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
Q06032 UniProt NPD GO	CST9_YEAST	Chromosome stability protein 9 (Molecular zipper protein 3)	0.90	-	nuc	0	Synapsed meiotic chromosomes	nuclear chromosome [IDA]			482
Q8N3U4 UniProt NPD GO	STAG2_HUMAN	Cohesin subunit SA-2 (Stromal antigen 2) (SCC3 homolog 2)	0.90	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	nucleus [TAS]	604359		1231
Q9H0G5 UniProt NPD GO	CCD55_HUMAN	Coiled-coil domain-containing protein 55	0.90	-	nuc	0					558
Q8VC31 UniProt NPD GO	CCDC9_MOUSE	Coiled-coil domain-containing protein 9	0.90	-	nuc	0					543
Q640U7 UniProt NPD GO	CCD93_XENTR	Coiled-coil domain-containing protein 93	0.90	+	nuc	0					610
Q29RS4 UniProt NPD GO	CCD95_BOVIN	Coiled-coil domain-containing protein 95	0.90	-	nuc	0					244
Q8NBZ0 UniProt NPD GO	CCD95_HUMAN	Coiled-coil domain-containing protein 95	0.90	-	nuc	0					244
Q6AYH2 UniProt NPD GO	CCD95_RAT	Coiled-coil domain-containing protein 95	0.90	-	nuc	0					244
P01142 UniProt NPD GO	CRF_SHEEP	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone) (E ...	0.90	-	nuc	0	Secreted protein				190
Q5NVA9 UniProt NPD GO	EME1_PONPY	Crossover junction endonuclease EME1 (EC 3.1.22.-)	0.90	-	nuc	0	Nucleus; nucleolus. Recruited to regions of DNA damage in S-phase cells (By similarity)				575
P87231 UniProt NPD GO	MUS81_SCHPO	Crossover junction endonuclease mus81 (EC 3.1.22.-)	0.90	-	nuc	0	Nucleus	Holliday junction resolvase complex [IDA]			608
Q61817 UniProt NPD GO	CREB3_MOUSE	Cyclic AMP-responsive element-binding protein 3 (Transcription factor LZIP)	0.90	+	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				404
Q5K9L9 UniProt NPD GO	ATG4_CRYNE	Cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.90	+	nuc	0	Cytoplasm (By similarity)				1193
Q8WWK9 UniProt NPD GO	CKAP2_HUMAN	Cytoskeleton-associated protein 2 (Tumor-associated microtubule-associated protein) (CTCL tumor anti ...	0.90	-	nuc	0	Cytoplasm. Colocalizes with microtubules throughout the cell cycle				683
Q2KN98 UniProt NPD GO	CYTSA_MOUSE	Cytospin-A	0.90	+	nuc	0					1118
Q2KNA1 UniProt NPD GO	CYTSA_PANTR	Cytospin-A	0.90	+	nuc	0					1117
Q69YQ0 UniProt NPD GO	CYTSA_HUMAN	Cytospin-A (NY-REN-22 antigen)	0.90	+	nuc	0					1117
P34420 UniProt NPD GO	DGC14_CAEEL	DGCR14 protein homolog (DiGeorge syndrome critical region 14 homolog)	0.90	+	nuc	0	Nucleus (By similarity)				531
Q92072 UniProt NPD GO	DNMT1_CHICK	DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) (Dnmt1) (DNA methyltransferase GgaI) (DNA MTase G ...	0.90	-	nuc	0	Nucleus (By similarity)				1537
Q08949 UniProt NPD GO	DDC1_YEAST	DNA damage checkpoint protein 1	0.90	-	nuc	0	Cytoplasm. Nucleus	condensed nuclear chromosome [IDA]			612
Q9MA98 UniProt NPD GO	ERCC1_ARATH	DNA excision repair protein ERCC-1 (EC 3.1.-.-) (AtERCC1) (AtRAD10) (Ultraviolet hypersensitive 7)	0.90	+	nuc	0	Nucleus (Probable)				410
P47110 UniProt NPD GO	DPOD3_YEAST	DNA polymerase subunit delta 3	0.90	-	nuc	0	Nucleus (By similarity)	delta DNA polymerase complex [TAS] nucleus [IDA]			350
Q6CJM4 UniProt NPD GO	RAD5_KLULA	DNA repair protein RAD5 (EC 3.6.1.-)	0.90	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1114
P36632 UniProt NPD GO	RAD26_SCHPO	DNA repair protein rad26	0.90	-	mit	0	Nucleus	nucleus [IDA]			614
P33991 UniProt NPD GO	MCM4_HUMAN	DNA replication licensing factor MCM4 (CDC21 homolog) (P1-CDC21)	0.90	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	602638		863
Q07050 UniProt NPD GO	TOP1_CRIGR	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.90	+	nuc	0					767
P93119 UniProt NPD GO	TOP1_DAUCA	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.90	-	nuc	0					790
P04786 UniProt NPD GO	TOP1_YEAST	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I) (Maintenance of killer protein 1)	0.90	+	nuc	0		nucleus [IDA]		1OIS	769
Q9Y8G8 UniProt NPD GO	TOP2_PENCH	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.90	+	nuc	0	Nucleus				1587
P08096 UniProt NPD GO	TOP2_SCHPO	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.90	+	nuc	0	Nucleus				1485
Q8QZV0 UniProt NPD GO	DEDD2_MOUSE	DNA-binding death effector domain-containing protein 2 (FADD-like anti-apoptotic molecule 3) (DED-co ...	0.90	+	nuc	0	Nucleus (By similarity). Nuclear, accumulated in subnuclear structures resembling nucleoli (By simil ...				330
P38935 UniProt NPD GO	SMBP2_HUMAN	DNA-binding protein SMUBP-2 (EC 3.6.1.-) (ATP-dependent helicase IGHMBP2) (Immunoglobulin mu-binding ...	0.90	-	nuc	0	Nucleus (Potential)		600502	1MSZ	993
Q9P7D9 UniProt NPD GO	RSV1_SCHPO	DNA-binding protein rsv1	0.90	-	nuc	0	Nucleus (By similarity)				428
Q8MA12 UniProt NPD GO	RPOB_CHAGL	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.90	-	nuc	0	Plastid; chloroplast				1070
P56299 UniProt NPD GO	RPOB_CHLVU	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.90	-	mit	0	Plastid; chloroplast				1301
P60283 UniProt NPD GO	RPOB_PHYPA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.90	+	mit	0	Plastid; chloroplast				1085
Q9TL05 UniProt NPD GO	RPOC1_NEPOL	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.90	-	nuc	0	Plastid; chloroplast				863
P49468 UniProt NPD GO	RPOC2_ODOSI	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.90	+	nuc	0	Plastid; chloroplast				1481
Q13426 UniProt NPD GO	XRCC4_HUMAN	DNA-repair protein XRCC4 (X-ray repair cross-complementing protein 4)	0.90	+	nuc	0	Nucleus	nucleus [NAS]	194363	1IK9	336
Q924T3 UniProt NPD GO	XRCC4_MOUSE	DNA-repair protein XRCC4 (X-ray repair cross-complementing protein 4)	0.90	-	nuc	0	Nucleus (By similarity)				326
Q673G8 UniProt NPD GO	DACT2_BRARE	Dapper homolog 2 (Frodo 2)	0.90	-	nuc	0	Cytoplasm. Predominantly. Endosome; late endosome. Nucleus. Cell membrane. Also found in late endoso ...				837
Q8BZN6 UniProt NPD GO	DOC10_MOUSE	Dedicator of cytokinesis protein 10 (Fragment)	0.90	-	nuc	0					1816
P18169 UniProt NPD GO	DEC11_DROME	Defective chorion-1 protein, FC125 isoform precursor	0.90	-	exc	0	Secreted protein	chorion [IDA] extracellular region [IDA]			1208
P20398 UniProt NPD GO	GV7_XENLA	Developmental protein XlGV7	0.90	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic (following oocyte maturation), then nuclear (blastula/gastrula stage ...				591
O75912 UniProt NPD GO	DGKI_HUMAN	Diacylglycerol kinase iota (EC 2.7.1.107) (Diglyceride kinase iota) (DGK-iota) (DAG kinase iota)	0.90	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]	604072		1065
P40358 UniProt NPD GO	JEM1_YEAST	DnaJ-like chaperone JEM1 precursor (DnaJ-like protein of the ER membrane 1)	0.90	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Nucleus; nuclear ...	endoplasmic reticulum [IDA] nuclear envelope-endoplasmic reticulum network [IDA] peripheral to membrane of membrane fraction [IDA]			645
Q63117 UniProt NPD GO	CLK3_RAT	Dual specificity protein kinase CLK3 (EC 2.7.12.1) (CDC-like kinase 3)	0.90	+	nuc	0	Nucleus (By similarity)				490
P22545 UniProt NPD GO	PVDA_PLAKN	Duffy receptor alpha form precursor (Erythrocyte-binding protein)	0.90	-	nuc	1	Membrane; single-pass type I membrane protein			2C6J	1073
Q96L91 UniProt NPD GO	EP400_HUMAN	E1A-binding protein p400 (EC 3.6.1.-) (p400 kDa SWI2/SNF2-related protein) (Domino homolog) (hDomino ...	0.90	+	nuc	0			606265		3160
Q5BU09 UniProt NPD GO	EAPP_MOUSE	E2F-associated phosphoprotein (EAPP)	0.90	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				281

You are viewing entries 4101 to 4150 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.