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
O46898 UniProt NPD GO	RR19_GUITH	Chloroplast 30S ribosomal protein S19	0.03	-	mit	0	Plastid; chloroplast				92
P35014 UniProt NPD GO	RR2_GALSU	Chloroplast 30S ribosomal protein S2	0.03	-	cyt	0	Plastid; chloroplast				233
Q40606 UniProt NPD GO	RR2_OCHNE	Chloroplast 30S ribosomal protein S2 (Fragment)	0.03	-	nuc	0	Plastid; chloroplast				34
P51338 UniProt NPD GO	RK1_PORPU	Chloroplast 50S ribosomal protein L1	0.03	-	mit	0	Plastid; chloroplast				229
P56345 UniProt NPD GO	RK12_CHLVU	Chloroplast 50S ribosomal protein L12	0.03	-	cyt	0	Plastid; chloroplast				131
Q85G10 UniProt NPD GO	RK12_CYAME	Chloroplast 50S ribosomal protein L12	0.03	-	cyt	0	Plastid; chloroplast				124
Q6B905 UniProt NPD GO	RK12_GRATL	Chloroplast 50S ribosomal protein L12	0.03	-	nuc	0	Plastid; chloroplast				131
Q9TL30 UniProt NPD GO	RK12_NEPOL	Chloroplast 50S ribosomal protein L12	0.03	-	cyt	0	Plastid; chloroplast				128
P41545 UniProt NPD GO	RK27_PLECA	Chloroplast 50S ribosomal protein L27	0.03	-	nuc	0	Plastid; chloroplast				82
O46917 UniProt NPD GO	RK31_GUITH	Chloroplast 50S ribosomal protein L31	0.03	-	nuc	0	Plastid; chloroplast				72
P49563 UniProt NPD GO	RK31_ODOSI	Chloroplast 50S ribosomal protein L31	0.03	-	nuc	0	Plastid; chloroplast				72
Q1XDF2 UniProt NPD GO	RK9_PORYE	Chloroplast 50S ribosomal protein L9	0.03	-	nuc	0	Plastid; chloroplast				155
Q8S8W5 UniProt NPD GO	CEMA_ATRBE	Chloroplast envelope membrane protein	0.03	-	nuc	3 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
P12213 UniProt NPD GO	CEMA_TOBAC	Chloroplast envelope membrane protein	0.03	-	nuc	3 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
P12811 UniProt NPD GO	HS22C_CHLRE	Chloroplast heat shock 22 kDa protein	0.03	-	cyt	0	Plastid; chloroplast				157
Q9LKN0 UniProt NPD GO	CHMO_ATRHO	Choline monooxygenase, chloroplast precursor (EC 1.14.15.7)	0.03	-	mit	0	Plastid; chloroplast; chloroplast stroma (By similarity)				438
P07185 UniProt NPD GO	CH15_DROME	Chorion protein S15	0.03	-	mit	0					115
Q5W111 UniProt NPD GO	CLLD6_HUMAN	Chronic lymphocytic leukemia deletion region gene 6 protein (CLL deletion region gene 6 protein)	0.03	-	cyt	0			607866		196
Q5ZHV7 UniProt NPD GO	CLLD6_CHICK	Chronic lymphocytic leukemia deletion region gene 6 protein homolog (CLL deletion region gene 6 prot ...	0.03	-	cyt	0					196
Q3TFQ1 UniProt NPD GO	CLLD6_MOUSE	Chronic lymphocytic leukemia deletion region gene 6 protein homolog (CLL deletion region gene 6 prot ...	0.03	-	cyt	0					196
Q5M7T2 UniProt NPD GO	CLLD6_RAT	Chronic lymphocytic leukemia deletion region gene 6 protein homolog (CLL deletion region gene 6 prot ...	0.03	-	cyt	0					196
P80646 UniProt NPD GO	CTRB_GADMO	Chymotrypsin B (EC 3.4.21.1) [Contains: Chymotrypsin B chain A; Chymotrypsin B chain B]	0.03	-	cyt	0	Secreted protein; extracellular space				245
P34952 UniProt NPD GO	IECI_ERYVA	Chymotrypsin inhibitor ECI	0.03	-	cyt	0					179
P17538 UniProt NPD GO	CTRB1_HUMAN	Chymotrypsinogen B precursor (EC 3.4.21.1) [Contains: Chymotrypsin B chain A; Chymotrypsin B chain B ...	0.03	-	end	1 *	Secreted protein; extracellular space	extracellular region [NAS]	118890		263
P23007 UniProt NPD GO	CISY_CHICK	Citrate synthase, mitochondrial (EC 2.3.3.1)	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [ISS]		6CTS	433
P79024 UniProt NPD GO	CISY_CANTR	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix				467
Q43175 UniProt NPD GO	CISY_SOLTU	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.03	-	nuc	0	Mitochondrion; mitochondrial matrix				471
P08679 UniProt NPD GO	CISY2_YEAST	Citrate synthase, peroxisomal (EC 2.3.3.1)	0.03	-	pox	0	Peroxisome	mitochondrion [IDA]			460
Q9NY35 UniProt NPD GO	CLDND_HUMAN	Claudin domain-containing protein 1 (Membrane protein GENX-3745)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				253
Q9Z0S6 UniProt NPD GO	CLD10_MOUSE	Claudin-10	0.03	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			231
Q9Y5I7 UniProt NPD GO	CLD16_HUMAN	Claudin-16 (Paracellin-1) (PCLN-1)	0.03	-	end	4	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]	603959		305
P56857 UniProt NPD GO	CLD18_MOUSE	Claudin-18	0.03	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			264
Q9D7U6 UniProt NPD GO	CLD22_MOUSE	Claudin-22	0.03	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			220
O15551 UniProt NPD GO	CLD3_HUMAN	Claudin-3 (Clostridium perfringens enterotoxin receptor 2) (CPE-receptor 2) (CPE-R 2) (Ventral prost ...	0.03	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS] tight junction [ISS]	602910		220
O35054 UniProt NPD GO	CLD4_MOUSE	Claudin-4 (Clostridium perfringens enterotoxin receptor) (CPE-receptor) (CPE-R)	0.03	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [NAS] tight junction [IDA]			210
Q9Z262 UniProt NPD GO	CLD6_MOUSE	Claudin-6 (Skullin)	0.03	-	end	5 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [NAS] plasma membrane [IDA] tight junction [IDA]			219
Q9Z1L1 UniProt NPD GO	CLD7_RAT	Claudin-7	0.03	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			211
Q9Z260 UniProt NPD GO	CLD8_MOUSE	Claudin-8	0.03	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [NAS] tight junction [IDA]			225
P16293 UniProt NPD GO	FA9_PIG	Coagulation factor IX (EC 3.4.21.22) (Christmas factor) [Contains: Coagulation factor IXa light chai ...	0.03	-	cyt	0	Secreted protein			1X7A	409
P23807 UniProt NPD GO	IXB_TRIFL	Coagulation factor IX/factor X-binding protein B chain precursor (IX/X-BP)	0.03	-	exc	0	Secreted protein			1X2W	146
P35604 UniProt NPD GO	COPZ1_BOVIN	Coatomer subunit zeta-1 (Zeta-1 coat protein) (Zeta-1 COP)	0.03	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]			177
P61923 UniProt NPD GO	COPZ1_HUMAN	Coatomer subunit zeta-1 (Zeta-1 coat protein) (Zeta-1 COP)	0.03	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]			177
P61924 UniProt NPD GO	COPZ1_MOUSE	Coatomer subunit zeta-1 (Zeta-1 coat protein) (Zeta-1 COP)	0.03	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				177
Q5R5F2 UniProt NPD GO	COPZ1_PONPY	Coatomer subunit zeta-1 (Zeta-1 coat protein) (Zeta-1 COP)	0.03	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				177
O42163 UniProt NPD GO	COCH_CHICK	Cochlin precursor (COCH-5B2)	0.03	-	end	0	Secreted protein (Potential)				547
Q62507 UniProt NPD GO	COCH_MOUSE	Cochlin precursor (COCH-5B2)	0.03	-	exc	0	Secreted protein; extracellular space (By similarity)				552
Q03048 UniProt NPD GO	COFI_YEAST	Cofilin	0.03	-	cyt	0	Cytoplasm. Cytoskeleton. Throughout the cytoplasm (but not on the cytoplasmic cables) and major comp ...	actin cortical patch [IDA]		1QPV	143
P29174 UniProt NPD GO	CSDE1_CAVPO	Cold shock domain-containing protein E1 (UNR protein) (Fragment)	0.03	-	cyt	0	Cytoplasm				114
P45452 UniProt NPD GO	MMP13_HUMAN	Collagenase 3 precursor (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13)	0.03	-	exc	0		extracellular space [TAS]	600108	830C	471
Q10835 UniProt NPD GO	MMP13_XENLA	Collagenase 3 precursor (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13) (Fragment)	0.03	-	exc	0					469

You are viewing entries 79401 to 79450 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.