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
Q9YHU9 UniProt NPD GO	NXS3_NAJAT	Cobrotoxin III (CBT III)	0.13	-	nuc	0	Secreted protein (By similarity)				62
Q9BDP9 UniProt NPD GO	CART_PIG	Cocaine- and amphetamine-regulated transcript protein [Contains: CART(55-102); CART(62-102)] (Fragme ...	0.13	-	nuc	0	Secreted protein (Potential)				66
P46525 UniProt NPD GO	CS120_WHEAT	Cold-shock protein CS120	0.13	-	cyt	0					391
P27658 UniProt NPD GO	CO8A1_HUMAN	Collagen alpha-1(VIII) chain precursor (Endothelial collagen)	0.13	-	exc	0		collagen type VIII [TAS]	120251		744
P14282 UniProt NPD GO	CO8A1_RABIT	Collagen alpha-1(VIII) chain precursor (Endothelial collagen)	0.13	-	exc	0					744
P23206 UniProt NPD GO	COAA1_BOVIN	Collagen alpha-1(X) chain precursor	0.13	-	exc	0					674
Q8K4G2 UniProt NPD GO	CONA1_MOUSE	Collagen alpha-1(XXIII) chain	0.13	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				532
P23097 UniProt NPD GO	MMP13_RAT	Collagenase 3 precursor (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13) (UMRCASE) (Fragment)	0.13	-	exc	0					466
Q5E9E3 UniProt NPD GO	C1QA_BOVIN	Complement C1q subcomponent subunit A precursor	0.13	-	exc	0	Secreted protein				244
P60827 UniProt NPD GO	C1QT8_HUMAN	Complement C1q tumor necrosis factor-related protein 8 precursor	0.13	-	exc	0	Secreted protein (Potential)				262
O35796 UniProt NPD GO	C1QBP_RAT	Complement component 1 Q subcomponent-binding protein, mitochondrial precursor (Glycoprotein gC1qBP) ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				278
P00746 UniProt NPD GO	CFAD_HUMAN	Complement factor D precursor (EC 3.4.21.46) (C3 convertase activator) (Properdin factor D) (Adipsin ...	0.13	-	exc	0	Secreted protein		134350	1HFD	253
O42106 UniProt NPD GO	CPLX1_NARJA	Complexin-1 (NJ-synaphin-2)	0.13	-	nuc	0	Cytoplasm; cytosol (By similarity)				133
Q8I6V7 UniProt NPD GO	CXP9_CONRE	Conotoxin Rg9.1 precursor	0.13	-	exc	1 *	Secreted protein				90
P69767 UniProt NPD GO	CX5C_CONVC	Conotoxin Vc5.3 precursor (Fragment)	0.13	-	exc	0	Secreted protein				53
P34998 UniProt NPD GO	CRFR1_HUMAN	Corticotropin-releasing factor receptor 1 precursor (CRF-R) (CRF1) (Corticotropin-releasing hormone ...	0.13	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	122561		444
P47866 UniProt NPD GO	CRFR2_RAT	Corticotropin-releasing factor receptor 2 precursor (CRF-R 2) (CRF2) (Corticotropin-releasing hormon ...	0.13	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IMP]			411
P56469 UniProt NPD GO	CORT_MOUSE	Cortistatin precursor [Contains: Cortistatin-14]	0.13	-	exc	0	Secreted protein				109
P47001 UniProt NPD GO	CIS3_YEAST	Covalently-linked cell wall protein 11 precursor (Protein CIS3) (Soluble cell wall protein 8)	0.13	-	exc	0	Cell wall. Attached to the cell wall	bud tip [IDA] cell wall (sensu Fungi) [IDA] endoplasmic reticulum [IDA] extracellular region [IDA] plasma membrane [IDA]			227
Q96524 UniProt NPD GO	CRY2_ARATH	Cryptochrome-2 (Blue light photoreceptor)	0.13	-	cyt	0					612
P84158 UniProt NPD GO	CUCN_CUCMA	Cucurmoschin (Fragment)	0.13	-		0					19
P15967 UniProt NPD GO	TXC1_HOLCU	Curtatoxin-1 (CT-I)	0.13	-	nuc	0	Secreted protein				36
Q24152 UniProt NPD GO	CKS1_DROME	Cyclin-dependent kinases regulatory subunit	0.13	-	cyt	0					74
P01034 UniProt NPD GO	CYTC_HUMAN	Cystatin C precursor (Neuroendocrine basic polypeptide) (Gamma-trace) (Post-gamma-globulin)	0.13	-	exc	1 *			105150	1TIJ	146
Q9Y600 UniProt NPD GO	CSAD_HUMAN	Cysteine sulfinic acid decarboxylase (EC 4.1.1.29) (Sulfinoalanine decarboxylase) (Cysteine-sulfinat ...	0.13	-	cyt	0					493
Q64611 UniProt NPD GO	CSAD_RAT	Cysteine sulfinic acid decarboxylase (EC 4.1.1.29) (Sulfinoalanine decarboxylase) (Cysteine-sulfinat ...	0.13	-	mit	0					493
Q4V7F2 UniProt NPD GO	CREL1_RAT	Cysteine-rich with EGF-like domain protein 1 precursor	0.13	-	end	2	Membrane; multi-pass membrane protein (Potential)				420
Q95328 UniProt NPD GO	CP17A_HORSE	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.13	-	mit	0					508
P79690 UniProt NPD GO	CP191_CARAU	Cytochrome P450 19 type 1 (EC 1.14.14.1) (Brain aromatase) (CYPXIXA1) (Estrogen synthetase) (P-450AR ...	0.13	-	end	2 *	Membrane; peripheral membrane protein				510
P79402 UniProt NPD GO	CP242_PIG	Cytochrome P450 2C42 (EC 1.14.14.1) (CYPIIC42) (Fragment)	0.13	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				327
Q9QYG6 UniProt NPD GO	CP2DR_MESAU	Cytochrome P450 2D27 (EC 1.14.14.-) (CYPIID27)	0.13	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				500
P24462 UniProt NPD GO	CP3A7_HUMAN	Cytochrome P450 3A7 (EC 1.14.14.1) (CYPIIIA7) (P450-HFLA)	0.13	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]	605340		503
O49340 UniProt NPD GO	C71AC_ARATH	Cytochrome P450 71A12 (EC 1.14.-.-)	0.13	-	nuc	0					497
P93531 UniProt NPD GO	C71D7_SOLCH	Cytochrome P450 71D7 (EC 1.14.-.-)	0.13	-	nuc	0					500
O65012 UniProt NPD GO	C78A4_PINRA	Cytochrome P450 78A4 (EC 1.14.-.-)	0.13	-	mit	1 *					553
O48956 UniProt NPD GO	C98A1_SORBI	Cytochrome P450 98A1 (EC 1.14.-.-)	0.13	-	nuc	1 *					512
Q9ZR03 UniProt NPD GO	UCRIA_ARATH	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sulfu ...	0.13	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...	thylakoid membrane (sensu Viridiplantae) [IDA]			229
Q96VP3 UniProt NPD GO	CYC_CURLU	Cytochrome c	0.13	-	cyt	0	Mitochondrion; mitochondrial matrix				108
Q9M3J1 UniProt NPD GO	CCSA_SPIOL	Cytochrome c biogenesis protein ccsA	0.13	-	end	7 *	Plastid; chloroplast				323
Q01359 UniProt NPD GO	COX6_NEUCR	Cytochrome c oxidase polypeptide VI, mitochondrial precursor (EC 1.9.3.1)	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane				148
P11950 UniProt NPD GO	CX6C1_RAT	Cytochrome c oxidase polypeptide VIc-1 (EC 1.9.3.1)	0.13	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane				75
P10606 UniProt NPD GO	COX5B_HUMAN	Cytochrome c oxidase polypeptide Vb, mitochondrial precursor (EC 1.9.3.1)	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane		123866		129
P29871 UniProt NPD GO	COX2_ADABI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.13	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
P50268 UniProt NPD GO	COX2_APIKO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.13	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				225
P20375 UniProt NPD GO	COX2_APILI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.13	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				225
Q37419 UniProt NPD GO	COX2_BOSTR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.13	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50678 UniProt NPD GO	COX2_BUBDE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.13	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q00528 UniProt NPD GO	COX2_PHOVI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.13	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37596 UniProt NPD GO	COX2_PHYHA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.13	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98048 UniProt NPD GO	COX2_YPOMA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.13	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228

You are viewing entries 59551 to 59600 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.