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
P32832 UniProt NPD GO	NPL6_YEAST	Chromatin structure remodeling complex protein RSC7 (Remodel the structure of chromatin complex subu ...	0.64	-	nuc	0	Nucleus	nucleus [IDA] RSC complex [IPI]			435
O95503 UniProt NPD GO	CBX6_HUMAN	Chromobox protein homolog 6	0.64	-	nuc	0	Nucleus (By similarity)				412
Q9DBY5 UniProt NPD GO	CBX6_MOUSE	Chromobox protein homolog 6	0.64	-	nuc	0	Nucleus (By similarity)				414
Q99PV5 UniProt NPD GO	BHLH3_MOUSE	Class B basic helix-loop-helix protein 3 (bHLHB3) (Differentially expressed in chondrocytes protein ...	0.64	-	nuc	0	Nucleus (By similarity)	transcriptional repressor complex [TAS]			410
O35779 UniProt NPD GO	BHLH3_RAT	Class B basic helix-loop-helix protein 3 (bHLHB3) (Enhancer-of-split and hairy-related protein 1) (S ...	0.64	-	nuc	0	Nucleus (By similarity)				410
P25473 UniProt NPD GO	CLUS_CANFA	Clusterin precursor (Glycoprotein 80) (Gp80) [Contains: Clusterin beta chain; Clusterin alpha chain] ...	0.64	-	exc	0	Secreted protein				445
Q9NUP7 UniProt NPD GO	CCD76_HUMAN	Coiled-coil domain-containing protein 76	0.64	-	nuc	0					481
Q14999 UniProt NPD GO	CUL7_HUMAN	Cullin-7 (CUL-7)	0.64	-	cyt	0		anaphase-promoting complex [NAS]	609577		1698
Q6ZQ38 UniProt NPD GO	CAND1_MOUSE	Cullin-associated NEDD8-dissociated protein 1 (Cullin-associated and neddylation-dissociated protein ...	0.64	-	mit	0	Nucleus (By similarity)				1230
P97536 UniProt NPD GO	CAND1_RAT	Cullin-associated NEDD8-dissociated protein 1 (Cullin-associated and neddylation-dissociated protein ...	0.64	-	mit	0	Nucleus	nucleus [ISS]			1230
P32963 UniProt NPD GO	CYHY_GIBBA	Cyanide hydratase (EC 4.2.1.66) (Formamide hydrolyase)	0.64	-	cyt	0					357
P97874 UniProt NPD GO	GAK_RAT	Cyclin G-associated kinase (EC 2.7.11.1)	0.64	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Golgi apparatus; trans-Golgi network (By similarity). ...				1305
P51946 UniProt NPD GO	CCNH_HUMAN	Cyclin-H (MO15-associated protein) (p37) (p34)	0.64	-	nuc	0	Nucleus	nucleus [TAS]	601953	1KXU	323
P61809 UniProt NPD GO	CD5R1_MOUSE	Cyclin-dependent kinase 5 activator 1 precursor (CDK5 activator 1) (Cyclin-dependent kinase 5 regula ...	0.64	-	nuc	0	Cyclin-dependent kinase 5 activator 1, p35: Cell membrane; lipid-anchor; cytoplasmic side (By simila ...	axon [ISS] cell soma [ISS] contractile fiber [ISS] cytoplasm [ISS] dendritic spine [ISS] growth cone [ISS] membrane [ISS] membrane fraction [TAS] neuromuscular junction [ISS] nucleus [ISS]			307
P61810 UniProt NPD GO	CD5R1_RAT	Cyclin-dependent kinase 5 activator 1 precursor (CDK5 activator 1) (Cyclin-dependent kinase 5 regula ...	0.64	-	nuc	0	Cyclin-dependent kinase 5 activator 1, p35: Cell membrane; lipid-anchor; cytoplasmic side (By simila ...	axon [IDA] cell soma [IDA] contractile fiber [IDA] cytoplasm [IDA] dendritic spine [IDA] growth cone [IDA] membrane [IDA] membrane fraction [ISS] neuromuscular junction [IDA] nucleus [IDA]			307
Q6E3C7 UniProt NPD GO	CPB1_CAEJA	Cytoplasmic polyadenylation element-binding protein 1	0.64	-	nuc	0					617
Q6E3F3 UniProt NPD GO	CPB2_CAEBR	Cytoplasmic polyadenylation element-binding protein 2	0.64	-	cyt	0					566
Q6C2T8 UniProt NPD GO	DAM1_YARLI	DASH complex subunit DAM1 (Outer kinetochore protein DAM1)	0.64	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				223
Q20870 UniProt NPD GO	DAZ1_CAEEL	DAZ protein 1	0.64	-	nuc	0					499
P09884 UniProt NPD GO	DPOLA_HUMAN	DNA polymerase alpha catalytic subunit (EC 2.7.7.7)	0.64	+	cyt	0	Nucleus	nucleus [NAS]	312040	1N5G	1462
P46588 UniProt NPD GO	DPOD_CANAL	DNA polymerase delta catalytic subunit (EC 2.7.7.7) (DNA polymerase III)	0.64	-	cyt	0	Nucleus				1038
Q9TL06 UniProt NPD GO	RPOB_NEPOL	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.64	-	cyt	0	Plastid; chloroplast				1109
Q4G3A5 UniProt NPD GO	RPOC2_EMIHU	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.64	-	nuc	0	Plastid; chloroplast				1267
Q6B8R6 UniProt NPD GO	RPOC2_GRATL	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.64	-	nuc	0	Plastid; chloroplast				1228
Q19038 UniProt NPD GO	DEL1_CAEEL	Degenerin del-1	0.64	-	end	2	Membrane; multi-pass membrane protein				664
Q8LFR2 UniProt NPD GO	DRE2C_ARATH	Dehydration-responsive element-binding protein 2C (DREB2C protein)	0.64	-	nuc	0	Nucleus (Probable)				341
P05066 UniProt NPD GO	PHR_YEAST	Deoxyribodipyrimidine photo-lyase, mitochondrial precursor (EC 4.1.99.3) (DNA photolyase) (Photoreac ...	0.64	-	mit	0	Nucleus. Mitochondrion	mitochondrion [IDA] nucleus [TAS]			565
O15061 UniProt NPD GO	DMN_HUMAN	Desmuslin	0.64	-	nuc	0	Cytoplasm (Probable). There are at least two distinct DMN subpopulations, one in which DMN interacts ...	intermediate filament [NAS]	606087		1565
Q9D4J3 UniProt NPD GO	DCBD1_MOUSE	Discoidin, CUB and LCCL domain-containing protein 1 precursor	0.64	+	exc	1	Membrane; single-pass type I membrane protein (Potential)				503
Q9QYI4 UniProt NPD GO	DNJBC_MOUSE	DnaJ homolog subfamily B member 12 (mDJ10)	0.64	-	nuc	1	Membrane; single-pass membrane protein (Potential)				376
Q9UBS3 UniProt NPD GO	DNJB9_HUMAN	DnaJ homolog subfamily B member 9 (Microvascular endothelial differentiation gene 1 protein) (Mdg-1) ...	0.64	-	nuc	1 *	Cytoplasm (By similarity). Nucleus (By similarity). Stress induces its translocation to the nucleus ...	cytoplasm [ISS] nucleolus [ISS]	602634	2CTR	223
Q5EA26 UniProt NPD GO	DJC18_BOVIN	DnaJ homolog subfamily C member 18	0.64	-	nuc	1	Membrane; single-pass membrane protein (Potential)				358
Q9NNZ3 UniProt NPD GO	DNJC4_HUMAN	DnaJ homolog subfamily C member 4 (Multiple endocrine neoplasia type 1 candidate protein number 18) ...	0.64	-	nuc	1	Membrane; single-pass membrane protein (Potential)	membrane [NAS] membrane fraction [TAS]	604189		241
P42824 UniProt NPD GO	DNJH2_ALLPO	DnaJ protein homolog 2	0.64	-	nuc	0	Membrane; lipid-anchor (Potential)				418
P43644 UniProt NPD GO	DNJH_ATRNU	DnaJ protein homolog ANJ1	0.64	-	nuc	0	Membrane; lipid-anchor (Potential)				417
Q9ZPY0 UniProt NPD GO	DOF25_ARATH	Dof zinc finger protein DOF2.5 (AtDOF2.5) (Dof affecting germination 2)	0.64	-	nuc	0	Nucleus (Probable)				369
Q9M2U1 UniProt NPD GO	DOF36_ARATH	Dof zinc finger protein DOF3.6 (AtDOF3.6) (OBF-binding protein 3)	0.64	-	nuc	0	Nucleus (Probable)				323
Q5ZM13 UniProt NPD GO	DRC1A_CHICK	Down-regulated by CTNNB1 protein A	0.64	-	nuc	0	Cytoplasm (By similarity)				515
Q16829 UniProt NPD GO	DUS7_HUMAN	Dual specificity protein phosphatase 7 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity protein phospha ...	0.64	-	nuc	0	Cytoplasm		602749		368
Q9MBF8 UniProt NPD GO	DYH1B_CHLRE	Dynein-1-beta heavy chain, flagellar inner arm I1 complex (1-beta DHC) (Dynein-1, subspecies f)	0.64	-	nuc	0	Flagellum				4513
Q5RBF2 UniProt NPD GO	NED4L_PONPY	E3 ubiquitin-protein ligase NEDD4-like protein (EC 6.3.2.-)	0.64	-	nuc	0	Cytoplasm (By similarity)				959
Q7M3M6 UniProt NPD GO	E74EF_DROVI	Ecdysone-induced protein 74EF (ETS-related protein E74A)	0.64	-	nuc	0	Nucleus (By similarity)				873
Q6CWT7 UniProt NPD GO	PPN1_KLULA	Endopolyphosphatase (EC 3.6.1.10)	0.64	+	mit	1 *	Vacuole; vacuolar membrane; single-pass type II membrane protein				681
O35177 UniProt NPD GO	CASL_MOUSE	Enhancer of filamentation 1 (MEF1) (CRK-associated substrate-related protein) (CAS-L) (p105) (Protei ...	0.64	-	nuc	0	Cytoplasm; cell cortex (By similarity). Nucleus (By similarity). Localizes to both the cell nucleus ...				833
Q8CHU3 UniProt NPD GO	EPN2_MOUSE	Epsin-2 (EPS-15-interacting protein 2) (Intersectin-EH-binding protein 2) (Ibp2)	0.64	-	nuc	0	Cytoplasm (By similarity). In punctate structures throughout the cell and particularly concentrated ...				595
Q6K7E6 UniProt NPD GO	ERF1_ORYSA	Ethylene-responsive transcription factor 1 (Ethylene-responsive element-binding factor 1) (EREBP-1) ...	0.64	-	nuc	0	Nucleus (Probable)				365
O13354 UniProt NPD GO	ERF2_CANAL	Eukaryotic peptide chain release factor GTP-binding subunit (ERF2) (Translation release factor 3) (P ...	0.64	-	nuc	0	Cytoplasm (Probable)				715
P09064 UniProt NPD GO	IF2B_YEAST	Eukaryotic translation initiation factor 2 subunit beta (eIF-2-beta)	0.64	+	nuc	0		eukaryotic translation initiation factor 2 ... [IMP] multi-eIF complex [IDA] ribosome [TAS]			285
P42525 UniProt NPD GO	ERK1_DICDI	Extracellular signal-regulated kinase 1 (EC 2.7.11.24) (ERK1) (MAP kinase 1)	0.64	-	nuc	0					415
Q8N693 UniProt NPD GO	ESX1L_HUMAN	Extraembryonic, spermatogenesis, homeobox 1-like protein	0.64	+	nuc	0	Nucleus (Potential)				406

You are viewing entries 16801 to 16850 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.