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
Q523C3 UniProt NPD GO	ATG4_MAGGR	Cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.40	-	nuc	0	Cytoplasm (By similarity)				572
Q7T3Q2 UniProt NPD GO	CRIM1_BRARE	Cysteine-rich motor neuron 1 protein precursor (CRIM-1)	0.40	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				1027
Q95078 UniProt NPD GO	CP18A_DROME	Cytochrome P450 18a1 (EC 1.14.-.-) (CYPXVIIIA1)	0.40	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				538
Q01741 UniProt NPD GO	CP1A2_CHICK	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2) (Fragment)	0.40	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				258
Q02318 UniProt NPD GO	CP27A_HUMAN	Cytochrome P450 27, mitochondrial precursor (EC 1.14.13.15) (Cytochrome P-450C27/25) (Sterol 26-hydr ...	0.40	-	nuc	0	Mitochondrion		213700	1MFX	531
P24903 UniProt NPD GO	CP2F1_HUMAN	Cytochrome P450 2F1 (EC 1.14.14.1) (CYPIIF1)	0.40	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		124070		491
Q462Q7 UniProt NPD GO	COX19_PARBR	Cytochrome c oxidase assembly protein COX19	0.40	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial intermembrane space (By similarity)				107
P07143 UniProt NPD GO	CY1_YEAST	Cytochrome c1, heme protein, mitochondrial precursor (Ubiquinol-cytochrome-c reductase complex cytoc ...	0.40	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein; intermembrane side	respiratory chain complex III (sensu Eukary... [IDA]		1P84	309
P35462 UniProt NPD GO	DRD3_HUMAN	D(3) dopamine receptor	0.40	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	126451		400
Q5IS72 UniProt NPD GO	DRD3_PANTR	D(3) dopamine receptor	0.40	-	end	7 *	Membrane; multi-pass membrane protein				400
Q42463 UniProt NPD GO	DCL_LYCES	DCL protein, chloroplast precursor (Defective chloroplasts and leaves protein)	0.40	+	mit	0	Plastid; chloroplast				224
Q3E9C3 UniProt NPD GO	RH58_ARATH	DEAD-box ATP-dependent RNA helicase 58, chloroplast precursor (EC 3.6.1.-)	0.40	-	mit	0					472
Q41382 UniProt NPD GO	RH7_SPIOL	DEAD-box ATP-dependent RNA helicase 7 (EC 3.6.1.-)	0.40	+	cyt	0	Nucleus				685
Q8RXK6 UniProt NPD GO	RH8_ARATH	DEAD-box ATP-dependent RNA helicase 8 (EC 3.6.1.-)	0.40	-	cyt	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				505
Q6EI05 UniProt NPD GO	GAIPB_CUCMA	DELLA protein GAIP-B (Gibberellic acid-insensitive phloem protein B) (GAIP-B) (CmGAIP-B)	0.40	-	nuc	0	Nucleus (By similarity)				587
Q6DRD3 UniProt NPD GO	DPOLB_BRARE	DNA polymerase beta (EC 2.7.7.7) (EC 4.2.99.-)	0.40	-	nuc	0	Nucleus (By similarity)				336
P27344 UniProt NPD GO	DPB3_YEAST	DNA polymerase epsilon subunit C (EC 2.7.7.7) (DNA polymerase II subunit C)	0.40	-	nuc	0	Nucleus	epsilon DNA polymerase complex [IDA] replication fork [TAS]			201
P33993 UniProt NPD GO	MCM7_HUMAN	DNA replication licensing factor MCM7 (CDC47 homolog) (P1.1-MCM3)	0.40	-	cyt	0	Nucleus (By similarity)	chromatin [TAS]	600592		719
O75001 UniProt NPD GO	MCM7_SCHPO	DNA replication licensing factor mcm7 (Minichromosome maintenance protein 7)	0.40	-	nuc	0	Nucleus	MCM complex [IDA]			760
Q7ZXB1 UniProt NPD GO	MCM7B_XENLA	DNA replication licensing factor mcm7-B (Minichromosome maintenance protein 7-B) (xMCM7-B) (CDC47 ho ...	0.40	-	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [IDA] MCM complex [IDA]			720
Q04841 UniProt NPD GO	3MG_MOUSE	DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase) (ADPG) (3-alkyladeni ...	0.40	-	nuc	0	Nucleus (Potential)				333
P97760 UniProt NPD GO	RPB3_MOUSE	DNA-directed RNA polymerase II 33 kDa polypeptide (EC 2.7.7.6) (RPB3) (RNA polymerase II subunit 3) ...	0.40	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			275
P05423 UniProt NPD GO	RPO3D_HUMAN	DNA-directed RNA polymerase III subunit D (EC 2.7.7.6) (DNA-directed RNA polymerase III 47 kDa polyp ...	0.40	-	nuc	0	Nucleus		187280		398
Q85FJ1 UniProt NPD GO	RPOA_ADICA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.40	-	cyt	0	Plastid; chloroplast				345
Q2L938 UniProt NPD GO	RPOA_GOSHI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.40	-	mit	0	Plastid; chloroplast				329
O78485 UniProt NPD GO	RPOB_GUITH	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.40	-	mit	0	Plastid; chloroplast				1096
Q5QA71 UniProt NPD GO	RPOC1_ACOGR	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.40	-	cyt	0	Plastid; chloroplast				682
P56763 UniProt NPD GO	RPOC1_ARATH	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.40	-	cyt	0	Plastid; chloroplast				680
Q5T2R2 UniProt NPD GO	DPS1_HUMAN	Decaprenyl-diphosphate synthase subunit 1 (EC 2.5.1.-) (Decaprenyl pyrophosphate synthetase subunit ...	0.40	-	mit	0			607429		415
Q9FJ93 UniProt NPD GO	DRE1D_ARATH	Dehydration-responsive element-binding protein 1D (DREB1D protein) (C-repeat-binding factor 4) (C-re ...	0.40	-	nuc	0	Nucleus (Probable)				224
O80917 UniProt NPD GO	DRE2E_ARATH	Dehydration-responsive element-binding protein 2E (DREB2E protein)	0.40	-	cyt	0	Nucleus (Probable)				244
Q60997 UniProt NPD GO	DMBT1_MOUSE	Deleted in malignant brain tumors 1 protein precursor (CRP-ductin) (Vomeroglandin)	0.40	-	nuc	1	Secreted protein (By similarity). Membrane (By similarity). Localized to the lumenal aspect of crypt ...	extracellular matrix (sensu Metazoa) [IDA] intracellular [IDA]			2085
O64404 UniProt NPD GO	TPSD4_ABIGR	Delta-selinene synthase (EC 4.2.3.-) (Agfdsel1)	0.40	-	cyt	0	Cytoplasm (Probable)				581
Q6W0C5 UniProt NPD GO	DPPA3_HUMAN	Developmental pluripotency-associated protein 3 (Stella-related protein)	0.40	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)		608408		159
P49619 UniProt NPD GO	DGKG_HUMAN	Diacylglycerol kinase gamma (EC 2.7.1.107) (Diglyceride kinase gamma) (DGK-gamma) (DAG kinase gamma) ...	0.40	-	cyt	0	Cytoplasm. Membrane. Can be loosely bound to the membranes		601854		791
P22316 UniProt NPD GO	CAC1S_CYPCA	Dihydropyridine-sensitive L-type, skeletal muscle calcium channel alpha-1 subunit	0.40	+	end	22 *	Membrane; multi-pass membrane protein				1852
Q99321 UniProt NPD GO	DDP1_YEAST	Diphosphoinositol polyphosphate phosphohydrolase DDP1 (EC 3.6.1.52) (Diadenosine and diphosphoinosit ...	0.40	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			187
Q62967 UniProt NPD GO	ERG19_RAT	Diphosphomevalonate decarboxylase (EC 4.1.1.33) (Mevalonate pyrophosphate decarboxylase) (Mevalonate ...	0.40	-	cyt	0		cytosol [IDA] peroxisomal matrix [IDA]			401
Q4IQ72 UniProt NPD GO	DPH1_GIBZE	Diphthamide biosynthesis protein 1	0.40	-	cyt	0	Cytoplasm (By similarity)				462
O64973 UniProt NPD GO	RPS5_ARATH	Disease resistance protein RPS5 (Resistance to Pseudomonas syringae protein 5) (pNd3/pNd10)	0.40	-	cyt	0					889
Q9ZV33 UniProt NPD GO	DOF22_ARATH	Dof zinc finger protein DOF2.2 (AtDOF2.2)	0.40	-	nuc	0	Nucleus (Probable)				340
Q8W1E3 UniProt NPD GO	DOF55_ARATH	Dof zinc finger protein DOF5.5 (AtDOF5.5)	0.40	-	nuc	0	Nucleus (Probable)				298
Q14184 UniProt NPD GO	DOC2B_HUMAN	Double C2-like domain-containing protein beta (Doc2-beta)	0.40	-	nuc	0	Membrane; peripheral membrane protein (By similarity)		604568		412
P08481 UniProt NPD GO	IPSG_PANLE	Double-headed protease inhibitor, submandibular gland	0.40	-	nuc	0	Secreted protein				112
Q5HYR2 UniProt NPD GO	DMRTC_HUMAN	Doublesex- and mab-3-related transcription factor C1	0.40	-	nuc	0					192
Q39578 UniProt NPD GO	DYI2_CHLRE	Dynein, 78 kDa intermediate chain, flagellar outer arm (IC78)	0.40	-	nuc	0					682
Q9BQY9 UniProt NPD GO	DBND2_HUMAN	Dysbindin domain-containing protein 2 (HSMNP1)	0.40	-	nuc	0					261
P98105 UniProt NPD GO	LYAM2_RAT	E-selectin precursor (Endothelial leukocyte adhesion molecule 1) (ELAM-1) (Leukocyte-endothelial cel ...	0.40	-	exc	1 *	Membrane; single-pass type I membrane protein				549
P22794 UniProt NPD GO	EVI2A_HUMAN	EVI2A protein precursor (Ecotropic viral integration site 2A protein)	0.40	-	nuc	1 *	Membrane; single-pass type I membrane protein		158380		232
O73694 UniProt NPD GO	EGR1_SERCA	Early growth response protein 1 (EGR-1) (Zinc finger protein ZENK) (Fragment)	0.40	-	mit	0	Nucleus				59

You are viewing entries 31751 to 31800 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.