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
Q9BXJ2 UniProt NPD GO	C1QT7_HUMAN	Complement C1q tumor necrosis factor-related protein 7 precursor	0.03	-	exc	0	Secreted protein (Potential)				289
Q8BVD7 UniProt NPD GO	C1QT7_MOUSE	Complement C1q tumor necrosis factor-related protein 7 precursor	0.03	-	exc	0	Secreted protein (Potential)	extracellular space [IDA]			289
P81364 UniProt NPD GO	CONA_CANMR	Concanavalin MA (Con MA)	0.03	-	cyt	0					236
P26788 UniProt NPD GO	LEG1_CONMY	Congerin-1 (Congerin I) (Beta-galactoside-binding lectin 1)	0.03	-	cyt	0				1C1L	135
Q9TWL8 UniProt NPD GO	COMB_CONMA	Conodipine-M beta chain	0.03	-	cyt	0	Secreted protein				42
P81727 UniProt NPD GO	CX2B_CONBE	Conotoxin BeTXIIb	0.03	-	nuc	0	Secreted protein				27
P58928 UniProt NPD GO	CXEX_CONCN	Conotoxin CcTx (Excitotoxin CcTx)	0.03	-	nuc	0	Secreted protein				30
P18512 UniProt NPD GO	CXKK1_CONTE	Conotoxin King-Kong 1 precursor (KK-1)	0.03	-	exc	0	Secreted protein				77
P0C1N6 UniProt NPD GO	CXM31_CONTE	Conotoxin Tx3.1 precursor	0.03	-	exc	1 *	Secreted protein (By similarity)				71
Q8IS41 UniProt NPD GO	CXO6B_CONVX	Conotoxin vx6b precursor	0.03	-	vac	1 *	Secreted protein				88
Q5K0B9 UniProt NPD GO	CXO2_CONIM	Conotoxin-2/7 precursor	0.03	+	exc	0	Secreted protein (By similarity)				80
P24031 UniProt NPD GO	PPA3_YEAST	Constitutive acid phosphatase precursor (EC 3.1.3.2)	0.03	-	vac	0		periplasmic space (sensu Fungi) [IMP]			467
Q9NDA5 UniProt NPD GO	COW2_CONTE	Contryphan-R/Tx precursor	0.03	-	vac	0	Secreted protein				63
P58787 UniProt NPD GO	COW_CONSE	Contryphan-Sm precursor	0.03	-	exc	0	Secreted protein			1DFZ	63
P38995 UniProt NPD GO	ATU2_YEAST	Copper-transporting ATPase (EC 3.6.3.4) (Cu(2+)-ATPase)	0.03	-	end	8	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein	trans-Golgi network transport vesicle membrane [IDA]		1FVS	1004
Q8K129 UniProt NPD GO	CTXN1_MOUSE	Cortexin-1	0.03	-	nuc	1 *					82
P81655 UniProt NPD GO	RK1_RABIT	Corticostatin-related peptide RK-1	0.03	-	nuc	0	Secreted protein			1EWS	32
P51975 UniProt NPD GO	DHI1_SHEEP	Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) (11-DH) (11-beta-hydroxysteroid dehydr ...	0.03	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				291
Q9XSC6 UniProt NPD GO	KCRM_BOVIN	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.03	-	nuc	0	Cytoplasm (By similarity)			1G0W	381
P05123 UniProt NPD GO	KCRM_CANFA	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.03	-	nuc	0	Cytoplasm				380
P06732 UniProt NPD GO	KCRM_HUMAN	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.03	-	nuc	0	Cytoplasm	cytoplasm [NAS]	123310	1I0E	381
P07310 UniProt NPD GO	KCRM_MOUSE	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.03	-	nuc	0	Cytoplasm				381
Q5XLD3 UniProt NPD GO	KCRM_PIG	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.03	-	nuc	0					381
P00563 UniProt NPD GO	KCRM_RABIT	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.03	-	nuc	0				2CRK	381
P00564 UniProt NPD GO	KCRM_RAT	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.03	-	nuc	0	Cytoplasm				381
P80364 UniProt NPD GO	CCB23_HOMAM	Crustacean calcium-binding protein 23 (CCBP-23 protein) (Fragments)	0.03	-	cyt	0					137
P30814 UniProt NPD GO	CHH_ARMVU	Crustacean hyperglycemic hormone (CHH)	0.03	-	cyt	0	Secreted protein				73
O97385 UniProt NPD GO	CHH3_PENMO	Crustacean hyperglycemic hormones 3 precursor (Pm-SGP-III) [Contains: CHH precursor-related peptide ...	0.03	-	vac	0	Secreted protein				102
O15982 UniProt NPD GO	CHH7_PENJP	Crustacean hyperglycemic hormones 7 precursor (Pej-SGP-VII) [Contains: CHH precursor-related peptide ...	0.03	-	exc	0	Secreted protein				122
P19667 UniProt NPD GO	CURC_CURLA	Curculin precursor	0.03	-	exc	1 *					158
P45583 UniProt NPD GO	CU19_LOCMI	Cuticle protein 19 (LM-19) (LM-ACP 19)	0.03	-	cyt	0					157
P80675 UniProt NPD GO	CU04_BLACR	Cuticle protein 4 (Bc-NCP4)	0.03	-	cyt	0					127
P83358 UniProt NPD GO	CU6B_LIMPO	Cuticle protein 6 isoform b (LpCP6b)	0.03	-	cyt	0					48
P83359 UniProt NPD GO	CU7A_LIMPO	Cuticle protein 7 isoform a (LpCP7a)	0.03	-	cyt	0					59
P83360 UniProt NPD GO	CU7B_LIMPO	Cuticle protein 7 isoform b (LpCP7b)	0.03	-	cyt	0					59
P83361 UniProt NPD GO	CU7C_LIMPO	Cuticle protein 7 isoform c (LpCP7c)	0.03	-	cyt	0					59
P81587 UniProt NPD GO	CUPC8_CANPG	Cuticle protein CP463 (CPCP463)	0.03	-	cyt	0					44
P81590 UniProt NPD GO	CUPC9_CANPG	Cuticle protein CP466 (CPCP466)	0.03	-	cyt	0					44
Q00298 UniProt NPD GO	CUTI_BOTCI	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.03	-	exc	0	Secreted protein (By similarity)				202
P30272 UniProt NPD GO	CUTI_MAGGR	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.03	-	end	0	Secreted protein				228
P13773 UniProt NPD GO	CAR1_DICDI	Cyclic AMP receptor 1 (cAMP receptor 1)	0.03	-	end	6 *	Membrane; multi-pass membrane protein				392
Q16280 UniProt NPD GO	CNGA2_HUMAN	Cyclic nucleotide-gated olfactory channel (Cyclic nucleotide-gated cation channel 2) (CNG channel 2) ...	0.03	-	nuc	1	Membrane; multi-pass membrane protein	intracellular cyclic nucleotide activated c... [NAS]	300338		261
P02785 UniProt NPD GO	CYGN_CYGAT	Cygnin	0.03	-	nuc	0					39
P32232 UniProt NPD GO	CBS_RAT	Cystathionine beta-synthase (EC 4.2.1.22) (Serine sulfhydrase) (Beta-thionase) (Hemoprotein H-450)	0.03	-	cyt	0	Cytoplasm				560
P81714 UniProt NPD GO	CYT_NAJAT	Cystatin (Fragment)	0.03	-	cyt	0	Secreted protein				99
Q10994 UniProt NPD GO	CYTB_SHEEP	Cystatin B (Stefin B)	0.03	-	cyt	0	Cytoplasm				98
Q91195 UniProt NPD GO	CYT_ONCMY	Cystatin precursor	0.03	-	cyt	1 *	Secreted protein (By similarity)				130
Q05158 UniProt NPD GO	CSRP2_COTJA	Cysteine and glycine-rich protein 2 (Cysteine-rich protein 2) (CRP2)	0.03	-	nuc	0	Nucleus			1QLI	193
P50460 UniProt NPD GO	CSRP2_CHICK	Cysteine and glycine-rich protein 2 (Cysteine-rich protein 2) (CRP2) (Beta-cysteine-rich protein) (B ...	0.03	-	nuc	0	Nucleus (Potential)				193
Q4U0T9 UniProt NPD GO	CSRP3_BOVIN	Cysteine and glycine-rich protein 3 (Cysteine-rich protein 3) (CRP3)	0.03	-	nuc	0	Nucleus (Potential). Cytoplasm. Nuclear, associates with the actin cytoskeleton (Potential)				194

You are viewing entries 79451 to 79500 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.