Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate N515DRAFT_3763 N515DRAFT_3763 N-acetylornithine carbamoyltransferase
Query= BRENDA::O93656 (317 letters) >FitnessBrowser__Dyella79:N515DRAFT_3763 Length = 335 Score = 176 bits (445), Expect = 9e-49 Identities = 125/342 (36%), Positives = 175/342 (51%), Gaps = 50/342 (14%) Query: 8 RDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVA 67 R L QDY+ EI +LE A K + + L GK++A++F PS RTR SFE+ Sbjct: 4 RHFLTTQDYSRAEIDALLEQAAAFKRSPR----GQQLAGKSVALLFFNPSMRTRTSFELG 59 Query: 68 MAHLGGHALYL----NAQDLQLRRG--------ETIADTARVLSRYVDAIMARVY----- 110 HLGGHA+ L +A ++ G E IA+ ARVLSRYVD I R + Sbjct: 60 AFHLGGHAIVLAPGKDAWPIEFDVGTVMDGDTEEHIAEVARVLSRYVDLIAVRAFPKFQD 119 Query: 111 ---DHKD--VEDLAKYASVPVINGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD-- 163 D +D ++ A+YASVPVIN + +HPCQ LA + + E G+++ K V Sbjct: 120 WTVDREDRVIKAFAQYASVPVIN-METITHPCQELAHALAMQEHLGSLQNKKYVLTWTYH 178 Query: 164 ----GNNVAHSLMIAGTKLGADVVVATPE-GYEPDEKVIKWAEQNAAESGGSFELLHDPV 218 VA+S ++ TK+G DV + P Y D++ ++ NA +GGS + HD Sbjct: 179 PKPLNTAVANSALLIATKMGMDVTLLCPTPDYVLDDRYMQAGYANAQANGGSLRISHDID 238 Query: 219 KAVKDADVIYTDVWASMGQEAEAEERRKIFRPFQVNKDLVKHAKPDY---------MFMH 269 +A ADV+Y W ++ E+ + I +D KH D +F H Sbjct: 239 EAYSGADVVYAKSWGALPFFGRWEQEKPI-------RDAHKHFIVDERKMALTNNGLFSH 291 Query: 270 CLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQKAVLALLLG 311 CLP R + TD V+D+P + DEAENRLH QKAV+A LLG Sbjct: 292 CLPLRRNVKATDAVMDAPYCIAIDEAENRLHVQKAVMATLLG 333 Lambda K H 0.319 0.134 0.400 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: 273 Number of extensions: 18 Number of successful extensions: 8 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: 317 Length of database: 335 Length adjustment: 28 Effective length of query: 289 Effective length of database: 307 Effective search space: 88723 Effective search space used: 88723 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 (21.7 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