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
Q71M36 UniProt NPD GO	CSPG5_MOUSE	Chondroitin sulfate proteoglycan 5 precursor (Neuroglycan C) (Acidic leucine-rich EGF-like domain-co ...	0.21	-	exc	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Partially enriched in lipid raft ...				566
Q04199 UniProt NPD GO	CAC2_YEAST	Chromatin assembly factor 1 subunit p60 (CAF-1 60 kDa subunit)	0.21	-	cyt	0	Nucleus	chromatin assembly complex [IDA] chromosome, pericentric region [IDA]			468
P02893 UniProt NPD GO	CSP_PLAFA	Circumsporozoite protein precursor (CS)	0.21	-	mit	0					412
P30515 UniProt NPD GO	1A01_SAGOE	Class I histocompatibility antigen, A alpha chain precursor	0.21	-	end	1	Membrane; single-pass type I membrane protein				365
P53622 UniProt NPD GO	COPA_YEAST	Coatomer subunit alpha (Alpha-coat protein) (Alpha-COP)	0.21	-	mit	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side. The coato ...	COPI vesicle coat [IMP]			1201
P41810 UniProt NPD GO	COPB_YEAST	Coatomer subunit beta (Beta-coat protein) (Beta-COP)	0.21	-	end	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IGI]			973
Q5RF83 UniProt NPD GO	CIRBP_PONPY	Cold-inducible RNA-binding protein (Glycine-rich RNA-binding protein CIRP)	0.21	+	nuc	0	Nucleus; nucleoplasm (By similarity)				172
Q14011 UniProt NPD GO	CIRBP_HUMAN	Cold-inducible RNA-binding protein (Glycine-rich RNA-binding protein CIRP) (A18 hnRNP)	0.21	+	nuc	0	Nucleus; nucleoplasm (By similarity)		602649	1X5S	172
Q9CQC2 UniProt NPD GO	COL_MOUSE	Colipase precursor	0.21	-	exc	1 *	Secreted protein				113
P04258 UniProt NPD GO	CO3A1_BOVIN	Collagen alpha-1(III) chain	0.21	-	nuc	0					1049
Q05707 UniProt NPD GO	COEA1_HUMAN	Collagen alpha-1(XIV) chain precursor (Undulin)	0.21	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)	collagen [NAS] collagen type XIV [NAS]	120324		1796
P39059 UniProt NPD GO	COFA1_HUMAN	Collagen alpha-1(XV) chain precursor [Contains: Endostatin (Endostatin-XV) (Restin) (Related to endo ...	0.21	-	exc	0			120325		1388
Q28668 UniProt NPD GO	CO1A2_RABIT	Collagen alpha-2(I) chain precursor (Fragment)	0.21	-	nuc	0					526
Q5R544 UniProt NPD GO	C1R_PONPY	Complement C1r subcomponent precursor (EC 3.4.21.41) (Complement component 1, r subcomponent) [Conta ...	0.21	-	mit	0					705
Q8IWV2 UniProt NPD GO	CNTN4_HUMAN	Contactin-4 precursor (Brain-derived immunoglobulin superfamily protein 2) (BIG-2)	0.21	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	axon [NAS] plasma membrane [NAS]	607280		1026
P05544 UniProt NPD GO	CPI3_RAT	Contrapsin-like protease inhibitor 3 precursor (CPI-23) (Serine protease inhibitor 1) (SPI-1)	0.21	-	end	0	Secreted protein (By similarity)				413
Q60543 UniProt NPD GO	CBG_MESAU	Corticosteroid-binding globulin precursor (CBG) (Transcortin) (Serpin A6)	0.21	-	end	0	Secreted protein (By similarity)				404
Q60571 UniProt NPD GO	CRHBP_MOUSE	Corticotropin-releasing factor-binding protein precursor (CRF-binding protein) (CRF-BP) (Corticotrop ...	0.21	-	exc	0					322
P34803 UniProt NPD GO	COL36_CAEEL	Cuticle collagen 36	0.21	-	nuc	1 *					307
P34688 UniProt NPD GO	DPY7_CAEEL	Cuticle collagen dpy-7 precursor (Protein dumpy-7)	0.21	-	nuc	1 *					318
P81387 UniProt NPD GO	CU03_HOMAM	Cuticle protein AMP3 (HA-AMP3)	0.21	-	nuc	0					105
P81388 UniProt NPD GO	CU04_HOMAM	Cuticle protein AMP4 (HA-AMP4)	0.21	-	nuc	0					105
P48125 UniProt NPD GO	RK1_CYAPA	Cyanelle 50S ribosomal protein L1	0.21	-	cyt	0	Plastid; cyanelle				237
P15769 UniProt NPD GO	RK33_CYAPA	Cyanelle 50S ribosomal protein L33	0.21	-	nuc	0	Plastid; cyanelle				64
P40782 UniProt NPD GO	CYPR1_CYNCA	Cyprosin precursor (EC 3.4.23.-) (Fragment)	0.21	-	cyt	0					473
P14841 UniProt NPD GO	CYTC_RAT	Cystatin C precursor	0.21	-	exc	0		extracellular space [IDA]			140
Q9U8F1 UniProt NPD GO	CDO_SCHJA	Cysteine dioxygenase (EC 1.13.11.20) (CDO)	0.21	-	cyt	0					212
Q811C2 UniProt NPD GO	ATG4C_MOUSE	Cysteine protease ATG4C (EC 3.4.22.-) (Autophagy-related protein 4 homolog C) (Autophagin-3) (Autoph ...	0.21	-	cyt	0	Cytoplasm (Probable)	cytoplasm [ISS] cytosol [ISS] microtubule associated complex [ISS]			458
Q9Y271 UniProt NPD GO	CLTR1_HUMAN	Cysteinyl leukotriene receptor 1 (CysLTR1) (Cysteinyl leukotriene D4 receptor) (LTD4 receptor) (HG55 ...	0.21	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	300201		337
Q28827 UniProt NPD GO	CP11A_RABIT	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.21	-	mit	0	Mitochondrion				445
P70085 UniProt NPD GO	CP17A_ORYLA	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.21	-	exc	1 *					517
P11511 UniProt NPD GO	CP19A_HUMAN	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.21	+	mit	0	Membrane; peripheral membrane protein	membrane fraction [TAS]	107910	1TQA	502
Q5KQT7 UniProt NPD GO	CP1A1_FELCA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.21	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				517
Q6JZS3 UniProt NPD GO	CP1A1_ORYLA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.21	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				521
O42457 UniProt NPD GO	CP1A1_SPAAU	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.21	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
Q92116 UniProt NPD GO	CP1A1_STECH	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.21	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
P33263 UniProt NPD GO	CP2CQ_MESAU	Cytochrome P450 2C26 (EC 1.14.14.1) (CYPIIC26) (P450 HSM2)	0.21	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P05181 UniProt NPD GO	CP2E1_HUMAN	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1) (P450-J)	0.21	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		124040		493
Q27664 UniProt NPD GO	CP6B2_HELAM	Cytochrome P450 6B2 (EC 1.14.14.1) (CYPVIB2)	0.21	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				504
Q27756 UniProt NPD GO	CP6B3_PAPPO	Cytochrome P450 6B3 (EC 1.14.14.1) (CYPVIB4) (CYP6B3V1/CYP6B3V2)	0.21	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				498
Q9FLC8 UniProt NPD GO	C79A2_ARATH	Cytochrome P450 79A2 (EC 1.-.-.-)	0.21	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				529
Q8GSQ1 UniProt NPD GO	C85A1_ORYSA	Cytochrome P450 85A1 (EC 1.14.-.-) (C6-oxidase) (OsDWARF) (Dwarf protein)	0.21	-	nuc	1 *					469
Q9MTI2 UniProt NPD GO	CCSA_OENHO	Cytochrome c biogenesis protein ccsA	0.21	-	end	7 *	Plastid; chloroplast				319
P40086 UniProt NPD GO	COX15_YEAST	Cytochrome c oxidase assembly protein COX15	0.21	-	end	8	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			486
P29875 UniProt NPD GO	COX2_LASSP	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.21	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P29879 UniProt NPD GO	COX2_SITGR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.21	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q9ZQ94 UniProt NPD GO	COGT3_ARATH	Cytokinin-O-glucosyltransferase 3 (EC 2.4.1.-) (UDP-glycosyltransferase 73C5) (Deoxynivalenol-glucos ...	0.21	-	cyt	0					495
Q6PDL0 UniProt NPD GO	DC1L2_MOUSE	Cytoplasmic dynein 1 light intermediate chain 2 (Dynein light intermediate chain 2, cytosolic)	0.21	-	nuc	0					492
Q7T2V2 UniProt NPD GO	ST1S3_BRARE	Cytosolic sulfotransferase 3 (EC 2.8.2.-) (SULT1 ST3)	0.21	-	cyt	0	Cytoplasm	cytoplasm [NAS]			301
P19004 UniProt NPD GO	CXH48_ASPSC	Cytotoxin homolog S4C8	0.21	-	mit	0	Secreted protein				64

You are viewing entries 49351 to 49400 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.