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
Q85WU8 UniProt NPD GO	RR15_PINKO	Chloroplast 30S ribosomal protein S15	0.72	-	nuc	0	Plastid; chloroplast				88
Q9M3K7 UniProt NPD GO	RR18_SPIOL	Chloroplast 30S ribosomal protein S18	0.72	-	nuc	0	Plastid; chloroplast				101
Q32RL5 UniProt NPD GO	RR4_ZYGCR	Chloroplast 30S ribosomal protein S4	0.72	+	mit	0	Plastid; chloroplast				199
Q9TLS0 UniProt NPD GO	RK20_CYACA	Chloroplast 50S ribosomal protein L20	0.72	-	nuc	0	Plastid; chloroplast				115
Q6B8T4 UniProt NPD GO	RK20_GRATL	Chloroplast 50S ribosomal protein L20	0.72	-	nuc	0	Plastid; chloroplast				118
Q95H54 UniProt NPD GO	RK20_WHEAT	Chloroplast 50S ribosomal protein L20	0.72	-	mit	0	Plastid; chloroplast				118
Q7QH73 UniProt NPD GO	PERC_ANOGA	Chorion peroxidase precursor (EC 1.11.1.7) [Contains: Chorion peroxidase light chain; Chorion peroxi ...	0.72	-	mit	0	Secreted protein. In the chorion layer of the mature eggs (By similarity)				767
O09102 UniProt NPD GO	GCM2_MOUSE	Chorion-specific transcription factor GCMb (Glial cells missing homolog 2) (GCM motif protein 2) (mG ...	0.72	-	nuc	0	Nucleus (By similarity)				504
P38210 UniProt NPD GO	LDB7_YEAST	Chromatin structure remodeling complex protein RSC14 (Remodel the structure of chromatin complex sub ...	0.72	-	nuc	0	Nucleus	RSC complex [IDA]			180
Q9QXV1 UniProt NPD GO	CBX8_MOUSE	Chromobox protein homolog 8 (Polycomb 3 homolog) (Pc3) (mPc3)	0.72	-	nuc	0	Nucleus				362
P10354 UniProt NPD GO	CMGA_RAT	Chromogranin A precursor (CgA) [Contains: Pancreastatin; Beta-granin; WE-14]	0.72	-	exc	0	Neuroendocrine and endocrine secretory granules				466
Q16204 UniProt NPD GO	CCDC6_HUMAN	Coiled-coil domain-containing protein 6 (H4 protein) (Papillary thyroid carcinoma-encoded protein)	0.72	-	nuc	0	Cytoplasm. May be a cytoskeletal protein		601985		585
Q9YHB5 UniProt NPD GO	CND3_XENLA	Condensin complex subunit 3 (Chromosome-associated protein G) (Chromosome assembly protein xCAP-G) ( ...	0.72	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...				1034
Q21444 UniProt NPD GO	COG2_CAEEL	Conserved oligomeric Golgi complex component 2 (LDLC protein homolog)	0.72	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity)				681
P47130 UniProt NPD GO	CSN12_YEAST	Cop9 signalosome complex subunit 12	0.72	+	nuc	0	Cytoplasm. Nucleus	signalosome complex [IDA]			423
Q04617 UniProt NPD GO	COLI1_ONCMY	Corticotropin-lipotropin A precursor (Pro-opiomelanocortin A) (POMC A) [Contains: NPP 1; Corticotrop ...	0.72	-	nuc	0	Secreted protein				253
P22923 UniProt NPD GO	COLI_RANRI	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.72	-	nuc	0					260
Q91ZJ0 UniProt NPD GO	MUS81_MOUSE	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.72	-	nuc	0	Nucleus; nucleolus. Recruited to foci of DNA damage in S-phase cells (By similarity)				551
Q4KM32 UniProt NPD GO	MUS81_RAT	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.72	-	nuc	0	Nucleus; nucleolus. Recruited to foci of DNA damage in S-phase cells (By similarity)				551
Q00858 UniProt NPD GO	CGPB_FUSSO	Cutinase gene palindrome-binding protein (PBP)	0.72	-	nuc	0	Nucleus				457
Q8MJD7 UniProt NPD GO	CNGB3_CANFA	Cyclic nucleotide-gated cation channel beta 3 (CNG channel beta 3) (Cyclic nucleotide-gated channel ...	0.72	-	nuc	3	Membrane; multi-pass membrane protein				782
Q2QLF9 UniProt NPD GO	CFTR_CALJA	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.72	-	end	11	Membrane; multi-pass membrane protein				1481
P26362 UniProt NPD GO	CFTR_SQUAC	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.72	-	end	9	Membrane; multi-pass membrane protein				1492
P14580 UniProt NPD GO	CP4A6_RABIT	Cytochrome P450 4A6 precursor (EC 1.14.15.3) (CYPIVA6) (Lauric acid omega-hydroxylase) (P450-KA-1)	0.72	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				510
Q2KI41 UniProt NPD GO	CYH2_BOVIN	Cytohesin-2	0.72	-	cyt	0					410
Q9FNM7 UniProt NPD GO	RH26_ARATH	DEAD-box ATP-dependent RNA helicase 26 (EC 3.6.1.-)	0.72	-	mit	0					850
Q91VV4 UniProt NPD GO	DEN2D_MOUSE	DENN domain-containing protein 2D	0.72	-	mit	0					469
O24617 UniProt NPD GO	MSH2_ARATH	DNA mismatch repair protein MSH2 (AtMsh2)	0.72	-	nuc	0					937
P39985 UniProt NPD GO	DPO5_YEAST	DNA polymerase V (EC 2.7.7.7) (POL V)	0.72	+	cyt	0		nucleolus [IDA]			1022
P28339 UniProt NPD GO	DPOD1_BOVIN	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.72	+	cyt	0	Nucleus	nucleus [IC]			1106
Q6FSW2 UniProt NPD GO	RAD52_CANGA	DNA repair and recombination protein RAD52	0.72	-	nuc	0	Nucleus (By similarity)				505
P15348 UniProt NPD GO	TOP2_DROME	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.72	+	nuc	0	Nucleus	chromatin accessibility complex [IDA] chromosome [IDA] insoluble fraction [IDA] nucleus [IDA] soluble fraction [IDA]			1447
Q64511 UniProt NPD GO	TOP2B_MOUSE	DNA topoisomerase 2-beta (EC 5.99.1.3) (DNA topoisomerase II, beta isozyme)	0.72	+	nuc	0	Nucleus; nucleolus	nucleus [IDA]			1612
O60126 UniProt NPD GO	TOP3_SCHPO	DNA topoisomerase 3 (EC 5.99.1.2) (DNA topoisomerase III)	0.72	-	cyt	0		RecQ helicase-Topo III complex [TAS]			622
Q13422 UniProt NPD GO	IKAR_HUMAN	DNA-binding protein Ikaros (Lymphoid transcription factor LyF-1)	0.72	-	nuc	0	Nucleus		603023		519
Q03267 UniProt NPD GO	IKAR_MOUSE	DNA-binding protein Ikaros (Lymphoid transcription factor LyF-1)	0.72	-	nuc	0	Nucleus	centric heterochromatin [IDA] nucleus [IDA] transcription factor complex [TAS]			517
Q04073 UniProt NPD GO	P3A2_STRPU	DNA-binding protein P3A2	0.72	+	nuc	0	Nucleus				459
O59958 UniProt NPD GO	CRE1_NEUCR	DNA-binding protein cre-1 (Carbon catabolite repressor)	0.72	-	nuc	0	Nucleus (By similarity)				430
Q93Y94 UniProt NPD GO	RPOT1_NICSY	DNA-directed RNA polymerase 1, mitochondrial precursor (EC 2.7.7.6) (T7 bacteriophage-type single su ...	0.72	-	mit	0	Mitochondrion	mitochondrion [IDA]			1002
Q01080 UniProt NPD GO	RPA3_YEAST	DNA-directed RNA polymerase I 49 kDa polypeptide (EC 2.7.7.6) (A49)	0.72	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [TAS]			415
P25441 UniProt NPD GO	RPC4_YEAST	DNA-directed RNA polymerase III 47 kDa polypeptide (EC 2.7.7.6) (C53) (RNA polymerase C subunit 4)	0.72	-	nuc	0	Nucleus	DNA-directed RNA polymerase III complex [TAS]			422
Q9BUI4 UniProt NPD GO	RPC62_HUMAN	DNA-directed RNA polymerase III 62 kDa polypeptide (EC 2.7.7.6) (RNA polymerase C subunit 3) (RPC3) ...	0.72	-	nuc	0	Nucleus (Potential)	DNA-directed RNA polymerase III complex [TAS]			534
P60314 UniProt NPD GO	RPOA_AMBTC	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.72	-	cyt	0	Plastid; chloroplast				334
P23579 UniProt NPD GO	RPOB_EUGGR	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.72	-	cyt	0	Plastid; chloroplast				1082
P49467 UniProt NPD GO	RPOC1_ODOSI	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.72	-	cyt	0	Plastid; chloroplast				843
P52733 UniProt NPD GO	RPOC1_PINTH	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.72	-	nuc	0	Plastid; chloroplast				696
Q3V544 UniProt NPD GO	RPOC2_ACOCL	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.72	+	cyt	0	Plastid; chloroplast				1386
Q8BKF1 UniProt NPD GO	RPOM_MOUSE	DNA-directed RNA polymerase, mitochondrial precursor (EC 2.7.7.6) (MtRPOL)	0.72	-	mit	0	Mitochondrion (By similarity)				1207
Q8CDG3 UniProt NPD GO	VCIP1_MOUSE	Deubiquitinating protein VCIP135 (EC 3.4.22.-) (Valosin-containing protein p97/p47 complex-interacti ...	0.72	-	nuc	0	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Associated with ...				1220
P33894 UniProt NPD GO	STE13_YEAST	Dipeptidyl aminopeptidase A (EC 3.4.14.-) (DPAP A) (YSCIV)	0.72	-	nuc	1	Vacuole; vacuolar membrane; single-pass type II membrane protein. Lysosome-like vacuoles	Golgi trans face [IDA]			931

You are viewing entries 12701 to 12750 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.