Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate Ac3H11_3978 Aspartate carbamoyltransferase (EC 2.1.3.2)
Query= curated2:O27495 (301 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3978 Length = 320 Score = 99.0 bits (245), Expect = 1e-25 Identities = 96/318 (30%), Positives = 143/318 (44%), Gaps = 36/318 (11%) Query: 3 HLLSVCDM--DNVVDLLDLADDYKEGKIRE----KILRGKTLAMIFEKSSTRTRVSFEVG 56 HLLS+ + D V +LD A ++ RE +LRGK++ +F ++STRTR +FE+ Sbjct: 17 HLLSIEGLPRDIVTHILDTAANFVSVNDREVKKVPLLRGKSVFNLFFENSTRTRTTFEIA 76 Query: 57 AFQMGAQPLYLSASDLQLGRGEPIADTARTLSRYVDGIMIRAISHSDVVELAGEASVP-- 114 A ++ A L L + +GE + DT LS + + S S L + P Sbjct: 77 AKRLSADVLNLDIARSSASKGESLLDTIANLSAMAADLFVVRHSESGAPYLIAQHVAPHV 136 Query: 115 -VIN-GLTDLEHPCQALADMQTIREKLGGFDGRLV-FVGD--GNNVCHSLLLITATLG-M 168 VIN G HP Q L DM TIR F V VGD + V S + TLG Sbjct: 137 HVINAGDGRHAHPTQGLLDMYTIRHYKKDFSNLTVAIVGDVLHSRVARSDIHGLTTLGCA 196 Query: 169 DMDVACPPGYEPDPGIREMAGKIADETGSRIRVIHDPSEAVRGADVVYTDVWVSMGYEDE 228 ++ V P P +D +RV H E ++ ADVV + + ++E Sbjct: 197 EVRVVGPRTLVP-----------SDMAQMGVRVCHTLEEGIKDADVV-----IMLRLQNE 240 Query: 229 ------AEDRLEVFRPYQVNMELMELAAPEAIFMHCLPAVRGQETTAEVIDGPHSVVWDQ 282 E F+ + + E ++LA P+AI MH P RG E + V+DG SV+ Q Sbjct: 241 RMSGALLPSSQEYFKSFGLTQEKLQLAKPDAIVMHPGPINRGVEIDSAVVDGKQSVILPQ 300 Query: 283 AENRLHAQKAIMHWLMGD 300 + + A+M + G+ Sbjct: 301 VTFGIAVRMAVMSIVAGN 318 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: 206 Number of extensions: 10 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: 320 Length adjustment: 27 Effective length of query: 274 Effective length of database: 293 Effective search space: 80282 Effective search space used: 80282 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