Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate Ac3H11_4531 Ornithine cyclodeaminase (EC 4.3.1.12)
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4531 Length = 353 Score = 419 bits (1077), Expect = e-122 Identities = 221/339 (65%), Positives = 259/339 (76%), Gaps = 4/339 (1%) Query: 2 TYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPVA 61 T ++ P + LV G+ P + +A + DF RW AFDKSARVASHS GVIELMP+A Sbjct: 9 TLYLSAPDVIALVQRKGIEPCLRGIADYIHADFLRWGAFDKSARVASHSRDGVIELMPIA 68 Query: 62 DKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMAA 121 D YAFKYVNGHP NT L TVMAFGVLADV +G P+LLSELT+ TALRTAA S +AA Sbjct: 69 DGETYAFKYVNGHPKNTRWGLPTVMAFGVLADVATGAPLLLSELTLTTALRTAAMSAVAA 128 Query: 122 QALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLT 181 +ALARP +R MALIGNGAQSEFQALAFH LGI+ + +DTDP ATAKL ANLK T Sbjct: 129 RALARPGSRTMALIGNGAQSEFQALAFHHLLGIDTLRLFDTDPAATAKLQANLKGTGPRT 188 Query: 182 IRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVLR 241 + +S AEAV+G D++TTVTADK ATI+TPDML PGMH+NAVGGDCPGKTELHADVLR Sbjct: 189 V-ACTSTAEAVRGADVVTTVTADKTNATILTPDMLAPGMHINAVGGDCPGKTELHADVLR 247 Query: 242 NARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDY 301 A+VFVEY PQTRIEG+IQQLPADF V +LW VL G+ GR SD+ VTVFDSVGFALED+ Sbjct: 248 QAQVFVEYAPQTRIEGDIQQLPADFAVTELWEVLAGQHGGRASDAAVTVFDSVGFALEDF 307 Query: 302 TVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLFS--HTR 338 + LR++ A + GMG I+L+P + DPK+LF HTR Sbjct: 308 SALRFLRDAAAELGMGQPIELIPQL-SDPKNLFGLLHTR 345 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: 352 Number of extensions: 7 Number of successful extensions: 2 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: 353 Length adjustment: 29 Effective length of query: 321 Effective length of database: 324 Effective search space: 104004 Effective search space used: 104004 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 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