Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate 3607012 Dshi_0433 ornithine carbamoyltransferase (RefSeq)
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Dino:3607012 Length = 333 Score = 114 bits (286), Expect = 3e-30 Identities = 109/357 (30%), Positives = 155/357 (43%), Gaps = 57/357 (15%) Query: 4 KHFLNTQDWSRAELDALLTQAALFKRNKL-GSE---LKGKSIALVFFNPSMRTRTSFELG 59 +HFL + ++ E+ LL +A K K G+E L+GK IAL+F S RTR FE+ Sbjct: 8 RHFLTLRGFTPEEIGFLLKLSADLKSAKYAGTEVPTLRGKEIALIFEKDSTRTRVGFEVA 67 Query: 60 AFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVD 119 A G L P GT + +E + + ARVLGR D I R F + Sbjct: 68 AHDQGATVTYLGPS----------GTHLG--KKETVKDTARVLGRVYDAIEYRGFGQ--- 112 Query: 120 WSKDREDQVLKSFAKYSPVPVINMETIT-HPCQELAHALALQEHFGTPDLRGKKYVLTWT 178 ++++ A ++ VPV N T HP Q LA L +QEH P LR Y Sbjct: 113 -------EIVQELADWAGVPVYNGLTDEFHPTQILADFLTMQEHCEKP-LREVAYCFMGD 164 Query: 179 YHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHD 238 + +S L +MGMDV L P + + + D A +G + ++ D Sbjct: 165 -----AGNNMGDSLLIGGAKMGMDVRLCAPRSLWPV-QSIQDEARAIAEHTGARVTLTED 218 Query: 239 IDSAYAGADVVYAKSWGALPF-FGNWEPEKPIRDQYQHFIVDERKMALTNNGV--FSHCL 295 +D A G D VY W ++ W + YQ V+ MA T N F HCL Sbjct: 219 VDKAVKGVDFVYTDVWVSMGEPVEKWAERIDLLMPYQ---VNADVMARTGNPRVRFMHCL 275 Query: 296 PLRRN-----------------VKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVG 335 P N ++ T+ V +SP I D+AENR+H KA++ A +G Sbjct: 276 PAFHNAETEVGCDIQDKFGLEAMEVTEEVFESPASIVFDQAENRMHTIKAVLVATLG 332 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: 272 Number of extensions: 18 Number of successful extensions: 6 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: 333 Length adjustment: 28 Effective length of query: 311 Effective length of database: 305 Effective search space: 94855 Effective search space used: 94855 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: 49 (23.5 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