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
Q71LE2 UniProt NPD GO	H33_PIG	Histone H3.3	0.49	-	nuc	0	Nucleus (By similarity)				135
P84246 UniProt NPD GO	H33_RABIT	Histone H3.3	0.49	-	nuc	0	Nucleus (By similarity)	nucleosome [ISS]			135
P84245 UniProt NPD GO	H33_RAT	Histone H3.3	0.49	-	nuc	0	Nucleus (By similarity)	nucleosome [ISS]			135
P84248 UniProt NPD GO	H33_SPISO	Histone H3.3	0.49	-	nuc	0	Nucleus (By similarity)	nucleosome [ISS]			135
P84247 UniProt NPD GO	H33_CHICK	Histone H3.3 (H3.3A/B) (Histone H3 class II)	0.49	-	nuc	0	Nucleus (By similarity)	nucleosome [ISS]			135
P84250 UniProt NPD GO	H33_DROHY	Histone H3.3 (H3.A/B)	0.49	-	nuc	0	Nucleus (By similarity)	nucleosome [ISS]			135
P84249 UniProt NPD GO	H33_DROME	Histone H3.3 (H3.A/B) (H3.3Q)	0.49	-	nuc	0	Nucleus (By similarity)	nucleosome [NAS]			135
Q9LZR5 UniProt NPD GO	HD2C_ARATH	Histone deacetylase 2c (HD-tuins protein 3)	0.49	-	nuc	0	Nucleus; nucleolus				294
O43463 UniProt NPD GO	SUV91_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-9 specific 1 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.49	-	mit	0	Nucleus. Associates with centromeric constitutive heterochromatin	condensed nuclear chromosome [TAS] nucleus [TAS]	300254		412
Q9UBX0 UniProt NPD GO	HESX1_HUMAN	Homeobox expressed in ES cells 1 (Homeobox protein ANF) (hAnf)	0.49	+	nuc	0	Nucleus (Probable)		601802		185
Q98876 UniProt NPD GO	DLX2B_BRARE	Homeobox protein Dlx2b (DLX-5) (Distal-less homeobox protein 2b)	0.49	+	nuc	0	Nucleus (Potential)				276
P31315 UniProt NPD GO	GSHI_MOUSE	Homeobox protein GSH-1	0.49	+	nuc	0	Nucleus				261
P35453 UniProt NPD GO	HXD13_HUMAN	Homeobox protein Hox-D13 (Hox-4I)	0.49	+	nuc	0	Nucleus		186000		335
P83949 UniProt NPD GO	UBX_DROME	Homeotic protein ultrabithorax	0.49	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [NAS]		1B8I	389
P83950 UniProt NPD GO	UBX_DROSI	Homeotic protein ultrabithorax	0.49	+	nuc	0	Nucleus	nucleus [ISS] transcription factor complex [ISS]			389
Q9Z2Y3 UniProt NPD GO	HOME1_MOUSE	Homer protein homolog 1 (VASP/Ena-related gene up-regulated during seizure and LTP) (Vesl-1)	0.49	-	nuc	0	Cytoplasm. Postsynaptic density of neuronal cells. Isoform 1 inhibits surface expression of GRM5 cau ...	cytoplasm [IDA] plasma membrane [IDA]			366
Q9V4C8 UniProt NPD GO	HCF_DROME	Host cell factor (dHcf) [Contains: HCF N-terminal chain; HCF C-terminal chain]	0.49	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			1500
Q14520 UniProt NPD GO	HABP2_HUMAN	Hyaluronan-binding protein 2 precursor (EC 3.4.21.-) (Plasma hyaluronan-binding protein) (Hepatocyte ...	0.49	-	exc	0	Secreted protein. Secreted as an inactive single-chain precursor and is then activated to a heterodi ...	extracellular region [NAS] extracellular space [TAS]	603924		560
P53240 UniProt NPD GO	YG27_YEAST	Hypothetical 14.4 kDa protein in SPT4-VHT1 intergenic region	0.49	-	mit	0					122
P53325 UniProt NPD GO	YG5K_YEAST	Hypothetical 16.1 kDa protein in MES1-FOL2 intergenic region	0.49	-	mit	1 *					136
P38856 UniProt NPD GO	YHW1_YEAST	Hypothetical 71.7 kDa protein in REC104-SOL3 intergenic region	0.49	-	nuc	0		actin cortical patch [IDA]			637
P39992 UniProt NPD GO	YEC3_YEAST	Hypothetical 78.3 kDa protein in RIP1-GEA2 intergenic region	0.49	-	nuc	0					682
Q9SUA9 UniProt NPD GO	DOF44_ARATH	Hypothetical Dof zinc finger protein DOF4.4 (AtDOF4.4)	0.49	-	nuc	0	Nucleus (Probable)				210
P03939 UniProt NPD GO	YBAS_PHAVU	Hypothetical basic polypeptide	0.49	-	mit	0					58
P14588 UniProt NPD GO	YDH2_PLAFS	Hypothetical protein 3' to Asp-rich and His-rich proteins (Fragment)	0.49	-	nuc	0					78
Q09217 UniProt NPD GO	YP68_CAEEL	Hypothetical protein B0495.8	0.49	+	nuc	0					313
O60098 UniProt NPD GO	YOX1_SCHPO	Hypothetical protein C14F5.01 in chromosome II	0.49	-	mit	0					278
Q09861 UniProt NPD GO	YAF7_SCHPO	Hypothetical protein C29E6.07 in chromosome I	0.49	-	cyt	1 *					116
O14084 UniProt NPD GO	YER1_SCHPO	Hypothetical protein C2F3.01 precursor	0.49	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				319
O14166 UniProt NPD GO	YDX3_SCHPO	Hypothetical protein C4C5.03 in chromosome I	0.49	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				302
O14185 UniProt NPD GO	YDSA_SCHPO	Hypothetical protein C4F8.10c in chromosome I	0.49	-	nuc	0		actin cortical patch [IDA]			174
Q20762 UniProt NPD GO	YAO6_CAEEL	Hypothetical protein F54D1.6 precursor	0.49	-	end	1					1423
Q05648 UniProt NPD GO	YD282_YEAST	Hypothetical protein YDR282C	0.49	-	nuc	0	Membrane; single-pass membrane protein (Potential)				414
P34653 UniProt NPD GO	YOT7_CAEEL	Hypothetical protein ZK632.7	0.49	+	nuc	0					632
Q99312 UniProt NPD GO	ISN1_YEAST	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.49	-	nuc	0					450
P01882 UniProt NPD GO	IGHDM_MOUSE	Ig delta chain C region membrane-bound form	0.49	-	nuc	1					290
Q5KNV7 UniProt NPD GO	TIM50_CRYNE	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.49	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				516
P38250 UniProt NPD GO	IST2_YEAST	Increased sodium tolerance protein 2	0.49	-	nuc	8	Cell membrane; multi-pass membrane protein. Correct localization requires BTN2. Localizes to the mot ...	bud [IDA] plasma membrane [IDA]			946
Q9UNL4 UniProt NPD GO	ING4_HUMAN	Inhibitor of growth protein 4 (p29ING4)	0.49	-	nuc	0	Nucleus	nucleus [IDA]	608524		249
Q01968 UniProt NPD GO	OCRL_HUMAN	Inositol polyphosphate 5-phosphatase OCRL-1 (EC 3.1.3.36) (Lowe oculocerebrorenal syndrome protein)	0.49	-	cyt	0		Golgi stack [TAS] Golgi-associated vesicle [TAS]	309000		901
Q9JHR7 UniProt NPD GO	IDE_MOUSE	Insulin-degrading enzyme (EC 3.4.24.56) (Insulysin) (Insulinase) (Insulin protease)	0.49	-	mit	0	Cytoplasm (By similarity)				1019
P47880 UniProt NPD GO	IBP6_MOUSE	Insulin-like growth factor-binding protein 6 precursor (IGFBP-6) (IBP-6) (IGF-binding protein 6)	0.49	-	nuc	1 *	Secreted protein				238
P08648 UniProt NPD GO	ITA5_HUMAN	Integrin alpha-5 precursor (Fibronectin receptor subunit alpha) (Integrin alpha-F) (VLA-5) (CD49e an ...	0.49	-	nuc	1	Membrane; single-pass type I membrane protein	integrin complex [TAS] ruffle [TAS]	135620		1049
P12080 UniProt NPD GO	ITA2_DROME	Integrin alpha-PS2 precursor (Position-specific antigen 2 alpha chain) (Protein inflated)	0.49	-	exc	2 *	Membrane; single-pass type I membrane protein	contractile fiber [IDA] integrin complex [TAS]			1396
Q8CFB4 UniProt NPD GO	GBP5_MOUSE	Interferon-induced guanylate-binding protein 5 (GTP-binding protein 5) (Guanine nucleotide-binding p ...	0.49	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				590
Q4V8C7 UniProt NPD GO	PRKRA_RAT	Interferon-inducible double stranded RNA-dependent protein kinase activator A (Protein kinase, inter ...	0.49	-	nuc	0					313
O75569 UniProt NPD GO	PRKRA_HUMAN	Interferon-inducible double stranded RNA-dependent protein kinase activator A (Protein kinase, inter ...	0.49	-	nuc	0			603424		313
Q9WTX2 UniProt NPD GO	PRKRA_MOUSE	Interferon-inducible double stranded RNA-dependent protein kinase activator A (Protein kinase, inter ...	0.49	-	nuc	0					313
Q865X7 UniProt NPD GO	IL1A_LAMGL	Interleukin-1 alpha precursor (IL-1 alpha)	0.49	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				268
P79340 UniProt NPD GO	IL1A_MACFA	Interleukin-1 alpha precursor (IL-1 alpha) (Hematopoietin-1)	0.49	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				271

You are viewing entries 25651 to 25700 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.