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
P30612 UniProt NPD GO	CP52P_CANTR	Cytochrome P450 52C1 (EC 1.14.14.-) (CYPLIIC1) (Alkane-inducible P450-ALK7)	0.53	-	mit	0					505
Q42569 UniProt NPD GO	C90A1_ARATH	Cytochrome P450 90A1 (EC 1.14.-.-)	0.53	-	mit	1 *					472
Q9V4I0 UniProt NPD GO	CP9B1_DROME	Cytochrome P450 9b1 (EC 1.14.-.-) (CYPIXB1)	0.53	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				505
Q9Y6A2 UniProt NPD GO	CP46A_HUMAN	Cytochrome p450 46A1 (EC 1.14.13.98) (Cholesterol 24-hydroxylase) (CH24H)	0.53	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	endoplasmic reticulum [TAS]	604087		500
Q32PF6 UniProt NPD GO	DBP_BOVIN	D site-binding protein (Albumin D box-binding protein) (Albumin D-element-binding protein)	0.53	+	nuc	0	Nucleus				325
Q9GJU1 UniProt NPD GO	DRD2_CANFA	D(2) dopamine receptor (Dopamine D2 receptor)	0.53	-	end	7 *	Membrane; multi-pass membrane protein				443
Q8C7W7 UniProt NPD GO	DCR1B_MOUSE	DNA cross-link repair 1B protein	0.53	-	mit	0	Nucleus (By similarity). Localizes to discrete foci (By similarity)				541
Q6CPH8 UniProt NPD GO	DPB2_KLULA	DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)	0.53	-	mit	0	Nucleus (By similarity)				710
Q9UNA4 UniProt NPD GO	POLI_HUMAN	DNA polymerase iota (EC 2.7.7.7) (RAD30 homolog B) (Eta2)	0.53	-	nuc	0	Nucleus. Accumulates at replication forks after DNA damage	nucleoplasm [TAS]	605252	2ALZ	715
Q9UJA3 UniProt NPD GO	MCM8_HUMAN	DNA replication licensing factor MCM8 (Minichromosome maintenance 8)	0.53	-	nuc	0	Nucleus		608187		840
O94666 UniProt NPD GO	RPC1_SCHPO	DNA-directed RNA polymerase III largest subunit (EC 2.7.7.6)	0.53	-	nuc	0	Nucleus (By similarity)				1405
P08968 UniProt NPD GO	RPC1_TRYBB	DNA-directed RNA polymerase III largest subunit (EC 2.7.7.6)	0.53	-	cyt	0	Nucleus				1530
Q6ENX3 UniProt NPD GO	RPOB_SACOF	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.53	-	nuc	0	Plastid; chloroplast				1075
Q8HVY5 UniProt NPD GO	RPOB_SOYBN	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.53	-	cyt	0	Plastid; chloroplast				1070
O75398 UniProt NPD GO	DEAF1_HUMAN	Deformed epidermal autoregulatory factor 1 homolog (Nuclear DEAF-1-related transcriptional regulator ...	0.53	-	nuc	1 *	Nucleus. Cytoplasmic in non-mucinous colorectal carcinoma. Isoforms 2, isoform 4: Secreted protein. ...	nucleus [TAS]	602635	2FV6	565
Q4A3R3 UniProt NPD GO	DMBT1_PIG	Deleted in malignant brain tumors 1 protein precursor	0.53	-	end	1	Secreted protein (By similarity). Membrane (By similarity). Localized to the lumenal aspect of crypt ...				1204
O89107 UniProt NPD GO	DNSL3_RAT	Deoxyribonuclease gamma precursor (EC 3.1.21.-) (DNase gamma) (Deoxyribonuclease I-like 3) (DNaseY)	0.53	-	end	1 *	Nucleus. May first pass through the ER membrane before being imported in the nucleus	nucleus [IDA]			310
Q05201 UniProt NPD GO	EYA_DROME	Developmental protein eyes absent (EC 3.1.3.48) (Protein Clift)	0.53	+	nuc	0	Nucleus	nucleus [IDA]			766
Q96EY1 UniProt NPD GO	DNJA3_HUMAN	DnaJ homolog subfamily A member 3, mitochondrial precursor (Tumorous imaginal discs protein Tid56 ho ...	0.53	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]	608382	2CTT	480
O89114 UniProt NPD GO	DNJB5_MOUSE	DnaJ homolog subfamily B member 5 (Heat shock protein Hsp40-3) (Heat shock protein cognate 40) (Hsc4 ...	0.53	-	cyt	0					348
P97554 UniProt NPD GO	DNJB9_RAT	DnaJ homolog subfamily B member 9 (Microvascular endothelial differentiation gene 1 protein) (Mdg-1) ...	0.53	-	nuc	1 *	Cytoplasm. Nucleus. Stress induces its translocation to the nucleus	cytoplasm [IDA] endoplasmic reticulum [TAS] nucleolus [IDA]			222
Q84K52 UniProt NPD GO	DOF47_ARATH	Dof zinc finger protein DOF4.7 (AtDOF4.7)	0.53	-	mit	0	Nucleus (Probable)				246
Q9TT01 UniProt NPD GO	DMRT1_PIG	Doublesex- and mab-3-related transcription factor 1	0.53	-	nuc	0	Nucleus (Potential)				373
Q9ES45 UniProt NPD GO	DUOX2_RAT	Dual oxidase 2 precursor (EC 1.6.3.1) (EC 1.11.1.-) (NADH/NADPH thyroid oxidase THOX2) (Thyroid oxid ...	0.53	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Localizes to the a ...	apical plasma membrane [ISS]			1517
Q01986 UniProt NPD GO	MP2K1_RAT	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPK ...	0.53	-	nuc	0		cytosol [IDA]			392
Q5ZLW3 UniProt NPD GO	DYM_CHICK	Dymeclin	0.53	-	end	0	Membrane; multi-pass membrane protein (Potential)				669
P39055 UniProt NPD GO	DYN1_CAEEL	Dynamin (EC 3.6.5.5)	0.53	-	nuc	0	Cytoplasm. Microtubule-associated	synapse [IDA]			830
Q7SXN5 UniProt NPD GO	DNM1L_BRARE	Dynamin-1-like protein (EC 3.6.5.5)	0.53	-	nuc	0	Cytoplasmic; mainly cytosolic. Also membrane-associated. May associate to mitochondria and peroxisom ...				691
P61556 UniProt NPD GO	EFR1_MACFA	ERV-FRD provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Syncytin-2) [Contains: ...	0.53	-	exc	2					537
Q90YC0 UniProt NPD GO	EF1G_CARAU	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.53	-	cyt	0					442
P29059 UniProt NPD GO	CHI3_TOBAC	Endochitinase 3 precursor (EC 3.2.1.14)	0.53	-	exc	0	Vacuole (Probable). Vacuolar and protoplast (Probable)				334
Q9STX5 UniProt NPD GO	ENPL_ARATH	Endoplasmin homolog precursor (GRP94 homolog) (Protein SHEPHERD) (HSP90-like protein 7)	0.53	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	mitochondrion [IDA]			823
O97177 UniProt NPD GO	ESM2_DROME	Enhancer of split M2 protein (E(spl)m2)	0.53	-	mit	0					218
Q9WV07 UniProt NPD GO	LOXE3_MOUSE	Epidermis-type lipoxygenase 3 (EC 1.13.11.-) (e-LOX-3)	0.53	-	cyt	0					711
Q61070 UniProt NPD GO	EI24_MOUSE	Etoposide-induced protein 2.4 (p53-induced protein 8)	0.53	-	end	6					358
Q96KP1 UniProt NPD GO	EXOC2_HUMAN	Exocyst complex component 2 (Exocyst complex component Sec5)	0.53	-	mit	0					924
Q9D4H1 UniProt NPD GO	EXOC2_MOUSE	Exocyst complex component 2 (Exocyst complex component Sec5)	0.53	-	mit	0		exocyst [TAS]		1HK6	924
Q6C238 UniProt NPD GO	EXO84_YARLI	Exocyst complex component EXO84	0.53	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				657
P22224 UniProt NPD GO	SEC15_YEAST	Exocyst complex component SEC15	0.53	-	cyt	0	Cytoplasm. 25%. Cell membrane; peripheral membrane protein. 75%	bud tip [IPI] exocyst [IPI]			910
Q9JKV7 UniProt NPD GO	EXTL1_MOUSE	Exostosin-like 1 (EC 2.4.1.224) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylgluc ...	0.53	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				669
Q6GMY9 UniProt NPD GO	XPO2_XENLA	Exportin-2 (Exp2) (Importin-alpha re-exporter) (Chromosome segregation 1-like protein)	0.53	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				971
Q9C0E2 UniProt NPD GO	XPO4_HUMAN	Exportin-4 (Exp4)	0.53	-	cyt	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm				1151
P70441 UniProt NPD GO	NHERF_MOUSE	Ezrin-radixin-moesin-binding phosphoprotein 50 (EBP50) (Na(+)/H(+) exchange regulatory cofactor NHE- ...	0.53	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity). Colocalizes with actin in mi ...	apical plasma membrane [IDA]			354
Q9UK96 UniProt NPD GO	FBX10_HUMAN	F-box only protein 10	0.53	-	cyt	0		ubiquitin ligase complex [NAS]	609092		954
Q8CHQ0 UniProt NPD GO	FBX4_MOUSE	F-box only protein 4	0.53	-	cyt	0					385
Q9QZN3 UniProt NPD GO	FBX8_MOUSE	F-box only protein 8	0.53	-	nuc	0		ubiquitin ligase complex [IPI]			319
O01683 UniProt NPD GO	SSP1B_CAEEL	FACT complex subunit ssrp1-B (Facilitates chromatin transcription complex subunit ssrp1-B) (Structur ...	0.53	-	nuc	0	Nucleus (By similarity)				689
P36888 UniProt NPD GO	FLT3_HUMAN	FL cytokine receptor precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor FLT3) (Stem cell tyro ...	0.53	-	vac	2	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	136351	1RJB	993
Q5SZK8 UniProt NPD GO	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2 precursor (ECM3 homolog)	0.53	-	end	1	Membrane; single-pass type I membrane protein (Potential)		608945		3169
P43592 UniProt NPD GO	FAR7_YEAST	Factor arrest protein 7	0.53	-	nuc	0					221

You are viewing entries 23051 to 23100 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.