Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate RR42_RS27330 RR42_RS27330 ornithine cyclodeaminase
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__Cup4G11:RR42_RS27330 Length = 310 Score = 97.1 bits (240), Expect = 6e-25 Identities = 77/233 (33%), Positives = 117/233 (50%), Gaps = 13/233 (5%) Query: 90 VLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPNARKMALIGNGAQSEFQALAFH 149 ++ + G P+ + T LRTAA S++AA+ LARP A +AL G G Q A Sbjct: 79 LIFSTEDGRPLASFDAGAITRLRTAACSVLAARHLARPGAEVLALFGAGTQGVQHARQLA 138 Query: 150 KHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYAT 209 L ++ I+ +DP A A + L G+ + A +AV DI+ VTA ++ Sbjct: 139 AALPLKRILL--SDPYADAAMPERLARQCGIPVDLAEP-DQAVAQADIV--VTASRSTTP 193 Query: 210 IITPDMLEPGMHLNAVGGDCPGKTELHADVL-RNARVFVEYEPQT-RIEGEI-----QQL 262 + + L+PG + A+G P EL L R AR+ VE+ PQ+ R G+I L Sbjct: 194 LFSGHSLKPGAFVAAIGSSLPHTRELDDVALSRAARLVVEWRPQSMREAGDIVLADPAVL 253 Query: 263 PADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRG 315 PAD VV+L V+ G + R +D+ + ++ SVG LED + + +Q E G Sbjct: 254 PAD-KVVELADVVTGSVKPRGNDTDILIYKSVGVGLEDVALAGFAYRQIEAAG 305 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: 197 Number of extensions: 7 Number of successful extensions: 3 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: 310 Length adjustment: 28 Effective length of query: 322 Effective length of database: 282 Effective search space: 90804 Effective search space used: 90804 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