Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate Ga0059261_0076 Ga0059261_0076 aspartate carbamoyltransferase (EC 2.1.3.2)
Query= curated2:A0RUE9 (301 letters) >FitnessBrowser__Korea:Ga0059261_0076 Length = 330 Score = 107 bits (267), Expect = 4e-28 Identities = 91/295 (30%), Positives = 135/295 (45%), Gaps = 29/295 (9%) Query: 9 LTGAE-LDRKEILGIIESAIRLKKGGRSKA---HPLDGRTLAMVFQKPSTRTRVSFAAGM 64 LTG L EIL +++ A + + RS+A H LDG T F + STRT +SF Sbjct: 24 LTGISGLQPHEILFLLDEAEQWIEANRSRAKSDHRLDGLTQINAFFENSTRTLLSFEIAG 83 Query: 65 FQLGGEAIYLPPGDMQLSRGETIPDTARALSGY-VDVIVARVFGHETIEEIAASASVPVI 123 +LG + + + + +GET+ DTA L+ DVIV R ++ IA PV+ Sbjct: 84 KRLGADVVNMHAAQSSVKKGETLIDTAMTLNAMRADVIVIRHMSSGAVQLIADKVDCPVL 143 Query: 124 N-GLSDTFHPCQILADLMTIKERKGRLKGLRAAWIGD--GNNVCNSLLYGCAAVGIDISV 180 N G HP Q L D +TI+ R+G + R GD + V S + A+ ++ V Sbjct: 144 NAGDGSHEHPTQALLDALTIRRRRGSIAHQRVVICGDILHSRVARSNILALTALAAEVRV 203 Query: 181 ATPAVFRPIPGVVDKCRESIDVKLTTDPAEAAAGADIVFTDTFASIHNMDKER------- 233 P+ P E + V TD A GAD+V + + ER Sbjct: 204 VAPSTLMP------AAIEKMGVTPYTDFDAALEGADVVM------MLRLQNERMSGAYIP 251 Query: 234 -ERKFLPKYRVNAPLMKKAADDAIFMHCLPAKRGQEVDGEVIDGP-QSAVWDEAE 286 R++ Y + +K+A DA+ MH P RG E+D V D P +SA+ ++ E Sbjct: 252 STREYHLNYGLTEERLKRAKPDALVMHPGPMNRGVEIDSSVADMPGRSAITEQVE 306 Lambda K H 0.320 0.137 0.398 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: 220 Number of extensions: 12 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: 301 Length of database: 330 Length adjustment: 27 Effective length of query: 274 Effective length of database: 303 Effective search space: 83022 Effective search space used: 83022 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 (21.8 bits) S2: 48 (23.1 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