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
Q8N137 UniProt NPD GO	CNTRB_HUMAN	Centrobin (LYST-interacting protein 8)	0.86	-	nuc	0	Centrosome. Centriole-associated, asymmetrically localizes to the daughter centriole	centriole [IDA]			903
O94986 UniProt NPD GO	CE152_HUMAN	Centrosomal protein of 152 kDa (Cep152 protein)	0.86	-	nuc	0	Centrosome				1275
Q60952 UniProt NPD GO	CP250_MOUSE	Centrosome-associated protein CEP250 (Centrosomal protein 2) (Centrosomal Nek2-associated protein 1) ...	0.86	-	nuc	0	Cytoplasm; perinuclear region. Centrosome. Component of the core centrosome where it is found at the ...				2414
Q24478 UniProt NPD GO	CP190_DROME	Centrosome-associated zinc finger protein CP190 (DMAP190) (Protein enhancer of mod(mdg4)4-1)	0.86	-	nuc	0	Nucleus. Nucleus in interphase. Colocalizes with other elements of the gypsy chromatin insulator com ...	centrosome [IDA] nucleus [IDA] polytene chromosome [IDA]			1096
Q9PWB0 UniProt NPD GO	CER1_CHICK	Cerberus precursor	0.86	-	nuc	0	Secreted protein (Probable)				272
Q569C1 UniProt NPD GO	CHM4C_RAT	Charged multivesicular body protein 4c (Chromatin-modifying protein 4c) (CHMP4c)	0.86	-	nuc	0	Cytoplasm (By similarity)				232
Q5SD32 UniProt NPD GO	RK20_HUPLU	Chloroplast 50S ribosomal protein L20	0.86	-	nuc	0	Plastid; chloroplast				136
Q59K07 UniProt NPD GO	EAF3_CANAL	Chromatin modification-related protein EAF3	0.86	-	nuc	0	Nucleus (By similarity)				369
Q12432 UniProt NPD GO	EAF3_YEAST	Chromatin modification-related protein EAF3 (ESA1-associated factor 3)	0.86	+	nuc	0	Nucleus	H4/H2A histone acetyltransferase complex [IPI]			401
Q6C626 UniProt NPD GO	EAF6_YARLI	Chromatin modification-related protein EAF6	0.86	+	nuc	0	Nucleus (By similarity)				135
O59773 UniProt NPD GO	VID21_SCHPO	Chromatin modification-related protein vid21	0.86	-	nuc	0	Nucleus (Probable)				985
P30658 UniProt NPD GO	CBX2_MOUSE	Chromobox protein homolog 2 (Modifier 3 protein) (M33)	0.86	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle				519
Q8VHE6 UniProt NPD GO	DYH5_MOUSE	Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (Mdnah5)	0.86	-	nuc	0		axonemal dynein complex [IMP]			4621
O14503 UniProt NPD GO	BHLH2_HUMAN	Class B basic helix-loop-helix protein 2 (bHLHB2) (Differentially expressed in chondrocytes protein ...	0.86	-	nuc	0	Nucleus	nucleus [NAS]	604256		412
Q502W7 UniProt NPD GO	CCD38_HUMAN	Coiled-coil domain-containing protein 38	0.86	-	nuc	0					563
Q9H0W5 UniProt NPD GO	CCDC8_HUMAN	Coiled-coil domain-containing protein 8	0.86	+	nuc	0					538
Q6GQI5 UniProt NPD GO	CCD93_XENLA	Coiled-coil domain-containing protein 93	0.86	+	nuc	0					609
P23508 UniProt NPD GO	CRCM_HUMAN	Colorectal mutant cancer protein (Protein MCC)	0.86	+	nuc	0			159350		829
O13360 UniProt NPD GO	FLUF_NEUCR	Conidial development protein fluffy	0.86	-	nuc	0	Nucleus (By similarity)				792
Q7SD49 UniProt NPD GO	MUS81_NEUCR	Crossover junction endonuclease mus-81 (EC 3.1.22.-)	0.86	-	nuc	0	Nucleus (By similarity)				645
Q24311 UniProt NPD GO	CUL1_DROME	Cullin homolog 1 (Lin-19 homolog protein)	0.86	-	nuc	0		SCF ubiquitin ligase complex [NAS]			774
P18846 UniProt NPD GO	ATF1_HUMAN	Cyclic AMP-dependent transcription factor ATF-1 (Activating transcription factor 1) (TREB36 protein) ...	0.86	+	nuc	0	Nucleus		123803		271
Q8R0S1 UniProt NPD GO	ATF7_MOUSE	Cyclic AMP-dependent transcription factor ATF-7 (Activating transcription factor 7) (Transcription f ...	0.86	+	nuc	0	Nucleus (By similarity)				413
Q2QLC5 UniProt NPD GO	CFTR_CARPS	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.86	-	end	11	Membrane; multi-pass membrane protein				1482
Q6E3D2 UniProt NPD GO	CPB3_CAEJA	Cytoplasmic polyadenylation element-binding protein 3	0.86	-	nuc	0					734
Q2KN97 UniProt NPD GO	CYTSA_CHICK	Cytospin-A	0.86	+	nuc	0					1118
Q6BHU0 UniProt NPD GO	SPC19_DEBHA	DASH complex subunit SPC19 (Outer kinetochore protein SPC19)	0.86	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				177
Q56X76 UniProt NPD GO	RH39_ARATH	DEAD-box ATP-dependent RNA helicase 39 (EC 3.6.1.-)	0.86	-	mit	0					621
Q9EQM6 UniProt NPD GO	DGCR8_MOUSE	DGCR8 protein (DiGeorge syndrome critical region 8 homolog) (Gy1)	0.86	+	nuc	0					773
Q8WYQ5 UniProt NPD GO	DGCR8_HUMAN	DGCR8 protein (DiGeorge syndrome critical region 8)	0.86	+	nuc	0		nucleus [IDA]	609030	1X47	773
Q6P1E8 UniProt NPD GO	DJBP_MOUSE	DJ-1-binding protein	0.86	-	nuc	0	Nucleus (By similarity)				1490
Q27746 UniProt NPD GO	DNMT1_PARLI	DNA (cytosine-5)-methyltransferase PliMCI (EC 2.1.1.37) (Dnmt1) (DNA methyltransferase PliMCI) (DNA ...	0.86	+	nuc	0	Nucleus (By similarity)				1612
P14607 UniProt NPD GO	DDIT3_CRIGR	DNA damage-inducible transcript 3 (DDIT-3) (Growth arrest and DNA-damage-inducible protein GADD153) ...	0.86	+	nuc	0	Nucleus				168
Q02870 UniProt NPD GO	ERCC3_DROME	DNA excision repair protein haywire (EC 3.6.1.-) (ATP-dependent DNA helicase hay) (ERCC-3 homolog pr ...	0.86	-	cyt	0	Nucleus	nucleus [IC]			798
Q15054 UniProt NPD GO	DPOD3_HUMAN	DNA polymerase subunit delta 3 (DNA polymerase subunit delta p66)	0.86	+	nuc	0	Nucleus	delta DNA polymerase complex [NAS]		1U76	466
Q920Q2 UniProt NPD GO	REV1_MOUSE	DNA repair protein REV1 (EC 2.7.7.-) (Rev1-like terminal deoxycytidyl transferase)	0.86	-	nuc	0	Nucleus (Probable)				1249
P55862 UniProt NPD GO	MCM5A_XENLA	DNA replication licensing factor mcm5-A (Minichromosome maintenance protein 5-A) (xMCM5-A) (CDC46 ho ...	0.86	-	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [IDA] MCM complex [IDA]			735
P41512 UniProt NPD GO	TOP1_XENLA	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.86	+	nuc	0					829
O24600 UniProt NPD GO	RPOT3_ARATH	DNA-directed RNA polymerase 3, chloroplast precursor (EC 2.7.7.6)	0.86	-	mit	0	Plastid; chloroplast				993
Q9TL28 UniProt NPD GO	RPOA_NEPOL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.86	-	nuc	0	Plastid; chloroplast				495
P56764 UniProt NPD GO	RPOC2_ARATH	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.86	+	cyt	0	Plastid; chloroplast				1376
Q9THV5 UniProt NPD GO	RPOC2_SINAL	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.86	-	nuc	0	Plastid; chloroplast				1384
Q9H7D0 UniProt NPD GO	DOCK5_HUMAN	Dedicator of cytokinesis protein 5 (Fragment)	0.86	-	nuc	0					804
Q7SIG6 UniProt NPD GO	DDEF2_MOUSE	Development and differentiation-enhancing factor 2 (Pyk2 C-terminus-associated protein) (PAP) (Paxil ...	0.86	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein. Cell mem ...			1DCQ	958
O95886 UniProt NPD GO	DLGP3_HUMAN	Disks large-associated protein 3 (DAP-3) (SAP90/PSD-95-associated protein 3) (SAPAP3) (PSD-95/SAP90- ...	0.86	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Postsynaptic density of neuronal cells ( ...				979
Q921R4 UniProt NPD GO	DCJ14_MOUSE	DnaJ homolog subfamily C member 14	0.86	+	mit	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				703
Q95J56 UniProt NPD GO	DCJ14_BOVIN	DnaJ homolog subfamily C member 14 (J-domain protein interacting with viral protein) (Jiv)	0.86	+	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				699
P78563 UniProt NPD GO	RED1_HUMAN	Double-stranded RNA-specific editase 1 (EC 3.5.-.-) (dsRNA adenosine deaminase) (RNA-editing deamina ...	0.86	+	nuc	0			601218	1ZY7	741
Q9JI20 UniProt NPD GO	RED2_MOUSE	Double-stranded RNA-specific editase B2 (EC 3.5.-.-) (dsRNA adenosine deaminase B2) (RNA-dependent a ...	0.86	+	mit	0	Nucleus (By similarity)				745
P97616 UniProt NPD GO	RED2_RAT	Double-stranded RNA-specific editase B2 (EC 3.5.-.-) (dsRNA adenosine deaminase B2) (RNA-dependent a ...	0.86	+	mit	0	Nucleus (By similarity)				746

You are viewing entries 6001 to 6050 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.