NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P27570 UniProt NPD GO	TOP2_CRIFA	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.70	-	nuc	0	Nucleus. Kinetoplast				1239
Q969P6 UniProt NPD GO	TOP1M_HUMAN	DNA topoisomerase I, mitochondrial precursor (EC 5.99.1.2) (TOP1mt)	0.70	-	mit	0	Mitochondrion		606387		601
P04050 UniProt NPD GO	RPB1_YEAST	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (RNA polymerase II subunit 1) (B220)	0.70	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS] mitochondrion [IDA]		2B8K	1733
Q9D483 UniProt NPD GO	RPC62_MOUSE	DNA-directed RNA polymerase III 62 kDa polypeptide (EC 2.7.7.6) (RNA polymerase C subunit 3) (RPC3) ...	0.70	-	cyt	0	Nucleus (Potential)				533
Q8HUG9 UniProt NPD GO	RPC1A_CHLRE	DNA-directed RNA polymerase beta' chain N-terminal subunit (EC 2.7.7.6) (PEP) (Plastid-encoded RNA p ...	0.70	-	nuc	0	Plastid; chloroplast				603
Q8QZY3 UniProt NPD GO	DPPA3_MOUSE	Developmental pluripotency-associated protein 3 (Compaction-associated protein 1) (Primordial germ c ...	0.70	-	nuc	0	Nucleus. Cytoplasm. Localized in the cytoplasm at the primary oocyte stage and in oocytes within mon ...	cytoplasm [IDA] female pronucleus [IDA] male pronucleus [IDA] nucleus [IDA]			150
Q90839 UniProt NPD GO	DKK3_CHICK	Dickkopf-related protein 3 precursor (Dkk-3) (Dickkopf-3) (Lens fiber protein CLFEST4)	0.70	-	mit	1 *	Secreted protein (Potential)				350
Q8N8Z6 UniProt NPD GO	DCBD1_HUMAN	Discoidin, CUB and LCCL domain-containing protein 1 precursor	0.70	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				715
Q62696 UniProt NPD GO	DLG1_RAT	Disks large homolog 1 (Synapse-associated protein 97) (SAP-97)	0.70	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Colocalizes with EPB41 at regions of intercel ...	basal plasma membrane [IDA] cell-cell adherens junction [ISS] plasma membrane [ISS] postsynaptic membrane [TAS] presynaptic membrane [IDA]		1ZOK	911
Q99615 UniProt NPD GO	DNJC7_HUMAN	DnaJ homolog subfamily C member 7 (Tetratricopeptide repeat protein 2) (TPR repeat protein 2)	0.70	-	cyt	0			601964		494
P50570 UniProt NPD GO	DYN2_HUMAN	Dynamin-2 (EC 3.6.5.5)	0.70	-	nuc	0	Cytoplasm. Microtubule-associated. Also found in the postsynaptic density of neuronal cells	cytoplasm [NAS] postsynaptic membrane [IDA]	602378		870
P58281 UniProt NPD GO	OPA1_MOUSE	Dynamin-like 120 kDa protein, mitochondrial precursor (Large GTP-binding protein) (LargeG)	0.70	-	mit	0	Mitochondrion	dendrite [IDA] mitochondrial crista [ISS] mitochondrial intermembrane space [IDA] mitochondrial outer membrane [ISS] mitochondrion [IDA]			960
O60313 UniProt NPD GO	OPA1_HUMAN	Dynamin-like 120 kDa protein, mitochondrial precursor (Optic atrophy 1 gene protein)	0.70	-	mit	0	Mitochondrion	dendrite [ISS] mitochondrial crista [IDA] mitochondrial intermembrane space [ISS] mitochondrial outer membrane [IDA]	605290		960
Q9Y048 UniProt NPD GO	DTN1_CAEEL	Dystrobrevin-1	0.70	-	nuc	0	Cytoplasm (By similarity)	dystrophin-associated glycoprotein complex [IDA]			590
P39940 UniProt NPD GO	RSP5_YEAST	E3 ubiquitin--protein ligase RSP5 (EC 6.3.2.-)	0.70	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytoplasm [IDA] endosome membrane [IDA] Golgi apparatus [IDA] mitochondrion [IDA] plasma membrane [IDA] ubiquitin ligase complex [IDA]			809
P22682 UniProt NPD GO	CBL_MOUSE	E3 ubiquitin-protein ligase CBL (EC 6.3.2.-) (Signal transduction protein CBL) (Proto-oncogene c-CBL ...	0.70	-	nuc	0	Cytoplasm				913
Q91ZD6 UniProt NPD GO	EAF2_MOUSE	ELL-associated factor 2 (Testosterone-regulated apoptosis inducer and tumor suppressor protein) (Ehr ...	0.70	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with ELL to nuclear speckles (By ...	nucleoplasm [IDA]			262
P42762 UniProt NPD GO	ERD1_ARATH	ERD1 protein, chloroplast precursor	0.70	+	mit	0	Plastid; chloroplast (Potential)				945
P11161 UniProt NPD GO	EGR2_HUMAN	Early growth response protein 2 (EGR-2) (Krox-20 protein) (AT591)	0.70	-	nuc	0	Nucleus		607678		476
Q2KID2 UniProt NPD GO	NTHL1_BOVIN	Endonuclease III-like protein 1 (EC 4.2.99.18)	0.70	-	mit	0	Mitochondrion (By similarity)				305
Q07872 UniProt NPD GO	ENT4_YEAST	Epsin-4	0.70	-	nuc	0		actin cortical patch [IPI]			247
Q40478 UniProt NPD GO	ERF5_TOBAC	Ethylene-responsive transcription factor 5 (Ethylene-responsive element-binding factor 5 homolog) (E ...	0.70	-	nuc	0	Nucleus				291
Q8R313 UniProt NPD GO	EXOC6_MOUSE	Exocyst complex component 6 (Exocyst complex component Sec15A) (Sec15-like 1)	0.70	-	cyt	0					802
Q4X0X6 UniProt NPD GO	EXO70_ASPFU	Exocyst complex protein exo70	0.70	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				628
Q5AZS0 UniProt NPD GO	EXO70_EMENI	Exocyst complex protein exo70	0.70	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				631
Q9W6K2 UniProt NPD GO	EXO1_XENLA	Exonuclease 1 (EC 3.1.-.-) (Exonuclease I)	0.70	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			734
Q92935 UniProt NPD GO	EXTL1_HUMAN	Exostosin-like 1 (EC 2.4.1.224) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylgluc ...	0.70	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...		601738		676
Q9HAV4 UniProt NPD GO	XPO5_HUMAN	Exportin-5 (Exp5) (Ran-binding protein 21)	0.70	+	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm		607845		1204
Q8NFZ0 UniProt NPD GO	FBX18_HUMAN	F-box only protein 18 (EC 3.6.1.-) (F-box DNA helicase 1)	0.70	-	nuc	0	Nucleus (Probable)		607222		1043
Q9D2Y6 UniProt NPD GO	FBX25_MOUSE	F-box only protein 25	0.70	+	cyt	0					357
Q8NEA4 UniProt NPD GO	FBX36_HUMAN	F-box only protein 36	0.70	-	cyt	0			609105		188
Q5R796 UniProt NPD GO	FBX36_PONPY	F-box only protein 36	0.70	-	cyt	0					188
Q9UH90 UniProt NPD GO	FBX40_HUMAN	F-box only protein 40 (Muscle disease-related protein)	0.70	+	nuc	0			609107		709
Q8NEE6 UniProt NPD GO	FXL13_HUMAN	F-box/LRR-repeat protein 13 (F-box and leucine-rich repeat protein 13)	0.70	-	nuc	0		cytoplasm [ISS]	609080		735
Q969H0 UniProt NPD GO	FBXW7_HUMAN	F-box/WD repeat protein 7 (F-box and WD-40 domain protein 7) (F-box protein FBX30) (hCdc4) (Archipel ...	0.70	-	nuc	0	Nucleus (By similarity)		606278		707
Q4P647 UniProt NPD GO	POB3_USTMA	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.70	-	nuc	0	Nucleus (By similarity)				558
Q04678 UniProt NPD GO	SSRP1_CHICK	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (Structure-sp ...	0.70	+	nuc	0	Nucleus (By similarity)				706
Q05344 UniProt NPD GO	SSRP1_DROME	FACT complex subunit Ssrp1 (Facilitates chromatin transcription complex subunit Ssrp1) (Recombinatio ...	0.70	+	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci	FACT complex [TAS]		1WXL	723
P97376 UniProt NPD GO	FRG1_MOUSE	FRG1 protein (FSHD region gene 1 protein)	0.70	-	nuc	0	Nucleus; nucleoplasm; Cajal body (By similarity). Nucleus; nucleoplasm; nuclear speckle (By similari ...				258
O15117 UniProt NPD GO	FYB_HUMAN	FYN-binding protein (FYN-T-binding protein) (FYB-120/130) (p120/p130) (SLP-76-associated phosphoprot ...	0.70	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]	602731	1RI9	783
Q9TV36 UniProt NPD GO	FBN1_PIG	Fibrillin-1 precursor	0.70	-	nuc	0					2871
P98177 UniProt NPD GO	FOXO4_HUMAN	Fork head domain transcription factor AFX1 (Forkhead box protein O4)	0.70	-	nuc	0	Cytoplasm. Nucleus. When phosphorylated, translocated from nucleus to cytoplasm. Dephosphorylation t ...	nucleus [TAS]	300033	1E17	505
Q92949 UniProt NPD GO	FOXJ1_HUMAN	Forkhead box protein J1 (Forkhead-related protein FKHL13) (Hepatocyte nuclear factor 3 forkhead homo ...	0.70	-	nuc	0	Nucleus	nucleus [TAS]	602291		421
P10158 UniProt NPD GO	FOSL1_RAT	Fos-related antigen 1 (FRA-1)	0.70	+	nuc	0	Nucleus				275
P32865 UniProt NPD GO	GPRK1_DROME	G protein-coupled receptor kinase 1 (EC 2.7.11.16)	0.70	-	cyt	0					700
P43250 UniProt NPD GO	GRK6_HUMAN	G protein-coupled receptor kinase 6 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK6)	0.70	+	cyt	0	Membrane; lipid-anchor		600869		576
O70293 UniProt NPD GO	GRK6_MOUSE	G protein-coupled receptor kinase 6 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK6)	0.70	+	cyt	0	Membrane; lipid-anchor				576
Q9Z238 UniProt NPD GO	CCNE2_MOUSE	G1/S-specific cyclin-E2	0.70	-	mit	0	Nucleus (By similarity)				404
P23770 UniProt NPD GO	GATA2_XENLA	GATA-binding factor 2 (GATA-2) (Transcription factor xGATA-2)	0.70	-	nuc	0	Nucleus				452
P91623 UniProt NPD GO	GATC_DROME	GATA-binding factor-C (Transcription factor GATA-C) (dGATA-C) (Protein grain)	0.70	-	nuc	0	Nucleus				486

You are viewing entries 13701 to 13750 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.