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
P14737 UniProt NPD GO	RAD9_YEAST	DNA repair protein RAD9	0.92	+	nuc	0	Nucleus	nucleus [IC]		2FF4	1309
P36617 UniProt NPD GO	RAD16_SCHPO	DNA repair protein rad16	0.92	+	end	0	Nucleus				892
Q5BHD6 UniProt NPD GO	RAD5_EMENI	DNA repair protein rad5 (EC 3.6.1.-)	0.92	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1202
P25206 UniProt NPD GO	MCM3_MOUSE	DNA replication licensing factor MCM3 (DNA polymerase alpha holoenzyme-associated protein P1) (P1-MC ...	0.92	+	nuc	0	Nucleus				812
P25205 UniProt NPD GO	MCM3_HUMAN	DNA replication licensing factor MCM3 (DNA polymerase alpha holoenzyme-associated protein P1) (RLF s ...	0.92	+	nuc	0	Nucleus	alpha DNA polymerase:primase complex [TAS]	602693		808
Q85C71 UniProt NPD GO	RPOC2_ANTFO	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.92	-	cyt	0	Plastid; chloroplast				1445
Q9XPS9 UniProt NPD GO	RPOC2_WHEAT	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.92	+	nuc	0	Plastid; chloroplast				1479
Q96BY6 UniProt NPD GO	DOC10_HUMAN	Dedicator of cytokinesis protein 10 (Protein zizimin 3)	0.92	-	nuc	0					2183
Q8NF50 UniProt NPD GO	DOCK8_HUMAN	Dedicator of cytokinesis protein 8	0.92	-	end	0					2031
Q9BZ29 UniProt NPD GO	DOCK9_HUMAN	Dedicator of cytokinesis protein 9 (Cdc42 guanine nucleotide exchange factor zizimin 1)	0.92	-	cyt	0	Intracytoplasmic membrane (Probable). Associated with membranes (Probable)		607325	1WG7	2069
Q9WV69 UniProt NPD GO	DEMA_MOUSE	Dematin (Erythrocyte membrane protein band 4.9)	0.92	-	nuc	0					405
Q86T65 UniProt NPD GO	DAAM2_HUMAN	Disheveled-associated activator of morphogenesis 2	0.92	-	nuc	0			606627		1068
Q9D415 UniProt NPD GO	DLGP1_MOUSE	Disks large-associated protein 1 (DAP-1) (Guanylate kinase-associated protein) (SAP90/PSD-95-associa ...	0.92	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Found in postsynaptic density of neurona ...	synapse [IDA]			992
O14490 UniProt NPD GO	DLGP1_HUMAN	Disks large-associated protein 1 (DAP-1) (Guanylate kinase-associated protein) (hGKAP) (SAP90/PSD-95 ...	0.92	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Found in postsynaptic density of neurona ...		605445		977
P97836 UniProt NPD GO	DLGP1_RAT	Disks large-associated protein 1 (DAP-1) (Guanylate kinase-associated protein) (rGKAP) (SAP90/PSD-95 ...	0.92	-	nuc	0	Cell membrane; peripheral membrane protein. Found in postsynaptic density of neuronal cells	postsynaptic membrane [IDA]			992
Q09446 UniProt NPD GO	DNJ5_CAEEL	DnaJ homolog dnj-5 (DnaJ domain protein 5)	0.92	+	nuc	2					915
Q16643 UniProt NPD GO	DREB_HUMAN	Drebrin (Developmentally-regulated brain protein)	0.92	-	nuc	0	Cytoplasm	actomyosin [NAS] cytoplasm [NAS] dendrite [NAS]	126660		648
Q09690 UniProt NPD GO	POM1_SCHPO	Dual specificity protein kinase pom1 (EC 2.7.12.1)	0.92	-	nuc	0	Present at both poles of the cell throughout the cell cycle whether they are growing or not. Located ...	barrier septum [IDA] cell cortex of cell tip [IDA] site of polarized growth [IDA]			1087
Q04195 UniProt NPD GO	SIZ1_YEAST	E3 SUMO--protein ligase SIZ1 (EC 6.-.-.-) (SAP and Miz-finger domain-containing protein 1) (Ubiquiti ...	0.92	-	nuc	0	Cytoplasm; cytosol. Nucleus. Present at the bud neck in early M-phase	septin ring [IDA]			904
P58283 UniProt NPD GO	UB7I1_MOUSE	E3 ubiquitin ligase TRIAD3 (EC 6.3.2.-) (Ubiquitin-conjugating enzyme 7-interacting protein 1) (UbcM ...	0.92	+	nuc	0	Cytoplasm				853
P17685 UniProt NPD GO	ELH1_APLPA	ELH type 1 precursor [Contains: Alpha-bag cell peptide (Alpha-BCP); Beta-bag cell peptide (Beta-BCP) ...	0.92	+	exc	0	Secreted protein				263
P14404 UniProt NPD GO	EVI1_MOUSE	Ecotropic virus integration 1 site protein	0.92	-	nuc	0	Nucleus				1042
Q9UI08 UniProt NPD GO	EVL_HUMAN	Ena/VASP-like protein (Ena/vasodilator-stimulated phosphoprotein-like)	0.92	-	nuc	0	Cytoplasm. Targeted to the leading edge of lamellipodia and the dital tip of stress fibers through i ...	cytoplasm [ISS] focal adhesion [ISS] lamellipodium [ISS]			416
Q9VCU9 UniProt NPD GO	DCR1_DROME	Endoribonuclease Dcr-1 (EC 3.1.26.-) (Protein dicer-1)	0.92	-	nuc	0		RNA-induced silencing complex [IDA]			2249
Q8R418 UniProt NPD GO	DICER_MOUSE	Endoribonuclease Dicer (EC 3.1.26.-) (Double-strand-specific ribonuclease mDCR-1)	0.92	-	nuc	0		intracellular [ISS]			1906
Q99PM1 UniProt NPD GO	CN092_RAT	Epidermal Langerhans cell protein LCP1	0.92	+	nuc	0	Nucleus (Probable)				619
P39936 UniProt NPD GO	IF4F2_YEAST	Eukaryotic initiation factor 4F subunit p130 (eIF4F p130) (eIF-4F p130) (mRNA cap-binding protein co ...	0.92	-	nuc	0		eukaryotic translation initiation factor 4F... [IGI] ribosome [TAS]			914
O43432 UniProt NPD GO	IF4G3_HUMAN	Eukaryotic translation initiation factor 4 gamma 3 (eIF-4-gamma 3) (eIF-4G 3) (eIF4G 3) (eIF-4-gamma ...	0.92	-	nuc	0		eukaryotic translation initiation factor 4F... [TAS]	603929	1HU3	1585
Q9UQ84 UniProt NPD GO	EXO1_HUMAN	Exonuclease 1 (EC 3.1.-.-) (hExo1) (Exonuclease I) (hExoI)	0.92	-	nuc	0	Nucleus. Colocalizes with PCNA to discrete nuclear foci in S-phase	nucleus [IDA]	606063		846
Q91Z62 UniProt NPD GO	FBX32_RAT	F-box only protein 32 (Muscle atrophy F-box protein) (MAFbx) (Atrogin-1)	0.92	+	cyt	0		SCF ubiquitin ligase complex [IPI]			350
Q8BMI0 UniProt NPD GO	FBX38_MOUSE	F-box only protein 38 (Modulator of KLF7 activity) (MoKA)	0.92	+	nuc	0	Cytoplasm. Nucleus				1194
Q08943 UniProt NPD GO	SSRP1_MOUSE	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (Structure-sp ...	0.92	+	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci (By ...				708
Q04931 UniProt NPD GO	SSRP1_RAT	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (Structure-sp ...	0.92	+	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci (By ...				709
Q9P2Q2 UniProt NPD GO	FRM4A_HUMAN	FERM domain-containing protein 4A	0.92	+	nuc	0					1024
O15360 UniProt NPD GO	FANCA_HUMAN	Fanconi anemia group A protein (Protein FACA)	0.92	-	nuc	0	Nucleus. Major form. Cytoplasm. Minor form	cytoplasm [TAS] nucleus [TAS]	607139		1455
Q9BX63 UniProt NPD GO	FANCJ_HUMAN	Fanconi anemia group J protein (EC 3.6.1.-) (ATP-dependent RNA helicase BRIP1) (Protein FACJ) (BRCA1 ...	0.92	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [NAS]	605882		1249
Q23935 UniProt NPD GO	TRSF_DROER	Female-specific protein transformer	0.92	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Speckled subnuclear compartment (By similarit ...				178
Q9CS72 UniProt NPD GO	FLIP1_MOUSE	Filamin-A-interacting protein 1 (FILIP)	0.92	-	nuc	0					1211
Q8K4T4 UniProt NPD GO	FLIP1_RAT	Filamin-A-interacting protein 1 (FILIP)	0.92	-	nuc	0	Cytoplasm. Isoform 1 is localized along actin stress fibres, except at their ends, suggesting coloca ...				1212
Q5NDM2 UniProt NPD GO	FXI2A_XENLA	Forkhead box protein I2-A (XlFoxI2-A)	0.92	+	nuc	0	Nucleus (Potential)				369
Q7TQC7 UniProt NPD GO	GPTC2_MOUSE	G patch domain-containing protein 2	0.92	+	nuc	0					527
Q92259 UniProt NPD GO	SREP_PENCH	GATA factor SREP	0.92	-	nuc	0	Nucleus (Probable)				532
Q5PP38 UniProt NPD GO	GAT29_ARATH	GATA transcription factor 29	0.92	-	nuc	0	Nucleus (Probable)				470
Q8VZP4 UniProt NPD GO	GATA5_ARATH	GATA transcription factor 5 (AtGATA-5)	0.92	+	nuc	0	Nucleus (Probable)				308
Q6DBP8 UniProt NPD GO	GATA6_ARATH	GATA transcription factor 6 (AtGATA-6)	0.92	+	nuc	0	Nucleus (Probable)				303
Q9P107 UniProt NPD GO	GMIP_HUMAN	GEM-interacting protein (GMIP)	0.92	-	nuc	0		intracellular [IC]	609694		970
Q755I4 UniProt NPD GO	GYP5_ASHGO	GTPase-activating protein GYP5	0.92	-	nuc	0	Cytoplasm (By similarity)				829
Q06648 UniProt NPD GO	GIC2_YEAST	GTPase-interacting component 2	0.92	-	nuc	0		actin cap [IDA] bud tip [IDA] incipient bud site [IDA] mating projection tip [IDA]			383
Q12514 UniProt NPD GO	NOT5_YEAST	General negative regulator of transcription subunit 5	0.92	-	nuc	0	Cytoplasm (Probable). Nucleus	CCR4-NOT core complex [IPI] cytoplasm [IDA]			560
Q08378 UniProt NPD GO	GOGA3_HUMAN	Golgin subfamily A member 3 (Golgin-160) (Golgi complex-associated protein of 170 kDa) (GCP170)	0.92	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein	Golgi apparatus [TAS] Golgi membrane [TAS] Golgi transport complex [IDA]	602581		1498

You are viewing entries 3201 to 3250 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.