Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate PP_4431 PP_4431 Ornithine cyclodeaminase 1
Query= SwissProt::Q59701 (356 letters) >FitnessBrowser__Putida:PP_4431 Length = 330 Score = 102 bits (255), Expect = 1e-26 Identities = 67/207 (32%), Positives = 111/207 (53%), Gaps = 10/207 (4%) Query: 109 LLSEMTILTALRTAATSALAAKYLARPNSKTMAIIGNGAQSEFQARAFRAILGIQKLRLF 168 LL + LTA+RTAA A+AA++LAR +S+ +A++G G Q+E Q +A + I+++R++ Sbjct: 104 LLLDNGYLTAVRTAAAGAVAARWLARQDSEEVALLGAGEQAELQLKALLLVRDIKRVRVW 163 Query: 169 DIDTSATRKCARNLTGP-GFDIVECGSVAEAVEGADVITTVTADKQFATILSDNHVGPGV 227 ++ ++ A L+ G + SV EA+ AD+ T T Q IL H+ PG+ Sbjct: 164 ARSSAKAQQLALQLSSLYGLEATAAESVDEAMSSADIAVTCTPSNQ--PILHRRHLRPGL 221 Query: 228 HINAVGGDCPGKTEISMEVLLRSDIFV-EYPPQTWIEGDIQQLPRT------HPVTELWQ 280 HI A+G D K E++ EV+ D +V + QT G++ EL Q Sbjct: 222 HITAMGADTEHKNEVAPEVIAAVDHYVADRVSQTATLGELHHAINAGVAQDLRVYAELGQ 281 Query: 281 VMTGEKTGRVGDRQITMFDSVGFAIED 307 V+ G++ GR+ +T+ D G ++D Sbjct: 282 VILGDRVGRLTPTDVTLCDLTGTGVQD 308 Lambda K H 0.320 0.137 0.405 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: 198 Number of extensions: 5 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: 356 Length of database: 330 Length adjustment: 29 Effective length of query: 327 Effective length of database: 301 Effective search space: 98427 Effective search space used: 98427 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