Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate AZOBR_RS19030 AZOBR_RS19030 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__azobra:AZOBR_RS19030 Length = 304 Score = 149 bits (376), Expect = 9e-41 Identities = 113/338 (33%), Positives = 173/338 (51%), Gaps = 43/338 (12%) Query: 2 SLKHFLNTQDWSRAELDALLTQAALFKRN--KLGSELKGKSIALVFFNPSMRTRTSFELG 59 +++HFL+ +A L +L AA K++ S G+++A++F PS RTR SFE+G Sbjct: 3 AVRHFLDIDRLDKATLRQILAMAATIKKDIPAYRSLFAGRTLAMIFEKPSTRTRVSFEVG 62 Query: 60 AFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVD 119 QLGG VVL+P + LG G+T I + ARVL RYVD + VR Sbjct: 63 MRQLGGDVVVLKPD------DMQLGR---GET---IGDTARVLSRYVDAVMVRTMG---- 106 Query: 120 WSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWT 178 ++ + A+++ VP+IN + +HPCQ +A + +EH G + R ++ Sbjct: 107 ------EERVHELAEFASVPIINGLTDQSHPCQIMADVMTFEEHRGPIEGRTVAWI---- 156 Query: 179 YHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHD 238 +N VA S + +A R+G+++ L CP Y +DW V GG + V+ Sbjct: 157 ---GDVNN-VAVSWVHVAVRLGVEIRLGCPEI-YGPAPELLDW----VKREGGRITVTTS 207 Query: 239 IDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHCLPL 297 + A GAD V +W ++ + + + YQ V+E MAL + +F HCLP Sbjct: 208 PEEAVRGADCVVTDAWASM-HNTDVDERAAVLGPYQ---VNEALMALAAPDALFMHCLPA 263 Query: 298 RRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVG 335 R + TD V+D + + DEAENRLH QKAI+A +G Sbjct: 264 HRGEEVTDGVIDGRHSVVWDEAENRLHAQKAILAWCLG 301 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: 260 Number of extensions: 11 Number of successful extensions: 7 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