Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 5208502 Shew_1013 aspartate carbamoyltransferase (RefSeq)
Query= curated2:Q7V8G9 (318 letters) >FitnessBrowser__PV4:5208502 Length = 339 Score = 102 bits (254), Expect = 1e-26 Identities = 96/286 (33%), Positives = 142/286 (49%), Gaps = 29/286 (10%) Query: 50 LGNRVLGLIFTKASTRTRVSFQVAMARLGG---QTVDLNPQVTQLGRGEPLEDTARVLSR 106 L +LG +F + STRTRVSF A LGG +TV + + L +GE L DTARVLS Sbjct: 43 LDGAILGNLFFEPSTRTRVSFGSAFNLLGGKVNETVGIG--TSSLSKGESLYDTARVLSS 100 Query: 107 FCDVMAVRTFAQQELLDYAHWASIPVLNALT-DLEHPCQAMADFLTIQEALG----SLTG 161 + DV+A+R + ++A + +PV+N EHP QA+ D TIQ+ L S++G Sbjct: 101 YSDVIAMRHPDAYSVREFAEGSRVPVINGGDGPNEHPTQALLDLFTIQKELAAGGRSISG 160 Query: 162 QTLAYVGD---GNNV-SHSLMLCGALLGVNVRIGCPQGFEPLPEVIDQARNLAVADARIE 217 +A VGD G V S S +LC V+ + P+ VID N A +I Sbjct: 161 MHIAMVGDLKFGRTVHSLSRLLC-MYKDVSFTLISPKELAMPDYVIDDIEN---AGHKIT 216 Query: 218 VMTDPVDAVRGAQALYTDVWASMGQEQEQSQREEA--FRG-FCLNEDLLA-HADPNAIVL 273 + D + G ++ + QE+ +EEA +RG F LN ++ H N +++ Sbjct: 217 I----TDQLEGNLDQADILYLTRIQEERFPSQEEANKYRGKFRLNHNIYTQHCKSNTVIM 272 Query: 274 HCLP---AHRGEEISSGVMEGEASRIFDQAENRLHVQQALLAAVLG 316 H LP + E+ + + IF QA+N L ++ AL A LG Sbjct: 273 HPLPRDSREQANELDNDLNSHPNLAIFRQADNGLLIRMALFALTLG 318 Lambda K H 0.321 0.135 0.391 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: 210 Number of extensions: 10 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: 318 Length of database: 339 Length adjustment: 28 Effective length of query: 290 Effective length of database: 311 Effective search space: 90190 Effective search space used: 90190 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: 49 (23.5 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