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
P47180 UniProt NPD GO	PGLR_YEAST	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase) (PGase SM)	0.09	-	mit	0		extracellular region [IDA]			361
P13446 UniProt NPD GO	HEM3_EUGGR	Porphobilinogen deaminase, chloroplast precursor (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) ...	0.09	-	end	2 *	Plastid; chloroplast				480
Q9H427 UniProt NPD GO	KCNKF_HUMAN	Potassium channel subfamily K member 15 (Acid-sensitive potassium channel protein TASK-5) (TWIK-rela ...	0.09	-	end	5 *	Membrane; multi-pass membrane protein		607368		330
O46028 UniProt NPD GO	KA101_CENNO	Potassium channel toxin alpha-KTx 10.1 precursor (Cobatoxin-1) (CoTx1) (gtIX)	0.09	-	vac	1 *	Secreted protein			1PJV	62
P83244 UniProt NPD GO	KA132_ORTSC	Potassium channel toxin alpha-KTx 13.2 (Toxin OsK2) (OsK-2)	0.09	-	nuc	0	Secreted protein	extracellular region [NAS]			28
P84777 UniProt NPD GO	KA156_TITDI	Potassium channel toxin alpha-KTx 15.6 (Discrepin)	0.09	-	nuc	0	Secreted protein	extracellular region [IDA]			38
P46111 UniProt NPD GO	KAX32_LEIQH	Potassium channel toxin alpha-KTx 3.2 (Agitoxin-2) (AGTX-2) (AgTx2)	0.09	-	nuc	0	Secreted protein			1AGT	38
P46112 UniProt NPD GO	KAX33_LEIQH	Potassium channel toxin alpha-KTx 3.3 (Agitoxin-3) (AGTX-3) (AgTx3)	0.09	-	nuc	0	Secreted protein				38
P58490 UniProt NPD GO	KAX65_PANIM	Potassium channel toxin alpha-KTx 6.5 (Pi7) (Pi-7) (Toxin-7)	0.09	-	nuc	0	Secreted protein			1QKY	38
Q86QV6 UniProt NPD GO	KGX12_CENEL	Potassium channel toxin gamma-KTx 1.2 (Ergtoxin-like protein 1) (ErgTx1) (CeErg1) (CeErgTx1)	0.09	-	nuc	0	Secreted protein				42
Q86QV3 UniProt NPD GO	KGX13_CENGR	Potassium channel toxin gamma-KTx 1.3 (Ergtoxin-like protein 1) (ErgTx1) (CgErg1) (CgErgTx1)	0.09	-	nuc	0	Secreted protein				42
Q86QV2 UniProt NPD GO	KGX34_CENGR	Potassium channel toxin gamma-KTx 3.4 (Ergtoxin-like protein 2) (ErgTx2) (CgErg2) (CgErgTx2)	0.09	-	nuc	0	Secreted protein				42
Q86QV4 UniProt NPD GO	KGX48_CENEL	Potassium channel toxin gamma-KTx 4.8 (Ergtoxin-like protein 3) (ErgTx3) (CeErg3) (CeErgTx3)	0.09	-	nuc	0	Secreted protein				43
Q9M7K4 UniProt NPD GO	POT5_ARATH	Potassium transporter 5 (AtPOT5) (AtHAK1) (AtHAK5)	0.09	-	end	12	Cell membrane; multi-pass membrane protein (Potential)				785
Q9XSP1 UniProt NPD GO	KCNE1_FELCA	Potassium voltage-gated channel subfamily E member 1 (IKs producing slow voltage-gated potassium cha ...	0.09	-	mit	1 *	Membrane; single-pass type I membrane protein				129
Q9H3M0 UniProt NPD GO	KCNF1_HUMAN	Potassium voltage-gated channel subfamily F member 1 (Voltage-gated potassium channel subunit Kv5.1) ...	0.09	-	end	4	Membrane; multi-pass membrane protein		603787		494
Q13412 UniProt NPD GO	3CL_HUMAN	Pre-T/NK cell-associated protein 3Cl	0.09	-	mit	0					51
Q75BY3 UniProt NPD GO	PRP46_ASHGO	Pre-mRNA-splicing factor PRP46 (Pre-mRNA-processing protein 46)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				425
Q6C709 UniProt NPD GO	PRP46_YARLI	Pre-mRNA-splicing factor PRP46 (Pre-mRNA-processing protein 46)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				472
Q28755 UniProt NPD GO	PAG1_SHEEP	Pregnancy-associated glycoprotein 1 precursor (EC 3.4.23.-) (PAG 1)	0.09	-	end	0	Secreted protein; extracellular space				382
P83497 UniProt NPD GO	PA66E_SHEEP	Pregnancy-associated glycoprotein 66e (EC 3.4.23.-) (ovPAG 66e) (Fragment)	0.09	-		0					15
P49769 UniProt NPD GO	PSN1_MOUSE	Presenilin-1 (EC 3.4.23.-) (PS-1) (Protein S182) [Contains: Presenilin-1 NTF subunit; Presenilin-1 C ...	0.09	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	axon [IDA] cell soma [IDA] ciliary rootlet [IDA] cytoplasmic vesicle [IDA] dendrite [IDA] endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to nuclear inner membrane [ISS] integral to plasma membrane [ISS] intracellular [IDA] kinetochore [ISS] membrane [IDA] membrane fraction [ISS] mitochondrion [ISS] nucleus [IDA]			467
P79802 UniProt NPD GO	PSN1_MICMU	Presenilin-1 (EC 3.4.23.-) (PS-1) [Contains: Presenilin-1 NTF subunit; Presenilin-1 CTF subunit; Pre ...	0.09	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to nuclear inner membrane [ISS] integral to plasma membrane [ISS] kinetochore [ISS] membrane fraction [ISS] mitochondrion [ISS]			467
O12976 UniProt NPD GO	PSN1_XENLA	Presenilin-1 (EC 3.4.23.-) (Presenilin alpha) (PS-alpha)	0.09	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to nuclear inner membrane [ISS] integral to plasma membrane [ISS] kinetochore [ISS] membrane fraction [ISS] mitochondrion [ISS]			433
O13035 UniProt NPD GO	SAP_CHICK	Proactivator polypeptide precursor [Contains: Saposin A; Saposin B; Saposin C; Saposin D]	0.09	-	exc	0	Lysosome (By similarity)				518
Q9VPS5 UniProt NPD GO	CH60B_DROME	Probable 60 kDa heat shock protein homolog 1, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (C ...	0.09	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				648
Q9P7W3 UniProt NPD GO	ACL1_SCHPO	Probable ATP-citrate synthase subunit 1 (EC 2.3.3.8) (ATP-citrate (pro-S-)-lyase 1) (Citrate cleavag ...	0.09	-	cyt	0	Cytoplasm (By similarity)				615
O78474 UniProt NPD GO	ABCX_GUITH	Probable ATP-dependent transporter ycf16	0.09	-	cyt	0	Plastid; chloroplast				253
Q694B4 UniProt NPD GO	ABEC2_PONPY	Probable C->U-editing enzyme APOBEC-2 (EC 3.5.4.-)	0.09	-	cyt	0					224
O22870 UniProt NPD GO	FKBP2_ARATH	Probable FKBP-type peptidyl-prolyl cis-trans isomerase 2, chloroplast precursor (EC 5.2.1.8) (PPIase ...	0.09	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen	thylakoid lumen (sensu Viridiplantae) [IDA]			223
Q8IZF4 UniProt NPD GO	GP114_HUMAN	Probable G-protein coupled receptor 114 precursor (G-protein coupled receptor PGR27)	0.09	-	end	6	Membrane; multi-pass membrane protein	integral to membrane [TAS]			570
Q9GZN0 UniProt NPD GO	GPR88_HUMAN	Probable G-protein coupled receptor 88 (Striatum-specific G-protein coupled receptor)	0.09	-	end	6 *	Membrane; multi-pass membrane protein		607468		384
Q9FSC1 UniProt NPD GO	ACS4_RUTGR	Probable acridone synthase 4 (EC 2.3.1.159) (Acridone synthase IV)	0.09	-	cyt	0					391
Q9SV31 UniProt NPD GO	PIP25_ARATH	Probable aquaporin PIP2.5 (Plasma membrane intrinsic protein 2d) (PIP2d)	0.09	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				286
Q9ZVX8 UniProt NPD GO	PIP28_ARATH	Probable aquaporin PIP2.8 (Plasma membrane intrinsic protein 3b) (PIP3b)	0.09	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				278
Q07747 UniProt NPD GO	AAD4_YEAST	Probable aryl-alcohol dehydrogenase AAD4 (EC 1.1.1.-)	0.09	-	cyt	0					329
Q9VQD2 UniProt NPD GO	CP391_DROME	Probable cytochrome P450 309a1 (EC 1.14.-.-) (CYPCCCIXA1)	0.09	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				529
Q9V774 UniProt NPD GO	C6A21_DROME	Probable cytochrome P450 6a21 (EC 1.14.-.-) (CYPVIA21)	0.09	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				504
Q23240 UniProt NPD GO	CYC2_CAEEL	Probable cytochrome c	0.09	-	cyt	0	Mitochondrion; mitochondrial matrix (Potential)				123
P36180 UniProt NPD GO	CCBS_MARPO	Probable cytochrome c biosynthesis protein	0.09	-	end	9 *					509
Q9VIU7 UniProt NPD GO	DPM1_DROME	Probable dolichol-phosphate mannosyltransferase (EC 2.4.1.83) (Dolichol-phosphate mannose synthase) ...	0.09	-	cyt	0	Endoplasmic reticulum (By similarity)				241
Q09605 UniProt NPD GO	LEC7_CAEEL	Probable galaptin lec-7	0.09	-	cyt	0					179
Q09740 UniProt NPD GO	GFA1_SCHPO	Probable glucosamine--fructose-6-phosphate aminotransferase [isomerizing] (EC 2.6.1.16) (Hexosephosp ...	0.09	-	cyt	0					695
Q9N4X8 UniProt NPD GO	GSTPA_CAEEL	Probable glutathione S-transferase P 10 (EC 2.5.1.18) (GST class-pi)	0.09	-	cyt	0					210
Q9T071 UniProt NPD GO	HXKL_ARATH	Probable hexokinase-like protein (EC 2.7.1.1)	0.09	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				493
Q9FJE8 UniProt NPD GO	H2A7_ARATH	Probable histone H2A.7 (HTA6)	0.09	-	nuc	0	Nucleus (By similarity)				150
Q8LLP5 UniProt NPD GO	H2AXA_ORYSA	Probable histone H2AXa	0.09	-	cyt	0	Nucleus (By similarity)				137
Q8LQM5 UniProt NPD GO	GH31_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.1 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.09	-	cyt	0					610
P50095 UniProt NPD GO	IMDH3_YEAST	Probable inosine-5'-monophosphate dehydrogenase IMD3 (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMP ...	0.09	-	cyt	0		cytoplasm [IDA]			523
Q58CU4 UniProt NPD GO	ZDH16_BOVIN	Probable palmitoyltransferase ZDHHC16 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 16) ( ...	0.09	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				377

You are viewing entries 66801 to 66850 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.