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
P63124 UniProt NPD GO	VPK9_HUMAN	HERV-K_5q13.3 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K104 Pro protein) (Protease) (Prote ...	0.07	-	cyt	0					156
P03992 UniProt NPD GO	HB25_HUMAN	HLA class II histocompatibility antigen, DQB1*0602 beta chain precursor (DQ(5)) (DC-1)	0.07	-	mit	1	Membrane; single-pass type I membrane protein (Potential)		604305		261
P01913 UniProt NPD GO	2B32_HUMAN	HLA class II histocompatibility antigen, DRB3-2 beta chain precursor (MHC class I antigen DRB3*2)	0.07	-	end	1 *	Membrane; single-pass type I membrane protein				266
P20163 UniProt NPD GO	HSP7D_CAEEL	Heat shock 70 kDa protein D precursor	0.07	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				657
P12076 UniProt NPD GO	HSP71_LEIMA	Heat shock 70-related protein 1, mitochondrial precursor	0.07	-	mit	0	Mitochondrion				634
O14368 UniProt NPD GO	HSP16_SCHPO	Heat shock protein 16 (16 kDa heat shock protein)	0.07	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			143
P15992 UniProt NPD GO	HSP26_YEAST	Heat shock protein 26 (26 kDa heat shock protein)	0.07	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			213
O60008 UniProt NPD GO	HSP60_PARBR	Heat shock protein 60, mitochondrial precursor (60 kDa chaperonin) (Protein Cpn60)	0.07	-	mit	0	Mitochondrion				592
P50142 UniProt NPD GO	HSP60_AJECA	Heat shock protein 60, mitochondrial precursor (Antigen HIS-62)	0.07	-	mit	0	Mitochondrion				590
Q09864 UniProt NPD GO	HSP60_SCHPO	Heat shock protein 60, mitochondrial precursor (HSP60)	0.07	-	mit	0	Mitochondrion	mitochondrion [IDA]			582
P87142 UniProt NPD GO	YDMC_SCHPO	Heat shock protein 70 homolog C57A7.12	0.07	-	cyt	0					566
Q74ZJ0 UniProt NPD GO	HSP7F_ASHGO	Heat shock protein homolog SSE1	0.07	-	cyt	0	Cytoplasm (By similarity)				697
P32589 UniProt NPD GO	HSP7F_YEAST	Heat shock protein homolog SSE1 (Chaperone protein MSI3)	0.07	-	cyt	0	Cytoplasm	cytoplasm [IC]			692
Q5EBG6 UniProt NPD GO	HSPB6_MOUSE	Heat-shock protein beta-6 (HspB6)	0.07	-	mit	0					162
P97541 UniProt NPD GO	HSPB6_RAT	Heat-shock protein beta-6 (HspB6) (Heat-shock 20 kDa-like protein p20)	0.07	-	mit	0					162
Q9JK92 UniProt NPD GO	HSPB8_MOUSE	Heat-shock protein beta-8 (HspB8) (Alpha crystallin C chain) (Small stress protein-like protein HSP2 ...	0.07	-	nuc	0					196
P51271 UniProt NPD GO	HO_PORPU	Heme oxygenase (EC 1.14.99.3)	0.07	-	cyt	0	Plastid; chloroplast				236
P37363 UniProt NPD GO	HEMI_PYRAP	Hemiptericin	0.07	-	cyt	0					133
P02243 UniProt NPD GO	HCYA_TACTR	Hemocyanin alpha chain (Fragment)	0.07	-	cyt	0	Secreted protein; extracellular space				87
P25033 UniProt NPD GO	HEMO_HYACE	Hemolin precursor (P4 protein) (Hemocyte aggregation inhibitor)	0.07	-	cyt	0	Secreted protein; extracellular space			1BIH	413
P26305 UniProt NPD GO	LPSBP_PERAM	Hemolymph lipopolysaccharide-binding protein precursor (LPS-binding protein) (LPS-BP)	0.07	-	exc	0	Secreted protein				256
Q60487 UniProt NPD GO	FGF2_CAVPO	Heparin-binding growth factor 2 (HBGF-2) (Fibroblast growth factor 2) (FGF-2) (Basic fibroblast grow ...	0.07	-	mit	0					170
P13571 UniProt NPD GO	HPTA_RABIT	Heptapoietin A light chain (HPTA) (Fragment)	0.07	-	nuc	0					24
P60992 UniProt NPD GO	TX1_HETMC	Heteroscodratoxin-1 (HmTx1)	0.07	-	nuc	0	Secreted protein				35
Q9SEK2 UniProt NPD GO	HXK1_TOBAC	Hexokinase-1 (EC 2.7.1.1) (NtHxK1)	0.07	-	mit	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (Probable)				497
P93834 UniProt NPD GO	HXK2_ARATH	Hexokinase-2 (EC 2.7.1.1)	0.07	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				502
P54862 UniProt NPD GO	HXT11_YEAST	Hexose transporter HXT11 (Low-affinity glucose transporter LGT3)	0.07	-	end	11	Membrane; multi-pass membrane protein (Probable)				567
P40885 UniProt NPD GO	HXT9_YEAST	Hexose transporter HXT9	0.07	-	end	11	Membrane; multi-pass membrane protein (Probable)				567
Q9BDR7 UniProt NPD GO	FCERG_BOVIN	High affinity immunoglobulin epsilon receptor gamma-subunit precursor (FceRI gamma) (IgE Fc receptor ...	0.07	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				85
Q28422 UniProt NPD GO	CXCR2_GORGO	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (CD182 antigen) (Fragment)	0.07	-	end	6 *	Membrane; multi-pass membrane protein				353
Q28807 UniProt NPD GO	CXCR2_PANTR	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (CD182 antigen) (Fragment)	0.07	-	end	6 *	Membrane; multi-pass membrane protein				353
Q9P3U6 UniProt NPD GO	GHT1_SCHPO	High-affinity glucose transporter ght1 (Hexose transporter 1)	0.07	-	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			557
P39003 UniProt NPD GO	HXT6_YEAST	High-affinity hexose transporter HXT6	0.07	-	end	11	Membrane; multi-pass membrane protein	mitochondrion [IDA]			570
P39004 UniProt NPD GO	HXT7_YEAST	High-affinity hexose transporter HXT6	0.07	-	end	11	Membrane; multi-pass membrane protein	mitochondrion [IDA] plasma membrane [IDA]			570
P50276 UniProt NPD GO	MUP1_YEAST	High-affinity methionine permease	0.07	-	end	12	Membrane; multi-pass membrane protein (Potential)				574
P09944 UniProt NPD GO	ITH2_HIRME	Hirudin PA	0.07	-	nuc	0	Secreted protein			1IHT	66
P17124 UniProt NPD GO	HRH2_CANFA	Histamine H2 receptor (H2R) (Gastric receptor I)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				359
Q9BX68 UniProt NPD GO	HINT2_HUMAN	Histidine triad nucleotide-binding protein 2 (EC 3.-.-.-) (HINT-2) (HINT-3) (HIT-17kDa) (PKCI-1-rela ...	0.07	-	mit	0		mitochondrion [ISS]			163
P05227 UniProt NPD GO	HRP1_PLAFA	Histidine-rich protein precursor (Clone PFHRP-II)	0.07	-	cyt	0				1L8M	332
P56099 UniProt NPD GO	HIS8_CANMA	Histidinol-phosphate aminotransferase (EC 2.6.1.9) (Imidazole acetol-phosphate transaminase)	0.07	-	cyt	0					389
O17536 UniProt NPD GO	H14_CAEEL	Histone H1.4 (Histone H1-like protein 4)	0.07	-	nuc	0	Nucleus (By similarity)				252
O01833 UniProt NPD GO	H15_CAEEL	Histone H1.5 (Histone H1-like protein 5)	0.07	-	nuc	0	Nucleus (By similarity)				224
P82899 UniProt NPD GO	H1B_OLILU	Histone H1B (Fragment)	0.07	-	nuc	0	Nucleus				42
P83863 UniProt NPD GO	H2B_PENVA	Histone H2B (Fragments)	0.07	-	nuc	0	Nucleus	nucleosome [ISS]			53
O59702 UniProt NPD GO	CLR6_SCHPO	Histone deacetylase clr6 (Cryptic loci regulator 6)	0.07	-	cyt	0	Nucleus	histone deacetylase complex [IDA] nuclear chromatin [IDA]			405
Q3MHL3 UniProt NPD GO	RBBP4_BOVIN	Histone-binding protein RBBP4 (Retinoblastoma-binding protein 4) (RBBP-4)	0.07	-	cyt	0	Nucleus (By similarity)				424
Q5M7K4 UniProt NPD GO	RBBP4_XENTR	Histone-binding protein RBBP4 (Retinoblastoma-binding protein 4) (RBBP-4)	0.07	-	cyt	0	Nucleus (By similarity)				424
Q09028 UniProt NPD GO	RBBP4_HUMAN	Histone-binding protein RBBP4 (Retinoblastoma-binding protein 4) (RBBP-4) (Retinoblastoma-binding pr ...	0.07	-	cyt	0	Nucleus	nucleus [TAS]	602923		424
Q60972 UniProt NPD GO	RBBP4_MOUSE	Histone-binding protein RBBP4 (Retinoblastoma-binding protein 4) (RBBP-4) (Retinoblastoma-binding pr ...	0.07	-	cyt	0	Nucleus	NuRD complex [IDA]			424
O93377 UniProt NPD GO	RBP4A_XENLA	Histone-binding protein RBBP4-A (Retinoblastoma-binding protein 4-A) (RBBP-4-A) (Retinoblastoma-bind ...	0.07	-	cyt	0	Nucleus				424

You are viewing entries 70151 to 70200 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.