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
P38845 UniProt NPD GO	YHU6_YEAST	Uncharacterized protein YHR146W	0.68	+	nuc	0		nucleus [IC]			465
Q08157 UniProt NPD GO	YOL19_YEAST	Uncharacterized protein YOL019W	0.68	-	nuc	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Cell membrane; multi-pass membrane protein	plasma membrane [IDA] vacuole (sensu Fungi) [IDA]			551
Q2V2P0 UniProt NPD GO	YP145_YEAST	Uncharacterized protein YPR145C-A	0.68	-	nuc	0					78
Q91YL3 UniProt NPD GO	UCKL1_MOUSE	Uridine/cytidine kinase-like 1	0.68	-	cyt	0					548
Q02948 UniProt NPD GO	VPS30_YEAST	Vacuolar protein sorting protein 30 (Autophagy-related protein 6)	0.68	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein. Vacuole; vacuolar membrane; peripheral me ...	membrane fraction [IDA]			557
P47161 UniProt NPD GO	VPS70_YEAST	Vacuolar protein sorting protein 70 (EC 3.4.-.-)	0.68	+	nuc	1					811
Q6CGJ5 UniProt NPD GO	BRO1_YARLI	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.68	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				867
Q12981 UniProt NPD GO	SEC20_HUMAN	Vesicle transport protein SEC20 (BCL2/adenovirus E1B 19 kDa protein-interacting protein 1)	0.68	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein	cytoplasm [IDA] endoplasmic reticulum [IDA] integral to endoplasmic reticulum membrane [TAS] nuclear envelope [IDA] SNARE complex [IDA]	603291		228
Q8VDJ3 UniProt NPD GO	VIGLN_MOUSE	Vigilin (High density lipoprotein-binding protein) (HDL-binding protein)	0.68	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1268
O55017 UniProt NPD GO	CAC1B_MOUSE	Voltage-dependent N-type calcium channel subunit alpha-1B (Voltage-gated calcium channel subunit alp ...	0.68	-	end	21	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]			2327
P59328 UniProt NPD GO	WDHD1_MOUSE	WD repeat and HMG-box DNA-binding protein 1 (Acidic nucleoplasmic DNA-binding protein 1) (And-1)	0.68	+	nuc	0	Nucleus; nucleoplasm (By similarity)				1117
O95389 UniProt NPD GO	WISP3_HUMAN	WNT1-inducible signaling pathway protein 3 precursor (WISP-3)	0.68	-	exc	0	Secreted protein (Probable)	soluble fraction [TAS]	603400		354
O04609 UniProt NPD GO	WRK22_ARATH	WRKY transcription factor 22 (WRKY DNA-binding protein 22)	0.68	-	nuc	0	Nucleus (Probable)				298
Q9EPK5 UniProt NPD GO	WWTR1_MOUSE	WW domain-containing transcription regulator protein 1 (Transcriptional coactivator with PDZ-binding ...	0.68	-	nuc	0	Nucleus. Cytoplasm. Concentrates along specific portions of the plasma membrane, and accumulates in ...	cytoplasm [IDA] nucleus [IDA] transcription factor complex [IDA]			395
Q8SW43 UniProt NPD GO	Z379_ENCCU	Zinc finger C2H2 protein ECU03_0790	0.68	-	nuc	0					190
Q9UJ78 UniProt NPD GO	ZMYM5_HUMAN	Zinc finger MYM-type protein 5 (Zinc finger protein 237) (Zinc finger protein 198-like 1)	0.68	-	nuc	0	Nucleus (Potential)			2DAS	382
P51786 UniProt NPD GO	ZN157_HUMAN	Zinc finger protein 157 (Zinc finger protein HZF22)	0.68	-	nuc	0	Nucleus (Potential)		300024		506
Q15697 UniProt NPD GO	ZN174_HUMAN	Zinc finger protein 174 (AW-1) (Zinc finger and SCAN domain-containing protein 8)	0.68	-	nuc	0	Nucleus		603900	1Y7Q	407
Q99676 UniProt NPD GO	ZN184_HUMAN	Zinc finger protein 184	0.68	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	602277		751
Q9UK13 UniProt NPD GO	ZN221_HUMAN	Zinc finger protein 221	0.68	-	nuc	0	Nucleus (Probable)				617
Q61116 UniProt NPD GO	ZN235_MOUSE	Zinc finger protein 235 (Zinc finger protein 93) (Zfp-93)	0.68	-	nuc	0	Nucleus (Probable)				645
Q8NF99 UniProt NPD GO	ZN397_HUMAN	Zinc finger protein 397 (Zinc finger and SCAN domain-containing protein 15)	0.68	-	nuc	0	Isoform 1, isoform 3: Nucleus. Isoform 3: Cytoplasm		609601		534
Q6PBT9 UniProt NPD GO	ZN533_BRARE	Zinc finger protein 533	0.68	-	nuc	0	Nucleus (Potential)				492
Q86XL7 UniProt NPD GO	ZN539_HUMAN	Zinc finger protein 539	0.68	-	nuc	0	Nucleus (Potential)				659
Q8N988 UniProt NPD GO	ZN557_HUMAN	Zinc finger protein 557	0.68	-	nuc	0	Nucleus (Potential)				423
Q9BR84 UniProt NPD GO	ZN559_HUMAN	Zinc finger protein 559	0.68	-	nuc	0	Nucleus (Potential)				538
P16374 UniProt NPD GO	ZFP60_MOUSE	Zinc finger protein 60 (Zfp-60) (Zinc finger protein Mfg-3)	0.68	-	nuc	0	Nucleus (Probable)				707
Q8N1W2 UniProt NPD GO	ZN710_HUMAN	Zinc finger protein 710	0.68	-	nuc	0	Nucleus (Potential)				664
O43830 UniProt NPD GO	ZNF73_HUMAN	Zinc finger protein 73 (Zinc finger protein 186) (hZNF2)	0.68	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	194547		326
Q20958 UniProt NPD GO	NAS29_CAEEL	Zinc metalloproteinase nas-29 precursor (EC 3.4.24.21) (Nematode astacin 29)	0.68	-	exc	1 *	Secreted protein (Potential)				532
Q8C145 UniProt NPD GO	S39A6_MOUSE	Zinc transporter SLC39A6 precursor (Solute carrier family 39 member 6) (Endoplasmic reticulum membra ...	0.68	+	end	6	Cell membrane; multi-pass membrane protein (By similarity). Endoplasmic reticulum; endoplasmic retic ...	endoplasmic reticulum [IDA]			765
Q759Y6 UniProt NPD GO	RNA14_ASHGO	mRNA 3'-end processing protein RNA14	0.68	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				661
O55236 UniProt NPD GO	MCE1_MOUSE	mRNA capping enzyme (HCE) (MCE1) [Includes: Polynucleotide 5'-triphosphatase (EC 3.1.3.33) (mRNA 5'- ...	0.68	-	mit	0	Nucleus			1I9T	597
O93803 UniProt NPD GO	CET1_CANAL	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.68	-	nuc	0	Nucleus (By similarity)				520
Q6FKK0 UniProt NPD GO	PALA_CANGA	pH-response regulator protein palA/RIM20	0.68	-	nuc	0					691
Q5KEK0 UniProt NPD GO	PALA_CRYNE	pH-response regulator protein palA/RIM20	0.68	-	nuc	0					902
Q8NCE0 UniProt NPD GO	SEN2_HUMAN	tRNA-splicing endonuclease subunit Sen2 (EC 3.1.27.9) (tRNA-intron endonuclease Sen2) (HsSen2 protei ...	0.68	-	nuc	0	Nucleus. Nucleus; nucleolus. May be transiently localized in the nucleolus		608753		465
P38631 UniProt NPD GO	GLS1_YEAST	1,3-beta-glucan synthase component GLS1 (EC 2.4.1.34) (1,3-beta-D-glucan-UDP glucosyltransferase) (P ...	0.67	+	end	13	Membrane; multi-pass membrane protein (Potential)	1,3-beta-glucan synthase complex [TAS] actin cap [IDA] actin cortical patch [IDA]			1876
P48601 UniProt NPD GO	PRS4_DROME	26S protease regulatory subunit 4 (P26s4)	0.67	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	proteasome regulatory particle (sensu Eukar... [IDA]			439
Q498P2 UniProt NPD GO	RT35_BRARE	28S ribosomal protein S35, mitochondrial precursor (S35mt) (MRP-S35)	0.67	-	mit	0	Mitochondrion (By similarity)				330
Q58DQ5 UniProt NPD GO	RT09_BOVIN	28S ribosomal protein S9, mitochondrial precursor (S9mt) (MRP-S9)	0.67	-	mit	0	Mitochondrion (By similarity)				396
O44406 UniProt NPD GO	ERI1_CAEEL	3'-5' exonuclease eri-1 (EC 3.1.-.-) (Enhanced RNAi protein)	0.67	-	nuc	0	Cytoplasm				582
P11891 UniProt NPD GO	RK18_PEA	50S ribosomal protein L18, chloroplast precursor (CL18)	0.67	-	mit	0	Plastid; chloroplast				145
Q9CUX1 UniProt NPD GO	P52K_MOUSE	52 kDa repressor of the inhibitor of the protein kinase (p58IPK-interacting protein) (58 kDa interfe ...	0.67	+	end	0		nucleus [IDA]			758
O13418 UniProt NPD GO	RL15_ASPNG	60S ribosomal protein L15	0.67	-	nuc	0					203
P05734 UniProt NPD GO	RL19_SCHPO	60S ribosomal protein L19 (YL15)	0.67	-	nuc	0					192
Q9NBK4 UniProt NPD GO	RL3_CAEBR	60S ribosomal protein L3	0.67	-	mit	0	Cytoplasm				401
P52814 UniProt NPD GO	RL39_CAEEL	60S ribosomal protein L39	0.67	-	nuc	0					51
P90702 UniProt NPD GO	RL44_BRUMA	60S ribosomal protein L44	0.67	-	nuc	0					104
O76190 UniProt NPD GO	RL5_BOMMO	60S ribosomal protein L5	0.67	+	nuc	0					299

You are viewing entries 15051 to 15100 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.