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
Q8WHY5 UniProt NPD GO	RK16_PSINU	Chloroplast 50S ribosomal protein L16	0.36	-	mit	0	Plastid; chloroplast				140
Q9TL18 UniProt NPD GO	RK2_NEPOL	Chloroplast 50S ribosomal protein L2	0.36	-	mit	0	Plastid; chloroplast				275
P49557 UniProt NPD GO	RK21_ODOSI	Chloroplast 50S ribosomal protein L21	0.36	+	cyt	0	Plastid; chloroplast				105
P19166 UniProt NPD GO	RK22_EUGGR	Chloroplast 50S ribosomal protein L22	0.36	-	nuc	0	Plastid; chloroplast				116
P06390 UniProt NPD GO	RK23_MARPO	Chloroplast 50S ribosomal protein L23	0.36	-	nuc	0	Plastid; chloroplast				91
Q85FH7 UniProt NPD GO	RK32_ADICA	Chloroplast 50S ribosomal protein L32	0.36	-	mit	0	Plastid; chloroplast				58
Q6B8S0 UniProt NPD GO	RK33_GRATL	Chloroplast 50S ribosomal protein L33	0.36	-	nuc	0	Plastid; chloroplast				65
P51255 UniProt NPD GO	RK33_PORPU	Chloroplast 50S ribosomal protein L33	0.36	-	nuc	0	Plastid; chloroplast				65
Q9PU41 UniProt NPD GO	CCKN_CHICK	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 70 (CCK70); Cholecystokinin 8 (CCK8); Ch ...	0.36	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			130
Q9Y5P2 UniProt NPD GO	CSAG2_HUMAN	Chondrosarcoma-associated protein 2 (Taxol-resistant-associated protein 3) (TRAG-3)	0.36	-	nuc	0					127
P27793 UniProt NPD GO	AROC_CORSE	Chorismate synthase, chloroplast precursor (EC 4.2.3.5) (5-enolpyruvylshikimate-3-phosphate phosphol ...	0.36	-	nuc	0	Plastid; chloroplast				447
Q9LXS6 UniProt NPD GO	CISY2_ARATH	Citrate synthase 2, peroxisomal precursor (EC 2.3.3.1)	0.36	-	nuc	0	Peroxisome	peroxisome [IDA]			514
Q05048 UniProt NPD GO	CSTF1_HUMAN	Cleavage stimulation factor 50 kDa subunit (CSTF 50 kDa subunit) (CF-1 50 kDa subunit) (CstF-50)	0.36	-	nuc	0	Nucleus	nucleus [TAS]	600369		431
Q5R8K2 UniProt NPD GO	CSTF1_PONPY	Cleavage stimulation factor 50 kDa subunit (CSTF 50 kDa subunit) (CF-1 50 kDa subunit) (CstF-50)	0.36	-	nuc	0	Nucleus (By similarity)				431
Q12996 UniProt NPD GO	CSTF3_HUMAN	Cleavage stimulation factor 77 kDa subunit (CSTF 77 kDa subunit) (CF-1 77 kDa subunit) (CstF-77)	0.36	+	cyt	0	Nucleus	nucleus [TAS]	600367		717
Q5RDW9 UniProt NPD GO	CSTF3_PONPY	Cleavage stimulation factor 77 kDa subunit (CSTF 77 kDa subunit) (CF-1 77 kDa subunit) (CstF-77)	0.36	+	cyt	0	Nucleus (By similarity)				717
Q27954 UniProt NPD GO	COPA_BOVIN	Coatomer subunit alpha (Alpha-coat protein) (Alpha-COP) (HEPCOP) (HEP-COP) [Contains: Xenin (Xenopsi ...	0.36	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]			1224
Q86WR0 UniProt NPD GO	CCD25_HUMAN	Coiled-coil domain-containing protein 25	0.36	+	nuc	0					208
Q9D1L0 UniProt NPD GO	CHCH2_MOUSE	Coiled-coil-helix-coiled-coil-helix domain-containing protein 2	0.36	-	mit	0		mitochondrion [IDA]			153
Q9Y6H1 UniProt NPD GO	CHCH2_HUMAN	Coiled-coil-helix-coiled-coil-helix domain-containing protein 2 (HCV NS2 trans-regulated protein) (N ...	0.36	-	mit	0					151
P98093 UniProt NPD GO	CO3_ONCMY	Complement C3-1 [Contains: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphylatoxin; C ...	0.36	-	cyt	0					1640
Q9CWX2 UniProt NPD GO	CIA30_MOUSE	Complex I intermediate-associated protein 30, mitochondrial precursor	0.36	-	cyt	0	Mitochondrion (Probable)	mitochondrion [IDA]			328
O42105 UniProt NPD GO	CPLX2_NARJA	Complexin-2 (NJ-synaphin-1A)	0.36	-	nuc	0	Cytoplasm; cytosol (By similarity)				134
Q9HCH3 UniProt NPD GO	CPNE5_HUMAN	Copine-5 (Copine V)	0.36	-	cyt	0			604209		593
P70079 UniProt NPD GO	KCRU_CHICK	Creatine kinase, ubiquitous mitochondrial precursor (EC 2.7.3.2) (U-MtCK) (Mia-CK) (Acidic-type mito ...	0.36	-	mit	0	Mitochondrion; mitochondrial inner membrane; intermembrane side				417
Q80YA8 UniProt NPD GO	CRUM2_MOUSE	Crumbs homolog 2 (Crumbs-like protein 2) (Fragment)	0.36	-	cyt	1	Membrane; single-pass type I membrane protein (By similarity)				1248
Q23628 UniProt NPD GO	LON3_CAEEL	Cuticle collagen lon-3 precursor	0.36	-	exc	1 *					324
Q9TX43 UniProt NPD GO	CAR4_DICDI	Cyclic AMP receptor 4 (cAMP receptor 4)	0.36	-	end	7 *	Membrane; multi-pass membrane protein				443
Q5R754 UniProt NPD GO	CDKL2_PONPY	Cyclin-dependent kinase-like 2 (EC 2.7.11.22)	0.36	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				493
Q9H114 UniProt NPD GO	CST1L_HUMAN	Cystatin-like 1 precursor (RCET11)	0.36	-	nuc	0	Secreted protein (Potential)				145
Q6PZ03 UniProt NPD GO	ATG4B_BOVIN	Cysteine protease ATG4B (EC 3.4.22.-) (Autophagy-related protein 4 homolog B) (Autophagy-related cys ...	0.36	-	cyt	0	Cytoplasm (Probable)				393
Q684M2 UniProt NPD GO	ATG4D_PIG	Cysteine protease ATG4D (EC 3.4.22.-) (Autophagy-related protein 4 homolog D)	0.36	-	cyt	0	Cytoplasm (Probable)				469
Q8AWW5 UniProt NPD GO	CRIM1_CHICK	Cysteine-rich motor neuron 1 protein precursor (CRIM-1)	0.36	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)				1048
Q6GUR1 UniProt NPD GO	CP1A1_MACMU	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.36	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				512
Q5KQT6 UniProt NPD GO	CP1A2_FELCA	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2)	0.36	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				512
Q6V0L0 UniProt NPD GO	CP26C_HUMAN	Cytochrome P450 26C1 (EC 1.14.-.-)	0.36	-	mit	1 *	Membrane; single-pass membrane protein (Potential)		608428		522
Q64409 UniProt NPD GO	CP3AH_CAVPO	Cytochrome P450 3A17 (EC 1.14.14.1) (CYPIIIA17)	0.36	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				503
Q9VA27 UniProt NPD GO	CP4C3_DROME	Cytochrome P450 4c3 (EC 1.14.-.-) (CYPIVC3)	0.36	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				535
Q4PJW3 UniProt NPD GO	CP51A_BOVIN	Cytochrome P450 51A1 (EC 1.14.13.70) (CYPLI) (P450LI) (Sterol 14-alpha demethylase) (Lanosterol 14-a ...	0.36	-	nuc	1 *	Microsome (By similarity)				502
O00061 UniProt NPD GO	CP67_UROFA	Cytochrome P450 67 (EC 1.14.-.-) (CYPLXVII) (Planta-induced rust protein 16) (Fragment)	0.36	-	exc	2 *					541
O48921 UniProt NPD GO	C97B2_SOYBN	Cytochrome P450 97B2 (EC 1.14.-.-)	0.36	-	cyt	0					576
P53702 UniProt NPD GO	CCHL_MOUSE	Cytochrome c-type heme lyase (EC 4.4.1.17) (CCHL) (Holocytochrome c-type synthase)	0.36	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)				272
Q9LUW5 UniProt NPD GO	RH53_ARATH	DEAD-box ATP-dependent RNA helicase 53 (EC 3.6.1.-)	0.36	+	mit	0		mitochondrion [IDA]			616
Q14129 UniProt NPD GO	DGCR6_HUMAN	DGCR6 protein (DiGeorge syndrome critical region 6)	0.36	-	nuc	0	Nucleus. Predominantly	extracellular matrix (sensu Metazoa) [TAS]	601279		220
Q27958 UniProt NPD GO	DPOLB_BOVIN	DNA polymerase beta (EC 2.7.7.7) (EC 4.2.99.-)	0.36	-	nuc	0	Nucleus				334
P06746 UniProt NPD GO	DPOLB_HUMAN	DNA polymerase beta (EC 2.7.7.7) (EC 4.2.99.-)	0.36	-	nuc	0	Nucleus	cytoplasm [IDA] spindle microtubule [IDA]	174760	9ICY	334
P06766 UniProt NPD GO	DPOLB_RAT	DNA polymerase beta (EC 2.7.7.7) (EC 4.2.99.-)	0.36	-	nuc	0	Nucleus			2BPG	334
P41137 UniProt NPD GO	ID2_RAT	DNA-binding protein inhibitor ID-2 (Inhibitor of DNA binding 2)	0.36	-	nuc	0	Nucleus	nucleus [IDA]			134
P21421 UniProt NPD GO	RPOB_PLAFA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6)	0.36	-	nuc	5 *	Plastid; apicoplast	apicoplast [NAS]			1024
P40422 UniProt NPD GO	RPC10_YEAST	DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide (EC 2.7.7.6) (ABC10-alpha)	0.36	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase II, core complex [TAS] DNA-directed RNA polymerase III complex [TAS]		2B8K	70

You are viewing entries 34851 to 34900 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.