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
O94614 UniProt NPD GO	CHR4_SCHPO	Chitin synthase regulatory factor 4 (Chs four homolog 3)	0.34	-	nuc	0	Cytoplasm. Localizes to the cell tips and septum during vegetative growth	barrier septum [IDA] cell tip [IDA]			633
P49498 UniProt NPD GO	RR10_ODOSI	Chloroplast 30S ribosomal protein S10	0.34	-	nuc	0	Plastid; chloroplast				103
P56802 UniProt NPD GO	RR11_ARATH	Chloroplast 30S ribosomal protein S11	0.34	-	nuc	0	Plastid; chloroplast				138
P56359 UniProt NPD GO	RR11_CHLVU	Chloroplast 30S ribosomal protein S11	0.34	-	nuc	0	Plastid; chloroplast				130
Q4VZK2 UniProt NPD GO	RR11_CUCSA	Chloroplast 30S ribosomal protein S11	0.34	-	mit	0	Plastid; chloroplast				138
Q3ZJ78 UniProt NPD GO	RR11_PSEAK	Chloroplast 30S ribosomal protein S11	0.34	-	mit	0	Plastid; chloroplast				130
Q8S8U3 UniProt NPD GO	RR15_ATRBE	Chloroplast 30S ribosomal protein S15	0.34	-	nuc	0	Plastid; chloroplast				87
Q9MTI7 UniProt NPD GO	RR3_OENHO	Chloroplast 30S ribosomal protein S3	0.34	-	cyt	0	Plastid; chloroplast				218
P59138 UniProt NPD GO	RR4_CYABU	Chloroplast 30S ribosomal protein S4	0.34	-	mit	0	Plastid; chloroplast				202
P06362 UniProt NPD GO	RR8_MARPO	Chloroplast 30S ribosomal protein S8	0.34	-	nuc	0	Plastid; chloroplast				132
Q85G11 UniProt NPD GO	RK1_CYAME	Chloroplast 50S ribosomal protein L1	0.34	-	nuc	0	Plastid; chloroplast				224
Q85C49 UniProt NPD GO	RK16_ANTFO	Chloroplast 50S ribosomal protein L16	0.34	-	nuc	0	Plastid; chloroplast				136
O78409 UniProt NPD GO	RK19_GUITH	Chloroplast 50S ribosomal protein L19	0.34	-	nuc	0	Plastid; chloroplast				118
Q85FK1 UniProt NPD GO	RK33_ADICA	Chloroplast 50S ribosomal protein L33	0.34	-	nuc	0	Plastid; chloroplast				66
Q85B74 UniProt NPD GO	RK33_ANTFO	Chloroplast 50S ribosomal protein L33	0.34	-	nuc	0	Plastid; chloroplast				65
Q6B8V4 UniProt NPD GO	RK4_GRATL	Chloroplast 50S ribosomal protein L4	0.34	-	nuc	0	Plastid; chloroplast				217
Q85FV1 UniProt NPD GO	RK5_CYAME	Chloroplast 50S ribosomal protein L5	0.34	-	mit	0	Plastid; chloroplast				177
O57312 UniProt NPD GO	CCKN_PAROL	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 8 (CCK8)]	0.34	-	exc	0					135
Q920C1 UniProt NPD GO	CRDL1_MOUSE	Chordin-like protein 1 precursor (Neuralin) (Ventroptin)	0.34	-	exc	0	Secreted protein (Potential)				447
Q9SHV5 UniProt NPD GO	CAP14_ARATH	Clathrin assembly protein At2g01920	0.34	-	mit	1					312
P49192 UniProt NPD GO	CART_RAT	Cocaine- and amphetamine-regulated transcript protein precursor [Contains: CART(1-52); CART(55-102); ...	0.34	-	exc	0	Secreted protein (Potential)				129
P45593 UniProt NPD GO	COF1B_XENLA	Cofilin-1-B	0.34	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				167
Q99LQ4 UniProt NPD GO	CCD23_MOUSE	Coiled-coil domain-containing protein 23	0.34	-	nuc	0					66
Q4KLG3 UniProt NPD GO	CCD23_RAT	Coiled-coil domain-containing protein 23	0.34	-	nuc	0					66
P02461 UniProt NPD GO	CO3A1_HUMAN	Collagen alpha-1(III) chain precursor	0.34	-	exc	0		collagen type III [TAS]	130050		1466
P08121 UniProt NPD GO	CO3A1_MOUSE	Collagen alpha-1(III) chain precursor	0.34	-	exc	0					1464
Q05722 UniProt NPD GO	CO9A1_MOUSE	Collagen alpha-1(IX) chain precursor	0.34	-	mit	1 *					921
Q07092 UniProt NPD GO	COGA1_HUMAN	Collagen alpha-1(XVI) chain precursor	0.34	-	exc	0		collagen type XVI [TAS]	120326		1603
P39061 UniProt NPD GO	COIA1_MOUSE	Collagen alpha-1(XVIII) chain precursor [Contains: Endostatin]	0.34	-	exc	0		basement membrane [IDA]		1KOE	1774
P05997 UniProt NPD GO	CO5A2_HUMAN	Collagen alpha-2(V) chain precursor	0.34	-	nuc	0		collagen type V [TAS]	120190	1A9A	1496
P29400 UniProt NPD GO	CO4A5_HUMAN	Collagen alpha-5(IV) chain precursor	0.34	-	exc	0		collagen type IV [TAS]	303630		1685
Q61476 UniProt NPD GO	DAF2_MOUSE	Complement decay-accelerating factor transmembrane isoform precursor (DAF-TM) (CD55 antigen)	0.34	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)				407
P52731 UniProt NPD GO	PDE6C_CHICK	Cone cGMP-specific 3',5'-cyclic phosphodiesterase alpha'-subunit (EC 3.1.4.35) (cGMP phosphodiestera ...	0.34	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				862
Q12556 UniProt NPD GO	AMO1_ASPNG	Copper amine oxidase 1 (EC 1.4.3.6)	0.34	-	cyt	0					671
P33522 UniProt NPD GO	CRU4_BRANA	Cruciferin CRU4 precursor (11S globulin) (12S storage protein) [Contains: Cruciferin CRU4 alpha chai ...	0.34	-	end	0	Endoplasmic reticulum; rough endoplasmic reticulum				465
Q16281 UniProt NPD GO	CNGA3_HUMAN	Cyclic nucleotide-gated cation channel alpha 3 (CNG channel alpha 3) (CNG-3) (CNG3) (Cyclic nucleoti ...	0.34	-	end	2	Membrane; multi-pass membrane protein		600053		694
P20248 UniProt NPD GO	CCNA2_HUMAN	Cyclin-A2 (Cyclin-A)	0.34	-	nuc	0			123835	2CJM	432
Q5R5D0 UniProt NPD GO	CCNG1_PONPY	Cyclin-G1	0.34	-	cyt	0	Nucleus (By similarity). DNA replication foci after DNA damage (By similarity)				295
P39950 UniProt NPD GO	CCNG1_RAT	Cyclin-G1 (Cyclin-G)	0.34	-	mit	0	Nucleus (By similarity)				294
Q8QZZ9 UniProt NPD GO	CD2A2_RAT	Cyclin-dependent kinase inhibitor 2A, isoform 2 (p19ARF)	0.34	-	mit	0	Nucleus; nucleolus (By similarity)	nucleus [NAS]			160
P01037 UniProt NPD GO	CYTN_HUMAN	Cystatin SN precursor (Salivary cystatin SA-1) (Cystain SA-I)	0.34	-	exc	0			123855		141
Q9Z1J3 UniProt NPD GO	NFS1_MOUSE	Cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7) (m-Nfs1)	0.34	-	mit	0	Mitochondrion (By similarity). Cytoplasm (By similarity)	mitochondrial matrix [IDA]			451
Q5VXU3 UniProt NPD GO	CHIC1_HUMAN	Cysteine-rich hydrophobic domain 1 protein (Brain X-linked protein)	0.34	-	nuc	1	Cell membrane (By similarity). Cytoplasmic vesicle (By similarity). Also present at a Golgi-like ves ...				224
P84806 UniProt NPD GO	CRV25_NAJHH	Cysteine-rich venom protein 25 (CRVP-25h) (Fragment)	0.34	-	nuc	0	Secreted protein	extracellular region [IDA]			25
O46515 UniProt NPD GO	CP11A_HORSE	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.34	-	mit	0	Mitochondrion				520
P19099 UniProt NPD GO	C11B2_HUMAN	Cytochrome P450 11B2, mitochondrial precursor (EC 1.14.15.4) (EC 1.14.15.5) (CYPXIB2) (P-450Aldo) (A ...	0.34	-	mit	0	Mitochondrion		203400		503
O42145 UniProt NPD GO	C19AA_BRARE	Cytochrome P450 19A1a (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.34	-	end	0	Membrane; peripheral membrane protein				509
P00186 UniProt NPD GO	CP1A2_MOUSE	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2) (P450-P2/P450-P3)	0.34	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				513
P08686 UniProt NPD GO	CP21A_HUMAN	Cytochrome P450 21 (EC 1.14.99.10) (Cytochrome P450 XXI) (Steroid 21-hydroxylase) (21-OHase) (P450-C ...	0.34	+	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		201910		494
O18809 UniProt NPD GO	CP2F3_CAPHI	Cytochrome P450 2F3 (EC 1.14.14.1) (CYPIIF3)	0.34	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491

You are viewing entries 36551 to 36600 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.