Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_058932370.1 AU252_RS21000 aspartate carbamoyltransferase catalytic subunit
Query= curated2:O27495 (301 letters) >NCBI__GCF_001484605.1:WP_058932370.1 Length = 356 Score = 90.9 bits (224), Expect = 4e-23 Identities = 100/338 (29%), Positives = 146/338 (43%), Gaps = 62/338 (18%) Query: 1 MKHLLSVCDMD--NVVDLLDLADDYKEGKIRE----KILRGKTLAMIFEKSSTRTRVSFE 54 MKHLLS D+ N + +LD A++ RE LRG+T+ +F + STRTR+SFE Sbjct: 1 MKHLLSTEDLSLANAIRILDTAEEMAAVGDREVKKLPALRGRTVVNLFFEDSTRTRISFE 60 Query: 55 VGAFQMGAQPLYLSASDLQLGRGEPIADTARTLSRY-VDGIMIRAISHSDVVELAGE--A 111 A ++ A + +A + +GE + DTA+TL+ D ++IR + LA Sbjct: 61 AAAKRLSADVINFAAKGSSVSKGESLKDTAQTLAAMGADAVVIRHWASGAPHRLAATDWI 120 Query: 112 SVPVIN-GLTDLEHPCQALADMQTIR---EKLGGFDG--------RLVFVGD--GNNVCH 157 VIN G EHP QAL D T+R KL G R+ GD + V Sbjct: 121 DAAVINAGDGTHEHPTQALLDAFTMRRHWSKLAGSASTGADLKGMRVAIAGDVLHSRVAR 180 Query: 158 SLLLITATLGMDMDVACPPGYEPDPGIREMAGKIA---DET--------------GSRIR 200 S + + TLG D+ + PP P G+ K++ D+T G R+ Sbjct: 181 SNVWLLRTLGADVTLVAPPTLLP-IGVEHWPCKVSYNMDDTLAQGVDAVMMLRVQGERMN 239 Query: 201 VIHDPSEAVRGADVVYTDVWVSMGYEDEAEDRLEVFRPYQVNMELMELAAPEAIFMHCLP 260 PS Y+ W G++D +RL L L + I MH P Sbjct: 240 ASFFPSTR------EYSRRW---GFDD---NRLRA---------LDSLGLKDTIIMHPGP 278 Query: 261 AVRGQETTAEVIDGPHSVVWDQAENRLHAQKAIMHWLM 298 RG E ++ D P S V Q N + + A ++ L+ Sbjct: 279 MNRGLEISSAAADSPRSTVLAQVRNGVSVRMATLYLLL 316 Lambda K H 0.320 0.137 0.405 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: 231 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 301 Length of database: 356 Length adjustment: 28 Effective length of query: 273 Effective length of database: 328 Effective search space: 89544 Effective search space used: 89544 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 Jul 25 2024. The underlying query database was built on Jul 25 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