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
Q9NQW8 UniProt NPD GO	CNGB3_HUMAN	Cyclic nucleotide-gated cation channel beta 3 (CNG channel beta 3) (Cyclic nucleotide-gated channel ...	0.59	+	nuc	4	Membrane; multi-pass membrane protein		605080		809
Q66HE7 UniProt NPD GO	CDKL1_RAT	Cyclin-dependent kinase-like 1 (EC 2.7.11.22)	0.59	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				352
P35071 UniProt NPD GO	CFTR_BOVIN	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.59	-	end	11	Membrane; multi-pass membrane protein				1481
P26955 UniProt NPD GO	IL3RB_MOUSE	Cytokine receptor common beta chain precursor (GM-CSF/IL-3/IL-5 receptor common beta-chain) (CD131 a ...	0.59	-	nuc	1 *	Membrane; single-pass type I membrane protein				896
P61168 UniProt NPD GO	DRD2_MOUSE	D(2) dopamine receptor (Dopamine D2 receptor)	0.59	-	end	7 *	Membrane; multi-pass membrane protein				444
P61169 UniProt NPD GO	DRD2_RAT	D(2) dopamine receptor (Dopamine D2 receptor)	0.59	-	end	7 *	Membrane; multi-pass membrane protein				444
Q75ED7 UniProt NPD GO	DUO1_ASHGO	DASH complex subunit DUO1 (Outer kinetochore protein DUO1)	0.59	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				209
Q38961 UniProt NPD GO	SNM1_ARATH	DNA cross-link repair protein SNM1 (AtSNM1)	0.59	-	nuc	0	Nucleus (By similarity)				484
Q9UGP5 UniProt NPD GO	DPOLL_HUMAN	DNA polymerase lambda (EC 2.7.7.7) (EC 4.2.99.-) (Pol Lambda) (DNA polymerase kappa) (DNA polymerase ...	0.59	-	nuc	0	Nucleus	nucleus [NAS]	606343	2BCV	575
Q13472 UniProt NPD GO	TOP3A_HUMAN	DNA topoisomerase 3-alpha (EC 5.99.1.2) (DNA topoisomerase III alpha)	0.59	-	nuc	0		nucleus [TAS]	601243		1001
P08518 UniProt NPD GO	RPB2_YEAST	DNA-directed RNA polymerase II 140 kDa polypeptide (EC 2.7.7.6) (B150) (RNA polymerase II subunit 2) ...	0.59	-	cyt	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]		2B8K	1224
O15514 UniProt NPD GO	RPB4_HUMAN	DNA-directed RNA polymerase II 16 kDa polypeptide (EC 2.7.7.6) (RPB4)	0.59	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [IC]	606017	2C35	142
Q9D7M8 UniProt NPD GO	RPB4_MOUSE	DNA-directed RNA polymerase II 16 kDa polypeptide (EC 2.7.7.6) (RPB4)	0.59	-	nuc	0	Nucleus (By similarity)				142
P36594 UniProt NPD GO	RPB1_SCHPO	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (RNA polymerase II subunit 1)	0.59	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]			1752
Q8MA10 UniProt NPD GO	RPOC2_CHAGL	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.59	-	cyt	0	Plastid; chloroplast				1373
P41606 UniProt NPD GO	RPOC2_PINTH	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.59	-	nuc	0	Plastid; chloroplast				1224
P51250 UniProt NPD GO	RPOC2_PORPU	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.59	-	nuc	0	Plastid; chloroplast				1224
Q9FKM5 UniProt NPD GO	XRCC3_ARATH	DNA-repair protein XRCC3 homolog (X-ray repair cross-complementing protein 3 homolog) (AtXRCC3)	0.59	-	nuc	0	Nucleus (Probable)				304
P98193 UniProt NPD GO	DMP1_RAT	Dentin matrix acidic phosphoprotein 1 precursor (Dentin matrix protein 1) (DMP-1) (AG1)	0.59	-	exc	0		extracellular matrix (sensu Metazoa) [IDA]			489
Q6IMK0 UniProt NPD GO	DPPA3_RAT	Developmental pluripotency-associated protein 3	0.59	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				158
P34100 UniProt NPD GO	PKD1_DICDI	Developmentally-regulated protein kinase 1 (EC 2.7.11.1) (Fragment)	0.59	-	nuc	0					416
Q2KI83 UniProt NPD GO	DJC17_BOVIN	DnaJ homolog subfamily C member 17	0.59	-	nuc	0					304
Q9H819 UniProt NPD GO	DJC18_HUMAN	DnaJ homolog subfamily C member 18	0.59	-	nuc	0	Membrane; single-pass membrane protein (Potential)				358
Q8WXX5 UniProt NPD GO	DNJC9_HUMAN	DnaJ homolog subfamily C member 9 (DnaJ protein SB73)	0.59	-	cyt	0					260
O80928 UniProt NPD GO	DOF24_ARATH	Dof zinc finger protein DOF2.4 (AtDOF2.4)	0.59	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			330
Q9UVN9 UniProt NPD GO	MRE11_COPCI	Double-strand break repair protein MRE11	0.59	-	nuc	0	Nucleus (By similarity)				731
Q9Z108 UniProt NPD GO	STAU1_MOUSE	Double-stranded RNA-binding protein Staufen homolog 1	0.59	-	nuc	0	Endoplasmic reticulum; rough endoplasmic reticulum. Localizes exclusively with the rough reticulum e ...	ribonucleoprotein complex [IDA]			487
P39053 UniProt NPD GO	DYN1_MOUSE	Dynamin-1 (EC 3.6.5.5)	0.59	-	nuc	0	Cytoplasm. Microtubule-associated	membrane coat [IDA]			867
Q9SMH3 UniProt NPD GO	DYH1A_CHLRE	Dynein-1-alpha heavy chain, flagellar inner arm I1 complex (1-alpha DHC) (Dynein-1, subspecies f)	0.59	-	end	0	Flagellum				4625
P51022 UniProt NPD GO	PNT1_DROME	ETS-like protein pointed, isoform P1 (D-ETS-2)	0.59	+	nuc	0	Nucleus (Potential)				623
Q58DT0 UniProt NPD GO	ELF5_BOVIN	ETS-related transcription factor Elf-5 (E74-like factor 5)	0.59	-	cyt	0					255
P21541 UniProt NPD GO	ZYG11_CAEEL	Early embryogenesis protein zyg-11	0.59	-	cyt	0					799
Q93ZB2 UniProt NPD GO	KO1_ARATH	Ent-kaurene oxidase (EC 1.14.13.78) (AtKO1) (Cytochrome P450 701A3)	0.59	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein				509
P43429 UniProt NPD GO	GATA1_RAT	Erythroid transcription factor (GATA-binding factor 1) (GATA-1) (Eryf1) (GF-1) (NF-E1 DNA-binding pr ...	0.59	+	nuc	0	Nucleus				413
Q9LW50 UniProt NPD GO	ERF2_NICSY	Ethylene-responsive transcription factor 2 (Ethylene-responsive element-binding factor 2) (EREBP-2) ...	0.59	-	nuc	0	Nucleus (Probable)				237
Q9UKV8 UniProt NPD GO	I2C2_HUMAN	Eukaryotic translation initiation factor 2C 2 (eIF2C 2) (eIF-2C 2) (Argonaute-2) (Slicer protein) (P ...	0.59	-	nuc	0	Cytoplasm; cytoplasmic bodies		606229		851
Q9C5Z2 UniProt NPD GO	IF33_ARATH	Eukaryotic translation initiation factor 3 subunit 3 (eIF-3 gamma) (eIF3 p38 subunit) (eIF3h)	0.59	-	cyt	0					337
Q96QU8 UniProt NPD GO	XPO6_HUMAN	Exportin-6 (Exp6) (Ran-binding protein 20)	0.59	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm		608411		1125
Q04623 UniProt NPD GO	ECM18_YEAST	Extracellular matrix protein 18	0.59	-	nuc	0	Mitochondrion	mitochondrion [IDA]			453
Q99504 UniProt NPD GO	EYA3_HUMAN	Eyes absent homolog 3 (EC 3.1.3.48)	0.59	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). With decreasing efficiency, translocalized to th ...		601655		573
Q9QXW0 UniProt NPD GO	FBXL6_MOUSE	F-box/LRR-repeat protein 6 (F-box and leucine-rich repeat protein 6) (F-box protein FBL6)	0.59	+	nuc	0					535
Q6C931 UniProt NPD GO	SPT16_YARLI	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.59	+	cyt	0	Nucleus (By similarity)				1003
P08021 UniProt NPD GO	FMR2_APLCA	FMRFamide neuropeptides type FMRF-2 precursor [Contains: FMRFamide]	0.59	-	cyt	0	Secreted protein				552
Q8BY35 UniProt NPD GO	FGD2_MOUSE	FYVE, RhoGEF and PH domain-containing protein 2	0.59	-	nuc	0	Cytoplasm (Probable)				655
P35556 UniProt NPD GO	FBN2_HUMAN	Fibrillin-2 precursor	0.59	-	nuc	1 *		extracellular matrix (sensu Metazoa) [TAS]	121050		2911
Q06002 UniProt NPD GO	BFSP1_BOVIN	Filensin (Beaded filament structural protein 1)	0.59	-	nuc	0	Membrane. Cytoplasm. Membrane- and cytoskeleton-associated				756
Q58DH8 UniProt NPD GO	FEN1_BOVIN	Flap endonuclease 1 (EC 3.1.-.-) (Flap structure-specific endonuclease 1) (FEN-1)	0.59	-	nuc	0	Nucleus (By similarity)				380
P48007 UniProt NPD GO	PIST_ARATH	Floral homeotic protein PISTILLATA (Transcription factor PI)	0.59	-	nuc	0	Nucleus				208
Q40505 UniProt NPD GO	FL2_TOBAC	Floricaula/leafy homolog 2 (NFL2)	0.59	-	cyt	0	Nucleus (Probable)				416
Q00944 UniProt NPD GO	FAK1_CHICK	Focal adhesion kinase 1 (EC 2.7.10.2) (FADK 1) (pp125FAK)	0.59	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...			2AL6	1053

You are viewing entries 19501 to 19550 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.