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
Q2F9P2 UniProt NPD GO	FA7_PANTR	Coagulation factor VII precursor (EC 3.4.21.21) (Serum prothrombin conversion accelerator) [Contains ...	0.39	-	vac	0					466
Q32LJ0 UniProt NPD GO	CCD23_BOVIN	Coiled-coil domain-containing protein 23	0.39	-	nuc	0					66
Q3SZX8 UniProt NPD GO	CCD25_BOVIN	Coiled-coil domain-containing protein 25	0.39	+	nuc	0					208
Q8BHX1 UniProt NPD GO	CCDC5_MOUSE	Coiled-coil domain-containing protein 5	0.39	-	nuc	0	Cytoplasm (By similarity). Spindle (By similarity). Localizes with the spindle poles in mitotic cell ...				278
Q5KS50 UniProt NPD GO	NPH3_ORYSA	Coleoptile phototropism protein 1 (Non-phototropic hypocotyl 3-like protein) (NPH3-like protein)	0.39	-	cyt	0					762
P12105 UniProt NPD GO	CO3A1_CHICK	Collagen alpha-1(III) chain precursor (Fragments)	0.39	-	exc	0					1262
Q32S24 UniProt NPD GO	COBA2_BOVIN	Collagen alpha-2(XI) chain precursor	0.39	-	exc	1 *					1736
Q64739 UniProt NPD GO	COBA2_MOUSE	Collagen alpha-2(XI) chain precursor	0.39	-	exc	1 *					1736
P01026 UniProt NPD GO	CO3_RAT	Complement C3 precursor [Contains: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphyla ...	0.39	-	exc	1 *		extracellular space [TAS]		1QSJ	1663
P98136 UniProt NPD GO	CO8A_RABIT	Complement component C8 alpha chain precursor (Complement component 8 subunit alpha)	0.39	-	nuc	0	Secreted protein				585
Q63135 UniProt NPD GO	CRRY_RAT	Complement regulatory protein Crry precursor (Antigen 5I2)	0.39	-	end	1	Membrane; single-pass type I membrane protein			1NTJ	559
P09931 UniProt NPD GO	CGD2L_LUPAN	Conglutin delta-2 large chain	0.39	-	nuc	0					80
Q9Y2V7 UniProt NPD GO	COG6_HUMAN	Conserved oligomeric Golgi complex component 6	0.39	-	cyt	0	Golgi apparatus (By similarity)		606977		605
Q8R3I3 UniProt NPD GO	COG6_MOUSE	Conserved oligomeric Golgi complex component 6	0.39	-	cyt	0	Golgi apparatus (By similarity)				605
O93327 UniProt NPD GO	H2AY_CHICK	Core histone macro-H2A.1 (Histone macroH2A1) (mH2A1) (H2A.y) (H2A/y)	0.39	-	mit	0	Nucleus				371
O75367 UniProt NPD GO	H2AY_HUMAN	Core histone macro-H2A.1 (Histone macroH2A1) (mH2A1) (H2A.y) (H2A/y) (Medulloblastoma antigen MU-MB- ...	0.39	+	mit	0	Nucleus. Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin	Barr body [IDA] nucleosome [NAS]		2F8N	371
O60494 UniProt NPD GO	CUBN_HUMAN	Cubilin precursor (Intrinsic factor-cobalamin receptor) (Intrinsic factor-vitamin B12 receptor) (460 ...	0.39	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysosomal membr ...	brush border membrane [NAS] extrinsic to external side of plasma membrane [NAS] membrane [TAS]	602997		3623
Q9Y4P1 UniProt NPD GO	ATG4B_HUMAN	Cysteine protease ATG4B (EC 3.4.22.-) (Autophagy-related protein 4 homolog B) (hAPG4B) (Autophagin-1 ...	0.39	-	cyt	0	Cytoplasm (Probable)	cytoplasm [ISS] cytosol [ISS] microtubule associated complex [ISS]		2D1I	393
Q8CBW7 UniProt NPD GO	CHIC1_MOUSE	Cysteine-rich hydrophobic domain 1 protein (Brain X-linked protein)	0.39	-	nuc	1	Cell membrane (By similarity). Cytoplasmic vesicle (By similarity). Also present at a Golgi-like ves ...				227
P53852 UniProt NPD GO	SYC_YEAST	Cysteinyl-tRNA synthetase (EC 6.1.1.16) (Cysteine--tRNA ligase) (CysRS)	0.39	-	mit	0		cytoplasm [IDA]			767
Q64658 UniProt NPD GO	C11B2_MESAU	Cytochrome P450 11B2, mitochondrial precursor (EC 1.14.15.4) (EC 1.14.15.5) (C450XIB2) (Aldosterone ...	0.39	-	mit	0	Mitochondrion				500
Q64678 UniProt NPD GO	CP1B1_RAT	Cytochrome P450 1B1 (EC 1.14.14.1) (CYPIB1) (P450RAP)	0.39	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			543
P93846 UniProt NPD GO	CP51_SORBI	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Obtusifoliol 14-alpha demethylase)	0.39	-	nuc	1 *					492
O64718 UniProt NPD GO	C71B9_ARATH	Cytochrome P450 71B9 (EC 1.14.-.-)	0.39	-	mit	2 *					500
Q9M066 UniProt NPD GO	C90C1_ARATH	Cytochrome P450 90C1 (EC 1.14.-.-) (ROTUNDIFOLIA3)	0.39	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				524
P40321 UniProt NPD GO	IL2RG_CANFA	Cytokine receptor common gamma chain precursor (Gamma-C) (Interleukin-2 receptor gamma chain) (IL-2R ...	0.39	-	exc	1	Membrane; single-pass type I membrane protein				373
Q2HJ53 UniProt NPD GO	CISH_BOVIN	Cytokine-inducible SH2-containing protein (CIS)	0.39	-	nuc	0					254
Q5U243 UniProt NPD GO	CLR59_XENLA	Cytoplasmic linker protein 170-related 59 kDa protein (CLIPR-59) (CLIP-170-related 59 kDa protein)	0.39	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi stack. Localized to Golgi stacks as well as on tubulovesicular ele ...				534
P42290 UniProt NPD GO	DRD5_XENLA	D(1B) dopamine receptor (D(5) dopamine receptor)	0.39	-	end	6 *	Membrane; multi-pass membrane protein				457
Q6CQ94 UniProt NPD GO	SPC19_KLULA	DASH complex subunit SPC19 (Outer kinetochore protein SPC19)	0.39	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				153
P87297 UniProt NPD GO	DAD1_SCHPO	DASH complex subunit dad1 (Outer kinetochore protein dad1)	0.39	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore. Unlike the other DASH complex memb ...	DASH complex [IDA] spindle microtubule [IDA] spindle pole body [IDA]			85
Q9UJW3 UniProt NPD GO	DNM3L_HUMAN	DNA (cytosine-5)-methyltransferase 3-like	0.39	-	cyt	0	Nucleus (By similarity)	nucleus [NAS]	606588		387
P43247 UniProt NPD GO	MSH2_MOUSE	DNA mismatch repair protein Msh2 (MutS protein homolog 2)	0.39	-	nuc	0		nucleus [ISS]			935
O74773 UniProt NPD GO	MSH2_SCHPO	DNA mismatch repair protein msh2	0.39	-	nuc	0	Nucleus (By similarity)				982
Q04603 UniProt NPD GO	DPB4_YEAST	DNA polymerase epsilon subunit D (EC 2.7.7.7) (DNA polymerase II subunit D)	0.39	-	nuc	0	Nucleus	chromatin accessibility complex [IPI] epsilon DNA polymerase complex [IDA]			196
Q04832 UniProt NPD GO	HEXP_LEIMA	DNA-binding protein HEXBP (Hexamer-binding protein)	0.39	-	nuc	0	Nucleus				271
O74633 UniProt NPD GO	RPA2_NEUCR	DNA-directed RNA polymerase I polypeptide 2 (EC 2.7.7.6) (RNA polymerase I subunit 2)	0.39	-	cyt	0	Nucleus				1234
Q332U5 UniProt NPD GO	RPOA_LACSA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.39	-	mit	0	Plastid; chloroplast				335
Q9XQN8 UniProt NPD GO	RPOA_SINAL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.39	-	mit	0	Plastid; chloroplast				327
Q96IM9 UniProt NPD GO	DYDC2_HUMAN	DPY30 domain-containing protein 2	0.39	-	nuc	0					177
Q33DR2 UniProt NPD GO	DPS1_MOUSE	Decaprenyl-diphosphate synthase subunit 1 (EC 2.5.1.-) (Decaprenyl pyrophosphate synthetase subunit ...	0.39	-	mit	0					409
Q9SGJ6 UniProt NPD GO	DRE1E_ARATH	Dehydration-responsive element-binding protein 1E (DREB1E protein)	0.39	-	cyt	0	Nucleus (Probable)				181
P42763 UniProt NPD GO	ERD14_ARATH	Dehydrin ERD14	0.39	+	nuc	0					185
O65797 UniProt NPD GO	ADS1_ARATH	Delta-9 acyl-lipid desaturase 1 (EC 1.14.19.-)	0.39	-	cyt	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				305
P43346 UniProt NPD GO	DCK_MOUSE	Deoxycytidine kinase (EC 2.7.1.74) (dCK)	0.39	-	cyt	0	Nucleus (By similarity)				260
Q90944 UniProt NPD GO	PGLB_CHICK	Dermatan sulfate proteoglycan 3 precursor (Epiphycan) (Small chondroitin/dermatan sulfate proteoglyc ...	0.39	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				316
P23283 UniProt NPD GO	DRPF_CRAPL	Desiccation-related protein PCC3-06	0.39	-	mit	0					201
O62654 UniProt NPD GO	DESM_BOVIN	Desmin	0.39	-	mit	0	Cytoplasm				469
P02540 UniProt NPD GO	DESM_PIG	Desmin	0.39	-	mit	0	Cytoplasm				470
P32926 UniProt NPD GO	DSG3_HUMAN	Desmoglein-3 precursor (130 kDa pemphigus vulgaris antigen) (PVA)	0.39	-	end	0	Membrane; single-pass type I membrane protein (By similarity)		169615		999

You are viewing entries 32501 to 32550 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.