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
Q9Z0W7 UniProt NPD GO	CLIC4_RAT	Chloride intracellular channel protein 4 (Intracellular chloride ion channel protein p64H1)	0.17	-	nuc	0	Endoplasmic reticulum	actin cytoskeleton [ISS] cytoplasm [ISS] endoplasmic reticulum [TAS] integral to membrane [TAS] microvillus [ISS] soluble fraction [ISS] vesicle [TAS]			252
Q6L3B6 UniProt NPD GO	RR19_SACHY	Chloroplast 30S ribosomal protein S19	0.17	-	mit	0	Plastid; chloroplast				93
Q6ENS3 UniProt NPD GO	RR19_SACOF	Chloroplast 30S ribosomal protein S19	0.17	-	mit	0	Plastid; chloroplast				93
Q9TKZ4 UniProt NPD GO	RK19_NEPOL	Chloroplast 50S ribosomal protein L19	0.17	-	nuc	0	Plastid; chloroplast				137
Q70XX1 UniProt NPD GO	RK22_AMBTC	Chloroplast 50S ribosomal protein L22	0.17	-	nuc	0	Plastid; chloroplast				124
Q8HTL3 UniProt NPD GO	RK23_CHLRE	Chloroplast 50S ribosomal protein L23	0.17	-	cyt	0	Plastid; chloroplast				95
Q85FR9 UniProt NPD GO	RK33_CYAME	Chloroplast 50S ribosomal protein L33	0.17	-	mit	0	Plastid; chloroplast				62
Q1XDH5 UniProt NPD GO	RK4_PORYE	Chloroplast 50S ribosomal protein L4	0.17	-	nuc	0	Plastid; chloroplast				214
Q9NRG0 UniProt NPD GO	CHRC1_HUMAN	Chromatin accessibility complex protein 1 (CHRAC-1) (CHRAC-15) (HuCHRAC15) (DNA polymerase epsilon s ...	0.17	-	nuc	0	Nucleus (Potential)	chromatin accessibility complex [NAS] epsilon DNA polymerase complex [NAS]	607268		131
Q6CX42 UniProt NPD GO	EAF5_KLULA	Chromatin modification-related protein EAF5	0.17	-	nuc	0	Nucleus (By similarity)				275
P23946 UniProt NPD GO	MCPT1_HUMAN	Chymase precursor (EC 3.4.21.39) (Mast cell protease I)	0.17	-	vac	0	Mast cell granules		118938	1T31	247
P00794 UniProt NPD GO	CHYM_BOVIN	Chymosin precursor (EC 3.4.23.4) (Preprorennin)	0.17	-	end	0				4CMS	381
P83987 UniProt NPD GO	CERI_CICAR	Cicerin (Fragment)	0.17	-		0					20
O02732 UniProt NPD GO	CNTF_PIG	Ciliary neurotrophic factor (CNTF)	0.17	-	mit	0	Cytoplasm				200
P08674 UniProt NPD GO	CSP_PLACG	Circumsporozoite protein precursor (CS)	0.17	-	nuc	0					401
P04973 UniProt NPD GO	CLCA_BOVIN	Clathrin light chain A (Lca)	0.17	-	nuc	0	Cytoplasmic face of coated pits and vesicles			1XI4	243
P59276 UniProt NPD GO	NXSC_NAJKA	Cobrotoxin c (CBT c) (Short neurotoxin)	0.17	-	nuc	0	Secreted protein			1JE9	61
Q63430 UniProt NPD GO	CSDC2_RAT	Cold shock domain-containing protein C2 (RNA-binding protein PIPPin)	0.17	-	nuc	0	Nucleus. Cytoplasm. PIPPin-RNA complexes are located to the nucleus				154
P46526 UniProt NPD GO	CS66_WHEAT	Cold shock protein CS66	0.17	-	cyt	0					469
P08123 UniProt NPD GO	CO1A2_HUMAN	Collagen alpha-2(I) chain precursor	0.17	-	exc	0			259420		1366
P08650 UniProt NPD GO	CO5_RAT	Complement C5 [Contains: C5a anaphylatoxin] (Fragment)	0.17	-	nuc	0		membrane attack complex [TAS]			77
P69745 UniProt NPD GO	CXKL_CONLY	Conantokin-L precursor	0.17	-	cyt	0	Secreted protein				101
P0C1N1 UniProt NPD GO	CXM32_CONMR	Conotoxin Mr3.2 precursor	0.17	-	exc	0	Secreted protein (By similarity)				67
P0C1N3 UniProt NPD GO	CXM34_CONMR	Conotoxin Mr3.4 precursor	0.17	-	exc	0	Secreted protein (By similarity)				68
Q5K0C5 UniProt NPD GO	CXO10_CONVR	Conotoxin-10 precursor	0.17	-	vac	0	Secreted protein (By similarity)				79
Q5K0D0 UniProt NPD GO	CXO12_CONVX	Conotoxin-12 precursor	0.17	-	vac	0	Secreted protein (By similarity)				79
Q5K0C9 UniProt NPD GO	CXO2_CONVX	Conotoxin-2 precursor	0.17	-	vac	0	Secreted protein				79
Q5K0C7 UniProt NPD GO	CXO3_CONVR	Conotoxin-3 precursor	0.17	-	vac	0	Secreted protein (By similarity)				79
Q5K0C8 UniProt NPD GO	CXO8_CONVX	Conotoxin-8 precursor	0.17	-	mit	1 *	Secreted protein (By similarity)				79
Q28106 UniProt NPD GO	CNTN1_BOVIN	Contactin-1 precursor (Neural cell surface protein F3)	0.17	-	end	1	Cell membrane; lipid-anchor; GPI-anchor				1018
Q64430 UniProt NPD GO	ATP7A_MOUSE	Copper-transporting ATPase 1 (EC 3.6.3.4) (Copper pump 1) (Menkes disease-associated protein homolog ...	0.17	-	end	7	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein (By ...	Golgi apparatus [ISS] integral to plasma membrane [ISS] trans-Golgi network transport vesicle [ISS]			1491
Q9V3D2 UniProt NPD GO	HEM6_DROME	Coproporphyrinogen III oxidase (EC 1.3.3.3) (Coproporphyrinogenase) (Coprogen oxidase) (COX)	0.17	-	mit	0					390
Q42946 UniProt NPD GO	HEM6_TOBAC	Coproporphyrinogen III oxidase, chloroplast precursor (EC 1.3.3.3) (Coproporphyrinogenase) (Coprogen ...	0.17	-	mit	0	Plastid; chloroplast (Probable)				397
Q9WUM4 UniProt NPD GO	COR1C_MOUSE	Coronin-1C (Coronin-3)	0.17	-	nuc	0		cytoskeleton [TAS]			474
Q5R7B5 UniProt NPD GO	KCRS_PONPY	Creatine kinase, sarcomeric mitochondrial precursor (EC 2.7.3.2) (S-MtCK)	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane. Outer side (By similarity)				419
Q3ZBP1 UniProt NPD GO	KCRS_BOVIN	Creatine kinase, sarcomeric mitochondrial precursor (EC 2.7.3.2) (S-MtCK) (Mib-CK) (Basic-type mitoc ...	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane. Outer side (By similarity)				419
P17540 UniProt NPD GO	KCRS_HUMAN	Creatine kinase, sarcomeric mitochondrial precursor (EC 2.7.3.2) (S-MtCK) (Mib-CK) (Basic-type mitoc ...	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane; intermembrane side	mitochondrion [TAS]	123295	2GL6	419
O15980 UniProt NPD GO	CHH1_PENJP	Crustacean hyperglycemic hormones 1 precursor (Pej-SGP-I) [Contains: CHH precursor-related peptide 1 ...	0.17	-	exc	1 *	Secreted protein				120
O97383 UniProt NPD GO	CHH1_PENMO	Crustacean hyperglycemic hormones 1 precursor (Pm-SGP-I) [Contains: CHH precursor-related peptide 1 ...	0.17	-	exc	1 *	Secreted protein				120
Q9U5D2 UniProt NPD GO	CHH2_PENJP	Crustacean hyperglycemic hormones 2 precursor (Pej-SGP-II) [Contains: CHH precursor-related peptide ...	0.17	-	exc	0	Secreted protein				120
P81384 UniProt NPD GO	CU1A_HOMAM	Cuticle protein AMP1A (HA-AMP1A)	0.17	-	nuc	0					105
P26205 UniProt NPD GO	BGLT_TRIRP	Cyanogenic beta-glucosidase precursor (EC 3.2.1.21) (Linamarase) (Fragment)	0.17	-	cyt	0				1CBG	425
Q00195 UniProt NPD GO	CNGA2_RAT	Cyclic nucleotide-gated olfactory channel (Cyclic nucleotide-gated cation channel 2) (CNG channel 2) ...	0.17	-	vac	3	Membrane; multi-pass membrane protein				664
P61024 UniProt NPD GO	CKS1_HUMAN	Cyclin-dependent kinases regulatory subunit 1 (CKS-1)	0.17	-	nuc	0			116900	2AST	79
P61025 UniProt NPD GO	CKS1_MOUSE	Cyclin-dependent kinases regulatory subunit 1 (CKS-1) (Sid 1334)	0.17	-	nuc	0					79
Q58DW2 UniProt NPD GO	CGL_BOVIN	Cystathionine gamma-lyase (EC 4.4.1.1) (Gamma-cystathionase)	0.17	-	cyt	0	Cytoplasm (By similarity)				405
O19092 UniProt NPD GO	CYTC_MACMU	Cystatin C precursor	0.17	-	exc	1 *					146
Q9D269 UniProt NPD GO	CST11_MOUSE	Cystatin-11 precursor	0.17	-	exc	1 *	Secreted protein (Potential)				139
Q5R699 UniProt NPD GO	ATG4A_PONPY	Cysteine protease ATG4A (EC 3.4.22.-) (Autophagy-related protein 4 homolog A)	0.17	-	cyt	0	Cytoplasm (Probable)				398
Q95V11 UniProt NPD GO	CMAH_ASTRU	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.17	+	cyt	0	Cytoplasm				653

You are viewing entries 54151 to 54200 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.