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
Q9BW62 UniProt NPD GO	KATL1_HUMAN	Katanin p60 ATPase-containing subunit A-like 1 (EC 3.6.4.3) (Katanin p60 subunit A-like 1) (p60 kata ...	0.43	-	nuc	0					490
Q5ZI33 UniProt NPD GO	KLHL7_CHICK	Kelch-like protein 7	0.43	+	nuc	0					586
Q8BUL5 UniProt NPD GO	KLHL7_MOUSE	Kelch-like protein 7	0.43	+	nuc	0					586
P02441 UniProt NPD GO	KRA3_SHEEP	Keratin, high-sulfur matrix protein, IIIA3	0.43	-	nuc	0					131
O93256 UniProt NPD GO	K1C19_CHICK	Keratin, type I cytoskeletal 19 (Cytokeratin-19) (CK-19) (Keratin-19) (K19) (GK-19)	0.43	-	nuc	0					423
Q29426 UniProt NPD GO	K2C3_RABIT	Keratin, type II cytoskeletal 3 (Cytokeratin-3) (CK-3) (Keratin-3) (K3)	0.43	-	cyt	0		keratin filament [ISS]			629
Q5XQN5 UniProt NPD GO	K2C5_BOVIN	Keratin, type II cytoskeletal 5 (Cytokeratin-5) (CK-5) (Keratin-5) (K5)	0.43	-	cyt	0		keratin filament [ISS]			601
O93532 UniProt NPD GO	K2CO_CHICK	Keratin, type II cytoskeletal cochleal (Cytokeratin otokeratin)	0.43	-	mit	0					492
Q26626 UniProt NPD GO	KIFA3_STRPU	Kinesin-associated protein 3 (SpKAP115)	0.43	-	nuc	0		kinesin II complex [IPI]			828
O45406 UniProt NPD GO	KBP3_CAEEL	Kinetochore-binding protein 3	0.43	-	nuc	0	Nucleus. Associated with kinetochores. Localize to kinetochores throughout mitosis. Begin to localiz ...				134
P83857 UniProt NPD GO	KNG_ANAMI	Kininogen [Contains: Bradykinin] (Fragments)	0.43	-	nuc	0					188
Q90W88 UniProt NPD GO	KNL1C_BOMMX	Kininogen-1c precursor (BMK-1) [Contains: Maximakinin (Bombinakinin M); Bradykinin]	0.43	-	exc	0	Secreted protein				152
P38169 UniProt NPD GO	BNA4_YEAST	Kynurenine 3-monooxygenase (EC 1.14.13.9) (Kynurenine 3-hydroxylase) (Biosynthesis of nicotinic acid ...	0.43	-	mit	0	Mitochondrion	mitochondrial outer membrane [IDA] mitochondrion [IDA]			460
P40126 UniProt NPD GO	TYRP2_HUMAN	L-dopachrome tautomerase precursor (EC 5.3.3.12) (DT) (DCT) (L-dopachrome delta-isomerase) (Tyrosina ...	0.43	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein	cytosol [ISS] integral to membrane [TAS] melanosome [ISS] microsome [ISS]	191275		519
P18337 UniProt NPD GO	LYAM1_MOUSE	L-selectin precursor (Lymph node homing receptor) (Leukocyte adhesion molecule 1) (LAM-1) (Lymphocyt ...	0.43	-	nuc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			372
Q9SZE8 UniProt NPD GO	LBD39_ARATH	LOB domain-containing protein 39	0.43	-	nuc	0					240
P08071 UniProt NPD GO	TRFL_MOUSE	Lactotransferrin precursor (EC 3.4.21.-) (Lactoferrin)	0.43	-	exc	0	Secreted protein				707
P11573 UniProt NPD GO	SEEP_RAPSA	Late seed maturation protein P8B6	0.43	-	nuc	0	Cytoplasm (Probable)				83
Q759U5 UniProt NPD GO	LCMT1_ASHGO	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.43	-	cyt	0					325
O60294 UniProt NPD GO	LCMT2_HUMAN	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-) (p21WAF1/CIP1 promoter-interacting protein)	0.43	-	cyt	0					686
O95202 UniProt NPD GO	LETM1_HUMAN	Leucine zipper-EF-hand-containing transmembrane protein 1, mitochondrial precursor	0.43	-	mit	1	Mitochondrion; mitochondrial membrane	integral to plasma membrane [TAS] mitochondrion [ISS]	604407		739
Q9BTT6 UniProt NPD GO	LRRC1_HUMAN	Leucine-rich repeat-containing protein 1 (LAP and no PDZ protein) (LANO adapter protein)	0.43	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Localized at the basolateral side of epithelial ce ...		608195		524
Q3ZC49 UniProt NPD GO	LRC39_BOVIN	Leucine-rich repeat-containing protein 39	0.43	-	nuc	0					334
Q8N653 UniProt NPD GO	LZTR1_HUMAN	Leucine-zipper-like transcriptional regulator 1 (LZTR-1)	0.43	-	cyt	0			600574		840
P42703 UniProt NPD GO	LIFR_MOUSE	Leukemia inhibitory factor receptor precursor (LIF receptor) (LIF-R) (D-factor/LIF receptor) (CD118 ...	0.43	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein				1092
Q5SCX2 UniProt NPD GO	CHLB_HUPLU	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.43	-	cyt	0	Plastid; chloroplast				511
Q9VKV5 UniProt NPD GO	LIN1_DROME	Lin1-like protein	0.43	-	nuc	0					319
Q7Z4F1 UniProt NPD GO	LRP10_HUMAN	Low-density lipoprotein receptor-related protein 10 precursor	0.43	-	exc	1	Membrane; single-pass type I membrane protein (Potential)		609921		713
Q9BE74 UniProt NPD GO	LRP12_MACFA	Low-density lipoprotein receptor-related protein 12 (Fragment)	0.43	-	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				701
Q05204 UniProt NPD GO	LAMP1_BOVIN	Lysosome-associated membrane glycoprotein 1 precursor (LAMP-1) (Chromaffin granule-associated membra ...	0.43	-	exc	2 *	Membrane; single-pass type I membrane protein. Chromaffin granule				408
Q2QQA3 UniProt NPD GO	MAD20_ORYSA	MADS-box transcription factor 20 (OsMADS20)	0.43	-	nuc	0	Nucleus (Probable)				233
Q2QW55 UniProt NPD GO	MAD33_ORYSA	MADS-box transcription factor 33 (OsMADS33)	0.43	-	mit	0	Nucleus (Probable)				202
Q8NFP4 UniProt NPD GO	MDGA1_HUMAN	MAM domain-containing glycosylphosphatidylinositol anchor protein 1 precursor (MAM domain-containing ...	0.43	-	nuc	0	Secreted protein (Potential)		609626		955
Q04912 UniProt NPD GO	RON_HUMAN	Macrophage-stimulating protein receptor precursor (EC 2.7.10.1) (MSP receptor) (p185-Ron) (CDw136 an ...	0.43	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600168		1400
Q6B8U1 UniProt NPD GO	ACSF_GRATL	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (EC 1.14.13.81) (Mg-protoporphyrin ...	0.43	-	cyt	0	Plastid; chloroplast				349
Q9UM22 UniProt NPD GO	EPDR1_HUMAN	Mammalian ependymin-related protein 1 precursor (MERP-1) (UCC1 protein)	0.43	-	exc	1 *	Secreted protein				224
Q5FWY4 UniProt NPD GO	MCM6M_XENLA	Maternal DNA replication licensing factor mcm6 (Maternal minichromosome maintenance protein 6) (mMCM ...	0.43	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [IDA] MCM complex [IDA]			821
Q6WRX7 UniProt NPD GO	MATMI_SCHKA	Mating-type M-specific polypeptide Mi	0.43	-	nuc	0					42
P10839 UniProt NPD GO	MATMI_SCHPO	Mating-type M-specific polypeptide Mi	0.43	-	nuc	0					42
Q874N0 UniProt NPD GO	MTAL1_KLUDE	Mating-type protein ALPHA1	0.43	-	nuc	0	Nucleus (By similarity)				194
P47841 UniProt NPD GO	MGP_RABIT	Matrix Gla-protein precursor (MGP)	0.43	-	exc	0	Secreted protein				103
P68750 UniProt NPD GO	MATK_LILCA	Maturase K (Intron maturase)	0.43	-	cyt	0	Plastid; chloroplast				512
P68751 UniProt NPD GO	MATK_LILMI	Maturase K (Intron maturase)	0.43	-	cyt	0	Plastid; chloroplast				512
P68752 UniProt NPD GO	MATK_LILSU	Maturase K (Intron maturase)	0.43	-	cyt	0	Plastid; chloroplast				512
Q58T64 UniProt NPD GO	M3112_BOMMX	Maximins 3/H11 type 2 precursor [Contains: Maximin-3; Maximin-H11]	0.43	-	end	0	Secreted protein				144
Q9CXU1 UniProt NPD GO	MED31_MOUSE	Mediator of RNA polymerase II transcription subunit 31 (Mediator complex subunit SOH1)	0.43	-	cyt	0	Nucleus (Potential)				131
Q6CTF5 UniProt NPD GO	MSC6_KLULA	Meiotic sister-chromatid recombination protein 6, mitochondrial precursor	0.43	-	mit	0	Mitochondrion (By similarity)				708
Q80TE3 UniProt NPD GO	MARH4_MOUSE	Membrane-associated RING finger protein 4 (Membrane-associated RING-CH protein IV) (MARCH-IV)	0.43	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				408
P35349 UniProt NPD GO	MGR6_RAT	Metabotropic glutamate receptor 6 precursor (mGluR6)	0.43	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			871
Q9H492 UniProt NPD GO	MLP3A_HUMAN	Microtubule-associated proteins 1A/1B light chain 3A precursor (MAP1A/MAP1B LC3 A) (MAP1A/1B light c ...	0.43	-	nuc	0	LC3-I: Cytoplasm. LC3-II: Intracytoplasmic membrane; lipid-anchor. LC3-II binds to the autophagic me ...	autophagic vacuole [IDA] organelle membrane [IDA]	601242		121

You are viewing entries 29751 to 29800 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.