Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate Pf1N1B4_762 Ornithine carbamoyltransferase (EC 2.1.3.3)
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 Length = 307 Score = 110 bits (275), Expect = 5e-29 Identities = 102/343 (29%), Positives = 150/343 (43%), Gaps = 47/343 (13%) Query: 1 MSLKHFLNTQDWSRAELDALLTQAALFK----RNKLGSELKGKSIALVFFNPSMRTRTSF 56 MS +HFL+ D + EL +++ + K R L LK + + ++F S RTR SF Sbjct: 2 MSARHFLSLMDCTPEELVSVIRRGVELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRISF 61 Query: 57 ELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPK 116 E G QLGG A+ L P + LG E I + A V+ +D + +R F Sbjct: 62 EAGMIQLGGQAIFLSPR------DTQLGR------GEPIGDCAIVMSSMLDAVMIRTFAH 109 Query: 117 FVDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVL 175 L FA S VPVIN + HPCQ LA EH G+ ++GK + Sbjct: 110 ----------STLTEFAANSRVPVINGLSDDLHPCQLLADMQTFLEHRGS--IQGK--TV 155 Query: 176 TWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQV 235 W + NS + A + + + CP E Y + + VA++G + + Sbjct: 156 AWIGD----GNNMCNSYIEAAIQFDFQLRIACP-------EGY-EPNPEFVAKAGDRVTI 203 Query: 236 SHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGV-FSHC 294 D A GA +V W ++ G E + F V+ + L V F HC Sbjct: 204 VRDPQEAVRGAHLVSTDVWTSM---GQEEETAKRLKLFAPFQVNRALLDLAAPDVLFMHC 260 Query: 295 LPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVGQS 337 LP R + + ++D +A D+AENRLH QKA++ LV S Sbjct: 261 LPAHRGEEISLDLLDDSRSVAWDQAENRLHAQKALLEFLVPPS 303 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: 214 Number of extensions: 5 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: 339 Length of database: 307 Length adjustment: 28 Effective length of query: 311 Effective length of database: 279 Effective search space: 86769 Effective search space used: 86769 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