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
Q9Y4A8 UniProt NPD GO	NF2L3_HUMAN	Nuclear factor erythroid 2-related factor 3 (NF-E2-related factor 3) (NFE2-related factor 3) (Nuclea ...	0.91	+	exc	1 *	Nucleus (By similarity)		604135		694
Q13469 UniProt NPD GO	NFAC2_HUMAN	Nuclear factor of activated T-cells, cytoplasmic 2 (T cell transcription factor NFAT1) (NFAT pre-exi ...	0.91	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic for the phosphorylated form and nuclear after activation that is con ...	cytoplasm [TAS] nucleus [TAS]	600490	1S9K	925
Q6P4L9 UniProt NPD GO	NFRKB_XENTR	Nuclear factor related to kappa-B-binding protein (DNA-binding protein R kappa-B)	0.91	+	nuc	0	Nucleus (Probable)				1265
O02151 UniProt NPD GO	NHR14_CAEEL	Nuclear hormone receptor family member nhr-14	0.91	-	nuc	0	Nucleus (Potential)				435
O18048 UniProt NPD GO	NH213_CAEEL	Nuclear hormone receptor family member nhr-213	0.91	-	nuc	0	Nucleus (Potential)				414
Q05952 UniProt NPD GO	STP2_HUMAN	Nuclear transition protein 2 (TP-2) (TP2)	0.91	+	mit	0	Nucleus		190232		138
Q9N1A5 UniProt NPD GO	STP2_GORGO	Nuclear transition protein 2 (TP-2) (TP2) (Fragment)	0.91	+	mit	0	Nucleus (By similarity)				133
P39744 UniProt NPD GO	NOC2_YEAST	Nucleolar complex protein 2	0.91	-	nuc	0	Nucleus; nucleolus	mitochondrion [IDA] Noc1p-Noc2p complex [IPI] Noc2p-Noc3p complex [IPI] nucleus [IDA]			710
Q6DRN3 UniProt NPD GO	NOC3L_BRARE	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				800
Q07896 UniProt NPD GO	NOC3_YEAST	Nucleolar complex-associated protein 3	0.91	+	nuc	0	Nucleus; nucleolus	Noc2p-Noc3p complex [IPI] nucleolus [TAS] nucleus [IDA]			663
Q6FUS6 UniProt NPD GO	NOP12_CANGA	Nucleolar protein 12	0.91	-	nuc	0	Nucleus; nucleolus (By similarity)				396
Q9UMY1 UniProt NPD GO	NOL7_HUMAN	Nucleolar protein 7 (Nucleolar protein of 27 kDa)	0.91	+	nuc	0	Nucleus; nucleolus				257
Q05166 UniProt NPD GO	NUP59_YEAST	Nucleoporin ASM4 (Nuclear pore protein NUP59)	0.91	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			528
Q5ZIP6 UniProt NPD GO	OTU6B_CHICK	OTU domain-containing protein 6B	0.91	+	nuc	0					302
Q99PG2 UniProt NPD GO	OGFR_MOUSE	Opioid growth factor receptor (OGFr) (Zeta-type opioid receptor)	0.91	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The OGF/OGFR complex is probably translocated to ...				633
Q60862 UniProt NPD GO	ORC2_MOUSE	Origin recognition complex subunit 2	0.91	-	nuc	0	Nucleus	inner kinetochore of condensed chromosome [IDA] nuclear origin of replication recognition c... [IDA]			576
Q9DBS9 UniProt NPD GO	OSBL3_MOUSE	Oxysterol-binding protein-related protein 3 (OSBP-related protein 3) (ORP-3)	0.91	+	nuc	0					855
Q9WTR8 UniProt NPD GO	PHLPP_RAT	PH domain leucine-rich repeat protein phosphatase (EC 3.1.3.16) (Pleckstrin homology domain-containi ...	0.91	-	nuc	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (Potential). May be membrane-associated				1696
Q8CHE4 UniProt NPD GO	PHLPP_MOUSE	PH domain leucine-rich repeat-containing protein phosphatase (EC 3.1.3.16) (PH domain leucine-rich r ...	0.91	-	nuc	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (By similarity). May be membrane-associa ...				1687
Q6ZPK0 UniProt NPD GO	PF21A_MOUSE	PHD finger protein 21A (BRAF35-HDAC complex protein BHC80) (mBHC80) (BHC80a)	0.91	-	nuc	0	Nucleus				659
P56224 UniProt NPD GO	POU12_BRARE	POU domain protein 12 (POU domain protein zp-12) (Class III POU domain protein taichi) (Brain-specif ...	0.91	+	nuc	0	Nucleus				437
P62515 UniProt NPD GO	PO3F4_MOUSE	POU domain, class 3, transcription factor 4 (Brain-specific homeobox/POU domain protein 4) (Brain-4) ...	0.91	+	nuc	0	Nucleus				361
P62516 UniProt NPD GO	PO3F4_RAT	POU domain, class 3, transcription factor 4 (Brain-specific homeobox/POU domain protein 4) (Brain-4) ...	0.91	+	nuc	0	Nucleus				361
P06198 UniProt NPD GO	MYSP_SCHMA	Paramyosin	0.91	-	nuc	0	Thick filaments of the myofibrils				866
Q05870 UniProt NPD GO	MYSP_SCHJA	Paramyosin (Antigen Sj97)	0.91	-	nuc	0	Thick filaments of the myofibrils				866
P52016 UniProt NPD GO	CYP8_CAEEL	Peptidyl-prolyl cis-trans isomerase 8 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-8)	0.91	+	nuc	0		nucleus [IDA]			466
Q7SBX8 UniProt NPD GO	CWC27_NEUCR	Peptidyl-prolyl isomerase cwc-27 (EC 5.2.1.8)	0.91	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				541
Q9QYK2 UniProt NPD GO	PRGC1_RAT	Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPAR gamma coactivator 1-alpha ...	0.91	+	nuc	0	Nucleus (By similarity)	DNA-directed RNA polymerase II, core complex [ISS] nucleus [ISS]			796
P54675 UniProt NPD GO	PI3K3_DICDI	Phosphatidylinositol 3-kinase 3 (EC 2.7.1.137) (PI3-kinase) (PtdIns-3-kinase) (PI3K) (Fragment)	0.91	-	nuc	0					1585
P97474 UniProt NPD GO	PITX2_MOUSE	Pituitary homeobox 2 (Orthodenticle-like homeobox 2) (Solurshin) (ALL1-responsive protein ARP1) (BRX ...	0.91	+	nuc	0	Nucleus	transcription factor complex [IDA]			317
Q99697 UniProt NPD GO	PITX2_HUMAN	Pituitary homeobox 2 (RIEG bicoid-related homeobox transcription factor) (Solurshin) (ALL1-responsiv ...	0.91	+	nuc	0	Nucleus	transcription factor complex [IDA]	137600	1YZ8	317
Q91169 UniProt NPD GO	PIT1_ONCKE	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.91	+	nuc	0	Nucleus				365
O02776 UniProt NPD GO	PARG_BOVIN	Poly(ADP-ribose) glycohydrolase (EC 3.2.1.143)	0.91	-	nuc	0	Nucleus (By similarity)				977
Q8L6Y4 UniProt NPD GO	EMF2_ARATH	Polycomb protein EMBRYONIC FLOWER 2	0.91	-	nuc	0	Nucleus (Probable)				631
P39769 UniProt NPD GO	PHP_DROME	Polyhomeotic-proximal chromatin protein	0.91	-	nuc	0	Nucleus			1PK1	1589
Q95L11 UniProt NPD GO	KCNB2_RABIT	Potassium voltage-gated channel subfamily B member 2 (Voltage-gated potassium channel subunit Kv2.2) ...	0.91	-	nuc	4	Membrane; multi-pass membrane protein				911
Q5BDW4 UniProt NPD GO	PRP5_EMENI	Pre-mRNA-processing ATP-dependent RNA helicase prp5 (EC 3.6.1.-)	0.91	+	nuc	0	Nucleus (By similarity)				1173
P33203 UniProt NPD GO	PRP40_YEAST	Pre-mRNA-processing protein PRP40	0.91	-	nuc	0	Nucleus	snRNP U1 [IDA]		2B7E	583
Q2UH00 UniProt NPD GO	PRP28_ASPOR	Pre-mRNA-splicing ATP-dependent RNA helicase prp28 (EC 3.6.1.-)	0.91	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				803
Q9P774 UniProt NPD GO	PRP16_SCHPO	Pre-mRNA-splicing factor ATP-dependent RNA helicase prp16 (EC 3.6.1.-)	0.91	-	nuc	0	Nucleus (By similarity)				1173
Q6FRY5 UniProt NPD GO	SLU7_CANGA	Pre-mRNA-splicing factor SLU7	0.91	+	nuc	0	Nucleus (By similarity)				318
Q02775 UniProt NPD GO	SLU7_YEAST	Pre-mRNA-splicing factor SLU7 (Synthetic lethal with U5 snRNA protein 7) (Synthetic lethal with U2 s ...	0.91	-	nuc	0	Nucleus	spliceosome complex [IDA]			382
P54683 UniProt NPD GO	TAGB_DICDI	Prestalk-specific protein tagB precursor (EC 3.4.21.-)	0.91	+	end	7 *	Membrane; multi-pass membrane protein (Potential)				1905
P82266 UniProt NPD GO	K125_ARATH	Probable 125 kDa kinesin-related protein	0.91	-	nuc	0	Cytoplasm (By similarity). Microtubule-associated (By similarity)				1056
P22516 UniProt NPD GO	CHL1_YEAST	Probable ATP-dependent RNA helicase CHL1 (EC 3.6.1.-)	0.91	-	nuc	0		nucleus [IDA]			861
Q13206 UniProt NPD GO	DDX10_HUMAN	Probable ATP-dependent RNA helicase DDX10 (EC 3.6.1.-) (DEAD box protein 10)	0.91	-	nuc	0			601235		875
Q03319 UniProt NPD GO	PRH1_SCHPO	Probable ATP-dependent RNA helicase prh1 (EC 3.6.1.-)	0.91	-	nuc	0					719
Q03735 UniProt NPD GO	YML7_YEAST	Probable RNA-binding protein YML117W	0.91	-	nuc	0		cytoplasm [IDA]			1134
O22176 UniProt NPD GO	WRK15_ARATH	Probable WRKY transcription factor 15 (WRKY DNA-binding protein 15)	0.91	-	nuc	0	Nucleus (Probable)				317
Q9STX0 UniProt NPD GO	WRKY7_ARATH	Probable WRKY transcription factor 7 (WRKY DNA-binding protein 7)	0.91	+	nuc	0	Nucleus (Probable)				353

You are viewing entries 3801 to 3850 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.