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
Q5R4R7 UniProt NPD GO	K1045_PONPY	Protein KIAA1045 homolog	0.59	-	nuc	0					400
P53185 UniProt NPD GO	MTC2_YEAST	Protein MTC2	0.59	-	nuc	0	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			909
P40091 UniProt NPD GO	PEA2_YEAST	Protein PEA2 (Protein PPF2)	0.59	-	nuc	0		actin cap [IDA] polarisome [TAS]			420
P32522 UniProt NPD GO	PT309_YEAST	Protein PET309, mitochondrial precursor	0.59	-	pox	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to membrane [IDA] mitochondrial inner membrane [IDA]			965
P16146 UniProt NPD GO	PZ02_LUPPO	Protein PPLZ02	0.59	-	nuc	0	Nucleus (Probable)				164
P25339 UniProt NPD GO	PUF4_YEAST	Protein PUF4	0.59	-	nuc	0		cytoplasm [IDA]			888
P53438 UniProt NPD GO	SOK2_YEAST	Protein SOK2	0.59	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			785
Q9QYS1 UniProt NPD GO	WNT16_MOUSE	Protein Wnt-16 precursor	0.59	-	exc	0	Secreted protein; extracellular space; extracellular matrix				364
Q8BG89 UniProt NPD GO	ZN365_MOUSE	Protein ZNF365 (Su48)	0.59	-	nuc	0					408
Q9QY17 UniProt NPD GO	PACN2_RAT	Protein kinase C and casein kinase substrate in neurons 2 protein (Synaptic dynamin-associated prote ...	0.59	-	nuc	0	Cytoplasmic vesicle. Vesicle-like cytoplasmic distribution				488
Q99MC0 UniProt NPD GO	PP14A_RAT	Protein phosphatase 1 regulatory subunit 14A (17 kDa PKC-potentiated inhibitory protein of PP1) (CPI ...	0.59	-	mit	0	Cytoplasm (By similarity)				147
Q8TAE6 UniProt NPD GO	PP14C_HUMAN	Protein phosphatase 1 regulatory subunit 14C (PKC-potentiated PP1 inhibitory protein) (Kinase-enhanc ...	0.59	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				165
Q8TE77 UniProt NPD GO	SSH3_HUMAN	Protein phosphatase Slingshot homolog 3 (EC 3.1.3.48) (EC 3.1.3.16) (SSH-3L) (hSSH-3L)	0.59	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		606780		659
Q45FX5 UniProt NPD GO	VAV_CAEEL	Protein vav-1	0.59	-	mit	0					1007
Q9R0C8 UniProt NPD GO	VAV3_MOUSE	Protein vav-3	0.59	-	cyt	0		cytoplasm [IDA] plasma membrane [IDA]			847
Q9Y5F7 UniProt NPD GO	PCDGL_HUMAN	Protocadherin gamma C4 precursor (PCDH-gamma-C4)	0.59	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)		606305		938
Q5DRA3 UniProt NPD GO	PCDGL_PANTR	Protocadherin gamma C4 precursor (PCDH-gamma-C4)	0.59	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)				938
Q9Y2W3 UniProt NPD GO	S45A1_HUMAN	Proton-associated sugar transporter A (PAST-A) (Solute carrier family 45 member 1) (Deleted in neuro ...	0.59	-	end	11	Membrane; multi-pass membrane protein (Potential)		605763		782
P34261 UniProt NPD GO	YKAA_CAEEL	Putative amino-acid permease B0303.11	0.59	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				903
Q4I1Q6 UniProt NPD GO	CRYD_GIBZE	Putative cryptochrome DASH	0.59	+	nuc	0					678
Q9XIF0 UniProt NPD GO	DRL13_ARATH	Putative disease resistance protein At1g59780	0.59	-	cyt	0					906
O14094 UniProt NPD GO	PPX1_SCHPO	Putative exopolyphosphatase (EC 3.6.1.11) (ExopolyPase) (Metaphosphatase)	0.59	-	cyt	0					384
Q9FX97 UniProt NPD GO	FUT12_ARATH	Putative fucosyltransferase-like protein (FucTB) (FucT2) (AtFUT12)	0.59	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				513
Q5H8A5 UniProt NPD GO	POLLU_LOTJA	Putative ion channel POLLUX, chloroplast precursor	0.59	+	end	3	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				917
Q6L400 UniProt NPD GO	R1B16_SOLDE	Putative late blight resistance protein homolog R1B-16	0.59	-	cyt	0	Cytoplasm (By similarity)				1284
Q58DP0 UniProt NPD GO	WBS22_BOVIN	Putative methyltransferase WBSCR22 (EC 2.1.1.-) (Williams-Beuren syndrome chromosome region 22 prote ...	0.59	+	nuc	0	Nucleus (Potential)				281
O43709 UniProt NPD GO	WBS22_HUMAN	Putative methyltransferase WBSCR22 (EC 2.1.1.-) (Williams-Beuren syndrome chromosome region 22 prote ...	0.59	-	nuc	0	Nucleus (Potential)		194050		281
Q8S403 UniProt NPD GO	PHO1_ARATH	Putative phosphate transporter 1	0.59	-	end	6	Membrane; multi-pass membrane protein (Probable)				782
Q10309 UniProt NPD GO	YD56_SCHPO	Putative phospholipid-transporting ATPase C6C3.06c (EC 3.6.3.1)	0.59	-	end	10	Membrane; multi-pass membrane protein				1033
Q9ZPV9 UniProt NPD GO	SY112_ARATH	Putative syntaxin-112 (AtSYP112)	0.59	-	cyt	0					285
Q20574 UniProt NPD GO	STX2_CAEEL	Putative syntaxin-2	0.59	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)	integral to membrane [ISS]			299
Q04526 UniProt NPD GO	YMI3_YEAST	Putative uncharacterized protein YML083C	0.59	-	nuc	0					418
Q5B2E9 UniProt NPD GO	P2OX_EMENI	Pyranose 2-oxidase (EC 1.1.3.10) (P2Ox) (Pyranose oxidase) (PROD) (POD) (POx) (Pyranose:oxygen 2-oxi ...	0.59	-	nuc	0					591
Q6NUQ1 UniProt NPD GO	RINT1_HUMAN	RAD50-interacting protein 1 (RAD50 interactor 1) (Protein RINT-1) (HsRINT-1)	0.59	-	cyt	0	Cytoplasm (Probable). Endoplasmic reticulum. The SNARE complex localizes to the endoplasmic reticulu ...	endoplasmic reticulum [IDA]	610089		792
Q5NVC7 UniProt NPD GO	RNF34_PONPY	RING finger protein 34	0.59	-	exc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Intracellular membrane; peripheral membrane p ...				372
Q9P7E1 UniProt NPD GO	YOF7_SCHPO	RING finger protein P4H10.07 in chromosome II	0.59	-	nuc	0	Membrane				583
Q9LX93 UniProt NPD GO	ATL5F_ARATH	RING-H2 finger protein ATL5F	0.59	-	exc	1 *					301
Q5B367 UniProt NPD GO	REXO3_EMENI	RNA exonuclease 3 (EC 3.1.-.-)	0.59	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				619
P53114 UniProt NPD GO	MED5_YEAST	RNA polymerase II mediator complex subunit 5 (Negative regulator of URS2 protein 1)	0.59	-	vac	0	Nucleus	nucleus [IDA]			1132
P33308 UniProt NPD GO	MED9_YEAST	RNA polymerase II mediator complex subunit 9 (Chromosome segregation protein 2)	0.59	-	nuc	0	Nucleus	mediator complex [IDA]			149
Q6BL86 UniProt NPD GO	TFB4_DEBHA	RNA polymerase II transcription factor B subunit 4 (RNA polymerase II transcription factor B p34 sub ...	0.59	+	nuc	0	Nucleus (By similarity)				387
O75319 UniProt NPD GO	DUS11_HUMAN	RNA/RNP complex-1-interacting phosphatase (EC 3.1.3.-) (Phosphatase that interacts with RNA/RNP comp ...	0.59	-	nuc	0	Nucleus	nucleus [TAS]	603092		330
P06494 UniProt NPD GO	ERBB2_RAT	Receptor tyrosine-protein kinase erbB-2 precursor (EC 2.7.10.1) (p185erbB2) (C-erbB-2) (NEU proto-on ...	0.59	-	exc	2	Membrane; single-pass type I membrane protein			1N8Y	1257
Q92932 UniProt NPD GO	PTPR2_HUMAN	Receptor-type tyrosine-protein phosphatase N2 precursor (EC 3.1.3.48) (R-PTP-N2) (Islet cell autoant ...	0.59	-	end	0	Membrane; single-pass type I membrane protein (Probable)	integral to plasma membrane [TAS]	601698		1015
P28828 UniProt NPD GO	PTPRM_MOUSE	Receptor-type tyrosine-protein phosphatase mu precursor (EC 3.1.3.48) (Protein-tyrosine phosphatase ...	0.59	-	end	1	Membrane; single-pass type I membrane protein				1452
O08674 UniProt NPD GO	RBPSL_MOUSE	Recombining binding protein suppressor of hairless-like protein (Transcription factor RBP-L)	0.59	-	cyt	0	Nucleus				515
P39531 UniProt NPD GO	RCY1_YEAST	Recyclin-1	0.59	-	nuc	0	Localized to sites of polarized growth	endosome [IDA] Golgi apparatus [IDA] site of polarized growth [IDA]			840
Q60841 UniProt NPD GO	RELN_MOUSE	Reelin precursor (EC 3.4.21.-) (Reeler protein)	0.59	-	cyt	1 *	Secreted protein	cytoplasm [IDA] extracellular matrix (sensu Metazoa) [TAS] extracellular space [IDA]			3461
P25171 UniProt NPD GO	RCC1_DROME	Regulator of chromosome condensation (Chromatin-binding protein Bj1)	0.59	-	nuc	0	Nucleus. Cytoplasm. Becomes dispersed throughout the cytoplasm during mitosis. Is associated with ch ...	nucleus [IDA]			547
P12959 UniProt NPD GO	OP2_MAIZE	Regulatory protein opaque-2	0.59	-	nuc	0	Nucleus				453

You are viewing entries 19801 to 19850 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.