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
Q7SBU6 UniProt NPD GO	VID21_NEUCR	Chromatin modification-related protein vid-21	0.85	+	nuc	0	Nucleus (Probable)				2189
P40381 UniProt NPD GO	SWI6_SCHPO	Chromatin-associated protein swi6	0.85	+	nuc	0	Nucleus (Probable)	nuclear telomeric heterochromatin [IDA]		1E0B	328
Q14781 UniProt NPD GO	CBX2_HUMAN	Chromobox protein homolog 2	0.85	+	nuc	0	Nucleus	nucleus [NAS]	602770		532
O13816 UniProt NPD GO	SCC3_SCHPO	Cohesin subunit psc3 (SCC3 homolog)	0.85	-	nuc	0	Nucleus. Associates with chromatin. Cohesin complex mainly associates with broad centromere region. ...	mitotic cohesin complex [IDA]			962
Q8IWA6 UniProt NPD GO	CCD60_HUMAN	Coiled-coil domain-containing protein 60	0.85	-	nuc	0					550
Q8C156 UniProt NPD GO	CND2_MOUSE	Condensin complex subunit 2 (Barren homolog protein 1) (Chromosome-associated protein H) (mCAP-H) (X ...	0.85	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...				731
P40094 UniProt NPD GO	COG3_YEAST	Conserved oligomeric Golgi complex subunit 3 (COG complex subunit 3) (Protein SEC34)	0.85	+	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein	Golgi transport complex [IPI] peripheral to membrane of membrane fraction [IDA] soluble fraction [IDA]			801
Q95MI6 UniProt NPD GO	CRF_BOVIN	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone)	0.85	-	exc	0	Secreted protein				190
Q96NY9 UniProt NPD GO	MUS81_HUMAN	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.85	-	nuc	0	Nucleus; nucleolus. Recruited to foci of DNA damage in S-phase cells		606591		551
O60583 UniProt NPD GO	CCNT2_HUMAN	Cyclin-T2 (CycT2)	0.85	-	nuc	0	Nucleus		603862		730
Q2QLA3 UniProt NPD GO	CFTR_HORSE	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.85	-	end	11	Membrane; multi-pass membrane protein				1481
Q2KN95 UniProt NPD GO	CYTSA_TETNG	Cytospin-A	0.85	-	nuc	0					1113
Q8GXD6 UniProt NPD GO	RH49_ARATH	DEAD-box ATP-dependent RNA helicase 49 (EC 3.6.1.-)	0.85	+	mit	0					558
Q96DF8 UniProt NPD GO	DGC14_HUMAN	DGCR14 protein (DiGeorge syndrome critical region 14) (ES2 protein)	0.85	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]	601755		476
Q5THR3 UniProt NPD GO	DJBP_HUMAN	DJ-1-binding protein (CAP-binding protein complex-interacting protein 1)	0.85	-	nuc	0	Nucleus			1WLZ	1501
Q9CWR8 UniProt NPD GO	DNM3L_MOUSE	DNA (cytosine-5)-methyltransferase 3-like	0.85	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nuclear heterochromatin [IDA] nucleus [ISS]			421
P40692 UniProt NPD GO	MLH1_HUMAN	DNA mismatch repair protein Mlh1 (MutL protein homolog 1)	0.85	-	nuc	0	Nucleus		609310		756
Q5K9M7 UniProt NPD GO	DPOE_CRYNE	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.85	+	nuc	0	Nucleus (By similarity)				2250
P25301 UniProt NPD GO	RAD57_YEAST	DNA repair protein RAD57	0.85	-	nuc	0	Nucleus (Potential)	nucleus [IPI]			460
P30666 UniProt NPD GO	MCM3_SCHPO	DNA replication licensing factor mcm3 (Minichromosome maintenance protein 3)	0.85	-	nuc	0	Nucleus	MCM complex [IDA]			879
Q561P5 UniProt NPD GO	MCM5_XENTR	DNA replication licensing factor mcm5 (Minichromosome maintenance protein 5)	0.85	-	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [ISS] MCM complex [ISS]			735
Q00313 UniProt NPD GO	TOP1_CANAL	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.85	+	nuc	0					778
O14086 UniProt NPD GO	RPA3_SCHPO	DNA-directed RNA polymerase I 49 kDa polypeptide (EC 2.7.7.6) (A49)	0.85	-	nuc	0	Nucleus (By similarity)				425
Q6GLI9 UniProt NPD GO	RPF53_XENLA	DNA-directed RNA polymerase I-associated factor 53 kDa subunit (EC 2.7.7.6) (RNA polymerase I-associ ...	0.85	-	nuc	0	Nucleus; nucleolus (By similarity)				419
Q9MTM3 UniProt NPD GO	RPOC2_OENHO	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.85	-	nuc	0	Plastid; chloroplast				1386
Q2VEI6 UniProt NPD GO	RPOC2_SOLTU	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.85	-	nuc	0	Plastid; chloroplast				1392
P11704 UniProt NPD GO	RPOC2_SPIOL	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.85	-	cyt	0	Plastid; chloroplast				1361
P38550 UniProt NPD GO	RPOC2_TOBAC	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.85	-	nuc	0	Plastid; chloroplast				1388
O54935 UniProt NPD GO	XRCC1_CRIGR	DNA-repair protein XRCC1 (X-ray repair cross-complementing protein 1)	0.85	+	nuc	0	Nucleus (Probable)				633
Q92608 UniProt NPD GO	DOCK2_HUMAN	Dedicator of cytokinesis protein 2	0.85	+	end	0	Intracytoplasmic membrane; peripheral membrane protein. Colocalizes with F-actin		603122		1830
Q8IZD9 UniProt NPD GO	DOCK3_HUMAN	Dedicator of cytokinesis protein 3 (Modifier of cell adhesion) (Presenilin-binding protein) (PBP pro ...	0.85	-	vac	0	Cytoplasm (By similarity)		603123		2030
Q8N1I0 UniProt NPD GO	DOCK4_HUMAN	Dedicator of cytokinesis protein 4	0.85	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein		607679		1966
Q24180 UniProt NPD GO	DEAF1_DROME	Deformed epidermal autoregulatory factor 1 (Protein DEAF-1)	0.85	+	nuc	0	Nucleus	nucleus [IDA] polytene chromosome [IDA]			576
O82132 UniProt NPD GO	DRE2A_ARATH	Dehydration-responsive element-binding protein 2A (DREB2A protein)	0.85	+	nuc	0	Nucleus (Probable)				335
Q8WZ79 UniProt NPD GO	DNS2B_HUMAN	Deoxyribonuclease-2-beta precursor (EC 3.1.22.1) (Deoxyribonuclease II beta) (DNase II beta) (DNase2 ...	0.85	-	exc	1 *	Lysosome (Probable)		608057		361
Q7Z7J5 UniProt NPD GO	DPPA2_HUMAN	Developmental pluripotency-associated protein 2 (Pluripotent embryonic stem cell-related protein 1)	0.85	-	nuc	0	Nucleus				298
Q5PYH7 UniProt NPD GO	DLG2_BRARE	Discs large homolog 2 (Postsynaptic density protein 93) (PSD-93)	0.85	-	nuc	0					881
Q8K4R9 UniProt NPD GO	DLG7_MOUSE	Discs large homolog 7 (Hepatoma up-regulated protein homolog) (HURP)	0.85	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Localizes to the spindle poles in mitotic cells. ...	nucleus [ISS] spindle pole centrosome [ISS]			808
Q5XIX0 UniProt NPD GO	DCJ14_RAT	DnaJ homolog subfamily C member 14 (Dopamine receptor interacting protein of 78 kDa) (DRiP78)	0.85	+	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				703
Q23255 UniProt NPD GO	MRE11_CAEEL	Double-strand break repair protein mre-11	0.85	-	nuc	0	Nucleus				728
Q9NS39 UniProt NPD GO	RED2_HUMAN	Double-stranded RNA-specific editase B2 (EC 3.5.-.-) (dsRNA adenosine deaminase B2) (RNA-dependent a ...	0.85	+	mit	0	Nucleus		602065		739
P59020 UniProt NPD GO	DSCR9_HUMAN	Down syndrome critical region protein 9	0.85	-	nuc	0					149
Q8GY23 UniProt NPD GO	UPL1_ARATH	E3 ubiquitin protein ligase UPL1 (EC 6.3.2.-) (Ubiquitin-protein ligase 1)	0.85	-	end	0					3684
O24606 UniProt NPD GO	EIN3_ARATH	ETHYLENE-INSENSITIVE3 protein	0.85	-	nuc	0	Nucleus	nucleus [TAS]			628
P41162 UniProt NPD GO	ETV3_HUMAN	ETS translocation variant 3 (ETS-domain transcriptional repressor PE1) (PE-1) (Mitogenic Ets transcr ...	0.85	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	164873		512
P49883 UniProt NPD GO	ECR_MANSE	Ecdysone receptor (Ecdysteroid receptor) (20-hydroxy-ecdysone receptor) (20E receptor) (EcRH)	0.85	-	mit	0	Nucleus				556
P23943 UniProt NPD GO	EDN2_RAT	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2) (Vasoactive intestinal contractor) (VIC)	0.85	-	exc	0	Secreted protein				176
Q01070 UniProt NPD GO	ESMC_DROME	Enhancer of split mgamma protein (E(spl)mgamma) (HLH-mgamma) (Split locus enhancer protein mB)	0.85	-	nuc	0	Nucleus (Probable)				205
Q8TE68 UniProt NPD GO	ES8L1_HUMAN	Epidermal growth factor receptor kinase substrate 8-like protein 1 (Epidermal growth factor receptor ...	0.85	-	nuc	0	Cytoplasm				723
Q8TE67 UniProt NPD GO	ES8L3_HUMAN	Epidermal growth factor receptor kinase substrate 8-like protein 3 (Epidermal growth factor receptor ...	0.85	+	nuc	0	Cytoplasm			1WXT	593

You are viewing entries 6451 to 6500 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.