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
P87317 UniProt NPD GO	YB2G_SCHPO	Protein C31F10.16 in chromosome II	0.20	-	cyt	0	Nucleus				679
Q6UWU4 UniProt NPD GO	CF089_HUMAN	Protein C6orf89	0.20	-	mit	1	Membrane; single-pass membrane protein (Potential)				347
Q8WUY3 UniProt NPD GO	CI065_HUMAN	Protein C9orf65	0.20	-	nuc	0					259
Q29611 UniProt NPD GO	CLN3_CANFA	Protein CLN3 (Battenin)	0.20	-	end	9 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				438
Q94KT8 UniProt NPD GO	COBRA_ARATH	Protein COBRA precursor (Cell expansion protein)	0.20	-	mit	1	Cell membrane; lateral cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). Locat ...	anchored to membrane [TAS]			456
O96002 UniProt NPD GO	CX001_HUMAN	Protein CXorf1	0.20	-	mit	2 *			300565		111
Q9NQM4 UniProt NPD GO	CX041_HUMAN	Protein CXorf41 (Sarcoma antigen NY-SAR-97)	0.20	-	nuc	0					214
Q6P1Z5 UniProt NPD GO	F113A_MOUSE	Protein FAM113A	0.20	-	cyt	0					449
Q6AYJ2 UniProt NPD GO	FA44B_RAT	Protein FAM44B	0.20	-	nuc	0					173
Q6C5P9 UniProt NPD GO	GRC3_YARLI	Protein GRC3	0.20	+	mit	0	Nucleus (By similarity)				599
Q8CHG5 UniProt NPD GO	K0317_MOUSE	Protein KIAA0317	0.20	-	cyt	1 *					823
P41821 UniProt NPD GO	MID1_YEAST	Protein MID1	0.20	-	nuc	0	Membrane; single-pass type II membrane protein (Potential)	endoplasmic reticulum [IDA] plasma membrane [IDA]			548
P31950 UniProt NPD GO	S10AB_PIG	Protein S100-A11 (S100 calcium-binding protein A11) (Protein S100C) (Calgizzarin)	0.20	-	nuc	0				1QLS	99
Q9TV56 UniProt NPD GO	S10A4_CANFA	Protein S100-A4 (S100 calcium-binding protein A4) (Metastasin)	0.20	-	cyt	0					101
P35466 UniProt NPD GO	S10A4_BOVIN	Protein S100-A4 (S100 calcium-binding protein A4) (Metastasin) (Placental calcium-binding protein ho ...	0.20	-	cyt	0					100
P82625 UniProt NPD GO	SCRL6_ARATH	Protein SCRL6 precursor	0.20	-	exc	0					95
P40318 UniProt NPD GO	SSM4_YEAST	Protein SSM4	0.20	-	end	14		integral to endoplasmic reticulum membrane [IDA] nuclear envelope [IDA]			1319
Q5R9S0 UniProt NPD GO	TMED8_PONPY	Protein TMED8	0.20	-	nuc	0					326
P38288 UniProt NPD GO	TOS1_YEAST	Protein TOS1 precursor (Target of SBF 1)	0.20	-	exc	0	Secreted protein (Potential)	cell wall (sensu Fungi) [IDA] vacuole (sensu Fungi) [IDA]			455
Q8S8I2 UniProt NPD GO	ULT2_ARATH	Protein ULTRAPETALA2	0.20	-	nuc	0	Cytoplasm. Nucleus	cytosol [IDA] nucleus [IDA]			228
Q8NJR6 UniProt NPD GO	URE2_SACBA	Protein URE2	0.20	-	mit	0					345
P22724 UniProt NPD GO	WNT4_MOUSE	Protein Wnt-4 precursor	0.20	-	gol	1 *	Secreted protein; extracellular space; extracellular matrix				351
O13267 UniProt NPD GO	WNT5A_PLEWA	Protein Wnt-5a precursor (PWnt-5a)	0.20	-	exc	0	Secreted protein; extracellular space; extracellular matrix				359
P28118 UniProt NPD GO	WNT5B_EUMSK	Protein Wnt-5b (Fragment)	0.20	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
Q06443 UniProt NPD GO	WNT5B_AMBME	Protein Wnt-5b precursor	0.20	-	exc	0	Secreted protein; extracellular space; extracellular matrix				357
P22726 UniProt NPD GO	WNT5B_MOUSE	Protein Wnt-5b precursor	0.20	-	exc	0	Secreted protein; extracellular space; extracellular matrix				359
P28144 UniProt NPD GO	WNT7B_SCEOC	Protein Wnt-7b (Fragment)	0.20	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P87127 UniProt NPD GO	ATP11_SCHPO	Protein atp11, mitochondrial precursor	0.20	-	nuc	0	Mitochondrion (By similarity)				286
Q02030 UniProt NPD GO	HUNB_LITFO	Protein hunchback (Fragment)	0.20	-	nuc	0	Nucleus (Probable)				50
Q02032 UniProt NPD GO	HUNB_PSYCI	Protein hunchback (Fragment)	0.20	-	nuc	0	Nucleus (Probable)				50
P05772 UniProt NPD GO	KPCB_RABIT	Protein kinase C beta type (EC 2.7.11.13) (PKC-beta) (PKC-B)	0.20	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				670
Q61220 UniProt NPD GO	NELL2_MOUSE	Protein kinase C-binding protein NELL2 precursor (NEL-like protein 2) (MEL91 protein)	0.20	-	mit	1 *	Secreted protein (By similarity)				816
Q02415 UniProt NPD GO	KRUP_CUPSA	Protein krueppel (Fragment)	0.20	-	nuc	0	Nucleus (Probable)				46
Q8J2P4 UniProt NPD GO	SC61B_KLULA	Protein transport protein SEC61 subunit beta	0.20	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				88
P10090 UniProt NPD GO	WHITE_DROME	Protein white	0.20	-	end	5	Integral membrane protein; pigment granules within pigment cells and retinula cells of the compound ...				687
Q9GLK0 UniProt NPD GO	TGM1_CANFA	Protein-glutamine gamma-glutamyltransferase K (EC 2.3.2.13) (Transglutaminase K) (TGase K) (TGK) (TG ...	0.20	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				815
Q5R537 UniProt NPD GO	THRB_PONPY	Prothrombin precursor (EC 3.4.21.5) (Coagulation factor II) [Contains: Activation peptide fragment 1 ...	0.20	-	exc	0					623
Q9Y5E2 UniProt NPD GO	PCDB7_HUMAN	Protocadherin beta 7 precursor (PCDH-beta7)	0.20	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]	606333		793
Q5DRC4 UniProt NPD GO	PCDB9_PANTR	Protocadherin beta 9 precursor (PCDH-beta9)	0.20	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				797
Q9Y5E1 UniProt NPD GO	PCDB9_HUMAN	Protocadherin beta 9 precursor (PCDH-beta9) (Protocadherin 3H)	0.20	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]	606335		797
Q9Y5G9 UniProt NPD GO	PCDG4_HUMAN	Protocadherin gamma A4 precursor (PCDH-gamma-A4)	0.20	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606291		931
Q12355 UniProt NPD GO	PST1_YEAST	Protoplast secreted protein 1 precursor	0.20	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein. Secreted by regenerating protoplasts	cell wall (sensu Fungi) [IDA]			444
Q06244 UniProt NPD GO	PUS5_YEAST	Pseudouridylate synthase PUS5 (EC 5.4.99.-) (Pseudouridine synthase 5) (Uracil hydrolyase PUS5)	0.20	-	nuc	0	Mitochondrion	mitochondrion [IMP]			254
Q80ZC9 UniProt NPD GO	PS1C2_MOUSE	Psoriasis susceptibility 1 candidate gene 2 protein homolog precursor (SPR1 protein)	0.20	-	exc	0	Secreted protein (Potential)				134
Q7YR45 UniProt NPD GO	PS1C2_PANTR	Psoriasis susceptibility 1 candidate gene 2 protein homolog precursor (SPR1 protein)	0.20	-	exc	0	Secreted protein (Potential)				136
Q9LPV3 UniProt NPD GO	R27A1_ARATH	Putative 60S ribosomal protein L27a-1	0.20	-	mit	0					104
Q9MUL7 UniProt NPD GO	RPOZ_MESVI	Putative DNA-directed RNA polymerase omega chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase ...	0.20	-	nuc	0	Plastid; chloroplast				75
P49671 UniProt NPD GO	FER1_ASCSU	Putative FERT-1 protein	0.20	-	nuc	0					137
Q960A0 UniProt NPD GO	YS9A_CAEEL	Putative G-protein coupled receptor B0244.10	0.20	-	end	13 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			628
P49048 UniProt NPD GO	GPI8_CAEEL	Putative GPI-anchor transamidase (EC 3.-.-.-) (GPI transamidase)	0.20	-	mit	0					322

You are viewing entries 51101 to 51150 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.