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
Q09947 UniProt NPD GO	YSH6_CAEEL	Hypothetical protein F12A10.6	0.14	-	nuc	0					125
P41883 UniProt NPD GO	YPT5_CAEEL	Hypothetical protein F37A4.5 in chromosome III	0.14	-	nuc	0					319
Q09341 UniProt NPD GO	YR24_CAEEL	Hypothetical protein W02B3.4 in chromosome III	0.14	-	mit	1 *					387
P34608 UniProt NPD GO	YO69_CAEEL	Hypothetical protein ZK1098.9	0.14	+	end	5 *					220
P34644 UniProt NPD GO	YOQ6_CAEEL	Hypothetical protein ZK512.6 in chromosome III	0.14	-	end	12	Membrane; multi-pass membrane protein (Potential)				576
P25408 UniProt NPD GO	YCA2_PLAFA	Hypothetical protein in calmodulin 3'region (Fragment)	0.14	-	nuc	0					241
P23086 UniProt NPD GO	HVC3_HETFR	Ig heavy chain C region (Clone 6121) (Fragment)	0.14	-	nuc	0					393
P03977 UniProt NPD GO	KV3D_MOUSE	Ig kappa chain V-III region 50S10.1	0.14	-	nuc	0					111
P06314 UniProt NPD GO	KV4C_HUMAN	Ig kappa chain V-IV region B17 precursor	0.14	-	exc	0		extracellular region [NAS]			134
P83593 UniProt NPD GO	KV4D_HUMAN	Ig kappa chain V-IV region STH (Fragment)	0.14	-	nuc	0					109
P01677 UniProt NPD GO	KV6C_MOUSE	Ig kappa chain V-VI region TEPC 601/TEPC 191	0.14	-	nuc	0					107
P06889 UniProt NPD GO	LV4E_HUMAN	Ig lambda chain V-IV region MOL	0.14	-	nuc	0		extracellular region [NAS]			106
P01843 UniProt NPD GO	LAC1_MOUSE	Ig lambda-1 chain C region	0.14	-	nuc	0				1JNH	105
P01875 UniProt NPD GO	MUC_CHICK	Ig mu chain C region	0.14	-	cyt	0					446
P01592 UniProt NPD GO	IGJ_MOUSE	Immunoglobulin J chain precursor	0.14	-	mit	0					159
P59888 UniProt NPD GO	IPTXI_PANIM	Imperatoxin-1 precursor (Imperatoxin I) (IpTxi) (Imperatoxin inhibitor) [Contains: Imperatoxin-1 lar ...	0.14	-	nuc	0	Secreted protein				167
P97812 UniProt NPD GO	IHH_MOUSE	Indian hedgehog protein precursor (IHH) (HHG-2) [Contains: Indian hedgehog protein N-product; Indian ...	0.14	-	mit	1 *	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				411
Q07820 UniProt NPD GO	MCL1_HUMAN	Induced myeloid leukemia cell differentiation protein Mcl-1 (Bcl-2-related protein EAT/mcl1) (mcl1/E ...	0.14	-	cyt	1	Membrane; single-pass membrane protein (Potential). Cytoplasm. Mitochondrion. Cytoplasmic, associate ...	cytoplasm [ISS] mitochondrial outer membrane [ISS]	159552		350
Q9WVS0 UniProt NPD GO	ICOS_MOUSE	Inducible T-cell co-stimulator precursor (Activation-inducible lymphocyte immunomediatory molecule) ...	0.14	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [IDA]			200
P98085 UniProt NPD GO	COLE_LEPMA	Inner ear-specific collagen precursor (Saccular collagen)	0.14	-	cyt	0					419
Q9VR82 UniProt NPD GO	INX6_DROME	Innexin inx6 (Innexin-6) (Gap junction protein prp6) (Pas-related protein 6)	0.14	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [IEP] integral to membrane [NAS]			481
O01634 UniProt NPD GO	INX12_CAEEL	Innexin-12	0.14	-	end	4 *	Membrane; multi-pass membrane protein				408
Q07152 UniProt NPD GO	IMDH_DROME	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD) (Protein ra ...	0.14	-	cyt	0					537
P20839 UniProt NPD GO	IMDH1_HUMAN	Inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) (IMP dehydrogenase 1) (IMPDH-I) (IMPD 1)	0.14	-	cyt	0			146690	1JCN	514
P12268 UniProt NPD GO	IMDH2_HUMAN	Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) (IMP dehydrogenase 2) (IMPDH-II) (IMPD 2)	0.14	-	cyt	0			146691	1NFB	514
Q9XYQ1 UniProt NPD GO	ITPK1_ENTHI	Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase) (EC 2.7.1.-) ( ...	0.14	-	cyt	0				1Z2P	319
P01323 UniProt NPD GO	INS2_RAT	Insulin-2 precursor [Contains: Insulin-2 B chain; Insulin-2 A chain]	0.14	-	exc	0	Secreted protein				110
O60478 UniProt NPD GO	G137B_HUMAN	Integral membrane protein GPR137B (Transmembrane 7 superfamily member 1)	0.14	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS] membrane fraction [TAS]	604658		399
Q62469 UniProt NPD GO	ITA2_MOUSE	Integrin alpha-2 precursor (Platelet membrane glycoprotein Ia) (GPIa) (Collagen receptor) (VLA-2 alp ...	0.14	-	end	1 *	Membrane; single-pass type I membrane protein				1178
P13598 UniProt NPD GO	ICAM2_HUMAN	Intercellular adhesion molecule 2 precursor (ICAM-2) (CD102 antigen)	0.14	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	146630	1ZXQ	275
Q9UMF0 UniProt NPD GO	ICAM5_HUMAN	Intercellular adhesion molecule 5 precursor (ICAM-5) (Telencephalin)	0.14	-	exc	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601852		924
Q66UW5 UniProt NPD GO	ISG20_PIG	Interferon-stimulated gene 20 kDa protein (EC 3.1.13.1)	0.14	-	cyt	0	Nucleus (By similarity)				181
Q7TP98 UniProt NPD GO	ILF2_RAT	Interleukin enhancer-binding factor 2 (Liver regeneration-related protein LRRG031)	0.14	-	cyt	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS] nucleus [ISS]			463
Q9XSQ5 UniProt NPD GO	IL12B_HORSE	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.14	-	exc	1 *	Secreted protein				329
Q28938 UniProt NPD GO	IL12B_PIG	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.14	-	exc	1 *	Secreted protein				324
Q95J68 UniProt NPD GO	IL13_PIG	Interleukin-13 precursor (IL-13)	0.14	-	exc	0	Secreted protein				131
P42203 UniProt NPD GO	IL13_RAT	Interleukin-13 precursor (IL-13) (T-cell activation protein P600)	0.14	-	nuc	0	Secreted protein				131
Q61098 UniProt NPD GO	IL18R_MOUSE	Interleukin-18 receptor 1 precursor (IL1 receptor-related protein) (IL-1Rrp)	0.14	-	nuc	1	Membrane; single-pass type I membrane protein				537
O95998 UniProt NPD GO	I18BP_HUMAN	Interleukin-18-binding protein precursor (IL-18BP) (Tadekinig-alfa)	0.14	-	vac	0	Secreted protein (Potential)	extracellular region [TAS]	604113		197
P26891 UniProt NPD GO	IL2_PIG	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.14	-	exc	0	Secreted protein				154
P21183 UniProt NPD GO	IL5RA_MOUSE	Interleukin-5 receptor alpha chain precursor (IL-5R-alpha) (CD125 antigen)	0.14	-	end	1	Membrane; single-pass type I membrane protein				415
P12661 UniProt NPD GO	IRBP_BOVIN	Interphotoreceptor retinoid-binding protein precursor (IRBP) (Interstitial retinol-binding protein) ...	0.14	-	vac	0	Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pi ...				1286
Q9QZ65 UniProt NPD GO	IRK13_CAVPO	Inward rectifier potassium channel 13 (Potassium channel, inwardly rectifying subfamily J member 13) ...	0.14	-	mit	2	Membrane; multi-pass membrane protein				360
Q75C07 UniProt NPD GO	ISU1_ASHGO	Iron sulfur cluster assembly protein 1, mitochondrial precursor (Iron sulfur cluster scaffold protei ...	0.14	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				154
P41565 UniProt NPD GO	IDH3G_RAT	Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.14	-	cyt	0	Mitochondrion	mitochondrion [TAS]			393
P28240 UniProt NPD GO	ACEA_YEAST	Isocitrate lyase (EC 4.1.3.1) (ICL) (Isocitrase) (Isocitratase) (Threo-D(S)-isocitrate glyoxylate-ly ...	0.14	-	cyt	0	Cytoplasm				557
P25248 UniProt NPD GO	ACEA_BRANA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.14	-	cyt	0	Glyoxysome				576
Q43097 UniProt NPD GO	ACEA_PINTA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.14	-	cyt	0	Glyoxysome				580
Q21926 UniProt NPD GO	SYIC_CAEEL	Isoleucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.14	-	mit	0	Cytoplasm				1141
Q10132 UniProt NPD GO	IDI1_SCHPO	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) (IPP isomerase) (Isopentenyl pyrophosphate isom ...	0.14	-	cyt	0	Cytoplasm				227

You are viewing entries 58501 to 58550 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.