Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate HSERO_RS07185 HSERO_RS07185 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__HerbieS:HSERO_RS07185 Length = 304 Score = 118 bits (295), Expect = 2e-31 Identities = 101/341 (29%), Positives = 157/341 (46%), Gaps = 49/341 (14%) Query: 1 MSLKHFLNTQDWSRAELDALLTQAALFKRNKLGSE----LKGKSIALVFFNPSMRTRTSF 56 M++KH+L D++ E + ++ ++ + KR E L +++ +VF S RTR SF Sbjct: 1 MAIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSF 60 Query: 57 ELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPK 116 E G Q+GG A+ L + LG E + + A+V+ R D+I +R + + Sbjct: 61 EAGMHQMGGAAIYLNTR------DSQLGR------GEPVEDAAQVMSRMCDVIMIRTYGQ 108 Query: 117 FVDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVL 175 ++++ FAK+S VPVIN + HPCQ LA EH G+ ++GK ++ Sbjct: 109 ----------EIIERFAKHSRVPVINGLTNEQHPCQVLADVFTYIEHHGS--IQGK--IV 154 Query: 176 TWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQV 235 W + S L A G V + P Y +D + +N Sbjct: 155 AWVGDANNM----LYSWLQAAEVFGFHVNVSTPK-GYDIDPAQVSPGNKNYTFFADPADA 209 Query: 236 SHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIR-DQYQHFIVDERKMALTN-NGVFSH 293 D AD+V W ++ F E E R + +IVD+ KMA + +F H Sbjct: 210 CQD-------ADLVTTDVWTSMGF----EAENNARLKAFDGWIVDQAKMARAKKDALFMH 258 Query: 294 CLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 CLP R + V+D P + +EAENRLHVQKA++ LV Sbjct: 259 CLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLV 299 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: 238 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: 339 Length of database: 304 Length adjustment: 28 Effective length of query: 311 Effective length of database: 276 Effective search space: 85836 Effective search space used: 85836 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