Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate 3607477 Dshi_0890 Ornithine cyclodeaminase (RefSeq)
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__Dino:3607477 Length = 330 Score = 107 bits (267), Expect = 4e-28 Identities = 73/253 (28%), Positives = 120/253 (47%), Gaps = 9/253 (3%) Query: 75 PANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPNARKMAL 134 P N A+ + + L D D+G L TA+RTAA+S ++ LAR +A+ + + Sbjct: 82 PNNMAKGIINHQSTVFLFDPDTGKLKALVGGNYLTAIRTAASSAVSIDQLARKDAKVLGM 141 Query: 135 IGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKG 194 +G G QS FQ A + E++V ++ P +I NL + + +V+ G Sbjct: 142 VGAGHQSTFQLRAAVEQRDFEKVVCWNPHP----DMIPNLGKVAAEIGIPFEAVSREELG 197 Query: 195 VDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTR 254 +T A+ +I ++PG HL +G D GK E+ A+++ A +F + Q+ Sbjct: 198 AQSDVIITITSAFEPLIEAGYIKPGTHLACMGTDTKGKQEVAAELVAKATLFTDEVAQST 257 Query: 255 IEGEIQQLPA-----DFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQ 309 GE Q A V + +V+ G+ GR SD ++T+FD G L+D V + Sbjct: 258 TIGETQHAIASGAITQDDVTPIGKVINGDHPGRTSDDEITLFDGTGVGLQDLAVAAVAAE 317 Query: 310 QAEKRGMGTKIDL 322 QA G T++ L Sbjct: 318 QAVATGAATRVSL 330 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: 222 Number of extensions: 10 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: 330 Length adjustment: 28 Effective length of query: 322 Effective length of database: 302 Effective search space: 97244 Effective search space used: 97244 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