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
P35694 UniProt NPD GO	BRU1_SOYBN	Brassinosteroid-regulated protein BRU1 precursor	0.24	-	mit	1 *					283
O35457 UniProt NPD GO	CCRL2_MOUSE	C-C chemokine receptor-like 2 (Lipopolysacharide-inducible C-C chemokine receptor) (L-CCR) (G-protei ...	0.24	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				360
Q9Y240 UniProt NPD GO	CLC11_HUMAN	C-type lectin domain family 11 member A precursor (Stem cell growth factor) (Lymphocyte secreted C-t ...	0.24	-	mit	0	Cytoplasm. Secreted protein	extracellular region [IDA]	604713		323
P18145 UniProt NPD GO	ANFC_ANGJA	C-type natriuretic peptide precursor (BNP-like peptide CNP-22)	0.24	-	vac	0	Secreted protein				131
Q91437 UniProt NPD GO	PYR1_SQUAC	CAD protein [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate carb ...	0.24	-	nuc	0	Cytoplasm				2242
Q9NPF0 UniProt NPD GO	CD320_HUMAN	CD320 antigen precursor (8D6 antigen) (FDC-signaling molecule 8D6) (FDC-SM-8D6)	0.24	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)		606475		282
Q17031 UniProt NPD GO	CDC42_ANOGA	CDC42 homolog (25 kDa GTP-binding protein)	0.24	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				191
Q6Z4G7 UniProt NPD GO	COBL6_ORYSA	COBRA-like 6 protein precursor (BRITTLE CULM1-like 7 protein)	0.24	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				451
Q9LJU0 UniProt NPD GO	CBL10_ARATH	COBRA-like protein 10 precursor	0.24	-	mit	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)	anchored to membrane [TAS]			672
Q8W575 UniProt NPD GO	CSN3_ARATH	COP9 signalosome complex subunit 3 (Signalosome subunit 3) (FUSCA protein 11) (FUSCA11)	0.24	-	cyt	0	Cytoplasm. Nucleus				429
O13895 UniProt NPD GO	CSN4_SCHPO	COP9 signalosome complex subunit 4 (CSN complex subunit 4) (SGN4)	0.24	-	mit	0	Cytoplasm. Nucleus				377
Q4P804 UniProt NPD GO	CSN5_USTMA	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.24	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				406
Q9FVU9 UniProt NPD GO	CSN5A_ARATH	COP9 signalosome complex subunit 5a (EC 3.4.-.-) (Signalosome subunit 5a) (Jun activation domain-bin ...	0.24	-	nuc	0	Cytoplasm. Nucleus				358
Q7ZUZ0 UniProt NPD GO	CSN8_BRARE	COP9 signalosome complex subunit 8 (Signalosome subunit 8)	0.24	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				191
P12399 UniProt NPD GO	CTL2A_MOUSE	CTLA-2-alpha protein precursor	0.24	-	nuc	1 *					136
Q5XHA8 UniProt NPD GO	PYG1A_XENLA	CTP synthase 1-A (EC 6.3.4.2) (UTP--ammonia ligase 1-A) (CTP synthetase 1-A)	0.24	-	cyt	0					591
Q7ZXP9 UniProt NPD GO	PYG1B_XENLA	CTP synthase 1-B (EC 6.3.4.2) (UTP--ammonia ligase 1-B) (CTP synthetase 1-B)	0.24	-	cyt	0					591
Q6GME1 UniProt NPD GO	PYRG2_XENLA	CTP synthase 2 (EC 6.3.4.2) (UTP--ammonia ligase 2) (CTP synthetase 2)	0.24	-	cyt	0					578
Q9H251 UniProt NPD GO	CAD23_HUMAN	Cadherin-23 precursor (Otocadherin)	0.24	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)	membrane [NAS]	605516		3354
Q5R4V1 UniProt NPD GO	CALB1_PONPY	Calbindin	0.24	-	cyt	0					260
P04354 UniProt NPD GO	CALB1_CHICK	Calbindin (Vitamin D-dependent calcium-binding protein, avian-type) (Calbindin D28) (D-28K)	0.24	-	cyt	0		postsynaptic membrane [IDA] vesicle membrane [NAS]			261
P05937 UniProt NPD GO	CALB1_HUMAN	Calbindin (Vitamin D-dependent calcium-binding protein, avian-type) (Calbindin D28) (D-28K)	0.24	-	cyt	0			114050		260
P10286 UniProt NPD GO	CALCA_CHICK	Calcitonin gene-related peptide precursor (CGRP)	0.24	-	cyt	0	Secreted protein				125
P07660 UniProt NPD GO	CALC_CHICK	Calcitonin precursor	0.24	-	nuc	0	Secreted protein				138
O23087 UniProt NPD GO	ECA2_ARATH	Calcium-transporting ATPase 2, endoplasmic reticulum-type (EC 3.6.3.8)	0.24	-	end	8	Membrane; multi-pass membrane protein				1054
P35565 UniProt NPD GO	CALX_RAT	Calnexin precursor	0.24	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				591
P07384 UniProt NPD GO	CAN1_HUMAN	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.24	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...		114220	2ARY	714
Q9UMQ6 UniProt NPD GO	CAN11_HUMAN	Calpain-11 (EC 3.4.22.-) (Calcium-activated neutral proteinase 11) (CANP 11)	0.24	-	nuc	0			604822		702
Q6ZSI9 UniProt NPD GO	CAN12_HUMAN	Calpain-12 (EC 3.4.22.-)	0.24	-	cyt	0			608839		719
Q9GK38 UniProt NPD GO	CNN1_MUSPF	Calponin-1 (Calponin H1, smooth muscle) (Basic calponin)	0.24	-	nuc	0					297
Q08092 UniProt NPD GO	CNN1_PIG	Calponin-1 (Calponin H1, smooth muscle) (Basic calponin)	0.24	-	nuc	0					297
Q948Z0 UniProt NPD GO	TPSD6_ABIGR	Camphene synthase, chloroplast precursor (EC 4.2.3.-) ((-)-(1S,4R)-camphene synthase) (Agg-cam)	0.24	-	mit	0	Plastid; chloroplast (By similarity)				618
Q95323 UniProt NPD GO	CAH4_BOVIN	Carbonic anhydrase 4 precursor (EC 4.2.1.1) (Carbonic anhydrase IV) (Carbonate dehydratase IV) (CA-I ...	0.24	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor				312
Q16790 UniProt NPD GO	CAH9_HUMAN	Carbonic anhydrase 9 precursor (EC 4.2.1.1) (Carbonic anhydrase IX) (Carbonate dehydratase IX) (CA-I ...	0.24	-	end	1	Found on the surface microvilli and in the nucleus, particularly in nucleolus	integral to membrane [TAS]	603179		459
Q90240 UniProt NPD GO	CBPD_ANAPL	Carboxypeptidase D precursor (EC 3.4.17.22) (Metallocarboxypeptidase D) (gp180) (p170)	0.24	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [IDA]			1389
Q63086 UniProt NPD GO	CTF1_RAT	Cardiotrophin-1 (CT-1)	0.24	-	cyt	0	Secreted protein (By similarity)				203
Q9UBD9 UniProt NPD GO	CLCF1_HUMAN	Cardiotrophin-like cytokine factor 1 precursor (B cell-stimulating factor 3) (BSF-3) (Novel neurotro ...	0.24	-	mit	0	Secreted protein (By similarity)	extracellular region [NAS]	607672		225
Q8IHZ9 UniProt NPD GO	KC1_PLAF7	Casein kinase I (EC 2.7.11.1)	0.24	-	cyt	0					323
Q7RBX5 UniProt NPD GO	KC1_PLAYO	Casein kinase I (EC 2.7.11.1)	0.24	-	cyt	0					323
P28523 UniProt NPD GO	CSK2A_MAIZE	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II) (CK2-alpha)	0.24	-	cyt	0				1ZOH	332
Q91398 UniProt NPD GO	CSK2B_BRARE	Casein kinase II subunit beta (CK II beta)	0.24	-	cyt	0					215
P55866 UniProt NPD GO	CASP3_XENLA	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) (Apopain) (Cysteine protease CPP32) (xCPP32) [Contains: C ...	0.24	-	cyt	0	Cytoplasm (By similarity)				282
P25890 UniProt NPD GO	CATA_PEA	Catalase (EC 1.11.1.6)	0.24	-	cyt	0	Peroxisome				494
P48351 UniProt NPD GO	CATA2_CUCPE	Catalase isozyme 2 (EC 1.11.1.6)	0.24	-	cyt	0	Peroxisome (Probable)				492
Q9XHH3 UniProt NPD GO	CATA2_LYCES	Catalase isozyme 2 (EC 1.11.1.6)	0.24	-	cyt	0	Peroxisome (By similarity)				492
Q06355 UniProt NPD GO	PPOB_SOLTU	Catechol oxidase B, chloroplast precursor (EC 1.10.3.1) (Polyphenol oxidase) (PPO) (Fragment)	0.24	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				588
P49929 UniProt NPD GO	SC52_SHEEP	Cathelin-related peptide SC5 precursor 2 (Antibacterial peptide SMAP-29) (Myeloid antibacterial pept ...	0.24	-	nuc	1 *	Secreted protein				160
Q9R1T3 UniProt NPD GO	CATZ_RAT	Cathepsin Z precursor (EC 3.4.22.-) (Cathepsin Y)	0.24	-	vac	0	Secreted protein				306
Q99967 UniProt NPD GO	CITE2_HUMAN	Cbp/p300-interacting transactivator 2 (MSG-related protein 1) (MRG-1) (P35srj)	0.24	-	nuc	0	Nucleus	nucleus [IMP]	602937	1P4Q	270
Q9Z0F6 UniProt NPD GO	RAD9A_MOUSE	Cell cycle checkpoint control protein RAD9A (EC 3.1.11.2) (DNA repair exonuclease rad9 homolog A) (R ...	0.24	-	nuc	0	Nucleus (By similarity)				389

You are viewing entries 46101 to 46150 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.