Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate GFF2391 PGA1_c24220 ornithine carbamoyltransferase ArgF
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__Phaeo:GFF2391 Length = 308 Score = 157 bits (396), Expect = 4e-43 Identities = 119/349 (34%), Positives = 171/349 (48%), Gaps = 58/349 (16%) Query: 3 LKHFLNTQDWSRAELDALLTQAALFKRNKLGSE---------LKGKSIALVFFNPSMRTR 53 + HFL+ +L A++ QA+ K+ +LG LK + +AL+F PS RTR Sbjct: 1 MNHFLDIHKTDATDLRAIIDQASATKQARLGRPKAAPDDELPLKDRMVALIFEKPSTRTR 60 Query: 54 TSFELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRA 113 SF++G Q+GG +VL G M E IA+ ARVL RYVD+I +R Sbjct: 61 VSFDVGVRQMGGQTMVLS------------GNDMQLGHGETIADTARVLSRYVDMIMIRT 108 Query: 114 FPKFVDWSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKK 172 F ++ VL A+Y+ VPVIN + THPCQ +A L +EH G ++GKK Sbjct: 109 F----------DETVLTEMAEYASVPVINGLTDRTHPCQIMADVLTYEEHRGP--IKGKK 156 Query: 173 YVLTWTYHPKPLNTAVANSALTIATRMGMDVTL-----LCPTPDYILDERYMDWAAQNVA 227 V W V S L A + G D+T L P P++I A+N Sbjct: 157 VV--WCGD----GNNVCASFLHAAAQFGFDLTFTGPAQLDPEPEFI-------GLARN-- 201 Query: 228 ESGGSLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN 287 +G + + D A GAD+V A +W ++ + ++ + + + V++ MA Sbjct: 202 -AGSQVIIERDAAKAVEGADLVVADTWVSM--HDSQSSKERRHNMLRGYQVNDALMAHAK 258 Query: 288 -NGVFSHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVG 335 + +F HCLP R + T AVMD P + DEAENRLH QKAIM +G Sbjct: 259 PDALFMHCLPAHREEEVTSAVMDGPQSVIFDEAENRLHAQKAIMRYCLG 307 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: 250 Number of extensions: 18 Number of successful extensions: 7 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: 308 Length adjustment: 28 Effective length of query: 311 Effective length of database: 280 Effective search space: 87080 Effective search space used: 87080 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