Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate 353243 BT3717 ornithine carbamoyltransferase (NCBI ptt file)
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Btheta:353243 Length = 318 Score = 187 bits (474), Expect = 4e-52 Identities = 115/313 (36%), Positives = 166/313 (53%), Gaps = 23/313 (7%) Query: 11 DWSRAELDALLTQAALFKRNKLGSELKGKSIALVFFNPSMRTRTSFELGAFQLGGHAVVL 70 D A +A Q FK +LG + K++ ++FFN S+RTR S + A LG + +VL Sbjct: 12 DLKSALAEAFEIQKDRFKYVELG---RNKTLMMIFFNSSLRTRLSTQKAALNLGMNVMVL 68 Query: 71 QPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSKDREDQVLK 130 + AW +E G +MDGD EH+ E V+G Y D+IGVR+F +F D D ++ +L Sbjct: 69 DINQGAWKLETERGVIMDGDKPEHLLEAIPVMGCYCDIIGVRSFARFEDRDFDYQETILN 128 Query: 131 SFAKYSPVPVINMETIT-HPCQELAHALALQEHFGTPDLRGKKYVLTWTYHPKPLNTAVA 189 F +YS PV +ME T HP Q A + ++E+ T K V+TW HP+PL AV Sbjct: 129 QFIQYSGRPVFSMEAATRHPLQSFADLITIEEYKKT---ARPKVVMTWAPHPRPLPQAVP 185 Query: 190 NSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDSAYAGADVV 249 NS D + P Y L +++ G+ +V +D A+ GAD + Sbjct: 186 NSFAEWMNATDYDFVITHP-EGYELAPQFV-----------GNAKVEYDQMKAFEGADFI 233 Query: 250 YAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLRRNVKATDAVMD 309 YAK+W A + I + + + V +R+MA+TNN F HCLP+RRN+ TD V++ Sbjct: 234 YAKNWAAY----TGDNYGQILSKDREWTVSDRQMAVTNNAFFMHCLPVRRNMIVTDDVIE 289 Query: 310 SPNCIAIDEAENR 322 SP I I EA NR Sbjct: 290 SPQSIVIPEAANR 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: 298 Number of extensions: 17 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: 318 Length adjustment: 28 Effective length of query: 311 Effective length of database: 290 Effective search space: 90190 Effective search space used: 90190 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