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
Q7YR44 UniProt NPD GO	CDSN_PANTR	Corneodesmosin precursor (S protein)	0.22	-	exc	1 *	Secreted protein. Found in corneodesmosomes, the intercellular structures that are involved in desqu ...				529
Q62266 UniProt NPD GO	SPR1A_MOUSE	Cornifin A (Small proline-rich protein 1A) (SPR1A) (SPR1 A)	0.22	-	nuc	0	Cytoplasm				144
Q8BH44 UniProt NPD GO	COR2B_MOUSE	Coronin-2B	0.22	-	mit	0					475
P31211 UniProt NPD GO	CBG_RAT	Corticosteroid-binding globulin precursor (CBG) (Transcortin) (Serpin A6)	0.22	-	end	0	Secreted protein				396
P06297 UniProt NPD GO	COLI_RABIT	Corticotropin-lipotropin (Pro-opiomelanocortin) (POMC) [Contains: Corticotropin (Adrenocorticotropic ...	0.22	-	nuc	0					39
Q28557 UniProt NPD GO	CRHBP_SHEEP	Corticotropin-releasing factor-binding protein precursor (CRF-binding protein) (CRF-BP) (Corticotrop ...	0.22	-	exc	0					324
Q03442 UniProt NPD GO	CRJ1A_TRICY	Crystallin J1A	0.22	-	nuc	0					322
P35799 UniProt NPD GO	DPY2_CAEEL	Cuticle collagen dpy-2 precursor (Protein dumpy-2)	0.22	-	nuc	1 *					360
P81385 UniProt NPD GO	CU1B_HOMAM	Cuticle protein AMP1B (HA-AMP1B)	0.22	-	nuc	0					105
P81386 UniProt NPD GO	CU02_HOMAM	Cuticle protein AMP2 (HA-AMP2)	0.22	-	nuc	0					105
Q91879 UniProt NPD GO	CKS2_XENLA	Cyclin-dependent kinases regulatory subunit 2 (Xe-p9)	0.22	-	nuc	0					79
P81061 UniProt NPD GO	CYT_COTJA	Cystatin (Egg-white cystatin)	0.22	-	nuc	0					116
P22283 UniProt NPD GO	22P2_RAT	Cystatin-related protein 2 precursor (Prostatic 22 kDa glycoprotein P22K15)	0.22	-	vac	1 *					176
P54639 UniProt NPD GO	CYSP4_DICDI	Cysteine proteinase 4 precursor (EC 3.4.22.-)	0.22	-	exc	0	Lysosome				442
P25781 UniProt NPD GO	CYSP_THEAN	Cysteine proteinase precursor (EC 3.4.22.-)	0.22	-	mit	1 *					441
P70687 UniProt NPD GO	CP17A_MESAU	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.22	-	end	0				1JO9	511
Q9YH64 UniProt NPD GO	CP1A1_PLAFE	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.22	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
Q62397 UniProt NPD GO	CP2BK_MOUSE	Cytochrome P450 2B20 (EC 1.14.14.1) (CYPIIB20) (P24) (Fragment)	0.22	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				470
P00181 UniProt NPD GO	CP2C2_RABIT	Cytochrome P450 2C2 (EC 1.14.14.1) (CYPIIC2) (P450 PBC2) (PHP2) (Laurate omega-1 hydroxylase)	0.22	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P56654 UniProt NPD GO	CP237_MOUSE	Cytochrome P450 2C37 (EC 1.14.14.1) (CYPIIC37)	0.22	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P56655 UniProt NPD GO	CP238_MOUSE	Cytochrome P450 2C38 (EC 1.14.14.1) (CYPIIC38)	0.22	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
Q29488 UniProt NPD GO	CP2DH_MACFA	Cytochrome P450 2D17 (EC 1.14.14.1) (CYPIID17)	0.22	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				497
P05180 UniProt NPD GO	CP2H1_CHICK	Cytochrome P450 2H1 (EC 1.14.14.1) (CYPIIH1) (PB15) (P450 PCHP3)	0.22	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
Q9DBX6 UniProt NPD GO	CP2S1_MOUSE	Cytochrome P450 2S1 (EC 1.14.14.1) (CYPIIS1)	0.22	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				501
O09158 UniProt NPD GO	CP3AP_MOUSE	Cytochrome P450 3A25 (EC 1.14.14.1) (CYPIIIA25)	0.22	-	vac	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				503
P10615 UniProt NPD GO	CP52A_CANTR	Cytochrome P450 52A1 (EC 1.14.14.-) (CYPLIIA1) (Alkane-inducible P450-ALK1)	0.22	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				543
Q9LIP4 UniProt NPD GO	C71BX_ARATH	Cytochrome P450 71B36 (EC 1.14.-.-)	0.22	-	end	2 *					500
O65787 UniProt NPD GO	C71B6_ARATH	Cytochrome P450 71B6 (EC 1.14.-.-)	0.22	-	mit	1 *					503
O81971 UniProt NPD GO	C71D9_SOYBN	Cytochrome P450 71D9 (EC 1.14.-.-) (P450 CP3)	0.22	-	nuc	1 *					496
Q7Y0C8 UniProt NPD GO	C74A1_ORYSA	Cytochrome P450 74A1, chloroplast precursor (EC 4.2.1.92) (Allene oxide synthase 1) (Hydroperoxide d ...	0.22	-	nuc	0	Plastid; chloroplast; chloroplast membrane (Potential)				512
O81972 UniProt NPD GO	C82A2_SOYBN	Cytochrome P450 82A2 (EC 1.14.-.-) (P450 CP4)	0.22	-	mit	1 *					522
P14066 UniProt NPD GO	CBS1_YEAST	Cytochrome b translational activator protein CBS1, mitochondrial precursor (COB-specific translation ...	0.22	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein	mitochondrial inner membrane [TAS] mitochondrial ribosome [IPI]			229
P13498 UniProt NPD GO	CY24A_HUMAN	Cytochrome b-245 light chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 22 kDa polypeptid ...	0.22	-	end	3 *			233690	1WLP	194
Q6CMC0 UniProt NPD GO	CTM1_KLULA	Cytochrome c lysine N-methyltransferase 1 (EC 2.1.1.59)	0.22	-	nuc	0	Cytoplasm; cytosol (By similarity)				503
O14056 UniProt NPD GO	COX19_SCHPO	Cytochrome c oxidase assembly protein cox19	0.22	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial intermembrane space (By similarity)				101
P00427 UniProt NPD GO	COX6_YEAST	Cytochrome c oxidase polypeptide VI, mitochondrial precursor (EC 1.9.3.1)	0.22	-	mit	0	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IPI]			148
Q7YRK2 UniProt NPD GO	COX6C_MACSL	Cytochrome c oxidase polypeptide VIc precursor (EC 1.9.3.1)	0.22	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				75
Q9UBD3 UniProt NPD GO	XCL2_HUMAN	Cytokine SCM-1 beta precursor (XCL2) (XC chemokine ligand 2)	0.22	-	exc	0	Secreted protein		604828		114
Q9LY71 UniProt NPD GO	CKX6_ARATH	Cytokinin dehydrogenase 6 precursor (EC 1.5.99.12) (Cytokinin oxidase 6) (CKO6) (AtCKX6) (AtCKX7)	0.22	-	vac	0	Secreted protein; extracellular space (By similarity)				504
Q90828 UniProt NPD GO	DC1L1_CHICK	Cytoplasmic dynein 1 light intermediate chain 1 (Dynein light intermediate chain 1, cytosolic) (Dyne ...	0.22	-	nuc	0					515
Q7ZUS4 UniProt NPD GO	ST2S2_BRARE	Cytosolic sulfotransferase 2 (EC 2.8.2.-) (SULT1 ST2)	0.22	-	cyt	0	Cytoplasm	cytoplasm [NAS]			301
Q9C718 UniProt NPD GO	RH20_ARATH	DEAD-box ATP-dependent RNA helicase 20 (EC 3.6.1.-)	0.22	-	nuc	0	Nucleus (By similarity)				501
Q9C8J1 UniProt NPD GO	RH34_ARATH	DEAD-box ATP-dependent RNA helicase 34 (EC 3.6.1.-)	0.22	-	cyt	0	Nucleus; nucleolus (By similarity)				392
Q84W89 UniProt NPD GO	RH37_ARATH	DEAD-box ATP-dependent RNA helicase 37 (EC 3.6.1.-)	0.22	+	cyt	0					633
Q84TQ7 UniProt NPD GO	GAI_GOSHI	DELLA protein GAI (Gibberellic acid-insensitive mutant protein) (GhGAI)	0.22	-	cyt	0	Nucleus (By similarity)				537
Q6CLM5 UniProt NPD GO	DPB3_KLULA	DNA polymerase epsilon subunit C (EC 2.7.7.7) (DNA polymerase II subunit C)	0.22	-	nuc	0	Nucleus (By similarity)				166
Q40134 UniProt NPD GO	RAD51_LYCES	DNA repair protein RAD51 homolog	0.22	-	cyt	0	Nucleus (Probable)				342
Q9CZ15 UniProt NPD GO	PSF1_MOUSE	DNA replication complex GINS protein PSF1	0.22	-	cyt	0	Nucleus (By similarity)				196
Q61J08 UniProt NPD GO	MCM6_CAEBR	DNA replication licensing factor mcm-6	0.22	-	nuc	0	Nucleus (Potential)				810
Q10002 UniProt NPD GO	APN1_CAEEL	DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP endonuclease) (Apurinic-apyrimidinic en ...	0.22	+	nuc	0	Nucleus (Potential)				396

You are viewing entries 48301 to 48350 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.