Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate CA265_RS18520 CA265_RS18520 acetylornithine carbamoyltransferase
Query= curated2:Q8TKT5 (302 letters) >FitnessBrowser__Pedo557:CA265_RS18520 Length = 324 Score = 109 bits (272), Expect = 1e-28 Identities = 98/321 (30%), Positives = 142/321 (44%), Gaps = 48/321 (14%) Query: 16 IYELLESAADLKAKRKAGESTEYLKNKSLGMIFEKSSTRTRVSFEVAMTDFGGHALYLN- 74 I + + A LKA A + KNK+LG++F S RTR+S + A + G + + +N Sbjct: 13 IKQFVNDALALKANPYAHQDLG--KNKTLGLVFMNPSLRTRLSTQKAALNLGMNVMVMNL 70 Query: 75 --------SRDIQVGRGETIE---DTARTLSGYLHGLMARVM----------SHDTVEKL 113 ++D V G T+E + A + Y L R S D K Sbjct: 71 DKEGWALETQDGVVMNGSTVEHIREAAAVMGQYCDILGLRSFPKLNNREEDYSEDFFNKF 130 Query: 114 AKYSTMPVINALSDREHPCQILGDFMTIME-FKKKFEGLK----FAWVGD--------GN 160 KY +PV++ S HP Q D +TI E + KK +G K AW N Sbjct: 131 VKYCAVPVVSLESATRHPLQSFADIITIHETWTKKPDGRKPKVVLAWAPHVKALPQAVPN 190 Query: 161 NVCNSALLGSAIMGMEFAVACPKGYEPKAEFLEQAKALGGKFTITDDPKVAAKDADIIYT 220 + A ++F +A P+GYE +F A I + + A AD +Y Sbjct: 191 SFAEWMCKAQAEGMIDFTIAQPEGYELSEDFTPDAN-------IQYNLEEALAGADYVYV 243 Query: 221 DVWVSMGDEAEQEKRLREFASFQVNTELLGVAKPDVIVMHCLPARRGLEITDEVMDGPNS 280 W S E K L + +N E L D VMHCLP RR LE++ E++DGPNS Sbjct: 244 KNWSSY---KEYGKVLTYPDGWMMNNEKLKFTN-DAKVMHCLPVRRDLELSSEILDGPNS 299 Query: 281 VIFEEAENRLHAQKALILKLM 301 ++ EA NRL A +A+I ++ Sbjct: 300 LVIHEAGNRLWAAQAVIKAML 320 Lambda K H 0.318 0.134 0.378 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: 204 Number of extensions: 9 Number of successful extensions: 3 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: 302 Length of database: 324 Length adjustment: 27 Effective length of query: 275 Effective length of database: 297 Effective search space: 81675 Effective search space used: 81675 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