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
Q8R4A3 UniProt NPD GO	DACT1_MOUSE	Dapper homolog 1 (MDpr1) (Frodo) (Thymus-expressed novel gene 3 protein)	0.81	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				778
Q9Z2K0 UniProt NPD GO	DEDD_RAT	Death effector domain-containing protein (Death effector domain-containing testicular molecule)	0.81	-	nuc	0	Cytoplasm (By similarity). Translocated to the nucleus during CD95-mediated apoptosis where it is lo ...	cytoplasm [ISS] nucleolus [ISS]			318
Q8BUR4 UniProt NPD GO	DOCK1_MOUSE	Dedicator of cytokinesis protein 1 (180 kDa protein downstream of CRK) (DOCK180) (Fragments)	0.81	+	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). Recruited to membranes via its interaction with ...				1027
Q8C147 UniProt NPD GO	DOCK8_MOUSE	Dedicator of cytokinesis protein 8	0.81	-	mit	0					1037
O82133 UniProt NPD GO	DRE2B_ARATH	Dehydration-responsive element-binding protein 2B (DREB2B protein)	0.81	-	nuc	0	Nucleus (Probable)				330
Q15700 UniProt NPD GO	DLG2_HUMAN	Discs large homolog 2 (Postsynaptic density protein PSD-93) (Channel-associated protein of synapse-1 ...	0.81	-	nuc	0	Membrane; lipid-anchor (By similarity). Concentrated in soma and postsynaptic density of a subset of ...	plasma membrane [TAS]	603583	2BYG	870
P07516 UniProt NPD GO	IPPD_BOVIN	Dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32)	0.81	-	nuc	0	Cytoplasm				202
Q5M7M7 UniProt NPD GO	STAU2_XENTR	Double-stranded RNA-binding protein Staufen homolog 2	0.81	-	nuc	0					624
P51400 UniProt NPD GO	RED1_RAT	Double-stranded RNA-specific editase 1 (EC 3.5.-.-) (dsRNA adenosine deaminase) (RNA-editing deamina ...	0.81	+	nuc	0		nucleolus [IMP] nucleoplasm [IMP]		2B7V	711
P59894 UniProt NPD GO	DCDC1_HUMAN	Doublecortin domain-containing protein 1	0.81	-	nuc	0			608062		354
Q23977 UniProt NPD GO	HEP_DROME	Dual specificity mitogen-activated protein kinase kinase hemipterous (EC 2.7.12.2) (MAPKK)	0.81	-	nuc	0					1178
O09112 UniProt NPD GO	DUS8_MOUSE	Dual specificity protein phosphatase 8 (EC 3.1.3.48) (EC 3.1.3.16) (Neuronal tyrosine threonine phos ...	0.81	-	nuc	0	Cytoplasm. Nucleus				663
Q09748 UniProt NPD GO	YB68_SCHPO	Dynamin-like protein C12C2.08	0.81	-	nuc	0	Cytoplasm (By similarity)				781
Q14204 UniProt NPD GO	DYHC_HUMAN	Dynein heavy chain, cytosolic (DYHC) (Cytoplasmic dynein heavy chain 1) (DHC1) (Dynein heavy chain 1 ...	0.81	-	nuc	0	Cytoplasm	cytoplasmic dynein complex [NAS]	600112		4646
Q12216 UniProt NPD GO	SIZ2_YEAST	E3 SUMO--protein ligase SIZ2 (EC 6.-.-.-) (SAP and Miz-finger domain-containing protein 2)	0.81	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			726
Q9VVI3 UniProt NPD GO	NEDD4_DROME	E3 ubiquitin-protein ligase Nedd-4 (EC 6.3.2.-) (DNedd4)	0.81	-	nuc	0	Cytoplasm	cytoplasm [IDA]		2EZ5	1007
Q9Z2U4 UniProt NPD GO	ELF4_MOUSE	ETS-related transcription factor Elf-4 (E74-like factor 4) (Myeloid Elf-1-like factor)	0.81	-	nuc	0	Nucleus (By similarity). Accumulation into PML nuclear bodies is mediated by PML (By similarity)	PML body [ISS]			655
P20105 UniProt NPD GO	E74EA_DROME	Ecdysone-induced protein 74EF isoform A (ETS-related protein E74A)	0.81	-	nuc	0	Nucleus				829
Q8K4Q6 UniProt NPD GO	NEIL1_MOUSE	Endonuclease VIII-like 1 (EC 3.2.2.-) (EC 4.2.99.18) (Nei-like 1) (DNA glycosylase/AP lyase Neil1) ( ...	0.81	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			388
Q9JHS1 UniProt NPD GO	EPAS1_RAT	Endothelial PAS domain-containing protein 1 (EPAS-1) (Hypoxia-inducible factor 2 alpha) (HIF-2 alpha ...	0.81	-	nuc	0	Nucleus (Potential)				874
P97481 UniProt NPD GO	EPAS1_MOUSE	Endothelial PAS domain-containing protein 1 (EPAS-1) (Hypoxia-inducible factor 2 alpha) (HIF-2 alpha ...	0.81	-	nuc	0	Nucleus (Potential)				874
Q867A9 UniProt NPD GO	EDN2_BOVIN	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2)	0.81	-	exc	0	Secreted protein				177
Q8BYZ7 UniProt NPD GO	ELMO3_MOUSE	Engulfment and cell motility protein 3	0.81	-	cyt	0	Cytoplasm (By similarity)				607
Q9XSB5 UniProt NPD GO	ESR2_BOVIN	Estrogen receptor beta (ER-beta)	0.81	+	nuc	0	Nucleus	nucleus [ISS]			527
O93511 UniProt NPD GO	ESR2_COTJA	Estrogen receptor beta (ER-beta)	0.81	+	nuc	0	Nucleus	nucleus [ISS]			472
P62509 UniProt NPD GO	ERR3_MOUSE	Estrogen-related receptor gamma (Estrogen receptor-related protein 3)	0.81	-	nuc	0	Nucleus (Potential)	nucleus [NAS]		1VJB	458
Q5RAM2 UniProt NPD GO	ERR3_PONPY	Estrogen-related receptor gamma (Estrogen receptor-related protein 3)	0.81	-	nuc	0	Nucleus (Potential)				435
P62510 UniProt NPD GO	ERR3_RAT	Estrogen-related receptor gamma (Estrogen receptor-related protein 3)	0.81	-	nuc	0	Nucleus (Potential)	nucleus [ISS]			458
P62508 UniProt NPD GO	ERR3_HUMAN	Estrogen-related receptor gamma (Estrogen receptor-related protein 3) (ERR gamma-2)	0.81	-	nuc	0	Nucleus (Potential)	nucleus [ISS]	602969	2EWP	458
P53695 UniProt NPD GO	EXO1_SCHPO	Exodeoxyribonuclease 1 (EC 3.1.-.-) (Exodeoxyribonuclease I) (Exonuclease I) (EXO I)	0.81	+	nuc	0	Nucleus (Potential)				571
Q5IGR8 UniProt NPD GO	EXT1A_BRARE	Exostosin-1a (EC 2.4.1.224) (EC 2.4.1.225) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylg ...	0.81	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	integral to endoplasmic reticulum membrane [ISS]			730
P15311 UniProt NPD GO	EZRI_HUMAN	Ezrin (p81) (Cytovillin) (Villin-2)	0.81	-	nuc	0	Membrane. Localization to the apical membrane of parietal cells depends on the interaction with MPP5 ...	actin filament [IDA] cortical cytoskeleton [TAS] microvillus [NAS]	123900	1NI2	585
O82491 UniProt NPD GO	SPT16_ARATH	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.81	+	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci				1074
Q9BXW9 UniProt NPD GO	FACD2_HUMAN	Fanconi anemia group D2 protein (Protein FACD2)	0.81	-	mit	0	Nucleus. Concentrates in nuclear foci during S phase and upon genotoxic stress		227650		1471
Q23949 UniProt NPD GO	TRSF_DROHY	Female-specific protein transformer	0.81	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Speckled subnuclear compartment (By similarit ...				201
O04407 UniProt NPD GO	NEED_PINRA	Floricaula/leafy-like protein FL1 (Protein NEEDLY)	0.81	-	nuc	0	Nucleus (Probable)				404
O93870 UniProt NPD GO	FCR1_CANAL	Fluconazole resistance protein 1	0.81	-	nuc	0	Nucleus (Probable)	nucleus [IC]			517
Q98937 UniProt NPD GO	FOXD1_CHICK	Forkhead box protein D1 (Brain factor 2) (HFH-BF-2) (CBF-2) (T-14-6)	0.81	-	nuc	0	Nucleus (Potential)				440
Q12778 UniProt NPD GO	FOXO1_HUMAN	Forkhead box protein O1A (Forkhead in rhabdomyosarcoma)	0.81	-	nuc	0	Cytoplasm. Nucleus. Shuttles between cytoplasm and nucleus		268220		655
O43524 UniProt NPD GO	FOXO3_HUMAN	Forkhead box protein O3A (Forkhead in rhabdomyosarcoma-like 1) (AF6q21 protein)	0.81	-	nuc	0	Cytoplasm; cytosol. Translocates to the nucleus upon oxidative stress	cytoplasm [TAS] nucleus [TAS]	602681		673
Q9H334 UniProt NPD GO	FOXP1_HUMAN	Forkhead box protein P1	0.81	-	nuc	0	Nucleus (Probable)		605515		677
Q8MJ99 UniProt NPD GO	FOXP2_GORGO	Forkhead box protein P2	0.81	-	nuc	0	Nucleus (Probable)				713
Q5QL03 UniProt NPD GO	FOXP2_HYLLA	Forkhead box protein P2	0.81	-	nuc	0	Nucleus (Probable)				713
Q8MJ97 UniProt NPD GO	FOXP2_MACMU	Forkhead box protein P2	0.81	-	nuc	0	Nucleus (Probable)				714
P58463 UniProt NPD GO	FOXP2_MOUSE	Forkhead box protein P2	0.81	-	nuc	0	Nucleus (Probable)				714
Q8HZ00 UniProt NPD GO	FOXP2_PANPA	Forkhead box protein P2	0.81	-	nuc	0	Nucleus (Probable)				716
Q8MJA0 UniProt NPD GO	FOXP2_PANTR	Forkhead box protein P2	0.81	-	nuc	0	Nucleus (Probable)				716
Q8MJ98 UniProt NPD GO	FOXP2_PONPY	Forkhead box protein P2	0.81	-	nuc	0	Nucleus (Probable)				714
O15409 UniProt NPD GO	FOXP2_HUMAN	Forkhead box protein P2 (CAG repeat protein 44) (Trinucleotide repeat-containing gene 10 protein)	0.81	-	nuc	0	Nucleus (Probable)		602081	2A07	715
P35905 UniProt NPD GO	FULI_ACHFU	Fulicin precursor [Contains: Fulicin; Fucilin gene-related peptide 1 (FGRP-1); Fucilin gene-related ...	0.81	-	exc	0					357

You are viewing entries 8301 to 8350 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.