Align Arginine deiminase; ADI; EC 3.5.3.6; Arginine dihydrolase; AD (uncharacterized)
to candidate Echvi_0116 Echvi_0116 Arginine deiminase
Query= curated2:O53088 (409 letters) >FitnessBrowser__Cola:Echvi_0116 Length = 405 Score = 257 bits (656), Expect = 5e-73 Identities = 154/410 (37%), Positives = 235/410 (57%), Gaps = 14/410 (3%) Query: 5 IHVNSEIGKLKTVLLKRPGKEVENITPDIMYRLLFDDIPYLPTIQKEHDQFAQTLRDN-G 63 + ++SE G LK VL+ RPGKE++ +TP LLF+D+PYL +Q+EHD F ++ G Sbjct: 3 LRIHSEFGTLKAVLMHRPGKEIDRLTPYNKELLLFEDVPYLEAMQQEHDYFTNIIKQTTG 62 Query: 64 VEVLYLENLAAEAIDAGDVKEAFLDKMLNESHIKSPQVQAALKDYLISMATLDMVEKIMA 123 V L L E + + L +M+ E+ + ++ + L ++T + ++A Sbjct: 63 ATVYSLHELLMETMS----DDGILFRMMEEA-LSFSRLSHFTESILGRLSTSECATALIA 117 Query: 124 GVRTNEIDIKSKALIDVSADDDYPFYMDPMPNLYFTRDPAASMGDGLTINKMTFEARQRE 183 G++ +E+ K L V D + F + P PNLYF RDP A G+ + M E RQRE Sbjct: 118 GIKVHELKKKISKLPMVDLMD-FAFVIPPCPNLYFQRDPIALTPGGVVFSSMKMEGRQRE 176 Query: 184 SMFMEVIMQHHPRFANQGAQVWRDRDHIDR--MEGGDELILSDKVLAIGISQRTSAQSIE 241 + + I ++HP F +Q Q++ H D +EGGD +++SDK +AIG S+RT ++I Sbjct: 177 ANVIRSIFENHPLFKDQVNQIYPIDGHKDPACIEGGDIIVISDKAVAIGNSERTDEKAIY 236 Query: 242 ELAKVLFANHSGFEKILAIKIPHKHAMMHLDTVFTMIDYDKFTIHPGIQGAGGMVDTYIL 301 +AK L A + E++ + +P + MHLDTVFT++D + +P A Y L Sbjct: 237 HVAKSLLAEGT-VERVYEVHLPQQRNFMHLDTVFTVLDENLVLTYPDAMEAVLQTSLYTL 295 Query: 302 EPGNNDEIKITHQTDLEKVLRDALE--VPELTLIPCGG-GDAVVAPREQWNDGSNTLAIA 358 + + D++ I +T L++ L LE +P L +I GG G+ A REQW DG+N AI Sbjct: 296 KSNDGDQVHIK-RTVLKESLLTVLEKEIPYLEIIHLGGNGNKDYALREQWFDGANVFAIG 354 Query: 359 PGVVVTYDRNYVSNENLRQYGIKVIEVPSSELSRGRGGPRCMSMPLVRRK 408 P V++Y RN +N LR G++V+++PSSELSRG GGPRCM+MPL R K Sbjct: 355 PRKVISYRRNKHTNRALRDMGVEVLDIPSSELSRGLGGPRCMTMPLSRSK 404 Lambda K H 0.319 0.136 0.392 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: 390 Number of extensions: 15 Number of successful extensions: 5 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: 409 Length of database: 405 Length adjustment: 31 Effective length of query: 378 Effective length of database: 374 Effective search space: 141372 Effective search space used: 141372 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 (21.7 bits) S2: 50 (23.9 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