Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_057687254.1 ABB28_RS15390 N-acetylornithine carbamoyltransferase
Query= BRENDA::O93656 (317 letters) >NCBI__GCF_001431535.1:WP_057687254.1 Length = 336 Score = 172 bits (437), Expect = 8e-48 Identities = 121/338 (35%), Positives = 177/338 (52%), Gaps = 40/338 (11%) Query: 8 RDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVA 67 + L QD++ E+ +L A + K K+G L+GK++A++F PS RTR SFE+ Sbjct: 4 KHFLNTQDWSRSELDALLTQAALFKR-NKLGDQ---LKGKSIALVFFNPSMRTRTSFELG 59 Query: 68 MAHLGGHALYL----NAQDLQLRRG--------ETIADTARVLSRYVDAIMARVY----- 110 LG HA+ L +A ++ G E IA+ A+VL RY D I R + Sbjct: 60 AFQLGAHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVAKVLGRYCDMIAVRAFPKFVD 119 Query: 111 ---DHKD--VEDLAKYASVPVINGLSDFSHPCQALADYMTIWEKKGT--IKGVKVVYVGD 163 D +D ++ AKY+ VPVIN + +HPCQ LA M + E GT ++G K V Sbjct: 120 WSVDREDTVLKSFAKYSPVPVIN-METITHPCQELAHAMALQEHFGTQDLRGKKYVLTWT 178 Query: 164 ------GNNVAHSLMIAGTKLGADVVVATPE-GYEPDEKVIKWAEQNAAESGGSFELLHD 216 VA+S + T++G DV + P Y DE+ + WAEQN AE+GGS ++ HD Sbjct: 179 YHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMGWAEQNVAENGGSLQVSHD 238 Query: 217 PVKAVKDADVIYTDVWASMGQEAEAEERRKI---FRPFQVNKDLVKHAKPDYMFMHCLPA 273 A ADV+Y W ++ E + I ++ F V++ + + +F HCLP Sbjct: 239 IESAYTGADVVYAKSWGALPFFGNWEPEKPIRDQYKHFIVDEQKMALTN-NGVFSHCLPL 297 Query: 274 HRGEEVTDDVIDSPNSVVWDEAENRLHAQKAVLALLLG 311 R + TD V+DSP + +EAENRLH QKA++A L G Sbjct: 298 RRNVKATDAVMDSPQCIAINEAENRLHVQKAIMAALAG 335 Lambda K H 0.319 0.134 0.400 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: 286 Number of extensions: 15 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: 317 Length of database: 336 Length adjustment: 28 Effective length of query: 289 Effective length of database: 308 Effective search space: 89012 Effective search space used: 89012 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 (21.7 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