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
Q876N4 UniProt NPD GO	ATG9_PICPA	Autophagy-related protein 9 (Glucose-induced selective autophagy protein 14)	0.84	-	nuc	4	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				885
Q9S7F3 UniProt NPD GO	BEH1_ARATH	BES1/BZR1 homolog protein 1	0.84	-	nuc	0					276
Q8TDC3 UniProt NPD GO	BRSK1_HUMAN	BR serine/threonine-protein kinase 1 (EC 2.7.11.1) (SAD1 kinase) (SAD1A)	0.84	-	nuc	0	Cytoplasm. Nucleus. Nuclear in the absence of DNA damage. Translocated to the nucleus in response to ...	cytoplasm [IDA] nucleus [IDA]	609235		794
Q7T2X7 UniProt NPD GO	BMP3_XENLA	Bone morphogenetic protein 3 precursor (BMP-3) (xBMP-3)	0.84	-	exc	1 *	Secreted protein				458
Q12186 UniProt NPD GO	MSL5_YEAST	Branchpoint-bridging protein MSL5 (MUD synthesis lethal 5 protein) (BBP) (Splicing factor 1)	0.84	-	nuc	0	Nucleus	commitment complex [IDA]			476
P43573 UniProt NPD GO	BUD27_YEAST	Bud site selection protein 27	0.84	+	nuc	0	Cytoplasm	cytoplasm [IDA]			796
Q8TDN4 UniProt NPD GO	CABL1_HUMAN	CDK5 and ABL1 enzyme substrate 1 (Interactor with CDK3 1) (Ik3-1)	0.84	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Located in the cell body and proximal region of ...		609194		633
Q9ESJ1 UniProt NPD GO	CABL1_MOUSE	CDK5 and ABL1 enzyme substrate 1 (Interactor with CDK3 1) (Ik3-1)	0.84	-	nuc	0	Nucleus. Cytoplasm. Located in the cell body and proximal region of the developing axonal shaft of i ...				568
Q9BE52 UniProt NPD GO	CK5P2_MACFA	CDK5 regulatory subunit-associated protein 2 (CDK5 activator-binding protein C48)	0.84	+	nuc	0	Centrosome (By similarity)	cytoskeleton [ISS]			862
Q96SN8 UniProt NPD GO	CK5P2_HUMAN	CDK5 regulatory subunit-associated protein 2 (CDK5 activator-binding protein C48) (Centrosome-associ ...	0.84	+	nuc	0	Centrosome	centrosome [IDA] cytoskeleton [NAS]	608201		1893
Q7Z460 UniProt NPD GO	CLAP1_HUMAN	CLIP-associating protein 1 (Cytoplasmic linker-associated protein 1) (Multiple asters homolog 1)	0.84	-	nuc	0	Cytoplasm. Localizes preferentially near the plus ends of growing spindle microtubules and is also a ...	centrosome [IDA] cortical microtubule cytoskeleton [IDA] cytoplasmic microtubule [IDA] Golgi apparatus [IDA] kinetochore [IDA] kinetochore microtubule [TAS]	605852		1538
Q9GS00 UniProt NPD GO	CSN1_CAEEL	COP9 signalosome complex subunit 1 (Signalosome subunit 1)	0.84	-	nuc	0	Cytoplasm. Nucleus				601
Q23658 UniProt NPD GO	CAPS_CAEEL	Calcium-dependent secretion activator (Uncoordinated protein 31)	0.84	-	nuc	0	Cytoplasmic vesicle (By similarity). Membrane-associated to vesicles (By similarity). Strongly enric ...				1260
P58660 UniProt NPD GO	CAR10_MOUSE	Caspase recruitment domain-containing protein 10 (Bcl10-interacting MAGUK protein 1) (Bimp1)	0.84	-	nuc	0		cytoplasm [ISS]			1021
Q9BWT7 UniProt NPD GO	CAR10_HUMAN	Caspase recruitment domain-containing protein 10 (CARD-containing MAGUK protein 3) (Carma 3)	0.84	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [NAS]	607209		1032
Q9Y239 UniProt NPD GO	CARD4_HUMAN	Caspase recruitment domain-containing protein 4 (Protein Nod1)	0.84	-	end	0	Cytoplasm	cytoplasm [TAS]	605980		953
P78746 UniProt NPD GO	CHSD_ASPFU	Chitin synthase D (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase D) (Class-VI chitin synt ...	0.84	+	end	5 *	Cell membrane; multi-pass membrane protein				745
Q9NP62 UniProt NPD GO	GCM1_HUMAN	Chorion-specific transcription factor GCMa (Glial cells missing homolog 1) (GCM motif protein 1) (hG ...	0.84	-	nuc	0	Nucleus (Potential)	nucleus [TAS] transcription factor complex [IDA]	603715		436
Q5AHB8 UniProt NPD GO	YNG2_CANAL	Chromatin modification-related protein YNG2 (ING1 homolog 2)	0.84	+	nuc	0	Nucleus (By similarity)				298
Q00737 UniProt NPD GO	SUDA_EMENI	Chromosome segregation protein sudA (DA-box protein sudA)	0.84	-	nuc	0	Nucleus (Potential)				1211
O35780 UniProt NPD GO	BHLH2_RAT	Class B basic helix-loop-helix protein 2 (bHLHB2) (Enhancer-of-split and hairy-related protein 2) (S ...	0.84	-	nuc	0	Nucleus (By similarity)	nucleus [IMP]			411
O35185 UniProt NPD GO	BHLH2_MOUSE	Class B basic helix-loop-helix protein 2 (bHLHB2) (Stimulated with retinoic acid 13) (E47 interactio ...	0.84	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			411
Q96AJ1 UniProt NPD GO	CLUA1_HUMAN	Clusterin-associated protein 1	0.84	-	nuc	0	Nucleus				413
Q6DJ13 UniProt NPD GO	CCD16_XENTR	Coiled-coil domain-containing protein 16	0.84	-	nuc	0	Nucleus (By similarity). Excluded from nucleolus (By similarity)				357
Q6P2H3 UniProt NPD GO	CCD21_HUMAN	Coiled-coil domain-containing protein 21	0.84	-	nuc	0					762
Q8N8E3 UniProt NPD GO	CCD46_HUMAN	Coiled-coil domain-containing protein 46	0.84	-	nuc	0					955
Q8C4J0 UniProt NPD GO	CCD60_MOUSE	Coiled-coil domain-containing protein 60	0.84	-	nuc	0					545
Q4V7C4 UniProt NPD GO	CCD71_RAT	Coiled-coil domain-containing protein 71	0.84	-	nuc	0					436
Q9Y7R3 UniProt NPD GO	CND2_SCHPO	Condensin complex subunit 2 (p105) (Barren homolog) (CAPH homolog)	0.84	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensin complex [IDA] cytoplasm [IDA] nucleus [IDA]			742
P04146 UniProt NPD GO	COPIA_DROME	Copia protein (Gag-int-pol protein) [Contains: Copia VLP protein; Copia protease (EC 3.4.23.-)]	0.84	-	nuc	0					1409
Q9YGK2 UniProt NPD GO	COLI_THUOB	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: Corticotropin (Adrenocor ...	0.84	-	exc	0					222
Q8BGU5 UniProt NPD GO	CFP1_MOUSE	Cyclin fold protein 1	0.84	-	nuc	0					341
Q9QWV9 UniProt NPD GO	CCNT1_MOUSE	Cyclin-T1 (CycT1) (Cyclin-T)	0.84	-	nuc	0	Nucleus (By similarity)				724
P38936 UniProt NPD GO	CDN1A_HUMAN	Cyclin-dependent kinase inhibitor 1 (p21) (CDK-interacting protein 1) (Melanoma differentiation-asso ...	0.84	-	nuc	0	Cytoplasm. Nucleus	nucleus [TAS]	116899	1AXC	163
Q8BLF2 UniProt NPD GO	CDKL3_MOUSE	Cyclin-dependent kinase-like 3 (EC 2.7.11.22)	0.84	-	nuc	0	Cytoplasm (By similarity)				595
Q9H8E8 UniProt NPD GO	CSR2B_HUMAN	Cysteine-rich protein 2-binding protein (CSRP2-binding protein) (CRP2BP) (CRP2-binding partner)	0.84	-	nuc	0	Nucleus. Mainly. Cytoplasm	nucleus [IPI]			782
P49589 UniProt NPD GO	SYC_HUMAN	Cysteinyl-tRNA synthetase (EC 6.1.1.16) (Cysteine--tRNA ligase) (CysRS)	0.84	-	nuc	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	123859		748
Q9Z0H8 UniProt NPD GO	CYLN2_MOUSE	Cytoplasmic linker protein 2 (Cytoplasmic linker protein 115) (CLIP-115)	0.84	-	nuc	0	Cytoplasm (By similarity). Associated with the cytoskeleton (By similarity)	cytoplasmic microtubule [IDA]			1047
Q91YE9 UniProt NPD GO	5NT1B_MOUSE	Cytosolic 5'-nucleotidase 1B (EC 3.1.3.5) (Cytosolic 5'-nucleotidase IB) (cN1B) (cN-IB) (Autoimmune ...	0.84	-	nuc	0	Cytoplasm	cytosol [IDA]			573
Q04377 UniProt NPD GO	LCD1_YEAST	DNA damage checkpoint protein LCD1 (Lethal, checkpoint-defective, DNA damage sensitive protein 1) (D ...	0.84	-	mit	0	Cytoplasm. Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response ...	nuclear chromosome [IDA]			747
P20457 UniProt NPD GO	PRI2_YEAST	DNA primase large subunit (EC 2.7.7.-) (DNA primase 58 kDa subunit) (DNA polymerase alpha:primase co ...	0.84	-	nuc	0		alpha DNA polymerase:primase complex [TAS] nuclear envelope [IDA] nucleus [IDA]			528
P41768 UniProt NPD GO	RAD52_KLULA	DNA repair and recombination protein RAD52	0.84	-	nuc	0	Nucleus (By similarity)				436
Q9QYM7 UniProt NPD GO	ERCC4_CRIGR	DNA repair endonuclease XPF (EC 3.1.-.-) (DNA excision repair protein ERCC-4)	0.84	-	cyt	0	Nucleus (By similarity)				902
Q7S1P9 UniProt NPD GO	RAD5_NEUCR	DNA repair protein rad-5 (EC 3.6.1.-)	0.84	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1222
P06272 UniProt NPD GO	RPOB_MARPO	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.84	+	mit	0	Plastid; chloroplast				1065
Q4VZP3 UniProt NPD GO	RPOC2_CUCSA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.84	+	cyt	0	Plastid; chloroplast				1394
Q24702 UniProt NPD GO	DVA1_DICVI	DVA-1 polyprotein precursor (Antigen 1) (Allergen 1) (Nematode polyprotein allergen DVA-1) (NPA DVA- ...	0.84	-	cyt	0					1557
Q9QYB2 UniProt NPD GO	DACH1_MOUSE	Dachshund homolog 1 (Dach1)	0.84	-	mit	0	Nucleus (By similarity)	nucleus [IDA] transcription factor complex [IDA]			751
Q8CIQ7 UniProt NPD GO	DOCK3_MOUSE	Dedicator of cytokinesis protein 3 (Modifier of cell adhesion) (Presenilin-binding protein) (PBP pro ...	0.84	-	vac	0	Cytoplasm	cytoplasm [IDA] soluble fraction [IDA]			2027
Q63603 UniProt NPD GO	DOCK9_RAT	Dedicator of cytokinesis protein 9 (Cdc42 guanine nucleotide exchange factor zizimin 1) (TRG protein ...	0.84	-	mit	0	Intracytoplasmic membrane (By similarity). Associated with membranes (By similarity)				720

You are viewing entries 6901 to 6950 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.