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
O17586 UniProt NPD GO	PSA6_CAEEL	Proteasome subunit alpha type 6 (EC 3.4.25.1) (Proteasome subunit alpha 1)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
Q9Z2U0 UniProt NPD GO	PSA7_MOUSE	Proteasome subunit alpha type 7 (EC 3.4.25.1) (Proteasome subunit RC6-1)	0.06	-	mit	0	Cytoplasm. Nucleus				248
P48004 UniProt NPD GO	PSA7_RAT	Proteasome subunit alpha type 7 (EC 3.4.25.1) (Proteasome subunit RC6-1)	0.06	-	mit	0	Cytoplasm. Nucleus				254
Q9PVQ1 UniProt NPD GO	PSA7B_XENLA	Proteasome subunit alpha type 7-B (EC 3.4.25.1) (Proteasome subunit alpha 4-B)	0.06	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				247
O24616 UniProt NPD GO	PSA7B_ARATH	Proteasome subunit alpha type 7-B (EC 3.4.25.1) (Proteasome subunit alpha type 4) (20S proteasome al ...	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
P40304 UniProt NPD GO	PSB1_DROME	Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome 26 kDa subunit)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				235
Q5R4W2 UniProt NPD GO	AF1Q_PONPY	Protein AF1q	0.06	-	cyt	0					90
Q3SZW3 UniProt NPD GO	ARV1_BOVIN	Protein ARV1	0.06	-	end	3	Membrane; multi-pass membrane protein (Potential)				282
P31386 UniProt NPD GO	ATS1_YEAST	Protein ATS1 (Alpha-tubulin suppressor 1)	0.06	-	cyt	0		cytoplasm [IPI]			333
Q94EG6 UniProt NPD GO	Y5224_ARATH	Protein At5g02240	0.06	-	mit	0				1YBM	253
Q9US39 UniProt NPD GO	YFZ2_SCHPO	Protein C1039.02 precursor	0.06	-	vac	0	Membrane				601
Q96DE5 UniProt NPD GO	CJ104_HUMAN	Protein C10orf104	0.06	-	cyt	0					110
Q58DR0 UniProt NPD GO	CJ104_BOVIN	Protein C10orf104 homolog	0.06	-	cyt	0					110
Q9CPV2 UniProt NPD GO	CJ104_MOUSE	Protein C10orf104 homolog	0.06	-	cyt	0					110
Q5REH8 UniProt NPD GO	CJ104_PONPY	Protein C10orf104 homolog	0.06	-	cyt	0					110
Q5ZK09 UniProt NPD GO	CK073_CHICK	Protein C11orf73 homolog	0.06	-	cyt	0	Cytoplasm (By similarity)				197
Q5M808 UniProt NPD GO	CK073_RAT	Protein C11orf73 homolog	0.06	-	cyt	0	Cytoplasm (By similarity)				158
Q99LS1 UniProt NPD GO	CB025_MOUSE	Protein C2orf25 homolog, mitochondrial precursor	0.06	-	mit	0	Mitochondrion (Potential)				296
Q6AYQ6 UniProt NPD GO	CB025_RAT	Protein C2orf25 homolog, mitochondrial precursor	0.06	-	mit	0	Mitochondrion (Potential)				296
Q9H0P7 UniProt NPD GO	CF059_HUMAN	Protein C6orf59	0.06	-	cyt	0			609891		198
Q6YKA8 UniProt NPD GO	DRK_DROSI	Protein E(sev)2B (Protein enhancer of sevenless 2B) (SH2-SH3 adapter protein drk) (Downstream of rec ...	0.06	-	cyt	0	Membrane; peripheral membrane protein (By similarity)	plasma membrane [ISS]			211
Q9Y3D0 UniProt NPD GO	FA96B_HUMAN	Protein FAM96B	0.06	-	cyt	0					163
Q9D187 UniProt NPD GO	FA96B_MOUSE	Protein FAM96B	0.06	-	cyt	0					163
O88823 UniProt NPD GO	JTB_RAT	Protein JTB precursor	0.06	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				146
Q870V7 UniProt NPD GO	PNS1_NEUCR	Protein PNS1	0.06	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				554
Q9UI25 UniProt NPD GO	P461_HUMAN	Protein PRO0461	0.06	-	nuc	0					63
Q9UI54 UniProt NPD GO	P628_HUMAN	Protein PRO0628	0.06	-	nuc	1 *					55
P31949 UniProt NPD GO	S10AB_HUMAN	Protein S100-A11 (S100 calcium-binding protein A11) (Protein S100C) (Calgizzarin) (MLN 70)	0.06	-	nuc	0		cytoplasm [TAS] nucleus [TAS]	603114	1V50	105
Q3MHP3 UniProt NPD GO	S10AE_BOVIN	Protein S100-A14 (S100 calcium-binding protein A14)	0.06	-	nuc	0	Cytoplasm (By similarity)				104
Q9D2Q8 UniProt NPD GO	S10AE_MOUSE	Protein S100-A14 (S100 calcium-binding protein A14) (S114)	0.06	-	nuc	0	Cytoplasm (By similarity)				104
Q754F0 UniProt NPD GO	SYM1_ASHGO	Protein SYM1	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				182
Q9CZR3 UniProt NPD GO	TM40L_MOUSE	Protein TOMM40-like	0.06	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				308
P53738 UniProt NPD GO	TR112_YEAST	Protein TRM112 (tRNA methyltransferase 112)	0.06	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]			135
P49338 UniProt NPD GO	WNT4_XENLA	Protein Wnt-4 precursor (XWnt-4)	0.06	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix				351
Q91VU1 UniProt NPD GO	YIPF1_MOUSE	Protein YIPF1 (YIP1 family member 1)	0.06	-	end	5	Membrane; multi-pass membrane protein (Potential)				306
Q5XIT3 UniProt NPD GO	YIPF2_RAT	Protein YIPF2 (YIP1 family member 2)	0.06	-	end	5	Membrane; multi-pass membrane protein (Potential)				311
Q9EQQ2 UniProt NPD GO	YIPF5_MOUSE	Protein YIPF5 (YIP1 family member 5) (YPT-interacting protein 1 A)	0.06	-	end	4	Golgi apparatus; Golgi stack; Golgi stack membrane; multi-pass membrane protein. COPII coated vesicl ...	nuclear envelope-endoplasmic reticulum network [IDA]			257
Q9R144 UniProt NPD GO	ANM2_MOUSE	Protein arginine N-methyltransferase 2 (EC 2.1.1.-)	0.06	-	nuc	0					448
Q27257 UniProt NPD GO	DIF1_CAEEL	Protein dif-1	0.06	-	cyt	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial envelope [IMP]			312
P32474 UniProt NPD GO	EUG1_YEAST	Protein disulfide-isomerase EUG1 precursor (EC 5.3.4.1) (PDI) (Endoplasmic reticulum protein EUG1)	0.06	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [IDA]			517
Q08012 UniProt NPD GO	DRK_DROME	Protein enhancer of sevenless 2B (Protein E(sev)2B) (SH2-SH3 adapter protein drk) (Downstream of rec ...	0.06	-	cyt	0	Membrane; peripheral membrane protein	plasma membrane [IDA]		2AZV	211
Q24188 UniProt NPD GO	LBM_DROME	Protein late bloomer	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	extracellular region [IDA]			208
O42335 UniProt NPD GO	PTC1_CYNPY	Protein patched homolog 1 (PTC1) (Fragment)	0.06	-	cyt	2	Membrane; multi-pass membrane protein				257
Q6CQZ5 UniProt NPD GO	PPME1_KLULA	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.06	-	cyt	0					395
Q23921 UniProt NPD GO	PKIA_DICDI	Protein pkiA	0.06	-	mit	0					172
Q9SM41 UniProt NPD GO	SUI1_SPOST	Protein translation factor SUI1 homolog	0.06	-	cyt	0					115
Q7SZU9 UniProt NPD GO	SC61G_GADMO	Protein transport protein SEC61 subunit gamma	0.06	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				68
Q9V3J8 UniProt NPD GO	WDS_DROME	Protein will die slowly	0.06	-	nuc	0					361
P62408 UniProt NPD GO	YELL_DROMA	Protein yellow precursor	0.06	-	exc	0	Secreted protein				541
P09957 UniProt NPD GO	YELL_DROME	Protein yellow precursor	0.06	-	exc	0	Secreted protein				541

You are viewing entries 72951 to 73000 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.