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
P36898 UniProt NPD GO	BMR1B_MOUSE	Bone morphogenetic protein receptor type IB precursor (EC 2.7.11.30) (Serine/threonine-protein kinas ...	0.43	-	nuc	1	Membrane; single-pass type I membrane protein				502
Q90322 UniProt NPD GO	BDNF_CYPCA	Brain-derived neurotrophic factor precursor (BDNF)	0.43	-	mit	0	Secreted protein				270
Q13895 UniProt NPD GO	BYST_HUMAN	Bystin	0.43	-	nuc	0	Cytoplasm	cytoplasm [TAS]	603871		437
Q9VG76 UniProt NPD GO	MYCBP_DROME	C-Myc-binding protein homolog	0.43	-	nuc	0	Nucleus (Potential)	nucleus [NAS]			181
Q8HY06 UniProt NPD GO	CLC4M_GORGO	C-type lectin domain family 4 member M (CD209 antigen-like protein 1) (CD299 antigen)	0.43	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				376
Q8HY10 UniProt NPD GO	CLC4M_HYLCO	C-type lectin domain family 4 member M (CD209 antigen-like protein 1) (CD299 antigen)	0.43	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				399
Q8HY12 UniProt NPD GO	CLC4M_HYLLA	C-type lectin domain family 4 member M (CD209 antigen-like protein 1) (CD299 antigen)	0.43	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				399
Q9H2X3 UniProt NPD GO	CLC4M_HUMAN	C-type lectin domain family 4 member M (CD209 antigen-like protein 1) (Dendritic cell-specific ICAM- ...	0.43	-	nuc	1 *	Isoform 1, isoform 2, isoform 3: Cell membrane; single-pass type II membrane protein (Potential). Is ...	integral to plasma membrane [TAS] membrane [TAS]	605872	1XPH	399
P13721 UniProt NPD GO	SIAT1_RAT	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,6-sialyltransferase (EC 2.4.99.1) (Beta-galactosi ...	0.43	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				403
Q9ULK4 UniProt NPD GO	CRSP3_HUMAN	CRSP complex subunit 3 (Cofactor required for Sp1 transcriptional activation subunit 3) (Transcripti ...	0.43	-	nuc	0	Nucleus	transcription factor complex [IDA]	605042		1368
Q80T79 UniProt NPD GO	CSMD3_MOUSE	CUB and sushi domain-containing protein 3 (CUB and sushi multiple domains protein 3) (Fragment)	0.43	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				2796
Q14517 UniProt NPD GO	FATH_HUMAN	Cadherin-related tumor suppressor homolog precursor (Protein fat homolog)	0.43	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	600976		4590
Q9N0T2 UniProt NPD GO	CALCA_HORSE	Calcitonin gene-related peptide 1 precursor (Calcitonin gene-related peptide I) (CGRP-I) (Alpha-type ...	0.43	-	nuc	0	Secreted protein				127
P53683 UniProt NPD GO	CDPK2_ORYSA	Calcium-dependent protein kinase, isoform 2 (EC 2.7.11.1) (CDPK 2)	0.43	-	mit	0					533
Q7L1S5 UniProt NPD GO	CHST9_HUMAN	Carbohydrate sulfotransferase 9 (EC 2.8.2.-) (N-acetylgalactosamine-4-O-sulfotransferase 2) (GalNAc- ...	0.43	-	mit	1 *	Isoform 1: Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity). Is ...	integral to membrane [NAS] intrinsic to Golgi membrane [ISS]			438
Q865C0 UniProt NPD GO	CAH6_CANFA	Carbonic anhydrase 6 precursor (EC 4.2.1.1) (Carbonic anhydrase VI) (Carbonate dehydratase VI) (CA-V ...	0.43	-	exc	0	Secreted protein				320
Q9D2L5 UniProt NPD GO	CPXM2_MOUSE	Carboxypeptidase-like protein X2 precursor	0.43	-	exc	1 *	Secreted protein (Probable)				764
Q92523 UniProt NPD GO	CPT1B_HUMAN	Carnitine O-palmitoyltransferase I, muscle isoform (EC 2.3.1.21) (CPT I) (CPTI-M) (Carnitine palmito ...	0.43	-	cyt	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrion [TAS]	601987		772
P40231 UniProt NPD GO	CSK2A_SCHPO	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II subunit alpha)	0.43	-	cyt	0		protein kinase CK2 complex [TAS]			332
Q9NPP4 UniProt NPD GO	CAR12_HUMAN	Caspase recruitment domain-containing protein 12 (Ice protease-activating factor) (Ipaf) (CARD, LRR, ...	0.43	-	cyt	0	Cytoplasm. Cytoplasmic filaments		606831		1024
Q8VEK0 UniProt NPD GO	CC50A_MOUSE	Cell cycle control protein 50A (Transmembrane protein 30A)	0.43	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				364
Q62623 UniProt NPD GO	CDC20_RAT	Cell division cycle protein 20 homolog (p55CDC)	0.43	-	nuc	0					499
Q9JJ66 UniProt NPD GO	CDC20_MOUSE	Cell division cycle protein 20 homolog (p55CDC) (mmCdc20)	0.43	-	nuc	0					499
P38739 UniProt NPD GO	WSC4_YEAST	Cell wall integrity and stress response component 4 precursor	0.43	-	exc	1		endoplasmic reticulum membrane [IDA]			605
Q8BJF9 UniProt NPD GO	CHM2B_MOUSE	Charged multivesicular body protein 2b (Chromatin-modifying protein 2b) (CHMP2b)	0.43	-	nuc	0	Cytoplasm; cytosol (By similarity)				213
Q7SYR0 UniProt NPD GO	CH2BA_XENLA	Charged multivesicular body protein 2b-A (Chromatin-modifying protein 2b-A) (CHMP2b-A)	0.43	-	nuc	0	Cytoplasm; cytosol (By similarity)				214
Q66IV6 UniProt NPD GO	CH2BB_XENLA	Charged multivesicular body protein 2b-B (Chromatin-modifying protein 2b-B) (CHMP2b-B)	0.43	-	nuc	0	Cytoplasm; cytosol (By similarity)				214
Q5RBR3 UniProt NPD GO	CHMP5_PONPY	Charged multivesicular body protein 5 (Chromatin-modifying protein 5)	0.43	-	nuc	0	Cytoplasm; cytosol (By similarity)				219
Q9NZZ3 UniProt NPD GO	CHMP5_HUMAN	Charged multivesicular body protein 5 (Chromatin-modifying protein 5) (Vacuolar protein sorting 60) ...	0.43	-	nuc	0	Cytoplasm; cytosol				219
O13395 UniProt NPD GO	CHS6_USTMA	Chitin synthase 6 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 6) (Class-V chitin synth ...	0.43	-	end	5	Cell membrane; multi-pass membrane protein				1103
O74756 UniProt NPD GO	CHS2_SCHPO	Chitin synthase-like protein 2	0.43	-	end	7	Integral membrane protein. Septum	barrier septum [IDA]			926
P09561 UniProt NPD GO	RR11_MAIZE	Chloroplast 30S ribosomal protein S11	0.43	-	nuc	0	Plastid; chloroplast				143
Q9BBN1 UniProt NPD GO	RR11_MARQU	Chloroplast 30S ribosomal protein S11	0.43	-	mit	0	Plastid; chloroplast				130
Q672I7 UniProt NPD GO	RR11_PENAM	Chloroplast 30S ribosomal protein S11	0.43	-	nuc	0	Plastid; chloroplast				143
Q4VZL1 UniProt NPD GO	RR15_CUCSA	Chloroplast 30S ribosomal protein S15	0.43	-	nuc	0	Plastid; chloroplast				90
Q6B8R5 UniProt NPD GO	RR2_GRATL	Chloroplast 30S ribosomal protein S2	0.43	-	mit	0	Plastid; chloroplast				231
Q68S04 UniProt NPD GO	RR4_PANGI	Chloroplast 30S ribosomal protein S4	0.43	-	mit	0	Plastid; chloroplast				201
Q32RY4 UniProt NPD GO	RR4_STAPU	Chloroplast 30S ribosomal protein S4	0.43	-	mit	0	Plastid; chloroplast				212
Q32RV1 UniProt NPD GO	RR8_STAPU	Chloroplast 30S ribosomal protein S8	0.43	-	mit	0	Plastid; chloroplast				132
Q68RW9 UniProt NPD GO	RK16_PANGI	Chloroplast 50S ribosomal protein L16	0.43	-	nuc	0	Plastid; chloroplast				135
Q8S8V4 UniProt NPD GO	RK22_ATRBE	Chloroplast 50S ribosomal protein L22	0.43	-	nuc	0	Plastid; chloroplast				155
Q85FV8 UniProt NPD GO	RK22_CYAME	Chloroplast 50S ribosomal protein L22	0.43	-	nuc	0	Plastid; chloroplast				95
P09594 UniProt NPD GO	RK22_SPIOL	Chloroplast 50S ribosomal protein L22 (Ribosomal protein CS-L13)	0.43	-	nuc	0	Plastid; chloroplast				199
P49546 UniProt NPD GO	RK4_ODOSI	Chloroplast 50S ribosomal protein L4	0.43	-	nuc	0	Plastid; chloroplast				215
O15335 UniProt NPD GO	CHAD_HUMAN	Chondroadherin precursor (Cartilage leucine-rich protein)	0.43	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [TAS]	602178		359
Q6WN34 UniProt NPD GO	CRDL2_HUMAN	Chordin-like protein 2 precursor (Chordin-related protein 2) (Breast tumor novel factor 1) (BNF-1)	0.43	-	nuc	0	Isoform 1, isoform 2: Secreted protein (Potential). Isoform 3, isoform 4, isoform 5: Cytoplasm (Pote ...				429
Q6CPA6 UniProt NPD GO	EAF6_KLULA	Chromatin modification-related protein EAF6	0.43	+	nuc	0	Nucleus (By similarity)				115
O13953 UniProt NPD GO	EAF3_SCHPO	Chromatin modification-related protein eaf3 (Altered polarity protein 13) (ESA1-associated factor 3) ...	0.43	-	nuc	0	Nucleus	histone deacetylase complex [IDA] nucleus [IDA]			337
Q754R8 UniProt NPD GO	SFH1_ASHGO	Chromatin structure remodeling complex protein SFH1 (SNF5 homolog 1)	0.43	+	cyt	0	Nucleus (By similarity)				383
P17891 UniProt NPD GO	CLC1_YEAST	Clathrin light chain (CLC)	0.43	-	nuc	0	Cytoplasmic face of coated pits and vesicles	clathrin vesicle coat [TAS]			233

You are viewing entries 29501 to 29550 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.