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
Q9ULI0 UniProt NPD GO	K1240_HUMAN	Protein KIAA1240 (Fragment)	0.97	+	nuc	0					733
Q02455 UniProt NPD GO	MLP1_YEAST	Protein MLP1 (Myosin-like protein 1)	0.97	-	nuc	0	Nucleus. Nuclear periphery	nuclear envelope [IDA] nucleoplasm [IDA]			1875
Q9SJQ6 UniProt NPD GO	ROS1_ARATH	Protein ROS1 (EC 3.2.2.-) (Repressor of silencing 1) (DEMETER-like protein 1)	0.97	+	nuc	0	Nucleus				1393
Q13123 UniProt NPD GO	RED_HUMAN	Protein Red (Protein RER) (IK factor) (Cytokine IK)	0.97	+	nuc	0	Nucleus	extracellular space [TAS] soluble fraction [TAS]	600549		557
Q9Z1M8 UniProt NPD GO	RED_MOUSE	Protein Red (Protein RER) (IK factor) (Cytokine IK)	0.97	+	nuc	0	Nucleus				557
P22470 UniProt NPD GO	SAN1_YEAST	Protein SAN1	0.97	+	nuc	0		nucleus [IDA]			610
Q10580 UniProt NPD GO	SWAP_CAEEL	Protein SWAP (Suppressor of white apricot protein homolog)	0.97	+	nuc	0					749
P54786 UniProt NPD GO	ZDS2_YEAST	Protein ZDS2	0.97	-	nuc	0		nucleus [IPI]			942
O88737 UniProt NPD GO	BSN_MOUSE	Protein bassoon	0.97	-	nuc	0	Cytoplasm. Localized to the active zone of presynaptic density	synapse [IDA]			3941
O88778 UniProt NPD GO	BSN_RAT	Protein bassoon	0.97	+	nuc	0	Cytoplasm. Localized to the active zone of presynaptic density. In retina, is localized in the outer ...				3937
O14064 UniProt NPD GO	BIR1_SCHPO	Protein bir1 (Chromosome segregation protein cut17)	0.97	-	nuc	0	Nucleus. Interacts with the outer centromeric regions of the chromosomes during interphase. After ch ...	condensed chromosome kinetochore [IDA] nucleus [IDA] spindle midzone [IDA]			997
P98081 UniProt NPD GO	DAB_DROME	Protein disabled	0.97	+	nuc	0	Cytoplasm	cytoplasm [IDA]			2224
P23792 UniProt NPD GO	DISC_DROME	Protein disconnected	0.97	-	nuc	0	Nucleus (Potential)				568
P43057 UniProt NPD GO	KPC1_CANAL	Protein kinase C-like 1 (EC 2.7.11.13) (PKC 1)	0.97	-	nuc	0					1097
P50535 UniProt NPD GO	MSL1_DROME	Protein male-specific lethal-1	0.97	+	nuc	0	Nucleus. Msl-1 is associated with hundreds of discrete sites along the length of the X chromosome in ...	dosage compensation complex (sensu Insecta) [TAS] X chromosome [NAS]			1039
Q07016 UniProt NPD GO	MAX_XENLA	Protein max (Myc-associated factor X) (xMAX)	0.97	+	nuc	0	Nucleus				163
Q27421 UniProt NPD GO	OSP_DROME	Protein outspread	0.97	-	nuc	0					1553
Q6NN85 UniProt NPD GO	SSH_DROME	Protein phosphatase Slingshot (EC 3.1.3.48) (EC 3.1.3.16)	0.97	+	nuc	0		apical part of cell [IDA]			1045
Q6IVY4 UniProt NPD GO	SSH_XENLA	Protein phosphatase Slingshot homolog (EC 3.1.3.48) (EC 3.1.3.16) (xSSH) (Slingshot-related protein) ...	0.97	-	nuc	0	Cytoplasm. Also localizes to the cleavage furrow and the midbody during cytokinesis				691
Q27934 UniProt NPD GO	PHYL_DROME	Protein phyllopod	0.97	-	nuc	0	Nucleus	nucleus [IDA]			400
Q86U86 UniProt NPD GO	PB1_HUMAN	Protein polybromo-1 (hPB1) (Polybromo-1D) (BRG1-associated factor 180) (BAF180)	0.97	+	nuc	0	Nucleus		606083		1689
P29617 UniProt NPD GO	PROS_DROME	Protein prospero	0.97	-	nuc	0	Nucleus	apical cortex [IDA] basal cortex [IDA] cell cortex [IDA] nucleus [IDA]		1MIJ	1403
Q9U6A1 UniProt NPD GO	PROS_DROVI	Protein prospero	0.97	-	nuc	0	Nucleus (By similarity)				1556
P91621 UniProt NPD GO	SIF1_DROME	Protein still life, isoform SIF type 1	0.97	-	nuc	0	Localizes to the submembranous region of synaptic terminals				2072
P22293 UniProt NPD GO	SUS_DROME	Protein suppressor of sable	0.97	+	nuc	0	Nucleus. Distributed in a reticulated pattern in embryo and salivary gland				1325
P40357 UniProt NPD GO	SEC9_YEAST	Protein transport protein SEC9	0.97	-	nuc	0		membrane [TAS]			651
Q9W517 UniProt NPD GO	WAPL_DROME	Protein wings apart-like (Protein parallel sister chromatids)	0.97	-	nuc	0					1741
Q3V4Z0 UniProt NPD GO	YCF2_ACOCL	Protein ycf2	0.97	+	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2076
Q2QD30 UniProt NPD GO	YCF2_CUCSA	Protein ycf2	0.97	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				1988
P30072 UniProt NPD GO	YCF2_EPIVI	Protein ycf2	0.97	+	nuc	0	Plastid; plastid stroma (By similarity)				2216
Q589A6 UniProt NPD GO	YCF2_SILLA	Protein ycf2	0.97	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2223
Q9SKN6 UniProt NPD GO	GATA7_ARATH	Putative GATA transcription factor 7	0.97	+	nuc	0	Nucleus (Probable)				315
P57052 UniProt NPD GO	RBM11_HUMAN	Putative RNA-binding protein 11 (RNA-binding motif protein 11)	0.97	+	nuc	0					281
Q10024 UniProt NPD GO	DGKM_CAEEL	Putative diacylglycerol kinase K06A1.6 (EC 2.7.1.107) (Diglyceride kinase) (DGK) (DAG kinase)	0.97	-	nuc	0					937
Q9LYP5 UniProt NPD GO	ARR21_ARATH	Putative two-component response regulator ARR21	0.97	+	nuc	0	Nucleus				592
Q99MI1 UniProt NPD GO	RB6I2_MOUSE	RAB6-interacting protein 2 (ERC protein 1) (ERC1) (CAZ-associated structural protein 2) (CAST2)	0.97	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Golgi apparatus; Golgi membrane; peripheral membra ...	cytoplasm [IDA]			1120
Q8NCN4 UniProt NPD GO	RN169_HUMAN	RING finger protein 169	0.97	-	nuc	0					708
P32786 UniProt NPD GO	RRN6_YEAST	RNA polymerase I-specific transcription initiation factor RRN6	0.97	-	nuc	0	Cytoplasm. Nucleus; nucleolus	RNA polymerase I transcription factor complex [TAS]			894
Q7TSG2 UniProt NPD GO	CTDP1_MOUSE	RNA polymerase II subunit A C-terminal domain phosphatase (EC 3.1.3.16) (TFIIF-associating CTD phosp ...	0.97	-	nuc	0	Nucleus (By similarity)				960
Q4QR29 UniProt NPD GO	CTR9_XENLA	RNA polymerase-associated protein CTR9 homolog (SH2 domain-binding protein 1)	0.97	+	nuc	0					1157
Q14498 UniProt NPD GO	RNPC2_HUMAN	RNA-binding region-containing protein 2 (Hepatocellular carcinoma protein 1) (Splicing factor HCC1)	0.97	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Concentrated in nuclear speckles. Colocalizes with the core s ...	nucleoplasm [TAS]	604739		530
Q9UJF2 UniProt NPD GO	NGAP_HUMAN	Ras GTPase-activating protein nGAP (RAS protein activator-like 1)	0.97	-	nuc	0			606136		1139
Q9D684 UniProt NPD GO	RIN2_MOUSE	Ras and Rab interactor 2 (Ras interaction/interference protein 2)	0.97	-	nuc	0	Cytoplasm (By similarity)				903
Q9DC04 UniProt NPD GO	RGS3_MOUSE	Regulator of G-protein signaling 3 (RGS3) (C2PA)	0.97	+	nuc	0	Cytoplasm. Nucleus. The long isoforms are cytoplasmic. Isoform 3 and probably also isoform 4 are nuc ...	cytoplasm [TAS] nucleus [IDA] plasma membrane [TAS]		1WHD	966
Q9HAU5 UniProt NPD GO	RENT2_HUMAN	Regulator of nonsense transcripts 2 (Nonsense mRNA reducing factor 2) (Up-frameshift suppressor 2 ho ...	0.97	+	nuc	0	Cytoplasm; perinuclear region	cytoplasm [IDA] nucleus [IDA]	605529	1UW4	1272
P97762 UniProt NPD GO	RP9_MOUSE	Retinitis pigmentosa 9 protein homolog (Pim-1-associated protein) (PAP-1)	0.97	+	nuc	0	Nucleus (Probable)				213
Q61818 UniProt NPD GO	RAI1_MOUSE	Retinoic acid-induced protein 1	0.97	-	nuc	0	Cytoplasm. Nucleus. In neurons, localized to neurites	nucleus [IDA]			1889
O43052 UniProt NPD GO	RGA1_SCHPO	Rho-type GTPase-activating protein 1	0.97	-	nuc	0	Cell poles and septum				1150
Q9Y7U6 UniProt NPD GO	RGF1_SCHPO	Rho1 guanine nucleotide exchange factor 1	0.97	+	nuc	0		barrier septum [IDA] cell cortex of cell tip [IDA]			1334
Q9Y7U5 UniProt NPD GO	RGF3_SCHPO	Rho1 guanine nucleotide exchange factor 3	0.97	-	nuc	0	Septum				1275

You are viewing entries 1151 to 1200 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.