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
P23881 UniProt NPD GO	TCEA3_MOUSE	Transcription elongation factor A protein 3 (Transcription elongation factor S-II protein 3) (Transc ...	0.82	-	nuc	0	Nucleus (Probable)			1WJT	347
Q9V460 UniProt NPD GO	SPT5H_DROME	Transcription elongation factor SPT5 (dSpt5) (DRB sensitivity-inducing factor large subunit) (DSIF l ...	0.82	+	nuc	0	Nucleus. Localizes predominantly to transcriptionally active regions of polytene chromosomes	nuclear exosome (RNase complex) [IPI] polytene chromosome interband [IDA] polytene chromosome puff [IDA] transcription elongation factor complex [IPI]			1078
Q4HYQ4 UniProt NPD GO	SPT6_GIBZE	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.82	-	cyt	0	Nucleus (By similarity)				1408
Q2U561 UniProt NPD GO	SPT6_ASPOR	Transcription elongation factor spt6 (Chromatin elongation factor spt6)	0.82	+	cyt	0	Nucleus (By similarity)				1422
Q5B7Q7 UniProt NPD GO	SPT6_EMENI	Transcription elongation factor spt6 (Chromatin elongation factor spt6)	0.82	+	cyt	0	Nucleus (By similarity)				1413
Q61286 UniProt NPD GO	HTF4_MOUSE	Transcription factor 12 (Transcription factor HTF-4) (E-box-binding protein) (DNA-binding protein HT ...	0.82	-	nuc	0	Nucleus	transcription factor complex [IDA]			706
P51514 UniProt NPD GO	HTF4_RAT	Transcription factor 12 (Transcription factor HTF-4) (E-box-binding protein) (Salivary-specific cAMP ...	0.82	-	nuc	0	Nucleus	nucleus [TAS]			707
P57074 UniProt NPD GO	SOX8_CHICK	Transcription factor SOX-8	0.82	+	nuc	0	Nucleus (Potential)				470
Q99551 UniProt NPD GO	MTERF_HUMAN	Transcription termination factor, mitochondrial precursor (mTERF) (Mitochondrial transcription termi ...	0.82	-	nuc	0	Mitochondrion	mitochondrion [TAS]	602318		399
P87000 UniProt NPD GO	ACU15_NEUCR	Transcriptional activator protein acu-15	0.82	-	nuc	0	Nucleus				926
Q86YP4 UniProt NPD GO	P66A_HUMAN	Transcriptional repressor p66 alpha (Hp66alpha) (GATA zinc finger domain-containing protein 2A)	0.82	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle	nucleus [IDA] NuRD complex [IDA]			633
Q9USY7 UniProt NPD GO	FZOL_SCHPO	Transmembrane GTPase fzo-like protein (EC 3.6.5.-)	0.82	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				758
P34576 UniProt NPD GO	MUA3_CAEEL	Transmembrane cell adhesion receptor mua-3 precursor (Muscle attachment abnormal protein 3)	0.82	-	end	1					3767
Q9V7H4 UniProt NPD GO	TM131_DROME	Transmembrane protein 131 homolog precursor	0.82	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				1567
Q8TEL6 UniProt NPD GO	TP4AP_HUMAN	Trpc4-associated protein (Short transient receptor potential channel 4-associated protein) (Trp4-ass ...	0.82	-	nuc	0		cytosol [NAS] endoplasmic reticulum lumen [IMP]	608430		797
Q7SXM7 UniProt NPD GO	PRP31_BRARE	U4/U6 small nuclear ribonucleoprotein Prp31 (Pre-mRNA-processing factor 31)	0.82	-	nuc	0	Nucleus (By similarity)				508
Q8WWY3 UniProt NPD GO	PRP31_HUMAN	U4/U6 small nuclear ribonucleoprotein Prp31 (Pre-mRNA-processing factor 31) (U4/U6 snRNP 61 kDa prot ...	0.82	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nucleus; nucleoplasm; Cajal body. Predominantly found in spec ...	Cajal body [IDA] nuclear speck [IDA] U4/U6 x U5 tri-snRNP complex [IDA]	606419		499
O75643 UniProt NPD GO	U520_HUMAN	U5 small nuclear ribonucleoprotein 200 kDa helicase (EC 3.6.1.-) (U5 snRNP-specific 200 kDa protein) ...	0.82	+	nuc	0	Nucleus	snRNP U5 [IDA] spliceosome complex [IDA]	601664		2136
P83369 UniProt NPD GO	LSM11_HUMAN	U7 snRNA-associated Sm-like protein LSm11	0.82	+	nuc	0	Nucleus				360
Q9VSS7 UniProt NPD GO	EVG1_DROME	UPF0193 protein EVG1 homolog	0.82	+	nuc	0					250
Q9D9S1 UniProt NPD GO	EVG1_MOUSE	UPF0193 protein EVG1 homolog	0.82	-	nuc	0					216
O94966 UniProt NPD GO	UBP19_HUMAN	Ubiquitin carboxyl-terminal hydrolase 19 (EC 3.1.2.15) (Ubiquitin thioesterase 19) (Ubiquitin-specif ...	0.82	+	nuc	1				1WH0	1371
Q5DU02 UniProt NPD GO	UBP22_MOUSE	Ubiquitin carboxyl-terminal hydrolase 22 (EC 3.1.2.15) (Ubiquitin thioesterase 22) (Ubiquitin-specif ...	0.82	-	nuc	0					525
Q9HBJ7 UniProt NPD GO	UBP29_HUMAN	Ubiquitin carboxyl-terminal hydrolase 29 (EC 3.1.2.15) (Ubiquitin thioesterase 29) (Ubiquitin-specif ...	0.82	-	nuc	0			609546		922
Q80X50 UniProt NPD GO	UBP2L_MOUSE	Ubiquitin-associated protein 2-like	0.82	+	nuc	0				1WJ7	1107
Q6BWW6 UniProt NPD GO	BRE1_DEBHA	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.82	-	nuc	0	Nucleus (By similarity)				691
P38213 UniProt NPD GO	YBL7_YEAST	Uncharacterized protein YBR007C	0.82	-	nuc	0					736
P38272 UniProt NPD GO	YBY0_YEAST	Uncharacterized protein YBR130C	0.82	-	nuc	0		actin cap [IDA] cytoplasm [IDA]			425
P38344 UniProt NPD GO	YB9M_YEAST	Uncharacterized protein YBR267W	0.82	-	nuc	0		cytoplasm [IDA]			393
P36165 UniProt NPD GO	YK69_YEAST	Uncharacterized protein YKR089C	0.82	-	nuc	0	Membrane; multi-pass membrane protein (Potential)	lipid particle [IDA]			910
P53939 UniProt NPD GO	YNH8_YEAST	Uncharacterized protein YNL078W	0.82	-	nuc	0		bud neck [IDA] nucleus [IDA]			407
P24271 UniProt NPD GO	RAG1_CHICK	V(D)J recombination-activating protein 1 (RAG-1)	0.82	+	nuc	0	Nucleus				1041
Q7Z7G8 UniProt NPD GO	VP13B_HUMAN	Vacuolar protein sorting 13B (Cohen syndrome protein 1)	0.82	-	cyt	0	Membrane; multi-pass membrane protein (Potential)		607817		4022
P49701 UniProt NPD GO	VDR_COTJA	Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor)	0.82	+	nuc	0	Nucleus				448
P13053 UniProt NPD GO	VDR_RAT	Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor)	0.82	+	nuc	0	Nucleus	nuclear chromosome [TAS]		1RKH	423
Q95MH5 UniProt NPD GO	VDR_SAGOE	Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor)	0.82	+	nuc	0	Nucleus (By similarity)				427
Q8WV16 UniProt NPD GO	WD21A_HUMAN	WD repeat protein 21A	0.82	-	nuc	0					495
P38873 UniProt NPD GO	YHY6_YEAST	WD repeat protein YHR186C	0.82	-	nuc	0		mitochondrion [IDA] plasma membrane [IDA] TORC 1 complex [IPI] vacuolar membrane (sensu Fungi) [IDA]			1541
Q9ULE0 UniProt NPD GO	WWC3_HUMAN	WWC family member 3	0.82	-	nuc	0					1030
Q5F3D1 UniProt NPD GO	ZCHC8_CHICK	Zinc finger CCHC domain-containing protein 8	0.82	-	nuc	0					613
Q9Y2K1 UniProt NPD GO	ZBTB1_HUMAN	Zinc finger and BTB domain-containing protein 1	0.82	-	nuc	0	Nucleus (Potential)				713
Q8IZC7 UniProt NPD GO	ZN101_HUMAN	Zinc finger protein 101 (Zinc finger protein HZF12)	0.82	-	nuc	0	Nucleus (Probable)		603983		436
Q8TCN5 UniProt NPD GO	ZN507_HUMAN	Zinc finger protein 507	0.82	-	nuc	0	Nucleus (Potential)				849
Q8TF47 UniProt NPD GO	ZFP90_HUMAN	Zinc finger protein 90 homolog (Zfp-90)	0.82	-	nuc	0	Nucleus (By similarity)		609451		636
P08151 UniProt NPD GO	GLI1_HUMAN	Zinc finger protein GLI1 (Glioma-associated oncogene) (Oncogene GLI)	0.82	-	nuc	0	Nucleus. Seems to translocate from the cytoplasm to the nucleus		165220	2GLI	1106
P34450 UniProt NPD GO	ZTF1_CAEEL	Zinc finger transcription factor family protein 1	0.82	-	nuc	0	Nucleus (Potential)				582
Q92782 UniProt NPD GO	DPF1_HUMAN	Zinc-finger protein neuro-d4 (D4, zinc and double PHD fingers family 1)	0.82	+	nuc	0	Cytoplasm (Potential). Nucleus (Potential)		601670		353
Q9VPQ6 UniProt NPD GO	USH_DROME	Zinc-finger protein ush (Protein U-shaped)	0.82	-	nuc	0	Nucleus	nucleus [IDA]		1Y0J	1191
Q24753 UniProt NPD GO	KNIR_DROVI	Zygotic gap protein knirps	0.82	-	nuc	0	Nucleus				481
Q13370 UniProt NPD GO	PDE3B_HUMAN	cGMP-inhibited 3',5'-cyclic phosphodiesterase B (EC 3.1.4.17) (Cyclic GMP-inhibited phosphodiesteras ...	0.82	-	end	5	Membrane; peripheral membrane protein (Potential)		602047	1SOJ	1112

You are viewing entries 8151 to 8200 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.