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
P32750 UniProt NPD GO	CHLE_CANFA	Cholinesterase (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylcholine estera ...	0.01	-	cyt	0					141
P05685 UniProt NPD GO	CHB4_BOMMO	Chorion class B protein B.L1 (410) (Fragment)	0.01	-	cyt	0					147
Q17213 UniProt NPD GO	CHCA3_BOMMO	Chorion class CA protein ERA.3 precursor	0.01	-	nuc	0					119
P08931 UniProt NPD GO	CHCB3_ANTPO	Chorion class CB protein PCH12 (Fragment)	0.01	-	cyt	0					37
P05687 UniProt NPD GO	CHHA2_BOMMO	Chorion class high-cysteine HCA protein 12 precursor (HC-A.12)	0.01	-	mit	0					124
P20730 UniProt NPD GO	CHHB2_BOMMO	Chorion class high-cysteine HCB protein 13 precursor (HC-B.13)	0.01	-	vac	0					178
P22977 UniProt NPD GO	CH16_DROME	Chorion protein S16	0.01	-	vac	0					138
P54219 UniProt NPD GO	VMAT1_HUMAN	Chromaffin granule amine transporter (Vesicular amine transporter 1) (VAT1) (Solute carrier family 1 ...	0.01	-	end	12 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein	membrane fraction [NAS]	193002		525
Q8R090 UniProt NPD GO	VMAT1_MOUSE	Chromaffin granule amine transporter (Vesicular amine transporter 1) (VAT1) (Solute carrier family 1 ...	0.01	-	end	11 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity)				521
Q01818 UniProt NPD GO	VMAT1_RAT	Chromaffin granule amine transporter (Vesicular amine transporter 1) (VAT1) (Solute carrier family 1 ...	0.01	-	end	11 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein				521
Q00871 UniProt NPD GO	CTRB1_PENVA	Chymotrypsin BI precursor (EC 3.4.21.1)	0.01	-	exc	0	Secreted protein; extracellular space				271
P10822 UniProt NPD GO	ICW3_PSOTE	Chymotrypsin inhibitor 3 precursor (WCI-3)	0.01	-	exc	0				4WBC	207
Q17025 UniProt NPD GO	CTR2_ANOGA	Chymotrypsin-2 precursor (EC 3.4.21.1)	0.01	-	exc	0					258
P56879 UniProt NPD GO	CIRB_CHAPA	Circulin-B (CIRB)	0.01	-	nuc	0				2ERI	31
Q29RK1 UniProt NPD GO	CISY_BOVIN	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				466
P81839 UniProt NPD GO	CT114_LITCI	Citropin-1.1.4	0.01	-		0	Secreted protein				18
P81845 UniProt NPD GO	CT125_LITCI	Citropin-1.2.5	0.01	-		0	Secreted protein				18
P02520 UniProt NPD GO	HSP12_SOYBN	Class I heat shock protein (Fragment)	0.01	-	nuc	0	Cytoplasm				74
Q925N4 UniProt NPD GO	CLD16_MOUSE	Claudin-16 (Paracellin-1)	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			235
Q91Y55 UniProt NPD GO	CLD16_RAT	Claudin-16 (Paracellin-1)	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			235
Q9ET38 UniProt NPD GO	CLD19_MOUSE	Claudin-19	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			224
Q5QT56 UniProt NPD GO	CLD19_RAT	Claudin-19	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein				224
Q6BBL6 UniProt NPD GO	CLD4_BOVIN	Claudin-4	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			209
O19005 UniProt NPD GO	CLD4_CERAE	Claudin-4 (Clostridium perfringens enterotoxin receptor) (CPE-receptor) (CPE-R)	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			209
O14493 UniProt NPD GO	CLD4_HUMAN	Claudin-4 (Clostridium perfringens enterotoxin receptor) (CPE-receptor) (CPE-R) (Williams-Beuren syn ...	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS] plasma membrane [TAS] tight junction [ISS]	602909		209
P56747 UniProt NPD GO	CLD6_HUMAN	Claudin-6 (Skullin 2)	0.01	-	end	5 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			220
O95484 UniProt NPD GO	CLD9_HUMAN	Claudin-9	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			217
Q9Z0S7 UniProt NPD GO	CLD9_MOUSE	Claudin-9	0.01	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			217
Q9YH91 UniProt NPD GO	CLDY_BRARE	Claudin-like protein ZF-A89 (Claudin d)	0.01	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			208
Q9YH90 UniProt NPD GO	CLDZ_BRARE	Claudin-like protein ZF-A9 (Claudin g)	0.01	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			209
P80711 UniProt NPD GO	CLAVB_STYCL	Clavanin-B	0.01	-	cyt	0	Secreted protein				23
Q01302 UniProt NPD GO	CCG6_NEUCR	Clock-controlled protein 6	0.01	-	exc	0					142
P16296 UniProt NPD GO	FA9_RAT	Coagulation factor IX (EC 3.4.21.22) (Christmas factor) (Fragment)	0.01	-	cyt	0	Secreted protein				282
P19090 UniProt NPD GO	COL_CANFA	Colipase precursor	0.01	-	exc	0	Secreted protein				112
P42890 UniProt NPD GO	COL_RABIT	Colipase precursor	0.01	-	exc	0	Secreted protein				107
P08897 UniProt NPD GO	COGS_HYPLI	Collagenase precursor (EC 3.4.21.-) (Hypodermin C) (HC)	0.01	-	exc	0	Secreted protein			2HLC	260
P34156 UniProt NPD GO	COG4_CHIOP	Collagenolytic protease 23 kDa (EC 3.4.24.7) (Fragment)	0.01	-		0					20
P34154 UniProt NPD GO	COG2_CHIOP	Collagenolytic protease 35 kDa 2 (EC 3.4.21.32) (Collagenolytic protease 35 kDa II) (Fragment)	0.01	-		0					20
P34155 UniProt NPD GO	COG3_CHIOP	Collagenolytic protease 36 kDa (EC 3.4.21.32) (Fragment)	0.01	-		0					20
P20732 UniProt NPD GO	COGA_PARCM	Collagenolytic protease 36 kDa A (EC 3.4.21.32) (Fragment)	0.01	-		0					20
P20733 UniProt NPD GO	COGB_PARCM	Collagenolytic protease 36 kDa B (EC 3.4.21.32) (Fragment)	0.01	-		0					20
P20734 UniProt NPD GO	COGC_PARCM	Collagenolytic protease 36 kDa C (EC 3.4.21.32) (Fragment)	0.01	-		0					20
Q8H9A8 UniProt NPD GO	COOMT_COPJA	Columbamine O-methyltransferase (EC 2.1.1.118) (CoOMT)	0.01	-	cyt	0					351
P19069 UniProt NPD GO	CO4_CAVPO	Complement C4 (Fragment)	0.01	-	mit	0					22
P81187 UniProt NPD GO	CFAB_BOVIN	Complement factor B (EC 3.4.21.47) (C3/C5 convertase) (EC-VMFB) [Contains: Complement factor B Bb fr ...	0.01	-		0	Secreted protein				16
Q25157 UniProt NPD GO	OPSC1_HEMSA	Compound eye opsin BCRH1	0.01	-	end	6 *	Membrane; multi-pass membrane protein				377
Q25158 UniProt NPD GO	OPSC2_HEMSA	Compound eye opsin BCRH2	0.01	-	end	7	Membrane; multi-pass membrane protein				377
Q9YIC2 UniProt NPD GO	LEG2_CONMY	Congerin-2 (Congerin II) (Beta-galactoside-binding lectin 2)	0.01	-	cyt	0				1WLW	135
P84700 UniProt NPD GO	CONO_CONGA	Conophan gld-V	0.01	-		0	Secreted protein	extracellular region [IDA]			8
P84701 UniProt NPD GO	CONO_CONMU	Conophan mus-V	0.01	-		0	Secreted protein	extracellular region [IDA]			8

You are viewing entries 87151 to 87200 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.