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
Q9URT2 UniProt NPD GO	YJU3_SCHPO	Hypothetical protein P25A2.03 in chromosome III	0.69	-	nuc	0					752
P34535 UniProt NPD GO	YNC2_CAEEL	Hypothetical protein R05D3.2	0.69	+	end	10 *					737
P30641 UniProt NPD GO	YNE2_CAEEL	Hypothetical protein R08D7.2	0.69	-	nuc	0					455
O88351 UniProt NPD GO	IKKB_MOUSE	Inhibitor of nuclear factor kappa B kinase subunit beta (EC 2.7.11.10) (I-kappa-B-kinase beta) (IkBK ...	0.69	-	nuc	0	Cytoplasm	cytoplasm [TAS]			757
Q9WU40 UniProt NPD GO	MAN1_MOUSE	Inner nuclear membrane protein Man1 (LEM domain-containing protein 3) (Fragment)	0.69	-	nuc	0	Nucleus; nuclear inner membrane; multi-pass membrane protein	nuclear envelope [IDA]			331
Q07079 UniProt NPD GO	IBP5_MOUSE	Insulin-like growth factor-binding protein 5 precursor (IGFBP-5) (IBP-5) (IGF-binding protein 5)	0.69	-	exc	0	Secreted protein	insulin-like growth factor binding protein ... [IC]			271
P07348 UniProt NPD GO	IFNA1_BOVIN	Interferon alpha-1 precursor	0.69	-	mit	1 *	Secreted protein				189
P10914 UniProt NPD GO	IRF1_HUMAN	Interferon regulatory factor 1 (IRF-1)	0.69	-	nuc	0	Nucleus		153550		325
Q9N0Y3 UniProt NPD GO	MX1_CANFA	Interferon-induced GTP-binding protein Mx1	0.69	-	cyt	0	Cytoplasm (By similarity)				657
Q8R5F7 UniProt NPD GO	IFIH1_MOUSE	Interferon-induced helicase C domain-containing protein 1 (EC 3.6.1.-) (Interferon induced with heli ...	0.69	-	nuc	0	Cytoplasm. Nucleus (Potential). May be found in the nucleus, during apoptosis				1025
Q03963 UniProt NPD GO	E2AK2_MOUSE	Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.11.1) (Interferon-inducible ...	0.69	-	nuc	0				1X49	515
O62802 UniProt NPD GO	IL2RA_CANFA	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (p55) ...	0.69	-	cyt	1	Membrane; single-pass type I membrane protein				268
Q9QY61 UniProt NPD GO	IRX4_MOUSE	Iroquois-class homeodomain protein IRX-4 (Iroquois homeobox protein 4) (Homeodomain protein IRXA3)	0.69	-	nuc	0	Nucleus (Probable)				515
P78412 UniProt NPD GO	IRX6_HUMAN	Iroquois-class homeodomain protein IRX-6 (Iroquois homeobox protein 6) (Homeodomain protein IRXB3)	0.69	-	nuc	0	Nucleus (Probable)		606196		445
Q8C863 UniProt NPD GO	ITCH_MOUSE	Itchy E3 ubiquitin protein ligase (EC 6.3.2.-)	0.69	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]		1YIU	864
Q9QXX0 UniProt NPD GO	JAG1_MOUSE	Jagged-1 precursor (Jagged1) (CD339 antigen)	0.69	-	nuc	1	Membrane; single-pass type I membrane protein	extracellular region [ISS] plasma membrane [IDA]			1218
Q6E0V2 UniProt NPD GO	KTNA1_RAT	Katanin p60 ATPase-containing subunit A1 (EC 3.6.4.3) (Katanin p60 subunit A1) (p60 katanin)	0.69	-	nuc	0	Cytoplasm (By similarity). Predominantly. Centrosome (By similarity). Also localized to the interpha ...				491
Q96AC6 UniProt NPD GO	KIFC2_HUMAN	Kinesin-like protein KIFC2	0.69	-	nuc	0					838
Q9BVG8 UniProt NPD GO	KIFC3_HUMAN	Kinesin-like protein KIFC3	0.69	-	nuc	0		kinesin complex [TAS]	604535		694
Q8CFA7 UniProt NPD GO	KLF17_MOUSE	Krueppel-like factor 17 (Zinc finger protein 393) (Germ cell-specific zinc finger protein)	0.69	-	nuc	0	Nucleus (Potential)				341
Q8IV42 UniProt NPD GO	PSTK_HUMAN	L-seryl-tRNA(Ser/Sec) kinase (EC 2.7.1.-) (Phosphoseryl-tRNA(Ser/Sec) kinase)	0.69	-	nuc	0					348
Q9XTB5 UniProt NPD GO	LEM2_CAEEL	LEM protein 2 (Ce-MAN1) (MAN1 homolog)	0.69	-	nuc	2	Nucleus; nuclear inner membrane; multi-pass membrane protein. Remains in the nuclear envelope until ...				500
P53413 UniProt NPD GO	LMX1B_CHICK	LIM/homeobox protein LMX-1.2 (Homeobox protein LMX-1) (LIM-homeobox protein 1) (LMX)	0.69	-	nuc	0	Nucleus				377
Q08282 UniProt NPD GO	LCMT2_YEAST	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.69	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			695
Q96QE4 UniProt NPD GO	LR37B_HUMAN	Leucine-rich repeat-containing protein 37B precursor (C66 SLIT-like testicular protein)	0.69	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				947
Q969E1 UniProt NPD GO	LEAP2_HUMAN	Liver-expressed antimicrobial peptide 2 precursor (LEAP-2)	0.69	-	exc	0	Secreted protein				77
Q91V13 UniProt NPD GO	LEAP2_MOUSE	Liver-expressed antimicrobial peptide 2 precursor (LEAP-2)	0.69	-	exc	0	Secreted protein				76
Q9JI18 UniProt NPD GO	LRP1B_MOUSE	Low-density lipoprotein receptor-related protein 1B precursor (Low-density lipoprotein receptor-rela ...	0.69	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	membrane fraction [IDA]			4599
P48967 UniProt NPD GO	MPIP3_MOUSE	M-phase inducer phosphatase 3 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25C)	0.69	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			447
Q05195 UniProt NPD GO	MAD_HUMAN	MAD protein (MAX dimerizer) (MAX dimerization protein 1)	0.69	-	nuc	0	Nucleus	nucleus [TAS]	600021	1S5Q	221
O42954 UniProt NPD GO	MBX1_SCHPO	MADS-box transcription factor 1	0.69	-	nuc	0	Nucleus (By similarity)	transcription factor complex [TAS]			436
Q40704 UniProt NPD GO	MADS3_ORYSA	MADS-box transcription factor 3 (OsMADS3) (Protein AGAMOUS-like) (RMADS222)	0.69	-	nuc	0	Nucleus (Probable)				236
Q6Z6W2 UniProt NPD GO	MAD57_ORYSA	MADS-box transcription factor 57 (OsMADS57)	0.69	-	nuc	0	Nucleus (Probable)				241
Q24618 UniProt NPD GO	EXU1_DROPS	Maternal protein exuperantia 1	0.69	-	nuc	0					495
Q53DU6 UniProt NPD GO	MATK_BERLA	Maturase K (Intron maturase)	0.69	-	cyt	0	Plastid; chloroplast				504
Q8MA20 UniProt NPD GO	MATK_DIOKA	Maturase K (Intron maturase)	0.69	-	cyt	0	Plastid; chloroplast				503
Q85ZM2 UniProt NPD GO	MATK_FAGES	Maturase K (Intron maturase)	0.69	-	cyt	0	Plastid; chloroplast				507
Q5J306 UniProt NPD GO	MATK_GOMPU	Maturase K (Intron maturase)	0.69	-	nuc	0	Plastid; chloroplast				505
Q8WJ26 UniProt NPD GO	MATK_MEMEL	Maturase K (Intron maturase)	0.69	-	nuc	0	Plastid; chloroplast				510
Q95DQ2 UniProt NPD GO	MATK_NICAL	Maturase K (Intron maturase)	0.69	-	cyt	0	Plastid; chloroplast				509
Q70D41 UniProt NPD GO	MATK_NICOT	Maturase K (Intron maturase)	0.69	-	cyt	0	Plastid; chloroplast				509
Q3MKB3 UniProt NPD GO	MATK_PERAC	Maturase K (Intron maturase)	0.69	-	nuc	0	Plastid; chloroplast				509
Q3MKA1 UniProt NPD GO	MATK_PORAR	Maturase K (Intron maturase)	0.69	-	nuc	0	Plastid; chloroplast				505
Q7YKM5 UniProt NPD GO	MATK_PROLU	Maturase K (Intron maturase)	0.69	-	pox	0	Plastid; chloroplast				500
O62991 UniProt NPD GO	MATK_RHOTS	Maturase K (Intron maturase)	0.69	-	nuc	0	Plastid; chloroplast				506
Q9MVV9 UniProt NPD GO	MATK_SCIVE	Maturase K (Intron maturase)	0.69	-	nuc	0	Plastid; chloroplast				505
P32088 UniProt NPD GO	MATK_SOLTU	Maturase K (Intron maturase)	0.69	-	cyt	0	Plastid; chloroplast				509
Q33134 UniProt NPD GO	MATK_SAXOP	Maturase K (Intron maturase) (Fragment)	0.69	-	cyt	0	Plastid; chloroplast				352
O95072 UniProt NPD GO	REC8L_HUMAN	Meiotic recombination protein REC8-like 1 (Cohesin Rec8p)	0.69	+	mit	0	Nucleus (By similarity). Localized along chromosome axis, but not chromosome ends (By similarity)	nucleus [TAS]	608193		547
Q5REE1 UniProt NPD GO	MIER1_PONPY	Mesoderm induction early response protein 1 (Mi-er1)	0.69	+	nuc	0	Nucleus (By similarity)				512

You are viewing entries 14301 to 14350 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.