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
P04933 UniProt NPD GO	MSP1_PLAFW	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (P195)	0.77	+	exc	1	Cell membrane; lipid-anchor; GPI-anchor			2FLG	1639
Q9BTC8 UniProt NPD GO	MTA3_HUMAN	Metastasis-associated protein MTA3	0.77	-	nuc	0	Nucleus		609050		594
Q924K8 UniProt NPD GO	MTA3_MOUSE	Metastasis-associated protein MTA3	0.77	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]		2CRG	591
Q8T5T1 UniProt NPD GO	MDN1_GIALA	Midasin (MIDAS-containing protein)	0.77	-	end	0	Nucleus (By similarity)				4835
O21264 UniProt NPD GO	RM19_RECAM	Mitochondrial 60S ribosomal protein L19	0.77	-	nuc	0	Mitochondrion				113
Q16891 UniProt NPD GO	IMMT_HUMAN	Mitochondrial inner membrane protein (Mitofilin) (p87/89) (Proliferation-inducing gene 4 protein)	0.77	-	nuc	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IEP]	600378		758
Q02779 UniProt NPD GO	M3K10_HUMAN	Mitogen-activated protein kinase kinase kinase 10 (EC 2.7.11.25) (Mixed lineage kinase 2) (Protein k ...	0.77	-	nuc	0			600137		954
P52962 UniProt NPD GO	MOES_LYTVA	Moesin	0.77	-	nuc	0					572
Q6QI89 UniProt NPD GO	MO4L2_RAT	Mortality factor 4-like protein 2 (MORF-related gene X protein) (Transcription factor-like protein M ...	0.77	-	nuc	0	Nucleus (By similarity)				288
P22980 UniProt NPD GO	MYOD1_CAEEL	Myoblast determination protein 1 homolog (MyoD protein 1) (Helix-loop-helix protein 1)	0.77	+	nuc	0	Nucleus	nucleus [IDA]			324
Q02080 UniProt NPD GO	MEF2B_HUMAN	Myocyte-specific enhancer factor 2B (Serum response factor-like protein 2) (XMEF2) (RSRFR2)	0.77	-	nuc	0	Nucleus	nucleus [TAS]	600661	1TQE	365
P20428 UniProt NPD GO	MYOG_RAT	Myogenin	0.77	+	nuc	0	Nucleus				287
P34109 UniProt NPD GO	MYOD_DICDI	Myosin ID heavy chain	0.77	-	nuc	0	Cytoplasm; cell cortex. Highest concentration just beneath the plasma membrane in the anterior pseud ...				1109
Q9WTI7 UniProt NPD GO	MYO1C_MOUSE	Myosin Ic (Myosin I beta) (MMIb)	0.77	-	cyt	0		myosin I [IDA]			1028
Q91WS2 UniProt NPD GO	NALP6_MOUSE	NACHT, LRR and PYD-containing protein 6 (PYRIN-containing APAF1-like protein 5-like)	0.77	-	mit	0	Cytoplasm (By similarity)				843
Q63035 UniProt NPD GO	NALP6_RAT	NACHT, LRR and PYD-containing protein 6 (PYRIN-containing APAF1-like protein 5-like) (Angiotensin II ...	0.77	-	cyt	0	Cytoplasm (By similarity)				854
Q62722 UniProt NPD GO	NAB1_RAT	NGFI-A-binding protein 1 (EGR-1-binding protein 1)	0.77	-	nuc	0	Nucleus				485
O15259 UniProt NPD GO	NPHP1_HUMAN	Nephrocystin-1 (Juvenile nephronophthisis 1 protein)	0.77	+	mit	0	Cell membrane; cell-cell junction; adherens junction (By similarity). Localizes at or near the cell- ...	membrane [NAS]	256100	1S1N	732
P48681 UniProt NPD GO	NEST_HUMAN	Nestin	0.77	-	nuc	0		intermediate filament [NAS]	600915		1618
P39923 UniProt NPD GO	NPR2_YEAST	Nitrogen permease regulator 2	0.77	-	nuc	0					615
Q5RFL9 UniProt NPD GO	NONO_PONPY	Non-POU domain-containing octamer-binding protein (NonO protein)	0.77	+	nuc	0	Nucleus (By similarity)				471
Q15233 UniProt NPD GO	NONO_HUMAN	Non-POU domain-containing octamer-binding protein (NonO protein) (54 kDa nuclear RNA- and DNA-bindin ...	0.77	+	nuc	0	Nucleus	nucleus [TAS]	300084		471
Q3UYV9 UniProt NPD GO	NCBP1_MOUSE	Nuclear cap-binding protein subunit 1 (80 kDa nuclear cap-binding protein) (NCBP 80 kDa subunit) (CB ...	0.77	+	mit	0	Nucleus (By similarity)	nucleus [ISS]			790
O18086 UniProt NPD GO	NH218_CAEEL	Nuclear hormone receptor family member nhr-218	0.77	-	nuc	0	Nucleus (Potential)				400
O76828 UniProt NPD GO	NHR42_CAEEL	Nuclear hormone receptor family member nhr-42	0.77	-	exc	0	Nucleus (Potential)				356
Q9SYH4 UniProt NPD GO	NFYA5_ARATH	Nuclear transcription factor Y subunit A-5 (AtNF-YA-5)	0.77	-	nuc	0	Nucleus (Probable)				308
P53742 UniProt NPD GO	NOG2_YEAST	Nucleolar GTP-binding protein 2	0.77	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleoplasm [IDA] nucleus [IDA]			486
Q6C2Q7 UniProt NPD GO	NOP12_YARLI	Nucleolar protein 12	0.77	+	nuc	0	Nucleus; nucleolus (By similarity)				509
P37838 UniProt NPD GO	NOP4_YEAST	Nucleolar protein 4 (Nucleolar protein NOP77)	0.77	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]			685
Q53GS7 UniProt NPD GO	GLE1_HUMAN	Nucleoporin GLE1 (GLE1-like protein) (hGLE1)	0.77	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm. Isoform 1: Nuclear envelope; nuc ...		603371		698
O08919 UniProt NPD GO	NUMBL_MOUSE	Numb-like protein	0.77	-	nuc	0	Cytoplasm	cytoplasm [IDA]			604
P18753 UniProt NPD GO	ZO84_XENLA	Oocyte zinc finger protein XLCOF8.4 (Fragment)	0.77	-	nuc	0	Nucleus (Potential)				780
Q91628 UniProt NPD GO	ORC2_XENLA	Origin recognition complex subunit 2 (XORC2)	0.77	-	nuc	0	Nucleus				558
Q24169 UniProt NPD GO	ORC5_DROME	Origin recognition complex subunit 5	0.77	-	cyt	0	Nucleus	nuclear origin of replication recognition c... [IDA]			460
Q07916 UniProt NPD GO	PO6F1_MOUSE	POU domain, class 6, transcription factor 1 (Octamer-binding transcription factor EMB) (Transcriptio ...	0.77	+	nuc	0	Nucleus	nucleus [IDA]			301
P63015 UniProt NPD GO	PAX6_MOUSE	Paired box protein Pax-6 (Oculorhombin)	0.77	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [TAS]			422
P26367 UniProt NPD GO	PAX6_HUMAN	Paired box protein Pax-6 (Oculorhombin) (Aniridia type II protein)	0.77	+	nuc	0	Nucleus		106210	6PAX	422
Q02770 UniProt NPD GO	CWC27_YEAST	Peptidyl-prolyl isomerase CWC27 (EC 5.2.1.8) (Complexed with CEF1 protein 27)	0.77	-	nuc	0	Cytoplasm. Nucleus	spliceosome complex [IPI]			301
P41219 UniProt NPD GO	PERI_HUMAN	Peripherin	0.77	-	mit	0		intermediate filament [TAS]	170710		471
P11746 UniProt NPD GO	MCM1_YEAST	Pheromone receptor transcription factor (GRM/PRTF protein)	0.77	-	nuc	0	Nucleus	nuclear chromatin [IDA] nucleus [IPI]		1MNM	286
Q6PF93 UniProt NPD GO	PK3C3_MOUSE	Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) (PtdIns-3-kinase type 3) (PI3- ...	0.77	-	cyt	0					887
O88763 UniProt NPD GO	PK3C3_RAT	Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) (PtdIns-3-kinase type 3) (PI3- ...	0.77	-	cyt	0					887
Q5ZJ58 UniProt NPD GO	PI51B_CHICK	Phosphatidylinositol-4-phosphate 5-kinase type-1 beta (EC 2.7.1.68) (Phosphatidylinositol-4-phosphat ...	0.77	-	nuc	0	Intracytoplasmic membrane (By similarity). Associated with membranes (By similarity)				540
Q43299 UniProt NPD GO	CAPP_AMAHP	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.77	-	nuc	0	Cytoplasm				964
P0C0R5 UniProt NPD GO	PI3R4_RAT	Phosphoinositide 3-kinase regulatory subunit 4 (EC 2.7.11.1) (PI3-kinase regulatory subunit 4)	0.77	-	nuc	0					1357
Q99570 UniProt NPD GO	PI3R4_HUMAN	Phosphoinositide 3-kinase regulatory subunit 4 (EC 2.7.11.1) (PI3-kinase regulatory subunit 4) (PI3- ...	0.77	-	nuc	0			602610		1357
Q91XR8 UniProt NPD GO	GPX42_RAT	Phospholipid hydroperoxide glutathione peroxidase, nuclear (EC 1.11.1.12) (GPX-4)	0.77	+	nuc	0	Nucleus	nucleus [ISS]			253
Q7Z3Z4 UniProt NPD GO	PIWL4_HUMAN	Piwi-like protein 4	0.77	-	nuc	0					852
P49162 UniProt NPD GO	RK20_LATCL	Plastid 50S ribosomal protein L20	0.77	-	mit	0	Plastid				127
Q9ERS5 UniProt NPD GO	PKHA2_MOUSE	Pleckstrin homology domain-containing family A member 2 (Tandem PH domain-containing protein 2) (TAP ...	0.77	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Nucleus. Locates to the plasma membrane after ...				425

You are viewing entries 10451 to 10500 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.