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
Q9HGQ2 UniProt NPD GO	YLH4_SCHPO	Hypothetical protein C17D4.04 in chromosome I	0.67	-	nuc	0					654
O14106 UniProt NPD GO	YEJ6_SCHPO	Hypothetical protein C31G5.06 in chromosome I	0.67	-	exc	0					234
Q10308 UniProt NPD GO	YD55_SCHPO	Hypothetical protein C6C3.05 in chromosome I	0.67	-	nuc	0					269
Q8SVF3 UniProt NPD GO	Y609_ENCCU	Hypothetical protein ECU06_0090	0.67	+	cyt	0					606
P34451 UniProt NPD GO	YMA6_CAEEL	Hypothetical protein F54F2.6	0.67	-	nuc	0					71
O43615 UniProt NPD GO	TIM44_HUMAN	Import inner membrane translocase subunit TIM44, mitochondrial precursor	0.67	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial matrix [TAS]	605058	2CW9	452
Q4PEW9 UniProt NPD GO	TIM50_USTMA	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.67	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				493
Q02821 UniProt NPD GO	IMA1_YEAST	Importin subunit alpha (Karyopherin subunit alpha) (Serine-rich RNA polymerase I suppressor protein) ...	0.67	-	nuc	0	Cytoplasm; perinuclear region. Mainly localized at the periphery of the nucleus	cytoplasm [IDA] nucleus [IDA]		2C1T	542
Q91YX0 UniProt NPD GO	ICB1_MOUSE	Induced by contact to basement membrane 1 protein homolog (ICB-1 protein)	0.67	+	nuc	0					663
Q9QY78 UniProt NPD GO	IKKB_RAT	Inhibitor of nuclear factor kappa B kinase subunit beta (EC 2.7.11.1) (I-kappa-B-kinase beta) (IkBKB ...	0.67	-	nuc	0	Cytoplasm				757
Q92551 UniProt NPD GO	IP6K1_HUMAN	Inositol hexaphosphate kinase 1 (EC 2.7.4.21) (InsP6 kinase 1) (Inositol hexakisphosphate kinase 1)	0.67	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]	606991		441
Q96A47 UniProt NPD GO	ISL2_HUMAN	Insulin gene enhancer protein ISL-2 (Islet-2)	0.67	+	nuc	0	Nucleus (By similarity)		609481		359
P15127 UniProt NPD GO	INSR_RAT	Insulin receptor precursor (EC 2.7.10.1) (IR) [Contains: Insulin receptor subunit alpha; Insulin rec ...	0.67	+	end	1	Membrane; single-pass type I membrane protein				1383
O35368 UniProt NPD GO	IFI3_MOUSE	Interferon-activable protein 203 (Ifi-203) (Interferon-inducible protein p203)	0.67	+	nuc	0	Nucleus				408
Q9JIL3 UniProt NPD GO	ILF3_RAT	Interleukin enhancer-binding factor 3	0.67	-	nuc	0	Nucleus; nucleolus (By similarity)				897
Q19782 UniProt NPD GO	IFD2_CAEEL	Intermediate filament protein ifd-2 (Intermediate filament protein D2) (IF-D2) (Cel IF D2)	0.67	+	nuc	0	Cytoplasm (Probable)				443
Q8VCE1 UniProt NPD GO	CU055_MOUSE	J domain-containing protein C21orf55 homolog	0.67	-	nuc	0					349
Q60976 UniProt NPD GO	JERKY_MOUSE	Jerky protein	0.67	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA] ribonucleoprotein complex [IDA]			557
Q63679 UniProt NPD GO	JHD2A_RAT	JmjC domain-containing histone demethylation protein 2A (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.67	+	nuc	0	Nucleus (By similarity)				1214
O60663 UniProt NPD GO	LMX1B_HUMAN	LIM homeobox transcription factor 1 beta (LIM/homeobox protein LMX1B) (LIM-homeobox protein 1.2) (LM ...	0.67	-	nuc	0	Nucleus (Potential)	nucleus [IDA]	602575		379
O88609 UniProt NPD GO	LMX1B_MOUSE	LIM homeobox transcription factor 1 beta (LIM/homeobox protein LMX1B) (LIM-homeobox protein 1.2) (LM ...	0.67	-	nuc	0	Nucleus (Potential)	nucleus [ISS]			372
Q60564 UniProt NPD GO	LMX1B_MESAU	LIM homeobox transcription factor 1 beta (LIM/homeobox protein LMX1B) (LIM-homeobox protein 1.2) (LM ...	0.67	-	nuc	0	Nucleus (Potential)				369
P11046 UniProt NPD GO	LAMB1_DROME	Laminin beta-1 chain precursor (Laminin B1 chain)	0.67	-	nuc	0	Secreted protein; extracellular space	basal lamina [IDA]			1790
P07942 UniProt NPD GO	LAMB1_HUMAN	Laminin beta-1 chain precursor (Laminin B1 chain)	0.67	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	laminin-1 [TAS]	150240		1786
Q18823 UniProt NPD GO	LAML1_CAEEL	Laminin-like protein C54D1.5 precursor	0.67	-	nuc	0					1535
Q50LG9 UniProt NPD GO	LRC24_HUMAN	Leucine-rich repeat-containing protein 24 precursor	0.67	+	exc	1	Membrane; single-pass membrane protein (Potential)				513
Q4R3P6 UniProt NPD GO	LRC40_MACFA	Leucine-rich repeat-containing protein 40	0.67	-	nuc	0					602
Q4KM95 UniProt NPD GO	LRC42_RAT	Leucine-rich repeat-containing protein 42	0.67	-	nuc	0					421
P98158 UniProt NPD GO	LRP2_RAT	Low-density lipoprotein receptor-related protein 2 precursor (Megalin) (Glycoprotein 330) (gp330)	0.67	-	exc	1	Cell membrane; single-pass type I membrane protein. Expressed in clathrin-coated pits; a soluble for ...	membrane fraction [IDA]			4660
Q8VHC8 UniProt NPD GO	MA2B1_CAVPO	Lysosomal alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase, alpha B) (Lysosomal acid alpha-man ...	0.67	-	nuc	0	Lysosome				1007
Q2QW53 UniProt NPD GO	MAD13_ORYSA	MADS-box transcription factor 13 (OsMADS13) (RMADS206)	0.67	-	nuc	0	Nucleus (Probable)				270
Q84NC5 UniProt NPD GO	MAD25_ORYSA	MADS-box transcription factor 25 (OsMADS25)	0.67	-	nuc	0	Nucleus (Probable)				227
Q6EP49 UniProt NPD GO	MAD27_ORYSA	MADS-box transcription factor 27 (OsMADS27) (RMADS218)	0.67	-	nuc	0	Nucleus (Probable)				240
P49071 UniProt NPD GO	MAPK2_DROME	MAP kinase-activated protein kinase 2 (EC 2.7.11.1) (MAPK-activated protein kinase 2) (MAPKAP kinase ...	0.67	-	mit	0					359
Q8CIP4 UniProt NPD GO	MARK4_MOUSE	MAP/microtubule affinity-regulating kinase 4 (EC 2.7.11.1)	0.67	-	nuc	0		centrosome [ISS] neuron projection [ISS]			752
Q8SM90 UniProt NPD GO	MATK_ACECA	Maturase K (Intron maturase)	0.67	-	nuc	0	Plastid; chloroplast				512
O47141 UniProt NPD GO	MATK_ACTCH	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				504
Q9GF39 UniProt NPD GO	MATK_AETGR	Maturase K (Intron maturase)	0.67	-	mit	0	Plastid; chloroplast				504
Q8SM20 UniProt NPD GO	MATK_ANTMA	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				508
Q8WJ31 UniProt NPD GO	MATK_CHOSU	Maturase K (Intron maturase)	0.67	-	nuc	0	Plastid; chloroplast				503
Q5GIZ6 UniProt NPD GO	MATK_EUCGL	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				503
Q6EIJ9 UniProt NPD GO	MATK_FRECA	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				502
Q9GGJ8 UniProt NPD GO	MATK_HAMJA	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				504
Q9MT47 UniProt NPD GO	MATK_HAMVI	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				504
Q8MCS1 UniProt NPD GO	MATK_LATAP	Maturase K (Intron maturase)	0.67	-	nuc	0	Plastid; chloroplast				506
Q5YJU6 UniProt NPD GO	MATK_LUPAG	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				504
Q95DN9 UniProt NPD GO	MATK_NICDE	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				509
Q5GAB0 UniProt NPD GO	MATK_OTACA	Maturase K (Intron maturase)	0.67	-	pox	0	Plastid; chloroplast				509
Q5D1B9 UniProt NPD GO	MATK_OXYPI	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				506
Q5J2W2 UniProt NPD GO	MATK_PHASI	Maturase K (Intron maturase)	0.67	-	nuc	0	Plastid; chloroplast				505

You are viewing entries 15301 to 15350 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.