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
Q62834 UniProt NPD GO	CD123_RAT	Cell division cycle protein 123 homolog (Protein D123)	0.35	-	cyt	0	Cytoplasm				336
Q94JQ6 UniProt NPD GO	CESA6_ARATH	Cellulose synthase A catalytic subunit 6 [UDP-forming] (EC 2.4.1.12) (AtCesA-6) (Isoxaben-resistant ...	0.35	+	end	8	Cell membrane; multi-pass membrane protein (Probable)				1084
Q9W4X9 UniProt NPD GO	ZW10_DROME	Centromere/kinetochore protein zw10 (Mitotic 15 protein)	0.35	-	cyt	0	Cytoplasm. Nucleus. Kinetochore. Excluded from the nucleus during interphase but migrates into the n ...	kinetochore [IDA] kinetochore microtubule [IDA] outer kinetochore of condensed chromosome [NAS]			721
Q8GYX8 UniProt NPD GO	DNJ10_ARATH	Chaperone protein dnaJ 10 (AtJ10) (AtDjC10)	0.35	-	nuc	0					398
P87073 UniProt NPD GO	CHS1_PHYBL	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-II chitin synt ...	0.35	-	end	7	Cell membrane; multi-pass membrane protein				841
Q12564 UniProt NPD GO	CHSA_AMPQU	Chitin synthase A (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase A) (Class-I chitin synth ...	0.35	-	end	9	Cell membrane; multi-pass membrane protein				910
P30584 UniProt NPD GO	CHSA_EMENI	Chitin synthase A (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase A) (Class-II chitin synt ...	0.35	-	end	7	Cell membrane; multi-pass membrane protein				1013
Q6BS98 UniProt NPD GO	ALG1_DEBHA	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.35	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				472
Q9BBQ3 UniProt NPD GO	RR11_LOTJA	Chloroplast 30S ribosomal protein S11	0.35	-	nuc	0	Plastid; chloroplast				138
O98461 UniProt NPD GO	RR11_SPIMX	Chloroplast 30S ribosomal protein S11	0.35	-	nuc	0	Plastid; chloroplast				130
Q3BAH6 UniProt NPD GO	RR15_PHAAO	Chloroplast 30S ribosomal protein S15	0.35	-	nuc	0	Plastid; chloroplast				91
Q6L3D3 UniProt NPD GO	RR15_SACHY	Chloroplast 30S ribosomal protein S15	0.35	-	nuc	0	Plastid; chloroplast				78
Q6ENQ1 UniProt NPD GO	RR15_SACOF	Chloroplast 30S ribosomal protein S15	0.35	-	nuc	0	Plastid; chloroplast				78
P27723 UniProt NPD GO	RR16_MAIZE	Chloroplast 30S ribosomal protein S16	0.35	-	mit	0	Plastid; chloroplast				85
Q6ENJ5 UniProt NPD GO	RR16_ORYNI	Chloroplast 30S ribosomal protein S16	0.35	-	nuc	0	Plastid; chloroplast				85
P12151 UniProt NPD GO	RR16_ORYSA	Chloroplast 30S ribosomal protein S16	0.35	-	nuc	0	Plastid; chloroplast				85
Q6L3B4 UniProt NPD GO	RR16_SACHY	Chloroplast 30S ribosomal protein S16	0.35	-	mit	0	Plastid; chloroplast				85
Q6ENY4 UniProt NPD GO	RR16_SACOF	Chloroplast 30S ribosomal protein S16	0.35	-	mit	0	Plastid; chloroplast				85
Q95H63 UniProt NPD GO	RR16_WHEAT	Chloroplast 30S ribosomal protein S16	0.35	-	mit	0	Plastid; chloroplast				85
Q6B8W2 UniProt NPD GO	RR17_GRATL	Chloroplast 30S ribosomal protein S17	0.35	-	nuc	0	Plastid; chloroplast				80
P49505 UniProt NPD GO	RR18_ODOSI	Chloroplast 30S ribosomal protein S18	0.35	-	nuc	0	Plastid; chloroplast				72
P49490 UniProt NPD GO	RR2_ODOSI	Chloroplast 30S ribosomal protein S2	0.35	-	cyt	0	Plastid; chloroplast				229
Q9M4C0 UniProt NPD GO	RR4_HAPHO	Chloroplast 30S ribosomal protein S4	0.35	-	mit	0	Plastid; chloroplast				202
P32060 UniProt NPD GO	RR9_EUGGR	Chloroplast 30S ribosomal protein S9	0.35	-	nuc	0	Plastid; chloroplast				134
Q70XX3 UniProt NPD GO	RK16_AMBTC	Chloroplast 50S ribosomal protein L16	0.35	-	mit	0	Plastid; chloroplast				135
Q49KW1 UniProt NPD GO	RK16_EUCGG	Chloroplast 50S ribosomal protein L16	0.35	-	mit	0	Plastid; chloroplast				135
Q85WS6 UniProt NPD GO	RK16_PINKO	Chloroplast 50S ribosomal protein L16	0.35	-	mit	0	Plastid; chloroplast				134
P52767 UniProt NPD GO	RK16_PINTH	Chloroplast 50S ribosomal protein L16	0.35	-	mit	0	Plastid; chloroplast				134
Q8HTL2 UniProt NPD GO	RK2_CHLRE	Chloroplast 50S ribosomal protein L2	0.35	+	mit	0	Plastid; chloroplast				278
Q20F12 UniProt NPD GO	RK2_OLTVI	Chloroplast 50S ribosomal protein L2	0.35	-	nuc	0	Plastid; chloroplast				275
Q85BJ7 UniProt NPD GO	RK23_ANTFO	Chloroplast 50S ribosomal protein L23	0.35	-	nuc	0	Plastid; chloroplast				91
P56360 UniProt NPD GO	RK36_CHLVU	Chloroplast 50S ribosomal protein L36	0.35	-	nuc	0	Plastid; chloroplast				37
Q6IQX7 UniProt NPD GO	CHSS2_MOUSE	Chondroitin sulfate synthase 2 (EC 2.4.1.175) (Glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-be ...	0.35	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)				774
P13826 UniProt NPD GO	CSP_PLAVS	Circumsporozoite protein (CS) (Fragment)	0.35	-	cyt	1					343
Q03110 UniProt NPD GO	CSP_PLASI	Circumsporozoite protein precursor (CS)	0.35	-	mit	1					386
P08677 UniProt NPD GO	CSP_PLAVB	Circumsporozoite protein precursor (CS)	0.35	-	mit	1					378
Q9SJH7 UniProt NPD GO	CISY3_ARATH	Citrate synthase 3, peroxisomal precursor (EC 2.3.3.1)	0.35	-	cyt	0	Peroxisome				509
P30377 UniProt NPD GO	1A03_GORGO	Class I histocompatibility antigen, GOGO-A0401 alpha chain precursor	0.35	-	end	1	Membrane; single-pass type I membrane protein				365
O60641 UniProt NPD GO	AP180_HUMAN	Clathrin coat assembly protein AP180 (Clathrin coat-associated protein AP180) (91 kDa synaptosomal-a ...	0.35	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane (By ...		607923		907
Q05140 UniProt NPD GO	AP180_RAT	Clathrin coat assembly protein AP180 (Clathrin coat-associated protein AP180) (91 kDa synaptosomal-a ...	0.35	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane	presynaptic membrane [IDA]			915
Q61548 UniProt NPD GO	AP180_MOUSE	Clathrin coat assembly protein AP180 (Clathrin coat-associated protein AP180) (91 kDa synaptosomal-a ...	0.35	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane				901
P03951 UniProt NPD GO	FA11_HUMAN	Coagulation factor XI precursor (EC 3.4.21.27) (Plasma thromboplastin antecedent) (PTA) (FXI) [Conta ...	0.35	-	cyt	0	Secreted protein	extracellular region [NAS] membrane [NAS]	264900	2FDA	625
P53621 UniProt NPD GO	COPA_HUMAN	Coatomer subunit alpha (Alpha-coat protein) (Alpha-COP) (HEPCOP) (HEP-COP) [Contains: Xenin (Xenopsi ...	0.35	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [ISS] cytoplasm [IDA] extracellular space [IDA] microsome [IDA] soluble fraction [IDA]	601924		1224
P45437 UniProt NPD GO	COPB_DROME	Coatomer subunit beta (Beta-coat protein) (Beta-COP)	0.35	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	Golgi apparatus [IDA]			964
Q9UBF2 UniProt NPD GO	COPG2_HUMAN	Coatomer subunit gamma-2 (Gamma-2 coat protein) (Gamma-2 COP)	0.35	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]	604355		871
Q99715 UniProt NPD GO	COCA1_HUMAN	Collagen alpha-1(XII) chain precursor	0.35	-	nuc	0		collagen type XII [TAS]	120320		3063
Q90584 UniProt NPD GO	COHA1_CHICK	Collagen alpha-1(XVII) chain (Bullous pemphigoid antigen 2) (180 kDa bullous pemphigoid antigen 2) ( ...	0.35	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				1146
P01027 UniProt NPD GO	CO3_MOUSE	Complement C3 precursor (HSE-MSF) [Contains: Complement C3 beta chain; Complement C3 alpha chain; C3 ...	0.35	-	exc	1 *					1663
Q61475 UniProt NPD GO	DAF1_MOUSE	Complement decay-accelerating factor, GPI-anchored precursor (DAF-GPI) (CD55 antigen)	0.35	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				390
Q9JMB8 UniProt NPD GO	CNTN6_MOUSE	Contactin-6 precursor (Neural recognition molecule NB-3) (mNB-3)	0.35	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				1028

You are viewing entries 35701 to 35750 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.