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
P26334 UniProt NPD GO	VSM6_TRYBB	Variant surface glycoprotein MITAT 1.6 precursor (VSG)	0.41	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				529
P25614 UniProt NPD GO	YCQ3_YEAST	Very hypothetical protein YCR013C	0.41	-	nuc	0					215
Q9JI51 UniProt NPD GO	VTI1A_RAT	Vesicle transport through interaction with t-SNAREs homolog 1A (Vesicle transport v-SNARE protein Vt ...	0.41	-	nuc	1	Membrane; single-pass type IV membrane protein. Enriched in small synaptic vesicles and clathrin-coa ...				224
Q6CRX0 UniProt NPD GO	BOS1_KLULA	Vesicular transport protein BOS1	0.41	-	nuc	1	Secretory vesicle; secretory vesicle membrane; peripheral membrane protein (By similarity). Secretor ...				248
Q13698 UniProt NPD GO	CAC1S_HUMAN	Voltage-dependent L-type calcium channel subunit alpha-1S (Voltage-gated calcium channel subunit alp ...	0.41	+	end	19	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	601887		1873
Q5RD06 UniProt NPD GO	WD51B_PONPY	WD repeat protein 51B	0.41	-	cyt	0					451
Q49LS3 UniProt NPD GO	XKR5_PANTR	XK-related protein 5	0.41	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				686
Q00519 UniProt NPD GO	XDH_MOUSE	Xanthine dehydrogenase/oxidase [Includes: Xanthine dehydrogenase (EC 1.17.1.4) (XD); Xanthine oxidas ...	0.41	-	mit	0	Peroxisome				1334
Q5QQ55 UniProt NPD GO	XYLT_CIOIN	Xylosyltransferase (EC 2.4.2.26) (Peptide O-xylosyltransferase)	0.41	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				848
Q9SJM6 UniProt NPD GO	ZF2N2_ARATH	Zinc finger A20 and AN1 domains-containing protein At2g36320	0.41	-	nuc	0				1WFH	161
Q9SWF9 UniProt NPD GO	ZFNL_PEA	Zinc finger CCCH domain-containing protein ZFN-like	0.41	-	nuc	0	Nucleus (By similarity)				417
Q9SQU4 UniProt NPD GO	ZFNL2_ARATH	Zinc finger CCCH domain-containing protein ZFN-like 2	0.41	-	nuc	0	Nucleus (By similarity)				437
Q13360 UniProt NPD GO	ZN177_HUMAN	Zinc finger protein 177	0.41	-	nuc	0	Nucleus (Probable)		601276		321
Q9NW07 UniProt NPD GO	ZN358_HUMAN	Zinc finger protein 358	0.41	-	nuc	0	Nucleus (Probable)				481
Q96PM9 UniProt NPD GO	ZN385_HUMAN	Zinc finger protein 385 (Hematopoietic zinc finger protein) (Retinal zinc finger protein)	0.41	-	nuc	0	Cytoplasm. Nucleus; nucleolus		609124		366
Q9C0G0 UniProt NPD GO	ZN407_HUMAN	Zinc finger protein 407 (Fragment)	0.41	-	nuc	0	Nucleus (Potential)				1165
Q8N8Z8 UniProt NPD GO	ZN441_HUMAN	Zinc finger protein 441	0.41	-	nuc	0	Nucleus (Potential)				626
Q6ZMY9 UniProt NPD GO	ZN517_HUMAN	Zinc finger protein 517	0.41	-	nuc	0	Nucleus (Potential)				492
Q4R882 UniProt NPD GO	ZN561_MACFA	Zinc finger protein 561	0.41	-	nuc	0	Nucleus (Potential)				486
P35789 UniProt NPD GO	ZNF93_HUMAN	Zinc finger protein 93 (Zinc finger protein 505) (Zinc finger protein HTF34)	0.41	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	603975		620
P97469 UniProt NPD GO	SLUG_MOUSE	Zinc finger protein SLUG (Neural crest transcription factor Slug) (Snail homolog 2)	0.41	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			269
Q7JLI1 UniProt NPD GO	NAS31_CAEEL	Zinc metalloproteinase nas-31 precursor (EC 3.4.24.21) (Nematode astacin 31)	0.41	-	exc	0	Secreted protein (Potential)				611
Q18206 UniProt NPD GO	NAS36_CAEEL	Zinc metalloproteinase nas-36 precursor (EC 3.4.24.21) (Nematode astacin 36)	0.41	-	mit	0	Secreted protein (Potential)				617
P91828 UniProt NPD GO	NAS5_CAEEL	Zinc metalloproteinase nas-5 precursor (EC 3.4.24.21) (Nematode astacin 5)	0.41	-	exc	0	Secreted protein (Potential)				360
Q62384 UniProt NPD GO	ZPR1_MOUSE	Zinc-finger protein ZPR1 (Zinc finger protein 259)	0.41	-	nuc	0	Cytoplasm. Nucleus. Translocates to the nucleus after treatment with mitogens	cytoplasm [IDA] nucleus [IDA]			459
P25367 UniProt NPD GO	RNQ1_YEAST	[PIN+] prion protein RNQ1 (Rich in asparagine and glutamine protein 1)	0.41	-	nuc	0	Cytoplasm. Nucleus	cytosol [IDA]			405
Q26619 UniProt NPD GO	KAPR_STRPU	cAMP-dependent protein kinase type II regulatory subunit	0.41	+	cyt	0					369
Q922S4 UniProt NPD GO	PDE2A_MOUSE	cGMP-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) (Cyclic GMP-stimulated phosphodiesterase ...	0.41	-	mit	0	Membrane; peripheral membrane protein (Potential)			1MC0	916
Q62927 UniProt NPD GO	CNGA1_RAT	cGMP-gated cation channel alpha 1 (CNG channel alpha 1) (CNG-1) (CNG1) (Cyclic nucleotide-gated chan ...	0.41	+	nuc	2	Membrane; multi-pass membrane protein				683
Q6CWR0 UniProt NPD GO	MCE1_KLULA	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.41	-	nuc	0	Nucleus (By similarity)				466
P40997 UniProt NPD GO	MCE1_SCHPO	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.41	-	cyt	0	Nucleus				402
Q6C783 UniProt NPD GO	MCE1_YARLI	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.41	-	cyt	0	Nucleus (By similarity)				391
P16658 UniProt NPD GO	SEN2_YEAST	tRNA-splicing endonuclease subunit SEN2 (EC 3.1.27.9) (tRNA-intron endonuclease SEN2) (Splicing endo ...	0.41	-	cyt	0	Nucleus. Intracellular membrane; peripheral membrane protein. Mitochondrion; mitochondrial outer mem ...	mitochondrial outer membrane [IDA] nuclear inner membrane [TAS] tRNA-intron endonuclease complex [TAS]			377
Q8AVQ3 UniProt NPD GO	143BB_XENLA	14-3-3 protein beta/alpha-B	0.40	-	nuc	0	Cytoplasm (By similarity)				244
Q9Y6K5 UniProt NPD GO	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3 (EC 2.7.7.-) ((2-5')oligo(A) synthetase 3) (2-5A synthetase 3) (p1 ...	0.40	+	cyt	0		microsome [TAS]	603351		1087
Q5RE15 UniProt NPD GO	PSD8_PONPY	26S proteasome non-ATPase regulatory subunit 8	0.40	-	mit	0					257
Q99N84 UniProt NPD GO	RT18B_MOUSE	28S ribosomal protein S18b, mitochondrial precursor (MRP-S18-b) (Mrps18b) (MRP-S18-2)	0.40	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [ISS]			254
Q5RCA3 UniProt NPD GO	RM17_PONPY	39S ribosomal protein L17, mitochondrial precursor (L17mt) (MRP-L17)	0.40	-	nuc	0	Mitochondrion (Potential)				175
Q3T142 UniProt NPD GO	RM45_BOVIN	39S ribosomal protein L45, mitochondrial precursor (L45mt) (MRP-L45)	0.40	-	mit	0	Mitochondrion				306
O81014 UniProt NPD GO	ISPE_ARATH	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, chloroplast precursor (EC 2.7.1.148) (CMK) (4-(cy ...	0.40	+	mit	0	Plastid; chloroplast (By similarity)				383
P93836 UniProt NPD GO	HPPD_ARATH	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.40	-	cyt	0	Cytoplasm			1TG5	445
O42387 UniProt NPD GO	RS24_FUGRU	40S ribosomal protein S24	0.40	-	nuc	0					132
O45499 UniProt NPD GO	RS26_CAEEL	40S ribosomal protein S26	0.40	-	nuc	0					117
P29504 UniProt NPD GO	RS27A_MANSE	40S ribosomal protein S27a	0.40	+	nuc	0					79
P49397 UniProt NPD GO	RS3A_ORYSA	40S ribosomal protein S3a (CYC07 protein)	0.40	-	nuc	0					261
P07997 UniProt NPD GO	HEM1_CHICK	5-aminolevulinate synthase, nonspecific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic aci ...	0.40	-	mit	0	Mitochondrion; mitochondrial matrix				635
Q8VC19 UniProt NPD GO	HEM1_MOUSE	5-aminolevulinate synthase, nonspecific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic aci ...	0.40	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				642
P24613 UniProt NPD GO	RK21_SPIOL	50S ribosomal protein L21, chloroplast precursor (CL21) (CS-L7)	0.40	-	mit	0	Plastid; chloroplast				256
P23408 UniProt NPD GO	RK22_PEA	50S ribosomal protein L22, chloroplast precursor (CL22)	0.40	-	mit	0	Plastid; chloroplast				204
O49937 UniProt NPD GO	RK4_SPIOL	50S ribosomal protein L4, chloroplast precursor (R-protein L4)	0.40	-	mit	0	Plastid; chloroplast				293

You are viewing entries 31551 to 31600 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.