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
Q04750 UniProt NPD GO	TOP1_MOUSE	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.91	+	nuc	0					767
P87078 UniProt NPD GO	TOP2_CANAL	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.91	-	nuc	0	Nucleus				1461
Q6ZQF0 UniProt NPD GO	TOPB1_MOUSE	DNA topoisomerase II-binding protein 1 (DNA topoisomerase IIbeta-binding protein 1) (TopBP1)	0.91	-	nuc	0	Nucleus. Has a uniform nuclear distribution during G phase. Colocalizes with BRCA1 at stalled replic ...	condensed nuclear chromosome [IDA]			1515
P87175 UniProt NPD GO	APN2_SCHPO	DNA-(apurinic or apyrimidinic site) lyase 2 (EC 4.2.99.18) (AP endonuclease 2) (Apurinic-apyrimidini ...	0.91	-	nuc	0	Nucleus (By similarity)				523
P11938 UniProt NPD GO	RAP1_YEAST	DNA-binding protein RAP1 (SBF-E) (Repressor/activator site-binding protein) (TUF)	0.91	+	nuc	0	Nucleus	nuclear telomere cap complex [IDA] nuclear telomeric heterochromatin [TAS] nucleus [TAS]		1IGN	827
Q05950 UniProt NPD GO	REB1_KLULA	DNA-binding protein REB1 (QBP)	0.91	-	nuc	0	Nucleus				595
P40694 UniProt NPD GO	SMBP2_MOUSE	DNA-binding protein SMUBP-2 (EC 3.6.1.-) (ATP-dependent helicase IGHMBP2) (Immunoglobulin mu-binding ...	0.91	-	nuc	0	Nucleus (Potential)	axon [IDA] cell soma [IDA] cytoplasm [IDA] nucleus [IDA]			993
Q9P6H9 UniProt NPD GO	REB1_SCHPO	DNA-binding protein reb1	0.91	-	nuc	0	Nucleus (By similarity)				504
Q9GZS1 UniProt NPD GO	RPF53_HUMAN	DNA-directed RNA polymerase I-associated factor 53 kDa subunit (EC 2.7.7.6) (RNA polymerase I-associ ...	0.91	+	nuc	0	Nucleus; nucleolus	nucleolus [ISS]			481
P56300 UniProt NPD GO	RPOC1_CHLVU	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.91	+	cyt	0	Plastid; chloroplast				836
Q32RY3 UniProt NPD GO	RPOC1_STAPU	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.91	+	nuc	0	Plastid; chloroplast				834
Q66KC9 UniProt NPD GO	DACT1_XENTR	Dapper 1	0.91	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				824
Q8BIK4 UniProt NPD GO	DOCK9_MOUSE	Dedicator of cytokinesis protein 9 (Cdc42 guanine nucleotide exchange factor zizimin 1)	0.91	-	gol	0	Intracytoplasmic membrane (By similarity). Associated with membranes (By similarity)				2055
Q10025 UniProt NPD GO	DEGZ_CAEEL	Degenerin-like protein T28D9.7 in chromosome II	0.91	-	nuc	2	Membrane; multi-pass membrane protein				982
P50617 UniProt NPD GO	DEND_RAT	Dendrin	0.91	+	nuc	0		dendritic spine [TAS] endoplasmic reticulum [TAS] integral to membrane [TAS]			653
Q9P1A6 UniProt NPD GO	DLGP2_HUMAN	Disks large-associated protein 2 (DAP-2) (SAP90/PSD-95-associated protein 2) (SAPAP2) (PSD-95/SAP90- ...	0.91	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Postsynaptic density of neuronal cells ( ...	neurofilament [NAS]	605438		1019
Q9NRI5 UniProt NPD GO	DISC1_HUMAN	Disrupted in schizophrenia 1 protein	0.91	+	nuc	0	Localizes to neurites (By similarity). Cytoplasm. Localizes to punctate cytoplasmic foci which overl ...		605210		854
O93310 UniProt NPD GO	RAD21_XENLA	Double-strand-break repair protein rad21 homolog (SCC1 homolog)	0.91	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...				629
P49760 UniProt NPD GO	CLK2_HUMAN	Dual specificity protein kinase CLK2 (EC 2.7.12.1) (CDC-like kinase 2)	0.91	+	nuc	0	Nucleus (By similarity)		602989		499
O35491 UniProt NPD GO	CLK2_MOUSE	Dual specificity protein kinase CLK2 (EC 2.7.12.1) (CDC-like kinase 2)	0.91	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			499
P35761 UniProt NPD GO	TTK_MOUSE	Dual specificity protein kinase TTK (EC 2.7.12.1) (ESK) (PYT)	0.91	-	nuc	0					856
O60729 UniProt NPD GO	CC14B_HUMAN	Dual specificity protein phosphatase CDC14B (EC 3.1.3.48) (EC 3.1.3.16) (CDC14 cell division cycle 1 ...	0.91	-	mit	0	Nucleus; nucleolus (By similarity). Nucleolar during interphase	nucleus [IDA]	603505	1OHE	498
Q9Z188 UniProt NPD GO	DYR1B_MOUSE	Dual specificity tyrosine-phosphorylation-regulated kinase 1B (EC 2.7.12.1)	0.91	+	nuc	0	Nucleus				589
Q9Y463 UniProt NPD GO	DYR1B_HUMAN	Dual specificity tyrosine-phosphorylation-regulated kinase 1B (EC 2.7.12.1) (Mirk protein kinase) (M ...	0.91	+	nuc	0	Nucleus	nucleus [TAS]	604556		629
P50493 UniProt NPD GO	PVDB_PLAKN	Duffy receptor beta form precursor (Erythrocyte-binding protein)	0.91	-	nuc	1	Membrane; single-pass type I membrane protein				1153
Q8S944 UniProt NPD GO	DRP3A_ARATH	Dynamin-related protein 3A (Dynamin-like protein 2) (Dynamin-like protein 2a)	0.91	-	nuc	0	Mitochondrion				808
Q91WZ8 UniProt NPD GO	DTBP1_MOUSE	Dystrobrevin-binding protein 1 (Dysbindin) (Hermansky-Pudlak syndrome 7 protein homolog)	0.91	-	nuc	0	Cytoplasm	axon [IDA] nucleus [IDA] sarcolemma [IDA] sarcoplasm [IDA]			352
Q6DFR2 UniProt NPD GO	CBLB_XENTR	E3 ubiquitin-protein ligase CBL-B (EC 6.3.2.-) (Signal transduction protein CBL-B) (SH3-binding prot ...	0.91	-	nuc	0	Cytoplasm (By similarity)				982
Q03112 UniProt NPD GO	EVI1_HUMAN	Ecotropic virus integration 1 site protein	0.91	-	nuc	0	Nucleus	nucleus [NAS]	165215		1051
P70429 UniProt NPD GO	EVL_MOUSE	Ena/VASP-like protein (Ena/vasodilator-stimulated phosphoprotein-like)	0.91	-	nuc	0	Cytoplasm. Targeted to the leading edge of lamellipodia and the dital tip of stress fibers through i ...	cytoplasm [IDA] focal adhesion [IDA] lamellipodium [IDA]		1QC6	414
Q5R896 UniProt NPD GO	EVL_PONPY	Ena/VASP-like protein (Ena/vasodilator-stimulated phosphoprotein-like)	0.91	-	nuc	0	Cytoplasm. Targeted to the leading edge of lamellipodia and the dital tip of stress fibers through i ...				422
Q12518 UniProt NPD GO	ENT1_YEAST	Epsin-1	0.91	-	mit	0	Cytoplasm. Membrane; peripheral membrane protein. Localizes in a punctate pattern. Found in the acti ...	actin cortical patch [IPI]			454
P57717 UniProt NPD GO	ESR1_BRARE	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.91	-	nuc	0	Nucleus				569
Q9NIV1 UniProt NPD GO	E2AK3_DROME	Eukaryotic translation initiation factor 2-alpha kinase precursor (EC 2.7.11.1) (PRKR-like endoplasm ...	0.91	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				1162
Q09103 UniProt NPD GO	DGK2_DROME	Eye-specific diacylglycerol kinase (EC 2.7.1.107) (Retinal degeneration A protein) (Diglyceride kina ...	0.91	-	nuc	0	Membrane; peripheral membrane protein				1457
Q2KHT6 UniProt NPD GO	FBX32_BOVIN	F-box only protein 32	0.91	+	cyt	0					355
Q80XI1 UniProt NPD GO	FBX34_MOUSE	F-box only protein 34	0.91	-	nuc	0					695
Q6FWT4 UniProt NPD GO	SPT16_CANGA	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.91	-	nuc	0	Nucleus (By similarity)				1027
Q08945 UniProt NPD GO	SSRP1_HUMAN	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (FACT 80 kDa ...	0.91	+	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci		604328		709
Q8BIE6 UniProt NPD GO	FRM4A_MOUSE	FERM domain-containing protein 4A	0.91	+	nuc	0					1020
Q80UZ0 UniProt NPD GO	FGD5_MOUSE	FYVE, RhoGEF and PH domain-containing protein 5	0.91	+	nuc	0	Cytoplasm (Probable)				1219
O01501 UniProt NPD GO	CCNE_CAEEL	G1/S-specific cyclin-E	0.91	+	nuc	0	Nucleus	nucleus [IDA]			524
P54733 UniProt NPD GO	CCNE_DROME	G1/S-specific cyclin-E (DmCycE)	0.91	-	exc	0	Nucleus	nucleus [IDA]			709
O65515 UniProt NPD GO	GAT12_ARATH	GATA transcription factor 12	0.91	-	nuc	0	Nucleus (Probable)				238
Q4V328 UniProt NPD GO	GRAP1_HUMAN	GRIP1-associated protein 1 (GRASP-1)	0.91	-	nuc	0			300408		841
P48566 UniProt NPD GO	GYP3_YEAST	GTPase-activating protein GYP3 (Protein MSB3) (Multicopy suppressor of bud emergence 3)	0.91	+	nuc	0	Cytoplasm. Bud. Bud neck. Localizes to the presumptive bud site, the bud tip and the mother-bud neck ...	bud tip [IDA] incipient bud site [IDA]			633
Q86X53 UniProt NPD GO	ERIC1_HUMAN	Glutamate-rich protein 1	0.91	+	nuc	0					443
Q8TBA6 UniProt NPD GO	GOGA5_HUMAN	Golgin subfamily A member 5 (Golgin-84) (RET-fused gene 5 protein) (Ret-II protein)	0.91	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein. Found throughout the Golgi, b ...	Golgi apparatus [IDA] Golgi cis-face [IDA] Golgi cisterna [IDA] integral to membrane [IDA]	606918		731
Q8TAE8 UniProt NPD GO	G45IP_HUMAN	Growth arrest and DNA-damage-inducible proteins-interacting protein 1 (CR6-interacting factor 1) (CR ...	0.91	+	mit	0	Nucleus				222
P33402 UniProt NPD GO	GCYA2_HUMAN	Guanylate cyclase soluble subunit alpha-2 (EC 4.6.1.2) (GCS-alpha-2)	0.91	-	mit	0	Cytoplasm		601244		732

You are viewing entries 3651 to 3700 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.