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
Q9W7L3 UniProt NPD GO	LDHA_PYTRG	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.00	-	mit	0	Cytoplasm (By similarity)				331
Q9W7L5 UniProt NPD GO	LDHA_SCEUN	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.00	-	mit	0	Cytoplasm (By similarity)				331
P79912 UniProt NPD GO	LDHA_SCEWO	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.00	-	cyt	0	Cytoplasm (By similarity)				331
Q9PT43 UniProt NPD GO	LDHA_TRASC	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.00	-	mit	0	Cytoplasm (By similarity)				331
P00339 UniProt NPD GO	LDHA_PIG	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.00	-	mit	0	Cytoplasm			9LDT	331
Q9BYZ2 UniProt NPD GO	LDH6B_HUMAN	L-lactate dehydrogenase A-like 6B (EC 1.1.1.27)	0.00	-	mit	0					381
Q8NK50 UniProt NPD GO	DCXR_TRIRE	L-xylulose reductase (EC 1.1.1.10) (XR)	0.00	-	cyt	0					266
Q11117 UniProt NPD GO	LMP1_CAEEL	LAMP family protein lmp-1 precursor	0.00	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				237
P13270 UniProt NPD GO	LABA_JATMU	Labaditin	0.00	-		0					10
P58809 UniProt NPD GO	CXL3_CONMR	Lambda-conotoxin CMrX	0.00	-		0	Secreted protein				12
P02839 UniProt NPD GO	LCP1_DROME	Larval cuticle protein 1 precursor (Larval cuticle protein I)	0.00	-	vac	0					130
P91627 UniProt NPD GO	LCP1_DROMI	Larval cuticle protein 1 precursor (Larval cuticle protein I)	0.00	-	vac	0					138
Q25504 UniProt NPD GO	CU16_MANSE	Larval cuticle protein 16/17 precursor	0.00	-	exc	0					110
P07187 UniProt NPD GO	LCP2_DROME	Larval cuticle protein 2 precursor (Larval cuticle protein II)	0.00	-	exc	0					126
P91629 UniProt NPD GO	LCP2_DROMI	Larval cuticle protein 2 precursor (Larval cuticle protein II)	0.00	-	exc	0					126
P07188 UniProt NPD GO	LCP3_DROME	Larval cuticle protein 3 precursor (Larval cuticle protein III)	0.00	-	exc	0					112
P07189 UniProt NPD GO	LCP4_DROME	Larval cuticle protein 4 precursor (Larval cuticle protein IV)	0.00	-	exc	0					112
P92192 UniProt NPD GO	LCP5_DROME	Larval cuticle protein 5 precursor (Larval cuticle protein V)	0.00	-	exc	0		extracellular region [NAS]			104
P92201 UniProt NPD GO	LCP8_DROME	Larval cuticle protein 8 precursor (Larval cuticle protein VIII)	0.00	-	vac	0		extracellular region [NAS]			105
P82384 UniProt NPD GO	LCP9_DROME	Larval cuticle protein 9 precursor (Larval cuticle protein IX)	0.00	-	exc	0		extracellular region [NAS]			92
O02387 UniProt NPD GO	CU17_BOMMO	Larval cuticle protein LCP-17 precursor	0.00	-	exc	0					143
P14486 UniProt NPD GO	CUP4_SARBU	Larval cuticle protein SC4 (Fragment)	0.00	-	cyt	0					37
P14487 UniProt NPD GO	CUP6_SARBU	Larval cuticle protein SC6 (Fragment)	0.00	-	cyt	0					39
P45590 UniProt NPD GO	CU66_HYACE	Larval/pupal rigid cuticle protein 66 precursor (HCCP66)	0.00	-	exc	0					129
P46518 UniProt NPD GO	LEA14_GOSHI	Late embryogenesis abundant protein Lea14-A	0.00	-	cyt	0					151
P84038 UniProt NPD GO	LEBCA_VIPLE	Lebecetin subunit alpha (Fragment)	0.00	-	cyt	0	Secreted protein				42
O95237 UniProt NPD GO	LRAT_HUMAN	Lecithin retinol acyltransferase (EC 2.3.1.135) (Phosphatidylcholine--retinol O-acyltransferase)	0.00	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)		604863		230
P16108 UniProt NPD GO	LECC_POLMI	Lectin	0.00	-	cyt	0				1TLG	125
P33888 UniProt NPD GO	AGI_EUPCH	Lectin (Fragment)	0.00	-		0					18
Q01806 UniProt NPD GO	LEC1_MEDTR	Lectin 1 precursor	0.00	-	mit	1 *					277
P07441 UniProt NPD GO	LECA_LATAP	Lectin alpha chain	0.00	-	cyt	0					53
P07442 UniProt NPD GO	LECA_LATAR	Lectin alpha chain	0.00	-	cyt	0					53
P02869 UniProt NPD GO	LECA_LATOD	Lectin alpha chain	0.00	-	cyt	0					54
P07444 UniProt NPD GO	LECA_LATTI	Lectin alpha chain	0.00	-	cyt	0					54
P07440 UniProt NPD GO	LECA_LATCI	Lectin alpha-1 chain [Contains: Lectin alpha-2 chain]	0.00	-	cyt	0					54
P07443 UniProt NPD GO	LECA_LATHI	Lectin alpha-1 chain [Contains: Lectin alpha-2 chain]	0.00	-	cyt	0					54
Q93WH6 UniProt NPD GO	LEC_LENCC	Lectin precursor [Contains: Lectin beta chain; Lectin alpha chain]	0.00	-	mit	1 *					275
P02870 UniProt NPD GO	LEC_LENCU	Lectin precursor [Contains: Lectin beta chain; Lectin alpha chain]	0.00	-	mit	1 *				2LAL	275
P84870 UniProt NPD GO	LEC1_HYPCE	Lectin-1 (HCA) [Contains: Lectin-1 N-terminal subunit; Lectin-1 C-terminal subunit]	0.00	-	cyt	0					90
P28587 UniProt NPD GO	LEC2_AXIDI	Lectin-2 (Lectin II) (Fragment)	0.00	-	cyt	0	Stored in spherulous cells in the sponge tissue				49
P28588 UniProt NPD GO	LEC3_AXIDI	Lectin-3 (Lectin III) (Fragment)	0.00	-		0	Stored in spherulous cells in the sponge tissue				15
O04939 UniProt NPD GO	LGB2_PHAVU	Leghemoglobin	0.00	-	cyt	0					145
P28010 UniProt NPD GO	LGB4_MEDSA	Leghemoglobin	0.00	-	cyt	0					147
P42511 UniProt NPD GO	LGB_CANLI	Leghemoglobin	0.00	-	cyt	0					149
Q9FEP8 UniProt NPD GO	LGB_LOTJA	Leghemoglobin	0.00	-	cyt	0					147
P27199 UniProt NPD GO	LGB_PSOTE	Leghemoglobin	0.00	-	cyt	0					145
P27992 UniProt NPD GO	LGB1_MEDTR	Leghemoglobin 1	0.00	-	cyt	0					147
P27993 UniProt NPD GO	LGB2_MEDTR	Leghemoglobin 2	0.00	-	cyt	0					146
P14848 UniProt NPD GO	LGB2_SESRO	Leghemoglobin 2 (Srglb2)	0.00	-	cyt	0					147
P93848 UniProt NPD GO	LGB2_VICFA	Leghemoglobin 29 (VfLb29)	0.00	-	cyt	0					148

You are viewing entries 95401 to 95450 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.