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
Q4ADK7 UniProt NPD GO	CFDP1_CAMDR	Craniofacial development protein 1 (Bucentaur)	0.78	+	nuc	0					297
O88271 UniProt NPD GO	CFDP1_MOUSE	Craniofacial development protein 1 (Bucentaur) (27 kDa craniofacial protein) (Protein Cp27)	0.78	-	nuc	0		basement membrane [TAS]			295
Q588U8 UniProt NPD GO	CFDP2_TRAJA	Craniofacial development protein 2 (p97 bucentaur protein)	0.78	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				574
P14810 UniProt NPD GO	RK35_CYAPA	Cyanelle 50S ribosomal protein L35	0.78	-	mit	0	Plastid; cyanelle				65
Q2QLE5 UniProt NPD GO	CFTR_PANTR	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.78	-	end	11	Membrane; multi-pass membrane protein				1480
Q91WL5 UniProt NPD GO	CP4AC_MOUSE	Cytochrome P450 4A12 (EC 1.14.14.1) (CYPIVA12)	0.78	+	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [ISS]			508
Q7XJN0 UniProt NPD GO	RH17_ARATH	DEAD-box ATP-dependent RNA helicase 17 (EC 3.6.1.-)	0.78	+	nuc	0					609
Q751Y8 UniProt NPD GO	LCD1_ASHGO	DNA damage checkpoint protein LCD1	0.78	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				694
Q8BTF7 UniProt NPD GO	DNL4_MOUSE	DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4)	0.78	-	cyt	0	Nucleus (By similarity)				911
Q07980 UniProt NPD GO	MLH2_YEAST	DNA mismatch repair protein MLH2 (MutL protein homolog 2)	0.78	-	nuc	0	Nucleus	nucleus [IPI]			695
P97679 UniProt NPD GO	MLH1_RAT	DNA mismatch repair protein Mlh1 (MutL protein homolog 1)	0.78	+	nuc	0	Nucleus (By similarity)				757
Q9DE46 UniProt NPD GO	DPOLA_XENLA	DNA polymerase alpha catalytic subunit (EC 2.7.7.7)	0.78	-	nuc	0	Nucleus				1458
Q6BJ51 UniProt NPD GO	RAD52_DEBHA	DNA repair and recombination protein RAD52	0.78	-	nuc	0	Nucleus (By similarity)				573
P43352 UniProt NPD GO	RAD52_MOUSE	DNA repair protein RAD52 homolog	0.78	-	nuc	0	Nucleus (Potential)				420
Q6PCI7 UniProt NPD GO	MCM5B_XENLA	DNA replication licensing factor mcm5-B (Minichromosome maintenance protein 5-B) (xMCM5-B) (CDC46 ho ...	0.78	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [ISS] MCM complex [ISS]			735
P30181 UniProt NPD GO	TOP1_ARATH	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.78	-	nuc	0					916
Q8VWF8 UniProt NPD GO	RPOT2_NICSY	DNA-directed RNA polymerase 2, chloroplast/mitochondrial precursor (EC 2.7.7.6) (T7 bacteriophage-ty ...	0.78	-	cyt	0	Plastid; chloroplast. Mitochondrion	mitochondrion [IDA] plastid [IDA]			1020
Q8L6J3 UniProt NPD GO	RPO2B_TOBAC	DNA-directed RNA polymerase 2B, chloroplast/mitochondrial precursor (EC 2.7.7.6) (T7 bacteriophage-t ...	0.78	-	cyt	0	Plastid; chloroplast. Mitochondrion				1021
P69242 UniProt NPD GO	RPOT3_NICSY	DNA-directed RNA polymerase 3, chloroplast precursor (EC 2.7.7.6) (T7 bacteriophage-type single subu ...	0.78	+	mit	0	Plastid; chloroplast				977
P69243 UniProt NPD GO	RPO3A_TOBAC	DNA-directed RNA polymerase 3A, chloroplast precursor (EC 2.7.7.6) (T7 bacteriophage-type single sub ...	0.78	+	mit	0	Plastid; chloroplast				977
Q8L6J1 UniProt NPD GO	RPO3B_TOBAC	DNA-directed RNA polymerase 3B, chloroplast precursor (EC 2.7.7.6) (T7 bacteriophage-type single sub ...	0.78	+	mit	0	Plastid; chloroplast				977
Q9UBU2 UniProt NPD GO	DKK2_HUMAN	Dickkopf-related protein 2 precursor (Dkk-2) (Dickkopf-2) (hDkk-2)	0.78	+	exc	0	Secreted protein	extracellular space [TAS]	605415		259
Q9UD71 UniProt NPD GO	IPPD_HUMAN	Dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32)	0.78	-	nuc	0	Cytoplasm	cytoplasm [NAS]	604399		204
O95793 UniProt NPD GO	STAU1_HUMAN	Double-stranded RNA-binding protein Staufen homolog 1	0.78	-	nuc	0	Endoplasmic reticulum; rough endoplasmic reticulum. Localizes exclusively with the rough reticulum e ...	microtubule associated complex [TAS] rough endoplasmic reticulum [TAS]	601716		577
Q13202 UniProt NPD GO	DUS8_HUMAN	Dual specificity protein phosphatase 8 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity protein phospha ...	0.78	+	nuc	0		cytoplasm [TAS]	602038		625
Q6PFY9 UniProt NPD GO	CC14B_MOUSE	Dual specificity protein phosphatase CDC14B (EC 3.1.3.48) (EC 3.1.3.16) (CDC14 cell division cycle 1 ...	0.78	-	nuc	1	Nucleus; nucleolus (By similarity). Nucleolar during interphase (By similarity)				485
Q19020 UniProt NPD GO	DYHC_CAEEL	Dynein heavy chain, cytosolic (DYHC)	0.78	-	nuc	0	Cytoplasm				4568
Q9PUQ1 UniProt NPD GO	PEA3_BRARE	ETS domain-containing transcription factor PEA3	0.78	-	nuc	0	Nucleus (By similarity)				494
Q99607 UniProt NPD GO	ELF4_HUMAN	ETS-related transcription factor Elf-4 (E74-like factor 4) (Myeloid Elf-1-like factor)	0.78	-	nuc	0	Nucleus. Accumulation into PML nuclear bodies is mediated by PML	PML body [IDA]			663
O18473 UniProt NPD GO	ECR_HELVI	Ecdysone receptor (Ecdysteroid receptor) (20-hydroxy-ecdysone receptor) (20E receptor) (EcRH) (HvEcR ...	0.78	-	nuc	0	Nucleus			1R20	576
Q8MJW9 UniProt NPD GO	EDN2_MUSPF	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2)	0.78	+	exc	0	Secreted protein				178
O95208 UniProt NPD GO	EPN2_HUMAN	Epsin-2 (EPS-15-interacting protein 2)	0.78	-	nuc	0	Cytoplasm. In punctate structures throughout the cell, associated with clathrin-coated vesicles, and ...		607263		642
P50240 UniProt NPD GO	ESR1_OREAU	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.78	+	nuc	0	Nucleus				583
O42132 UniProt NPD GO	ESR1_PAGMA	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.78	-	nuc	0	Nucleus				581
Q9PVE2 UniProt NPD GO	ESR2_STUVU	Estrogen receptor beta (ER-beta)	0.78	+	nuc	0	Nucleus	nucleus [ISS]			554
Q9PTU5 UniProt NPD GO	ESR2_CHICK	Estrogen receptor beta (ER-beta) (cERb)	0.78	+	nuc	0	Nucleus				472
Q9W669 UniProt NPD GO	ESRB1_CARAU	Estrogen receptor beta-1 (ER-beta-1)	0.78	+	nuc	0	Nucleus				568
P89102 UniProt NPD GO	SEC5_YEAST	Exocyst complex component SEC5	0.78	-	nuc	0		bud neck [IDA] bud tip [IDA] exocyst [IPI] incipient bud site [IDA]			971
Q9V730 UniProt NPD GO	EXT1_DROME	Exostosin-1 (EC 2.4.1.224) (EC 2.4.1.225) (Protein tout-velu)	0.78	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to membrane [NAS]			760
Q03214 UniProt NPD GO	ECM5_YEAST	Extracellular matrix protein 5	0.78	-	cyt	0	Nucleus	nucleus [IDA]			1411
Q9W602 UniProt NPD GO	SSRP1_XENLA	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit ssrp1) (Structure-sp ...	0.78	+	nuc	0	Nucleus				693
Q80V62 UniProt NPD GO	FACD2_MOUSE	Fanconi anemia group D2 protein homolog (Protein FACD2)	0.78	+	nuc	0	Nucleus (By similarity). Concentrates in nuclear foci during S phase and upon genotoxic stress (By s ...	condensed chromosome [IDA]			1450
P61150 UniProt NPD GO	FGF12_RAT	Fibroblast growth factor 12 (FGF-12) (Fibroblast growth factor homologous factor 1) (FHF-1)	0.78	-	nuc	0	Nucleus (Probable)				243
P61328 UniProt NPD GO	FGF12_HUMAN	Fibroblast growth factor 12 (FGF-12) (Fibroblast growth factor homologous factor 1) (FHF-1) (Myocyte ...	0.78	-	nuc	0	Nucleus (Probable)		601513	1Q1U	243
P61329 UniProt NPD GO	FGF12_MOUSE	Fibroblast growth factor 12 (FGF-12) (Fibroblast growth factor homologous factor 1) (FHF-1) (Myocyte ...	0.78	-	nuc	0	Nucleus (Probable)				243
P48802 UniProt NPD GO	FGF3_BRARE	Fibroblast growth factor 3 precursor (FGF-3) (HBGF-3)	0.78	+	exc	0	Secreted protein (Probable)	extracellular matrix (sensu Metazoa) [IDA] extracellular space [IDA]			256
P32029 UniProt NPD GO	FD5_DROME	Fork head domain-containing protein FD5	0.78	-	nuc	0	Nucleus				271
Q12951 UniProt NPD GO	FOXI1_HUMAN	Forkhead box protein I1 (Forkhead-related protein FKHL10) (Forkhead-related transcription factor 6) ...	0.78	+	nuc	0	Nucleus	nucleus [NAS]	601093		351
Q63248 UniProt NPD GO	FOXI2_RAT	Forkhead box protein I2 (Hepatocyte nuclear factor 3 forkhead homolog 5) (HFH-5) (Fragment)	0.78	+	mit	0	Nucleus				101
Q9UPW0 UniProt NPD GO	FOXJ3_HUMAN	Forkhead box protein J3	0.78	+	nuc	0	Nucleus (Potential)				622

You are viewing entries 9801 to 9850 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.