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
O43151 UniProt NPD GO	K0401_HUMAN	Protein KIAA0401 (Fragment)	0.58	-	nuc	0					344
P38271 UniProt NPD GO	OPY1_YEAST	Protein OPY1 (Overproduction-induced pheromone resistant yeast protein 1)	0.58	+	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			328
P39684 UniProt NPD GO	PES4_YEAST	Protein PES4 (DNA polymerase epsilon suppressor 4)	0.58	-	nuc	0	Nucleus (Potential)				611
Q12460 UniProt NPD GO	SIK1_YEAST	Protein SIK1 (Nucleolar protein NOP56)	0.58	+	nuc	0	Nucleus; nucleolus	box C/D snoRNP complex [IDA] nucleolus [IDA] nucleus [IDA] small nuclear ribonucleoprotein complex [TAS]			504
Q12600 UniProt NPD GO	SIS2_CANTR	Protein SIS2 (Halotolerance protein HAL3)	0.58	-	nuc	0	Or: Nucleus (By similarity). Or: Cytoplasm (By similarity)				531
Q6CQE5 UniProt NPD GO	TAR1_KLULA	Protein TAR1	0.58	-	nuc	0	Mitochondrion				109
P47980 UniProt NPD GO	TIS1_DROME	Protein TIS11 (dTIS11)	0.58	-	nuc	0	Nucleus (Potential)	nucleus [ISS]			436
Q8LL11 UniProt NPD GO	WUS_PETHY	Protein WUSCHEL (PhWUS) (Protein TERMINATOR)	0.58	-	nuc	0	Nucleus (By similarity)				307
P43446 UniProt NPD GO	WN10A_BRARE	Protein Wnt-10a precursor	0.58	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				442
Q70YC5 UniProt NPD GO	ZN365_HUMAN	Protein ZNF365	0.58	-	nuc	0			607818		407
Q5R9L2 UniProt NPD GO	ZN365_PONPY	Protein ZNF365	0.58	-	nuc	0					407
Q91712 UniProt NPD GO	ETS2B_XENLA	Protein c-ets-2-B (C-ets-2B)	0.58	+	nuc	0	Nucleus				472
O77027 UniProt NPD GO	CID_DROYA	Protein cubitus interruptus (Fragment)	0.58	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			403
P25932 UniProt NPD GO	ESCA_DROME	Protein escargot (Protein fleabag)	0.58	-	nuc	0	Nucleus	nucleus [IC]			470
P42287 UniProt NPD GO	GRK_DROME	Protein gurken precursor	0.58	-	exc	1	Membrane; single-pass type I membrane protein	endoplasmic reticulum [TAS] extracellular region [NAS]			295
O43593 UniProt NPD GO	HAIR_HUMAN	Protein hairless	0.58	-	nuc	0	Nucleus	nucleus [NAS]	602302		1189
P05709 UniProt NPD GO	SIM_DROME	Protein single-minded	0.58	-	nuc	0	Nucleus (Potential)	nucleus [IEP]			697
O16845 UniProt NPD GO	TLL_DROVI	Protein tailless	0.58	-	nuc	0	Nucleus (Potential)				450
Q9Y5F8 UniProt NPD GO	PCDGJ_HUMAN	Protocadherin gamma B7 precursor (PCDH-gamma-B7)	0.58	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606304		929
P59469 UniProt NPD GO	LBD34_ARATH	Putative LOB domain-containing protein 34	0.58	-	nuc	0					141
Q8LI34 UniProt NPD GO	MYST1_ORYSA	Putative MYST-like histone acetyltransferase 1 (EC 2.3.1.48)	0.58	-	cyt	0	Nucleus (Probable)				450
Q03770 UniProt NPD GO	SSY1_YEAST	Putative amino-acid permease SSY1	0.58	+	end	12	Membrane; multi-pass membrane protein (Probable)	plasma membrane [IDA]			852
Q03175 UniProt NPD GO	SRT1_YEAST	Putative dehydrodolichyl diphosphate synthetase (EC 2.5.1.-) (DEDOL-PP synthase)	0.58	-	cyt	1 *		lipid particle [IDA]			343
Q6RHR6 UniProt NPD GO	DMI1_MEDTR	Putative ion channel DMI-1 (Does not make infections protein 1)	0.58	+	end	3	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				882
Q9USL4 UniProt NPD GO	NGK7_SCHPO	Putative nucleoporin C18B5.07c	0.58	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear pore [TAS]			565
Q09691 UniProt NPD GO	RF1M_SCHPO	Putative peptide chain release factor 1, mitochondrial precursor	0.58	-	nuc	0					396
Q9SYM2 UniProt NPD GO	STHY_ARATH	Putative salt tolerance-like protein At1g78600	0.58	-	nuc	0	Nucleus (Potential)				299
Q04585 UniProt NPD GO	YDR09_YEAST	Putative sugar kinase YDR109C (EC 2.7.1.-)	0.58	-	nuc	0					715
Q05536 UniProt NPD GO	BOFH_BRAOB	Putative transcription factor BOFH	0.58	+	cyt	0	Nucleus (Probable)				415
Q01214 UniProt NPD GO	MTF1_RHIRA	Putative transcription factor MTF1	0.58	-	mit	3	Nucleus (Probable)	nucleus [IC]			353
Q12504 UniProt NPD GO	RMS1_YEAST	Putative transcription regulator RMS1	0.58	-	nuc	0	Nucleus	nucleus [IDA]			494
Q80TZ3 UniProt NPD GO	AUXI_MOUSE	Putative tyrosine-protein phosphatase auxilin (EC 3.1.3.48) (DnaJ homolog subfamily C member 6)	0.58	-	nuc	0					938
P40462 UniProt NPD GO	YIN7_YEAST	Putative zinc aminopeptidase YIL137C (EC 3.4.11.-)	0.58	-	cyt	0		cytoplasm [IDA]			946
Q9LJ44 UniProt NPD GO	COL12_ARATH	Putative zinc finger protein CONSTANS-LIKE 12	0.58	-	nuc	0	Nucleus (Potential)				337
P05625 UniProt NPD GO	RAF1_CHICK	RAF proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (RAF-1) (C-RAF) (MIL proto-oncogene ...	0.58	-	nuc	0					647
Q59E36 UniProt NPD GO	RCOR_DROME	REST corepressor (CoREST)	0.58	-	nuc	0	Nucleus				657
Q9VS46 UniProt NPD GO	RINT1_DROME	RINT1-like protein (DmRINT-1)	0.58	-	cyt	0					724
P40356 UniProt NPD GO	MED3_YEAST	RNA polymerase II mediator complex subunit 3 (Poly-glutamine domain protein 1) (Hyper-recombination ...	0.58	-	nuc	0	Nucleus	mediator complex [IDA]			397
Q14690 UniProt NPD GO	RRP5_HUMAN	RRP5 protein homolog (Programmed cell death protein 11)	0.58	+	nuc	0	Nucleus; nucleolus	nucleus [IDA]		1WI5	1871
Q9H2T7 UniProt NPD GO	RBP17_HUMAN	Ran-binding protein 17	0.58	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Nucleus; nuclear envelope; nuclear pore complex ...	nuclear pore [NAS]	606141		1088
P09959 UniProt NPD GO	SWI6_YEAST	Regulatory protein SWI6 (Cell-cycle box factor subunit SWI6) (Trans-acting activator of HO endonucle ...	0.58	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]		1SW6	803
P67854 UniProt NPD GO	ZEST_DROMA	Regulatory protein zeste (Fragment)	0.58	-	nuc	0	Nucleus (By similarity)				268
P67855 UniProt NPD GO	ZEST_DROSE	Regulatory protein zeste (Fragment)	0.58	-	nuc	0	Nucleus (By similarity)				268
P67856 UniProt NPD GO	ZEST_DROSI	Regulatory protein zeste (Fragment)	0.58	-	nuc	0	Nucleus (By similarity)				268
Q8R323 UniProt NPD GO	RFC3_MOUSE	Replication factor C subunit 3 (Replication factor C 38 kDa subunit) (RFC38) (Activator 1 38 kDa sub ...	0.58	-	nuc	0	Nucleus (Probable)				356
Q9PVY0 UniProt NPD GO	RX1_CHICK	Retinal homeobox protein Rx1 (cRax1)	0.58	+	nuc	0	Nucleus (By similarity)				228
P23443 UniProt NPD GO	KS6B1_HUMAN	Ribosomal protein S6 kinase beta-1 (EC 2.7.11.1) (Ribosomal protein S6 kinase I) (S6K) (S6K1) (70 kD ...	0.58	+	mit	0	Cytoplasm. Synaptosome (By similarity). Also found in the soluble synaptosomal fractions (By similar ...		608938		525
P16960 UniProt NPD GO	RYR1_PIG	Ryanodine receptor 1 (Skeletal muscle-type ryanodine receptor) (RyR1) (RYR-1) (Skeletal muscle calci ...	0.58	+	end	6	Membrane; multi-pass membrane protein (Potential)				5035
Q9UPN7 UniProt NPD GO	SAPS1_HUMAN	SAPS domain family member 1	0.58	-	nuc	0					881
Q9NVD3 UniProt NPD GO	SETD4_HUMAN	SET domain-containing protein 4	0.58	-	nuc	0					440

You are viewing entries 20401 to 20450 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.