Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate GFF3435 PS417_17585 ornithine cyclodeaminase
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__WCS417:GFF3435 Length = 348 Score = 407 bits (1045), Expect = e-118 Identities = 208/335 (62%), Positives = 256/335 (76%), Gaps = 1/335 (0%) Query: 1 MTYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPV 60 MT +IDV + LV G+ I E+A +R D+ RWQ F+K AR+A+HS GVIELMPV Sbjct: 1 MTRYIDVNDLCYLVSQKGLQTCITEMAEYIRADYLRWQDFEKCARLANHSPDGVIELMPV 60 Query: 61 ADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMA 120 +D S YAFKYVNGHP NT + TVMAFG L DVD+G PVLL+E+T+ TA+RTAATS + Sbjct: 61 SDASLYAFKYVNGHPKNTLAGMLTVMAFGALGDVDTGLPVLLAEMTLTTAIRTAATSALV 120 Query: 121 AQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGL 180 A+ LAR N+R MALIGNG+QSEFQALAFH LGI EI +D D ATAKL ANLK + + Sbjct: 121 ARYLARDNSRSMALIGNGSQSEFQALAFHAMLGITEIRLFDIDAKATAKLAANLKAFPAI 180 Query: 181 TIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVL 240 + A SVAEAVKG DI+TTVTADKAYATI+T +M+EPGMHLNAVGGDCPGKTEL ++ Sbjct: 181 KVILAGSVAEAVKGADIVTTVTADKAYATILTDEMIEPGMHLNAVGGDCPGKTELDRRIV 240 Query: 241 RNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALED 300 ARV VEYEPQ+RIEGEIQ +P D PV +LW+V+ G+ GR++ QVT+FDSVGFA+ED Sbjct: 241 ERARVIVEYEPQSRIEGEIQHMPEDSPVTELWQVINGQQPGRENARQVTLFDSVGFAIED 300 Query: 301 YTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLFS 335 Y+ LRYVL A+ +G+ ++LVP + DPKDLF+ Sbjct: 301 YSALRYVLDVAKALDVGSDLELVPDLA-DPKDLFA 334 Lambda K H 0.320 0.134 0.387 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: 316 Number of extensions: 4 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: 350 Length of database: 348 Length adjustment: 29 Effective length of query: 321 Effective length of database: 319 Effective search space: 102399 Effective search space used: 102399 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 Aug 03 2021. The underlying query database was built on Aug 03 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