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
O43896 UniProt NPD GO	KIF1C_HUMAN	Kinesin-like protein KIF1C	0.97	-	nuc	0		endoplasmic reticulum [TAS] Golgi apparatus [TAS]	603060	2G1L	1103
Q9HAQ2 UniProt NPD GO	KIF9_HUMAN	Kinesin-like protein KIF9	0.97	-	nuc	0			607910		790
Q86U70 UniProt NPD GO	LDB1_HUMAN	LIM domain-binding protein 1 (Carboxyl-terminal LIM domain-binding protein 2) (CLIM-2) (LIM domain-b ...	0.97	+	nuc	0	Nucleus (By similarity)		603451		375
P70662 UniProt NPD GO	LDB1_MOUSE	LIM domain-binding protein 1 (Nuclear LIM interactor)	0.97	+	nuc	0	Nucleus			1RUT	375
P70060 UniProt NPD GO	LDB1_XENLA	LIM domain-binding protein 1 (XLDB1)	0.97	+	nuc	0	Nucleus				375
P25579 UniProt NPD GO	LRE1_YEAST	Laminarase-resistance protein LRE1	0.97	-	nuc	0		cell wall (sensu Fungi) [TAS]			583
Q6MG48 UniProt NPD GO	BAT2_RAT	Large proline-rich protein BAT2 (HLA-B-associated transcript 2)	0.97	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				2161
Q8MI28 UniProt NPD GO	LBN_BOVIN	Limbin	0.97	+	nuc	1					1209
Q91ZP3 UniProt NPD GO	LPIN1_MOUSE	Lipin-1 (Fatty liver dystrophy protein)	0.97	+	nuc	0	Nucleus	nucleus [IEP]			924
Q21049 UniProt NPD GO	LIPA_CAEEL	Liprin-alpha (LAR-interacting protein alpha) (Synapse defective protein 2)	0.97	+	nuc	0	Presynaptic region	axon [IDA] cytoplasm [IDA] synapse [IDA]			1139
Q94071 UniProt NPD GO	LIPB_CAEEL	Liprin-beta (LAR-interacting protein beta)	0.97	-	nuc	0					920
P40971 UniProt NPD GO	LYS14_YEAST	Lysine biosynthesis regulatory protein LYS14	0.97	+	nuc	0	Nucleus	nucleus [IDA]			790
Q9TTK4 UniProt NPD GO	LYST_BOVIN	Lysosomal-trafficking regulator	0.97	+	end	0	Cytoplasm (Potential)				3796
P30308 UniProt NPD GO	MPI1A_XENLA	M-phase inducer phosphatase 1-A (EC 3.1.3.48)	0.97	+	nuc	0					550
O44628 UniProt NPD GO	MPIP2_CAEEL	M-phase inducer phosphatase cdc-25.2 (EC 3.1.3.48) (Cell division cycle-related protein 25.2)	0.97	-	nuc	0					480
Q8N5Y2 UniProt NPD GO	MS3L1_HUMAN	Male-specific lethal 3-like 1 (MSL3-like 1) (Male-specific lethal-3 homolog 1)	0.97	+	nuc	0	Nucleus (Probable)	nucleus [TAS]	604880		521
Q5PSV9 UniProt NPD GO	MDC1_MOUSE	Mediator of DNA damage checkpoint protein 1	0.97	-	nuc	0	Nucleus. Associated with chromatin. Relocalizes to discrete nuclear foci following DNA damage, this ...				1707
Q767L8 UniProt NPD GO	MDC1_PIG	Mediator of DNA damage checkpoint protein 1	0.97	-	nuc	0	Nucleus (By similarity). Associated with chromatin. Relocalizes to discrete nuclear foci following D ...				2042
Q9P7T4 UniProt NPD GO	MRC1_SCHPO	Mediator of replication checkpoint protein 1 (DNA replication checkpoint mediator mrc1)	0.97	-	nuc	0	Nucleus. Associated with chromatin	chromatin [IDA] nucleus [TAS] replication fork [TAS]			1019
O43068 UniProt NPD GO	MDE4_SCHPO	Mei4-dependent protein 4	0.97	-	nuc	0					421
Q96QZ7 UniProt NPD GO	MAGI1_HUMAN	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 (BAI1-associated protei ...	0.97	+	nuc	0	Cell membrane; cell-cell junction; tight junction; peripheral membrane protein. Localizes to epithel ...	intercellular junction [TAS] plasma membrane [TAS]	602625		1491
Q8NEM0 UniProt NPD GO	MCPH1_HUMAN	Microcephalin	0.97	+	nuc	0	Centrosome		607117		835
Q5IFK1 UniProt NPD GO	MCPH1_MACFA	Microcephalin	0.97	+	nuc	0	Centrosome (By similarity)				842
Q9UPN3 UniProt NPD GO	MACF1_HUMAN	Microtubule-actin crosslinking factor 1, isoforms 1/2/3/5 (Actin cross-linking family protein 7) (Ma ...	0.97	-	nuc	0	Cytoplasm	cytoplasm [IDA] cytoskeleton [NAS]	608271		5430
Q31708 UniProt NPD GO	RT04_ARATH	Mitochondrial ribosomal protein S4	0.97	-	nuc	0	Mitochondrion				362
Q99LX5 UniProt NPD GO	MMTA2_MOUSE	Multiple myeloma tumor-associated protein 2 homolog	0.97	+	nuc	0					260
Q95YM8 UniProt NPD GO	MBLK1_APIME	Mushroom body large-type Kenyon cell-specific protein 1	0.97	+	nuc	0	Nucleus	nucleus [IC]			1598
Q19272 UniProt NPD GO	MSH5_CAEEL	MutS protein homolog 5	0.97	+	nuc	0					1369
Q12457 UniProt NPD GO	YD026_YEAST	Myb domain-containing protein YDR026C	0.97	+	nuc	0	Nucleus. Nucleus; nucleolus	nucleolus [IDA] nucleus [IC]			570
Q9BQG0 UniProt NPD GO	MBB1A_HUMAN	Myb-binding protein 1A	0.97	+	nuc	0	Cytoplasm. Nucleus. Nucleus; nucleolus. Shuttles between the nucleus and cytoplasm. Nuclear import m ...	cytoplasm [ISS] NLS-dependent protein nuclear import complex [ISS] nucleolus [ISS] nucleus [ISS]	604885		1328
O35821 UniProt NPD GO	MBB1A_RAT	Myb-binding protein 1A (PAR-interacting protein) (PIP)	0.97	+	nuc	0	Nucleus; nucleolus (By similarity). Predominantly. Cytoplasm (By similarity). Also shuttles between ...	cytoplasm [ISS] NLS-dependent protein nuclear import complex [ISS] nucleolus [ISS] nucleus [ISS]			1344
P10243 UniProt NPD GO	MYBA_HUMAN	Myb-related protein A (A-Myb)	0.97	+	nuc	0	Nucleus	nucleus [NAS]	159405		752
Q9UL68 UniProt NPD GO	MYT1L_HUMAN	Myelin transcription factor 1-like protein (MyT1L protein) (MyT1-L)	0.97	-	nuc	0	Nucleus (By similarity)				1186
O14686 UniProt NPD GO	MLL2_HUMAN	Myeloid/lymphoid or mixed-lineage leukemia protein 2 (ALL1-related protein)	0.97	+	nuc	0	Nucleus (Probable)	nucleus [NAS]	602113		5262
Q8NEV4 UniProt NPD GO	MYO3A_HUMAN	Myosin IIIA (EC 2.7.11.1)	0.97	+	nuc	0			607101		1616
Q99105 UniProt NPD GO	MYSU_RABIT	Myosin heavy chain, embryonic smooth muscle isoform (Fragment)	0.97	-	nuc	0	Thick filaments of the myofibrils				501
P02565 UniProt NPD GO	MYH3_CHICK	Myosin heavy chain, fast skeletal muscle, embryonic	0.97	+	nuc	0	Thick filaments of the myofibrils				1940
P79114 UniProt NPD GO	MYO10_BOVIN	Myosin-10 (Myosin X)	0.97	-	nuc	0					2052
Q92614 UniProt NPD GO	MY18A_HUMAN	Myosin-18A (Myosin XVIIIa) (Myosin containing PDZ domain) (Molecule associated with JAK3 N-terminus) ...	0.97	-	nuc	0	Isoform 1: Endoplasmic reticulum-Golgi intermediate compartment (By similarity). Isoform 2: Cytoplas ...		609517		2054
Q8IUG5 UniProt NPD GO	MY18B_HUMAN	Myosin-18B (Myosin XVIIIb)	0.97	-	nuc	0	Cytoplasm. Punctate pattern in undifferentiated myoblasts. Nucleus. Nuclear, on primary cardiomyocyt ...	unconventional myosin [IDA]	607295		2567
P02566 UniProt NPD GO	MYO4_CAEEL	Myosin-4 (Myosin heavy chain B) (MHC B) (Uncoordinated protein 54)	0.97	+	nuc	0	Thick filaments of the myofibrils				1966
Q9UM54 UniProt NPD GO	MYO6_HUMAN	Myosin-6 (Myosin VI)	0.97	+	nuc	0		unconventional myosin [TAS]	607821		1285
Q13459 UniProt NPD GO	MYO9B_HUMAN	Myosin-9B (Myosin IXb) (Unconventional myosin-9b)	0.97	-	nuc	0	Cytoplasm; cell cortex. Cytoplasm; perinuclear region. In undifferentiated cells colocalizes with F- ...	actin cytoskeleton [TAS]	609753		2158
Q9QY06 UniProt NPD GO	MYO9B_MOUSE	Myosin-9B (Myosin IXb) (Unconventional myosin-9b)	0.97	-	nuc	0	Cytoplasm; cell cortex. Cytoplasm; perinuclear region (By similarity). In undifferentiated cells col ...				2114
Q56NI9 UniProt NPD GO	ESCO2_HUMAN	N-acetyltransferase ESCO2 (EC 2.3.1.-) (Establishment of cohesion 1 homolog 2) (ECO1 homolog 2)	0.97	-	nuc	0	Nucleus (Probable)		609353		601
Q8IXF0 UniProt NPD GO	NPAS3_HUMAN	Neuronal PAS domain-containing protein 3 (Neuronal PAS3) (Member of PAS protein 6) (MOP6)	0.97	+	nuc	0	Nucleus		609430		933
Q9DE07 UniProt NPD GO	NBN_CHICK	Nibrin (Nijmegen breakage syndrome protein 1 homolog)	0.97	+	nuc	0	Nucleus (By similarity)	Mre11 complex [ISS] nuclear inclusion body [ISS]			753
O74689 UniProt NPD GO	NDE1_EMENI	Nuclear distribution protein nudE	0.97	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules				586
Q14980 UniProt NPD GO	NUMA1_HUMAN	Nuclear mitotic apparatus protein 1 (NuMA protein) (SP-H antigen)	0.97	-	nuc	0	Nucleus. Dissociates from condensing chromosomes during early prophase, before the complete disinteg ...	nucleus [TAS] spindle microtubule [TAS]	164009		2115
O57539 UniProt NPD GO	NCOA3_XENLA	Nuclear receptor coactivator 3 (EC 2.3.1.48) (Retinoid X receptor-interacting coactivator xSRC-3)	0.97	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Mainly cytoplasmic and weakly nuclear (By simila ...				1391

You are viewing entries 1051 to 1100 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.)

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