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
Q8AYC2 UniProt NPD GO	MRTFA_XENLA	Myocardin-related transcription factor A (MRTF-A) (xMRTF-A)	0.90	+	nuc	0	Nucleus (By similarity)				936
P04460 UniProt NPD GO	MYH6_RABIT	Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha) (Alpha isomyosin) (Fragment)	0.90	+	nuc	0	Thick filaments of the myofibrils				465
P02562 UniProt NPD GO	MYSS_RABIT	Myosin heavy chain, skeletal muscle (Fragments)	0.90	+	nuc	0	Thick filaments of the myofibrils				1084
Q61879 UniProt NPD GO	MYH10_MOUSE	Myosin-10 (Myosin heavy chain, nonmuscle IIb) (Nonmuscle myosin heavy chain IIb) (NMMHC II-b) (NMMHC ...	0.90	+	nuc	0		cytoplasm [IDA] stress fiber [IDA]			1976
P12845 UniProt NPD GO	MYO2_CAEEL	Myosin-2 (Myosin heavy chain C) (MHC C)	0.90	-	nuc	0	Thick filaments of the myofibrils				1947
Q04439 UniProt NPD GO	MYO5_YEAST	Myosin-5	0.90	-	nuc	0		actin cortical patch [IDA]		1YP5	1219
Q9NQX4 UniProt NPD GO	MYO5C_HUMAN	Myosin-5C (Myosin Vc)	0.90	-	nuc	0					1742
P14105 UniProt NPD GO	MYH9_CHICK	Myosin-9 (Myosin heavy chain, nonmuscle IIa) (Nonmuscle myosin heavy chain IIa) (NMMHC II-a) (NMMHC- ...	0.90	+	nuc	0					1959
Q62812 UniProt NPD GO	MYH9_RAT	Myosin-9 (Myosin heavy chain, nonmuscle IIa) (Nonmuscle myosin heavy chain IIa) (NMMHC II-a) (NMMHC- ...	0.90	+	nuc	0					1960
Q9H0A0 UniProt NPD GO	NAT10_HUMAN	N-acetyltransferase 10 (EC 2.3.1.-)	0.90	+	mit	0	Nucleus; nucleolus	nucleus [NAS]	609221		1025
O15226 UniProt NPD GO	NKRF_HUMAN	NF-kappa-B-repressing factor (NFKB-repressing factor) (Transcription factor NRF) (ITBA4 protein)	0.90	+	nuc	0	Nucleus; nucleolus	nucleus [IDA]	300440		690
Q9P2E3 UniProt NPD GO	ZNFX1_HUMAN	NFX1-type zinc finger-containing protein 1	0.90	+	nuc	0					1918
Q641K5 UniProt NPD GO	NUAK1_MOUSE	NUAK family SNF1-like kinase 1 (EC 2.7.11.1)	0.90	-	nuc	0					658
O60285 UniProt NPD GO	NUAK1_HUMAN	NUAK family SNF1-like kinase 1 (EC 2.7.11.1) (AMPK-related protein kinase 5)	0.90	-	nuc	0			608130		661
O77774 UniProt NPD GO	NCF1_BOVIN	Neutrophil cytosol factor 1 (NCF-1) (Neutrophil NADPH oxidase factor 1) (47 kDa neutrophil oxidase f ...	0.90	-	nuc	0	Cytoplasm				392
Q5RCV3 UniProt NPD GO	NBN_PONPY	Nibrin (Nijmegen breakage syndrome protein 1 homolog)	0.90	-	nuc	0	Nucleus (By similarity)	Mre11 complex [ISS] nuclear inclusion body [ISS]			754
O60934 UniProt NPD GO	NBN_HUMAN	Nibrin (Nijmegen breakage syndrome protein 1) (Cell cycle regulatory protein p95)	0.90	-	nuc	0	Nucleus (By similarity). Localizes to discrete nuclear foci after treatment with genotoxic agents (B ...	Mre11 complex [IDA] nuclear inclusion body [IDA]	609135		754
Q01582 UniProt NPD GO	AREA_PENCH	Nitrogen regulatory protein areA (Nitrogen regulator nre)	0.90	-	nuc	0	Nucleus				725
P08651 UniProt NPD GO	NFIC_HUMAN	Nuclear factor 1 C-type (Nuclear factor 1/C) (NF1-C) (NFI-C) (NF-I/C) (CCAAT-box-binding transcripti ...	0.90	-	nuc	0	Nucleus		600729		508
P21999 UniProt NPD GO	NFIC_PIG	Nuclear factor 1 C-type (Nuclear factor 1/C) (NF1-C) (NFI-C) (NF-I/C) (CCAAT-box-binding transcripti ...	0.90	-	nuc	0	Nucleus				506
O73630 UniProt NPD GO	NFKB2_XENLA	Nuclear factor NF-kappa-B p100 subunit (DNA-binding factor KBF2) [Contains: Nuclear factor NF-kappa- ...	0.90	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear, but also found in the cytoplasm in an i ...				958
Q9WTM4 UniProt NPD GO	NF2L3_MOUSE	Nuclear factor erythroid 2-related factor 3 (NF-E2-related factor 3) (NFE2-related factor 3) (Nuclea ...	0.90	+	nuc	1 *	Nucleus (By similarity)				660
Q641W3 UniProt NPD GO	NUFP1_RAT	Nuclear fragile X mental retardation-interacting protein 1 (Nuclear FMRP-interacting protein 1)	0.90	+	nuc	0	Nucleus. Distributed in the nucleus in a dot-like pattern (By similarity)				486
Q13823 UniProt NPD GO	NOG2_HUMAN	Nucleolar GTP-binding protein 2 (Autoantigen NGP-1)	0.90	+	nuc	0	Nucleus; nucleolus	nucleus [TAS]	609365		731
Q9VI82 UniProt NPD GO	NOC3L_DROME	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS] nucleus [ISS]			822
Q6BTS9 UniProt NPD GO	NOP12_DEBHA	Nucleolar protein 12	0.90	-	nuc	0	Nucleus; nucleolus (By similarity)				462
Q3UHX0 UniProt NPD GO	NOL8_MOUSE	Nucleolar protein 8	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS]			1147
Q95KF9 UniProt NPD GO	NO40_MACFA	Nucleolar protein of 40 kDa (pNO40) (Zinc finger CCHC domain-containing protein 17) (Putative S1 RNA ...	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)				193
Q7ZV00 UniProt NPD GO	OTU6B_BRARE	OTU domain-containing protein 6B	0.90	+	nuc	0					293
Q9NZT2 UniProt NPD GO	OGFR_HUMAN	Opioid growth factor receptor (OGFr) (Zeta-type opioid receptor) (7-60 protein)	0.90	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The OGF/OGFR complex is probably translocated to ...		606459		677
Q9ER64 UniProt NPD GO	OSBL5_MOUSE	Oxysterol-binding protein-related protein 5 (OSBP-related protein 5) (ORP-5) (Oxysterol-binding prot ...	0.90	-	nuc	1		cytosol [ISS]			874
Q5E9B6 UniProt NPD GO	NR1H3_BOVIN	Oxysterols receptor LXR-alpha (Liver X receptor alpha) (Nuclear orphan receptor LXR-alpha)	0.90	-	nuc	0					447
Q86YI8 UniProt NPD GO	PHF13_HUMAN	PHD finger protein 13	0.90	+	nuc	0					300
P79746 UniProt NPD GO	POU47_BRARE	POU domain protein ZP-47	0.90	+	nuc	0	Nucleus				378
P49335 UniProt NPD GO	PO3F4_HUMAN	POU domain, class 3, transcription factor 4 (Brain-specific homeobox/POU domain protein 4) (Brain-4) ...	0.90	+	nuc	0	Nucleus		304400		361
Q812B1 UniProt NPD GO	PO3F4_MESAU	POU domain, class 3, transcription factor 4 (Brain-specific homeobox/POU domain protein 4) (Brain-4) ...	0.90	+	nuc	0	Nucleus (By similarity)				361
P23760 UniProt NPD GO	PAX3_HUMAN	Paired box protein Pax-3 (HUP2)	0.90	+	nuc	0	Nucleus		606597		479
Q4ZHW1 UniProt NPD GO	PTF1A_XENLA	Pancreas transcription factor 1 subunit alpha (Pancreas-specific transcription factor 1a) (Transcrip ...	0.90	+	nuc	0	Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS] transcription factor complex [ISS]			270
Q7ZSX3 UniProt NPD GO	PTF1A_BRARE	Pancreas transcription factor 1 subunit alpha (Pancreas-specific transcription factor 1a) (bHLH tran ...	0.90	-	nuc	0	Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS] transcription factor complex [ISS]			265
P22858 UniProt NPD GO	PTHR_MOUSE	Parathyroid hormone-related protein precursor (PTH-rP) (PTHrP) (PLP) [Contains: Osteostatin]	0.90	+	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity)	extracellular space [TAS]			175
P17251 UniProt NPD GO	PTHR_CHICK	Parathyroid hormone-related protein precursor (PTH-rP) (PTHrP) [Contains: Osteostatin (PTHrP[107-139 ...	0.90	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity)				176
Q96RV3 UniProt NPD GO	PCX1_HUMAN	Pecanex-like protein 1 (Pecanex homolog)	0.90	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				2341
Q17062 UniProt NPD GO	PER_ANTPE	Period circadian protein	0.90	-	nuc	0	Nucleus. Nuclear at specific periods of the day. Interaction with TIM is required for nuclear locali ...				849
O70343 UniProt NPD GO	PRGC1_MOUSE	Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPAR gamma coactivator 1-alpha ...	0.90	+	nuc	0	Nucleus (By similarity)	DNA-directed RNA polymerase II, core complex [ISS] nucleus [ISS]			797
Q94131 UniProt NPD GO	PIE1_CAEEL	Pharynx and intestine in excess protein 1 (Protein pie-1)	0.90	-	nuc	0	Nucleus. Centrosome. Initially associates with both centrosomes of the mitotic spindle. Rapidly disa ...	centrosome [IDA] nucleus [IDA]			335
Q8UUU2 UniProt NPD GO	P85AA_XENLA	Phosphatidylinositol 3-kinase regulatory subunit alpha (PI3-kinase p85-subunit alpha) (PtdIns-3-kina ...	0.90	-	nuc	0		phosphoinositide 3-kinase complex, class IA [ISS]			722
Q9UW24 UniProt NPD GO	PIK1A_CANAL	Phosphatidylinositol 4-kinase PIK1a (EC 2.7.1.67) (PI4-kinase) (PtdIns-4-kinase)	0.90	+	nuc	0	Nucleus (By similarity)				956
Q96BK5 UniProt NPD GO	PINX1_HUMAN	Pin2-interacting protein X1 (TRF1-interacting protein 1) (Liver-related putative tumor suppressor) ( ...	0.90	+	nuc	0	Nucleus. Nucleus; nucleolus. In nucleoli and at telomere speckles		606505		328
Q9W5Z2 UniProt NPD GO	PITX2_BRARE	Pituitary homeobox 2a	0.90	+	nuc	0	Nucleus				314
P10037 UniProt NPD GO	PIT1_RAT	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.90	+	nuc	0	Nucleus			1AU7	291

You are viewing entries 4251 to 4300 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.