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
Q9PUB4 UniProt NPD GO	CP26A_CHICK	Cytochrome P450 26A1 (EC 1.14.-.-) (Retinoic acid-degrading enzyme CYP26)	0.54	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				492
Q9VGH1 UniProt NPD GO	CP315_DROME	Cytochrome P450 315a1, mitochondrial precursor (EC 1.14.99.-) (CYPCCCXVA1) (Shadow protein)	0.54	-	cyt	0	Mitochondrion	mitochondrion [IDA]			520
Q9HBI6 UniProt NPD GO	CP4FB_HUMAN	Cytochrome P450 4F11 (EC 1.14.14.1) (CYPIVF11)	0.54	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				524
Q63100 UniProt NPD GO	DC1I1_RAT	Cytoplasmic dynein 1 intermediate chain 1 (Dynein intermediate chain 1, cytosolic) (DH IC-1) (Cytopl ...	0.54	+	cyt	0		cytoplasmic dynein complex [IDA]			643
Q6FU86 UniProt NPD GO	SPC19_CANGA	DASH complex subunit SPC19 (Outer kinetochore protein SPC19)	0.54	-	cyt	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				154
Q90YB1 UniProt NPD GO	DNL4_CHICK	DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4)	0.54	-	cyt	0	Nucleus (By similarity)				912
O02789 UniProt NPD GO	TDT_MONDO	DNA nucleotidylexotransferase (EC 2.7.7.31) (Terminal addition enzyme) (Terminal deoxynucleotidyltra ...	0.54	-	cyt	0	Nucleus				518
O57486 UniProt NPD GO	TDT_AMBME	DNA nucleotidylexotransferase (EC 2.7.7.31) (Terminal addition enzyme) (Terminal deoxynucleotidyltra ...	0.54	-	nuc	0	Nucleus (By similarity)				510
P12531 UniProt NPD GO	TOP2_TRYBB	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.54	-	cyt	0	Nucleus				1221
Q04688 UniProt NPD GO	ELG_DROME	DNA-binding protein D-ELG	0.54	+	nuc	0	Nucleus				464
P22138 UniProt NPD GO	RPA2_YEAST	DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6) (A135) (RNA polymerase I subunit 2)	0.54	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [TAS]			1203
Q4VZK3 UniProt NPD GO	RPOA_CUCSA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.54	+	mit	0	Plastid; chloroplast				333
Q9XPS7 UniProt NPD GO	RPOB_WHEAT	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.54	-	nuc	0	Plastid; chloroplast				1076
Q68S15 UniProt NPD GO	RPOC1_PANGI	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.54	-	cyt	0	Plastid; chloroplast				682
Q23933 UniProt NPD GO	DEC1_DROER	Defective chorion-1 protein precursor (Fragments)	0.54	-	exc	0	Secreted protein	chorion [ISS]			557
P28310 UniProt NPD GO	DEF3_MOUSE	Defensin-related cryptdin 3 precursor	0.54	-	exc	0	Secreted protein				93
P50707 UniProt NPD GO	DEF9_MOUSE	Defensin-related cryptdin 9 precursor	0.54	-	exc	0	Secreted protein				93
P24612 UniProt NPD GO	MEC4_CAEEL	Degenerin mec-4 (Mechanosensory abnormality protein 4)	0.54	-	vac	1	Membrane; multi-pass membrane protein				768
P23239 UniProt NPD GO	DESM_XENLA	Desmin	0.54	-	mit	0	Cytoplasm				458
Q9BGX5 UniProt NPD GO	DAB1_MACFA	Disabled homolog 1	0.54	-	nuc	0					555
P59584 UniProt NPD GO	RP8HA_ARATH	Disease resistance protein RPH8A (RPP8 homolog A)	0.54	-	cyt	0					910
P98149 UniProt NPD GO	DIF_DROME	Dorsal-related immunity factor Dif	0.54	+	nuc	0	Cytoplasm. Nucleus. Accumulates in the nucleus upon bacterial infection of injury	cytoplasm [IDA] nucleus [IDA]			667
P49959 UniProt NPD GO	MRE11_HUMAN	Double-strand break repair protein MRE11A (MRE11 homolog 1) (MRE11 meiotic recombination 11 homolog ...	0.54	-	nuc	0	Nucleus (By similarity). Localizes to discrete nuclear foci after treatment with genotoxic agents (B ...	nucleoplasm [TAS] nucleus [TAS]	604391		708
Q60HE6 UniProt NPD GO	MRE11_MACFA	Double-strand break repair protein MRE11A (MRE11 homolog 1) (MRE11 meiotic recombination 11 homolog ...	0.54	-	nuc	0	Nucleus (By similarity). Localizes to discrete nuclear foci after treatment with genotoxic agents (B ...				707
Q5DU00 UniProt NPD GO	DCDC2_MOUSE	Doublecortin domain-containing protein 2	0.54	-	nuc	0					475
Q9PTQ7 UniProt NPD GO	DMRT1_CHICK	Doublesex- and mab-3-related transcription factor 1 (Fragment)	0.54	-	nuc	0	Nucleus (Potential)				311
Q8CFG4 UniProt NPD GO	DMRTA_MOUSE	Doublesex- and mab-3-related transcription factor A1 (Doublesex- and mab-3-related transcription fac ...	0.54	-	nuc	0	Nucleus (Potential)				490
Q1KKS3 UniProt NPD GO	PDE11_FUGRU	Dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11A (EC 3.1.4.17) (EC 3.1.4.35) (cAMP and cGMP phos ...	0.54	-	mit	0	Cytoplasm; cytosol (By similarity)				903
Q8VCT9 UniProt NPD GO	TESK2_MOUSE	Dual specificity testis-specific protein kinase 2 (EC 2.7.12.1) (Testicular protein kinase 2)	0.54	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			570
P14044 UniProt NPD GO	PRO2_TRYBB	Duplicate procyclin	0.54	+	mit	0					99
Q6FNV5 UniProt NPD GO	HRD3_CANGA	ERAD-associated E3 ubiquitin-protein ligase component HRD3 precursor	0.54	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				833
P61555 UniProt NPD GO	EFR1_HYLML	ERV-FRD provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Syncytin-2) [Contains: ...	0.54	-	exc	2					538
P61558 UniProt NPD GO	EFR1_PONPY	ERV-FRD provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Syncytin-2) [Contains: ...	0.54	-	end	2					538
Q8VD58 UniProt NPD GO	EVI2B_MOUSE	EVI2B protein precursor (Ecotropic viral integration site 2B protein)	0.54	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				444
Q9GL77 UniProt NPD GO	S4A4_BOVIN	Electrogenic sodium bicarbonate cotransporter 1 (Sodium bicarbonate cotransporter) (Solute carrier f ...	0.54	+	end	9	Cell membrane; basolateral cell membrane; multi-pass membrane protein				1079
Q7SEY9 UniProt NPD GO	ERO1_NEUCR	Endoplasmic oxidoreductin-1 precursor (EC 1.8.4.-)	0.54	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				668
O13889 UniProt NPD GO	E2AK1_SCHPO	Eukaryotic translation initiation factor 2-alpha kinase 1 (EC 2.7.11.1) (Heme-regulated eukaryotic i ...	0.54	-	nuc	0					704
Q8CJF8 UniProt NPD GO	I2C4_MOUSE	Eukaryotic translation initiation factor 2C 4 (eIF2C 4) (eIF-2C 4) (Argonaute-4) (Piwi/argonaute fam ...	0.54	-	cyt	0					861
O15371 UniProt NPD GO	IF37_HUMAN	Eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta) (eIF3 p66) (eIF3d)	0.54	-	nuc	0		eukaryotic translation initiation factor 3 ... [TAS]	603915		548
O70194 UniProt NPD GO	IF37_MOUSE	Eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta) (eIF3 p66) (eIF3d)	0.54	-	nuc	0					547
O54921 UniProt NPD GO	EXOC2_RAT	Exocyst complex component 2 (Exocyst complex component Sec5) (rSec5)	0.54	-	mit	0		exocyst [IDA]		1UAD	924
Q4ILI9 UniProt NPD GO	EXO70_GIBZE	Exocyst complex protein EXO70	0.54	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				632
Q9Y169 UniProt NPD GO	EXT2_DROME	Exostosin-2 (EC 2.4.1.224) (EC 2.4.1.225) (Protein sister of tout-velu)	0.54	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA]			717
Q9ERK4 UniProt NPD GO	XPO2_MOUSE	Exportin-2 (Exp2) (Importin-alpha re-exporter) (Chromosome segregation 1-like protein)	0.54	-	cyt	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm (By similarity)				971
Q5R9J2 UniProt NPD GO	XPO2_PONPY	Exportin-2 (Exp2) (Importin-alpha re-exporter) (Chromosome segregation 1-like protein)	0.54	-	cyt	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm (By similarity)				971
P55060 UniProt NPD GO	XPO2_HUMAN	Exportin-2 (Exp2) (Importin-alpha re-exporter) (Chromosome segregation 1-like protein) (Cellular apo ...	0.54	-	cyt	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm	cytoplasm [TAS] nucleus [TAS]	601342		971
Q9ESJ0 UniProt NPD GO	XPO4_MOUSE	Exportin-4 (Exp4)	0.54	-	cyt	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm (By similarity)				1151
Q9QZN4 UniProt NPD GO	FBX6_MOUSE	F-box only protein 6 (F-box only protein 6b)	0.54	-	cyt	0					295
O94334 UniProt NPD GO	POF13_SCHPO	F-box protein pof13	0.54	-	cyt	0					396
O04235 UniProt NPD GO	SSRP1_VICFA	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (Recombinatio ...	0.54	+	cyt	0	Nucleus (By similarity)				642

You are viewing entries 22451 to 22500 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.