Align N-succinylornithine carbamoyltransferase (EC 2.1.3.11) (characterized)
to candidate N515DRAFT_3763 N515DRAFT_3763 N-acetylornithine carbamoyltransferase
Query= reanno::Cola:Echvi_3849 (313 letters) >FitnessBrowser__Dyella79:N515DRAFT_3763 Length = 335 Score = 198 bits (504), Expect = 1e-55 Identities = 116/327 (35%), Positives = 185/327 (56%), Gaps = 22/327 (6%) Query: 5 TQFENKSLADQLIQKALEYKKAPLSDNNLGRGKRIGLLFLNPSLRTRVSTQIAASNLGME 64 TQ +++ D L+++A +K++P G K + LLF NPS+RTR S ++ A +LG Sbjct: 9 TQDYSRAEIDALLEQAAAFKRSPRGQQLAG--KSVALLFFNPSMRTRTSFELGAFHLGGH 66 Query: 65 SIVLNMDKESWALEMEDGVIMNQGKAEHIRDAAGVLGSYFDILALRAFPSLTNKDEDSED 124 +IVL K++W +E + G +M+ EHI + A VL Y D++A+RAFP + D ED Sbjct: 67 AIVLAPGKDAWPIEFDVGTVMDGDTEEHIAEVARVLSRYVDLIAVRAFPKFQDWTVDRED 126 Query: 125 FILHQFAKHSGLPLISLESAIRHPLQSLADMVTIQEH-KQKEKPKVVLTWAPHIKAIPHA 183 ++ FA+++ +P+I++E+ I HP Q LA + +QEH + K VLTW H K + A Sbjct: 127 RVIKAFAQYASVPVINMET-ITHPCQELAHALAMQEHLGSLQNKKYVLTWTYHPKPLNTA 185 Query: 184 VANSFAEWSIGCGHDVTITHP-EGYELDERFTQGA-----------TIEHDQDKALANAD 231 VANS + G DVT+ P Y LD+R+ Q I HD D+A + AD Sbjct: 186 VANSALLIATKMGMDVTLLCPTPDYVLDDRYMQAGYANAQANGGSLRISHDIDEAYSGAD 245 Query: 232 FVYVKNWSAFNEYGK------ILCTDESWMLNEQKLSQAPNAKVMHCLPVRRNVELSDEI 285 VY K+W A +G+ I + ++++E+K++ N HCLP+RRNV+ +D + Sbjct: 246 VVYAKSWGALPFFGRWEQEKPIRDAHKHFIVDERKMALTNNGLFSHCLPLRRNVKATDAV 305 Query: 286 LDGPRSLVQHQAKNRVFAAQAALSELL 312 +D P + +A+NR+ +A ++ LL Sbjct: 306 MDAPYCIAIDEAENRLHVQKAVMATLL 332 Lambda K H 0.317 0.132 0.384 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: 271 Number of extensions: 14 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: 313 Length of database: 335 Length adjustment: 28 Effective length of query: 285 Effective length of database: 307 Effective search space: 87495 Effective search space used: 87495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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