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
P41223 UniProt NPD GO	G10_HUMAN	Protein G10 homolog (EDG-2)	0.51	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	603477		144
O70454 UniProt NPD GO	G10_RAT	Protein G10 homolog (EDG-2)	0.51	-	nuc	0	Nucleus (Potential)				144
Q9BPW8 UniProt NPD GO	NIPS1_HUMAN	Protein NipSnap1	0.51	-	mit	0		mitochondrion [ISS]	603249		284
Q5A4J4 UniProt NPD GO	PBN1_CANAL	Protein PBN1	0.51	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				489
P10355 UniProt NPD GO	PT122_YEAST	Protein PET122, mitochondrial precursor	0.51	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein	mitochondrial inner membrane [IDA]			254
Q07327 UniProt NPD GO	ROP_DROME	Protein ROP	0.51	-	cyt	0	Cytoplasm; cytosol (Probable). Membrane; peripheral membrane protein (Probable). Soluble or bound to ...	cytoplasm [NAS]			597
P45978 UniProt NPD GO	SCD6_YEAST	Protein SCD6	0.51	-	nuc	0		cytoplasm [IDA]			349
P22213 UniProt NPD GO	SLY1_YEAST	Protein SLY1 (Suppressor of loss of YPT1 protein 1)	0.51	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytoplasm [NAS] endoplasmic reticulum [IDA] ER to Golgi transport vesicle [IDA] Golgi apparatus [IDA] membrane [NAS]		1MQS	666
Q84PB7 UniProt NPD GO	THF1_ORYSA	Protein THYLAKOID FORMATION1, chloroplast precursor	0.51	-	mit	0	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein. Plastid; chloroplast ...				287
Q9SB92 UniProt NPD GO	WUS_ARATH	Protein WUSCHEL (AtWUS) (Plant growth activator 6)	0.51	-	nuc	0	Nucleus				292
P28090 UniProt NPD GO	WNT3_EVATR	Protein Wnt-3 (Fragment)	0.51	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				124
P31291 UniProt NPD GO	WNT8B_XENLA	Protein Wnt-8b precursor (XWnt-8b)	0.51	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				428
O42280 UniProt NPD GO	WNT9A_CHICK	Protein Wnt-9a precursor (Wnt-14)	0.51	-	exc	0	Secreted protein; extracellular space; extracellular matrix				354
P12428 UniProt NPD GO	BROWN_DROME	Protein brown	0.51	-	end	5	Membrane; multi-pass membrane protein				675
Q24292 UniProt NPD GO	DS_DROME	Protein dachsous precursor (Adherin)	0.51	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [ISS]			3503
Q4WID9 UniProt NPD GO	GRC3_ASPFU	Protein grc3	0.51	-	nuc	0	Nucleus (By similarity)				455
P41005 UniProt NPD GO	MES1_SCHPO	Protein mes1	0.51	-	nuc	0					101
Q91ZD1 UniProt NPD GO	OSR2_MOUSE	Protein odd-skipped-related 2	0.51	-	nuc	0					312
Q24118 UniProt NPD GO	PIGE_DROME	Protein pigeon (Protein linotte)	0.51	-	mit	0					915
Q9SFU0 UniProt NPD GO	SC24A_ARATH	Protein transport protein Sec24-like At3g07100	0.51	-	nuc	0					1038
Q9C0W8 UniProt NPD GO	TIP20_SCHPO	Protein transport protein tip20	0.51	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				678
Q27237 UniProt NPD GO	TID_DROME	Protein tumorous imaginal discs, mitochondrial precursor (Protein lethal(2)tumorous imaginal discs) ...	0.51	-	mit	0	Mitochondrion; mitochondrial outer membrane	mitochondrion [IDA]			520
P09615 UniProt NPD GO	WNTG_DROME	Protein wingless precursor (Protein Wnt-1) (dWnt-1) (Protein int-1) (dInt-1)	0.51	-	nuc	0	Secreted protein. Membrane; lipid-anchor. Palmitoylation converts wg into a membrane-anchored protei ...	cytoplasmic membrane-bound vesicle [NAS] extracellular region [TAS] lipid raft [IDA]			468
O88807 UniProt NPD GO	PADI4_RAT	Protein-arginine deiminase type-4 (EC 3.5.3.15) (Protein-arginine deiminase type IV) (Peptidylargini ...	0.51	-	cyt	0	Cytoplasmic granule (By similarity)				666
P02855 UniProt NPD GO	VCLA_PEA	Provicilin (Type A) (Fragment)	0.51	-	nuc	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				275
P16381 UniProt NPD GO	PL10_MOUSE	Putative ATP-dependent RNA helicase Pl10 (EC 3.6.1.-)	0.51	-	nuc	0					660
Q09965 UniProt NPD GO	YS96_CAEEL	Putative G-protein coupled receptor B0244.6	0.51	-	end	17	Membrane; multi-pass membrane protein (Potential)				982
O14470 UniProt NPD GO	YEPA_SCHPO	Putative chromatin regulator protein C23H3.10	0.51	-	nuc	0	Nucleus (By similarity)				503
Q9STE5 UniProt NPD GO	R13L2_ARATH	Putative disease resistance RPP13-like protein 2	0.51	-	cyt	0					847
Q9LQZ7 UniProt NPD GO	STHX_ARATH	Putative salt tolerance-like protein At1g75540	0.51	-	nuc	0	Nucleus (Potential)				331
Q9M9B9 UniProt NPD GO	ARR19_ARATH	Putative two-component response regulator ARR19	0.51	-	nuc	0	Nucleus				407
Q5VZQ5 UniProt NPD GO	CJ122_HUMAN	Putative uncharacterized protein C10orf122	0.51	-	nuc	0					186
Q96QF0 UniProt NPD GO	RAB3I_HUMAN	RAB3A-interacting protein (Rabin-3) (SSX2-interacting protein)	0.51	-	nuc	0	Cytoplasm. Nucleus. Predominantly cytoplasmic but a small proportion colocalizes with SSX2 in the nu ...	cytosol [IDA] nucleus [IDA]	608686		476
P09560 UniProt NPD GO	RAF1_XENLA	RAF proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (C-RAF)	0.51	-	nuc	0					638
O00237 UniProt NPD GO	RN103_HUMAN	RING finger protein 103 (Zinc finger protein 103 homolog) (Zfp-103) (KF-1) (hKF-1)	0.51	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		602507		685
P38823 UniProt NPD GO	YHR5_YEAST	RING finger protein YHR115C	0.51	-	nuc	0		cytoplasm [IDA]			416
Q9LY41 UniProt NPD GO	ATL3J_ARATH	RING-H2 finger protein ATL3J (RING-H2 finger protein ATL4) (RING-H2 finger protein RHX1a)	0.51	-	nuc	1 *					334
Q6CJB5 UniProt NPD GO	REXO3_KLULA	RNA exonuclease 3 (EC 3.1.-.-)	0.51	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				478
Q5EA36 UniProt NPD GO	RBM14_BOVIN	RNA-binding protein 14 (RNA-binding motif protein 14)	0.51	-	nuc	0	Nucleus (By similarity)				669
Q9CWZ3 UniProt NPD GO	RBM8A_MOUSE	RNA-binding protein 8A (RNA-binding motif protein 8A) (Ribonucleoprotein RBM8A)	0.51	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IDA]			174
Q9Y5S9 UniProt NPD GO	RBM8A_HUMAN	RNA-binding protein 8A (RNA-binding motif protein 8A) (Ribonucleoprotein RBM8A) (RNA-binding protein ...	0.51	+	cyt	0	Cytoplasm. Nucleus	cytoplasm [NAS] nucleus [NAS]	605313	1P27	174
Q9QXG2 UniProt NPD GO	RAE1_MOUSE	Rab proteins geranylgeranyltransferase component A 1 (Rab escort protein 1) (REP-1) (Choroideraemia ...	0.51	-	nuc	0					665
P37727 UniProt NPD GO	RAE1_RAT	Rab proteins geranylgeranyltransferase component A 1 (Rab escort protein 1) (REP-1) (Choroideraemia ...	0.51	-	nuc	0				1VG9	650
Q22720 UniProt NPD GO	GAP1_CAEEL	Ras GTPase-activating protein gap-1 (GTPase-activating protein 1)	0.51	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]			629
Q86WH2 UniProt NPD GO	RASF3_HUMAN	Ras association domain-containing protein 3	0.51	-	nuc	0	Cytoplasm. Localized to microtubules in vascular endothelial cells		607019		238
P70424 UniProt NPD GO	ERBB2_MOUSE	Receptor tyrosine-protein kinase erbB-2 precursor (EC 2.7.10.1) (p185erbB2) (C-erbB-2) (NEU proto-on ...	0.51	-	exc	2	Membrane; single-pass type I membrane protein	apical plasma membrane [IDA] cytoplasm [IDA] integral to membrane [NAS]			1256
Q9Y572 UniProt NPD GO	RIPK3_HUMAN	Receptor-interacting serine/threonine-protein kinase 3 (EC 2.7.11.1) (RIP-like protein kinase 3) (Re ...	0.51	-	nuc	0	Cytoplasm (Probable)		605817		518
Q13332 UniProt NPD GO	PTPRS_HUMAN	Receptor-type tyrosine-protein phosphatase S precursor (EC 3.1.3.48) (R-PTP-S) (Protein-tyrosine pho ...	0.51	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]	601576	2FH7	1948
Q63259 UniProt NPD GO	PTPRN_RAT	Receptor-type tyrosine-protein phosphatase-like N precursor (R-PTP-N) (105 kDa islet cell antigen) ( ...	0.51	-	end	1	Membrane; single-pass type I membrane protein				983
Q9JL25 UniProt NPD GO	RGS1_MOUSE	Regulator of G-protein signaling 1 (RGS1)	0.51	+	nuc	0		plasma membrane [TAS]			196

You are viewing entries 24551 to 24600 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.