::: {#tbl-annotation-report .cell tbl-cap='Full annotations' tbl-colwidths='[60,40]' hash='index_cache/html/tbl-annotation-report_c7037e429e58ec83c7c6c701f1b7953a'}

```{.r .cell-code}
library(kableExtra)

annotations.df <- read.csv("https://gannet.fish.washington.edu/Atumefaciens/20231109-mmag-trinotate-transcriptome/20231109.trinity_denovo.Trinity.fasta.trinotate_annotation_report.txt",
header = TRUE,
sep = "\t")

knitr::kable(head(annotations.df))
```

::: {.cell-output-display}
`````{=html}
<table>
 <thead>
  <tr>
   <th style="text-align:left;"> X.gene_id </th>
   <th style="text-align:left;"> transcript_id </th>
   <th style="text-align:left;"> sprot_Top_BLASTX_hit </th>
   <th style="text-align:left;"> RNAMMER </th>
   <th style="text-align:left;"> prot_id </th>
   <th style="text-align:left;"> prot_coords </th>
   <th style="text-align:left;"> sprot_Top_BLASTP_hit </th>
   <th style="text-align:left;"> Pfam </th>
   <th style="text-align:left;"> SignalP </th>
   <th style="text-align:left;"> TmHMM </th>
   <th style="text-align:left;"> eggnog </th>
   <th style="text-align:left;"> Kegg </th>
   <th style="text-align:left;"> gene_ontology_blast </th>
   <th style="text-align:left;"> gene_ontology_pfam </th>
   <th style="text-align:left;"> transcript </th>
   <th style="text-align:left;"> peptide </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1 </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i1 </td>
   <td style="text-align:left;"> sp|Q63089|S22A1_RAT^sp|Q63089|S22A1_RAT^Q:905-18,H:87-381^36.2%ID^E:1.09e-38^.^. </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i1.p1 </td>
   <td style="text-align:left;"> 908-3[-] </td>
   <td style="text-align:left;"> S22A1_RAT^S22A1_RAT^Q:2-297,H:87-381^36.156%ID^E:5.87e-43^RecName: Full=Solute carrier family 22 member 1;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus </td>
   <td style="text-align:left;"> PF00083.24^Sugar_tr^Sugar (and other) transporter^57-276^E:4.5e-21`PF07690.16^MFS_1^Major Facilitator Superfamily^61-278^E:7e-18 </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> ExpAA=119.03^PredHel=5^Topology=i59-81o91-109i116-138o148-170i177-196o </td>
   <td style="text-align:left;"> ENOG410XR5P^Major facilitator superfamily MFS_1 </td>
   <td style="text-align:left;"> KEGG:rno:24904`KO:K08198 </td>
   <td style="text-align:left;"> GO:0016323^cellular_component^basolateral plasma membrane`GO:0005887^cellular_component^integral component of plasma membrane`GO:0005277^molecular_function^acetylcholine transmembrane transporter activity`GO:0005330^molecular_function^dopamine:sodium symporter activity`GO:0042802^molecular_function^identical protein binding`GO:0008504^molecular_function^monoamine transmembrane transporter activity`GO:0005334^molecular_function^norepinephrine:sodium symporter activity`GO:0015101^molecular_function^organic cation transmembrane transporter activity`GO:0042803^molecular_function^protein homodimerization activity`GO:0015651^molecular_function^quaternary ammonium group transmembrane transporter activity`GO:0008513^molecular_function^secondary active organic cation transmembrane transporter activity`GO:0015872^biological_process^dopamine transport`GO:0006855^biological_process^drug transmembrane transport`GO:0048241^biological_process^epinephrine transport`GO:0010248^biological_process^establishment or maintenance of transmembrane electrochemical gradient`GO:0015844^biological_process^monoamine transport`GO:0015874^biological_process^norepinephrine transport`GO:0015695^biological_process^organic cation transport`GO:0051260^biological_process^protein homooligomerization`GO:0015697^biological_process^quaternary ammonium group transport </td>
   <td style="text-align:left;"> GO:0022857^molecular_function^transmembrane transporter activity`GO:0055085^biological_process^transmembrane transport`GO:0016021^cellular_component^integral component of membrane </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
  </tr>
  <tr>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1 </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i1 </td>
   <td style="text-align:left;"> sp|Q63089|S22A1_RAT^sp|Q63089|S22A1_RAT^Q:905-18,H:87-381^36.2%ID^E:1.09e-38^.^. </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i1.p2 </td>
   <td style="text-align:left;"> 810-1[-] </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
  </tr>
  <tr>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1 </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i4 </td>
   <td style="text-align:left;"> sp|Q9VIK2|CART_DROME^sp|Q9VIK2|CART_DROME^Q:1209-529,H:114-344^33.8%ID^E:2.21e-27^.^. </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i4.p1 </td>
   <td style="text-align:left;"> 1212-475[-] </td>
   <td style="text-align:left;"> CART_DROME^CART_DROME^Q:2-242,H:114-358^32.661%ID^E:6.98e-33^RecName: Full=Carcinine transporter {ECO:0000303|PubMed:26653853, ECO:0000303|PubMed:26713872};^Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora </td>
   <td style="text-align:left;"> PF00083.24^Sugar_tr^Sugar (and other) transporter^56-219^E:7.4e-19`PF07690.16^MFS_1^Major Facilitator Superfamily^61-209^E:1e-15 </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> ExpAA=106.03^PredHel=5^Topology=i59-81o91-109i116-138o148-170i177-196o </td>
   <td style="text-align:left;"> ENOG410XSRI^solute carrier family 22 </td>
   <td style="text-align:left;"> KEGG:dme:Dmel_CG9317 </td>
   <td style="text-align:left;"> GO:0043679^cellular_component^axon terminus`GO:0016021^cellular_component^integral component of membrane`GO:0005886^cellular_component^plasma membrane`GO:1905131^molecular_function^carcinine transmembrane transporter activity`GO:0005326^molecular_function^neurotransmitter transporter activity`GO:1905130^biological_process^carcinine import across plasma membrane`GO:0050908^biological_process^detection of light stimulus involved in visual perception`GO:0001504^biological_process^neurotransmitter uptake`GO:0046956^biological_process^positive phototaxis`GO:0007601^biological_process^visual perception </td>
   <td style="text-align:left;"> GO:0022857^molecular_function^transmembrane transporter activity`GO:0055085^biological_process^transmembrane transport`GO:0016021^cellular_component^integral component of membrane </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
  </tr>
  <tr>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1 </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i4 </td>
   <td style="text-align:left;"> sp|Q9VIK2|CART_DROME^sp|Q9VIK2|CART_DROME^Q:1209-529,H:114-344^33.8%ID^E:2.21e-27^.^. </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i4.p2 </td>
   <td style="text-align:left;"> 1114-494[-] </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
  </tr>
  <tr>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1 </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i4 </td>
   <td style="text-align:left;"> sp|Q9VIK2|CART_DROME^sp|Q9VIK2|CART_DROME^Q:1209-529,H:114-344^33.8%ID^E:2.21e-27^.^. </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g1_i4.p3 </td>
   <td style="text-align:left;"> 497-126[-] </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> ExpAA=41.12^PredHel=2^Topology=i13-35o104-122i </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
  </tr>
  <tr>
   <td style="text-align:left;"> TRINITY_DN8_c0_g2 </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g2_i1 </td>
   <td style="text-align:left;"> sp|Q6NY98|MCE1_DANRE^sp|Q6NY98|MCE1_DANRE^Q:665-84,H:7-198^57.7%ID^E:2.12e-77^.^. </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> TRINITY_DN8_c0_g2_i1.p1 </td>
   <td style="text-align:left;"> 707-3[-] </td>
   <td style="text-align:left;"> MCE1_MOUSE^MCE1_MOUSE^Q:14-203,H:6-193^56.842%ID^E:4.77e-75^RecName: Full=mRNA-capping enzyme;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus </td>
   <td style="text-align:left;"> PF00782.20^DSPc^Dual specificity phosphatase, catalytic domain^65-182^E:5.3e-10 </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> COG5226^Second step of mRNA capping. Transfer of the GMP moiety of GTP to the 5'-end of RNA via an enzyme-GMP covalent reaction intermediate (By similarity) </td>
   <td style="text-align:left;"> KEGG:mmu:24018`KO:K13917 </td>
   <td style="text-align:left;"> GO:0005634^cellular_component^nucleus`GO:0005525^molecular_function^GTP binding`GO:0004484^molecular_function^mRNA guanylyltransferase activity`GO:0004651^molecular_function^polynucleotide 5'-phosphatase activity`GO:0004725^molecular_function^protein tyrosine phosphatase activity`GO:0008138^molecular_function^protein tyrosine/serine/threonine phosphatase activity`GO:0008192^molecular_function^RNA guanylyltransferase activity`GO:0050355^molecular_function^triphosphatase activity`GO:0006370^biological_process^7-methylguanosine mRNA capping`GO:0006396^biological_process^RNA processing </td>
   <td style="text-align:left;"> GO:0008138^molecular_function^protein tyrosine/serine/threonine phosphatase activity`GO:0016311^biological_process^dephosphorylation </td>
   <td style="text-align:left;"> . </td>
   <td style="text-align:left;"> . </td>
  </tr>
</tbody>
</table>

`````
:::
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