Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate CCNA_02325 CCNA_02325 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Caulo:CCNA_02325 Length = 311 Score = 125 bits (313), Expect = 2e-33 Identities = 104/343 (30%), Positives = 165/343 (48%), Gaps = 50/343 (14%) Query: 4 KHFLNTQDWSRAELDALLTQAALFKRNKLG---------SELKGKSIALVFFNPSMRTRT 54 +HF++ A L LL A K + G + K + ++++F S RTR Sbjct: 5 RHFIDLWKLDGATLRLLLDDAHARKAARKGWPQGKVDADAPAKDRVLSMIFQKNSTRTRF 64 Query: 55 SFELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAF 114 SF+ QLGG A++ + LG G+T I + A+VL R VD + +RA Sbjct: 65 SFDAAMRQLGGSAIISTAS------DMQLGR---GET---IEDTAKVLSRMVDAVMIRA- 111 Query: 115 PKFVDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKY 173 ++ FA+ S VP+IN + +HPCQ +A L ++EH G + GK Sbjct: 112 ---------NSHADVERFAQVSTVPIINGLTDKSHPCQIMADILTIEEHRGP--IAGK-- 158 Query: 174 VLTWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSL 233 + W V +S + A +G ++ + CP + D A + G + Sbjct: 159 TIAWVGD----GNNVCSSFIHAAPLLGFELKIACPA---VYHADLHDLARAEGLQ--GKV 209 Query: 234 QVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALT-NNGVFS 292 ++ D +A +GADVV A +W ++ G+ + ++ + + + VD+R M L NGVF Sbjct: 210 SMTTDPKAAVSGADVVVADTWVSM---GDTDHDERLA-ALEPYQVDDRLMDLAAGNGVFL 265 Query: 293 HCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVG 335 HCLP R + TDAV+D P + DEAENR+H QK+++A G Sbjct: 266 HCLPAHRGEEVTDAVLDGPRSLVWDEAENRIHAQKSVLAWCFG 308 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: 224 Number of extensions: 8 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: 311 Length adjustment: 28 Effective length of query: 311 Effective length of database: 283 Effective search space: 88013 Effective search space used: 88013 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: 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