Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate NP_662679.1 CT1800 aspartate carbamoyltransferase
Query= curated2:Q3A9W4 (311 letters) >NCBI__GCF_000006985.1:NP_662679.1 Length = 308 Score = 117 bits (293), Expect = 3e-31 Identities = 89/267 (33%), Positives = 135/267 (50%), Gaps = 22/267 (8%) Query: 13 MNDLTG------EEIEEVLDLASELK--IRQKKGISTPILKGKTLAMIFSKNSTRTRVSF 64 MN LTG + E+LDLA+ + + ++ P+L + +A++F +NSTRTR SF Sbjct: 1 MNHLTGLFGLPASTLVELLDLATGYREGLNREPETFAPLLSNRRIALVFFENSTRTRFSF 60 Query: 65 EVGMVQLGGYPLFITATDSQLSRGEPIADTARVLSRM-VDGIMIRTYSHSEVEELAYYAD 123 E+ LG L TA S +S+GE ++DT R L M VD ++R S E +A Sbjct: 61 ELAARHLGAGTLSFTAASSSVSKGETLSDTIRNLEAMKVDAFVLRHPSSGAAEFVASITK 120 Query: 124 VPVIN-GLTDYEHPCQIMADLLTIKEHKGQLRGLKVAWVGD--GNNVCHSLMIGAAKVGM 180 PVIN G +EHP Q + DLLT++E+ G++ GLK+ +GD + V S +IG +G Sbjct: 121 RPVINAGDGTHEHPTQALLDLLTLREYFGKIEGLKIMILGDILHSRVARSNIIGLKTLGA 180 Query: 181 EVAVATPPGYEPDQKVSLIAQ-----KETSRWGTKLLLTHDPVEAVTGADVVVTDVW-AS 234 E+AV P P + L + E W ++ +E TG + + + AS Sbjct: 181 EIAVCAPTTLLPGRIDQLGVRVFTGIDEALAWADAAIVLRLQLERATGGYIPSLEEYSAS 240 Query: 235 MGQEAESAERVK----VFEPYQVNGEL 257 G E +R+K V P +N E+ Sbjct: 241 YGLTDEKLDRLKRLMPVLHPGPINREI 267 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: 168 Number of extensions: 7 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: 311 Length of database: 308 Length adjustment: 27 Effective length of query: 284 Effective length of database: 281 Effective search space: 79804 Effective search space used: 79804 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 10 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