Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_013451026.1 CALNI_RS04515 aspartate carbamoyltransferase catalytic subunit
Query= curated2:Q3A9W4 (311 letters) >NCBI__GCF_000183405.1:WP_013451026.1 Length = 311 Score = 129 bits (323), Expect = 1e-34 Identities = 100/308 (32%), Positives = 157/308 (50%), Gaps = 17/308 (5%) Query: 8 RDFLSMNDLTGEEIEEVLDLASELK-IRQKKGISTPILKGKTLAMIFSKNSTRTRVSFEV 66 +D + D+T EEI E+LD A + K I ++ P LKGKT+A +F + STRTR SFE+ Sbjct: 5 KDLTGLVDVTKEEILEILDTAEKFKEINSREIKKVPALKGKTIANLFFEPSTRTRTSFEI 64 Query: 67 GMVQLGGYPLFITATDSQLSRGEPIADTARVLSRM-VDGIMIRTYSHSEVEELAYYADVP 125 +L + TA+ S ++GE + DT + + M VD ++R Y V +A Sbjct: 65 AGKRLSADVINFTASASSTTKGETLIDTVKNIESMGVDMFVVRHYYSGSVRFIAQNTKAH 124 Query: 126 VIN-GLTDYEHPCQIMADLLTIKEHKGQLRGLKVAWVGD--GNNVCHSLMIGAAKVGMEV 182 VIN G EHP Q + DL TIKE KG+L GLKVA +GD + V S K+G+++ Sbjct: 125 VINAGDGTNEHPTQSLLDLYTIKEQKGKLEGLKVAIIGDITHSRVARSNAWAMKKLGIDL 184 Query: 183 AVATPPGYEPDQKVSLIAQKETSRWGTKLLLTHDPVEAVTGADVVVTDVWASMGQEAESA 242 + P P ++ +G K+ + + EA+ DVV+ Q Sbjct: 185 RLYGPKTMIP---------RDYLPFGCKVCNSME--EALEDCDVVMMLRIQLERQGIALL 233 Query: 243 ERVKVFEP-YQVNGELVSHAKQDFIFLHCLPAHRGEEVTAEVIDGEHSVVFAEAENRLHA 301 +K + + +N + AK+D I +H P +RG E+ + + D + SV+ + EN + Sbjct: 234 PSLKEYSKLFGLNKNRLDLAKKDAIIMHPGPINRGVELPSYLADCDKSVILTQVENGVAV 293 Query: 302 QKAILTLL 309 + A++ LL Sbjct: 294 RMAVMYLL 301 Lambda K H 0.317 0.134 0.382 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: 178 Number of extensions: 11 Number of successful extensions: 4 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: 311 Length of database: 311 Length adjustment: 27 Effective length of query: 284 Effective length of database: 284 Effective search space: 80656 Effective search space used: 80656 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 (21.7 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