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
P40308 UniProt NPD GO	YM93_YEAST	Hypothetical 73.6 kDa protein in GLC8-PRE5 intergenic region	0.40	-	cyt	1	Membrane; multi-pass membrane protein (Potential)	lipid particle [IDA]			642
P53326 UniProt NPD GO	YG5L_YEAST	Hypothetical 81.2 kDa protein in MES1-FOL2 intergenic region	0.40	-	cyt	0		mitochondrial outer membrane [IDA] mitochondrion [IDA] plasma membrane [IDA]			701
P68941 UniProt NPD GO	YCF15_OENPI	Hypothetical 9.4 kDa protein ycf15 (ORF 80)	0.40	-	cyt	0	Plastid; chloroplast				80
P68942 UniProt NPD GO	YCF15_OENVI	Hypothetical 9.4 kDa protein ycf15 (ORF 80)	0.40	-	cyt	0	Plastid; chloroplast				80
P93310 UniProt NPD GO	M550_ARATH	Hypothetical mitochondrial protein AtMg00550 (ORF160)	0.40	-	cyt	0	Mitochondrion (Potential)				196
P92522 UniProt NPD GO	M850_ARATH	Hypothetical mitochondrial protein AtMg00850 (ORF107e)	0.40	-	nuc	0	Mitochondrion (Potential)				107
P34292 UniProt NPD GO	YKO4_CAEEL	Hypothetical protein C05B5.4	0.40	-	end	1 *					315
Q9UT68 UniProt NPD GO	YJ53_SCHPO	Hypothetical protein C4F11.03c in chromosome III	0.40	-	nuc	0					335
Q92361 UniProt NPD GO	YDHG_SCHPO	Hypothetical protein C6G9.16c in chromosome I	0.40	-	nuc	0					132
O13679 UniProt NPD GO	YJ15_SCHPO	Hypothetical protein C737.05 in chromosome III	0.40	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				264
P34557 UniProt NPD GO	YNP4_CAEEL	Hypothetical protein T05G5.4	0.40	-	nuc	0					78
P34582 UniProt NPD GO	YN23_CAEEL	Hypothetical protein T26G10.3 in chromosome III	0.40	-	nuc	0					91
P51392 UniProt NPD GO	YCF26_PORPU	Hypothetical sensor-like histidine kinase ycf26 (EC 2.7.13.3)	0.40	-	end	3 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Probable)				656
P49249 UniProt NPD GO	IN22_MAIZE	IN2-2 protein	0.40	-	cyt	0					306
P01600 UniProt NPD GO	KV1H_HUMAN	Ig kappa chain V-I region Hau	0.40	-	nuc	0		extracellular region [NAS]		1F6L	108
Q5VY09 UniProt NPD GO	IER5_HUMAN	Immediate early response gene 5 protein	0.40	-	nuc	0			607177		327
Q5RAJ8 UniProt NPD GO	TIM50_PONPY	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.40	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)	mitochondrial inner membrane presequence tr... [ISS]			353
O35343 UniProt NPD GO	IMA4_MOUSE	Importin alpha-4 subunit (Karyopherin alpha-4 subunit) (Importin alpha Q1)	0.40	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				521
Q9ZPY7 UniProt NPD GO	CSE1_ARATH	Importin-alpha re-exporter (Cellular apoptosis susceptibility protein homolog)	0.40	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				972
P32617 UniProt NPD GO	IES6_YEAST	Ino eighty subunit 6	0.40	-	nuc	0	Nucleus	nucleus [IDA]			166
Q5F480 UniProt NPD GO	ITPK1_CHICK	Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase) (EC 2.7.1.-) ( ...	0.40	-	cyt	0					407
P35559 UniProt NPD GO	IDE_RAT	Insulin-degrading enzyme (EC 3.4.24.56) (Insulysin) (Insulinase) (Insulin protease)	0.40	-	mit	0	Cytoplasm				1019
Q9WUK0 UniProt NPD GO	INSL3_RAT	Insulin-like 3 precursor (Leydig insulin-like peptide) (Ley-I-L) (Relaxin-like factor) [Contains: In ...	0.40	-	exc	0	Secreted protein				128
Q05688 UniProt NPD GO	IGF1R_BOVIN	Insulin-like growth factor 1 receptor precursor (EC 2.7.10.1) (Insulin-like growth factor I receptor ...	0.40	+	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			640
P11688 UniProt NPD GO	ITA5_MOUSE	Integrin alpha-5 precursor (Fibronectin receptor subunit alpha) (Integrin alpha-F) (VLA-5) (CD49e an ...	0.40	-	end	1	Membrane; single-pass type I membrane protein	ruffle [ISS] synaptosome [IDA]			1053
P01572 UniProt NPD GO	IFNA1_MOUSE	Interferon alpha-1 precursor	0.40	-	exc	0	Secreted protein				189
P05011 UniProt NPD GO	IFNA1_RAT	Interferon alpha-1 precursor	0.40	-	end	0	Secreted protein				192
P28171 UniProt NPD GO	IFNT_CAPHI	Interferon tau precursor (IFN-tau) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin) ( ...	0.40	-	vac	1 *	Secreted protein. Secreted into the uterine lumen				195
Q7ZYA5 UniProt NPD GO	PRKRA_XENLA	Interferon-inducible double stranded RNA-dependent protein kinase activator A homolog	0.40	-	nuc	0					309
Q865X0 UniProt NPD GO	IL12A_LAMGL	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.40	-	exc	0	Secreted protein				222
Q60819 UniProt NPD GO	I15RA_MOUSE	Interleukin-15 receptor alpha chain precursor (IL-15R-alpha) (IL-15RA)	0.40	-	exc	2 *	Membrane; single-pass type I membrane protein. Secreted protein. Isoform 1, isoform 3, isoform 4 and ...				263
P04351 UniProt NPD GO	IL2_MOUSE	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.40	-	exc	0	Secreted protein	extracellular space [IDA]			169
P12342 UniProt NPD GO	IL2RA_BOVIN	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (p55) ...	0.40	-	mit	1	Membrane; single-pass type I membrane protein				275
Q9HBE5 UniProt NPD GO	IL21R_HUMAN	Interleukin-21 receptor precursor (IL-21R) (Novel interleukin receptor)	0.40	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	605383		538
Q969J5 UniProt NPD GO	I22RA_HUMAN	Interleukin-22 receptor alpha-2 chain precursor (IL-22R-alpha-2) (Interleukin 22-binding protein) (I ...	0.40	-	exc	0	Secreted protein	extracellular space [NAS]	606648		263
P26951 UniProt NPD GO	IL3RA_HUMAN	Interleukin-3 receptor alpha chain precursor (IL-3R-alpha) (CD123 antigen)	0.40	-	end	1	Membrane; single-pass type I membrane protein		430000		378
Q6WG24 UniProt NPD GO	IL4RA_HORSE	Interleukin-4 receptor alpha chain precursor (IL-4R-alpha) (CD124 antigen)	0.40	-	exc	0	Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein (Probable)				809
P98089 UniProt NPD GO	MUC2L_RAT	Intestinal mucin-like protein (MLP) (Fragment)	0.40	-	mit	0	Secreted protein				837
P18174 UniProt NPD GO	INVO_CANFA	Involucrin	0.40	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope				285
P17941 UniProt NPD GO	INVO_HYLLA	Involucrin	0.40	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope	cornified envelope [ISS] cytoplasm [ISS]			522
Q9NPI9 UniProt NPD GO	IRK16_HUMAN	Inward rectifier potassium channel 16 (Potassium channel, inwardly rectifying subfamily J member 16) ...	0.40	+	mit	2	Membrane; multi-pass membrane protein		605722		418
P41252 UniProt NPD GO	SYIC_HUMAN	Isoleucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS) (IRS)	0.40	-	nuc	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	600709		1266
Q8SPJ1 UniProt NPD GO	PLAK_BOVIN	Junction plakoglobin (Desmoplakin III)	0.40	-	nuc	0	Cytoplasm (By similarity). Cytoplasmic in a soluble and membrane-associated form (By similarity)	cytoplasm [ISS] cytoskeleton [ISS] membrane fraction [ISS]			745
Q9BVA0 UniProt NPD GO	KTNB1_HUMAN	Katanin p80 WD40-containing subunit B1 (Katanin p80 subunit B1) (p80 katanin)	0.40	-	nuc	0	Cytoplasm. Predominantly. Centrosome. Spindle. Also localized to the interphase centrosome and mitot ...	cytoplasm [IDA] katanin [TAS]	602703		655
Q8VCK5 UniProt NPD GO	KLH20_MOUSE	Kelch-like protein 20 (Kelch-like ECT2-interacting protein)	0.40	-	mit	0					604
Q8IXQ5 UniProt NPD GO	KLHL7_HUMAN	Kelch-like protein 7	0.40	+	nuc	0					586
O76013 UniProt NPD GO	K1H6_HUMAN	Keratin, type I cuticular Ha6 (Hair keratin, type I Ha6)	0.40	-	mit	0			604540		467
Q6IFV4 UniProt NPD GO	K1C13_RAT	Keratin, type I cytoskeletal 13 (Cytokeratin-13) (CK-13) (Keratin-13) (K13) (Type I keratin Ka13)	0.40	-	nuc	0					438
Q61781 UniProt NPD GO	K1C14_MOUSE	Keratin, type I cytoskeletal 14 (Cytokeratin-14) (CK-14) (Keratin-14) (K14)	0.40	-	nuc	0		keratin filament [IDA]			484
O77727 UniProt NPD GO	K1C15_SHEEP	Keratin, type I cytoskeletal 15 (Cytokeratin-15) (CK-15) (Keratin-15) (K15)	0.40	-	cyt	0					453

You are viewing entries 31901 to 31950 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.