Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate HSERO_RS00300 HSERO_RS00300 ornithine cyclodeaminase
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__HerbieS:HSERO_RS00300 Length = 347 Score = 400 bits (1027), Expect = e-116 Identities = 204/312 (65%), Positives = 247/312 (79%), Gaps = 2/312 (0%) Query: 23 IGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPVADKSRYAFKYVNGHPANTARNL 82 IG + A L D+ RW+ FDK+ARVASHS GVIELMP++D Y FKYVNGHPANTA+ L Sbjct: 23 IGGMLAYLHHDYLRWREFDKTARVASHSAQGVIELMPISDGRLYCFKYVNGHPANTAQGL 82 Query: 83 HTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPNARKMALIGNGAQSE 142 TV AFGVLADV SGYP LLSELT+ TALRTAATS++AA+ +AR ++R MA+IGNGAQSE Sbjct: 83 LTVTAFGVLADVASGYPRLLSELTLTTALRTAATSVLAARQMARSDSRVMAVIGNGAQSE 142 Query: 143 FQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVT 202 FQ LAFH +GIE + YDTDP ATA+L+ NL+ SGL + +S AEAV+G DI+TT+T Sbjct: 143 FQILAFHHQMGIEVVRLYDTDPAATARLMRNLRACSGLQLIPCASAAEAVRGADIVTTLT 202 Query: 203 ADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQL 262 ADK A II+P MLE GMHLNAVGGDCPGKTELHADVL+ ARV VE+ PQ+RIEGE+QQ+ Sbjct: 203 ADKRRACIISPAMLEAGMHLNAVGGDCPGKTELHADVLKAARVVVEFAPQSRIEGEVQQM 262 Query: 263 PADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGMGTKIDL 322 PADFPV +LW+VL G GR S ++VTVFDSVGFALED+ LRY+ +Q + R ++DL Sbjct: 263 PADFPVTELWQVLAGHAPGRSSAAEVTVFDSVGFALEDFAALRYLDEQVDAR-FTRQLDL 321 Query: 323 VPWVEDDPKDLF 334 +P DDPKDL+ Sbjct: 322 IP-AMDDPKDLY 332 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: 328 Number of extensions: 7 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: 347 Length adjustment: 29 Effective length of query: 321 Effective length of database: 318 Effective search space: 102078 Effective search space used: 102078 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