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
P28740 UniProt NPD GO	KIF2_MOUSE	Kinesin-like protein KIF2	0.95	-	nuc	0					716
P17120 UniProt NPD GO	BIMC_EMENI	Kinesin-like protein bimC	0.95	-	nuc	0					1184
P10166 UniProt NPD GO	MYCL1_MOUSE	L-myc-1 proto-oncogene protein	0.95	-	nuc	0	Nucleus (Potential)				368
P08548 UniProt NPD GO	LIN1_NYCCO	LINE-1 reverse transcriptase homolog	0.95	-	nuc	0					1260
P08928 UniProt NPD GO	LAM0_DROME	Lamin Dm0	0.95	-	nuc	0	Nucleus. Nuclear periphery	lamin filament [TAS]			622
P21910 UniProt NPD GO	LAML2_XENLA	Lamin-L(II)	0.95	+	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side				623
Q7TSC1 UniProt NPD GO	BAT2_MOUSE	Large proline-rich protein BAT2 (HLA-B-associated transcript 2)	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				2158
P60469 UniProt NPD GO	LIPA3_MOUSE	Liprin-alpha-3 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3 ...	0.95	-	nuc	0	Cytoplasm (By similarity). Cell surface (By similarity). Colocalizes with PTPRF at the cell surface ...				1043
Q91Z79 UniProt NPD GO	LIPA3_RAT	Liprin-alpha-3 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3 ...	0.95	-	nuc	0	Cytoplasm (By similarity). Cell surface (By similarity). Colocalizes with PTPRF at the cell surface ...				1192
P30309 UniProt NPD GO	MPI1B_XENLA	M-phase inducer phosphatase 1-B (EC 3.1.3.48)	0.95	+	nuc	0					550
P48966 UniProt NPD GO	MPIP2_RAT	M-phase inducer phosphatase 2 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25B)	0.95	-	nuc	0	Centrosome (By similarity)				574
Q8JHF4 UniProt NPD GO	MPP5_BRARE	MAGUK p55 subfamily member 5 (Nagie oko protein) (MAGUK family factor)	0.95	+	nuc	0	Cell membrane; apical cell membrane; peripheral membrane protein. Localizes to the apical region of ...				677
Q9Y6X9 UniProt NPD GO	MORC2_HUMAN	MORC family CW-type zinc finger 2 (Zinc finger CW-type coiled-coil domain protein 1)	0.95	-	nuc	0					970
Q2TLZ3 UniProt NPD GO	MACOI_BOVIN	Macoilin (Transmembrane protein 57)	0.95	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				664
Q2TLZ1 UniProt NPD GO	MACOI_CANFA	Macoilin (Transmembrane protein 57)	0.95	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				664
Q8N5G2 UniProt NPD GO	MACOI_HUMAN	Macoilin (Transmembrane protein 57)	0.95	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				664
Q2TLZ5 UniProt NPD GO	MACOI_PANTR	Macoilin (Transmembrane protein 57)	0.95	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				664
Q2TLZ2 UniProt NPD GO	MACOI_PIG	Macoilin (Transmembrane protein 57)	0.95	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				664
Q7TQE6 UniProt NPD GO	MACOI_MOUSE	Macoilin (Transmembrane protein 57) (Brain-specific adaptor protein C61)	0.95	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)	nucleus [IDA]			664
P37934 UniProt NPD GO	MAAY3_SCHCO	Mating-type protein A-alpha Y3	0.95	+	nuc	0	Nucleus (Potential)				926
P40333 UniProt NPD GO	MAB11_COPCI	Mating-type protein beta1-1	0.95	+	nuc	0	Nucleus				681
O47135 UniProt NPD GO	MATK_PHYCU	Maturase K (Intron maturase)	0.95	-	cyt	0	Plastid; chloroplast				506
Q5TM68 UniProt NPD GO	MDC1_MACMU	Mediator of DNA damage checkpoint protein 1	0.95	-	nuc	0	Nucleus (By similarity). Associated with chromatin. Relocalizes to discrete nuclear foci following D ...				2173
O94713 UniProt NPD GO	MEU27_SCHPO	Meiotic expression up-regulated protein 27	0.95	+	nuc	0					736
Q9BV36 UniProt NPD GO	MELPH_HUMAN	Melanophilin (Exophilin-3) (Synaptotagmin-like protein 2a) (Slp homolog lacking C2 domains a)	0.95	-	nuc	0	Cytoplasm		609227		600
Q9BZ72 UniProt NPD GO	PITM2_HUMAN	Membrane-associated phosphatidylinositol transfer protein 2 (Phosphatidylinositol transfer protein, ...	0.95	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (Probable)	integral to membrane [NAS]	608920		1349
P61591 UniProt NPD GO	MCPH1_GORGO	Microcephalin	0.95	+	nuc	0	Centrosome (By similarity)				835
P61593 UniProt NPD GO	MCPH1_PANTR	Microcephalin	0.95	+	nuc	0	Centrosome (By similarity)				835
O42667 UniProt NPD GO	SSM4_SCHPO	Microtubule-associated protein ssm4	0.95	+	nuc	0	Spindle. Mitotic spindle	cortical microtubule cytoskeleton [IDA] spindle pole body [IDA]			670
Q6P0Q8 UniProt NPD GO	MAST2_HUMAN	Microtubule-associated serine/threonine-protein kinase 2 (EC 2.7.11.1)	0.95	-	nuc	0	Cytoplasm. Recruited to the sub-membranous area on interaction with PC-LKC				1798
O43283 UniProt NPD GO	M3K13_HUMAN	Mitogen-activated protein kinase kinase kinase 13 (EC 2.7.11.25) (Mixed lineage kinase) (MLK) (Leuci ...	0.95	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	membrane fraction [IDA]	604915		966
Q80YF0 UniProt NPD GO	MD1L1_CRIGR	Mitotic spindle assembly checkpoint protein MAD1 (Mitotic arrest deficient-like protein 1) (MAD1-lik ...	0.95	-	nuc	0	Nucleus (By similarity). From the beginning to the end of mitosis, it is seen to move from a diffuse ...				717
Q9BU76 UniProt NPD GO	MMTA2_HUMAN	Multiple myeloma tumor-associated protein 2 (hMMTAG2)	0.95	+	nuc	0					263
P52550 UniProt NPD GO	MYBA_CHICK	Myb-related protein A (A-Myb)	0.95	+	nuc	0	Nucleus				757
Q03237 UniProt NPD GO	MYBB_CHICK	Myb-related protein B (B-Myb)	0.95	+	nuc	0	Nucleus			1A5J	686
Q2HJ27 UniProt NPD GO	MYC_BOVIN	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.95	+	nuc	0	Nucleus				439
Q9MZT8 UniProt NPD GO	MYC_PTEHP	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.95	+	nuc	0	Nucleus				440
Q28566 UniProt NPD GO	MYC_SHEEP	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.95	+	nuc	0	Nucleus				439
Q9MZT7 UniProt NPD GO	MYC_TADBR	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.95	+	nuc	0	Nucleus				439
Q9MZT9 UniProt NPD GO	MYC_TUPGL	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.95	+	nuc	0	Nucleus				439
P70047 UniProt NPD GO	MYT1_XENLA	Myelin transcription factor 1 (X-MyT1)	0.95	+	nuc	0	Nucleus (Potential)				1122
P11055 UniProt NPD GO	MYH3_HUMAN	Myosin heavy chain, fast skeletal muscle, embryonic (Muscle embryonic myosin heavy chain) (SMHCE)	0.95	+	nuc	0	Thick filaments of the myofibrils		160720		1940
P13538 UniProt NPD GO	MYSS_CHICK	Myosin heavy chain, skeletal muscle, adult	0.95	+	nuc	0	Thick filaments of the myofibrils			2MYS	1938
P24733 UniProt NPD GO	MYS_AEQIR	Myosin heavy chain, striated muscle	0.95	-	nuc	0	Thick filaments of the myofibrils			1WDC	1938
P12882 UniProt NPD GO	MYH1_HUMAN	Myosin-1 (Myosin heavy chain, skeletal muscle, adult 1) (Myosin heavy chain IIx/d) (MyHC-IIx/d)	0.95	+	nuc	0	Thick filaments of the myofibrils		160730		1939
P10587 UniProt NPD GO	MYH11_CHICK	Myosin-11 (Myosin heavy chain, gizzard smooth muscle)	0.95	+	nuc	0	Thick filaments of the myofibrils			1I84	1978
P32492 UniProt NPD GO	MYO4_YEAST	Myosin-4	0.95	-	cyt	0	Accumulates preferentially in growing buds	actin cap [IDA] mitochondrion [IDA]			1471
Q5SX39 UniProt NPD GO	MYH4_MOUSE	Myosin-4 (Myosin heavy chain, skeletal muscle, fetal)	0.95	+	nuc	0	Thick filaments of the myofibrils				1939
Q9Y623 UniProt NPD GO	MYH4_HUMAN	Myosin-4 (Myosin heavy chain, skeletal muscle, fetal) (Myosin heavy chain IIb) (MyHC-IIb)	0.95	+	nuc	0	Thick filaments of the myofibrils		160742		1939
P97479 UniProt NPD GO	MYO7A_MOUSE	Myosin-7A (Myosin VIIa)	0.95	+	nuc	0	Cytoplasm (Probable)	cytoplasm [IDA]			2215

You are viewing entries 1901 to 1950 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.