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
Q29257 UniProt NPD GO	TSN31_PIG	Tetraspanin-31 (Tspan-31) (Sarcoma amplified sequence homolog) (Fragment)	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
Q7ZWW7 UniProt NPD GO	TS31B_XENLA	Tetraspanin-31 B (Tspan-31 B) (Sarcoma amplified sequence homolog B)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				212
Q9DCK3 UniProt NPD GO	TSN4_MOUSE	Tetraspanin-4 (Tspan-4) (Transmembrane 4 superfamily member 7)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				238
O14817 UniProt NPD GO	TSN4_HUMAN	Tetraspanin-4 (Tspan-4) (Transmembrane 4 superfamily member 7) (Novel antigen 2) (NAG-2)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	602644		238
Q68VK5 UniProt NPD GO	TSN5_RAT	Tetraspanin-5 (Tspan-5) (Transmembrane 4 superfamily member 9)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				268
P62079 UniProt NPD GO	TSN5_HUMAN	Tetraspanin-5 (Tspan-5) (Transmembrane 4 superfamily member 9) (Tetraspan NET-4)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				268
P62080 UniProt NPD GO	TSN5_MOUSE	Tetraspanin-5 (Tspan-5) (Transmembrane 4 superfamily member 9) (Tetraspan NET-4)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				268
Q32KU6 UniProt NPD GO	TSN6_BOVIN	Tetraspanin-6 (Tspan-6)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				245
Q7YQL0 UniProt NPD GO	TSN7_PANTR	Tetraspanin-7 (Tspan-7) (Transmembrane 4 superfamily member 2) (CD231 antigen)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				244
O75954 UniProt NPD GO	TSN9_HUMAN	Tetraspanin-9 (Tspan-9) (Tetraspan NET-5)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS] membrane fraction [TAS]			239
Q8BJU2 UniProt NPD GO	TSN9_MOUSE	Tetraspanin-9 (Tspan-9) (Tetraspan NET-5)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				239
P83958 UniProt NPD GO	TLP_ACTCH	Thaumatin-like protein (Allergen Act c 2) (Fragment)	0.00	-		0	Secreted protein				20
P81954 UniProt NPD GO	TLP1_CHRCO	Thaumatin-like protein 1 (CTLP1) (Fragment)	0.00	-	cyt	0					43
P81956 UniProt NPD GO	TLP5_CHRCO	Thaumatin-like protein 5 (CTLP5) (Fragment)	0.00	-	cyt	0					44
O19915 UniProt NPD GO	THIG_CYACA	Thiazole biosynthesis protein thiG	0.00	-	cyt	0	Plastid; chloroplast				291
P84548 UniProt NPD GO	THI4_POPEU	Thiazole biosynthetic enzyme (Fragments)	0.00	-	cyt	0					48
P32318 UniProt NPD GO	THI4_YEAST	Thiazole biosynthetic enzyme, mitochondrial precursor	0.00	-	cyt	1	Mitochondrion (Potential)	cytosol [IDA] mitochondrion [IMP]			326
Q5RBJ3 UniProt NPD GO	TPMT_PONPY	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.00	-	cyt	0	Cytoplasm (By similarity)				245
Q9Z0T0 UniProt NPD GO	TPMT_RAT	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.00	-	cyt	0	Cytoplasm				240
P37395 UniProt NPD GO	THIO_CYACA	Thioredoxin	0.00	-	mit	0	Plastid; chloroplast				107
O22022 UniProt NPD GO	THIO_CYAME	Thioredoxin	0.00	-	mit	0	Plastid; chloroplast				102
O17486 UniProt NPD GO	THIO_ECHGR	Thioredoxin	0.00	-	cyt	0					107
P29429 UniProt NPD GO	THIO_EMENI	Thioredoxin	0.00	-	cyt	0					109
P50338 UniProt NPD GO	THIO_GRIPA	Thioredoxin	0.00	-	cyt	0	Plastid; chloroplast				109
Q9DGI3 UniProt NPD GO	THIO_ICTPU	Thioredoxin	0.00	-	cyt	0					107
P42115 UniProt NPD GO	THIO_NEUCR	Thioredoxin	0.00	-	cyt	0					127
P34723 UniProt NPD GO	THIO_PENCH	Thioredoxin	0.00	-	cyt	0					106
Q7KQL8 UniProt NPD GO	THIO_PLAF7	Thioredoxin	0.00	-	cyt	0				1SYR	104
P51225 UniProt NPD GO	THIO_PORPU	Thioredoxin	0.00	-	cyt	0	Plastid; chloroplast				107
P50254 UniProt NPD GO	THIO_PORYE	Thioredoxin	0.00	-	cyt	0	Plastid; chloroplast				107
Q9UW02 UniProt NPD GO	THIO_COPCM	Thioredoxin (Allergen Cop c 2)	0.00	-	cyt	0					106
O14463 UniProt NPD GO	THIO_SCHPO	Thioredoxin (TR)	0.00	-	cyt	0		cytoplasm [TAS]			102
Q9XFH9 UniProt NPD GO	TRXF2_ARATH	Thioredoxin F-type 2, chloroplast precursor (TRX-F2)	0.00	-	cyt	0	Plastid; chloroplast (By similarity)				185
Q96419 UniProt NPD GO	TRXH_FAGES	Thioredoxin H-type (TRX-H)	0.00	-	cyt	0	Cytoplasm (By similarity)				116
P84564 UniProt NPD GO	TRXH_POPEU	Thioredoxin H-type (TRX-H) (Fragments)	0.00	-	nuc	0	Cytoplasm (By similarity)				26
Q42443 UniProt NPD GO	TRXH_ORYSA	Thioredoxin H-type (TRX-H) (Phloem sap 13 kDa protein 1)	0.00	-	cyt	0	Cytoplasm (By similarity)			1WMJ	122
P80028 UniProt NPD GO	TRXH_CHLRE	Thioredoxin H-type (TRX-H) (Thioredoxin CH1)	0.00	-	cyt	0	Cytoplasm			1TOF	112
O64394 UniProt NPD GO	TRXH_WHEAT	Thioredoxin H-type (TRX-H) (TrxTa)	0.00	-	cyt	0	Cytoplasm				126
Q38879 UniProt NPD GO	TRXH2_ARATH	Thioredoxin H-type 2 (TRX-H-2)	0.00	-	mit	0	Cytoplasm (By similarity)				133
Q42403 UniProt NPD GO	TRXH3_ARATH	Thioredoxin H-type 3 (TRX-H-3)	0.00	-	cyt	0	Cytoplasm (By similarity)				118
Q39239 UniProt NPD GO	TRXH4_ARATH	Thioredoxin H-type 4 (TRX-H-4)	0.00	-	cyt	0	Cytoplasm (By similarity)				119
Q39241 UniProt NPD GO	TRXH5_ARATH	Thioredoxin H-type 5 (TRX-H-5)	0.00	-	cyt	0	Cytoplasm (By similarity)				118
P22803 UniProt NPD GO	TRX2_YEAST	Thioredoxin II (TR-II) (Thioredoxin 1)	0.00	-	cyt	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. Nucleus	cytosol [IDA] vacuole (sensu Fungi) [IPI]			103
Q9ZP21 UniProt NPD GO	TRXM_WHEAT	Thioredoxin M-type, chloroplast precursor (TRX-M)	0.00	-	cyt	0	Plastid; chloroplast (By similarity)				175
P91883 UniProt NPD GO	TDX_FASHE	Thioredoxin peroxidase (EC 1.11.1.15) (Peroxiredoxin) (Thioredoxin-dependent peroxide reductase) (Th ...	0.00	-	cyt	0	Cytoplasm (By similarity)				194
P48822 UniProt NPD GO	TDX1_BRUMA	Thioredoxin peroxidase 1 (EC 1.11.1.15) (Peroxiredoxin 1) (Thioredoxin-dependent peroxide reductase ...	0.00	-	mit	0	Cytoplasm (By similarity)			1W65	229
Q75CM8 UniProt NPD GO	TRXB_ASHGO	Thioredoxin reductase (EC 1.8.1.9)	0.00	-	cyt	0	Cytoplasm (By similarity)				319
Q92375 UniProt NPD GO	TRXB_SCHPO	Thioredoxin reductase (EC 1.8.1.9) (Caffeine resistance protein 4)	0.00	-	cyt	0	Cytoplasm				322
Q25861 UniProt NPD GO	TRXR_PLAF5	Thioredoxin reductase (EC 1.8.1.9) (TrxR)	0.00	-	cyt	0	Cytoplasm (By similarity)				541
P61076 UniProt NPD GO	TRXR_PLAF7	Thioredoxin reductase (EC 1.8.1.9) (TrxR)	0.00	-	cyt	0	Cytoplasm (By similarity)				541

You are viewing entries 98251 to 98300 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.