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
Q61330 UniProt NPD GO	CNTN2_MOUSE	Contactin-2 precursor (Axonin-1) (Axonal glycoprotein TAG-1) (Transient axonal glycoprotein 1) (TAX- ...	0.24	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Attached to the neuronal membrane by a GPI- ...	axon [IDA]			1040
Q62845 UniProt NPD GO	CNTN4_RAT	Contactin-4 precursor (Brain-derived immunoglobulin superfamily protein 2) (BIG-2)	0.24	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	axon [ISS] plasma membrane [ISS]			1026
Q99829 UniProt NPD GO	CPNE1_HUMAN	Copine-1 (Copine I)	0.24	-	cyt	0			604205		537
O46406 UniProt NPD GO	AOCY_BOVIN	Copper amine oxidase, lung isozyme precursor (EC 1.4.3.6) (Amine oxidase [copper-containing]) (BOLAO ...	0.24	-	nuc	0	Secreted protein; extracellular space (By similarity)				762
P01196 UniProt NPD GO	COLI_STRCA	Corticotropin (Adrenocorticotropic hormone) (ACTH) [Contains: Melanotropin alpha (Alpha-MSH); Cortic ...	0.24	-	nuc	0					39
Q8VHS2 UniProt NPD GO	CRUM1_MOUSE	Crumbs homolog 1 precursor	0.24	-	exc	1	Isoform 1: Membrane; single-pass type I membrane protein. In the retina, localizes to the Mueller ce ...				1405
P35352 UniProt NPD GO	CAR3_DICDI	Cyclic AMP receptor 3 (cAMP receptor 3)	0.24	-	end	7 *	Membrane; multi-pass membrane protein				490
Q9R0Z3 UniProt NPD GO	CD2A1_RAT	Cyclin-dependent kinase inhibitor 2A, isoform 1 (Cyclin-dependent kinase 4 inhibitor A) (CDK4I) (p16 ...	0.24	-	nuc	0		nucleus [NAS]			159
Q8N726 UniProt NPD GO	CD2A2_HUMAN	Cyclin-dependent kinase inhibitor 2A, isoform 4 (p14ARF) (p19ARF)	0.24	-	nuc	0	Nucleus; nucleolus (By similarity)		600160		173
P33552 UniProt NPD GO	CKS2_HUMAN	Cyclin-dependent kinases regulatory subunit 2 (CKS-2)	0.24	-	nuc	0			116901	1CKS	79
P56390 UniProt NPD GO	CKS2_MOUSE	Cyclin-dependent kinases regulatory subunit 2 (CKS-2)	0.24	-	nuc	0					79
P47164 UniProt NPD GO	MET7_YEAST	Cystathionine gamma-synthase (EC 2.5.1.48) (O-succinylhomoserine (thiol)-lyase)	0.24	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			639
Q9WV23 UniProt NPD GO	CMAH_CRIGR	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.24	-	nuc	0	Cytoplasm (By similarity)				563
P79202 UniProt NPD GO	CP11A_SHEEP	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(SCC)) (Cholesterol side ...	0.24	-	mit	0	Mitochondrion				520
P97720 UniProt NPD GO	C11B1_MESAU	Cytochrome P450 11B1, mitochondrial precursor (EC 1.14.15.4) (CYPXIB1) (P450C11) (Steroid 11-beta-hy ...	0.24	-	mit	0	Mitochondrion				499
Q29624 UniProt NPD GO	CP191_PIG	Cytochrome P450 19 type I (EC 1.14.14.1) (Aromatase) (CYPXIXA1) (Estrogen synthetase) (P-450AROM)	0.24	+	nuc	2 *	Membrane; peripheral membrane protein				503
Q92109 UniProt NPD GO	CP1A3_ONCMY	Cytochrome P450 1A3 (EC 1.14.14.1) (CYP1A3) (CYP1A1)	0.24	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				522
Q29510 UniProt NPD GO	CP2CU_RABIT	Cytochrome P450 2C30 (EC 1.14.14.1) (CYPIIC30)	0.24	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				489
P52786 UniProt NPD GO	CP2J1_RABIT	Cytochrome P450 2J1 (EC 1.14.14.1) (CYPIIJ1) (P-450IB)	0.24	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
Q12588 UniProt NPD GO	CP52J_CANMA	Cytochrome P450 52A10 (EC 1.14.14.-) (CYPLIIA10) (Alkane-inducible P450-ALK7)	0.24	-	cyt	1 *					519
O61387 UniProt NPD GO	CP6B7_HELAM	Cytochrome P450 6B7 (EC 1.14.14.1) (CYPVIB7)	0.24	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				504
Q9LTM6 UniProt NPD GO	C71BH_ARATH	Cytochrome P450 71B17 (EC 1.14.-.-)	0.24	-	mit	0					502
P93530 UniProt NPD GO	C71D6_SOLCH	Cytochrome P450 71D6 (EC 1.14.-.-)	0.24	-	nuc	0					501
O81346 UniProt NPD GO	C79B2_ARATH	Cytochrome P450 79B2 (EC 1.14.-.-)	0.24	-	nuc	1 *					541
Q964T2 UniProt NPD GO	CP9E2_BLAGE	Cytochrome P450 9e2 (EC 1.14.-.-) (CYPIXE2)	0.24	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				533
P21595 UniProt NPD GO	CP56_YEAST	Cytochrome P450-DIT2 (EC 1.14.14.-) (Cytochrome P450 56)	0.24	-	end	1 *					489
P79010 UniProt NPD GO	COX4_SCHPO	Cytochrome c oxidase polypeptide IV, mitochondrial precursor (EC 1.9.3.1)	0.24	-	mit	0	Mitochondrion; mitochondrial inner membrane				164
P10382 UniProt NPD GO	D5_DICDI	D5 protein	0.24	-	nuc	1					193
Q02574 UniProt NPD GO	MEC3_YEAST	DNA damage checkpoint control protein MEC3	0.24	-	nuc	0	Nucleus (Potential)	nucleus [TAS]			474
P43246 UniProt NPD GO	MSH2_HUMAN	DNA mismatch repair protein Msh2 (MutS protein homolog 2)	0.24	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	609309		934
Q24317 UniProt NPD GO	PRI1_DROME	DNA primase small subunit (EC 2.7.7.-) (DNA primase 50 kDa subunit) (DNA polymerase subunit A) (dPRI ...	0.24	-	cyt	0					438
Q8RY99 UniProt NPD GO	RECAM_ARATH	DNA repair protein recA homolog 2, mitochondrial precursor (Recombinase A homolog 2)	0.24	-	mit	0	Mitochondrion				389
P13099 UniProt NPD GO	TOP3_YEAST	DNA topoisomerase 3 (EC 5.99.1.2) (DNA topoisomerase III)	0.24	-	cyt	0		nucleus [IC] RecQ helicase-Topo III complex [IPI]			656
Q9Z321 UniProt NPD GO	TOP3B_MOUSE	DNA topoisomerase 3-beta-1 (EC 5.99.1.2) (DNA topoisomerase III beta-1)	0.24	-	cyt	0		condensed chromosome [IDA]			862
Q93VI0 UniProt NPD GO	S1FA3_ARATH	DNA-binding protein S1FA3	0.24	-	nuc	1 *	Nucleus (Probable)				73
Q8S8V9 UniProt NPD GO	RPOA_ATRBE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.24	-	mit	0	Plastid; chloroplast				337
O19897 UniProt NPD GO	RPOC1_CYACA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.24	-	cyt	0	Plastid; chloroplast				633
P48011 UniProt NPD GO	RPC10_SCHPO	DNA-directed RNA polymerases I, II, and III 7.3 kDa polypeptide (EC 2.7.7.6) (ABC10-alpha)	0.24	-	nuc	0	Nucleus				63
P51397 UniProt NPD GO	DAP1_HUMAN	Death-associated protein 1 (DAP-1)	0.24	-	nuc	0			600954		101
P17350 UniProt NPD GO	DECO_MACDE	Decorsin	0.24	-	nuc	0	Secreted protein			1DEC	39
Q60YT5 UniProt NPD GO	DCN1_CAEBR	Defective in cullin neddylation protein 1	0.24	-	cyt	0	Nucleus (By similarity)				292
P50714 UniProt NPD GO	DEF16_MOUSE	Defensin-related cryptdin 16 precursor	0.24	-	exc	0	Secreted protein				93
P50716 UniProt NPD GO	DFR12_MOUSE	Defensin-related cryptdin, related sequence 12 precursor (Cryptdin-related protein 4C-5) (CRS4C)	0.24	-	exc	0	Secreted protein				91
P50715 UniProt NPD GO	DEFR7_MOUSE	Defensin-related cryptdin, related sequence 7 precursor (Cryptdin-related protein 4C-2) (CRS4C)	0.24	-	exc	0	Secreted protein				91
P12952 UniProt NPD GO	DHN2_HORVU	Dehydrin DHN2 (B9)	0.24	-	nuc	0					143
P35196 UniProt NPD GO	RER2_YEAST	Dehydrodolichyl diphosphate synthetase (EC 2.5.1.-) (DEDOL-PP synthase)	0.24	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [IDA]			286
Q8NBQ5 UniProt NPD GO	DHRS8_HUMAN	Dehydrogenase/reductase SDR family member 8 precursor (EC 1.1.1.-) (17-beta-hydroxysteroid dehydroge ...	0.24	-	end	0	Secreted protein (Potential)			1YB1	300
Q9NR90 UniProt NPD GO	DAZ3_HUMAN	Deleted in azoospermia protein 3	0.24	-	cyt	0	Cytoplasm. Predominantly. Nucleus. Nuclear at some stages of spermatozoide development. Localizes bo ...		415000		486
Q86SG3 UniProt NPD GO	DAZ4_HUMAN	Deleted in azoospermia protein 4	0.24	-	cyt	0	Cytoplasm. Predominantly. Nucleus. Nuclear at some stages of spermatozoide development. Localizes bo ...		415000		579
P45623 UniProt NPD GO	HEM2_SELMA	Delta-aminolevulinic acid dehydratase, chloroplast precursor (EC 4.2.1.24) (Porphobilinogen synthase ...	0.24	-	cyt	0	Plastid; chloroplast				417

You are viewing entries 46201 to 46250 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.