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
P31161 UniProt NPD GO	SODM1_CAEEL	Superoxide dismutase [Mn] 1, mitochondrial precursor (EC 1.15.1.1)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				221
P28762 UniProt NPD GO	SODM_EPTST	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix				144
P28766 UniProt NPD GO	SODM_PARCL	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix				144
P28767 UniProt NPD GO	SODM_PETMA	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix				144
P28768 UniProt NPD GO	SODM_PIG	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix				144
P35017 UniProt NPD GO	SODM_HEVBR	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				233
P41981 UniProt NPD GO	SODM_ONCVO	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix				223
Q6CBN5 UniProt NPD GO	SVF1_YARLI	Survival factor 1	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				398
O55101 UniProt NPD GO	SNG2_MOUSE	Synaptogyrin-2 (Cellugyrin)	0.02	-	end	4 *	Membrane; multi-pass membrane protein	synaptic vesicle [IDA]			224
P20488 UniProt NPD GO	SYPH_BOVIN	Synaptophysin (Major synaptic vesicle protein p38)	0.02	-	end	3 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein				313
P08247 UniProt NPD GO	SYPH_HUMAN	Synaptophysin (Major synaptic vesicle protein p38)	0.02	-	end	3 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein	integral to synaptic vesicle membrane [NAS]	313475		313
Q8BGN8 UniProt NPD GO	SYNPR_MOUSE	Synaptoporin	0.02	-	end	4 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)	integral to synaptic vesicle membrane [TAS]			265
P01407 UniProt NPD GO	TS24_DENJA	Synergistic-type venom protein S2C4	0.02	-	nuc	0	Secreted protein				62
P57738 UniProt NPD GO	TCTA_HUMAN	T-cell leukemia translocation-associated gene protein	0.02	-	nuc	1 *			600690		103
P04213 UniProt NPD GO	TVB5_MOUSE	T-cell receptor beta chain V region C5 precursor (Fragment)	0.02	-	cyt	0				1U3H	122
P23042 UniProt NPD GO	CD1B_RABIT	T-cell surface glycoprotein CD1b precursor (Leukocyte differentiation-like antigen Ta) (Fragment)	0.02	-	exc	0	Membrane; single-pass type I membrane protein				109
Q9QZY6 UniProt NPD GO	CD1C3_CAVPO	T-cell surface glycoprotein CD1c3 precursor (CD1-c3 antigen)	0.02	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				332
P04234 UniProt NPD GO	CD3D_HUMAN	T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)	0.02	-	nuc	0	Membrane; single-pass type I membrane protein	cytoplasm [NAS] T cell receptor complex [NAS]	186790	1XIW	171
Q95LI8 UniProt NPD GO	CD3D_MACFA	T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)	0.02	-	nuc	0	Membrane; single-pass type I membrane protein				171
P19377 UniProt NPD GO	CD3D_RAT	T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)	0.02	-	nuc	0	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			173
Q98910 UniProt NPD GO	CD3E_CHICK	T-cell surface glycoprotein CD3 epsilon chain precursor	0.02	-	end	1 *	Membrane; single-pass type I membrane protein				175
P47207 UniProt NPD GO	TCPB_CAEEL	T-complex protein 1 subunit beta (TCP-1-beta) (CCT-beta)	0.02	-	nuc	0	Cytoplasm				529
Q29236 UniProt NPD GO	TCPZ_PIG	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta) (Fragment)	0.02	-	cyt	0	Cytoplasm				104
P17871 UniProt NPD GO	TBP_SCHPO	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.02	-	cyt	0	Nucleus				231
Q5ZKH0 UniProt NPD GO	TF2H5_CHICK	TFIIH basal transcription factor complex TTD-A subunit (General transcription factor IIH polypeptide ...	0.02	-	cyt	0	Nucleus (By similarity)				71
Q6ZYL4 UniProt NPD GO	TF2H5_HUMAN	TFIIH basal transcription factor complex TTD-A subunit (General transcription factor IIH polypeptide ...	0.02	-	cyt	0	Nucleus		601675	1YDL	71
Q8K2X8 UniProt NPD GO	TF2H5_MOUSE	TFIIH basal transcription factor complex TTD-A subunit (General transcription factor IIH polypeptide ...	0.02	-	cyt	0	Nucleus (By similarity)				71
P38962 UniProt NPD GO	TVP23_YEAST	TLG2-vesicle protein of 23 kDa	0.02	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] integral to Golgi membrane [IDA]			199
Q9VP65 UniProt NPD GO	TR112_DROME	TRM112-like protein	0.02	-	cyt	0					124
Q9UI30 UniProt NPD GO	TR112_HUMAN	TRM112-like protein	0.02	-	mit	0					125
Q9DCG9 UniProt NPD GO	TR112_MOUSE	TRM112-like protein	0.02	-	mit	0					125
Q8LFJ5 UniProt NPD GO	T112A_ARATH	TRM112-like protein At1g22270	0.02	-	mit	0					124
Q9C9R3 UniProt NPD GO	T112B_ARATH	TRM112-like protein At1g78190	0.02	-	mit	0					124
P81737 UniProt NPD GO	TRP5_LEUMA	Tachykinin-related peptide 5 (LemTRP 5)	0.02	-		0	Secreted protein				10
P81741 UniProt NPD GO	TRP9_LEUMA	Tachykinin-related peptide 9 (LemTRP 9)	0.02	-		0	Secreted protein				10
Q6IV83 UniProt NPD GO	TAZ_GORGO	Tafazzin	0.02	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				292
Q6IV84 UniProt NPD GO	TAZ_PANTR	Tafazzin	0.02	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				292
Q6IV82 UniProt NPD GO	TAZ_PONPY	Tafazzin	0.02	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				292
Q16635 UniProt NPD GO	TAZ_HUMAN	Tafazzin (Protein G4.5)	0.02	-	cyt	1 *	Membrane; single-pass membrane protein. Cytoplasm. Isoforms with hydrophobic N-terminus are thought ...		604169		292
P29288 UniProt NPD GO	PPA5_RAT	Tartrate-resistant acid phosphatase type 5 precursor (EC 3.1.3.2) (TR-AP) (Tartrate-resistant acid A ...	0.02	-	nuc	0	Lysosome	integral to membrane [TAS] lysosome [TAS]		1QHW	327
Q646E0 UniProt NPD GO	T2R44_PANPA	Taste receptor type 2 member 44 (T2R44)	0.02	-	end	6 *	Membrane; multi-pass membrane protein				309
P59538 UniProt NPD GO	T2R44_HUMAN	Taste receptor type 2 member 44 (T2R44) (T2R53)	0.02	-	end	6 *	Membrane; multi-pass membrane protein				309
Q5Y4Z8 UniProt NPD GO	T2R45_PANPA	Taste receptor type 2 member 45 (T2R45)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				309
Q645Z0 UniProt NPD GO	T2R60_GORGO	Taste receptor type 2 member 60 (T2R60) (T2R56)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				318
Q5Y4Z0 UniProt NPD GO	T2R62_PANPA	Taste receptor type 2 member 62 (T2R62)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				312
Q5Y4Y9 UniProt NPD GO	T2R64_PANPA	Taste receptor type 2 member 64 (T2R64)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				309
O61064 UniProt NPD GO	TCT2_PHYPO	Tectonin-2 (Tectonin II)	0.02	-	cyt	0	Cell surface. Cytoplasmic vesicle; cytoplasmic vesicle membrane. Also bound to inner membrane of cer ...				353
P82882 UniProt NPD GO	TE1CC_RANCL	Temporin-1Cc	0.02	-		0	Secreted protein				13
P56923 UniProt NPD GO	TEMK_RANTE	Temporin-K	0.02	-		0	Secreted protein				10
P80941 UniProt NPD GO	ECDE_LYMDI	Testis ecdysiotropin peptide E (TE)	0.02	-		0					13

You are viewing entries 85851 to 85900 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.