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
P80205 UniProt NPD GO	OTX1_MOUSE	Homeobox protein OTX1	0.59	-	nuc	0	Nucleus (Probable)	nucleus [IC]			355
O95343 UniProt NPD GO	SIX3_HUMAN	Homeobox protein SIX3 (Sine oculis homeobox homolog 3)	0.59	-	exc	0	Nucleus		603714		332
Q8NE63 UniProt NPD GO	HIPK4_HUMAN	Homeodomain-interacting protein kinase 4 (EC 2.7.11.1)	0.59	-	nuc	0	Cytoplasm (Probable)				616
P20914 UniProt NPD GO	HM20_XENLA	Homeotic protein NRL-20 (Fragment)	0.59	+	nuc	0	Nucleus				105
O94740 UniProt NPD GO	CDC37_SCHPO	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (Cell division control p ...	0.59	-	nuc	0	Nucleus. Cytoplasm. When in the nucleus associated with chromatin	cytoplasm [IDA] nucleus [IDA]			466
P54868 UniProt NPD GO	HMCS2_HUMAN	Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor (EC 2.3.3.10) (HMG-CoA synthase) (3-hydr ...	0.59	-	mit	0	Mitochondrion	mitochondrion [TAS]	600234		508
P47007 UniProt NPD GO	YJO7_YEAST	Hypothetical 44.9 kDa protein in INO1-IDS2 intergenic region	0.59	-	nuc	0		mitochondrion [IDA]			382
P34263 UniProt NPD GO	YKAD_CAEEL	Hypothetical protein B0303.14	0.59	-	nuc	0					407
Q09716 UniProt NPD GO	YA3B_SCHPO	Hypothetical protein C18B11.11 in chromosome I	0.59	-	cyt	0	Membrane; multi-pass membrane protein (Potential)				1294
O14202 UniProt NPD GO	YDQA_SCHPO	Hypothetical protein C5D6.10c in chromosome I	0.59	+	mit	1 *					135
Q8ST44 UniProt NPD GO	Y7I5_ENCCU	Hypothetical protein ECU07_1850/ECU10_0050	0.59	+	cyt	0					634
P34550 UniProt NPD GO	YNJ6_CAEEL	Hypothetical protein R10E11.6	0.59	-	nuc	0					371
P45972 UniProt NPD GO	YNZB_CAEEL	Hypothetical protein T09A5.12	0.59	-	nuc	1					708
P45966 UniProt NPD GO	YNZ6_CAEEL	Hypothetical protein T09A5.6	0.59	-	nuc	0					173
Q09354 UniProt NPD GO	YRY4_CAEEL	Hypothetical protein T15H9.4	0.59	-	nuc	0					431
Q9XUB9 UniProt NPD GO	YGJI_CAEEL	Hypothetical protein T28F3.1 in chromosome IV	0.59	-	nuc	0					634
Q09374 UniProt NPD GO	YS48_CAEEL	Hypothetical protein ZK177.8	0.59	-	nuc	0					587
P34680 UniProt NPD GO	YO42_CAEEL	Hypothetical protein ZK757.2 in chromosome III	0.59	-	mit	0					294
P34735 UniProt NPD GO	YLU2_PICAN	Hypothetical protein in LEU2 3'region (Fragment)	0.59	-	nuc	1					373
O08717 UniProt NPD GO	INHBE_MOUSE	Inhibin beta E chain precursor (Activin beta-E chain)	0.59	-	exc	0	Secreted protein (By similarity)				350
P05008 UniProt NPD GO	IFNAB_BOVIN	Interferon alpha-B precursor	0.59	-	mit	1 *	Secreted protein				189
P79135 UniProt NPD GO	MX1_BOVIN	Interferon-induced GTP-binding protein Mx1	0.59	-	cyt	0	Cytoplasm				648
Q96PP8 UniProt NPD GO	GBP5_HUMAN	Interferon-induced guanylate-binding protein 5 (GTP-binding protein 5) (Guanine nucleotide-binding p ...	0.59	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				586
Q64112 UniProt NPD GO	IFIT2_MOUSE	Interferon-induced protein with tetratricopeptide repeats 2 (IFIT-2) (Interferon-induced 54 kDa prot ...	0.59	-	nuc	0					472
O46613 UniProt NPD GO	IL1A_FELCA	Interleukin-1 alpha precursor (IL-1 alpha)	0.59	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				270
Q60480 UniProt NPD GO	IL1A_CAVPO	Interleukin-1 alpha precursor (IL-1 alpha) (Fragment)	0.59	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				204
Q60837 UniProt NPD GO	I12R1_MOUSE	Interleukin-12 receptor beta-1 chain precursor (IL-12R-beta1) (Interleukin-12 receptor beta) (IL-12 ...	0.59	-	exc	1	Membrane; single-pass type I membrane protein				738
Q99665 UniProt NPD GO	I12R2_HUMAN	Interleukin-12 receptor beta-2 chain precursor (IL-12 receptor beta-2) (IL-12R-beta2)	0.59	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601642		862
Q14005 UniProt NPD GO	IL16_HUMAN	Interleukin-16 precursor (IL-16) (Lymphocyte chemoattractant factor) (LCF)	0.59	-	nuc	0	Secreted protein	extracellular space [TAS]	603035	1X6D	631
O62676 UniProt NPD GO	IL16_MACFA	Interleukin-16 precursor (IL-16) (Lymphocyte chemoattractant factor) (LCF)	0.59	-	nuc	0	Secreted protein (By similarity)				630
O62675 UniProt NPD GO	IL16_MACMU	Interleukin-16 precursor (IL-16) (Lymphocyte chemoattractant factor) (LCF)	0.59	-	nuc	0	Secreted protein (By similarity)				630
O62666 UniProt NPD GO	IL16_PANTR	Interleukin-16 precursor (IL-16) (Lymphocyte chemoattractant factor) (LCF)	0.59	-	nuc	0	Secreted protein (By similarity)				631
Q9EQI6 UniProt NPD GO	IL17B_MESAU	Interleukin-17B precursor (IL-17B) (Neuronal interleukin-17-related factor) (Fragment)	0.59	-	nuc	0	Secreted protein				178
O02733 UniProt NPD GO	IL2RA_PIG	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (CD25 ...	0.59	-	cyt	1	Membrane; single-pass type I membrane protein				270
Q76LU5 UniProt NPD GO	IL21_BOVIN	Interleukin-21 precursor (IL-21)	0.59	-	nuc	0	Secreted protein				146
Q19286 UniProt NPD GO	IFB2_CAEEL	Intermediate filament protein ifb-2 (Intermediate filament protein B2) (IF-B2) (Cel IF B2)	0.59	-	nuc	0	Cytoplasm				543
P24709 UniProt NPD GO	INVO_CEBAL	Involucrin	0.59	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope	cornified envelope [ISS] cytoplasm [ISS]			428
Q90Y54 UniProt NPD GO	JAG1B_BRARE	Jagged-1b precursor (Jagged1b) (Jagged3)	0.59	-	exc	1	Membrane; single-pass type I membrane protein (Probable)	integral to membrane [NAS]			1213
Q80WT0 UniProt NPD GO	JPH4_MOUSE	Junctophilin-4 (Junctophilin-like 1 protein)	0.59	-	cyt	0	Membrane; single-pass type IV membrane protein (By similarity)	microsome [IDA]			628
Q6CN28 UniProt NPD GO	SMI1_KLULA	KNR4/SMI1 homolog	0.59	+	nuc	0					535
Q13351 UniProt NPD GO	KLF1_HUMAN	Krueppel-like factor 1 (Erythroid krueppel-like transcription factor) (EKLF) (Erythroid transcriptio ...	0.59	-	nuc	0	Nucleus		600599		362
O35819 UniProt NPD GO	KLF6_RAT	Krueppel-like factor 6 (Core promoter element-binding protein) (Transcription factor Zf9)	0.59	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			283
P25369 UniProt NPD GO	LSB5_YEAST	LAS seventeen-binding protein 5 (LAS17-binding protein 5)	0.59	-	nuc	0	Cytoplasm; cell cortex. Localizes independently of F-actin	cell cortex [IDA]			354
P53411 UniProt NPD GO	LHX1_CHICK	LIM/homeobox protein Lhx1 (Homeobox protein LIM-1)	0.59	+	nuc	0	Nucleus (Probable)				406
P29674 UniProt NPD GO	LHX1_XENLA	LIM/homeobox protein Lhx1 (Homeobox protein LIM-1) (xLIM-1)	0.59	+	nuc	0	Nucleus (Probable)				403
P25391 UniProt NPD GO	LAMA1_HUMAN	Laminin alpha-1 chain precursor (Laminin A chain)	0.59	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	laminin-1 [NAS] laminin-3 [NAS]	150320		3075
O15230 UniProt NPD GO	LAMA5_HUMAN	Laminin alpha-5 chain precursor	0.59	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component		601033		3695
P15838 UniProt NPD GO	LEGA2_PEA	Legumin A2 precursor [Contains: Legumin A2 alpha chain (Legumin A2 acidic chain); Legumin A2 beta ch ...	0.59	-	exc	0					520
Q3T0H0 UniProt NPD GO	LCMT1_BOVIN	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-)	0.59	-	mit	0					332
Q9UIC8 UniProt NPD GO	LCMT1_HUMAN	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein-leucine O-methyltransferase)	0.59	-	exc	0					334

You are viewing entries 19601 to 19650 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.