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
Q9UBI1 UniProt NPD GO	COMD3_HUMAN	COMM domain-containing protein 3 (Bup protein) (PIL protein)	0.39	-	nuc	0					195
Q96PZ7 UniProt NPD GO	CSMD1_HUMAN	CUB and sushi domain-containing protein 1 precursor (CUB and sushi multiple domains protein 1)	0.39	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)		608397		3565
Q6URK6 UniProt NPD GO	CADH5_BOVIN	Cadherin-5 precursor (Vascular endothelial-cadherin) (VE-cadherin) (CD144 antigen)	0.39	+	end	2 *	Cell membrane; cell-cell junction; single-pass type I membrane protein. Cell membrane; cell-matrix j ...				783
Q9SUA6 UniProt NPD GO	CNBL7_ARATH	Calcineurin B-like protein 7 (SOS3-like calcium-binding protein 3)	0.39	-	cyt	0					214
Q9UKA8 UniProt NPD GO	CCP3_HUMAN	Calcipressin-3 (Down syndrome candidate region 1-like protein 2) (Myocyte-enriched calcineurin-inter ...	0.39	-	nuc	0			605860		241
P01256 UniProt NPD GO	CALCA_RAT	Calcitonin gene-related peptide 1 precursor (Calcitonin gene-related peptide I) (CGRP-I) (Alpha-type ...	0.39	-	vac	0	Secreted protein				128
P01261 UniProt NPD GO	CALC_SHEEP	Calcitonin precursor	0.39	-	exc	0	Secreted protein				143
Q9Y691 UniProt NPD GO	KCMB2_HUMAN	Calcium-activated potassium channel subunit beta 2 (Calcium-activated potassium channel, subfamily M ...	0.39	-	nuc	2 *	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [IDA]	605214	1JO6	235
Q9DB16 UniProt NPD GO	CB39L_MOUSE	Calcium-binding protein 39-like (Mo25-like protein)	0.39	-	nuc	0					337
Q16975 UniProt NPD GO	KPC2_APLCA	Calcium-independent protein kinase C (EC 2.7.11.13) (APL II)	0.39	-	mit	0	Membrane; peripheral membrane protein				743
P14100 UniProt NPD GO	PDE1A_BOVIN	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A (EC 3.1.4.17) (Cam-PDE 1A) ...	0.39	-	cyt	0					529
Q9DBB9 UniProt NPD GO	CPN2_MOUSE	Carboxypeptidase N subunit 2 precursor (Carboxypeptidase N polypeptide 2) (Carboxypeptidase N 83 kDa ...	0.39	-	exc	0	Secreted protein (By similarity)				547
P35507 UniProt NPD GO	KC1B_BOVIN	Casein kinase I isoform beta (EC 2.7.11.1) (CKI-beta)	0.39	-	cyt	0	Cytoplasm				336
Q02720 UniProt NPD GO	CSK2A_DICDI	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II subunit alpha)	0.39	-	mit	0					337
P33674 UniProt NPD GO	CSK21_RABIT	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II)	0.39	-	mit	0					391
Q53B87 UniProt NPD GO	CAR15_PANTR	Caspase recruitment domain-containing protein 15	0.39	-	cyt	0	Cytoplasm (By similarity)				1040
Q9HC29 UniProt NPD GO	CAR15_HUMAN	Caspase recruitment domain-containing protein 15 (Protein Nod2) (Inflammatory bowel disease protein ...	0.39	-	cyt	0	Cytoplasm	cytoplasm [TAS] cytosol [IDA] plasma membrane [IDA] vesicle [IDA]	609464		1040
Q9MZV6 UniProt NPD GO	CASP1_FELCA	Caspase-1 precursor (EC 3.4.22.36) (CASP-1) (Interleukin-1 beta convertase) (IL-1BC) (IL-1 beta-conv ...	0.39	-	nuc	0	Cytoplasm				410
P43527 UniProt NPD GO	CASP1_RAT	Caspase-1 precursor (EC 3.4.22.36) (CASP-1) (Interleukin-1 beta convertase) (IL-1BC) (IL-1 beta-conv ...	0.39	-	cyt	0	Cytoplasm				402
O08736 UniProt NPD GO	CASPC_MOUSE	Caspase-12 precursor (EC 3.4.22.-) (CASP-12)	0.39	-	mit	0		endoplasmic reticulum [TAS]			419
Q9TST1 UniProt NPD GO	CATW_FELCA	Cathepsin W precursor (EC 3.4.22.-)	0.39	-	exc	0					374
Q00587 UniProt NPD GO	BORG5_HUMAN	Cdc42 effector protein 1 (Binder of Rho GTPases 5) (Serum protein MSE55)	0.39	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein		606084		391
Q5E9X8 UniProt NPD GO	RAD9B_BOVIN	Cell cycle checkpoint control protein RAD9B homolog (RAD9 homolog B)	0.39	-	nuc	0					442
Q9NV96 UniProt NPD GO	CC50A_HUMAN	Cell cycle control protein 50A (Transmembrane protein 30A)	0.39	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				361
Q6PC40 UniProt NPD GO	CD123_BRARE	Cell division cycle protein 123 homolog	0.39	-	cyt	0	Cytoplasm (By similarity)				348
P54685 UniProt NPD GO	CDK7_DICDI	Cell division protein kinase 7 (EC 2.7.11.22) (EC 2.7.11.23) (CDK-activating kinase) (CAK) (MO15 hom ...	0.39	-	cyt	0	Nucleus (By similarity)				362
Q03147 UniProt NPD GO	CDK7_MOUSE	Cell division protein kinase 7 (EC 2.7.11.22) (EC 2.7.11.23) (CDK-activating kinase) (CAK) (TFIIH ba ...	0.39	-	mit	0	Nucleus	nucleus [IDA]			346
P97586 UniProt NPD GO	CGRE1_RAT	Cell growth regulator with EF hand domain 1 (Cell growth regulatory gene 11 protein)	0.39	-	exc	0					281
Q8L778 UniProt NPD GO	CESA5_ARATH	Cellulose synthase A catalytic subunit 5 [UDP-forming] (EC 2.4.1.12) (AtCesA-5)	0.39	+	end	8	Cell membrane; multi-pass membrane protein (Probable)				1069
Q06162 UniProt NPD GO	NKP2_YEAST	Central kinetochore subunit NKP2 (Non-essential kinetochore protein 2)	0.39	-	nuc	0	Nucleus. Associated with kinetochores	kinetochore [IDA]			153
Q8K4Q7 UniProt NPD GO	CERK1_MOUSE	Ceramide kinase (EC 2.7.1.138) (Acylsphingosine kinase) (mCERK)	0.39	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	integral to membrane of membrane fraction [ISS]			531
P48400 UniProt NPD GO	CHSA_IPOPL	Chalcone synthase A (EC 2.3.1.74) (Naringenin-chalcone synthase A) (CHS-A) (Fragment)	0.39	-	mit	0					362
P19461 UniProt NPD GO	RR12_GUITH	Chloroplast 30S ribosomal protein S12	0.39	-	nuc	0	Plastid; chloroplast				123
O46912 UniProt NPD GO	RR13_GUITH	Chloroplast 30S ribosomal protein S13	0.39	-	nuc	0	Plastid; chloroplast				122
Q9TM39 UniProt NPD GO	RR18_CYACA	Chloroplast 30S ribosomal protein S18	0.39	-	nuc	0	Plastid; chloroplast				68
Q8MA09 UniProt NPD GO	RR2_CHAGL	Chloroplast 30S ribosomal protein S2	0.39	-	mit	0	Plastid; chloroplast				236
Q9TLT8 UniProt NPD GO	RR3_CYACA	Chloroplast 30S ribosomal protein S3	0.39	-	mit	0	Plastid; chloroplast				207
Q3ZJ85 UniProt NPD GO	RR3_PSEAK	Chloroplast 30S ribosomal protein S3	0.39	-	mit	0	Plastid; chloroplast				229
Q49KW3 UniProt NPD GO	RR8_EUCGG	Chloroplast 30S ribosomal protein S8	0.39	-	nuc	0	Plastid; chloroplast				134
O20029 UniProt NPD GO	RR9_CHLRE	Chloroplast 30S ribosomal protein S9	0.39	-	nuc	0	Plastid; chloroplast				191
P49497 UniProt NPD GO	RR9_ODOSI	Chloroplast 30S ribosomal protein S9	0.39	-	nuc	0	Plastid; chloroplast				138
O98456 UniProt NPD GO	RK16_SPIMX	Chloroplast 50S ribosomal protein L16	0.39	-	mit	0	Plastid; chloroplast				143
Q4VZM9 UniProt NPD GO	RK22_CUCSA	Chloroplast 50S ribosomal protein L22	0.39	-	nuc	0	Plastid; chloroplast				162
Q332T7 UniProt NPD GO	RK22_LACSA	Chloroplast 50S ribosomal protein L22	0.39	-	mit	0	Plastid; chloroplast				157
Q8TDX6 UniProt NPD GO	CGAT1_HUMAN	Chondroitin beta-1,4-N-acetylgalactosaminyltransferase 1 (EC 2.4.1.174) (beta4GalNAcT-1)	0.39	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)	integral to Golgi membrane [NAS] intracellular [ISS] soluble fraction [IDA]			532
Q13112 UniProt NPD GO	CAF1B_HUMAN	Chromatin assembly factor 1 subunit B (CAF-1 subunit B) (Chromatin assembly factor I p60 subunit) (C ...	0.39	-	nuc	0	Nucleus. DNA replication foci. Cytoplasm. Cytoplasmic in M phase	chromatin assembly complex [TAS] cytoplasm [NAS] nucleus [NAS]	601245		559
P30379 UniProt NPD GO	1B01_GORGO	Class I histocompatibility antigen, GOGO-B0101 alpha chain precursor	0.39	-	end	1	Membrane; single-pass type I membrane protein				362
P30381 UniProt NPD GO	1B03_GORGO	Class I histocompatibility antigen, GOGO-B0103 alpha chain precursor	0.39	-	end	1	Membrane; single-pass type I membrane protein				362
P30382 UniProt NPD GO	1B04_GORGO	Class I histocompatibility antigen, GOGO-B0201 alpha chain precursor	0.39	-	end	1	Membrane; single-pass type I membrane protein				363
Q10570 UniProt NPD GO	CPSF1_HUMAN	Cleavage and polyadenylation specificity factor 160 kDa subunit (CPSF 160 kDa subunit)	0.39	-	nuc	0	Nucleus; nucleoplasm	mRNA cleavage and polyadenylation specifici... [IDA]	606027		1443

You are viewing entries 32451 to 32500 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.