Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate WP_051955498.1 DL88_RS02250 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >NCBI__GCF_000745425.1:WP_051955498.1 Length = 318 Score = 139 bits (349), Expect = 1e-37 Identities = 118/345 (34%), Positives = 162/345 (46%), Gaps = 52/345 (15%) Query: 5 HFLNTQDWSRAELDALLTQAALFK-RNKLGSE-----LKGKSIALVFFNPSMRTRTSFEL 58 HFL+ AEL A+L AA FK R + G + L+G+++A+VF PS RTR SF+L Sbjct: 15 HFLDLSQLDTAELRAILDLAAEFKARRRRGQKSRERPLEGRTLAMVFDQPSTRTRVSFDL 74 Query: 59 GAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFV 118 G +LGG ++L G M E IA+ ARVL R+VD I +R Sbjct: 75 GMRELGGETIMLT------------GQEMQLGRGETIADTARVLSRFVDSIVIRIL---- 118 Query: 119 DWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTW 177 + L A+++ VPVIN + +HPCQ +A L +EH G ++G+ + W Sbjct: 119 ------DHANLLELAEHAEVPVINGLTKRSHPCQIMADILTFEEHRGP--IKGR--TIAW 168 Query: 178 TYHPKPLNTAVANSALTIATRMGMDVTLLCP---TPDYILDERYMDWAAQNVAESGGSLQ 234 T + V S + A R + + CP TP L A N E + Sbjct: 169 TGD----SNNVLASWIEAARRFDFTLNVACPEELTPAQDL------LAFANAHEK--KVH 216 Query: 235 VSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALT-NNGVFSH 293 V D A +GAD V + W ++ G+ E F V+ R MA + VF H Sbjct: 217 VLRDPFEAVSGADAVISDCWVSM---GDEAEEARRHALLAPFQVNARLMATAAKDAVFLH 273 Query: 294 CLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVGQSR 338 CLP R + TD V+D P + DEAENRLH QK I+A G R Sbjct: 274 CLPAHRGEEVTDEVIDGPQSVVFDEAENRLHAQKGILAWCFGVGR 318 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: 259 Number of extensions: 21 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: 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 10 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