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
P00744 UniProt NPD GO	PROZ_BOVIN	Vitamin K-dependent protein Z	0.17	-	cyt	0	Secreted protein				396
Q8VHW7 UniProt NPD GO	CCG6_RAT	Voltage-dependent calcium channel gamma-6 subunit (Neuronal voltage-gated calcium channel gamma-6 su ...	0.17	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				260
Q9PWR1 UniProt NPD GO	KCAB1_CHICK	Voltage-gated potassium channel subunit beta-1 (K(+) channel subunit beta-1) (Kv-beta-1)	0.17	-	cyt	0	Cytoplasm (Potential)				401
Q28528 UniProt NPD GO	KCAB1_MUSPU	Voltage-gated potassium channel subunit beta-1 (K(+) channel subunit beta-1) (Kv-beta-1)	0.17	-	cyt	0	Cytoplasm (Potential)				408
Q8CHN3 UniProt NPD GO	WFDC2_RAT	WAP four-disulfide core domain protein 2 precursor (Epididymal secretory protein 4) (RE4)	0.17	-	exc	0	Secreted protein (Potential)				168
Q6DCN1 UniProt NPD GO	WIPI1_XENLA	WD repeat domain phosphoinositide-interacting protein 1 (WIPI-1)	0.17	-	nuc	0	Trans elements of the Golgi and peripheral endosomes. Dynamically cycles through these compartments ...				433
Q4VBE8 UniProt NPD GO	WDR18_MOUSE	WD repeat protein 18	0.17	-	cyt	0					431
Q8NEZ3 UniProt NPD GO	WDR19_HUMAN	WD repeat protein 19	0.17	-	cyt	0			608151		1342
P58930 UniProt NPD GO	WAG2_TRIWA	Waglerin-2 (Waglerin II) (Lethal peptide II)	0.17	-	nuc	0	Secreted protein				22
Q9C6W5 UniProt NPD GO	WBC14_ARATH	White-brown complex homolog protein 14	0.17	-	nuc	7	Membrane; multi-pass membrane protein (By similarity)				648
Q9LZJ3 UniProt NPD GO	XT1_ARATH	Xyloglucan 6-xylosyltransferase (EC 2.4.2.39) (AtXT1)	0.17	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				460
O95365 UniProt NPD GO	ZBT7A_HUMAN	Zinc finger and BTB domain-containing protein 7A (Leukemia/lymphoma-related factor) (Factor that bin ...	0.17	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]	605878		584
P35273 UniProt NPD GO	ZN123_HUMAN	Zinc finger protein 123 (HZF-1) (Fragment)	0.17	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194630		74
Q22710 UniProt NPD GO	NAS26_CAEEL	Zinc metalloproteinase nas-26 precursor (EC 3.4.24.21) (Nematode astacin 26) (Tollish protein 1)	0.17	-	cyt	0	Secreted protein (Potential)				414
Q18439 UniProt NPD GO	NAS8_CAEEL	Zinc metalloproteinase nas-8 precursor (EC 3.4.24.21) (Nematode astacin 8)	0.17	-	end	1 *	Secreted protein (Potential)				403
P21754 UniProt NPD GO	ZP3_HUMAN	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Zona pellucida p ...	0.17	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...	extracellular matrix (sensu Metazoa) [NAS]	182889		424
Q9HEP7 UniProt NPD GO	KAPR_BLUGR	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.17	-	cyt	0					389
Q6C922 UniProt NPD GO	YTH1_YARLI	mRNA 3'-end-processing protein YTH1	0.17	-	nuc	0	Nucleus (By similarity)				193
Q59YK4 UniProt NPD GO	PALH_CANAL	pH-response regulator protein palH/RIM21	0.17	-	end	6	Membrane; multi-pass membrane protein (Potential)				529
Q9P8G9 UniProt NPD GO	PACC_COLSU	pH-response transcription factor pacC/RIM101 (Fragment)	0.17	-	nuc	0					71
Q5E9M5 UniProt NPD GO	SNPC3_BOVIN	snRNA-activating protein complex subunit 3 (SNAPc subunit 3) (snRNA-activating protein complex 50 kD ...	0.17	-	cyt	0	Nucleus (By similarity)				412
Q8K1J6 UniProt NPD GO	TRNT1_MOUSE	tRNA-nucleotidyltransferase 1, mitochondrial precursor (EC 2.7.7.25) (mitochondrial tRNA nucleotidyl ...	0.17	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			434
Q9URQ3 UniProt NPD GO	TAD3_YEAST	tRNA-specific adenosine deaminase subunit TAD3 (EC 3.5.4.-) (tRNA-specific adenosine-34 deaminase su ...	0.17	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			322
Q9P8U4 UniProt NPD GO	GEL2_ASPFU	1,3-beta-glucanosyltransferase gel2 precursor (EC 2.4.1.-) (Glucan elongating glucanosyltransferase ...	0.16	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				475
Q6T308 UniProt NPD GO	GLGB_FELCA	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme) (Brancher enzyme)	0.16	-	cyt	0					699
Q10184 UniProt NPD GO	HIS4_SCHPO	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.16	-	cyt	0	Cytoplasm (By similarity)				264
Q9NRZ7 UniProt NPD GO	PLCC_HUMAN	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (EC 2.3.1.51) (1-AGP acyltransferase 3) (1-AGPA ...	0.16	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				376
Q5RA57 UniProt NPD GO	PLCC_PONPY	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (EC 2.3.1.51) (1-AGP acyltransferase 3) (1-AGPA ...	0.16	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				376
P54632 UniProt NPD GO	1433_DICDI	14-3-3-like protein	0.16	-	nuc	0					252
P42654 UniProt NPD GO	1433B_VICFA	14-3-3-like protein B (VFA-1433B)	0.16	-	cyt	0					261
Q96299 UniProt NPD GO	14339_ARATH	14-3-3-like protein GF14 mu (General regulatory factor 9)	0.16	-	cyt	0					263
Q7Z5P4 UniProt NPD GO	DHB13_HUMAN	17-beta hydroxysteroid dehydrogenase 13 precursor (EC 1.1.-.-) (Short-chain dehydrogenase/reductase ...	0.16	-	mit	1 *	Secreted protein (Potential)				300
P19242 UniProt NPD GO	HSP21_PEA	17.1 kDa class II heat shock protein	0.16	-	cyt	0	Cytoplasm				152
Q05058 UniProt NPD GO	RASL_COPCI	24 kDa RAS-like protein	0.16	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				215
Q94AU2 UniProt NPD GO	SEC22_ARATH	25.3 kDa vesicle transport protein (AtSEC22)	0.16	-	cyt	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				218
Q9FXT9 UniProt NPD GO	PRS7_ORYSA	26S protease regulatory subunit 7 (26S proteasome subunit 7) (26S proteasome AAA-ATPase subunit RPT1 ...	0.16	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				426
Q41365 UniProt NPD GO	PRS7_SPIOL	26S protease regulatory subunit 7 (26S proteasome subunit 7) (26S proteasome AAA-ATPase subunit RPT1 ...	0.16	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				426
O88761 UniProt NPD GO	PSD1_RAT	26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit RPN2) (26S proteas ...	0.16	-	cyt	0					953
P32565 UniProt NPD GO	RPN2_YEAST	26S proteasome regulatory subunit RPN2	0.16	-	cyt	0		nucleus [IDA] proteasome regulatory particle, base subcom... [IPI]			944
P82912 UniProt NPD GO	RT11_HUMAN	28S ribosomal protein S11, mitochondrial precursor (S11mt) (MRP-S11) (Cervical cancer proto-oncogene ...	0.16	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [ISS]			194
Q9NWU1 UniProt NPD GO	OXSM_HUMAN	3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial precursor (EC 2.3.1.41) (Beta-ketoacyl synt ...	0.16	-	mit	0	Mitochondrion	mitochondrion [IMP]		2C9H	459
P34753 UniProt NPD GO	PHYA_ASPAW	3-phytase A precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase A) (3 phytase A) ( ...	0.16	-	mit	0	Secreted protein				467
Q949R4 UniProt NPD GO	DIOXL_ARATH	4,5-DOPA dioxygenase extradiol-like protein	0.16	-	cyt	0					269
Q9LTF2 UniProt NPD GO	RS10C_ARATH	40S ribosomal protein S10-3	0.16	-	cyt	0	Cytoplasm (By similarity)				179
Q03334 UniProt NPD GO	RS13_DROME	40S ribosomal protein S13	0.16	-	nuc	0					150
Q96W53 UniProt NPD GO	RS14_CANAL	40S ribosomal protein S14	0.16	-	mit	0					134
P33095 UniProt NPD GO	RS15A_STRPU	40S ribosomal protein S15a (Ribosomal protein S24)	0.16	-	cyt	0					129
P63273 UniProt NPD GO	RS17_CANFA	40S ribosomal protein S17	0.16	-	nuc	0					134
P63274 UniProt NPD GO	RS17_CRIGR	40S ribosomal protein S17	0.16	-	nuc	0					134
P63275 UniProt NPD GO	RS17_FELCA	40S ribosomal protein S17	0.16	-	nuc	0					134

You are viewing entries 55151 to 55200 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.