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
Q85WX8 UniProt NPD GO	RR4_PINKO	Chloroplast 30S ribosomal protein S4	0.53	-	mit	0	Plastid; chloroplast				228
P13788 UniProt NPD GO	RR4_SPIOL	Chloroplast 30S ribosomal protein S4	0.53	-	mit	0	Plastid; chloroplast				201
O19992 UniProt NPD GO	RR4_BOBGL	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				194
P69635 UniProt NPD GO	RR4_BRAPI	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				196
P69636 UniProt NPD GO	RR4_BRASY	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				196
P69639 UniProt NPD GO	RR4_CRONU	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				183
O20103 UniProt NPD GO	RR4_CROSP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				183
O20215 UniProt NPD GO	RR4_FRESP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				183
P69643 UniProt NPD GO	RR4_GLACO	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				183
O20235 UniProt NPD GO	RR4_IRILU	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				182
P36461 UniProt NPD GO	RR4_IRIPA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				196
P69647 UniProt NPD GO	RR4_MICJU	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				183
O20265 UniProt NPD GO	RR4_NERBO	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				182
O20280 UniProt NPD GO	RR4_ROMRE	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				195
O36054 UniProt NPD GO	RR4_SPASP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.53	-	mit	0	Plastid; chloroplast				183
Q6EM87 UniProt NPD GO	RR7_HYDMC	Chloroplast 30S ribosomal protein S7	0.53	-	nuc	0	Plastid; chloroplast				155
Q9ME90 UniProt NPD GO	RR7_OENHO	Chloroplast 30S ribosomal protein S7	0.53	-	nuc	0	Plastid; chloroplast				155
Q6YXS0 UniProt NPD GO	RR7_PHYPA	Chloroplast 30S ribosomal protein S7	0.53	-	nuc	0	Plastid; chloroplast				155
Q9GFK3 UniProt NPD GO	RR7_SAUCE	Chloroplast 30S ribosomal protein S7	0.53	-	nuc	0	Plastid; chloroplast				155
Q6EM56 UniProt NPD GO	RR7_STEPS	Chloroplast 30S ribosomal protein S7	0.53	-	nuc	0	Plastid; chloroplast				155
Q70XX5 UniProt NPD GO	RR8_AMBTC	Chloroplast 30S ribosomal protein S8	0.53	-	nuc	0	Plastid; chloroplast				132
Q6END8 UniProt NPD GO	RR8_ORYNI	Chloroplast 30S ribosomal protein S8	0.53	-	cyt	0	Plastid; chloroplast				136
P12148 UniProt NPD GO	RR8_ORYSA	Chloroplast 30S ribosomal protein S8	0.53	-	cyt	0	Plastid; chloroplast				136
Q6B8X6 UniProt NPD GO	RR9_GRATL	Chloroplast 30S ribosomal protein S9	0.53	-	nuc	0	Plastid; chloroplast				137
P60406 UniProt NPD GO	RK2_AMBTC	Chloroplast 50S ribosomal protein L2	0.53	+	nuc	0	Plastid; chloroplast				273
Q4VZK5 UniProt NPD GO	RK2_CUCSA	Chloroplast 50S ribosomal protein L2	0.53	+	nuc	0	Plastid; chloroplast				274
Q4G362 UniProt NPD GO	RK2_EMIHU	Chloroplast 50S ribosomal protein L2	0.53	-	mit	0	Plastid; chloroplast				276
Q332R5 UniProt NPD GO	RK2_LACSA	Chloroplast 50S ribosomal protein L2	0.53	-	nuc	0	Plastid; chloroplast				274
Q3BAJ4 UniProt NPD GO	RK2_PHAAO	Chloroplast 50S ribosomal protein L2	0.53	+	nuc	0	Plastid; chloroplast				273
P27107 UniProt NPD GO	RK2_SINAL	Chloroplast 50S ribosomal protein L2	0.53	+	nuc	0	Plastid; chloroplast				274
P06509 UniProt NPD GO	RK2_SPIOL	Chloroplast 50S ribosomal protein L2 (Ribosomal protein CS-L4)	0.53	+	mit	0	Plastid; chloroplast				271
Q6YXQ4 UniProt NPD GO	RK32_PHYPA	Chloroplast 50S ribosomal protein L32	0.53	-	nuc	0	Plastid; chloroplast				59
Q85AP4 UniProt NPD GO	CEMA_ANTFO	Chloroplast envelope membrane protein	0.53	-	end	1	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				508
Q6CSR7 UniProt NPD GO	SFH1_KLULA	Chromatin structure remodeling complex protein SFH1 (SNF5 homolog 1)	0.53	+	cyt	0	Nucleus (By similarity)				442
Q8R2N2 UniProt NPD GO	CIR1A_MOUSE	Cirhin (Testis-expressed gene 292 protein)	0.53	-	mit	0	Nucleus; nucleolus (By similarity)				686
P30386 UniProt NPD GO	1C03_GORGO	Class I histocompatibility antigen, GOGO-C0202 alpha chain precursor	0.53	-	end	1	Membrane; single-pass type I membrane protein				366
P11442 UniProt NPD GO	CLH_RAT	Clathrin heavy chain	0.53	-	cyt	0	Cytoplasmic face of coated pits and vesicles	clathrin coat [TAS]		1C9L	1675
P49951 UniProt NPD GO	CLH1_BOVIN	Clathrin heavy chain 1	0.53	-	cyt	0	Cytoplasmic face of coated pits and vesicles			1XI5	1675
Q00610 UniProt NPD GO	CLH1_HUMAN	Clathrin heavy chain 1 (CLH-17)	0.53	-	cyt	0	Cytoplasmic face of coated pits and vesicles	clathrin coat [NAS]	118955		1674
P98094 UniProt NPD GO	CO3_EPTBU	Complement C3 [Contains: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphylatoxin; Com ...	0.53	-	nuc	0					1620
Q2UVX4 UniProt NPD GO	CO3_BOVIN	Complement C3 precursor [Contains: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphyla ...	0.53	-	end	0					1661
P48770 UniProt NPD GO	CO9_HORSE	Complement component C9 precursor	0.53	-	mit	0	Secreted protein				547
Q9C0A0 UniProt NPD GO	CNTP4_HUMAN	Contactin-associated protein-like 4 precursor (Cell recognition molecule Caspr4)	0.53	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1308
Q43125 UniProt NPD GO	CRY1_ARATH	Cryptochrome-1 (Blue light photoreceptor)	0.53	-	nuc	0				1U3D	681
O75155 UniProt NPD GO	CAND2_HUMAN	Cullin-associated NEDD8-dissociated protein 2 (Cullin-associated and neddylation-dissociated protein ...	0.53	-	cyt	0	Nucleus (By similarity)	intracellular [IDA]			1119
P48138 UniProt NPD GO	RR14_CYAPA	Cyanelle 30S ribosomal protein S14	0.53	-	nuc	0	Plastid; cyanelle				100
Q14094 UniProt NPD GO	CCNI_HUMAN	Cyclin-I	0.53	-	nuc	0					377
Q9QUK0 UniProt NPD GO	CDKL2_MOUSE	Cyclin-dependent kinase-like 2 (EC 2.7.11.22) (Serine/threonine-protein kinase KKIAMRE)	0.53	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				568
P15539 UniProt NPD GO	C11B2_MOUSE	Cytochrome P450 11B2, mitochondrial precursor (EC 1.14.15.4) (EC 1.14.15.5) (CYPXIB2) (P450C11) (Ste ...	0.53	-	mit	0	Mitochondrion				500
Q9DBW0 UniProt NPD GO	CP4V3_MOUSE	Cytochrome P450 4V3 (EC 1.14.-.-)	0.53	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				525

You are viewing entries 23001 to 23050 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.