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
Q9YHE8 UniProt NPD GO	T7L1A_BRARE	Transcription factor 7-like 1-A (HMG box transcription factor 3-A) (TCF-3-A) (TCF-3) (zTcf-3) (Prote ...	0.97	+	nuc	0	Nucleus				560
Q9NQB0 UniProt NPD GO	TF7L2_HUMAN	Transcription factor 7-like 2 (HMG box transcription factor 4) (T-cell-specific transcription factor ...	0.97	+	nuc	0	Nucleus	nucleus [NAS]	602228	1JPW	619
P36197 UniProt NPD GO	TCF8_CHICK	Transcription factor 8 (Delta-crystallin enhancer-binding factor) (Delta EF1)	0.97	+	nuc	0	Nucleus (Probable)				1114
Q62947 UniProt NPD GO	TCF8_RAT	Transcription factor 8 (Zinc finger homeodomain enhancer-binding protein) (Zfhep)	0.97	+	nuc	0	Nucleus (By similarity)				1109
P19532 UniProt NPD GO	TFE3_HUMAN	Transcription factor E3	0.97	+	nuc	0	Nucleus		314310		743
Q4IJ11 UniProt NPD GO	IWS1_GIBZE	Transcription factor IWS1	0.97	+	nuc	0	Nucleus (By similarity)				428
P39678 UniProt NPD GO	MBP1_YEAST	Transcription factor MBP1 (MBF subunit p120)	0.97	-	nuc	0	Nucleus	nucleus [IDA]		1MB1	833
P33200 UniProt NPD GO	PDR3_YEAST	Transcription factor PDR3 (Pleiotropic drug resistance protein 3)	0.97	-	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			976
Q64127 UniProt NPD GO	TIF1A_MOUSE	Transcription intermediary factor 1-alpha (TIF1-alpha) (Tripartite motif-containing protein 24)	0.97	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [ISS]			1051
O15164 UniProt NPD GO	TIF1A_HUMAN	Transcription intermediary factor 1-alpha (TIF1-alpha) (Tripartite motif-containing protein 24) (RIN ...	0.97	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	603406		1050
P34739 UniProt NPD GO	TTF2_DROME	Transcription termination factor 2 (EC 3.6.1.-) (RNA polymerase II termination factor) (Transcriptio ...	0.97	-	nuc	0	Nucleus (Probable)				1061
P35177 UniProt NPD GO	SPT7_YEAST	Transcriptional activator SPT7	0.97	-	nuc	0	Nucleus	mitochondrion [IDA] SAGA complex [IDA] SLIK (SAGA-like) complex [IPI]			1332
P53968 UniProt NPD GO	CRZ1_YEAST	Transcriptional regulator CRZ1	0.97	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			678
Q12986 UniProt NPD GO	NFX1_HUMAN	Transcriptional repressor NF-X1 (EC 6.3.2.-) (Nuclear transcription factor, X box-binding, 1)	0.97	-	nuc	0	Nucleus		603255		1104
Q6IEG0 UniProt NPD GO	CF151_HUMAN	U11/U12 snRNP 48 kDa protein	0.97	+	nuc	0	Nucleus	minor (U12-dependent) spliceosome complex [IDA]			339
Q02724 UniProt NPD GO	ULP1_YEAST	Ubiquitin-like-specific protease 1 (EC 3.4.22.-)	0.97	+	nuc	0		nuclear envelope [IDA] nuclear pore [IDA]		1EUV	621
P40537 UniProt NPD GO	ULP2_YEAST	Ubiquitin-like-specific protease 2 (EC 3.4.22.-)	0.97	-	nuc	0		nucleus [IDA]			1034
Q7YRZ8 UniProt NPD GO	MDM2_FELCA	Ubiquitin-protein ligase E3 Mdm2 (EC 6.3.2.-) (p53-binding protein Mdm2) (Double minute 2 protein)	0.97	-	nuc	0	Nucleus; nucleoplasm (By similarity). Cytoplasm (By similarity). Expressed predominantly in the nucl ...	nucleolus [ISS] nucleoplasm [ISS]			491
Q80TP3 UniProt NPD GO	EDD1_MOUSE	Ubiquitin-protein ligase EDD1 (EC 6.3.2.-) (Hyperplastic discs protein homolog)	0.97	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			2792
Q8WUQ7 UniProt NPD GO	CS029_HUMAN	Uncharacterized protein C19orf29 (NY-REN-24 antigen)	0.97	+	nuc	0					690
P40095 UniProt NPD GO	YEY8_YEAST	Uncharacterized protein YER158C	0.97	-	nuc	0					573
Q03661 UniProt NPD GO	YM67_YEAST	Uncharacterized protein YMR219W	0.97	+	nuc	0		nucleus [IDA]			1658
Q99248 UniProt NPD GO	YO019_YEAST	Uncharacterized protein YOR019W	0.97	+	nuc	0					730
Q91829 UniProt NPD GO	RAG1_XENLA	V(D)J recombination-activating protein 1 (RAG-1)	0.97	+	nuc	0	Nucleus				1045
P15918 UniProt NPD GO	RAG1_HUMAN	V(D)J recombination-activating protein 1 (RAG-1) (RING finger protein 74)	0.97	+	nuc	0	Nucleus		609889		1043
Q00731 UniProt NPD GO	VEGFA_MOUSE	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.97	+	nuc	0	Isoform VEGF-1, isoform VEGF-2: Secreted protein. Isoform VEGF-3: Cell membrane; peripheral membrane ...	cytoplasm [IDA]			214
Q5EB97 UniProt NPD GO	ZCH10_RAT	Zinc finger CCHC domain-containing protein 10	0.97	+	nuc	0					173
Q80X44 UniProt NPD GO	ZBT24_MOUSE	Zinc finger and BTB domain-containing protein 24 (Zinc finger protein 450) (Bone morphogenetic prote ...	0.97	-	nuc	0	Nucleus (Potential)	nucleus [IC]			710
Q9R0G7 UniProt NPD GO	SIP1_MOUSE	Zinc finger homeobox protein 1b (Smad-interacting protein 1)	0.97	-	nuc	0	Nucleus	nucleus [IC]			1215
O60315 UniProt NPD GO	SIP1_HUMAN	Zinc finger homeobox protein 1b (Smad-interacting protein 1) (SMADIP1)	0.97	-	nuc	0	Nucleus	nucleus [IC]	605802		1214
Q9H2Y7 UniProt NPD GO	ZF106_HUMAN	Zinc finger protein 106 homolog (Zfp-106) (Zinc finger protein 474)	0.97	+	nuc	0					1883
Q9BY12 UniProt NPD GO	ZN291_HUMAN	Zinc finger protein 291	0.97	-	nuc	0					1399
Q86YF9 UniProt NPD GO	DZIP1_HUMAN	Zinc finger protein DZIP1 (DAZ-interacting protein 1/2)	0.97	-	nuc	0	Nucleus. Cytoplasm. In testis, it is predominantly nuclear, with some cytoplasmic localization in sp ...	cytoplasm [IDA] nucleus [IDA]	608671		867
Q7T019 UniProt NPD GO	DZIP1_BRARE	Zinc finger protein Dzip1 (DAZ-interacting protein 1 homolog) (Iguana protein)	0.97	-	nuc	0	Nucleus. Cytoplasm. In the cytoplasm, it is localized in large vesicles. These vesicles correspond t ...	cytoplasm [ISS] nucleus [ISS]			898
P33749 UniProt NPD GO	MSN4_YEAST	Zinc finger protein MSN4 (Multicopy suppressor of SNF1 protein 4)	0.97	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [IDA]			630
Q11107 UniProt NPD GO	LIN13_CAEEL	Zinc finger protein lin-13 (Abnormal cell lineage protein 13)	0.97	-	nuc	0	Nucleus	nucleus [IDA]			2248
Q9UKY1 UniProt NPD GO	ZHX1_HUMAN	Zinc fingers and homeoboxes protein 1	0.97	+	exc	0	Nucleus	nucleus [IDA]	604764	2GHF	873
Q9P8W3 UniProt NPD GO	ACE1_TRIRE	Zinc-finger transcription factor ace1 (ACEI)	0.97	-	nuc	0	Nucleus (Probable)				733
Q9W4S9 UniProt NPD GO	PDE4C_DROME	cAMP-specific 3',5'-cyclic phosphodiesterase, isoforms N/G (EC 3.1.4.17) (Learning/memory process pr ...	0.97	-	nuc	0					983
Q6BND2 UniProt NPD GO	CET1_DEBHA	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.97	-	nuc	0	Nucleus (By similarity)				476
Q51NJ3 UniProt NPD GO	PALA_MAGGR	pH-response regulator protein palA/RIM20	0.97	-	nuc	0					849
Q8BP86 UniProt NPD GO	SNPC4_MOUSE	snRNA-activating protein complex subunit 4 (SNAPc subunit 4) (snRNA-activating protein complex 190 k ...	0.97	-	nuc	0	Nucleus (Potential)	nucleus [ISS] snRNA-activating protein complex [ISS]			1333
Q5SXM2 UniProt NPD GO	SNPC4_HUMAN	snRNA-activating protein complex subunit 4 (SNAPc subunit 4) (snRNA-activating protein complex 190 k ...	0.97	+	nuc	0	Nucleus (Potential)	nucleus [IC] snRNA-activating protein complex [IDA]	602777		1469
Q9Z1B3 UniProt NPD GO	PLCB1_MOUSE	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 1 (EC 3.1.4.11) (Phosphoinositide pho ...	0.96	+	nuc	0					1216
O61308 UniProt NPD GO	PUMA_PARUN	227 kDa spindle- and centromere-associated protein (PUMA1)	0.96	-	nuc	0	Centrosome. Kinetochore. Spindle. Centrosomes and kinetochore microtubles of mitotic cells. Also loc ...				1955
Q9W0V1 UniProt NPD GO	PDPK1_DROME	3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) (dPDK-1) (Serine/threonine-protein kinas ...	0.96	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] plasma membrane [ISS]			836
Q9BMX5 UniProt NPD GO	RS6_APLCA	40S ribosomal protein S6	0.96	-	nuc	0					247
Q62036 UniProt NPD GO	AZI1_MOUSE	5-azacytidine-induced protein 1 (Pre-acrosome localization protein 1)	0.96	+	nuc	0					1060
P24588 UniProt NPD GO	AKAP5_HUMAN	A-kinase anchor protein 5 (A-kinase anchor protein 79 kDa) (AKAP 79) (cAMP-dependent protein kinase ...	0.96	+	nuc	0	Membrane. Associated with particulate fractions	plasma membrane [NAS]	604688		427
P51816 UniProt NPD GO	AFF2_HUMAN	AF4/FMR2 family member 2 (Fragile X mental retardation 2 protein) (Protein FMR-2) (FMR2P) (Protein O ...	0.96	-	nuc	0			309548		1311

You are viewing entries 1251 to 1300 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.