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
Q92143 UniProt NPD GO	P53_XIPMA	Cellular tumor antigen p53 (Tumor suppressor p53)	0.81	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				342
Q8WWN8 UniProt NPD GO	CEND3_HUMAN	Centaurin-delta 3 (Cnt-d3) (Arf-GAP, Rho-GAP, ankyrin repeat and pleckstrin homology domain-containi ...	0.81	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Cytoplasmic, ...	cytoplasm [IC] lamellipodium [ISS] ruffle [ISS]	606647		1544
O15078 UniProt NPD GO	CE290_HUMAN	Centrosomal protein Cep290	0.81	-	nuc	0	Centrosome	centrosome [IDA] cytoplasm [IDA]			1539
Q6GNN8 UniProt NPD GO	CHM4C_XENLA	Charged multivesicular body protein 4c (Chromatin-modifying protein 4c) (CHMP4c)	0.81	+	nuc	0	Cytoplasm (By similarity)				227
Q6GMA4 UniProt NPD GO	CHM6A_XENLA	Charged multivesicular body protein 6-A (Chromatin-modifying protein 6-A)	0.81	-	nuc	0	Intracytoplasmic membrane; lipid-anchor (By similarity)				199
O78495 UniProt NPD GO	RK20_GUITH	Chloroplast 50S ribosomal protein L20	0.81	-	nuc	0	Plastid; chloroplast				114
Q85X37 UniProt NPD GO	RK20_PINKO	Chloroplast 50S ribosomal protein L20	0.81	-	nuc	0	Plastid; chloroplast				120
P41610 UniProt NPD GO	RK20_PINTH	Chloroplast 50S ribosomal protein L20	0.81	-	mit	0	Plastid; chloroplast				118
Q70JA7 UniProt NPD GO	CHSS3_HUMAN	Chondroitin sulfate synthase 3 (EC 2.4.1.175) (Glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-be ...	0.81	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)		609963		882
Q91713 UniProt NPD GO	CHRD_XENLA	Chordin precursor (Organizer-specific secreted dorsalizing factor)	0.81	-	nuc	0	Secreted protein				941
Q6BNL6 UniProt NPD GO	YNG2_DEBHA	Chromatin modification-related protein YNG2 (ING1 homolog 2)	0.81	+	nuc	0	Nucleus (By similarity)				285
P41877 UniProt NPD GO	ISW1_CAEEL	Chromatin remodelling complex ATPase chain isw-1 (EC 3.6.1.-)	0.81	-	nuc	0	Nucleus (Probable)				1009
O74964 UniProt NPD GO	RSC1_SCHPO	Chromatin structure remodeling complex protein rsc1 (Remodel the structure of chromatin complex subu ...	0.81	-	nuc	0	Nucleus (By similarity). Localizes to centromeric and flanking chromatin (By similarity)				803
Q99KN9 UniProt NPD GO	EPN4_MOUSE	Clathrin interactor 1 (Epsin-4) (Epsin-related protein) (EpsinR) (Enthoprotin)	0.81	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Membrane; peripheral membr ...				631
Q14677 UniProt NPD GO	EPN4_HUMAN	Clathrin interactor 1 (Epsin-4) (Epsin-related protein) (EpsinR) (Enthoprotin) (Clathrin-interacting ...	0.81	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region. Membrane; peripheral membrane protein. Found throughout th ...	Golgi apparatus [IDA]	607265	1XGW	625
Q8BTV2 UniProt NPD GO	CPSF7_MOUSE	Cleavage and polyadenylation specificity factor 7	0.81	-	nuc	0	Nucleus (By similarity)				471
Q8N684 UniProt NPD GO	CPSF7_HUMAN	Cleavage and polyadenylation specificity factor 7 (Cleavage and polyadenylation specificity factor 5 ...	0.81	-	nuc	0	Nucleus (Probable)				471
Q06890 UniProt NPD GO	CLUS_MOUSE	Clusterin precursor (Sulfated glycoprotein 2) (SGP-2) (Clustrin) (Apolipoprotein J) (Apo-J) [Contain ...	0.81	-	nuc	0	Secreted protein				448
P05371 UniProt NPD GO	CLUS_RAT	Clusterin precursor (Sulfated glycoprotein 2) (SGP-2) (Dimeric acid glycoprotein) (DAG) (Testosteron ...	0.81	-	exc	0	Secreted protein				447
Q8R3P7 UniProt NPD GO	CLUA1_MOUSE	Clusterin-associated protein 1	0.81	-	nuc	0	Nucleus (By similarity)				413
P12263 UniProt NPD GO	FA8_PIG	Coagulation factor VIII precursor (Procoagulant component)	0.81	-	nuc	0	Secreted protein; extracellular space				2133
Q8R1N0 UniProt NPD GO	CCD16_MOUSE	Coiled-coil domain-containing protein 16 (Ovus mutant candidate gene 1 protein)	0.81	-	nuc	0	Nucleus. Excluded from nucleolus. In metaphase II oocytes and in mitotic blastomeres, it is detected ...	nucleus [IDA]			363
Q2M329 UniProt NPD GO	CCD96_HUMAN	Coiled-coil domain-containing protein 96	0.81	-	nuc	0					555
P0C0L4 UniProt NPD GO	CO4A_HUMAN	Complement C4-A precursor (Acidic complement C4) [Contains: Complement C4 beta chain; Complement C4- ...	0.81	+	mit	0			120790	1HZF	1744
P07358 UniProt NPD GO	CO8B_HUMAN	Complement component C8 beta chain precursor (Complement component 8 subunit beta)	0.81	-	mit	1 *	Secreted protein	membrane [TAS]	120960		591
Q8K2Z4 UniProt NPD GO	CND1_MOUSE	Condensin complex subunit 1 (Chromosome condensation-related SMC-associated protein 1) (Chromosome-a ...	0.81	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...	condensed chromosome [IDA] condensin core heterodimer [ISS] cytoplasm [ISS] pronucleus [IDA]			1392
Q91082 UniProt NPD GO	COLI_LEPOS	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Gamma-melanotropin- ...	0.81	-	nuc	0					259
Q9UEE9 UniProt NPD GO	CFDP1_HUMAN	Craniofacial development protein 1 (Bucentaur)	0.81	+	nuc	0			608108		299
P63154 UniProt NPD GO	CRNL1_MOUSE	Crooked neck-like protein 1 (Crooked neck homolog)	0.81	+	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				690
P63155 UniProt NPD GO	CRNL1_RAT	Crooked neck-like protein 1 (Crooked neck homolog) (Crooked neck protein)	0.81	+	cyt	0	Nucleus. Detected in the splicing complex carrying pre-mRNA				690
P37366 UniProt NPD GO	CCL1_YEAST	Cyclin CCL1	0.81	-	nuc	0		mitochondrion [IDA] transcription factor TFIIH complex [TAS]			393
Q22197 UniProt NPD GO	CKI1_CAEEL	Cyclin-dependent kinase inhibitor 1	0.81	-	nuc	0	Nucleus				184
P14581 UniProt NPD GO	CP4A7_RABIT	Cytochrome P450 4A7 precursor (EC 1.14.15.3) (CYPIVA7) (Lauric acid omega-hydroxylase) (P450-KA-2)	0.81	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				511
Q9PW73 UniProt NPD GO	SOJO_XENLA	Cytoskeletal protein Sojo (p170)	0.81	-	nuc	0					1335
Q9UBC3 UniProt NPD GO	DNM3B_HUMAN	DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) (Dnmt3b) (DNA methyltransferase HsaIIIB) (DNA MT ...	0.81	-	nuc	0	Nucleus	nucleus [TAS]	602900		853
P34881 UniProt NPD GO	DNMT1_ARATH	DNA (cytosine-5)-methyltransferase AthI (EC 2.1.1.37) (DNA methyltransferase AthI) (DNA Metase AthI) ...	0.81	-	nuc	0	Nucleus (By similarity)				1534
Q5R6L3 UniProt NPD GO	DNL4_PONPY	DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4)	0.81	+	cyt	0	Nucleus (By similarity)				911
Q4WXH8 UniProt NPD GO	DPOE_ASPFU	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.81	+	mit	0	Nucleus (By similarity)				2230
Q27607 UniProt NPD GO	DPOG1_DROME	DNA polymerase subunit gamma 1, mitochondrial precursor (EC 2.7.7.7) (Mitochondrial DNA polymerase c ...	0.81	-	mit	0	Mitochondrion	gamma DNA polymerase complex [IDA] mitochondrion [NAS]			1145
P49643 UniProt NPD GO	PRI2_HUMAN	DNA primase large subunit (EC 2.7.7.-) (DNA primase 58 kDa subunit) (p58)	0.81	-	nuc	0			176636		509
P33610 UniProt NPD GO	PRI2_MOUSE	DNA primase large subunit (EC 2.7.7.-) (DNA primase 58 kDa subunit) (p58)	0.81	+	nuc	0					505
O89044 UniProt NPD GO	PRI2_RAT	DNA primase large subunit (EC 2.7.7.-) (DNA primase 58 kDa subunit) (p58)	0.81	+	nuc	0					507
P97310 UniProt NPD GO	MCM2_MOUSE	DNA replication licensing factor MCM2 (Minichromosome maintenance protein 2 homolog) (Nuclear protei ...	0.81	-	nuc	0	Nucleus (Probable)	nuclear origin of replication recognition c... [IDA] nucleus [IDA]			904
O61078 UniProt NPD GO	TOP2_LEICH	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.81	-	cyt	0	Nucleus (By similarity)				1236
P41001 UniProt NPD GO	TOP2_PLAFK	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.81	+	nuc	0	Nucleus				1398
O35134 UniProt NPD GO	RPA1_MOUSE	DNA-directed RNA polymerase I largest subunit (EC 2.7.7.6) (RNA polymerase I 194 kDa subunit) (RPA19 ...	0.81	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [IDA]			1717
P18616 UniProt NPD GO	RPB1_ARATH	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	0.81	-	nuc	0	Nucleus				1840
P27059 UniProt NPD GO	RPOB_ASTLO	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.81	+	nuc	0	Plastid				1076
Q8HTL6 UniProt NPD GO	RPOB1_CHLRE	DNA-directed RNA polymerase beta chain N-terminal subunit (EC 2.7.7.6) (PEP) (Plastid-encoded RNA po ...	0.81	-	nuc	0	Plastid; chloroplast				822
P18887 UniProt NPD GO	XRCC1_HUMAN	DNA-repair protein XRCC1 (X-ray repair cross-complementing protein 1)	0.81	+	nuc	0	Nucleus (Probable)		194360	1XNT	633

You are viewing entries 8251 to 8300 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.