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
Q8CD91 UniProt NPD GO	SMOC2_MOUSE	SPARC-related modular calcium-binding protein 2 precursor (Secreted modular calcium-binding protein ...	0.85	-	exc	0	Secreted protein (Probable)				447
Q9UH99 UniProt NPD GO	UN84B_HUMAN	Sad1/unc-84-like protein 2 (Rab5-interacting protein) (Rab5IP)	0.85	-	nuc	1	Nucleus; nuclear membrane; single-pass membrane protein. Endosome; endosomal membrane; single-pass m ...	nuclear envelope [TAS]			717
Q15424 UniProt NPD GO	SAFB1_HUMAN	Scaffold attachment factor B (Scaffold attachment factor B1) (SAF-B) (HSP27 estrogen response elemen ...	0.85	-	nuc	0	Nucleus	nucleus [TAS]	602895		915
P59222 UniProt NPD GO	SREC2_MOUSE	Scavenger receptor class F member 2 precursor (Scavenger receptor expressed by endothelial cells 2 p ...	0.85	-	nuc	0	Membrane; single-pass type I membrane protein (Potential)				833
Q9W7J1 UniProt NPD GO	SE3AA_BRARE	Semaphorin-3aa precursor (Semaphorin-1A) (Semaphorin Z1A) (Sema-Z1A)	0.85	-	nuc	0	Secreted protein (By similarity)				860
P33144 UniProt NPD GO	BIMB_EMENI	Separin (EC 3.4.22.49) (Separase) (Cell division-associated protein bimB)	0.85	+	nuc	0	Nucleus				2067
Q9JI10 UniProt NPD GO	STK3_MOUSE	Serine/threonine-protein kinase 3 (EC 2.7.11.1) (STE20-like kinase MST2) (MST-2) (Mammalian STE20-li ...	0.85	-	nuc	0	Cytoplasm; the caspase-cleaved form cycles between nucleus and cytoplasm (By similarity)				497
Q9VXG8 UniProt NPD GO	ATR_DROME	Serine/threonine-protein kinase ATR (EC 2.7.11.1) (Ataxia telangiectasia and Rad3-related protein ho ...	0.85	+	nuc	0	Nucleus (Probable)				2517
Q9JKK8 UniProt NPD GO	ATR_MOUSE	Serine/threonine-protein kinase ATR (EC 2.7.11.1) (Ataxia telangiectasia and Rad3-related protein)	0.85	-	end	0	Nucleus (By similarity). Recruited to chromatin during S-phase. Redistributes to discrete nuclear fo ...	nucleus [TAS]			2635
Q62829 UniProt NPD GO	PAK3_RAT	Serine/threonine-protein kinase PAK 3 (EC 2.7.11.1) (p21-activated kinase 3) (PAK-3) (Beta-PAK) (p65 ...	0.85	-	nuc	0					544
O96013 UniProt NPD GO	PAK4_HUMAN	Serine/threonine-protein kinase PAK 4 (EC 2.7.11.1) (p21-activated kinase 4) (PAK-4)	0.85	-	nuc	0		Golgi apparatus [TAS]	605451	2CDZ	591
P38110 UniProt NPD GO	ATM_YEAST	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.85	-	cyt	0	Nucleus. Localizes to nuclear DNA repair foci in response to DNA double strand breaks	mitochondrion [IDA] nucleus [TAS]			2787
Q80X41 UniProt NPD GO	VRK1_MOUSE	Serine/threonine-protein kinase VRK1 (EC 2.7.11.1) (Vaccinia-related kinase 1) (Serine/threonine-pro ...	0.85	+	nuc	0	Nucleus. Dispersed throughout the cell but not located on mitotic spindle or chromatids during mitos ...	nucleus [IDA]			440
P50527 UniProt NPD GO	STE20_SCHPO	Serine/threonine-protein kinase shk1/pak1 (EC 2.7.11.1)	0.85	-	nuc	0	Cytoplasm. Localizes at cell ends, septum forming regions and at the mitotic spindle				658
P36389 UniProt NPD GO	SRY_HORSE	Sex-determining region Y protein (Testis-determining factor)	0.85	+	nuc	0	Nucleus				223
Q9QUQ5 UniProt NPD GO	TRPC4_MOUSE	Short transient receptor potential channel 4 (TrpC4) (Receptor-activated cation channel TRP4) (Capac ...	0.85	-	end	8	Membrane; multi-pass membrane protein (Probable)				974
Q9QX29 UniProt NPD GO	TRPC5_MOUSE	Short transient receptor potential channel 5 (TrpC5) (Transient receptor protein 5) (Mtrp5) (trp-rel ...	0.85	-	end	7	Membrane; multi-pass membrane protein (Probable)				975
P38687 UniProt NPD GO	SRP68_YEAST	Signal recognition particle subunit SRP68 (Signal recognition particle 68 kDa protein homolog)	0.85	-	nuc	0	Cytoplasm (By similarity). Nucleus	signal recognition particle (sensu Eukaryota) [IDA]			599
Q8MR31 UniProt NPD GO	SLIP1_DROME	Slo-interacting protein 1 (dSLIP1)	0.85	-	nuc	0					767
Q759T1 UniProt NPD GO	SNX41_ASHGO	Sorting nexin-41	0.85	+	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				603
Q9D5A0 UniProt NPD GO	SPESP_MOUSE	Sperm equatorial segment protein 1 precursor	0.85	-	exc	0	Acrosome (By similarity). Small proacrosomal granules (during the Golgi phase), enlarged acrosomal v ...				399
Q8WNZ2 UniProt NPD GO	HSP1_OTOHE	Sperm protamine P1	0.85	+	nuc	0	Nucleus (By similarity)				49
P42147 UniProt NPD GO	HSP1_PERGU	Sperm protamine P1	0.85	+	nuc	0	Nucleus				68
P42148 UniProt NPD GO	HSP1_PLAIN	Sperm protamine P1	0.85	+	nuc	0	Nucleus				61
Q5U2X2 UniProt NPD GO	SPAG1_RAT	Sperm-associated antigen 1 (Infertility-related sperm protein Spag-1) (HSD-3.8)	0.85	-	nuc	0	Cytoplasm (By similarity)				893
Q8VIJ6 UniProt NPD GO	SFPQ_MOUSE	Splicing factor, proline- and glutamine-rich (Polypyrimidine tract-binding protein-associated-splici ...	0.85	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity). Predominantly in nuclear matrix (By similarity ...				699
Q01443 UniProt NPD GO	SSP2_PLAYO	Sporozoite surface protein 2 precursor	0.85	-	exc	1	Cell membrane; single-pass membrane protein				827
Q5REG1 UniProt NPD GO	SART3_PONPY	Squamous cell carcinoma antigen recognized by T-cells 3 (SART-3)	0.85	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized in speckles (By similarity)				981
O75159 UniProt NPD GO	SOCS5_HUMAN	Suppressor of cytokine signaling 5 (SOCS-5) (Cytokine-inducible SH2-containing protein 5) (Cytokine- ...	0.85	-	nuc	0		cytoplasm [ISS]	607094		536
Q86YH2 UniProt NPD GO	SUHW2_HUMAN	Suppressor of hairy wing homolog 2 (5'OY11.1) (Zinc finger protein 632)	0.85	-	nuc	0	Nucleus (Potential)				543
Q8TDW5 UniProt NPD GO	SYTL5_HUMAN	Synaptotagmin-like protein 5	0.85	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				730
Q80T23 UniProt NPD GO	SYTL5_MOUSE	Synaptotagmin-like protein 5	0.85	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				753
P08921 UniProt NPD GO	CD2_RAT	T-cell surface antigen CD2 precursor (T-cell surface antigen T11/Leu-5) (LFA-2) (LFA-3 receptor) (OX ...	0.85	-	exc	1	Membrane; single-pass type I membrane protein	cytoplasm [IMP] extracellular space [IMP]		1T6W	344
Q68US1 UniProt NPD GO	TCP1L_PANTR	T-complex protein 10A homolog 2 (T-complex protein 10A-2) (TCP10A-2) (TCP10-like)	0.85	-	nuc	0					217
Q5ZM41 UniProt NPD GO	TEX10_CHICK	Testis-expressed sequence 10 protein homolog	0.85	+	nuc	0	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Nucleus; nucleolus (By simil ...				927
Q28571 UniProt NPD GO	THB1_SHEEP	Thyroid hormone receptor beta-1 (Fragment)	0.85	+	nuc	0	Nucleus				411
Q71F56 UniProt NPD GO	T240L_HUMAN	Thyroid hormone receptor-associated protein 2 (Thyroid hormone receptor-associated protein complex 2 ...	0.85	-	nuc	0	Nucleus (By similarity)		608808		2210
P03872 UniProt NPD GO	REP2_YEAST	Trans-acting factor C (REP2) (Protein charlie)	0.85	-	nuc	0					296
P56931 UniProt NPD GO	E2F2_MOUSE	Transcription factor E2F2 (E2F-2)	0.85	-	nuc	0	Nucleus	nucleus [IDA]			443
Q8CFK2 UniProt NPD GO	TF3B_MOUSE	Transcription factor IIIB 90 kDa subunit (TFIIIB90) (hTFIIIB90) (B-related factor 1) (BRF-1)	0.85	-	nuc	0	Nucleus (By similarity)				676
Q9S7L2 UniProt NPD GO	MYB98_ARATH	Transcription factor MYB98 (Myb-related protein 98) (AtMYB98)	0.85	-	nuc	0	Nucleus (By similarity)				427
P56693 UniProt NPD GO	SOX10_HUMAN	Transcription factor SOX-10	0.85	+	nuc	0	Cytoplasm. Nucleus		609136		466
P48430 UniProt NPD GO	SOX2_CHICK	Transcription factor SOX-2	0.85	+	nuc	0	Nucleus				315
P48431 UniProt NPD GO	SOX2_HUMAN	Transcription factor SOX-2	0.85	+	nuc	0	Nucleus	nucleus [NAS]	184429	1O4X	317
P54231 UniProt NPD GO	SOX2_SHEEP	Transcription factor SOX-2	0.85	+	nuc	0	Nucleus				320
Q6DGL6 UniProt NPD GO	SOX1A_BRARE	Transcription factor Sox-1a	0.85	+	nuc	0	Nucleus				336
Q6P0E1 UniProt NPD GO	SOX2_BRARE	Transcription factor Sox-2	0.85	+	nuc	0	Nucleus. Cytoplasm	transcription factor complex [IC]			315
O74252 UniProt NPD GO	STE12_EMENI	Transcription factor steA	0.85	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			692
Q10424 UniProt NPD GO	ZIP1_SCHPO	Transcription factor zip1	0.85	-	nuc	0	Nucleus (Probable)				330
Q9P3W1 UniProt NPD GO	T2EA_SCHPO	Transcription initiation factor IIE subunit alpha (TFIIE-alpha)	0.85	-	nuc	0	Nucleus (Probable)	transcription factor TFIIE complex [IDA]			448

You are viewing entries 6751 to 6800 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.