Taxon-GO Checks and Commentary - Part 3
ELECTRONIC ANNOTATIONS
MAPPING/ANNOTATION INCORRECT. 1 HAMAP:MF_00099 - an E.coli annotation to GO:sensory perception of chemical stimulus ; GO:0007606. Definition has been clarified to indicate the organism must have a neurological system. HAMAP contacted.
MAPPING/ANNOTATION INCORRECT. 1 HAMAP:MF_01314 - an E.coli annotation to GO:sensory perception; GO:0007600. Definition has been clarified to indicate the organism must have a neurological system. HAMAP contacted.
TAXON RULE INCORRECT? 1 HAMAP:MF_01631 - TAXON RULE INCORRECT? an E.coli annotation to GO:0000902 cell morphogenesis. Definition appears to include non-eukaryotes?
INTERPRO MAPPING/ANNOTATION CONCERN; taxon spread. 3 InterPro:IPR000098 > GO:0006955 "immune response" only_in NCBITaxon:131567 "cellular organisms" wide taxon spread as there are interleukin and interleukin-like proteins; both of which produce effects on the immune system.
TAXON RULE INCORRECT?. InterPro:IPR000149 > GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms"
TAXON RULE INCORRECT? InterPro:IPR000176 > GO:0006397 "mRNA processing" only_in NCBITaxon:131567 "cellular organisms" Viruses also carry out this process on its own mRNAs; see PMID:8612277 . Should this term be moved from underneath 'GO:0044237 cellular metabolic process'?
TAXON RULE INCORRECT? InterPro:IPR000176 > GO:0006370 "mRNA capping" only_in NCBITaxon:131567 "cellular organisms". Viruses also carry out this process on its own mRNAs; see PMID:8612277 . Should this term be moved from underneath 'GO:0044237 cellular metabolic process'?
NEW GO TERM REQUESTED (DNA EXCISION) 3 InterPro:IPR000305 GO:0006281 "DNA repair" only_in NCBITaxon:131567 "cellular organisms" Both viral and cellular organism proteins carry out DNA excision, however cellular organisms tend to do this during DNA repair, whereas viruses excise DNA to tranpose their DNA into the hosts. Would be good to have a simple 'DNA excision' term, without any indication of the end intent of the organism.
TAXON RULE INCORRECT? 3 InterPro:IPR000386 GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms"
TAXON RULE INCORRECT? InterPro:IPR000398 GO:0006231 "dTMP biosynthetic process" only_in NCBITaxon:131567 "cellular organisms". Well some viruses do encode proteins involved in pyrimidine biosynthesis; from PMID: 10026292 "Bacteriophage T4 thymidylate synthase (T4TS) interacts with a dNTP synthetase complex which contains several phage-coded proteins and at least two enzymes of the bacteriophage's natural host, E. coli (9). This organization of enzymes permits rapid DNA synthesis and thus maintains very high rates of DNA replication in infected cells (10). For example, T4TS and deoxycytidylate deaminase (T4CD) catalyze sequential reactions and have been shown to be functionally associated with one another (11). The advantage conferred by such a dNTP synthetase complex could explain why the bacteriophage T4 encodes most of its own enzymes for dNTP synthesis."
TAXON RULE INCORRECT? 215 InterPro:IPR000477 GO:0006278 "RNA-dependent DNA replication" only_in NCBITaxon:131567 "cellular organisms". Viral DNA-directed DNA polymerase, Heptitis protein P, which is a multifunctional enzyme that converts the viral RNA genome into dsDNA in viral cytoplasmic capsids. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3'- to 5'-endonucleasic mode., e.g. PMID: 17206754
INTERPRO DOMAIN NO LONGER EXISTS; MAPPING WILL DISAPPEAR. 1 InterPro:IPR000480 GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" ::
TAXON RULE INCORRECT? 18 InterPro:IPR000484
GO:0009772 "photosynthetic electron transport in photosystem II" only_in ID:0000000 "Viridiplantae or Bacteria"
GO:0030077 "plasma membrane light-harvesting complex" only_in JD:0000004 "Prokaryota" :: 2 InterPro:IPR000523
GO:0019684 "photosynthesis, light reaction" only_in ID:0000000 "Viridiplantae or Bacteria"
-- this mapping includes viral proteins, which infect marine cyanobacteria. See PMID: 15263091, from this paper:
Viral genes psbA and psbD from bacteriophage S-PM2 , encode the D1 and D2 core components of the photosynthetic reaction center PSII (photosystem II). D1 and D2 binds the pigments and cofactors necessary for primary photochemistry. "During active photosynthesis, D1 and, to a lesser extent, D2 turn over rapidly as a result of photodamage and are replaced by newly synthesized polypeptides in a repair cycle..[snip]..It is speculated that the expression of phage-encoded D1 and D2 proteins in infected cells would permit a continued PSII repair cycle to operate after host protein synthesis had been shut down, thus maintaining the photosynthetic activity of the cells and concomitant oxygen evolution and ensuring the provision of energy for extended viral replication."
Unfortunately the InterPro annotation prediction method cannot distinguish which of the proteins its matches originate from plants/cynobacteria/viruses - therefore creating a virus-specific term would not address this annotation issue.
THIS MAPPING NO LONGER EXISTS; ANNOTATIONS WILL DISAPPEAR. InterPro:IPR000551 GO:0005634 "nucleus" only_in NCBITaxon:2759 "Eukaryota"
TAXON RULE INCORRECT? ALL ANNOTATIONS REFER TO SEED STORAGE PROTEINS. 3 InterPro:IPR000617 GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda"
- TO DO LIST: *********
5 InterPro:IPR000692 GO:0005634 "nucleus" only_in NCBITaxon:2759 "Eukaryota" 32 InterPro:IPR000721 GO:0016032 "viral reproduction" only_in NCBITaxon:10239 "Viruses" 6 InterPro:IPR000814 GO:0005634 "nucleus" only_in NCBITaxon:2759 "Eukaryota" 3 InterPro:IPR000827 GO:0006955 "immune response" only_in NCBITaxon:131567 "cellular organisms" 10 InterPro:IPR000840 GO:0019028 "viral capsid" only_in NCBITaxon:10239 "Viruses" 68 InterPro:IPR000931
GO:0008037 "cell recognition" only_in NCBITaxon:131567 "cellular organisms" GO:0007155 "cell adhesion" only_in NCBITaxon:131567 "cellular organisms"
20 InterPro:IPR000939
GO:0008037 "cell recognition" only_in NCBITaxon:131567 "cellular organisms" GO:0007155 "cell adhesion" only_in NCBITaxon:131567 "cellular organisms"
68 InterPro:IPR000978
GO:0008037 "cell recognition" only_in NCBITaxon:131567 "cellular organisms" GO:0007155 "cell adhesion" only_in NCBITaxon:131567 "cellular organisms"
19 InterPro:IPR001098 GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms"
32 InterPro:IPR001177 34 InterPro:IPR001205 8 InterPro:IPR001339 193 InterPro:IPR001364 7 InterPro:IPR001476 3 InterPro:IPR001564 59 InterPro:IPR001584 12 InterPro:IPR001615 1 InterPro:IPR001631 2 InterPro:IPR001796 7 InterPro:IPR001811 20 InterPro:IPR001818 57 InterPro:IPR001889 6 InterPro:IPR002043 20 InterPro:IPR002050 1 InterPro:IPR002050|InterPro:IPR008981 15 InterPro:IPR002052 2 InterPro:IPR002054 12 InterPro:IPR002092 106 InterPro:IPR002104 5 InterPro:IPR002109 23 InterPro:IPR002166 15 InterPro:IPR002294 19 InterPro:IPR002298 6 InterPro:IPR002527 10 InterPro:IPR002552 6 InterPro:IPR002592 2 InterPro:IPR002693 2 InterPro:IPR002877 4 InterPro:IPR003084 11 InterPro:IPR003133 12 InterPro:IPR003176 4 InterPro:IPR003202 2 InterPro:IPR003299 18 InterPro:IPR003308 45 InterPro:IPR003322 3 InterPro:IPR003376 2 InterPro:IPR003469 18 InterPro:IPR003512 1 InterPro:IPR003573 1 InterPro:IPR003574 4 InterPro:IPR003626 3 InterPro:IPR003860 1 InterPro:IPR004099 8 InterPro:IPR004107 6 InterPro:IPR004189 9 InterPro:IPR004190 10 InterPro:IPR004196 12 InterPro:IPR004228 27 InterPro:IPR004295 5 InterPro:IPR004302 2 InterPro:IPR004519 5 InterPro:IPR004578 4 InterPro:IPR004753 10 InterPro:IPR004868 4 InterPro:IPR005005 2 InterPro:IPR005080 7 InterPro:IPR005166 6 InterPro:IPR005376 3 InterPro:IPR005515 12 InterPro:IPR006044 66 InterPro:IPR006045 15 InterPro:IPR006133 11 InterPro:IPR006134 9 InterPro:IPR006154 25 InterPro:IPR006172 9 InterPro:IPR006245 37 InterPro:IPR006246 33 InterPro:IPR006247 2 InterPro:IPR006290 2 InterPro:IPR006291 3 InterPro:IPR007142 2 InterPro:IPR007596 23 InterPro:IPR007694 6 InterPro:IPR007798 1 InterPro:IPR008018 12 InterPro:IPR008029 6 InterPro:IPR008047 3 InterPro:IPR008063 20 InterPro:IPR008180 2 InterPro:IPR008213 27 InterPro:IPR008916 2 InterPro:IPR008918 30 InterPro:IPR008919 4 InterPro:IPR008921 125 InterPro:IPR008980 74 InterPro:IPR008982 26 InterPro:IPR009013 1 InterPro:IPR009052 1 InterPro:IPR009084 10 InterPro:IPR010194 1 InterPro:IPR010311 192 InterPro:IPR010659 193 InterPro:IPR010661 25 InterPro:IPR010932 32 InterPro:IPR010999 2 InterPro:IPR011064 2 InterPro:IPR011134 2 InterPro:IPR011161 2 InterPro:IPR011162 5 InterPro:IPR011767 127 InterPro:IPR012128 2 InterPro:IPR012259 9 InterPro:IPR012310 15 InterPro:IPR012326 15 InterPro:IPR012327 11 InterPro:IPR012344 3 InterPro:IPR012352 1 InterPro:IPR012512 4 InterPro:IPR012884 5 InterPro:IPR012915 2 InterPro:IPR013150 1 InterPro:IPR013500 2 InterPro:IPR013590 106 InterPro:IPR013762 36 InterPro:IPR013827 3 InterPro:IPR013828 193 InterPro:IPR013829 15 InterPro:IPR014237 10 InterPro:IPR014416 2 InterPro:IPR014711 3 InterPro:IPR014831 4 InterPro:IPR015094 2 InterPro:IPR015233 1 InterPro:IPR015346 3 InterPro:IPR016075 1 InterPro:IPR016177 27 InterPro:IPR016197 29 InterPro:IPR016392 38 InterPro:IPR016396 8 InterPro:IPR016678 7 InterPro:IPR016848 1 InterPro:IPR017956 1 SP_KW:KW-0167 41 SP_KW:KW-0261 1 SP_KW:KW-0733 4 SP_KW:KW-0758 29 SP_KW:KW-0946 2 SP_SL:SL-0008 29 SP_SL:SL-0154