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
Q9Y468 UniProt NPD GO	LMBTL_HUMAN	Lethal(3)malignant brain tumor-like protein (L(3)mbt-like) (L(3)mbt protein homolog) (H-l(3)mbt prot ...	0.91	+	nuc	0	Nucleus. Excluded from the nucleolus. Does not colocalizes with the PcG protein BMI1, suggesting tha ...		608802	1OZ3	772
Q8R4U7 UniProt NPD GO	LUZP1_MOUSE	Leucine zipper protein 1 (Leucine zipper motif-containing protein)	0.91	-	nuc	0	Nucleus. Also detected in soma and dendrites of neurons (By similarity)				1068
Q9Y608 UniProt NPD GO	LRRF2_HUMAN	Leucine-rich repeat flightless-interacting protein 2 (LRR FLI-II-interacting protein 2)	0.91	-	nuc	0					721
Q4V7E8 UniProt NPD GO	LRRF2_RAT	Leucine-rich repeat flightless-interacting protein 2 (LRR FLI-II-interacting protein 2)	0.91	-	nuc	0					437
Q86VH4 UniProt NPD GO	LRTM4_HUMAN	Leucine-rich repeat transmembrane neuronal protein 4 precursor	0.91	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				518
Q99PI4 UniProt NPD GO	LPIN3_MOUSE	Lipin-3	0.91	+	nuc	0	Nucleus (Potential)				848
Q13136 UniProt NPD GO	LIPA1_HUMAN	Liprin-alpha-1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-1 ...	0.91	-	nuc	0	Cytoplasm. Colocalizes with PTPRF at the ends of focal adhesions most proximal to the cell nucleus	cytoplasm [TAS]			1202
Q6NYD4 UniProt NPD GO	RBM13_BRARE	MAK16-like protein RBM13 (RNA-binding motif protein 13)	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				303
Q9LW85 UniProt NPD GO	MFP1_ARATH	MAR-binding filament-like protein 1	0.91	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)				726
O02193 UniProt NPD GO	MOF_DROME	Males-absent on the first protein (EC 2.3.1.-) (Putative acetyl transferase MOF)	0.91	-	nuc	0		dosage compensation complex (sensu Insecta) [TAS]		2BUD	827
P37938 UniProt NPD GO	MAAZ4_SCHCO	Mating-type protein A-alpha Z4	0.91	-	nuc	0	Nucleus				940
Q9HG13 UniProt NPD GO	MATA2_KLULA	Mating-type protein A2 (A2 HMG-domain transcription factor)	0.91	+	mit	0	Nucleus (By similarity)				257
P43243 UniProt NPD GO	MATR3_HUMAN	Matrin-3	0.91	-	nuc	0	Nucleus; nucleoplasm; nuclear matrix	nuclear inner membrane [TAS]	604706		847
P78957 UniProt NPD GO	RE114_SACPS	Meiotic recombination protein REC114	0.91	-	nuc	0					431
Q92380 UniProt NPD GO	REC11_SCHPO	Meiotic recombination protein rec11	0.91	-	end	0					923
Q5R7T9 UniProt NPD GO	MTF2_PONPY	Metal-response element-binding transcription factor 2 (Metal-regulatory transcription factor 2)	0.91	+	nuc	0	Nucleus (By similarity)				593
Q9Y483 UniProt NPD GO	MTF2_HUMAN	Metal-response element-binding transcription factor 2 (Metal-response element DNA-binding protein M9 ...	0.91	+	nuc	0	Nucleus (By similarity)		609882		593
O43312 UniProt NPD GO	MTSS1_HUMAN	Metastasis suppressor protein 1 (Missing in metastasis protein) (Metastasis suppressor YGL-1)	0.91	-	nuc	0		actin cytoskeleton [IDA] cytoplasm [TAS] endocytic vesicle [TAS] ruffle [NAS]	608486		755
Q9R1L5 UniProt NPD GO	MAST1_MOUSE	Microtubule-associated serine/threonine-protein kinase 1 (EC 2.7.11.1) (Syntrophin-associated serine ...	0.91	-	nuc	0	Cell membrane; peripheral membrane protein. Colocalizes with syntrophins at the cell membrane	membrane [IDA]			1566
Q810W7 UniProt NPD GO	MAST1_RAT	Microtubule-associated serine/threonine-protein kinase 1 (EC 2.7.11.1) (Syntrophin-associated serine ...	0.91	-	nuc	0	Isoform 1: Cell membrane; peripheral membrane protein. Colocalizes with syntrophins at the cell memb ...				1570
O60307 UniProt NPD GO	MAST3_HUMAN	Microtubule-associated serine/threonine-protein kinase 3 (EC 2.7.11.1)	0.91	-	nuc	0				1V9V	1309
P53083 UniProt NPD GO	MDM34_YEAST	Mitochondrial distribution and morphology protein 34 (Mitochondrial outer membrane protein MMM2)	0.91	+	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein. Punctate structures in the ...	cytoplasm [IDA] mitochondrial outer membrane [IDA]			459
Q95749 UniProt NPD GO	RT03_ARATH	Mitochondrial ribosomal protein S3	0.91	-	nuc	0	Mitochondrion				556
P49386 UniProt NPD GO	RT03_BRANA	Mitochondrial ribosomal protein S3	0.91	-	nuc	0	Mitochondrion				555
Q8BGT6 UniProt NPD GO	MILK1_MOUSE	Molecule interacting with Rab13 (MIRab13) (MICAL-like protein 1)	0.91	-	nuc	0	Cytoplasm (By similarity)				870
P21339 UniProt NPD GO	MSB1_YEAST	Morphogenesis-related protein MSB1 (Multicopy suppressor of bud emergence 1)	0.91	-	nuc	0		bud neck [TAS] bud tip [TAS] mitochondrion [IDA]			1137
Q5BGA9 UniProt NPD GO	MRD1_EMENI	Multiple RNA-binding domain-containing protein 1	0.91	-	nuc	0	Nucleus (By similarity)				819
Q06106 UniProt NPD GO	MRD1_YEAST	Multiple RNA-binding domain-containing protein 1	0.91	-	nuc	0	Nucleus	nucleolus [IDA]			887
P04197 UniProt NPD GO	MYB_DROME	Myb protein	0.91	-	nuc	0	Nucleus	Myb complex [IDA]			657
P22035 UniProt NPD GO	BAS1_YEAST	Myb-like DNA-binding protein BAS1	0.91	-	nuc	0	Nucleus	nucleus [IDA]			811
P48972 UniProt NPD GO	MYBB_MOUSE	Myb-related protein B (B-Myb)	0.91	+	nuc	0	Nucleus				704
Q90342 UniProt NPD GO	MYC2_CYPCA	Myc II protein (C-MYC II)	0.91	+	nuc	0	Nucleus				401
Q8CFC2 UniProt NPD GO	MYT1_MOUSE	Myelin transcription factor 1 (MyT1) (Neural zinc finger factor 2) (NZF-2)	0.91	+	nuc	0	Nucleus (By similarity)				1127
P16075 UniProt NPD GO	MYOD1_CHICK	Myoblast determination protein 1 homolog (MYOD1 homolog)	0.91	+	nuc	0	Nucleus				298
P16076 UniProt NPD GO	MYODB_XENLA	Myoblast determination protein 1 homolog B (Myogenic factor 25)	0.91	+	nuc	0	Nucleus (Probable)				287
Q8R5I7 UniProt NPD GO	MYCD_RAT	Myocardin	0.91	-	nuc	0	Nucleus				938
Q8AYC1 UniProt NPD GO	MRTFB_XENLA	Myocardin-related transcription factor B (MRTF-B) (xMRTF-B)	0.91	-	nuc	0	Nucleus (By similarity)				1067
Q01989 UniProt NPD GO	MYS9_DROME	Myosin heavy chain 95F (95F MHC) (Jaguar protein)	0.91	-	nuc	0	Cytoplasm. Microtubule-associated	endocytic vesicle [IDA] microtubule associated complex [IDA] unconventional myosin [IDA]			1256
P05661 UniProt NPD GO	MYSA_DROME	Myosin heavy chain, muscle	0.91	+	nuc	0	Thick filaments of the myofibrils	muscle myosin [IDA] striated muscle thick filament [IDA]			1962
P35749 UniProt NPD GO	MYH11_HUMAN	Myosin-11 (Myosin heavy chain, smooth muscle isoform) (SMMHC)	0.91	+	nuc	0	Thick filaments of the myofibrils	muscle myosin [TAS]	160745		1972
P35748 UniProt NPD GO	MYH11_RABIT	Myosin-11 (Myosin heavy chain, smooth muscle isoform) (SMMHC)	0.91	-	nuc	0	Thick filaments of the myofibrils				1972
P36006 UniProt NPD GO	MYO3_YEAST	Myosin-3	0.91	-	nuc	0		actin cortical patch [IPI]		2BTT	1273
Q8VDD5 UniProt NPD GO	MYH9_MOUSE	Myosin-9 (Myosin heavy chain, nonmuscle IIa) (Nonmuscle myosin heavy chain IIa) (NMMHC II-a) (NMMHC- ...	0.91	+	nuc	0		cell-cell adherens junction [IDA] cytoplasm [IDA]			1959
P18444 UniProt NPD GO	MYCN_CHICK	N-myc proto-oncogene protein	0.91	+	nuc	0	Nucleus				441
P26014 UniProt NPD GO	MYCN_SERCA	N-myc proto-oncogene protein	0.91	-	nuc	0	Nucleus (Potential)				427
Q9VJZ7 UniProt NPD GO	NNP1_DROME	NNP-1 protein homolog	0.91	+	nuc	0	Nucleus (Potential)				687
Q9ULJ8 UniProt NPD GO	NEB1_HUMAN	Neurabin-1 (Neurabin-I) (Neural tissue-specific F-actin-binding protein I) (Protein phosphatase 1 re ...	0.91	-	nuc	0	Cytoplasm. Synaptosome (By similarity). Also found in the soluble synaptosomal fractions (By similar ...		602468	1WF8	1098
O35867 UniProt NPD GO	NEB1_RAT	Neurabin-1 (Neurabin-I) (Neural tissue-specific F-actin-binding protein I) (Protein phosphatase 1 re ...	0.91	-	nuc	0	Cytoplasm. Synaptosome. Also found in the soluble synaptosomal fractions				1095
O15240 UniProt NPD GO	VGF_HUMAN	Neurosecretory protein VGF precursor	0.91	-	exc	0	Stored in secretory vesicles and then secreted (By similarity)		602186		616
Q02780 UniProt NPD GO	NFIA_MOUSE	Nuclear factor 1 A-type (Nuclear factor 1/A) (NF1-A) (NFI-A) (NF-I/A) (CCAAT-box-binding transcripti ...	0.91	-	nuc	0	Nucleus				532

You are viewing entries 3751 to 3800 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.