Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate 8499267 DvMF_0046 ornithine carbamoyltransferase (RefSeq)
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Miya:8499267 Length = 300 Score = 123 bits (308), Expect = 7e-33 Identities = 102/330 (30%), Positives = 147/330 (44%), Gaps = 41/330 (12%) Query: 4 KHFLNTQDWSRAELDALLTQAALFKRNK-LGSELKGKSIALVFFNPSMRTRTSFELGAFQ 62 +HF +D LL +A K G ++GK+ L+F S RTR SFE+ Sbjct: 3 RHFTRIRDLGYEGAWKLLQRAKEMKDTAHRGKIMEGKTAILIFEKASTRTRVSFEMAVRH 62 Query: 63 LGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSK 122 LGG + + P E LG E + + ARVL RY D + VR F + Sbjct: 63 LGGSTIFMTPA------ESQLGR------SEPLRDTARVLSRYADCMVVRTFGQ------ 104 Query: 123 DREDQVLKSFAKYSPVPVINMETIT-HPCQELAHALALQEHFGTPDLRGKKYVLTWTYHP 181 + A+Y +PVIN T HPCQ + L + E TPDL + + W Sbjct: 105 ----SKITELAEYGSIPVINALTDEGHPCQVMGDVLTMYER--TPDLSTVR--VAWVGD- 155 Query: 182 KPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDS 241 +ANS + A ++ + P Y D + +A +G + ++HD Sbjct: 156 ---GNNMANSWIEAAVYFPFELFMAFPE-GYEPDRDLLGYALN----AGAKIFLTHDPRM 207 Query: 242 AYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHCLPLRRN 300 A GA V W ++ G E +K ++ + +D MAL + F HCLP R Sbjct: 208 AVEGAHYVNTDVWASM---GQEEEQKKREAAFKGYCIDTEMMALAAPDAKFMHCLPAHRG 264 Query: 301 VKATDAVMDSPNCIAIDEAENRLHVQKAIM 330 + TD VM+SP I D+AENRLH+QKAI+ Sbjct: 265 EEVTDEVMESPASIIFDQAENRLHIQKAIL 294 Lambda K H 0.320 0.134 0.412 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: 257 Number of extensions: 18 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: 339 Length of database: 300 Length adjustment: 28 Effective length of query: 311 Effective length of database: 272 Effective search space: 84592 Effective search space used: 84592 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 Apr 09 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