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
Q4P9P3 UniProt NPD GO	DRS1_USTMA	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.95	+	nuc	0	Nucleus; nucleolus (By similarity)				932
Q5BFU1 UniProt NPD GO	DBP4_EMENI	ATP-dependent RNA helicase dbp4 (EC 3.6.1.-)	0.95	+	nuc	0	Nucleus; nucleolus (By similarity)				812
Q9UTP9 UniProt NPD GO	DBP4_SCHPO	ATP-dependent RNA helicase dbp4 (EC 3.6.1.-)	0.95	+	nuc	0	Nucleus; nucleolus (By similarity)				735
Q9VVN4 UniProt NPD GO	ATRIP_DROME	ATR-interacting protein mus304 (Mutagen-sensitive protein 304)	0.95	-	nuc	0	Cytoplasm	cytoplasm [IDA]			846
Q8IZT6 UniProt NPD GO	ASPM_HUMAN	Abnormal spindle-like microcephaly-associated protein (Abnormal spindle protein homolog) (Asp homolo ...	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...		608716		3477
P62283 UniProt NPD GO	ASPM_AOTVO	Abnormal spindle-like microcephaly-associated protein homolog	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3473
P62287 UniProt NPD GO	ASPM_COLGU	Abnormal spindle-like microcephaly-associated protein homolog	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3477
P62289 UniProt NPD GO	ASPM_GORGO	Abnormal spindle-like microcephaly-associated protein homolog	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3476
P62291 UniProt NPD GO	ASPM_MACFA	Abnormal spindle-like microcephaly-associated protein homolog	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3476
P62292 UniProt NPD GO	ASPM_MACMU	Abnormal spindle-like microcephaly-associated protein homolog	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3479
P62293 UniProt NPD GO	ASPM_PANTR	Abnormal spindle-like microcephaly-associated protein homolog	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3477
P62296 UniProt NPD GO	ASPM_SAIBB	Abnormal spindle-like microcephaly-associated protein homolog	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3469
P62288 UniProt NPD GO	ASPM_FELCA	Abnormal spindle-like microcephaly-associated protein homolog (Fragment)	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3461
Q01593 UniProt NPD GO	ABI3_ARATH	Abscisic acid-insensitive protein 3	0.95	-	nuc	0	Nucleus (Potential)				720
Q4WK35 UniProt NPD GO	AMDR_ASPFU	Acetamidase regulatory protein	0.95	-	nuc	0	Nucleus (By similarity)				772
Q9V4P1 UniProt NPD GO	ANLN_DROME	Actin-binding protein anillin (Actin-binding protein 8) (ABP8) (Protein scraps)	0.95	-	nuc	0	Nucleus. Mainly found in the nucleus during interphase. Colocalizes with cortical F-actin upon nucle ...	contractile ring [IDA] cytoplasm [IDA] nucleus [IDA] ring canal (sensu Insecta) [IDA]			1239
Q91WR3 UniProt NPD GO	ASCC2_MOUSE	Activating signal cointegrator 1 complex subunit 2 (ASC-1 complex subunit p100) (Trip4 complex subun ...	0.95	-	nuc	0					749
P23466 UniProt NPD GO	CYAA_SACKL	Adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase)	0.95	-	nuc	0					1839
Q7TN31 UniProt NPD GO	AGGF1_MOUSE	Angiogenic factor with G patch and FHA domains 1 (Angiogenic factor VG5Q) (mVG5Q)	0.95	+	nuc	0	Cytoplasm (By similarity). Secreted protein (By similarity). Cytoplasmic in microvascular endothelia ...	cytoplasm [ISS] extracellular region [ISS] perinuclear region [ISS]			711
Q01484 UniProt NPD GO	ANK2_HUMAN	Ankyrin-2 (Brain ankyrin) (Ankyrin-B) (Ankyrin, nonerythroid)	0.95	+	nuc	0			600919		3924
Q13796 UniProt NPD GO	APXL_HUMAN	Apical-like protein (Protein APXL)	0.95	-	nuc	0			300103		1616
Q9V9K7 UniProt NPD GO	ARS2_DROME	Arsenite-resistance protein 2 homolog	0.95	+	nuc	0					943
Q5RGE5 UniProt NPD GO	DCR1C_BRARE	Artemis protein (EC 3.1.-.-) (DNA cross-link repair 1C protein)	0.95	+	nuc	0	Nucleus (By similarity)				639
P35869 UniProt NPD GO	AHR_HUMAN	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.95	-	nuc	0	Cytoplasm. Nucleus. First cytoplasmic, upon binding with ligand and interaction with a HSP90, it tra ...	nucleus [IDA]	600253		848
Q9HFR4 UniProt NPD GO	ATG2_PICPA	Autophagy-related protein 2 (Glucose-induced selective autophagy protein 11) (Pexophagy zeocin-resis ...	0.95	-	nuc	0	Perivacuolar compartment				1862
Q5ANC9 UniProt NPD GO	ATG9_CANAL	Autophagy-related protein 9	0.95	+	nuc	6	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				952
Q9WV92 UniProt NPD GO	E41L3_MOUSE	Band 4.1-like protein 3 (4.1B) (Differentially expressed in adenocarcinoma of the lung protein 1) (D ...	0.95	-	nuc	0	Membrane; peripheral membrane protein				929
P46863 UniProt NPD GO	KL61_DROME	Bipolar kinesin KRP-130 (Kinesin-like protein Klp61F)	0.95	+	nuc	0		cytoplasm [IDA] kinesin complex [IDA]			1066
P49002 UniProt NPD GO	BMP3_RAT	Bone morphogenetic protein 3 precursor (BMP-3)	0.95	+	exc	0	Secreted protein				468
P12645 UniProt NPD GO	BMP3_HUMAN	Bone morphogenetic protein 3 precursor (BMP-3) (Osteogenin) (BMP-3A)	0.95	-	nuc	0	Secreted protein		112263		472
Q6AXW0 UniProt NPD GO	BOREA_RAT	Borealin (Cell division cycle-associated protein 8)	0.95	+	nuc	0	Nucleus; nucleolus. Cytoplasm. Localizes on chromosome arms and inner centromeres from prophase thro ...				288
O95696 UniProt NPD GO	BRD1_HUMAN	Bromodomain-containing protein 1 (BR140-like protein)	0.95	-	mit	0	Nucleus	nucleus [TAS]	604589		1058
Q6NVM8 UniProt NPD GO	BRD9_XENTR	Bromodomain-containing protein 9	0.95	+	nuc	0					596
Q08492 UniProt NPD GO	BUD21_YEAST	Bud site selection protein 21 (U3 small nucleolar RNA-associated protein 16) (U3 snoRNA-associated p ...	0.95	-	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			214
P53569 UniProt NPD GO	CEBPZ_MOUSE	CCAAT/enhancer-binding protein zeta (CCAAT-box-binding transcription factor) (CCAAT-binding factor) ...	0.95	+	nuc	0	Nucleus				1052
Q9FY74 UniProt NPD GO	CMTA1_ARATH	Calmodulin-binding transcription activator 1 (Signal-responsive protein 2) (Ethylene-induced calmodu ...	0.95	-	nuc	0	Nucleus				1007
Q95208 UniProt NPD GO	ICAL_SHEEP	Calpastatin (Calpain inhibitor)	0.95	-	nuc	0					723
Q09909 UniProt NPD GO	CWF19_SCHPO	Cell cycle control protein cwf19	0.95	-	nuc	0	Nucleus (Probable)	spliceosome complex [IDA]			639
P09119 UniProt NPD GO	CDC6_YEAST	Cell division control protein 6	0.95	-	nuc	0	Cell membrane	pre-replicative complex [TAS]			513
P11927 UniProt NPD GO	KAR1_YEAST	Cell division control protein KAR1	0.95	+	nuc	1		half bridge of spindle pole body [IDA]		1OQP	433
Q5BQN8 UniProt NPD GO	CENPJ_PANTR	Centromere protein J (CENP-J)	0.95	-	nuc	0	Centrosome. Localized within the center of microtubule asters (By similarity)				1338
Q865V0 UniProt NPD GO	CEP57_BOVIN	Centrosomal protein of 57 kDa (Cep57 protein) (Testis-specific protein 57) (Translokin)	0.95	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Associated with microtubules and the centrosome ...	centrosome [ISS] microtubule [ISS]			499
Q8CEE0 UniProt NPD GO	CEP57_MOUSE	Centrosomal protein of 57 kDa (Cep57 protein) (Testis-specific protein 57) (Translokin)	0.95	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Associated with microtubules and the centrosome ...	centrosome [ISS] cytoplasm [IDA] microtubule [ISS] nucleus [IDA]			500
Q09897 UniProt NPD GO	CHR3_SCHPO	Chitin synthase regulatory factor 3 (Chs four homolog 1)	0.95	-	nuc	0					932
Q6CMB8 UniProt NPD GO	VID21_KLULA	Chromatin modification-related protein VID21	0.95	-	nuc	0	Nucleus (Probable)				1005
Q6C7K8 UniProt NPD GO	VID21_YARLI	Chromatin modification-related protein VID21	0.95	+	nuc	0	Nucleus (Probable)				967
Q6FSB1 UniProt NPD GO	YNG2_CANGA	Chromatin modification-related protein YNG2 (ING1 homolog 2)	0.95	+	nuc	0	Nucleus (By similarity)				274
O14240 UniProt NPD GO	EAF6_SCHPO	Chromatin modification-related protein eaf6	0.95	-	nuc	0	Nucleus (By similarity)				138
Q4WP03 UniProt NPD GO	VID21_ASPFU	Chromatin modification-related protein vid21	0.95	-	nuc	0	Nucleus (Probable)				1467
P53236 UniProt NPD GO	RSC1_YEAST	Chromatin structure remodeling complex protein RSC1 (Remodel the structure of chromatin complex subu ...	0.95	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	RSC complex [IDA]			928

You are viewing entries 1751 to 1800 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.