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
O75131 UniProt NPD GO	CPNE3_HUMAN	Copine-3 (Copine III)	0.37	-	mit	0		cytoplasm [NAS] cytosol [IDA]	604207		537
Q9D2V7 UniProt NPD GO	CORO7_MOUSE	Coronin-7 (70 kDa WD repeat tumor rejection antigen homolog)	0.37	-	mit	0	Cytoplasm; cytosol. Predominantly. Membrane. Also found in membrane fractions. Detected on vesicle-l ...	Golgi apparatus [IDA] integral to membrane of membrane fraction [IDA] soluble fraction [IDA]			922
Q06440 UniProt NPD GO	CORO_YEAST	Coronin-like protein	0.37	-	nuc	0		actin cortical patch [IDA]			651
Q9R066 UniProt NPD GO	CXAR_RAT	Coxsackievirus and adenovirus receptor homolog precursor (rCAR)	0.37	-	exc	1	Cell membrane; cell-cell junction; single-pass type I membrane protein (By similarity). Localized at ...	tight junction [IDA]			365
Q02498 UniProt NPD GO	CRU1_RAPSA	Cruciferin PGCRURSE5 precursor (11S globulin) (12S storage protein) [Contains: Cruciferin PGCRURSE5 ...	0.37	-	exc	0					479
Q651U1 UniProt NPD GO	CRYD_ORYSA	Cryptochrome DASH, chloroplast/mitochondrial precursor	0.37	-	mit	0	Plastid; chloroplast (By similarity). Mitochondrion (By similarity)				582
P48137 UniProt NPD GO	RR13_CYAPA	Cyanelle 30S ribosomal protein S13	0.37	-	nuc	0	Plastid; cyanelle				126
Q64417 UniProt NPD GO	CP3AE_CAVPO	Cytochrome P450 3A14 (EC 1.14.14.1) (CYPIIIA14)	0.37	-	vac	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				503
Q64654 UniProt NPD GO	CP51A_RAT	Cytochrome P450 51A1 (EC 1.14.13.70) (CYPLI) (P450LI) (Sterol 14-alpha demethylase) (Lanosterol 14-a ...	0.37	-	end	1 *	Microsome (Potential)				503
P30610 UniProt NPD GO	CP52H_CANTR	Cytochrome P450 52A8 (EC 1.14.14.-) (CYPLIIA8) (Alkane-inducible P450-ALK5)	0.37	+	cyt	1 *					517
Q964Q7 UniProt NPD GO	CP6D3_MUSDO	Cytochrome P450 6d3 (EC 1.14.-.-) (CYPVID3) (Pyrethroid resistance cytochrome P450)	0.37	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				520
O64635 UniProt NPD GO	C76C4_ARATH	Cytochrome P450 76C4 (EC 1.14.-.-)	0.37	-	mit	1 *					511
Q69F95 UniProt NPD GO	C85A_PHAVU	Cytochrome P450 85A (EC 1.14.-.-) (C6-oxidase)	0.37	-	end	1 *					466
Q9LUW6 UniProt NPD GO	RH9_ARATH	DEAD-box ATP-dependent RNA helicase 9 (EC 3.6.1.-)	0.37	+	mit	0					610
Q9BY27 UniProt NPD GO	DGC6L_HUMAN	DGCR6L protein (DiGeorge syndrome critical region 6-like protein)	0.37	-	nuc	0	Nucleus. Predominantly		609459		220
Q9AXT8 UniProt NPD GO	CMT1_MAIZE	DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) (Chromomethylase 1) (Zea methyltransferase2) (Zme ...	0.37	+	mit	0	Nucleus (By similarity)				912
O14717 UniProt NPD GO	DNMT2_HUMAN	DNA (cytosine-5)-methyltransferase-like protein 2 (Dnmt2) (DNA methyltransferase homolog HsaIIP) (DN ...	0.37	-	cyt	0	Nucleus (Probable)		602478	1G55	391
Q694C1 UniProt NPD GO	ABC3G_GORGO	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.37	-	cyt	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				384
Q694C2 UniProt NPD GO	ABC3G_MACFA	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.37	-	mit	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				384
Q694B6 UniProt NPD GO	ABC3G_PANPA	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.37	-	cyt	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				384
Q7YR24 UniProt NPD GO	ABC3G_PANTR	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.37	-	cyt	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				384
Q9HC16 UniProt NPD GO	ABC3G_HUMAN	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-) (APOBEC-related cytidine deaminase) (ARCD) (APOBEC- ...	0.37	-	mit	0	Cytoplasm. Mainly. Nucleus. Small amount are found in the nucleus. During HIV-1 infection, virion-en ...		607113		384
Q9LQQ2 UniProt NPD GO	RA51D_ARATH	DNA repair protein RAD51 homolog 4 (AtRAD51D)	0.37	-	nuc	0	Nucleus (By similarity)				322
Q9UUL2 UniProt NPD GO	RAD57_SCHPO	DNA repair protein rhp57 (RAD57 homolog)	0.37	-	nuc	0	Nucleus (Potential)				354
P29372 UniProt NPD GO	3MG_HUMAN	DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase) (ADPG) (3-alkyladeni ...	0.37	-	nuc	0	Nucleus (Potential)	nucleoplasm [TAS]	156565	1F6O	298
Q92383 UniProt NPD GO	MAG1_SCHPO	DNA-3-methyladenine glycosylase 1 (EC 3.2.2.21) (3-methyladenine DNA glycosidase 1) (3MEA DNA glycos ...	0.37	-	nuc	0					228
P05476 UniProt NPD GO	TRF1_KLULA	DNA-binding protein TRF1 (Terminal region recognition factor 1)	0.37	-	nuc	0					103
Q02363 UniProt NPD GO	ID2_HUMAN	DNA-binding protein inhibitor ID-2 (Inhibitor of DNA binding 2)	0.37	-	nuc	0	Nucleus	nucleus [IC]	600386		134
Q4R5J7 UniProt NPD GO	ID2_MACFA	DNA-binding protein inhibitor ID-2 (Inhibitor of DNA binding 2)	0.37	-	nuc	0	Nucleus (By similarity)				134
Q5RCH7 UniProt NPD GO	ID2_PONPY	DNA-binding protein inhibitor ID-2 (Inhibitor of DNA binding 2)	0.37	-	nuc	0	Nucleus (By similarity)				134
P25167 UniProt NPD GO	RPC2_DROME	DNA-directed RNA polymerase III 128 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subunit 2)	0.37	-	cyt	0	Nucleus				1137
Q8SL86 UniProt NPD GO	RPOA_EUGVI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.37	-	mit	0	Plastid; chloroplast				214
O78484 UniProt NPD GO	RPOC1_GUITH	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.37	-	cyt	0	Plastid; chloroplast				623
Q6FQA6 UniProt NPD GO	RPB5_CANGA	DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.37	-	cyt	0	Nucleus (By similarity)				215
P78560 UniProt NPD GO	CRADD_HUMAN	Death domain-containing protein CRADD (Caspase and RIP adapter with death domain) (RIP-associated pr ...	0.37	-	cyt	0			603454	3CRD	199
Q9QX60 UniProt NPD GO	DGUOK_MOUSE	Deoxyguanosine kinase, mitochondrial precursor (EC 2.7.1.113) (dGK)	0.37	-	mit	0	Isoform 1: Mitochondrion. Isoform 2: Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			277
P42781 UniProt NPD GO	XPR6_YARLI	Dibasic-processing endoprotease precursor (EC 3.4.21.-)	0.37	+	end	1	Membrane; multi-pass membrane protein (Potential)				976
Q6C0S8 UniProt NPD GO	DPH1_YARLI	Diphthamide biosynthesis protein 1	0.37	-	cyt	0	Cytoplasm (By similarity)				439
Q14689 UniProt NPD GO	DIP2A_HUMAN	Disco-interacting protein 2 homolog A	0.37	-	end	0	Nucleus (Potential)		607711		1571
Q8BWT5 UniProt NPD GO	DIP2A_MOUSE	Disco-interacting protein 2 homolog A	0.37	-	end	0	Nucleus (Potential)				1523
Q9VLK4 UniProt NPD GO	DIUX_DROME	Diuretic hormone class-II precursor (Diuretic peptide) (DP) (DH(31))	0.37	-	exc	1 *	Secreted protein (By similarity)				116
Q5E954 UniProt NPD GO	DNJA1_BOVIN	DnaJ homolog subfamily A member 1	0.37	-	cyt	0	Membrane; lipid-anchor (Potential)				397
Q80TN4 UniProt NPD GO	DJC16_MOUSE	DnaJ homolog subfamily C member 16 precursor	0.37	-	end	1 *	Membrane; single-pass type IV membrane protein (Potential)			2CUG	772
P57055 UniProt NPD GO	DSCR6_HUMAN	Down syndrome critical region protein 6	0.37	-	nuc	0			609892		190
P36507 UniProt NPD GO	MP2K2_HUMAN	Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.12.2) (MAP kinase kinase 2) (MAPK ...	0.37	-	mit	0		extracellular region [NAS]	601263	1S9I	400
Q9GZS0 UniProt NPD GO	DNAI2_HUMAN	Dynein intermediate chain 2, axonemal (Axonemal dynein intermediate chain 2)	0.37	-	nuc	0		axonemal dynein complex [IMP] cilium axoneme [IMP]	605483		605
P16581 UniProt NPD GO	LYAM2_HUMAN	E-selectin precursor (Endothelial leukocyte adhesion molecule 1) (ELAM-1) (Leukocyte-endothelial cel ...	0.37	-	mit	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	131210	1KJA	610
Q6IE77 UniProt NPD GO	NEIL2_BOVIN	Endonuclease VIII-like 2 (EC 3.2.2.-) (EC 4.2.99.18) (Nei-like 2) (DNA glycosylase/AP lyase Neil2) ( ...	0.37	-	cyt	0	Nucleus (By similarity)				328
Q4PZA2 UniProt NPD GO	ECE1_MOUSE	Endothelin-converting enzyme 1 (EC 3.4.24.71) (ECE-1)	0.37	-	mit	1	Membrane; single-pass type II membrane protein (By similarity)				769
P98073 UniProt NPD GO	ENTK_HUMAN	Enteropeptidase precursor (EC 3.4.21.9) (Enterokinase) [Contains: Enteropeptidase non-catalytic heav ...	0.37	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)	brush border [TAS]	606635		1019

You are viewing entries 34101 to 34150 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.