Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate N515DRAFT_3763 N515DRAFT_3763 N-acetylornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Dyella79:N515DRAFT_3763 Length = 335 Score = 563 bits (1452), Expect = e-165 Identities = 270/336 (80%), Positives = 303/336 (90%), Gaps = 2/336 (0%) Query: 1 MSLKHFLNTQDWSRAELDALLTQAALFKRNKLGSELKGKSIALVFFNPSMRTRTSFELGA 60 M+L+HFL TQD+SRAE+DALL QAA FKR+ G +L GKS+AL+FFNPSMRTRTSFELGA Sbjct: 1 MTLRHFLTTQDYSRAEIDALLEQAAAFKRSPRGQQLAGKSVALLFFNPSMRTRTSFELGA 60 Query: 61 FQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDW 120 F LGGHA+VL PGKDAWPIEF++GTVMDGDTEEHIAEVARVL RYVDLI VRAFPKF DW Sbjct: 61 FHLGGHAIVLAPGKDAWPIEFDVGTVMDGDTEEHIAEVARVLSRYVDLIAVRAFPKFQDW 120 Query: 121 SKDREDQVLKSFAKYSPVPVINMETITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYH 180 + DRED+V+K+FA+Y+ VPVINMETITHPCQELAHALA+QEH G+ L+ KKYVLTWTYH Sbjct: 121 TVDREDRVIKAFAQYASVPVINMETITHPCQELAHALAMQEHLGS--LQNKKYVLTWTYH 178 Query: 181 PKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDID 240 PKPLNTAVANSAL IAT+MGMDVTLLCPTPDY+LD+RYM N +GGSL++SHDID Sbjct: 179 PKPLNTAVANSALLIATKMGMDVTLLCPTPDYVLDDRYMQAGYANAQANGGSLRISHDID 238 Query: 241 SAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLRRN 300 AY+GADVVYAKSWGALPFFG WE EKPIRD ++HFIVDERKMALTNNG+FSHCLPLRRN Sbjct: 239 EAYSGADVVYAKSWGALPFFGRWEQEKPIRDAHKHFIVDERKMALTNNGLFSHCLPLRRN 298 Query: 301 VKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVGQ 336 VKATDAVMD+P CIAIDEAENRLHVQKA+MA L+GQ Sbjct: 299 VKATDAVMDAPYCIAIDEAENRLHVQKAVMATLLGQ 334 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: 467 Number of extensions: 17 Number of successful extensions: 2 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: 335 Length adjustment: 28 Effective length of query: 311 Effective length of database: 307 Effective search space: 95477 Effective search space used: 95477 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 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