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
Q75BG6 UniProt NPD GO	JID1_ASHGO	J domain-containing protein 1	0.45	-	nuc	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (By similarity)				305
P97607 UniProt NPD GO	JAG2_RAT	Jagged-2 (Jagged2) (Fragment)	0.45	+	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			1202
Q9Y219 UniProt NPD GO	JAG2_HUMAN	Jagged-2 precursor (Jagged2) (HJ2)	0.45	+	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]	602570		1238
P02442 UniProt NPD GO	KRA3_CAPHI	Keratin, high-sulfur matrix protein, IIIA3 (M2.6 protein)	0.45	-	nuc	0					132
Q61765 UniProt NPD GO	K1H1_MOUSE	Keratin, type I cuticular Ha1 (Hair keratin, type I Ha1) (HKA-1)	0.45	-	nuc	0					416
Q14532 UniProt NPD GO	K1H2_HUMAN	Keratin, type I cuticular Ha2 (Hair keratin, type I Ha2)	0.45	-	nuc	0			602760		448
Q62168 UniProt NPD GO	K1H2_MOUSE	Keratin, type I cuticular Ha2 (Hair keratin, type I Ha2)	0.45	-	mit	0					407
O76011 UniProt NPD GO	K1H4_HUMAN	Keratin, type I cuticular Ha4 (Hair keratin, type I Ha4)	0.45	-	nuc	0			602763		394
Q28706 UniProt NPD GO	K1C12_RABIT	Keratin, type I cytoskeletal 12 (Cytokeratin-12) (CK-12) (Keratin-12) (K12) (Fragment)	0.45	-	nuc	0					411
Q5BJY9 UniProt NPD GO	K1C18_RAT	Keratin, type I cytoskeletal 18 (Cytokeratin-18) (CK-18) (Keratin-18) (K18)	0.45	-	mit	0	Nucleus; nucleoplasm; nuclear matrix				422
Q63279 UniProt NPD GO	K1C19_RAT	Keratin, type I cytoskeletal 19 (Cytokeratin-19) (CK-19) (Keratin-19) (K19) (Type I keratin Ka19)	0.45	-	mit	0					403
Q99M74 UniProt NPD GO	KRHB2_MOUSE	Keratin, type II cuticular Hb2 (Hair keratin, type II Hb2)	0.45	-	mit	0					516
P16878 UniProt NPD GO	K2C5_XENLA	Keratin, type II cytoskeletal (XENCK55(5/6))	0.45	-	mit	0					512
P50446 UniProt NPD GO	K2C6A_MOUSE	Keratin, type II cytoskeletal 6A (Cytokeratin-6A) (CK 6A) (K6a keratin) (Keratin-6 alpha) (mK6-alpha ...	0.45	-	nuc	0		intermediate filament [ISS]			552
Q9Z331 UniProt NPD GO	K2C6B_MOUSE	Keratin, type II cytoskeletal 6B (Cytokeratin-6B) (CK 6B) (K6b keratin) (Keratin-6 beta) (mK6-beta)	0.45	-	nuc	1		intermediate filament [ISS] mitochondrion [IDA]			561
Q6NWF6 UniProt NPD GO	K2C8_BRARE	Keratin, type II cytoskeletal 8 (Cytokeratin-8) (CK-8) (Keratin-8) (K8)	0.45	-	nuc	0					520
Q9BYP9 UniProt NPD GO	KRA99_HUMAN	Keratin-associated protein 9-9 (Keratin-associated protein 9.9) (Ultrahigh sulfur keratin-associated ...	0.45	-	mit	0					154
Q92845 UniProt NPD GO	KIFA3_HUMAN	Kinesin-associated protein 3 (Smg GDS-associated protein)	0.45	+	nuc	0		endoplasmic reticulum [TAS] kinesin II complex [ISS]	601836		792
Q14847 UniProt NPD GO	LASP1_HUMAN	LIM and SH3 domain protein 1 (LASP-1) (MLN 50)	0.45	-	nuc	0	Cytoplasm (By similarity). Associated with the F-actin rich cortical cytoskeleton (By similarity)	cortical actin cytoskeleton [ISS]	602920		261
P53668 UniProt NPD GO	LIMK1_MOUSE	LIM domain kinase 1 (EC 2.7.11.1) (LIMK-1) (KIZ-1)	0.45	-	nuc	0	Cytoplasm (By similarity)	focal adhesion [IDA] nucleus [IDA]			647
Q9AT61 UniProt NPD GO	LBD13_ARATH	LOB domain-containing protein 13	0.45	-	nuc	0					268
Q9SLB6 UniProt NPD GO	LBD17_ARATH	LOB domain-containing protein 17	0.45	-	nuc	0					244
O22131 UniProt NPD GO	LBD18_ARATH	LOB domain-containing protein 18	0.45	-	nuc	0					262
Q9ZW96 UniProt NPD GO	LBD40_ARATH	LOB domain-containing protein 40	0.45	-	nuc	0					233
Q5T7P2 UniProt NPD GO	LCE1A_HUMAN	Late cornified envelope protein 1A (Late envelope protein 1)	0.45	-	mit	0					110
P16078 UniProt NPD GO	LEGB2_VICFA	Legumin type B [Contains: Legumin type B alpha chain (Legumin type B acidic chain); Legumin type B b ...	0.45	-	nuc	0					335
Q80Y17 UniProt NPD GO	L2GL1_MOUSE	Lethal(2) giant larvae protein homolog 1 (LLGL) (Mlgl) (Mgl-1)	0.45	-	nuc	0	Cytoplasm. Localized to the lateral membrane during the polarization and formation cell-cell contact ...	cytoplasm [IDA]			1036
Q6UXK5 UniProt NPD GO	LRRN1_HUMAN	Leucine-rich repeats neuronal protein 1 precursor (Neuronal leucine-rich repeat protein 1) (NLRR-1)	0.45	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				716
Q5RA63 UniProt NPD GO	LIGA_PONPY	Ligatin	0.45	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				584
P41214 UniProt NPD GO	LIGA_HUMAN	Ligatin (Hepatocellular carcinoma-associated antigen 56)	0.45	-	nuc	0	Membrane; peripheral membrane	cytoplasm [TAS]	151625		584
Q85FG6 UniProt NPD GO	CHLN_ADICA	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.45	+	cyt	0	Plastid; chloroplast				460
Q99MT8 UniProt NPD GO	MRGRH_MOUSE	Mas-related G-protein coupled receptor member H (G-protein coupled receptor 90)	0.45	-	end	7 *	Membrane; multi-pass membrane protein				321
Q10115 UniProt NPD GO	MATC_NEUCR	Mating-type protein A-2 (Mt A-2)	0.45	-	cyt	0					373
Q5YJU7 UniProt NPD GO	MATK_CHAFS	Maturase K (Intron maturase)	0.45	-	cyt	0	Plastid; chloroplast				499
Q85V93 UniProt NPD GO	MATK_FICCA	Maturase K (Intron maturase)	0.45	-	nuc	0	Plastid; chloroplast				505
Q8R456 UniProt NPD GO	OPN4_RAT	Melanopsin (Opsin-4)	0.45	-	end	6	Membrane; multi-pass membrane protein. Found in soma, dendrites and proximal part of axons of retina ...				474
P41594 UniProt NPD GO	MGR5_HUMAN	Metabotropic glutamate receptor 5 precursor (mGluR5)	0.45	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604102		1212
Q4WN24 UniProt NPD GO	GEM1_ASPFU	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.45	+	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				632
Q9XGX8 UniProt NPD GO	TIM9_MESCR	Mitochondrial import inner membrane translocase subunit Tim9	0.45	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				93
P82873 UniProt NPD GO	TO202_ARATH	Mitochondrial import receptor subunit TOM20-2 (Translocase of outer membrane 20 kDa subunit 2)	0.45	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				210
O14225 UniProt NPD GO	TOM20_SCHPO	Mitochondrial import receptor subunit tom20 (Mitochondrial 20 kDa outer membrane protein) (Transloca ...	0.45	+	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				152
O42781 UniProt NPD GO	MAPK2_PNECA	Mitogen-activated protein kinase 2 (EC 2.7.11.24) (PCM)	0.45	-	nuc	0	Nucleus (By similarity)				351
Q15796 UniProt NPD GO	SMAD2_HUMAN	Mothers against decapentaplegic homolog 2 (SMAD 2) (Mothers against DPP homolog 2) (Mad-related prot ...	0.45	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...	nucleus [ISS] transcription factor complex [ISS]	601366	1U7V	467
Q8BSU7 UniProt NPD GO	MOL2A_MOUSE	Mps one binder kinase activator-like 2A (Mob1 homolog 2A)	0.45	-	nuc	0					217
O75970 UniProt NPD GO	MPDZ_HUMAN	Multiple PDZ domain protein (Multi PDZ domain protein 1) (Multi-PDZ-domain protein 1)	0.45	-	nuc	0	Cell membrane; cytoplasmic side. Associated with membranes. Colocalizes with HTR2C on the apical mem ...		603785	2FNE	2042
O88281 UniProt NPD GO	MEGF6_RAT	Multiple epidermal growth factor-like domains 6 precursor (EGF-like domain-containing protein 3) (Mu ...	0.45	-	mit	1 *					1574
O08539 UniProt NPD GO	BIN1_MOUSE	Myc box-dependent-interacting protein 1 (Bridging integrator 1) (Amphiphysin-like protein) (Amphiphy ...	0.45	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				588
P70331 UniProt NPD GO	MDFI_MOUSE	MyoD family inhibitor (Myogenic repressor I-mf)	0.45	-	nuc	0	Cytoplasm				251
P50426 UniProt NPD GO	GL6S_CAPHI	N-acetylglucosamine-6-sulfatase precursor (EC 3.1.6.14) (G6S) (Glucosamine-6-sulfatase)	0.45	-	mit	0	Lysosome				559
Q93015 UniProt NPD GO	NAT6_HUMAN	N-acetyltransferase 6 (EC 2.3.1.-) (Fus-2 protein) (Fusion 2 protein)	0.45	-	nuc	0	Cytoplasm		607073		286

You are viewing entries 28401 to 28450 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.