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
Q923Y5 UniProt NPD GO	TAAR6_RAT	Trace amine-associated receptor 6 (Trace amine receptor 4) (TaR-4)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				345
Q5QD07 UniProt NPD GO	TAA8A_MOUSE	Trace amine-associated receptor 8a	0.00	-	end	7 *	Membrane; multi-pass membrane protein				344
Q9CQP2 UniProt NPD GO	TPPC2_MOUSE	Trafficking protein particle complex protein 2 (Sedlin)	0.00	-	cyt	0	Cytoplasm; perinuclear region (By similarity). Localized in perinuclear granular structures (By simi ...			1H3Q	140
O14582 UniProt NPD GO	TPPC2_HUMAN	Trafficking protein particle complex protein 2 (Sedlin) (MBP-1-interacting protein 2A) (MIP-2A)	0.00	-	cyt	0	Cytoplasm; perinuclear region. Localized in perinuclear granular structures		313400		140
Q9ES56 UniProt NPD GO	TPPC4_MOUSE	Trafficking protein particle complex subunit 4 (Synbindin) (TRS23 homolog)	0.00	-	cyt	0	Membrane. Associated with postsynaptic membranes and in intracellular cisterns and vesicles (Golgi)	dendrite [IDA] Golgi stack [IDA] synapse [IDA] synaptic vesicle [IDA]			219
Q2KII4 UniProt NPD GO	ELOC_BOVIN	Transcription elongation factor B polypeptide 1 (RNA polymerase II transcription factor SIII subunit ...	0.00	-	cyt	0	Nucleus (Probable)				112
Q15369 UniProt NPD GO	ELOC_HUMAN	Transcription elongation factor B polypeptide 1 (RNA polymerase II transcription factor SIII subunit ...	0.00	-	cyt	0	Nucleus (Probable)		600788	2C9W	112
P83940 UniProt NPD GO	ELOC_MOUSE	Transcription elongation factor B polypeptide 1 (RNA polymerase II transcription factor SIII subunit ...	0.00	-	cyt	0	Nucleus (Probable)			2FNJ	112
P83941 UniProt NPD GO	ELOC_RAT	Transcription elongation factor B polypeptide 1 (RNA polymerase II transcription factor SIII subunit ...	0.00	-	cyt	0	Nucleus (Probable)				112
P36951 UniProt NPD GO	TRLC_DROME	Transient receptor potential locus C protein precursor (GIP-like protein)	0.00	-	cyt	0					264
Q42675 UniProt NPD GO	TKTA_CRAPL	Transketolase 10 (EC 2.2.1.1) (TK)	0.00	-	cyt	0					679
P51854 UniProt NPD GO	TKT2_HUMAN	Transketolase-like 1 (EC 2.2.1.1) (Transketolase 2) (TK 2) (Transketolase-related protein)	0.00	-	nuc	0			300044		557
Q5E984 UniProt NPD GO	TCTP_BOVIN	Translationally-controlled tumor protein (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				172
Q9DGK4 UniProt NPD GO	TCTP_BRARE	Translationally-controlled tumor protein (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				171
Q98SJ7 UniProt NPD GO	TCTP_LABRO	Translationally-controlled tumor protein (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				171
Q6XSH4 UniProt NPD GO	TCTP_LATJA	Translationally-controlled tumor protein (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				170
Q7ZYF2 UniProt NPD GO	TCTP_XENLA	Translationally-controlled tumor protein (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				172
Q66JC5 UniProt NPD GO	TCTP_XENTR	Translationally-controlled tumor protein (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				172
P63029 UniProt NPD GO	TCTP_RAT	Translationally-controlled tumor protein (TCTP) (Lens epithelial protein)	0.00	-	cyt	0	Cytoplasm (By similarity)				172
P63028 UniProt NPD GO	TCTP_MOUSE	Translationally-controlled tumor protein (TCTP) (p23) (21 kDa polypeptide) (p21)	0.00	-	cyt	0	Cytoplasm (By similarity)				172
P43347 UniProt NPD GO	TCTP_CHICK	Translationally-controlled tumor protein (TCTP) (p23) (pCHK23)	0.00	-	cyt	0	Cytoplasm (By similarity)				172
Q7QCK2 UniProt NPD GO	TCTP_ANOGA	Translationally-controlled tumor protein homolog (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				171
Q9VGS2 UniProt NPD GO	TCTP_DROME	Translationally-controlled tumor protein homolog (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			172
Q6XIN1 UniProt NPD GO	TCTP_DROYA	Translationally-controlled tumor protein homolog (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			172
Q94587 UniProt NPD GO	TCTP_HYDAT	Translationally-controlled tumor protein homolog (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				184
Q5MGM6 UniProt NPD GO	TCTP_LONON	Translationally-controlled tumor protein homolog (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				172
O18477 UniProt NPD GO	TCTP_LUMRU	Translationally-controlled tumor protein homolog (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				167
Q60FS1 UniProt NPD GO	TCTP_PLUXY	Translationally-controlled tumor protein homolog (TCTP)	0.00	-	cyt	0	Cytoplasm (By similarity)				172
P35758 UniProt NPD GO	TCTP_TRYBB	Translationally-controlled tumor protein homolog (TCTP) (22 kDa calcium-binding protein) (Fragment)	0.00	-	cyt	0	Cytoplasm				37
Q10344 UniProt NPD GO	TCTP_SCHPO	Translationally-controlled tumor protein homolog (TCTP) (p23fyp)	0.00	-	cyt	0	Cytoplasm (By similarity)			1H7Y	168
P30408 UniProt NPD GO	T4S1_HUMAN	Transmembrane 4 L6 family member 1 (Tumor-associated antigen L6) (Membrane component surface marker ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]	191155		202
Q5R6Z4 UniProt NPD GO	T4S4_PONPY	Transmembrane 4 L6 family member 4	0.00	-	end	4 *	Membrane; multi-pass membrane protein				202
Q9EQL5 UniProt NPD GO	T4S4_RAT	Transmembrane 4 L6 family member 4	0.00	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				202
P48230 UniProt NPD GO	T4S4_HUMAN	Transmembrane 4 L6 family member 4 (Intestine and liver tetraspan membrane protein) (IL-TMP)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	606567		202
Q9HC24 UniProt NPD GO	TMBI4_HUMAN	Transmembrane BAX inhibitor motif-containing protein 4 (Z-protein) (S1R protein)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				238
Q924P2 UniProt NPD GO	TM14C_RAT	Transmembrane protein 14C (p11)	0.00	-	cyt	4 *	Membrane; multi-pass membrane protein (Potential)				115
Q5R4C3 UniProt NPD GO	TM50B_PONPY	Transmembrane protein 50B	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				158
P56557 UniProt NPD GO	TM50B_HUMAN	Transmembrane protein 50B (HCV p7-transregulated protein 3)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			158
Q969K7 UniProt NPD GO	TMM54_HUMAN	Transmembrane protein 54 (Beta-casein-like protein) (Protein CAC-1)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				222
Q3MHQ7 UniProt NPD GO	TM86A_BOVIN	Transmembrane protein 86A	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				240
Q8N2M4 UniProt NPD GO	TM86A_HUMAN	Transmembrane protein 86A	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				240
Q9D8N3 UniProt NPD GO	TM86A_MOUSE	Transmembrane protein 86A	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				241
Q8N661 UniProt NPD GO	TM86B_HUMAN	Transmembrane protein 86B	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				226
Q497J1 UniProt NPD GO	TM86B_MOUSE	Transmembrane protein 86B	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				226
P07489 UniProt NPD GO	TTHY_RABIT	Transthyretin (Prealbumin)	0.00	-	cyt	0	Secreted protein				127
O55245 UniProt NPD GO	TTHY_CROPO	Transthyretin precursor (Prealbumin)	0.00	-	exc	1 *	Secreted protein				150
P42204 UniProt NPD GO	TTHY_MACEU	Transthyretin precursor (Prealbumin)	0.00	-	end	0	Secreted protein				149
Q29616 UniProt NPD GO	TTHY_MACGI	Transthyretin precursor (Prealbumin)	0.00	-	exc	0	Secreted protein				149
P49141 UniProt NPD GO	TTHY_MONDO	Transthyretin precursor (Prealbumin)	0.00	-	exc	0	Secreted protein				149
P07309 UniProt NPD GO	TTHY_MOUSE	Transthyretin precursor (Prealbumin)	0.00	-	exc	0	Secreted protein				147

You are viewing entries 98351 to 98400 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.