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
Q5EA61 UniProt NPD GO	KCRB_BOVIN	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK)	0.08	-	nuc	0	Cytoplasm (By similarity)				381
P05124 UniProt NPD GO	KCRB_CANFA	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK)	0.08	-	nuc	0	Cytoplasm				381
P12277 UniProt NPD GO	KCRB_HUMAN	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK)	0.08	-	nuc	0	Cytoplasm		123280		381
Q29577 UniProt NPD GO	KCRU_PIG	Creatine kinase, ubiquitous mitochondrial (EC 2.7.3.2) (U-MtCK) (Mia-CK) (Acidic-type mitochondrial ...	0.08	-	cyt	0	Mitochondrion; mitochondrial inner membrane. Outer side (By similarity)				78
P01475 UniProt NPD GO	MYXC_CRODU	Crotamine (Crt) (Myotoxin)	0.08	-	nuc	0	Secreted protein			1Z99	42
P63327 UniProt NPD GO	MYX_CRODR	Crotamine Ile-19 (CRO_Ile-19)	0.08	-	nuc	0	Secreted protein				42
P56687 UniProt NPD GO	CHH_JASLA	Crustacean hyperglycemic hormone (CHH) (JAL-CHH-I)	0.08	-	nuc	0	Secreted protein				73
P25779 UniProt NPD GO	CYSP_TRYCR	Cruzipain precursor (EC 3.4.22.51) (Major cysteine proteinase) (Cruzaine)	0.08	-	exc	1 *				2AIM	467
P83992 UniProt NPD GO	CU16A_LOCMI	Cuticle protein 16.5, isoform A (LM-16.5A) (LM-ACP 16.5A)	0.08	-	mit	5 *					175
P83993 UniProt NPD GO	CU16B_LOCMI	Cuticle protein 16.5, isoform B (LM-16.5B) (LM-ACP 16.5B)	0.08	-	mit	5 *					175
P81576 UniProt NPD GO	CUPA2_CANPG	Cuticle protein AM1159 (CPAM1159)	0.08	-	cyt	0					105
Q9FWK4 UniProt NPD GO	CYNS_ORYSA	Cyanate hydratase (EC 4.2.1.104) (Cyanase) (Cyanate lyase) (Cyanate hydrolase)	0.08	-	cyt	0					168
P55272 UniProt NPD GO	CDN2B_RAT	Cyclin-dependent kinase 4 inhibitor B (p14-INK4b) (p15-INK4b)	0.08	-	cyt	0					130
Q8VCN5 UniProt NPD GO	CGL_MOUSE	Cystathionine gamma-lyase (EC 4.4.1.1) (Gamma-cystathionase)	0.08	-	cyt	0	Cytoplasm (By similarity)				398
P28325 UniProt NPD GO	CYTD_HUMAN	Cystatin D precursor	0.08	-	end	0			123858	1ROA	142
Q9H4G1 UniProt NPD GO	CST9_HUMAN	Cystatin-9-like precursor	0.08	-	exc	1 *	Secreted protein (Potential)				147
O88969 UniProt NPD GO	CST8_RAT	Cystatin-related epididymal spermatogenic protein precursor (Cystatin-8)	0.08	-	exc	0	Secreted protein (By similarity)				142
P60334 UniProt NPD GO	CDO1_MOUSE	Cysteine dioxygenase type 1 (EC 1.13.11.20) (Cysteine dioxygenase type I) (CDO) (CDO-I)	0.08	-	mit	0		cytosol [IDA]		2ATF	200
P21816 UniProt NPD GO	CDO1_RAT	Cysteine dioxygenase type 1 (EC 1.13.11.20) (Cysteine dioxygenase type I) (CDO) (CDO-I)	0.08	-	mit	0		cytosol [TAS]		2GH2	200
P54108 UniProt NPD GO	CRIS3_HUMAN	Cysteine-rich secretory protein 3 precursor (CRISP-3) (SGP28 protein)	0.08	-	exc	0	Secreted protein. In neutrophils, localized in specific granules	extracellular matrix (sensu Metazoa) [NAS] extracellular region [IDA] specific granule [IDA]			245
Q8T0W3 UniProt NPD GO	CVP3_PIMHY	Cysteine-rich venom protein 3 precursor	0.08	-	exc	1 *	Secreted protein				63
Q8MMH0 UniProt NPD GO	CVP7_PIMHY	Cysteine-rich venom protein 7 precursor	0.08	-	nuc	1 *	Secreted protein				109
Q96HD1 UniProt NPD GO	CREL1_HUMAN	Cysteine-rich with EGF-like domain protein 1 precursor	0.08	-	end	2	Membrane; multi-pass membrane protein (Potential)		607170		420
Q09500 UniProt NPD GO	CTNS_CAEEL	Cystinosin homolog	0.08	-	end	7 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				404
P11715 UniProt NPD GO	CP17A_RAT	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.08	-	end	0					507
Q5QQX7 UniProt NPD GO	CP19A_CANFA	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.08	-	cyt	2 *	Membrane; peripheral membrane protein				503
Q6YI21 UniProt NPD GO	CP19A_CAPHI	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.08	-	cyt	2 *	Membrane; peripheral membrane protein				503
Q9XS28 UniProt NPD GO	CP19A_SHEEP	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.08	-	cyt	2 *	Membrane; peripheral membrane protein				503
O46512 UniProt NPD GO	CP19A_HORSE	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM) (P450 17- ...	0.08	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				503
P79716 UniProt NPD GO	CP1A1_DICLA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.08	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				520
P11371 UniProt NPD GO	CP2C4_RABIT	Cytochrome P450 2C4 (EC 1.14.14.1) (CYPIIC4) (Progesterone 21-hydroxylase) (P450 PBC4) (P1-88)	0.08	-	end	0					487
P12939 UniProt NPD GO	CP2DA_RAT	Cytochrome P450 2D10 (EC 1.14.14.1) (CYPIID10) (P450-DB5) (P450-CMF1B) (Debrisoquine 4-hydroxylase)	0.08	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				504
P51581 UniProt NPD GO	CP2E1_MESAU	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1) (P450-J)	0.08	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				493
P04800 UniProt NPD GO	CP3A1_RAT	Cytochrome P450 3A1 (EC 1.14.14.1) (CYPIIIA1) (P450-PCN1)	0.08	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum membrane [IMP] microsome [IDA]			504
Q9JMA7 UniProt NPD GO	CP341_MOUSE	Cytochrome P450 3A41 (EC 1.14.14.1)	0.08	-	vac	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				504
P51538 UniProt NPD GO	CP3A9_RAT	Cytochrome P450 3A9 (EC 1.14.14.1) (CYPIIIA9) (P450-OLF3) (Olfactive) (3AH15)	0.08	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]			503
O14442 UniProt NPD GO	CP51_UNCNE	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Eburicol 14-al ...	0.08	-	nuc	2 *					524
Q9ZU07 UniProt NPD GO	C71BC_ARATH	Cytochrome P450 71B12 (EC 1.14.-.-)	0.08	-	nuc	1 *					496
P58051 UniProt NPD GO	C71BE_ARATH	Cytochrome P450 71B14 (EC 1.14.-.-)	0.08	-	nuc	1 *					496
O65788 UniProt NPD GO	C71B2_ARATH	Cytochrome P450 71B2 (EC 1.14.-.-)	0.08	-	mit	1 *					502
O65784 UniProt NPD GO	C71B5_ARATH	Cytochrome P450 71B5 (EC 1.14.-.-)	0.08	-	end	0					498
O23066 UniProt NPD GO	C86A2_ARATH	Cytochrome P450 86A2 (EC 1.14.-.-)	0.08	-	cyt	0					553
O79205 UniProt NPD GO	CYB_HALMI	Cytochrome b	0.08	-	end	9 *					380
O79206 UniProt NPD GO	CYB_HYDPE	Cytochrome b	0.08	-	end	9 *					380
O79210 UniProt NPD GO	CYB_OCEFU	Cytochrome b	0.08	-	end	8 *					380
O79211 UniProt NPD GO	CYB_OCEMA	Cytochrome b	0.08	-	end	9 *					380
O79212 UniProt NPD GO	CYB_OCETE	Cytochrome b	0.08	-	end	9 *					380
P92723 UniProt NPD GO	CYB_PONPP	Cytochrome b	0.08	-	end	9 *					380
Q35614 UniProt NPD GO	CYB_PONPY	Cytochrome b	0.08	-	end	9 *					380
Q9ZZD2 UniProt NPD GO	CYB_TODTO	Cytochrome b	0.08	-	end	8 *					380

You are viewing entries 67801 to 67850 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.