Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate GFF1258 Psest_1291 ornithine carbamoyltransferase
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__psRCH2:GFF1258 Length = 306 Score = 120 bits (301), Expect = 4e-32 Identities = 104/341 (30%), Positives = 156/341 (45%), Gaps = 49/341 (14%) Query: 1 MSLKHFLNTQDWSRAELDALLTQAA----LFKRNKLGSELKGKSIALVFFNPSMRTRTSF 56 MS +HFL+ D + EL++L+ + L KR L LK + + ++F S RTR SF Sbjct: 1 MSARHFLSLMDCTPQELNSLVRRGIELKDLRKRGVLFEPLKNRVLGMIFEKASTRTRLSF 60 Query: 57 ELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPK 116 E G QLGG A+ L P + LG E I++ A V+ R +D + +R F Sbjct: 61 EAGMIQLGGQAIFLSPR------DTQLGR------GEPISDSAIVMSRMLDAVMIRTFAH 108 Query: 117 FVDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVL 175 L FA S VPVIN + HPCQ +A EH G+ + GK + Sbjct: 109 ----------STLTDFAANSSVPVINGLSDDLHPCQLMADMQTFHEHRGS--IAGK--TV 154 Query: 176 TWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQV 235 W + N+ + A + + + CP E Y + A+ + +G +Q+ Sbjct: 155 AWIGD----GNNMCNTYIEAAIQFDFQLKVACP-------EGY-EPNAELMGRAGDRVQI 202 Query: 236 SHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIR-DQYQHFIVDERKMALTNNGV-FSH 293 D A AGA ++ W ++ E E R ++ + VD + V F H Sbjct: 203 LRDPREAAAGAHLISTDVWASM----GQEDEAAARLATFRPYQVDRALLDCAAADVLFMH 258 Query: 294 CLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334 CLP R + + ++D P +A D+AENRLHVQKA++ LV Sbjct: 259 CLPAHRGEEISHDLLDDPRSVAWDQAENRLHVQKALLEFLV 299 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: 218 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: 306 Length adjustment: 28 Effective length of query: 311 Effective length of database: 278 Effective search space: 86458 Effective search space used: 86458 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