---HPKVGAARLASEFADVPVIN 120 Query: 129 GLTDK-YHPCQALADLLTIKEIKGKLKGVKVAYIGD--GNNVAHSLMIGCAKMGCDISIA 185 G HP Q L DL TI + L +K+ +GD HSL + +I Sbjct: 121 GGDGAGQHPSQTLIDLYTIHQ-SMPLDRIKIGLVGDLMYGRTTHSLAYALTRYNAEIHAI 179 Query: 186 SPKGYEVLDEAAEAAKTYALQSGSSVTLTDDPIEAVKDADVIYSDVFTSMGQEAEEQERL 245 SPKG + E+ K ++G V D E ++D DV+Y F + + Sbjct: 180 SPKGLGL----PESLKHDLREAGCEVIEHDSIEEIIRDLDVLYVTRF-QRERFPDPASFF 234 Query: 246 AVFAPYQVNAALVSHAKPDYTFLHCLPAHREEEVTAEIIDGPNSAVFQQAENRLHVQKAL 305 V A Y++ +L+ K + LH LP R +E+ + P + FQQA N + V+ A+ Sbjct: 235 DVAASYRITPSLLQGVKDNLILLHPLP--RVDEIDPAVDSLPYARYFQQARNGVPVRMAM 292 Query: 306 LKAIL 310 L ++ Sbjct: 293 LLEVM 297 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: 188 Number of extensions: 13 Number of successful extensions: 5 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: 298 Length adjustment: 27 Effective length of query: 292 Effective length of database: 271 Effective search space: 79132 Effective search space used: 79132 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 Apr 09 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