Taxon-GO Checks and Commentary - Part 3

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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