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
O94588 UniProt NPD GO	CUF2_SCHPO	Copper-binding regulatory protein cuf2 (Copper homeostasis protein)	0.35	-	nuc	0	Nucleus (Potential)				177
Q84KJ5 UniProt NPD GO	CRYD_ARATH	Cryptochrome DASH, chloroplast/mitochondrial precursor	0.35	-	mit	0	Plastid; chloroplast. Mitochondrion				569
Q09455 UniProt NPD GO	COL39_CAEEL	Cuticle collagen 39 precursor	0.35	-	nuc	1 *					323
P48131 UniProt NPD GO	RK36_CYAPA	Cyanelle 50S ribosomal protein L36	0.35	-	nuc	0	Plastid; cyanelle				37
Q9Z2V9 UniProt NPD GO	CCNI_MOUSE	Cyclin-I	0.35	-	nuc	0					377
Q99P39 UniProt NPD GO	NFS1_RAT	Cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7)	0.35	-	mit	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				451
Q6NWZ9 UniProt NPD GO	CDO1_BRARE	Cysteine dioxygenase type 1 (EC 1.13.11.20) (Cysteine dioxygenase type I) (CDO) (CDO-I)	0.35	-	nuc	0					201
Q5ZIW7 UniProt NPD GO	ATG4A_CHICK	Cysteine protease ATG4A (EC 3.4.22.-) (Autophagy-related protein 4 homolog A)	0.35	-	cyt	0	Cytoplasm (Probable)				380
Q01532 UniProt NPD GO	BLH1_YEAST	Cysteine proteinase 1 (EC 3.4.22.40) (Y3) (Bleomycin hydrolase) (BLM hydrolase)	0.35	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]		3GCB	454
Q9UKJ5 UniProt NPD GO	CHIC2_HUMAN	Cysteine-rich hydrophobic domain 2 protein (BrX-like translocated in leukemia)	0.35	-	cyt	1	Cell membrane. Cytoplasmic vesicle. Also present at a Golgi-like vesicular compartment and at scatte ...		604332		165
Q9NZV1 UniProt NPD GO	CRIM1_HUMAN	Cysteine-rich motor neuron 1 protein precursor (CRIM-1) (Cysteine-rich repeat-containing protein S52 ...	0.35	-	exc	1 *	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein. A soluble N-te ...	integral to membrane [TAS]	606189		1036
P84805 UniProt NPD GO	CRV25_NAJKA	Cysteine-rich venom protein 25 (CRVP-25k) (Fragment)	0.35	-	nuc	0	Secreted protein	extracellular region [IDA]			25
Q924T8 UniProt NPD GO	CLTR1_RAT	Cysteinyl leukotriene receptor 1 (CysLTR1)	0.35	-	end	7 *	Membrane; multi-pass membrane protein				339
P15538 UniProt NPD GO	C11B1_HUMAN	Cytochrome P450 11B1, mitochondrial precursor (EC 1.14.15.4) (CYPXIB1) (P450C11) (P-450c11) (Steroid ...	0.35	-	mit	0	Mitochondrion		202010		503
P00185 UniProt NPD GO	CP1A1_RAT	Cytochrome P450 1A1 (EC 1.14.14.1) (CYP1A1) (CYPIA1) (P450-C) (P450MT2) [Contains: Cytochrome P450MT ...	0.35	-	end	0	Cytochrome P450 1A1: Cytoplasm. Cytochrome P450MT2A, cytochrome P450MT2B: Endoplasmic reticulum. Cyt ...				524
P33616 UniProt NPD GO	CP1A1_MACFA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.35	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				512
P24453 UniProt NPD GO	CP1A2_MESAU	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2) (P450-MC4) (Hepatic cytochrome P-450MC1)	0.35	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				512
P33266 UniProt NPD GO	CP2E1_MACFA	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1) (P450-MKJ1) (Fragment)	0.35	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				449
Q6ENA8 UniProt NPD GO	CCSA_ORYNI	Cytochrome c biogenesis protein ccsA	0.35	-	end	7 *	Plastid; chloroplast				321
P12215 UniProt NPD GO	CCSA_ORYSA	Cytochrome c biogenesis protein ccsA	0.35	-	end	7 *	Plastid; chloroplast				321
Q00873 UniProt NPD GO	CYT2_YEAST	Cytochrome c1 heme lyase (EC 4.4.1.-) (CC1HL)	0.35	-	nuc	0	Mitochondrion; mitochondrial inner membrane. Partially exposed to the intermembrane space	mitochondrial intermembrane space [IDA]			224
Q9PW70 UniProt NPD GO	CISH_CHICK	Cytokine-inducible SH2-containing protein (CIS) (CIS-1) (Suppressor of cytokine signaling) (SOCS)	0.35	-	nuc	0					249
Q96GG9 UniProt NPD GO	DCNL1_HUMAN	DCN1-like protein 1 (Defective in cullin neddylation protein 1-like protein 1) (DCUN1 domain-contain ...	0.35	-	cyt	0			605905		259
Q9QZ73 UniProt NPD GO	DCNL1_MOUSE	DCN1-like protein 1 (Defective in cullin neddylation protein 1-like protein 1) (DCUN1 domain-contain ...	0.35	-	cyt	0					259
Q74ZB0 UniProt NPD GO	MEC3_ASHGO	DNA damage checkpoint control protein MEC3	0.35	-	nuc	0	Nucleus (Potential)				387
P54275 UniProt NPD GO	MSH2_RAT	DNA mismatch repair protein Msh2 (MutS protein homolog 2)	0.35	-	nuc	0		nucleus [ISS]			933
Q9W088 UniProt NPD GO	DPOD2_DROME	DNA polymerase delta small subunit (EC 2.7.7.7)	0.35	-	cyt	0	Nucleus (By similarity)				431
P40359 UniProt NPD GO	PSF2_YEAST	DNA replication complex GINS protein PSF2 (Partner of Sld five 2)	0.35	-	cyt	0	Nucleus	GINS complex [IPI] nucleus [IDA]			213
P41136 UniProt NPD GO	ID2_MOUSE	DNA-binding protein inhibitor ID-2 (Inhibitor of DNA binding 2)	0.35	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			134
P13469 UniProt NPD GO	MODU_DROME	DNA-binding protein modulo	0.35	-	nuc	0	Nucleus				542
Q49KW6 UniProt NPD GO	RPOA_EUCGG	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.35	-	mit	0	Plastid; chloroplast				337
Q9BBQ4 UniProt NPD GO	RPOA_LOTJA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.35	-	mit	0	Plastid; chloroplast				333
Q4MY95 UniProt NPD GO	RPOB_THEPA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6)	0.35	-	nuc	0	Plastid; apicoplast				1005
P42080 UniProt NPD GO	RPOC1_CYAPA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.35	+	cyt	0	Plastid; cyanelle				636
P51251 UniProt NPD GO	RPOC1_PORPU	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.35	-	cyt	0	Plastid; chloroplast				629
Q8WWB3 UniProt NPD GO	DYDC1_HUMAN	DPY30 domain-containing protein 1 (RSD-9)	0.35	-	nuc	0					177
Q5R6I4 UniProt NPD GO	CRADD_PONPY	Death domain-containing protein CRADD (Caspase and RIP adapter with death domain)	0.35	-	cyt	0					199
Q9LN86 UniProt NPD GO	DRE1F_ARATH	Dehydration-responsive element-binding protein 1F (DREB1F protein)	0.35	-	nuc	0	Nucleus (Probable)				209
P30185 UniProt NPD GO	DHR18_ARATH	Dehydrin Rab18	0.35	-	cyt	0					186
Q25540 UniProt NPD GO	GRA2_NEOCA	Dense granule protein 2 (NcDG2) (Antigen Nc14.1)	0.35	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				193
Q99645 UniProt NPD GO	PGLB_HUMAN	Dermatan sulfate proteoglycan 3 precursor (Epiphycan) (Small chondroitin/dermatan sulfate proteoglyc ...	0.35	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		601657		322
P33545 UniProt NPD GO	DSC2_BOVIN	Desmocollin-2 precursor (Epithelial type 2 desmocollin) (Fragment)	0.35	-	mit	1	Membrane; single-pass type I membrane protein				863
P36235 UniProt NPD GO	DISG_ORNMO	Disagregin (Platelet aggregation activation inhibitor)	0.35	-	nuc	0					60
Q96PD2 UniProt NPD GO	DCBD2_HUMAN	Discoidin, CUB and LCCL domain-containing protein 2 precursor (Endothelial and smooth muscle cell-de ...	0.35	-	mit	1 *	Membrane; single-pass type I membrane protein	cell surface [IDA] integral to plasma membrane [IDA]	608698		775
P23465 UniProt NPD GO	DIUH_LOCMI	Diuretic hormone (DH) (Diuretic peptide) (DP)	0.35	-	nuc	0	Secreted protein				46
P16226 UniProt NPD GO	IPSG_MELME	Double-headed protease inhibitor, submandibular gland	0.35	-	nuc	0	Secreted protein				122
P47809 UniProt NPD GO	MP2K4_MOUSE	Dual specificity mitogen-activated protein kinase kinase 4 (EC 2.7.12.2) (MAP kinase kinase 4) (MAPK ...	0.35	-	nuc	0					397
Q15569 UniProt NPD GO	TESK1_HUMAN	Dual specificity testis-specific protein kinase 1 (EC 2.7.12.1) (Testicular protein kinase 1)	0.35	-	nuc	0			601782		626
O95967 UniProt NPD GO	FBLN4_HUMAN	EGF-containing fibulin-like extracellular matrix protein 2 precursor (Fibulin-4) (FIBL-4) (UPH1 prot ...	0.35	-	exc	0	Secreted protein	basement membrane [TAS]	604633		443
Q9QXY6 UniProt NPD GO	EHD3_MOUSE	EH-domain-containing protein 3	0.35	-	nuc	0		endocytic vesicle [IDA]			535

You are viewing entries 35751 to 35800 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.