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
P52747 UniProt NPD GO	ZN143_HUMAN	Zinc finger protein 143 (SPH-binding factor)	0.27	-	nuc	0	Nucleus (Potential)		603433		626
P51522 UniProt NPD GO	ZNF83_HUMAN	Zinc finger protein 83 (Zinc finger protein HPF1)	0.27	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	194558		428
Q19269 UniProt NPD GO	NAS14_CAEEL	Zinc metalloproteinase nas-14 precursor (EC 3.4.24.21) (Nematode astacin 14)	0.27	-	nuc	1 *	Secreted protein (Potential)				503
P91137 UniProt NPD GO	NAS9_CAEEL	Zinc metalloproteinase nas-9 precursor (EC 3.4.24.21) (Nematode astacin 9)	0.27	-	exc	0	Secreted protein (Potential)				546
Q62522 UniProt NPD GO	ZPBP1_MOUSE	Zona pellucida-binding protein 1 precursor (Sp38)	0.27	-	nuc	1 *	Secreted protein (Potential)				350
Q29108 UniProt NPD GO	ZPBP1_PIG	Zona pellucida-binding protein 1 precursor (Sp38)	0.27	-	nuc	0	Secreted protein (Potential). Acrosome. Detected in the acrosome of sperm cells. Released after the ...				350
Q9JK42 UniProt NPD GO	PDK2_MOUSE	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.27	-	mit	0	Mitochondrion; mitochondrial matrix				407
O88483 UniProt NPD GO	PDP1_RAT	[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1, mitochondrial precursor (EC 3.1.3.43) (PDP 1) (P ...	0.27	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS] mitochondrion [ISS]			538
Q758T3 UniProt NPD GO	YTH1_ASHGO	mRNA 3'-end-processing protein YTH1	0.27	-	nuc	0	Nucleus (By similarity)				209
P34232 UniProt NPD GO	MTR2_YEAST	mRNA transport regulator MTR2	0.27	-	nuc	0	Nucleus	nuclear pore [IDA]		1OF5	184
Q75DK9 UniProt NPD GO	MRT4_ASHGO	mRNA turnover protein 4 homolog	0.27	-	mit	0	Nucleus; nucleolus (By similarity)				236
Q9UKD2 UniProt NPD GO	MRT4_HUMAN	mRNA turnover protein 4 homolog	0.27	-	nuc	0	Nucleus; nucleolus				239
Q92966 UniProt NPD GO	SNPC3_HUMAN	snRNA-activating protein complex subunit 3 (SNAPc subunit 3) (snRNA-activating protein complex 50 kD ...	0.27	-	cyt	0	Nucleus	nucleus [TAS]	602348		411
Q12272 UniProt NPD GO	TPT1_YEAST	tRNA 2'phosphotransferase (EC 2.7.-.-)	0.27	-	nuc	0		nucleus [TAS]			230
Q9WU56 UniProt NPD GO	TRUA_MOUSE	tRNA pseudouridine synthase A (EC 5.4.99.12) (tRNA-uridine isomerase I) (tRNA pseudouridylate syntha ...	0.27	-	nuc	0	Nucleus (By similarity)	nucleolus [IDA] nucleus [IDA] transcription factor complex [IDA]			393
Q5ZL43 UniProt NPD GO	MTND_CHICK	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.26	-	cyt	0					180
P93209 UniProt NPD GO	14333_LYCES	14-3-3 protein 3 (PBLT3)	0.26	-	nuc	0					260
Q7T356 UniProt NPD GO	143BA_BRARE	14-3-3 protein beta/alpha-A	0.26	-	nuc	0	Cytoplasm (By similarity)				242
Q5ZMD1 UniProt NPD GO	1433T_CHICK	14-3-3 protein theta	0.26	-	nuc	0	Cytoplasm (By similarity)				245
O65352 UniProt NPD GO	1433_HELAN	14-3-3-like protein	0.26	-	cyt	0					259
P93343 UniProt NPD GO	1433C_TOBAC	14-3-3-like protein C (14-3-3-like protein B)	0.26	-	nuc	0				1O9F	260
O49998 UniProt NPD GO	1433F_TOBAC	14-3-3-like protein F	0.26	-	nuc	0					258
P46077 UniProt NPD GO	14334_ARATH	14-3-3-like protein GF14 phi (General regulatory factor 4)	0.26	-	nuc	0					267
Q05961 UniProt NPD GO	OAS1_RAT	2'-5'-oligoadenylate synthetase 1 (EC 2.7.7.-) ((2-5')oligo(A) synthetase 1) (2-5A synthetase 1)	0.26	-	nuc	0					358
Q63569 UniProt NPD GO	PRS6A_RAT	26S protease regulatory subunit 6A (TAT-binding protein 1) (TBP-1) (Spermatogenic cell/sperm-associa ...	0.26	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				439
Q18115 UniProt NPD GO	PSD1_CAEEL	26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit rpn-2)	0.26	-	mit	0		proteasome complex (sensu Eukaryota) [NAS]			965
Q99JI4 UniProt NPD GO	PSD6_MOUSE	26S proteasome non-ATPase regulatory subunit 6 (26S proteasome regulatory subunit S10) (p42A)	0.26	-	cyt	0		proteasome complex (sensu Eukaryota) [ISS]			389
Q5RB32 UniProt NPD GO	RT12_PONPY	28S ribosomal protein S12, mitochondrial precursor (S12mt) (MRP-S12) (MT-RPS12)	0.26	-	mit	0	Mitochondrion (By similarity)				139
P49313 UniProt NPD GO	ROC1_NICPL	30 kDa ribonucleoprotein, chloroplast precursor (CP-RBP30)	0.26	-	mit	0	Plastid; chloroplast				279
Q5KBT4 UniProt NPD GO	RT10_CRYNE	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.26	-	mit	0	Mitochondrion (By similarity)				255
Q9ARF9 UniProt NPD GO	HPPD_SOLSC	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.26	-	cyt	0	Cytoplasm (By similarity)				436
Q95V31 UniProt NPD GO	RS16_SPOFR	40S ribosomal protein S16	0.26	-	cyt	0					151
Q9XEK7 UniProt NPD GO	RS16_TORRU	40S ribosomal protein S16	0.26	-	mit	0	Cytoplasm				142
Q9VH69 UniProt NPD GO	RS29_DROME	40S ribosomal protein S29	0.26	-	nuc	0					56
Q6UZG0 UniProt NPD GO	RS29_HIPCM	40S ribosomal protein S29	0.26	-	mit	0					55
Q90YP2 UniProt NPD GO	RS29_ICTPU	40S ribosomal protein S29	0.26	-	mit	0					55
Q6QAP6 UniProt NPD GO	RS29_PIG	40S ribosomal protein S29	0.26	-	mit	0					55
P62908 UniProt NPD GO	RS3_MOUSE	40S ribosomal protein S3	0.26	-	cyt	0		cytoplasm [IDA]			243
P62909 UniProt NPD GO	RS3_RAT	40S ribosomal protein S3	0.26	-	cyt	0					243
P02350 UniProt NPD GO	RS31_XENLA	40S ribosomal protein S3-A (S1A)	0.26	-	cyt	0					246
P47835 UniProt NPD GO	RS32_XENLA	40S ribosomal protein S3-B (S1B)	0.26	-	cyt	0					246
P33514 UniProt NPD GO	RS7_ANOGA	40S ribosomal protein S7	0.26	-	nuc	0					192
Q9NPB1 UniProt NPD GO	NT5M_HUMAN	5'(3')-deoxyribonucleotidase, mitochondrial precursor (EC 3.1.3.-) (5',3'-nucleotidase, mitochondria ...	0.26	-	mit	0	Mitochondrion	mitochondrion [TAS]	605292	1Z4Q	228
P55027 UniProt NPD GO	TYRP1_AMBME	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (EC 1.14.18.-) (DHICA oxidase) (Tyrosinase-r ...	0.26	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (Potential)				534
P38092 UniProt NPD GO	HEM1_EMENI	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.26	-	mit	0	Mitochondrion; mitochondrial matrix				648
Q9WUA3 UniProt NPD GO	K6PP_MOUSE	6-phosphofructokinase type C (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosphofruct ...	0.26	+	cyt	0					784
Q9N4I4 UniProt NPD GO	RL10A_CAEEL	60S ribosomal protein L10a	0.26	+	nuc	0					216
P50881 UniProt NPD GO	RL11_CHLRE	60S ribosomal protein L11	0.26	-	mit	0	Cytoplasm				170
P42794 UniProt NPD GO	RL112_ARATH	60S ribosomal protein L11-2 (L16)	0.26	-	cyt	0	Cytoplasm				182
P07279 UniProt NPD GO	RL18_YEAST	60S ribosomal protein L18 (RP28)	0.26	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	186

You are viewing entries 43851 to 43900 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.