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
Q6L3C7 UniProt NPD GO	RR12_SACHY	Chloroplast 30S ribosomal protein S12	0.27	-	mit	0	Plastid; chloroplast				124
Q6ENU0 UniProt NPD GO	RR12_SACOF	Chloroplast 30S ribosomal protein S12	0.27	-	mit	0	Plastid; chloroplast				124
Q5SD19 UniProt NPD GO	RR3_HUPLU	Chloroplast 30S ribosomal protein S3	0.27	-	cyt	0	Plastid; chloroplast				219
Q32RV4 UniProt NPD GO	RR3_STAPU	Chloroplast 30S ribosomal protein S3	0.27	-	mit	0	Plastid; chloroplast				219
P09597 UniProt NPD GO	RR8_SPIOL	Chloroplast 30S ribosomal protein S8	0.27	-	cyt	0	Plastid; chloroplast				133
Q8MCA4 UniProt NPD GO	RK16_PHAAN	Chloroplast 50S ribosomal protein L16	0.27	-	nuc	0	Plastid; chloroplast				136
P42353 UniProt NPD GO	RK16_VIGUN	Chloroplast 50S ribosomal protein L16 (Fragment)	0.27	-	nuc	0	Plastid; chloroplast				137
Q85CH6 UniProt NPD GO	RK22_ANTFO	Chloroplast 50S ribosomal protein L22	0.27	-	nuc	0	Plastid; chloroplast				119
P16634 UniProt NPD GO	RK22_GRATE	Chloroplast 50S ribosomal protein L22	0.27	-	mit	0	Plastid; chloroplast				114
Q6B8V8 UniProt NPD GO	RK22_GRATL	Chloroplast 50S ribosomal protein L22	0.27	-	nuc	0	Plastid; chloroplast				114
Q6YXK7 UniProt NPD GO	RK22_PHYPA	Chloroplast 50S ribosomal protein L22	0.27	-	nuc	0	Plastid; chloroplast				118
P49559 UniProt NPD GO	RK23_ODOSI	Chloroplast 50S ribosomal protein L23	0.27	-	nuc	0	Plastid; chloroplast				102
Q5SD36 UniProt NPD GO	RK33_HUPLU	Chloroplast 50S ribosomal protein L33	0.27	-	nuc	0	Plastid; chloroplast				64
Q8M9V3 UniProt NPD GO	RK5_CHAGL	Chloroplast 50S ribosomal protein L5	0.27	-	mit	0	Plastid; chloroplast				186
P29357 UniProt NPD GO	HSP7E_SPIOL	Chloroplast envelope membrane 70 kDa heat shock-related protein	0.27	-	cyt	0	Plastid; chloroplast; chloroplast membrane				652
P01356 UniProt NPD GO	CCKN_PIG	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 58 (CCK58); Cholecystokinin 39 (CCK39); ...	0.27	-	exc	0					114
Q9PU29 UniProt NPD GO	CCKN_STRCA	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 70 (CCK70); Cholecystokinin 8 (CCK8); Ch ...	0.27	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			130
Q8IZ52 UniProt NPD GO	CHSS2_HUMAN	Chondroitin sulfate synthase 2 (EC 2.4.1.175) (Glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-be ...	0.27	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)				775
P17111 UniProt NPD GO	CH36_DROVI	Chorion protein S36	0.27	-	nuc	0					293
Q6FTV3 UniProt NPD GO	SFH1_CANGA	Chromatin structure remodeling complex protein SFH1 (SNF5 homolog 1)	0.27	-	mit	0	Nucleus (By similarity)				403
Q9USM3 UniProt NPD GO	SFH1_SCHPO	Chromatin structure remodeling complex protein SFH1 (SNF5 homolog 1)	0.27	-	mit	0	Nucleus				418
P20294 UniProt NPD GO	CNTF_RAT	Ciliary neurotrophic factor (CNTF)	0.27	-	cyt	0	Cytoplasm	axon [IDA] cell soma [IDA] cytosol [IDA] nucleus [IDA]			200
P13815 UniProt NPD GO	CSP_PLAMA	Circumsporozoite protein precursor (CS)	0.27	-	mit	0					429
P04923 UniProt NPD GO	CRA_PLAFA	Circumsporozoite protein-related antigen precursor (CRA)	0.27	-	end	1					162
Q5NTB3 UniProt NPD GO	FA11_BOVIN	Coagulation factor XI precursor (EC 3.4.21.27) (Plasma thromboplastin antecedent) (PTA) (FXI) [Conta ...	0.27	-	nuc	0	Secreted protein (By similarity)				625
P05160 UniProt NPD GO	F13B_HUMAN	Coagulation factor XIII B chain precursor (Protein-glutamine gamma-glutamyltransferase B chain) (Tra ...	0.27	-	exc	0		extracellular region [NAS]	134580		661
P53620 UniProt NPD GO	COPG_BOVIN	Coatomer subunit gamma (Gamma-coat protein) (Gamma-COP)	0.27	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]		1PZD	874
Q9Y678 UniProt NPD GO	COPG_HUMAN	Coatomer subunit gamma (Gamma-coat protein) (Gamma-COP)	0.27	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [ISS]		1R4X	874
Q6NSX1 UniProt NPD GO	CCD70_HUMAN	Coiled-coil domain-containing protein 70 precursor	0.27	-	mit	0	Secreted protein (Potential)				233
P02457 UniProt NPD GO	CO1A1_CHICK	Collagen alpha-1(I) chain precursor	0.27	-	exc	0					1453
P12106 UniProt NPD GO	CO9A1_CHICK	Collagen alpha-1(IX) chain precursor	0.27	-	mit	1 *					920
Q14993 UniProt NPD GO	COJA1_HUMAN	Collagen alpha-1(XIX) chain precursor (Collagen alpha-1(Y) chain)	0.27	-	exc	0		collagen [NAS]	120165		1142
P08572 UniProt NPD GO	CO4A2_HUMAN	Collagen alpha-2(IV) chain precursor	0.27	-	mit	1 *		collagen type IV [TAS]	120090	1LI1	1712
P12110 UniProt NPD GO	CO6A2_HUMAN	Collagen alpha-2(VI) chain precursor	0.27	-	vac	0	Secreted protein. Membrane. Recruited on membranes by CSPG4	extracellular matrix (sensu Metazoa) [NAS]	254090		1019
Q02788 UniProt NPD GO	CO6A2_MOUSE	Collagen alpha-2(VI) chain precursor	0.27	-	exc	0	Secreted protein (By similarity). Membrane (By similarity). Recruited on membranes by CSPG4 (By simi ...				1029
Q29442 UniProt NPD GO	CO4A4_BOVIN	Collagen alpha-4(IV) chain (Fragment)	0.27	-	nuc	0	Cell surface (Potential)				453
Q14031 UniProt NPD GO	CO4A6_HUMAN	Collagen alpha-6(IV) chain precursor	0.27	-	exc	0	Cell surface (Potential)	collagen type IV [NAS]	303631		1691
O95741 UniProt NPD GO	CPNE6_HUMAN	Copine-6 (Copine VI) (Neuronal-copine) (N-copine)	0.27	-	cyt	0			605688		557
P49573 UniProt NPD GO	CTR1_YEAST	Copper transport protein CTR1 (Copper transporter 1)	0.27	-	nuc	3	Membrane; multi-pass membrane protein	plasma membrane [IDA]			406
P11280 UniProt NPD GO	COLI_MUSVI	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: Corticotropin (Adrenocor ...	0.27	-	mit	0					142
O00230 UniProt NPD GO	CORT_HUMAN	Cortistatin precursor [Contains: Cortistatin-29; Cortistatin-17]	0.27	-	exc	0	Secreted protein	soluble fraction [TAS]	602784		105
P12532 UniProt NPD GO	KCRU_HUMAN	Creatine kinase, ubiquitous mitochondrial precursor (EC 2.7.3.2) (U-MtCK) (Mia-CK) (Acidic-type mito ...	0.27	-	mit	0	Mitochondrion; mitochondrial inner membrane; intermembrane side	mitochondrion [TAS]	123290	1QK1	417
Q03443 UniProt NPD GO	CRJ1B_TRICY	Crystallin J1B	0.27	-	nuc	0					322
Q86N75 UniProt NPD GO	CORZ_BOMMO	Crz precursor (BmCrz) [Contains: Corazonin; Corazonin-precursor-related peptide (CPRP)]	0.27	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			101
Q9JJZ8 UniProt NPD GO	CNGA3_MOUSE	Cyclic nucleotide-gated cation channel alpha 3 (CNG channel alpha 3) (CNG-3) (CNG3) (Cyclic nucleoti ...	0.27	-	end	2	Membrane; multi-pass membrane protein	photoreceptor outer segment [IDA]			631
Q90805 UniProt NPD GO	CNG1_CHICK	Cyclic nucleotide-gated channel cone photoreceptor subunit alpha (CNG channel 1) (CNG-1)	0.27	-	end	2	Membrane; multi-pass membrane protein				735
O74627 UniProt NPD GO	CG1C_SCHPO	Cyclin pch1 (Pombe cyclin c homolog 1)	0.27	-	nuc	0	Nucleus (By similarity)				342
Q62447 UniProt NPD GO	CCNC_MOUSE	Cyclin-C	0.27	-	nuc	0	Nucleus (By similarity)				304
Q5RD50 UniProt NPD GO	CCNL1_PONPY	Cyclin-L1	0.27	-	exc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). More specifically found in nuclear intrachrom ...				172
Q64364 UniProt NPD GO	CD2A2_MOUSE	Cyclin-dependent kinase inhibitor 2A, isoform 3 (p19ARF)	0.27	-	nuc	1	Nucleus; nucleolus	cytoplasm [IDA] nucleolus [IDA] nucleoplasm [IDA]		1HN3	169

You are viewing entries 43051 to 43100 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.