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
Q10261 UniProt NPD GO	YD2D_SCHPO	Very hypothetical protein C56F8.13 in chromosome I	0.40	-	mit	0					101
Q28520 UniProt NPD GO	PROS_MACMU	Vitamin K-dependent protein S precursor (Fragment)	0.40	-	nuc	0	Secreted protein				649
Q58DT8 UniProt NPD GO	WDR55_BOVIN	WD repeat protein 55	0.40	-	cyt	0					382
O13856 UniProt NPD GO	YEX2_SCHPO	WD repeat protein C1A6.02	0.40	+	nuc	0					361
P53877 UniProt NPD GO	YNS2_YEAST	WD repeat protein YNL182C	0.40	-	nuc	0		nucleoplasm [IDA] nucleus [IDA]			555
Q8K1I7 UniProt NPD GO	WASIP_MOUSE	Wiskott-Aldrich syndrome protein-interacting protein (WASP-interacting protein)	0.40	-	nuc	0	Vesicle surfaces and along actin tails. Co-localized with actin stress fibers. When co-expressed wit ...	actin cytoskeleton [IDA]			493
Q3SZY7 UniProt NPD GO	Z20D3_BOVIN	Zinc finger A20 domain-containing protein 3	0.40	-	nuc	0					208
Q8SUR9 UniProt NPD GO	Z856_ENCCU	Zinc finger C2H2 protein ECU08_0560	0.40	-	nuc	0					449
Q8SQW0 UniProt NPD GO	ZB99_ENCCU	Zinc finger C2H2 protein ECU11_0990	0.40	-	nuc	0					165
Q8N8U3 UniProt NPD GO	ZCHC5_HUMAN	Zinc finger CCHC domain-containing protein 5	0.40	-	nuc	0					475
P52737 UniProt NPD GO	ZN136_HUMAN	Zinc finger protein 136	0.40	-	nuc	0	Nucleus (Potential)		604078		540
P08043 UniProt NPD GO	ZFP2_MOUSE	Zinc finger protein 2 (Zfp-2) (Protein mKR2)	0.40	-	nuc	0	Nucleus (Probable)				347
Q16600 UniProt NPD GO	ZN239_HUMAN	Zinc finger protein 239 (Zinc finger protein MOK-2) (HOK-2)	0.40	-	nuc	0	Nucleus (Potential)		601069		458
Q8BLB0 UniProt NPD GO	ZFP3_MOUSE	Zinc finger protein 3 (Zfp-3)	0.40	-	nuc	0	Nucleus (Potential)				497
Q9ET26 UniProt NPD GO	ZN313_MOUSE	Zinc finger protein 313	0.40	-	nuc	0					229
Q8IVP9 UniProt NPD GO	ZN547_HUMAN	Zinc finger protein 547	0.40	-	nuc	0	Nucleus (Potential)				402
Q5RCX4 UniProt NPD GO	ZN547_PONPY	Zinc finger protein 547	0.40	-	nuc	0	Nucleus (Probable)				402
Q80W31 UniProt NPD GO	ZN569_MOUSE	Zinc finger protein 569 (Zinc finger protein 74) (Zfp-74) (Mszf21)	0.40	-	nuc	0	Nucleus (By similarity)				679
Q96I27 UniProt NPD GO	ZN625_HUMAN	Zinc finger protein 625	0.40	-	nuc	0	Nucleus (Probable)				306
Q15915 UniProt NPD GO	ZIC1_HUMAN	Zinc finger protein ZIC 1 (Zinc finger protein of the cerebellum 1)	0.40	-	nuc	0	Nucleus	nucleus [IDA]	600470		447
Q21432 UniProt NPD GO	NAS11_CAEEL	Zinc metalloproteinase nas-11 precursor (EC 3.4.24.21) (Nematode astacin 11)	0.40	-	exc	0	Secreted protein (Potential)				579
Q22401 UniProt NPD GO	NAS21_CAEEL	Zinc metalloproteinase nas-21 precursor (EC 3.4.24.-) (Nematode astacin 21)	0.40	-	cyt	0	Secreted protein (Potential)				391
Q7Z0M7 UniProt NPD GO	NAS23_CAEEL	Zinc metalloproteinase nas-23 precursor (EC 3.4.24.21) (Nematode astacin 23)	0.40	-	exc	0	Secreted protein (By similarity)				537
Q61EX6 UniProt NPD GO	NAS36_CAEBR	Zinc metalloproteinase nas-36 precursor (EC 3.4.24.21) (Nematode astacin 36)	0.40	-	exc	0	Secreted protein (Potential)				614
Q6ZMH5 UniProt NPD GO	S39A5_HUMAN	Zinc transporter ZIP5 precursor (Solute carrier family 39 member 5)	0.40	-	end	6 *	Cell membrane; basolateral cell membrane; multi-pass membrane protein (By similarity)		608730		539
P20107 UniProt NPD GO	ZRC1_YEAST	Zinc/cadmium resistance protein	0.40	-	end	6 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			442
Q8UVD9 UniProt NPD GO	ZBP2_CHICK	Zipcode-binding protein 2	0.40	-	nuc	0	Nucleus. Predominantly. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			769
P91622 UniProt NPD GO	PDK_DROME	[Pyruvate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (EC 2.7.11.2) (Pyruvate dehydro ...	0.40	-	mit	0	Mitochondrion; mitochondrial matrix				413
P00515 UniProt NPD GO	KAP2_BOVIN	cAMP-dependent protein kinase type II-alpha regulatory subunit	0.40	-	cyt	0				2BPK	400
P46959 UniProt NPD GO	TRM61_YEAST	tRNA (adenine-N(1)-)-methyltransferase catalytic subunit TRM61 (EC 2.1.1.36) (tRNA(m1A58)-methyltran ...	0.40	-	cyt	0	Nucleus	nucleus [IDA]			383
P21269 UniProt NPD GO	CCA1_YEAST	tRNA nucleotidyltransferase, mitochondrial precursor (EC 2.7.7.25) (tRNA adenylyltransferase) (tRNA ...	0.40	-	mit	0	Mitochondrion. Cytoplasm. Nucleus	cytoplasm [NAS] mitochondrial matrix [IDA] nucleus [NAS]			546
Q8C2P3 UniProt NPD GO	DUS1L_MOUSE	tRNA-dihydrouridine synthase 1-like (EC 1.-.-.-)	0.40	-	cyt	0					475
O08810 UniProt NPD GO	U5S1_MOUSE	116 kDa U5 small nuclear ribonucleoprotein component (U5 snRNP-specific protein, 116 kDa) (U5-116 kD ...	0.39	-	cyt	0	Nucleus	nucleus [IDA]			971
Q15029 UniProt NPD GO	U5S1_HUMAN	116 kDa U5 small nuclear ribonucleoprotein component (U5 snRNP-specific protein, 116 kDa) (U5-116 kD ...	0.39	-	cyt	0	Nucleus	spliceosome complex [TAS]	603892		972
Q9BYN8 UniProt NPD GO	RT26_HUMAN	28S ribosomal protein S26, mitochondrial precursor (MRP-S26) (MRP-S13)	0.39	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [NAS]			205
Q78JT3 UniProt NPD GO	3HAO_MOUSE	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.39	-	mit	0	Cytoplasm (By similarity)				286
Q9NRX2 UniProt NPD GO	RM17_HUMAN	39S ribosomal protein L17, mitochondrial precursor (L17mt) (MRP-L17) (LYST-interacting protein 2)	0.39	-	nuc	0	Mitochondrion (Potential)			2CQM	175
Q9EQI8 UniProt NPD GO	RM46_MOUSE	39S ribosomal protein L46, mitochondrial precursor (L46mt) (MRP-L46)	0.39	-	mit	0	Mitochondrion (By similarity)				283
P56848 UniProt NPD GO	ISPE_MENPI	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, chloroplast precursor (EC 2.7.1.148) (CMK) (4-(cy ...	0.39	+	mit	0	Plastid; chloroplast (By similarity)				405
P41115 UniProt NPD GO	RS11_XENLA	40S ribosomal protein S11	0.39	-	cyt	0					158
P78571 UniProt NPD GO	RS13_AGABI	40S ribosomal protein S13	0.39	-	mit	0					151
P27770 UniProt NPD GO	RS17_NEUCR	40S ribosomal protein S17 (CRP3)	0.39	-	nuc	0					146
Q9SJ36 UniProt NPD GO	RS17B_ARATH	40S ribosomal protein S17-2	0.39	-	nuc	0					139
P62980 UniProt NPD GO	RS27A_LYCES	40S ribosomal protein S27a	0.39	+	nuc	0					80
P62981 UniProt NPD GO	RS27A_SOLTU	40S ribosomal protein S27a	0.39	+	nuc	0					80
P59272 UniProt NPD GO	RS27A_DAUCA	40S ribosomal protein S27a (Fragment)	0.39	+	nuc	0					67
P46781 UniProt NPD GO	RS9_HUMAN	40S ribosomal protein S9	0.39	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603631		193
Q6ZWN5 UniProt NPD GO	RS9_MOUSE	40S ribosomal protein S9	0.39	-	mit	0					193
P29314 UniProt NPD GO	RS9_RAT	40S ribosomal protein S9	0.39	-	mit	0					193
P52810 UniProt NPD GO	RS9_PODAN	40S ribosomal protein S9 (S7)	0.39	-	mit	0					190

You are viewing entries 32301 to 32350 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.