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
Q61129 UniProt NPD GO	CFAI_MOUSE	Complement factor I precursor (EC 3.4.21.45) (C3B/C4B inactivator) [Contains: Complement factor I he ...	0.52	-	exc	0	Secreted protein; extracellular space				603
Q06096 UniProt NPD GO	COG4_YEAST	Conserved oligomeric Golgi complex subunit 4 (COG complex subunit 4) (Complexed with DOR1 protein 1) ...	0.52	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	Golgi transport complex [IPI]			861
Q8CIT0 UniProt NPD GO	CRF_MOUSE	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone)	0.52	-	mit	1 *	Secreted protein				187
P01143 UniProt NPD GO	CRF_RAT	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone)	0.52	-	mit	0	Secreted protein	extracellular space [TAS]			187
Q9R0L4 UniProt NPD GO	CAND2_RAT	Cullin-associated NEDD8-dissociated protein 2 (Cullin-associated and neddylation-dissociated protein ...	0.52	-	cyt	0	Nucleus	nucleus [IDA]			1273
Q07973 UniProt NPD GO	CP24A_HUMAN	Cytochrome P450 24A1, mitochondrial precursor (EC 1.14.-.-) (P450-CC24) (Vitamin D(3) 24-hydroxylase ...	0.52	-	mit	0	Mitochondrion		126065		514
Q08477 UniProt NPD GO	CP4F3_HUMAN	Cytochrome P450 4F3 (EC 1.14.13.30) (CYPIVF3) (Leukotriene-B(4) omega-hydroxylase) (Leukotriene-B(4) ...	0.52	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)		601270		520
Q6ZWL3 UniProt NPD GO	CP4V2_HUMAN	Cytochrome P450 4V2 (EC 1.14.-.-)	0.52	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)		608614		525
Q64505 UniProt NPD GO	CP7A1_MOUSE	Cytochrome P450 7A1 (EC 1.14.13.17) (Cholesterol 7-alpha-monooxygenase) (CYPVII) (Cholesterol 7-alph ...	0.52	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			503
P16443 UniProt NPD GO	DBP_RAT	D site-binding protein (Albumin D box-binding protein) (Albumin D-element-binding protein) (D site a ...	0.52	+	nuc	0	Nucleus				325
Q10586 UniProt NPD GO	DBP_HUMAN	D site-binding protein (Albumin D box-binding protein) (Albumin D-element-binding protein) (TAXREB30 ...	0.52	+	nuc	0	Nucleus		124097		325
Q6TLI9 UniProt NPD GO	DRD2_MUSPF	D(2) dopamine receptor (Dopamine D2 receptor)	0.52	-	end	7 *	Membrane; multi-pass membrane protein				443
P53453 UniProt NPD GO	DRD2L_FUGRU	D(2)-like dopamine receptor	0.52	+	end	7 *	Membrane; multi-pass membrane protein				463
Q75EQ0 UniProt NPD GO	DAM1_ASHGO	DASH complex subunit DAM1 (Outer kinetochore protein DAM1)	0.52	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				268
Q50HP3 UniProt NPD GO	SPC19_SCHPO	DASH complex subunit spc19 (Outer kinetochore protein spc19)	0.52	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore. Kinetochore associ ...	DASH complex [IDA]			152
Q94C75 UniProt NPD GO	RH25_ARATH	DEAD-box ATP-dependent RNA helicase 25 (EC 3.6.1.-)	0.52	+	nuc	0					563
Q9SMV7 UniProt NPD GO	MSH7_ARATH	DNA mismatch repair protein MSH6-2 (AtMsh6-2) (MutS homolog 7)	0.52	-	mit	0					1109
O13396 UniProt NPD GO	MSH2_NEUCR	DNA mismatch repair protein msh-2	0.52	-	mit	0					937
Q9ZWM9 UniProt NPD GO	RAV1_ARATH	DNA-binding protein RAV1	0.52	-	nuc	0	Nucleus (Probable)			1WID	344
Q42877 UniProt NPD GO	RPB2_LYCES	DNA-directed RNA polymerase II 135 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 2)	0.52	-	cyt	0	Nucleus				1191
P48118 UniProt NPD GO	RPOA_CYAPA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (RNAP alpha subunit) (Transcriptase alpha chain ...	0.52	-	cyt	0	Plastid; cyanelle				315
P51252 UniProt NPD GO	RPOB_PORPU	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.52	-	cyt	0	Plastid; chloroplast				1143
Q1XDN5 UniProt NPD GO	RPOB_PORYE	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.52	-	cyt	0	Plastid; chloroplast				1143
P11705 UniProt NPD GO	RPOC1_SPIOL	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.52	-	cyt	0	Plastid; chloroplast				677
Q9TM34 UniProt NPD GO	RPOC2_CYACA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.52	-	cyt	0	Plastid; chloroplast				1269
P53803 UniProt NPD GO	RPC10_HUMAN	DNA-directed RNA polymerases I, II, and III 7.0 kDa polypeptide (EC 2.7.7.6) (ABC10-alpha) (RPB7.0) ...	0.52	-	nuc	0	Nucleus		606033		58
P27089 UniProt NPD GO	XPA_CHICK	DNA-repair protein complementing XP-A cells homolog (Xeroderma pigmentosum group A-complementing pro ...	0.52	+	nuc	0	Nucleus				267
Q7T1H5 UniProt NPD GO	DND1_BRARE	Dead end protein 1	0.52	-	nuc	0	Cytoplasm. Perinuclear germ granules				411
P50713 UniProt NPD GO	DEF15_MOUSE	Defensin-related cryptdin 15 precursor	0.52	-	exc	0	Secreted protein				93
Q9Z1T5 UniProt NPD GO	DEAF1_MOUSE	Deformed epidermal autoregulatory factor 1 homolog (Nuclear DEAF-1-related transcriptional regulator ...	0.52	-	nuc	0	Nucleus (By similarity)	transcription factor complex [IDA]			566
O77562 UniProt NPD GO	DEAF1_PANTR	Deformed epidermal autoregulatory factor 1 homolog (Nuclear DEAF-1-related transcriptional regulator ...	0.52	-	nuc	1 *	Nucleus (By similarity)				565
O88450 UniProt NPD GO	DEAF1_RAT	Deformed epidermal autoregulatory factor 1 homolog (Nuclear DEAF-1-related transcriptional regulator ...	0.52	-	nuc	0	Nucleus. Secreted protein. Secreted in some cell types	nucleus [IMP]			565
Q8BLA1 UniProt NPD GO	DLEC1_MOUSE	Deleted in lung and esophageal cancer protein 1 homolog	0.52	-	mit	0	Cytoplasm (By similarity)	cytoplasm [ISS]			635
O55070 UniProt NPD GO	DNSL3_MOUSE	Deoxyribonuclease gamma precursor (EC 3.1.21.-) (DNase gamma) (Deoxyribonuclease I-like 3) (DNase I ...	0.52	+	end	0	Nucleus (By similarity). May first pass through the ER membrane before being imported in the nucleus ...	nucleus [IDA]			310
Q5IS50 UniProt NPD GO	DPP6_PANTR	Dipeptidyl aminopeptidase-like protein 6 (Dipeptidylpeptidase VI) (Dipeptidylpeptidase 6)	0.52	-	cyt	1 *	Membrane; single-pass type II membrane protein (Probable)				803
Q92796 UniProt NPD GO	DLG3_HUMAN	Discs large homolog 3 (Synapse-associated protein 102) (SAP102) (Neuroendocrine-DLG) (XLMR)	0.52	-	nuc	0			300189	2FE5	817
Q925T0 UniProt NPD GO	DJC12_RAT	DnaJ homolog subfamily C member 12 (J domain-containing protein 1)	0.52	-	nuc	0					198
Q03363 UniProt NPD GO	DNJH1_ALLPO	DnaJ protein homolog 1 (DNAJ-1) (Fragment)	0.52	-	nuc	0	Membrane; lipid-anchor (Potential)				397
Q8LE43 UniProt NPD GO	DOF21_ARATH	Dof zinc finger protein DOF2.1 (AtDOF2.1)	0.52	-	nuc	0	Nucleus (Probable)				288
Q9M1E6 UniProt NPD GO	DOF32_ARATH	Dof zinc finger protein DOF3.2 (AtDOF3.2)	0.52	-	nuc	0	Nucleus (Probable)				245
P38564 UniProt NPD GO	MNB1A_MAIZE	Dof zinc finger protein MNB1A	0.52	-	nuc	0	Nucleus (Probable)				238
O24463 UniProt NPD GO	PBF_MAIZE	Dof zinc finger protein PBF (Prolamin box-binding factor)	0.52	-	nuc	0	Nucleus				328
P22192 UniProt NPD GO	PAC1_SCHPO	Double-strand-specific pac1 ribonuclease (EC 3.1.26.3) (HCS protein)	0.52	-	nuc	0					363
Q9UHG0 UniProt NPD GO	DCDC2_HUMAN	Doublecortin domain-containing protein 2 (RU2S protein)	0.52	-	nuc	0			605755		476
Q9Y5R6 UniProt NPD GO	DMRT1_HUMAN	Doublesex- and mab-3-related transcription factor 1 (DM domain expressed in testis protein 1)	0.52	-	nuc	0	Nucleus (Potential)		602424		373
Q5VZB9 UniProt NPD GO	DMRTA_HUMAN	Doublesex- and mab-3-related transcription factor A1	0.52	+	nuc	0	Nucleus (Potential)				504
Q9NRD8 UniProt NPD GO	DUOX2_HUMAN	Dual oxidase 2 precursor (EC 1.6.3.1) (EC 1.11.1.-) (NADPH oxidase/peroxidase DUOX2) (NADPH thyroid ...	0.52	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein. Localizes to the apical membrane o ...	apical plasma membrane [ISS]	607200		1548
O09110 UniProt NPD GO	MP2K3_MOUSE	Dual specificity mitogen-activated protein kinase kinase 3 (EC 2.7.12.2) (MAP kinase kinase 3) (MAPK ...	0.52	-	cyt	0					347
Q62767 UniProt NPD GO	DUS4_RAT	Dual specificity protein phosphatase 4 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinase ...	0.52	-	nuc	0	Nucleus (By similarity)				395
Q63340 UniProt NPD GO	DUS7_RAT	Dual specificity protein phosphatase 7 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity protein phospha ...	0.52	-	nuc	0	Cytoplasm	cytosol [IDA]			280

You are viewing entries 23651 to 23700 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.