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
Q5QQ57 UniProt NPD GO	XYLT1_PANTR	Xylosyltransferase 1 (EC 2.4.2.26) (Xylosyltransferase I) (Peptide O-xylosyltransferase 1)	0.56	+	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				945
Q965Q8 UniProt NPD GO	XYLT_CAEEL	Xylosyltransferase sqv-6 (EC 2.4.2.26) (Peptide O-xylosyltransferase) (Squashed vulva protein 6)	0.56	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				806
Q8VIG0 UniProt NPD GO	ZCH14_MOUSE	Zinc finger CCHC domain-containing protein 14 (BDG-29)	0.56	-	nuc	0					956
Q6P2D0 UniProt NPD GO	ZFP1_HUMAN	Zinc finger protein 1 homolog (Zfp-1)	0.56	-	nuc	0	Nucleus (Probable)				407
P17022 UniProt NPD GO	ZNF18_HUMAN	Zinc finger protein 18 (Zinc finger protein KOX11) (Heart development-specific gene 1 protein)	0.56	-	nuc	0	Nucleus (Potential)		194524		549
Q9NYT6 UniProt NPD GO	ZN226_HUMAN	Zinc finger protein 226	0.56	-	nuc	0	Nucleus (Probable)				803
Q9HBT8 UniProt NPD GO	ZN286_HUMAN	Zinc finger protein 286	0.56	-	nuc	0	Nucleus (Probable)				521
Q39263 UniProt NPD GO	ZFP4_ARATH	Zinc finger protein 4	0.56	-	nuc	0					260
Q9H9D4 UniProt NPD GO	ZN408_HUMAN	Zinc finger protein 408 (PR-domain zinc finger protein 17)	0.56	-	nuc	0	Nucleus (Potential)				720
O94892 UniProt NPD GO	ZN432_HUMAN	Zinc finger protein 432	0.56	-	nuc	0	Nucleus (Probable)				652
Q9UK33 UniProt NPD GO	ZN580_HUMAN	Zinc finger protein 580 (LDL-induced EC protein)	0.56	-	nuc	0	Nucleus (Probable)				172
Q96NL3 UniProt NPD GO	ZN599_HUMAN	Zinc finger protein 599	0.56	-	nuc	0	Nucleus (Probable)				588
Q9H6B1 UniProt NPD GO	ZN659_HUMAN	Zinc finger protein 659	0.56	-	nuc	0	Nucleus (Potential)				395
Q9NV72 UniProt NPD GO	ZN701_HUMAN	Zinc finger protein 701	0.56	-	nuc	0	Nucleus (Potential)				465
Q9UM63 UniProt NPD GO	PLAL1_HUMAN	Zinc finger protein PLAGL1 (Pleiomorphic adenoma-like protein 1)	0.56	-	nuc	0	Nucleus (Probable)		603044		411
P53243 UniProt NPD GO	YG2A_YEAST	Zinc finger protein YGR067C	0.56	-	nuc	0	Nucleus (Potential)				794
P41995 UniProt NPD GO	ODD1_CAEEL	Zinc finger protein odd-1	0.56	-	nuc	0	Nucleus (Potential)				242
Q9BQ52 UniProt NPD GO	RNZ2_HUMAN	Zinc phosphodiesterase ELAC protein 2 (EC 3.1.26.11) (Ribonuclease Z 2) (RNase Z 2) (tRNase Z 2) (tR ...	0.56	+	cyt	0	Nucleus (Probable)		605367		826
Q12057 UniProt NPD GO	PIN2_YEAST	[PSI+] induction protein 2	0.56	-	nuc	1 *	Membrane; single-pass membrane protein				282
P05987 UniProt NPD GO	KAPR_DICDI	cAMP-dependent protein kinase regulatory subunit	0.56	-	nuc	0					327
Q6FQ31 UniProt NPD GO	MCE1_CANGA	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.56	-	nuc	0	Nucleus (By similarity)				449
Q7SB53 UniProt NPD GO	MCE1_NEUCR	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.56	-	cyt	0	Nucleus (By similarity)				402
Q8IZD4 UniProt NPD GO	DCP1B_HUMAN	mRNA decapping enzyme 1B (EC 3.-.-.-)	0.56	-	nuc	0	Cytoplasm. In discrete foci (By similarity)		609843		618
P84149 UniProt NPD GO	MEX67_CANAL	mRNA export factor MEX67	0.56	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Localizes at both the nuclear and cytoplasmic si ...			1Q40	617
Q9P4S5 UniProt NPD GO	CCA1_CANGA	tRNA nucleotidyltransferase, mitochondrial precursor (EC 2.7.7.25) (tRNA adenylyltransferase) (tRNA ...	0.56	-	mit	0	Mitochondrion (By similarity). Cytoplasm (By similarity). Nucleus (By similarity)				531
Q74ZY5 UniProt NPD GO	SEN2_ASHGO	tRNA-splicing endonuclease subunit SEN2 (EC 3.1.27.9) (tRNA-intron endonuclease SEN2)	0.56	-	mit	0					356
P23745 UniProt NPD GO	ABRA_PLAFG	101 kDa malaria antigen (p101) (Acidic basic repeat antigen) (Fragment)	0.55	-	nuc	0	Cell surface. Parasitophorous vacuole. At the merozoite surface and within the parasitophorous vacuo ...				600
Q7TMF2 UniProt NPD GO	THEX1_MOUSE	3' histone mRNA exonuclease 1 (EC 3.1.-.-) (3'-5' exonuclease ERI1) (Eri-1 homolog)	0.55	-	nuc	0					345
Q8IV48 UniProt NPD GO	THEX1_HUMAN	3' histone mRNA exonuclease 1 (EC 3.1.-.-) (3'-5' exonuclease ERI1) (Eri-1 homolog) (Histone mRNA 3' ...	0.55	-	nuc	0			608739	1W0H	348
Q6CJI3 UniProt NPD GO	RT10_KLULA	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.55	-	mit	0	Mitochondrion (By similarity)				207
P61922 UniProt NPD GO	GABT_MOUSE	4-aminobutyrate aminotransferase, mitochondrial precursor (EC 2.6.1.19) ((S)-3-amino-2-methylpropion ...	0.55	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			500
Q9GT45 UniProt NPD GO	RS26_ANOGA	40S ribosomal protein S26	0.55	-	nuc	0					115
P14799 UniProt NPD GO	RS27A_NEUCR	40S ribosomal protein S27a (CRP6) (S37)	0.55	+	nuc	0					78
P19474 UniProt NPD GO	RO52_HUMAN	52 kDa Ro protein (Sjoegren syndrome type A antigen) (SS-A) (Ro(SS-A)) (52 kDa ribonucleoprotein aut ...	0.55	-	cyt	0	Cytoplasm. Nucleus	ribonucleoprotein complex [TAS]	109092		475
Q9FF90 UniProt NPD GO	RL133_ARATH	60S ribosomal protein L13-3	0.55	-	mit	0		cytosolic ribosome (sensu Eukaryota) [IDA]			206
O74895 UniProt NPD GO	RL15A_SCHPO	60S ribosomal protein L15-A	0.55	-	nuc	0					201
Q8TFH1 UniProt NPD GO	RL18B_SCHPO	60S ribosomal protein L18-B	0.55	-	nuc	0					187
P51414 UniProt NPD GO	RL261_ARATH	60S ribosomal protein L26-1	0.55	-	nuc	0					146
Q24154 UniProt NPD GO	RL29_DROME	60S ribosomal protein L29 (L43)	0.55	-	nuc	0					76
P27659 UniProt NPD GO	RL3_MOUSE	60S ribosomal protein L3 (J1 protein)	0.55	-	mit	0	Cytoplasm				402
P21531 UniProt NPD GO	RL3_RAT	60S ribosomal protein L3 (L4)	0.55	-	mit	0	Cytoplasm				402
Q8JHJ1 UniProt NPD GO	RL35_BRARE	60S ribosomal protein L35	0.55	-	nuc	0					122
P39741 UniProt NPD GO	RL35_YEAST	60S ribosomal protein L35	0.55	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	120
Q8L8W6 UniProt NPD GO	RL392_ARATH	60S ribosomal protein L39-2	0.55	-	nuc	0					51
P51423 UniProt NPD GO	RL40_BRARA	60S ribosomal protein L40 (CEP52)	0.55	-	nuc	0					52
P0C015 UniProt NPD GO	RL40_SCHPO	60S ribosomal protein L40 (CEP52)	0.55	-	nuc	0					52
P27076 UniProt NPD GO	RL44_KLUMA	60S ribosomal protein L44 (60S ribosomal protein L41)	0.55	-	nuc	0					105
Q26481 UniProt NPD GO	RL5_STYCL	60S ribosomal protein L5	0.55	-	mit	0	Cytoplasm				294
O76732 UniProt NPD GO	RL7A_ANOGA	60S ribosomal protein L7a	0.55	+	nuc	0					271
P10398 UniProt NPD GO	ARAF_HUMAN	A-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (A-raf-1) (Proto-oncogene Pks)	0.55	-	nuc	0			311010	1WXM	606

You are viewing entries 21751 to 21800 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.