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
Q86WR7 UniProt NPD GO	CJ047_HUMAN	Protein C10orf47	0.55	-	nuc	0					435
Q9NXX6 UniProt NPD GO	CJ086_HUMAN	Protein C10orf86	0.55	+	nuc	0					385
Q9BQ75 UniProt NPD GO	CC026_HUMAN	Protein C3orf26	0.55	+	nuc	0					279
Q8NC60 UniProt NPD GO	CD014_HUMAN	Protein C4orf14	0.55	-	mit	0					698
Q15884 UniProt NPD GO	CI061_HUMAN	Protein C9orf61 (Protein X123)	0.55	-	nuc	0			607710		289
Q8IA98 UniProt NPD GO	CASP_CAEEL	Protein CASP	0.55	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				621
O43247 UniProt NPD GO	EAN57_HUMAN	Protein EAN57	0.55	-	nuc	0					280
Q5T8I3 UniProt NPD GO	F102B_HUMAN	Protein FAM102B	0.55	-	nuc	0					329
Q9Z1X1 UniProt NPD GO	FA62A_RAT	Protein FAM62A (Membrane-bound C2 domain-containing protein) (vp115)	0.55	-	nuc	1	Membrane; multi-pass membrane protein (Potential). Found in the plasma membrane and in high density ...				1088
Q753Y3 UniProt NPD GO	GRC3_ASHGO	Protein GRC3	0.55	-	nuc	0	Nucleus (By similarity)				633
Q944N1 UniProt NPD GO	LHP1_LYCES	Protein LIKE HETEROCHROMATIN PROTEIN1 (Sl LHP1)	0.55	-	nuc	0	Nucleus; punctuated distribution and in heterochromatic chromocenters				399
Q16385 UniProt NPD GO	SSX2_HUMAN	Protein SSX2 (Synovial sarcoma, X breakpoint 2) (SSX) (HOM-MEL-40)	0.55	-	nuc	0	Nucleus		300192		188
Q960N3 UniProt NPD GO	CORT_DROME	Protein cortex	0.55	-	nuc	0	Cytoplasm	cytoplasm [IDA]			483
Q9VQS6 UniProt NPD GO	DRM_DROME	Protein drumstick	0.55	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			81
P14734 UniProt NPD GO	FKH_DROME	Protein fork head	0.55	+	nuc	0	Nucleus				510
Q02156 UniProt NPD GO	KPCE_HUMAN	Protein kinase C epsilon type (EC 2.7.11.13) (nPKC-epsilon)	0.55	-	cyt	0		membrane fraction [TAS]	176975		737
P16054 UniProt NPD GO	KPCE_MOUSE	Protein kinase C epsilon type (EC 2.7.11.13) (nPKC-epsilon)	0.55	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			737
P50536 UniProt NPD GO	MSL3_DROME	Protein male-specific lethal-3	0.55	-	nuc	0	Nucleus. Msl-3 is associated with hundreds of discrete sites along the length of the X chromosome in ...	dosage compensation complex (sensu Insecta) [TAS] X chromosome [NAS]			512
Q09614 UniProt NPD GO	PTC1_CAEEL	Protein patched homolog 1	0.55	+	end	11	Integral membrane protein; highly concentrated in a punctate pattern at the apices and internal memb ...				1405
Q8C669 UniProt NPD GO	PELI1_MOUSE	Protein pellino homolog 1 (Pellino-1)	0.55	-	nuc	0					418
Q3T0W4 UniProt NPD GO	PP1R7_BOVIN	Protein phosphatase 1 regulatory subunit 7 (Protein phosphatase 1 regulatory subunit 22)	0.55	-	nuc	0	Nucleus (By similarity)				360
Q15435 UniProt NPD GO	PP1R7_HUMAN	Protein phosphatase 1 regulatory subunit 7 (Protein phosphatase 1 regulatory subunit 22)	0.55	-	nuc	0	Nucleus (By similarity)	cytoplasm [TAS] nucleus [TAS]	602877		360
Q00362 UniProt NPD GO	2ABA_YEAST	Protein phosphatase PP2A regulatory subunit B (PR55) (Cell division control protein 55)	0.55	-	nuc	0		bud neck [IDA] bud tip [IDA] nucleus [IDA] protein phosphatase type 2A complex [TAS]			526
P40996 UniProt NPD GO	SCD2_SCHPO	Protein scd2/ral3	0.55	-	nuc	0					536
O94855 UniProt NPD GO	SC24D_HUMAN	Protein transport protein Sec24D (SEC24-related protein D)	0.55	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity)	COPII vesicle coat [NAS]	607186		1032
P06803 UniProt NPD GO	PIM1_MOUSE	Proto-oncogene serine/threonine-protein kinase Pim-1 (EC 2.7.11.1)	0.55	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				397
O88277 UniProt NPD GO	FAT2_RAT	Protocadherin Fat 2 precursor (Multiple epidermal growth factor-like domains 1)	0.55	-	end	1					4351
Q6X862 UniProt NPD GO	PC11X_GORGO	Protocadherin-11 X-linked precursor (Protocadherin-11) (Protocadherin on the X chromosome)	0.55	+	nuc	0	Membrane; single-pass type I membrane protein (Potential)				1347
Q71M42 UniProt NPD GO	PC11X_PANTR	Protocadherin-11 X-linked precursor (Protocadherin-11) (Protocadherin on the X chromosome)	0.55	+	nuc	0	Membrane; single-pass type I membrane protein (Potential)				1347
Q5BCK8 UniProt NPD GO	COX10_EMENI	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.55	-	mit	8	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				506
Q9P7W0 UniProt NPD GO	OPA3_SCHPO	Putative OPA3-like protein C1703.11	0.55	+	nuc	1					218
Q9C8N9 UniProt NPD GO	ARFU_ARATH	Putative auxin response factor 21	0.55	-	nuc	0	Nucleus				606
Q8SQP3 UniProt NPD GO	H3L_ENCCU	Putative histone H3-like protein	0.55	-	nuc	0	Nucleus (By similarity)				140
Q98TR3 UniProt NPD GO	RENT1_FUGRU	Putative regulator of nonsense transcripts 1 (EC 3.6.1.-) (ATP-dependent helicase RENT1)	0.55	-	nuc	0	Cytoplasm (Potential)				1097
Q9CZW6 UniProt NPD GO	RN146_MOUSE	RING finger protein 146	0.55	+	nuc	0				1UJR	359
O94332 UniProt NPD GO	RRN11_SCHPO	RNA polymerase I-specific transcription initiation factor rrn11	0.55	-	nuc	0	Nucleus (Potential)	RNA polymerase I transcription factor complex [IDA]			200
P19263 UniProt NPD GO	MED14_YEAST	RNA polymerase II mediator complex subunit 14 (Glucose repression regulatory protein 1)	0.55	-	nuc	0	Nucleus	mediator complex [IDA]			1082
Q03570 UniProt NPD GO	MED14_CAEEL	RNA polymerase II mediator complex subunit 14 (Mediator complex subunit rgr-1)	0.55	-	mit	0	Nucleus				1374
Q3T042 UniProt NPD GO	NOB1_BOVIN	RNA-binding protein NOB1	0.55	-	nuc	0	Nucleus (By similarity)				413
Q8GYN5 UniProt NPD GO	RIN4_ARATH	RPM1-interacting protein 4	0.55	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein				211
Q8BMG7 UniProt NPD GO	RBGPR_MOUSE	Rab3 GTPase-activating protein non-catalytic subunit (Rab3 GTPase-activating protein 150 kDa subunit ...	0.55	-	cyt	0	Cytoplasm (By similarity). In neurons, it is enriched in the synaptic soluble fraction (By similarit ...	soluble fraction [ISS]			1366
Q9Z1C8 UniProt NPD GO	RPGF3_RAT	Rap guanine nucleotide exchange factor 3 (cAMP-regulated guanine nucleotide exchange factor I) (cAMP ...	0.55	-	mit	0	Cytoplasm. Membrane; peripheral membrane protein (By similarity)				884
Q5A1U8 UniProt NPD GO	ERFD_CANAL	Ras modification protein ERF4	0.55	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				232
P49795 UniProt NPD GO	RGS19_HUMAN	Regulator of G-protein signaling 19 (RGS19) (G-alpha-interacting protein) (GAIP protein)	0.55	-	nuc	0	Membrane; lipid-anchor	Golgi apparatus [TAS] membrane fraction [TAS]	605071	1CMZ	217
Q8BXT1 UniProt NPD GO	RGS8_MOUSE	Regulator of G-protein signaling 8 (RGS8)	0.55	-	mit	0					180
P49804 UniProt NPD GO	RGS8_RAT	Regulator of G-protein signaling 8 (RGS8)	0.55	-	mit	0					180
Q99P72 UniProt NPD GO	RTN4_MOUSE	Reticulon-4 (Neurite outgrowth inhibitor) (Nogo protein)	0.55	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	cell projection [IDA] cell soma [IDA] endoplasmic reticulum [IDA] integral to endoplasmic reticulum membrane [ISS] nuclear envelope [ISS]			1162
O35602 UniProt NPD GO	RX_MOUSE	Retinal homeobox protein Rx (Retina and anterior neural fold homeobox protein)	0.55	+	nuc	0	Nucleus				342
Q9I9A2 UniProt NPD GO	RX2_ORYLA	Retinal homeobox protein Rx2	0.55	+	nuc	0	Nucleus (By similarity)				327
Q12128 UniProt NPD GO	BAG7_YEAST	Rho-GTPase-activating protein BAG7	0.55	-	nuc	0		intracellular [TAS]			409

You are viewing entries 22151 to 22200 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.