Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_084275279.1 B8779_RS04075 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_900176045.1:WP_084275279.1 Length = 308 Score = 128 bits (321), Expect = 2e-34 Identities = 101/337 (29%), Positives = 167/337 (49%), Gaps = 41/337 (12%) Query: 3 LKHFLNTQDWSRAELDALLTQAALFK----RNKLGSELKGKSIALVFFNPSMRTRTSFEL 58 ++HFL +D+++ E+ ++T A K R + L+ +++A++F S RTR SFE+ Sbjct: 1 MRHFLTLKDFTKEEILEIITLAEQIKTETKRKEFVPYLENQTLAMIFEKSSTRTRVSFEV 60 Query: 59 GAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFV 118 G +QLGG + L + LG E + + ARV+ R D++ +R F Sbjct: 61 GIYQLGGIGLFLSKN------DLQLGR------GEPMKDTARVVSRMCDMVMIRTF---- 104 Query: 119 DWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTW 177 E L+ FA YS VPVIN + HP Q +A L ++E FG + YV Sbjct: 105 ------EQAKLEEFAAYSKVPVINGLTNEYHPVQLMADYLTMRE-FGKAENPVVAYVGD- 156 Query: 178 TYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSH 237 +A+S L + +++G + + P Y + ++ A + ESG ++ ++ Sbjct: 157 -------GNNMAHSWLMLVSKLGFTLRIATPK-GYEPAKNVVEDALRFAKESGAKIEFTN 208 Query: 238 DIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHCLP 296 D A A ADVV +W + E EK ++D +Q ++VD++ MAL + +F HCLP Sbjct: 209 DPKEAVANADVVTTDTW--ISMGQEDEKEKRLKD-FQGYMVDKQMMALAKPDAIFLHCLP 265 Query: 297 LRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAAL 333 R + ++ + ++ EAENRLH QK +M L Sbjct: 266 AYRGYEVSEEIFEAHAEEIFTEAENRLHAQKGVMVWL 302 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: 212 Number of extensions: 10 Number of successful extensions: 5 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: 308 Length adjustment: 28 Effective length of query: 311 Effective length of database: 280 Effective search space: 87080 Effective search space used: 87080 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 10 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