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
Q9D9Z7 UniProt NPD GO	H2BV_MOUSE	Histone H2B subacrosomal variant	0.55	-	mit	0	Cytoplasm. Subacrosomal region. Does not localize in nucleus (By similarity)				122
P62807 UniProt NPD GO	H2B1C_HUMAN	Histone H2B type 1-C/E/F/G/I (H2B.a/g/h/k/l) (H2B.1 A) (H2B/a) (H2B/g) (H2B/h) (H2B/k) (H2B/l)	0.55	+	nuc	0	Nucleus	nucleosome [NAS]	602847		124
Q2PFX4 UniProt NPD GO	H2B1K_MACFA	Histone H2B type 1-K (H2B K)	0.55	+	nuc	0	Nucleus				125
Q8CGP0 UniProt NPD GO	H2B3B_MOUSE	Histone H2B type 3-B	0.55	+	nuc	0	Nucleus				125
Q8N257 UniProt NPD GO	H2B3B_HUMAN	Histone H2B type 3-B (H2B type 12)	0.55	+	nuc	0	Nucleus				125
P35068 UniProt NPD GO	H2B1_TIGCA	Histone H2B.1/H2B.2	0.55	-	nuc	0	Nucleus				122
Q8J1F8 UniProt NPD GO	H2B2_ASHGO	Histone H2B.2	0.55	-	nuc	0					126
Q6FKS5 UniProt NPD GO	HAT1_CANGA	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.55	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				388
Q84WW6 UniProt NPD GO	ASHH1_ARATH	Histone-lysine N-methyltransferase ASHH1 (EC 2.1.1.43) (ASH1-homolog protein 1) (Protein SET DOMAIN ...	0.55	-	nuc	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				492
Q946J2 UniProt NPD GO	SUVR1_ARATH	Histone-lysine N-methyltransferase SUVR1 (EC 2.1.1.43) (Suppressor of variegation 3-9-related protei ...	0.55	+	nuc	0	Nucleus (By similarity). Associates with euchromatic regions (By similarity)				630
O08686 UniProt NPD GO	BARX2_MOUSE	Homeobox protein BarH-like 2	0.55	+	nuc	0	Nucleus	transcription factor complex [IDA]			228
Q98879 UniProt NPD GO	DLX4A_BRARE	Homeobox protein Dlx4a (DLX-8) (Distal-less homeobox protein 4a)	0.55	+	nuc	0	Nucleus (Potential)				250
P50223 UniProt NPD GO	HMGX7_CHICK	Homeobox protein GHOX-7 (CHOX-7) (Hox-7)	0.55	+	nuc	0	Nucleus (Probable)				288
Q99687 UniProt NPD GO	MEIS3_HUMAN	Homeobox protein Meis3 (Meis1-related protein 2)	0.55	-	nuc	0	Nucleus (Probable)				375
P53188 UniProt NPD GO	YGC9_YEAST	Hypothetical 14.4 kDa protein in RPL30-CWH41 intergenic region	0.55	-	nuc	0		nucleolus [IDA]			120
P09363 UniProt NPD GO	YCX1_SOYBN	Hypothetical 16.8 kDa protein (ORF 143)	0.55	-	nuc	0	Plastid; chloroplast				143
P53177 UniProt NPD GO	YGF0_YEAST	Hypothetical 30.8 kDa protein in DUP2-TIF4632 intergenic region	0.55	+	nuc	0					273
P40476 UniProt NPD GO	YIL7_YEAST	Hypothetical 34.7 kDa protein in RHO3-HIS5 intergenic region	0.55	-	nuc	1					318
P53208 UniProt NPD GO	YG19_YEAST	Hypothetical 37.9 kDa protein in MSB2-UGA1 intergenic region	0.55	-	nuc	0		mitochondrion [IDA]			328
P53878 UniProt NPD GO	YNS1_YEAST	Hypothetical 46.5 kDa protein in NPR1-RPS3 intergenic region	0.55	-	mit	1		endoplasmic reticulum [IDA] nuclear envelope [IDA]			407
P53264 UniProt NPD GO	YG2V_YEAST	Hypothetical 52.0 kDa protein in CLB6-SHY1 intergenic region	0.55	-	mit	0					445
P47048 UniProt NPD GO	YJE9_YEAST	Hypothetical 52.8 kDa protein in MTR4-GYP6 intergenic region	0.55	-	nuc	0					450
P53235 UniProt NPD GO	YG22_YEAST	Hypothetical 71.3 kDa protein in SCM4-MUP1 intergenic region	0.55	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]			642
Q09523 UniProt NPD GO	YQN2_CAEEL	Hypothetical GTP-binding protein E02H1.2 in chromosome II	0.55	-	mit	0					394
Q09866 UniProt NPD GO	YAG1_SCHPO	Hypothetical WD repeat protein C12G12.01c in chromosome I	0.55	-	nuc	0					905
P87177 UniProt NPD GO	YB1C_SCHPO	Hypothetical WD repeat protein C3D6.12 in chromosome II	0.55	+	cyt	0					922
P93275 UniProt NPD GO	M010_ARATH	Hypothetical mitochondrial protein AtMg00010 (ORF153a)	0.55	-	nuc	0	Mitochondrion (Potential)				153
Q11081 UniProt NPD GO	YT65_CAEEL	Hypothetical protein B0563.5	0.55	-	nuc	0					90
Q9UTN2 UniProt NPD GO	YII1_SCHPO	Hypothetical protein C139.01c	0.55	-	nuc	0					802
Q09796 UniProt NPD GO	YAA2_SCHPO	Hypothetical protein C22G7.02 in chromosome I	0.55	-	end	0					990
O13915 UniProt NPD GO	YDWA_SCHPO	Hypothetical protein C23C11.10 in chromosome I	0.55	-	nuc	0					265
O74780 UniProt NPD GO	YGB8_SCHPO	Hypothetical protein C25B2.08 in chromosome II	0.55	-	nuc	0					125
Q09889 UniProt NPD GO	YC9F_SCHPO	Hypothetical protein C584.15c in chromosome III	0.55	-	nuc	0					594
Q09529 UniProt NPD GO	YQO2_CAEEL	Hypothetical protein EEED8.2	0.55	-	nuc	0					299
P34396 UniProt NPD GO	YLU2_CAEEL	Hypothetical protein F10E9.2	0.55	-	nuc	0					286
Q09307 UniProt NPD GO	YQR2_CAEEL	Hypothetical protein F19C6.2	0.55	-	nuc	0					495
Q03610 UniProt NPD GO	YN81_CAEEL	Hypothetical protein ZC84.1 in chromosome III	0.55	-	nuc	0					1416
O60084 UniProt NPD GO	TIM44_SCHPO	Import inner membrane translocase subunit tim44, mitochondrial precursor	0.55	-	mit	0	Mitochondrion; mitochondrial inner membrane (Potential)				427
Q3T095 UniProt NPD GO	ING4_BOVIN	Inhibitor of growth protein 4 (p29ING4)	0.55	-	nuc	0	Nucleus (By similarity)				248
Q4I298 UniProt NPD GO	MRS2_GIBZE	Inner membrane magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.55	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				498
Q96PC2 UniProt NPD GO	IP6K3_HUMAN	Inositol hexaphosphate kinase 3 (EC 2.7.4.21) (InsP6 kinase 3) (Inositol hexakisphosphate kinase 3)	0.55	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]	606993		410
Q59KN8 UniProt NPD GO	IPK1_CANAL	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.55	-	nuc	0	Nucleus (By similarity)				361
P14735 UniProt NPD GO	IDE_HUMAN	Insulin-degrading enzyme (EC 3.4.24.56) (Insulysin) (Insulinase) (Insulin protease)	0.55	-	cyt	0	Cytoplasm	extracellular space [TAS] peroxisome [TAS] soluble fraction [TAS]	146680		1018
Q90WW4 UniProt NPD GO	IGF2A_XENLA	Insulin-like growth factor II-A precursor (IGF-II-A) (Insulin-like growth factor 2-A) (xIGF-2)	0.55	-	nuc	0	Secreted protein (By similarity)				217
Q90873 UniProt NPD GO	IFNB_CHICK	Interferon type B precursor	0.55	-	exc	0	Secreted protein (Probable)				203
O82391 UniProt NPD GO	JOSL_ARATH	Josephin-like protein	0.55	+	nuc	0					360
Q96G42 UniProt NPD GO	KLD7B_HUMAN	Kelch domain-containing protein 7B	0.55	-	mit	0					495
Q9NSB4 UniProt NPD GO	KRHB2_HUMAN	Keratin, type II cuticular Hb2 (Hair keratin, type II Hb2)	0.55	-	mit	0			601078		513
Q60660 UniProt NPD GO	KLRA2_MOUSE	Killer cell lectin-like receptor 2 (T-cell surface glycoprotein Ly-49B) (Ly49-B antigen) (Lymphocyte ...	0.55	-	nuc	1 *	Membrane; single-pass type II membrane protein	plasma membrane [TAS]			288
Q8MI05 UniProt NPD GO	KLRF1_MACFA	Killer cell lectin-like receptor subfamily F member 1 (Lectin-like receptor F1) (Activating corecept ...	0.55	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)				231

You are viewing entries 22001 to 22050 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.)

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