Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate GFF1617 PGA1_c16390 ornithine cyclodeaminase ArcB
Query= SwissProt::Q59701 (356 letters) >FitnessBrowser__Phaeo:GFF1617 Length = 348 Score = 468 bits (1205), Expect = e-137 Identities = 224/339 (66%), Positives = 279/339 (82%) Query: 9 VVPFISVDHMMKLVLKVGIDTFLTELAAEIEKDFRRWPIFDKKPRVGSHSQDGVIELMPT 68 +VPF+SVD+MM+L+ VGIDT + +LA IE+DF+RW +FDK PRV SHS GVIELMPT Sbjct: 9 LVPFVSVDNMMRLIHHVGIDTVMKDLATYIEEDFKRWELFDKTPRVASHSDVGVIELMPT 68 Query: 69 SDGSLYGFKYVNGHPKNTHQGRQTVTAFGVLSDVGNGYPLLLSEMTILTALRTAATSALA 128 SDG YGFKYVNGHPKNT +G QTVTAFG+L+DV GYP+LL+EMTILTALRTAATSA+ Sbjct: 69 SDGEAYGFKYVNGHPKNTSEGLQTVTAFGLLADVYTGYPVLLTEMTILTALRTAATSAMV 128 Query: 129 AKYLARPNSKTMAIIGNGAQSEFQARAFRAILGIQKLRLFDIDTSATRKCARNLTGPGFD 188 AK+LA + TMA+IGNGAQSEFQ+ A +AI G++ +RL+D+D +AT KCA NL G G Sbjct: 129 AKHLAPKGATTMAMIGNGAQSEFQSLAMQAICGLKSVRLYDVDPAATAKCAANLAGTGLA 188 Query: 189 IVECGSVAEAVEGADVITTVTADKQFATILSDNHVGPGVHINAVGGDCPGKTEISMEVLL 248 +V C + EA+EGA ++TT TADKQ+ATIL+DN VG GVHINA+GGDCPGKTE++ +L Sbjct: 189 VVSCKTPEEAIEGAQILTTCTADKQYATILTDNMVGSGVHINAIGGDCPGKTELAPGILS 248 Query: 249 RSDIFVEYPPQTWIEGDIQQLPRTHPVTELWQVMTGEKTGRVGDRQITMFDSVGFAIEDF 308 RSD+FVE+PPQT +EG+IQQ+P VTELWQV+ G+K GR D+QIT+FDSVGFAIEDF Sbjct: 249 RSDVFVEFPPQTRVEGEIQQMPEDFEVTELWQVILGQKPGRRDDKQITLFDSVGFAIEDF 308 Query: 309 SALRYVRAKITDFEMFTELDLLADPDEPRDLYGMLLRCE 347 SALRY+R +I D + F ELD+LADPD+PRDL+GM+ R + Sbjct: 309 SALRYIRDRIKDTDFFLELDMLADPDDPRDLFGMVQRAK 347 Lambda K H 0.320 0.137 0.405 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: 403 Number of extensions: 10 Number of successful extensions: 1 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: 356 Length of database: 348 Length adjustment: 29 Effective length of query: 327 Effective length of database: 319 Effective search space: 104313 Effective search space used: 104313 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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