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
Q6YBR5 UniProt NPD GO	NGF_BRARE	Nerve growth factor precursor (NGF) (zNGF)	0.74	+	exc	0	Secreted protein (By similarity)				194
Q6UXZ4 UniProt NPD GO	UNC5D_HUMAN	Netrin receptor UNC5D precursor (Unc-5 homolog D) (Unc-5 homolog 4)	0.74	-	exc	0	Membrane; single-pass type I membrane protein (By similarity)				953
Q8WMG7 UniProt NPD GO	NLGNX_MACMU	Neuroligin-4, X-linked (Fragment)	0.74	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				213
Q09528 UniProt NPD GO	NHR19_CAEEL	Nuclear hormone receptor family member nhr-19	0.74	-	nuc	0	Nucleus (Potential)				477
Q09565 UniProt NPD GO	NHR20_CAEEL	Nuclear hormone receptor family member nhr-20	0.74	-	nuc	0	Nucleus (Potential)				457
Q966I0 UniProt NPD GO	NHR98_CAEEL	Nuclear hormone receptor family member nhr-98	0.74	-	cyt	0	Nucleus (Potential)				433
P38996 UniProt NPD GO	NAB3_YEAST	Nuclear polyadenylated RNA-binding protein 3	0.74	-	nuc	0	Nucleus; nucleoplasm	nucleus [IDA]			802
Q5R4V4 UniProt NPD GO	HCC1_PONPY	Nuclear protein Hcc-1	0.74	+	nuc	0	Nucleus (By similarity)				209
P82979 UniProt NPD GO	HCC1_HUMAN	Nuclear protein Hcc-1 (Proliferation-associated cytokine-inducible protein CIP29)	0.74	+	nuc	0	Nucleus	nucleus [NAS]			209
Q9N1A6 UniProt NPD GO	STP2_PANPA	Nuclear transition protein 2 (TP-2) (TP2) (Fragment)	0.74	+	mit	0	Nucleus (By similarity)				133
P21331 UniProt NPD GO	GAGJ_DROFU	Nucleic-acid-binding protein from mobile element jockey (ORF1)	0.74	-	nuc	0					574
Q02630 UniProt NPD GO	NU116_YEAST	Nucleoporin NUP116/NSP116 (Nuclear pore protein NUP116/NSP116)	0.74	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...	nuclear pore [IDA]		2AIV	1113
O74796 UniProt NPD GO	ORC6_SCHPO	Origin recognition complex subunit 6	0.74	-	nuc	0	Nucleus	nuclear origin of replication recognition c... [IDA]			264
Q9XTA8 UniProt NPD GO	OLR1_RABIT	Oxidized low-density lipoprotein receptor 1 (Ox-LDL receptor 1) (Lectin-type oxidized LDL receptor 1 ...	0.74	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Secreted protein (By similarity ...				274
Q9UIL8 UniProt NPD GO	PHF11_HUMAN	PHD finger protein 11 (BRCA1 C-terminus-associated protein) (NY-REN-34 antigen)	0.74	-	nuc	0			607796		292
P54277 UniProt NPD GO	PMS1_HUMAN	PMS1 protein homolog 1 (DNA mismatch repair protein PMS1)	0.74	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	600258	2CS1	932
P20264 UniProt NPD GO	PO3F3_HUMAN	POU domain, class 3, transcription factor 3 (Brain-specific homeobox/POU domain protein 1) (Brain-1) ...	0.74	+	nuc	0	Nucleus		602480		500
P31361 UniProt NPD GO	PO3F3_MOUSE	POU domain, class 3, transcription factor 3 (Brain-specific homeobox/POU domain protein 1) (Brain-1) ...	0.74	+	nuc	0	Nucleus				495
Q63262 UniProt NPD GO	PO3F3_RAT	POU domain, class 3, transcription factor 3 (Brain-specific homeobox/POU domain protein 1) (Brain-1) ...	0.74	+	nuc	0	Nucleus (By similarity)				497
P39768 UniProt NPD GO	OPA_DROME	Pair-rule protein odd-paired	0.74	-	nuc	0	Nucleus (Probable)				609
P47237 UniProt NPD GO	PAX6_CHICK	Paired box protein Pax-6 (Fragment)	0.74	+	nuc	0	Nucleus				216
P26630 UniProt NPD GO	PAX6_BRARE	Paired box protein Pax[Zf-a] (Pax-6)	0.74	+	nuc	0	Nucleus				437
Q8JZM7 UniProt NPD GO	CDC73_MOUSE	Parafibromin (Cell division cycle protein 73 homolog) (Hyperparathyroidism 2 protein homolog)	0.74	-	nuc	0	Nucleus (By similarity)				531
Q6P1J9 UniProt NPD GO	CDC73_HUMAN	Parafibromin (Cell division cycle protein 73 homolog) (Hyperparathyroidism 2 protein)	0.74	-	nuc	0	Nucleus		607393		531
Q9Z301 UniProt NPD GO	PER2_RAT	Period circadian protein 2 (rPER2)	0.74	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			1257
Q5D891 UniProt NPD GO	PK3C3_PIG	Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) (PtdIns-3-kinase type 3) (PI3- ...	0.74	-	cyt	0					887
Q84VW9 UniProt NPD GO	CAPP3_ARATH	Phosphoenolpyruvate carboxylase 3 (EC 4.1.1.31) (PEPCase 3) (PEPC 3) (AtPPC3)	0.74	-	cyt	0	Cytoplasm (By similarity)				968
Q9HB20 UniProt NPD GO	PKHA3_HUMAN	Pleckstrin homology domain-containing family A member 3 (Phosphoinositol 4-phosphate adaptor protein ...	0.74	-	nuc	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (Probable)		607774		300
Q6MGB6 UniProt NPD GO	RING1_RAT	Polycomb complex protein RING1 (RING finger protein 1)	0.74	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				406
Q9W3C1 UniProt NPD GO	U202_DROME	Polycomb protein l(1)G0020 (p110 protein)	0.74	-	nuc	0	Nucleus	nucleus [NAS]			1008
Q527H0 UniProt NPD GO	CLF1_MAGGR	Pre-mRNA-splicing factor CLF1	0.74	+	cyt	0	Nucleus (By similarity)				691
Q59PD3 UniProt NPD GO	CWC15_CANAL	Pre-mRNA-splicing factor CWC15	0.74	-	nuc	0	Nucleus (Probable)				224
Q6C9I7 UniProt NPD GO	ISY1_YARLI	Pre-mRNA-splicing factor ISY1	0.74	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				220
P78814 UniProt NPD GO	SRP2_SCHPO	Pre-mRNA-splicing factor srp2	0.74	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			365
Q91VN6 UniProt NPD GO	DDX41_MOUSE	Probable ATP-dependent RNA helicase DDX41 (EC 3.6.1.-) (DEAD box protein 41)	0.74	-	cyt	0	Nucleus (Potential)				622
Q9UJV9 UniProt NPD GO	DDX41_HUMAN	Probable ATP-dependent RNA helicase DDX41 (EC 3.6.1.-) (DEAD box protein 41) (DEAD box protein abstr ...	0.74	-	cyt	0	Nucleus (Potential)		608170		622
Q9H2U1 UniProt NPD GO	DHX36_HUMAN	Probable ATP-dependent RNA helicase DHX36 (EC 3.6.1.-) (DEAH box protein 36) (MLE-like protein 1) (R ...	0.74	-	mit	0	Nucleus and cytoplasm. Isoform 1 preferentially localized to the nucleus and isoform 2 localized to ...				1008
Q8IY37 UniProt NPD GO	DHX37_HUMAN	Probable ATP-dependent RNA helicase DHX37 (EC 3.6.1.-) (DEAH box protein 37)	0.74	+	nuc	0					1157
Q53NI2 UniProt NPD GO	NADK2_ORYSA	Probable NAD kinase 2, chloroplast precursor (EC 2.7.1.23)	0.74	-	nuc	0	Plastid; chloroplast (By similarity)				981
Q9CZJ1 UniProt NPD GO	UTP11_MOUSE	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11) (UTP11-like ...	0.74	-	nuc	0	Nucleus; nucleolus (By similarity)	cytoplasm [ISS] extracellular space [ISS] nucleus [ISS]			253
Q9SZ67 UniProt NPD GO	WRK19_ARATH	Probable WRKY transcription factor 19 (WRKY DNA-binding protein 19)	0.74	-	nuc	0	Nucleus (Probable)				1895
Q9ZSI7 UniProt NPD GO	WRK47_ARATH	Probable WRKY transcription factor 47 (WRKY DNA-binding protein 47)	0.74	-	nuc	0	Nucleus (Potential)				489
Q94HW3 UniProt NPD GO	DRL11_ARATH	Probable disease resistance protein RDL6/RF9	0.74	+	cyt	0					1049
Q9XWS2 UniProt NPD GO	EXOC4_CAEEL	Probable exocyst complex component 4 (Exocyst complex component Sec8)	0.74	-	nuc	0					893
Q10925 UniProt NPD GO	KIN25_CAEEL	Probable tyrosine-protein kinase kin-25 (EC 2.7.10.2)	0.74	-	nuc	0					1237
Q9P7S5 UniProt NPD GO	UBP7_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 7 (EC 3.1.2.15) (Ubiquitin thioesterase 7) (Ubiquitin ...	0.74	-	nuc	0					875
Q7Z7K6 UniProt NPD GO	PRR6_HUMAN	Proline-rich protein 6 (Nuclear protein p30)	0.74	-	mit	0	Nucleus. Enriched at the nuclear periphery and around the nucleolus		608139		275
P82295 UniProt NPD GO	PROML_DROME	Prominin-like protein	0.74	+	end	6 *	Membrane; multi-pass membrane protein (Potential)				1013
P35312 UniProt NPD GO	PRM2_ALOSE	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.74	+	nuc	0	Nucleus				100
Q8BI22 UniProt NPD GO	CN145_MOUSE	Protein C14orf145 homolog	0.74	-	nuc	0					524

You are viewing entries 11951 to 12000 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.