Mercurial > repos > proteore > proteore_prot_features_3orga

changeset 6:21a88e16dfef draft

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planemo upload commit c9d70181a2b587e53dcc4b5885b74b625def6b8c-dirty
author proteore
date Mon, 16 Dec 2019 10:20:05 +0000
parents 3257978fe4f8
children ca8d8d379588
files add_protein_features_3orga.xml tool-data/uniprot_features_human.tsv tool-data/uniprot_features_mouse.tsv tool-data/uniprot_features_rat.tsv
diffstat 4 files changed, 16 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/add_protein_features_3orga.xml	Mon Dec 16 09:50:35 2019 +0000
+++ b/add_protein_features_3orga.xml	Mon Dec 16 10:20:05 2019 +0000
@@ -1,4 +1,4 @@
-<tool id="prot_features_3orga" name="Add protein features (3 orga)" version="2019.12.16.1">
+<tool id="prot_features_3orga" name="Add protein features (3 orga)" version="2019.12.16.2">
 <description>[UniProt]
 </description>
 <requirements>
@@ -68,22 +68,22 @@
   </param>
 
     <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="false">
-      <option value="Entry name" selected="false">Entry name (e.g. PLK3_MOUSE)</option>
-      <option value="Protein names" selected="false">Protein names (e.g. Serine/threonine-protein kinase PLK3 (EC 2.7.11.21))</option>
+      <option value="Entry.name" selected="false">Entry name (e.g. PLK3_MOUSE)</option>
+      <option value="Protein.names" selected="false">Protein names (e.g. Serine/threonine-protein kinase PLK3 (EC 2.7.11.21))</option>
       <option value="Length" selected="false">Sequence length</option>
       <option value="Mass" selected="false">Molecular Mass (Da)</option>
       <option value="Features" selected="false">Features (e.g. Chain (1); Transmembrane (4))</option>
       <option value="Intramembrane" selected="false">Intramembrane (e.g. INTRAMEM 104 116 Helical; Name=Pore helix 1. {ECO:0000250|UniProtKB:O00180})</option>
       <option value="Transmembrane" selected="false">Transmembrane (e.g. TRANSMEM 1 21 Helical. {ECO:0000255})</option>
-      <option value="Topological domain" selected="false">Topological domain (e.g. TOPO_DOM 33 64 Extracellular. {ECO:0000250|UniProtKB:P11169})</option>
+      <option value="Topological.domain" selected="false">Topological domain (e.g. TOPO_DOM 33 64 Extracellular. {ECO:0000250|UniProtKB:P11169})</option>
       <option value="Pathway" selected="false">Pathway (e.g. Steroid metabolism; cholesterol metabolism)</option>
-      <option value="Function [CC]" selected="false">Function (e.g. FUNCTION: Serine/threonine-protein kinase involved in cell cycle regulation)</option>
-      <option value="Post-translational modification" selected="false">Post-translational modification (e.g. PTM: Phosphorylation on Ser-300 or Ser-302 and on Ser-420)</option>
-      <option value="Subcellular location [CC]" selected="false">Subcellular location (e.g. SUBCELLULAR LOCATION: Secreted)</option>
-      <option value="Subunit structure [CC]" selected="false">Subunit structure (e.g. SUBUNIT: Homodimer. Heterodimerizes with YWHAE (By similarity))</option>
-      <option value="Domain [CC]" selected="false">Domain (e.g. DOMAIN: The Walker motif (consensus sequence G-X-X-G-X-G-K-[ST]-T) is expected to bind ATP)</option>
-      <option value="Tissue specificity" selected="false">Tissue specificity (e.g. TISSUE SPECIFICITY: Highest expression in fat cells {ECO:0000269|PubMed:7629182})</option>
-      <option value="Involvement in disease" selected="false">Involvement in disease (e.g. DISEASE: Note=Defects in Btk are the cause of murine X-linked immunodeficiency (XID))</option>     
+      <option value="Function.[CC]" selected="false">Function (e.g. FUNCTION: Serine/threonine-protein kinase involved in cell cycle regulation)</option>
+      <option value="Post-translational.modification" selected="false">Post-translational modification (e.g. PTM: Phosphorylation on Ser-300 or Ser-302 and on Ser-420)</option>
+      <option value="Subcellular.location.[CC]" selected="false">Subcellular location (e.g. SUBCELLULAR LOCATION: Secreted)</option>
+      <option value="Subunit.structure.[CC]" selected="false">Subunit structure (e.g. SUBUNIT: Homodimer. Heterodimerizes with YWHAE (By similarity))</option>
+      <option value="Domain.[CC]" selected="false">Domain (e.g. DOMAIN: The Walker motif (consensus sequence G-X-X-G-X-G-K-[ST]-T) is expected to bind ATP)</option>
+      <option value="Tissue.specificity" selected="false">Tissue specificity (e.g. TISSUE SPECIFICITY: Highest expression in fat cells {ECO:0000269|PubMed:7629182})</option>
+      <option value="Involvement.in.disease" selected="false">Involvement in disease (e.g. DISEASE: Note=Defects in Btk are the cause of murine X-linked immunodeficiency (XID))</option>     
     </param>
 
 </inputs>
--- a/tool-data/uniprot_features_human.tsv	Mon Dec 16 09:50:35 2019 +0000
+++ b/tool-data/uniprot_features_human.tsv	Mon Dec 16 10:20:05 2019 +0000
@@ -1,4 +1,4 @@
-Entry	Entry name	Protein names	Length	Mass	Features	Intramembrane	Transmembrane	Topological domain	Pathway	Function [CC]	Post-translational modification	Subcellular location [CC]	Subunit structure [CC]	Domain [CC]	Tissue specificity	Involvement in disease
+Entry	Entry.name	Protein.names	Length	Mass	Features	Intramembrane	Transmembrane	Topological.domain	Pathway	Function.[CC]	Post-translational.modification	Subcellular.location.[CC]	Subunit.structure.[CC]	Domain.[CC]	Tissue.specificity	Involvement.in.disease
 Q96IY4	CBPB2_HUMAN	Carboxypeptidase B2 (EC 3.4.17.20) (Carboxypeptidase U) (CPU) (Plasma carboxypeptidase B) (pCPB) (Thrombin-activable fibrinolysis inhibitor) (TAFI)	423	48,424	Active site (1); Alternative sequence (2); Beta strand (14); Binding site (2); Chain (1); Disulfide bond (3); Glycosylation (5); Helix (17); Metal binding (3); Natural variant (2); Propeptide (1); Region (3); Sequence conflict (1); Signal peptide (1); Site (1); Turn (7)					FUNCTION: Cleaves C-terminal arginine or lysine residues from biologically active peptides such as kinins or anaphylatoxins in the circulation thereby regulating their activities. Down-regulates fibrinolysis by removing C-terminal lysine residues from fibrin that has already been partially degraded by plasmin. {ECO:0000269|PubMed:10574983}.	PTM: N-glycosylated. N-glycan at Asn-108: Hex5HexNAc4. {ECO:0000269|PubMed:16335952, ECO:0000269|PubMed:16445295, ECO:0000269|PubMed:18559974, ECO:0000269|PubMed:19159218, ECO:0000269|PubMed:22171320}.	SUBCELLULAR LOCATION: Secreted.			TISSUE SPECIFICITY: Plasma; synthesized in the liver.	
 P22362	CCL1_HUMAN	C-C motif chemokine 1 (Small-inducible cytokine A1) (T lymphocyte-secreted protein I-309)	96	10,992	Beta strand (5); Chain (1); Disulfide bond (3); Glycosylation (1); Helix (3); Signal peptide (1)					FUNCTION: Cytokine that is chemotactic for monocytes but not for neutrophils. Binds to CCR8. {ECO:0000269|PubMed:1557400}.		SUBCELLULAR LOCATION: Secreted.	SUBUNIT: Monomer.			
 Q8NCR9	CLRN3_HUMAN	Clarin-3 (Transmembrane protein 12) (Usher syndrome type-3A-like protein 1)	226	25,321	Alternative sequence (2); Chain (1); Erroneous initiation (1); Glycosylation (1); Natural variant (2); Transmembrane (4)		TRANSMEM 8 28 Helical. {ECO:0000255}.; TRANSMEM 92 112 Helical. {ECO:0000255}.; TRANSMEM 129 149 Helical. {ECO:0000255}.; TRANSMEM 181 201 Helical. {ECO:0000255}.					SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.				
@@ -74447,4 +74447,4 @@
 H0YJ03	H0YJ03_HUMAN	Proteasome subunit alpha type-3 (Fragment)	83	9,716	Non-terminal residue (1)											
 R4GMT5	R4GMT5_HUMAN	Selenoprotein P	171	19,372	Chain (1); Domain (1); Signal peptide (1); Transmembrane (3)		TRANSMEM 45 64 Helical. {ECO:0000256|SAM:Phobius}.; TRANSMEM 93 111 Helical. {ECO:0000256|SAM:Phobius}.; TRANSMEM 123 143 Helical. {ECO:0000256|SAM:Phobius}.									
 F8WF70	F8WF70_HUMAN	Omega-amidase NIT2	92	10,199	Domain (1)											
-F8WE09	F8WE09_HUMAN	Lipase member H	47	5,550	Chain (1); Signal peptide (1)											
\ No newline at end of file
+F8WE09	F8WE09_HUMAN	Lipase member H	47	5,550	Chain (1); Signal peptide (1)											
--- a/tool-data/uniprot_features_mouse.tsv	Mon Dec 16 09:50:35 2019 +0000
+++ b/tool-data/uniprot_features_mouse.tsv	Mon Dec 16 10:20:05 2019 +0000
@@ -1,4 +1,4 @@
-Entry	Entry name	Protein names	Length	Mass	Features	Intramembrane	Transmembrane	Topological domain	Pathway	Function [CC]	Post-translational modification	Subcellular location [CC]	Subunit structure [CC]	Domain [CC]	Tissue specificity	Involvement in disease
+Entry	Entry.name	Protein.names	Length	Mass	Features	Intramembrane	Transmembrane	Topological.domain	Pathway	Function.[CC]	Post-translational.modification	Subcellular.location.[CC]	Subunit.structure.[CC]	Domain.[CC]	Tissue.specificity	Involvement.in.disease
 Q8K4K6	PANK1_MOUSE	Pantothenate kinase 1 (mPank) (mPank1) (EC 2.7.1.33) (Pantothenic acid kinase 1)	548	60,091	Alternative sequence (2); Binding site (3); Chain (1); Modified residue (2)				Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. 	FUNCTION: Plays a role in the physiological regulation of the intracellular CoA concentration.			SUBUNIT: Homodimer. {ECO:0000250}.	DOMAIN: The N-terminal extension, present in isoform 1 may be the regulatory domain.	TISSUE SPECIFICITY: Expressed in liver and kidney. Isoform 1 is highly expressed in heart and skeletal muscle, whereas isoform 2 is expressed exclusively in testis.	
 Q60967	PAPS1_MOUSE	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 (PAPS synthase 1) (PAPSS 1) (Sulfurylase kinase 1) (SK 1) (SK1) [Includes: Sulfate adenylyltransferase (EC 2.7.7.4) (ATP-sulfurylase) (Sulfate adenylate transferase) (SAT); Adenylyl-sulfate kinase (EC 2.7.1.25) (3'-phosphoadenosine-5'-phosphosulfate synthase) (APS kinase) (Adenosine-5'-phosphosulfate 3'-phosphotransferase) (Adenylylsulfate 3'-phosphotransferase)]	624	70,794	Binding site (5); Chain (1); Modified residue (2); Nucleotide binding (3); Region (6)				Sulfur metabolism; sulfate assimilation. 	FUNCTION: Bifunctional enzyme with both ATP sulfurylase and APS kinase activity, which mediates two steps in the sulfate activation pathway. The first step is the transfer of a sulfate group to ATP to yield adenosine 5'-phosphosulfate (APS), and the second step is the transfer of a phosphate group from ATP to APS yielding 3'-phosphoadenylylsulfate (PAPS: activated sulfate donor used by sulfotransferase). In mammals, PAPS is the sole source of sulfate; APS appears to be only an intermediate in the sulfate-activation pathway (PubMed:7493984). Required for normal biosynthesis of sulfated L-selectin ligands in endothelial cells (By similarity). {ECO:0000250|UniProtKB:O43252, ECO:0000269|PubMed:7493984}.			SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:O43252}.		TISSUE SPECIFICITY: Expressed in the neonatal brain and in cartilage. {ECO:0000269|PubMed:7493984}.	
 Q9DCU0	PAQR5_MOUSE	Membrane progestin receptor gamma (mPR gamma) (Membrane progesterone P4 receptor gamma) (Membrane progesterone receptor gamma) (Progesterone and adipoQ receptor family member 5) (Progestin and adipoQ receptor family member 5) (Progestin and adipoQ receptor family member V)	330	38,151	Chain (1); Erroneous initiation (1); Sequence caution (1); Topological domain (8); Transmembrane (7)		TRANSMEM 52 72 Helical; Name=1. {ECO:0000255}.; TRANSMEM 82 101 Helical; Name=2. {ECO:0000255}.; TRANSMEM 114 134 Helical; Name=3. {ECO:0000255}.; TRANSMEM 142 162 Helical; Name=4. {ECO:0000255}.; TRANSMEM 187 207 Helical; Name=5. {ECO:0000255}.; TRANSMEM 254 274 Helical; Name=6. {ECO:0000255}.; TRANSMEM 295 315 Helical; Name=7. {ECO:0000255}.	TOPO_DOM 1 51 Cytoplasmic. {ECO:0000255}.; TOPO_DOM 73 81 Extracellular. {ECO:0000255}.; TOPO_DOM 102 113 Cytoplasmic. {ECO:0000255}.; TOPO_DOM 135 141 Extracellular. {ECO:0000255}.; TOPO_DOM 163 186 Cytoplasmic. {ECO:0000255}.; TOPO_DOM 208 253 Extracellular. {ECO:0000255}.; TOPO_DOM 275 294 Cytoplasmic. {ECO:0000255}.; TOPO_DOM 316 330 Extracellular. {ECO:0000255}.		FUNCTION: Plasma membrane progesterone (P4) receptor coupled to G proteins. Seems to act through a G(i) mediated pathway. May be involved in oocyte maturation. {ECO:0000250|UniProtKB:Q9NXK6}.		SUBCELLULAR LOCATION: Cell membrane {ECO:0000250|UniProtKB:Q9NXK6}; Multi-pass membrane protein {ECO:0000255}.				
--- a/tool-data/uniprot_features_rat.tsv	Mon Dec 16 09:50:35 2019 +0000
+++ b/tool-data/uniprot_features_rat.tsv	Mon Dec 16 10:20:05 2019 +0000
@@ -1,4 +1,4 @@
-Entry	Entry name	Protein names	Length	Mass	Features	Intramembrane	Transmembrane	Topological domain	Pathway	Function [CC]	Post-translational modification	Subcellular location [CC]	Subunit structure [CC]	Domain [CC]	Tissue specificity	Involvement in disease
+Entry	Entry.name	Protein.names	Length	Mass	Features	Intramembrane	Transmembrane	Topological.domain	Pathway	Function.[CC]	Post-translational.modification	Subcellular.location.[CC]	Subunit.structure.[CC]	Domain.[CC]	Tissue.specificity	Involvement.in.disease
 F1LN63	F1LN63_RAT	Toll-like receptor 3	905	103,015	Domain (1); Transmembrane (2)		TRANSMEM 7 24 Helical. {ECO:0000256|SAM:Phobius}.; TRANSMEM 705 726 Helical. {ECO:0000256|SAM:Phobius}.									
 G3V802	G3V802_RAT	Cyclin A2 (Cyclin A2, isoform CRA_b)	418	47,054	Compositional bias (1); Domain (1); Region (1)											
 F1M7X4	F1M7X4_RAT	Receptor protein-tyrosine kinase (EC 2.7.10.1)	1231	138,371	Active site (1); Binding site (1); Domain (1); Nucleotide binding (1); Region (1); Transmembrane (1)		TRANSMEM 575 598 Helical. {ECO:0000256|SAM:Phobius}.									
@@ -28119,4 +28119,4 @@
 A0A0S2LUU2	A0A0S2LUU2_MNPV	Protein E7	92	10,290	Motif (2); Region (1); Zinc finger (1)					FUNCTION: E7 protein has both transforming and trans-activating activities. {ECO:0000256|PIRNR:PIRNR003407}.; FUNCTION: Plays a role in viral genome replication by driving entry of quiescent cells into the cell cycle. Stimulation of progression from G1 to S phase allows the virus to efficiently use the cellular DNA replicating machinery to achieve viral genome replication. E7 protein has both transforming and trans-activating activities. Induces the disassembly of the E2F1 transcription factor from RB1, with subsequent transcriptional activation of E2F1-regulated S-phase genes. Interferes with host histone deacetylation mediated by HDAC1 and HDAC2, leading to transcription activation. Plays also a role in the inhibition of both antiviral and antiproliferative functions of host interferon alpha. Interaction with host TMEM173/STING impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta). {ECO:0000256|HAMAP-Rule:MF_04004, ECO:0000256|SAAS:SAAS00955501}.	PTM: Highly phosphorylated. {ECO:0000256|HAMAP-Rule:MF_04004}.	SUBCELLULAR LOCATION: Host cytoplasm {ECO:0000256|HAMAP-Rule:MF_04004}. Host nucleus {ECO:0000256|HAMAP-Rule:MF_04004, ECO:0000256|SAAS:SAAS00614351}. Note=Predominantly found in the host nucleus. {ECO:0000256|HAMAP-Rule:MF_04004}.	SUBUNIT: Homodimer. Homooligomer. Interacts with host RB1; this interaction induces dissociation of RB1-E2F1 complex thereby disrupting RB1 activity. Interacts with host EP300; this interaction represses EP300 transcriptional activity. Interacts with protein E2; this interaction inhibits E7 oncogenic activity. Interacts with host TMEM173/STING; this interaction impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta). {ECO:0000256|HAMAP-Rule:MF_04004}.			
 A0A0H4PK94	A0A0H4PK94_9POLY	Large T antigen	776	87,343	Compositional bias (4); DNA binding (1); Domain (3); Region (1)											
 A0A0S2LV84	A0A0S2LV84_MNPV	Replication protein E1 (EC 3.6.4.12) (ATP-dependent helicase E1)	600	68,697	Cross-link (1); Domain (1); Modified residue (2); Motif (2); Nucleotide binding (1); Region (3)					FUNCTION: ATP-dependent DNA helicase required for initiation of viral DNA replication. It forms a complex with the viral E2 protein. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins. During the initial step, a dimer of E1 interacts with a dimer of protein E2 leading to a complex that binds the viral origin of replication with high specificity. Then, a second dimer of E1 displaces the E2 dimer in an ATP-dependent manner to form the E1 tetramer. Following this, two E1 monomers are added to each half of the site, which results in the formation of two E1 trimers on the viral ori. Subsequently, two hexamers will be created. The double hexamer acts as a bi-directional helicase machinery and unwinds the viral DNA and then recruits the host DNA polymerase to start replication. {ECO:0000256|HAMAP-Rule:MF_04000, ECO:0000256|SAAS:SAAS01053033}.	PTM: Phosphorylated. {ECO:0000256|HAMAP-Rule:MF_04000}.; PTM: Sumoylated. {ECO:0000256|HAMAP-Rule:MF_04000}.	SUBCELLULAR LOCATION: Host nucleus {ECO:0000256|HAMAP-Rule:MF_04000, ECO:0000256|SAAS:SAAS01053029}.	SUBUNIT: Can form hexamers. Interacts with E2 protein; this interaction increases E1 DNA binding specificity. Interacts with host DNA polymerase subunit POLA2. Interacts with host single stranded DNA-binding protein RPA1. Interacts with host TOP1; this interaction stimulates the enzymatic activity of TOP1. {ECO:0000256|HAMAP-Rule:MF_04000, ECO:0000256|SAAS:SAAS01053038}.			
-A0A0S2LUM1	A0A0S2LUM1_MNPV	Protein E6	135	15,424	Zinc finger (2)					FUNCTION: Plays a major role in the induction and maintenance of cellular transformation. E6 associates with host UBE3A/E6-AP ubiquitin-protein ligase and modulates its activity. Protects host keratinocytes from apoptosis by mediating the degradation of host BAK1. May also inhibit host immune response. {ECO:0000256|HAMAP-Rule:MF_04006}.		SUBCELLULAR LOCATION: Host cytoplasm {ECO:0000256|HAMAP-Rule:MF_04006, ECO:0000256|RuleBase:RU363123}. Host nucleus {ECO:0000256|HAMAP-Rule:MF_04006, ECO:0000256|RuleBase:RU363123, ECO:0000256|SAAS:SAAS01013177}.	SUBUNIT: Forms homodimers. Interacts with ubiquitin-protein ligase UBE3A/E6-AP; this interaction stimulates UBE3A ubiquitin activity. Interacts with host BAK1. {ECO:0000256|HAMAP-Rule:MF_04006}.			
\ No newline at end of file
+A0A0S2LUM1	A0A0S2LUM1_MNPV	Protein E6	135	15,424	Zinc finger (2)					FUNCTION: Plays a major role in the induction and maintenance of cellular transformation. E6 associates with host UBE3A/E6-AP ubiquitin-protein ligase and modulates its activity. Protects host keratinocytes from apoptosis by mediating the degradation of host BAK1. May also inhibit host immune response. {ECO:0000256|HAMAP-Rule:MF_04006}.		SUBCELLULAR LOCATION: Host cytoplasm {ECO:0000256|HAMAP-Rule:MF_04006, ECO:0000256|RuleBase:RU363123}. Host nucleus {ECO:0000256|HAMAP-Rule:MF_04006, ECO:0000256|RuleBase:RU363123, ECO:0000256|SAAS:SAAS01013177}.	SUBUNIT: Forms homodimers. Interacts with ubiquitin-protein ligase UBE3A/E6-AP; this interaction stimulates UBE3A ubiquitin activity. Interacts with host BAK1. {ECO:0000256|HAMAP-Rule:MF_04006}.