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
Q9BZ71 UniProt NPD GO	PITM3_HUMAN	Membrane-associated phosphatidylinositol transfer protein 3 (Phosphatidylinositol transfer protein, ...	0.84	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (Probable)	integral to membrane [TAS]	608921		974
Q8NHZ7 UniProt NPD GO	MB3L2_HUMAN	Methyl-CpG-binding domain protein 3-like 2 (MBD3-like 2)	0.84	-	nuc	0			607964		204
Q96DN6 UniProt NPD GO	MBD6_HUMAN	Methyl-CpG-binding domain protein 6 (Methyl-CpG-binding protein MBD6)	0.84	-	nuc	0					1003
P20357 UniProt NPD GO	MAP2_MOUSE	Microtubule-associated protein 2 (MAP 2)	0.84	-	nuc	0		cytoplasm [IDA] dendritic shaft [IDA] microtubule associated complex [TAS]			1828
P11137 UniProt NPD GO	MAP2_HUMAN	Microtubule-associated protein 2 (MAP 2) (MAP-2)	0.84	-	nuc	0		microtubule associated complex [TAS]	157130		1827
P27928 UniProt NPD GO	RT03_MAIZE	Mitochondrial ribosomal protein S3	0.84	-	nuc	0	Mitochondrion				559
P27754 UniProt NPD GO	RT03_OENBE	Mitochondrial ribosomal protein S3	0.84	-	nuc	0	Mitochondrion				550
P47907 UniProt NPD GO	RMS5_PENUR	Mitochondrial ribosomal protein S5	0.84	+	nuc	0	Mitochondrion				399
P46756 UniProt NPD GO	RT07_ACACA	Mitochondrial ribosomal protein S7	0.84	-	mit	0	Mitochondrion				337
Q9ESL4 UniProt NPD GO	MLTK_MOUSE	Mitogen-activated protein kinase kinase kinase MLT (EC 2.7.11.25) (MLK-like mitogen-activated protei ...	0.84	-	nuc	0	Cytoplasm. Nucleus. Isoform 2 appears to shuttle between nucleus and cytoplasm	cytoplasm [IDA] nucleus [IDA]			802
P07527 UniProt NPD GO	WEE1_SCHPO	Mitosis inhibitor protein kinase wee1 (EC 2.7.11.1) (P107 protein kinase homolog)	0.84	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			877
Q75A83 UniProt NPD GO	MRD1_ASHGO	Multiple RNA-binding domain-containing protein 1	0.84	-	nuc	0	Nucleus (By similarity)				838
P20309 UniProt NPD GO	ACM3_HUMAN	Muscarinic acetylcholine receptor M3	0.84	+	vac	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	118494	2CSA	590
P15172 UniProt NPD GO	MYOD1_HUMAN	Myoblast determination protein 1 (Myogenic factor 3) (Myf-3)	0.84	+	nuc	0	Nucleus	nucleus [TAS]	159970		319
Q91205 UniProt NPD GO	MYOD1_ONCMY	Myoblast determination protein 1 homolog 1 (Myogenic factor 1-1)	0.84	+	nuc	0	Nucleus				276
Q8VIM5 UniProt NPD GO	MYCD_MOUSE	Myocardin (SRF cofactor protein) (Basic SAP coiled-coil transcription activator 2)	0.84	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear, with a punctate intranuclear pattern with exclusion ...	nucleus [IDA]			935
Q14814 UniProt NPD GO	MEF2D_HUMAN	Myocyte-specific enhancer factor 2D	0.84	-	nuc	0	Nucleus		600663		521
Q63943 UniProt NPD GO	MEF2D_MOUSE	Myocyte-specific enhancer factor 2D	0.84	-	nuc	0	Nucleus	nucleus [IDA]			514
Q3YFL6 UniProt NPD GO	MYF6_PIG	Myogenic factor 6 (Myf-6)	0.84	+	nuc	0	Nucleus (By similarity)				242
Q5DTJ9 UniProt NPD GO	MYPN_MOUSE	Myopalladin	0.84	-	nuc	0	Cytoplasm. Bound to sarcomere both at the Z-line periphery and in the central I-band region. Nucleus ...				1315
O43795 UniProt NPD GO	MYO1B_HUMAN	Myosin Ib (Myosin I alpha) (MMI-alpha) (MMIa) (MYH-1c)	0.84	-	nuc	0			606537		1136
P47068 UniProt NPD GO	BBC1_YEAST	Myosin tail region-interacting protein MTI1 (Protein BBC1)	0.84	-	nuc	0	Actin patch. Colocalizes with cortical actin patches	actin cortical patch [IDA]		1WDX	1157
Q876G9 UniProt NPD GO	MYO2_SACBA	Myosin-2 (Class V unconventional myosin MYO2) (Type V myosin heavy chain MYO2) (Myosin V MYO2)	0.84	-	cyt	0					1568
Q875Q8 UniProt NPD GO	MYO2_SACKL	Myosin-2 (Class V unconventional myosin MYO2) (Type V myosin heavy chain MYO2) (Myosin V MYO2)	0.84	-	nuc	0					1554
Q9QYF3 UniProt NPD GO	MYO5A_RAT	Myosin-5A (Myosin Va) (Dilute myosin heavy chain, non-muscle)	0.84	-	nuc	0		secretory granule [TAS]			1828
Q9DBB4 UniProt NPD GO	NARGL_MOUSE	NMDA receptor-regulated 1-like protein (NARG1-like protein)	0.84	-	nuc	0					864
P92204 UniProt NPD GO	NELFE_DROME	Negative elongation factor E	0.84	-	nuc	0	Nucleus. Associates with polytene chromosomes. Associates with the hsp70 promoter when it is inactiv ...	transcription elongation factor complex [IPI] transcriptional repressor complex [IDA]			280
P34072 UniProt NPD GO	MKS1_YEAST	Negative regulator of RAS-cAMP pathway	0.84	-	nuc	0	Nucleus	intracellular [IC]			584
O17972 UniProt NPD GO	NPHP1_CAEEL	Nephrocystin-1-like protein (Nephronophthisis homolog)	0.84	-	nuc	0					682
Q7Z494 UniProt NPD GO	NPHP3_HUMAN	Nephrocystin-3	0.84	-	gol	0			608002		1330
O62647 UniProt NPD GO	PNOC_BOVIN	Nociceptin precursor [Contains: Neuropeptide 1; Nociceptin (Orphanin FQ) (PPNOC); Neuropeptide 2]	0.84	-	exc	0	Secreted protein				176
O88984 UniProt NPD GO	NXF1_RAT	Nuclear RNA export factor 1 (Tip-associating protein) (Tip-associated protein) (mRNA export factor T ...	0.84	-	nuc	0	Nucleus; nucleoplasm (By similarity). Cytoplasm (By similarity). Localized predominantly in the nucl ...				618
P70257 UniProt NPD GO	NFIX_MOUSE	Nuclear factor 1 X-type (Nuclear factor 1/X) (NF1-X) (NFI-X) (NF-I/X) (CCAAT-box-binding transcripti ...	0.84	-	nuc	0	Nucleus				488
Q23294 UniProt NPD GO	NHR11_CAEEL	Nuclear hormone receptor family member nhr-11	0.84	-	nuc	0	Nucleus (By similarity)				459
Q9XYB7 UniProt NPD GO	NHR8_CAEEL	Nuclear hormone receptor family member nhr-8	0.84	-	nuc	0	Nucleus (Potential)				560
Q9N1A3 UniProt NPD GO	STP2_MACMU	Nuclear transition protein 2 (TP-2) (TP2) (Fragment)	0.84	+	mit	0	Nucleus (By similarity)				137
O94818 UniProt NPD GO	NOL4_HUMAN	Nucleolar protein 4 (Nucleolar-localized protein)	0.84	-	nuc	0	Nucleus; nucleolus	nucleolus [TAS]	603577		524
Q3SZ63 UniProt NPD GO	NOP56_BOVIN	Nucleolar protein Nop56 (Nucleolar protein 5A)	0.84	+	nuc	0	Nucleus; nucleolus (By similarity)				596
P52593 UniProt NPD GO	NU188_YEAST	Nucleoporin NUP188 (Nuclear pore protein NUP188)	0.84	-	end	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			1655
Q03790 UniProt NPD GO	NUP53_YEAST	Nucleoporin NUP53 (Nuclear pore protein NUP53)	0.84	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			475
Q04913 UniProt NPD GO	NR4A2_XENLA	Orphan nuclear receptor NR4A2 (Orphan nuclear receptor NURR1) (Nerve growth factor-induced protein I ...	0.84	-	nuc	0	Nucleus				577
P45448 UniProt NPD GO	NR5A2_MOUSE	Orphan nuclear receptor NR5A2 (Liver receptor homolog 1) (LRH-1)	0.84	+	nuc	0	Nucleus (Probable)			1ZH7	560
P20240 UniProt NPD GO	OTE_DROME	Otefin	0.84	+	nuc	1	Nucleus; nuclear inner membrane; single-pass type I membrane protein. It is a component of the spind ...	nuclear inner membrane [IDA]			424
Q6BJM5 UniProt NPD GO	OXR1_DEBHA	Oxidation resistance protein 1	0.84	-	nuc	0	Mitochondrion (By similarity)				323
Q969R2 UniProt NPD GO	OSBP2_HUMAN	Oxysterol-binding protein 2 (Oxysterol-binding protein-related protein 4) (OSBP-related protein 4) ( ...	0.84	+	nuc	0	Membrane; peripheral membrane protein		606729		916
P38151 UniProt NPD GO	PBP2_YEAST	PAB1-binding protein 2	0.84	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA]			413
Q6ZVD8 UniProt NPD GO	PHLPL_HUMAN	PH domain leucine-rich repeat protein phosphatase-like (EC 3.1.3.16)	0.84	-	nuc	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (By similarity). May be membrane-associa ...				1323
O60346 UniProt NPD GO	PHLPP_HUMAN	PH domain leucine-rich repeat-containing protein phosphatase (EC 3.1.3.16) (PH domain leucine-rich r ...	0.84	-	nuc	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (By similarity). May be membrane-associa ...		609396		1717
P38835 UniProt NPD GO	YHT1_YEAST	PH domain-containing protein YHR131C	0.84	+	nuc	0	Cytoplasm	cytoplasm [IDA]			850
Q9D4J7 UniProt NPD GO	PHF6_MOUSE	PHD finger protein 6	0.84	+	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Nuclear, it particularly localizes to t ...				364

You are viewing entries 7051 to 7100 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.