Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_012283661.1 HM1_RS12045 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000019165.1:WP_012283661.1 Length = 334 Score = 142 bits (357), Expect = 2e-38 Identities = 111/357 (31%), Positives = 184/357 (51%), Gaps = 57/357 (15%) Query: 4 KHFLNTQDWSRAELDALLTQAA-LFKRNKLGSE---LKGKSIALVFFNPSMRTRTSFELG 59 +HF++ +++++ E+D +L + L K+ +G L K++ ++FF S RTR S E G Sbjct: 8 RHFIDLEEFTKEEIDTMLEVSFDLKKQFAMGVPTPYLLHKTMFMMFFEQSTRTRNSMEAG 67 Query: 60 AFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVD 119 QLGGHA L D+ ++ G E + A +L R+ I R + + Sbjct: 68 LAQLGGHAGFL----DSSSMQIAHG--------ESAKDTAIILSRFGHAIACR----YCN 111 Query: 120 WSKDREDQVLKSFAKYSPVPVINMET-ITHPCQELAHALALQEHFGTPDLRGKKYVLTWT 178 W ++ L A++S VP++N++ + HP Q LA + ++E G DL+ K + W Sbjct: 112 WGYG--NKYLTEMARWSKVPIMNLQCDLYHPFQALADLMTMKEKIG--DLKRTKVSIIWA 167 Query: 179 Y---HPKPLNTAVANSALTIATRMGMDVTLLCPT----PDYILDERYMDWAAQNVAESGG 231 Y H KP++ V S + + R GMDV L P PD+++++ A N A+ GG Sbjct: 168 YAESHKKPISVPV--SQILLFPRYGMDVCLAHPRGWELPDWVIEK-----AKANAAKFGG 220 Query: 232 SLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDER---------- 281 ++ V+++ + AY A +V K+WG+ + N + + + +VDE+ Sbjct: 221 TVTVTNNEEEAYENAHIVIPKNWGS---WVNDQTGASVAGAAK--VVDEKLMAQKSWKCT 275 Query: 282 --KMALTNNGV-FSHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVG 335 KMA+ + V + H LP RN + D+V+D P+ I DEAENRLH KA+M L+G Sbjct: 276 EAKMAMADKDVMYMHALPADRNNEVEDSVIDGPHSIVFDEAENRLHTAKAVMTLLMG 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: 320 Number of extensions: 15 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: 334 Length adjustment: 28 Effective length of query: 311 Effective length of database: 306 Effective search space: 95166 Effective search space used: 95166 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 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