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
Q9PSN5 UniProt NPD GO	PA2E_NOTSC	Toxic phospholipase A2 HTe (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.18	-	nuc	0	Secreted protein				125
P03871 UniProt NPD GO	REP1_YEAST	Trans-acting factor B (REP1) (Protein Baker)	0.18	-	cyt	0					373
Q13890 UniProt NPD GO	BT3L1_HUMAN	Transcription factor BTF3 homolog 1 (Basic transcription factor 3-like 1)	0.18	-	nuc	0	Nucleus (Potential)		602543		111
P52657 UniProt NPD GO	T2AG_HUMAN	Transcription initiation factor IIA gamma chain (TFIIA P12 subunit) (TFIIA-12) (TFIIAS) (TFIIA-gamma ...	0.18	-	mit	0	Nucleus	transcription factor TFIIA complex [NAS]	600519	1NVP	109
O08950 UniProt NPD GO	T2AG_RAT	Transcription initiation factor IIA gamma chain (TFIIA P12 subunit) (TFIIA-12) (TFIIAS) (TFIIA-gamma ...	0.18	-	mit	0	Nucleus				109
Q27272 UniProt NPD GO	TAF9_DROME	Transcription initiation factor TFIID subunit 9 (Transcription initiation factor TFIID 42 kDa subuni ...	0.18	-	cyt	0	Nucleus	SAGA complex [IPI]		1TAF	278
Q9GLD3 UniProt NPD GO	TFR1_CANFA	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen)	0.18	-	cyt	1	Membrane; single-pass type II membrane protein (By similarity)				770
Q07891 UniProt NPD GO	TFR1_CRIGR	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen)	0.18	-	cyt	1	Membrane; single-pass type II membrane protein (By similarity)				757
Q8R4D5 UniProt NPD GO	TRPM8_MOUSE	Transient receptor potential cation channel subfamily M member 8	0.18	-	end	7	Membrane; multi-pass membrane protein (Probable)	membrane [IDA]			1104
Q6B855 UniProt NPD GO	TKT_BOVIN	Transketolase (EC 2.2.1.1) (TK)	0.18	-	cyt	0					623
Q5R4C1 UniProt NPD GO	TKT_PONPY	Transketolase (EC 2.2.1.1) (TK)	0.18	-	cyt	0					623
Q62348 UniProt NPD GO	TSN_MOUSE	Translin	0.18	-	cyt	0	Nucleus	cytoplasm [IDA] nucleus [IDA]		1KEY	228
Q9GKZ4 UniProt NPD GO	TRAM1_BOVIN	Translocation-associated membrane protein 1	0.18	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				373
Q5R7Z3 UniProt NPD GO	TRAM1_PONPY	Translocation-associated membrane protein 1	0.18	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				373
Q9CXE7 UniProt NPD GO	TMED5_MOUSE	Transmembrane emp24 domain-containing protein 5 precursor	0.18	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				229
Q3T133 UniProt NPD GO	TMED9_BOVIN	Transmembrane emp24 domain-containing protein 9 precursor	0.18	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				235
Q91VP7 UniProt NPD GO	TM101_MOUSE	Transmembrane protein 101	0.18	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				257
Q96IK0 UniProt NPD GO	TM101_HUMAN	Transmembrane protein 101 (Putative NF-kappa-B-activating protein 130)	0.18	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				257
Q3UBX0 UniProt NPD GO	TM109_MOUSE	Transmembrane protein 109 precursor (Mitsugumin-23) (Mg23)	0.18	+	end	5 *	Nucleus; nuclear outer membrane; multi-pass membrane protein (By similarity). Endoplasmic reticulum; ...				243
Q4V888 UniProt NPD GO	TM55A_RAT	Transmembrane protein 55A (EC 3.1.3.-) (Type II phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.18	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				257
Q9UT70 UniProt NPD GO	BET5_SCHPO	Transport protein particle subunit bet5	0.18	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				155
P32359 UniProt NPD GO	TREA_TENMO	Trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.18	-	exc	0	It is incorporated into the wall of the spermatophore				555
Q9NVH6 UniProt NPD GO	TMLH_HUMAN	Trimethyllysine dioxygenase, mitochondrial precursor (EC 1.14.11.8) (Epsilon-trimethyllysine 2-oxogl ...	0.18	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				421
Q86UV7 UniProt NPD GO	TRI73_HUMAN	Tripartite motif-containing protein 73 (Tripartite motif-containing protein 50B)	0.18	-	cyt	0					250
Q64514 UniProt NPD GO	TPP2_MOUSE	Tripeptidyl-peptidase 2 (EC 3.4.14.10) (Tripeptidyl-peptidase II) (TPP-II) (Tripeptidyl aminopeptida ...	0.18	-	cyt	0	Cytoplasm				1261
P10294 UniProt NPD GO	ITR1_MOMCH	Trypsin inhibitor 1 (Trypsin inhibitor I) (MCTI-I)	0.18	-	nuc	0	Secreted protein			1EWU	30
P43284 UniProt NPD GO	TRPB2_MAIZE	Tryptophan synthase beta chain 2, chloroplast precursor (EC 4.2.1.20) (Orange pericarp 2) (Fragment) ...	0.18	-	nuc	0	Plastid; chloroplast (Probable)				443
Q9CYK1 UniProt NPD GO	SYWM_MOUSE	Tryptophanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS) ...	0.18	-	cyt	0	Mitochondrion; mitochondrial matrix				360
P92120 UniProt NPD GO	TBA_ENCHE	Tubulin alpha chain (Fragment)	0.18	-	cyt	0					380
Q962P8 UniProt NPD GO	TBA6_NAEGR	Tubulin alpha-6 chain	0.18	-	nuc	0	Spindle. Present in the nuclei and mitotic spindle-fibers but absent in flagellar axonemes or cytosk ...				452
P22012 UniProt NPD GO	TBB_ASPFL	Tubulin beta chain (Beta tubulin)	0.18	-	cyt	0					448
Q00264 UniProt NPD GO	TBB_ASPPA	Tubulin beta chain (Beta tubulin)	0.18	-	cyt	0					448
P11857 UniProt NPD GO	TBB_STYLE	Tubulin beta chain (Beta tubulin)	0.18	-	cyt	0					442
Q9SEV2 UniProt NPD GO	TBBN_GUITH	Tubulin beta chain, nucleomorph (Nucleomorph beta tubulin)	0.18	-	cyt	0					441
P32928 UniProt NPD GO	TBB1_COLGL	Tubulin beta-1 chain (Beta-1 tubulin)	0.18	-	cyt	0					448
Q43594 UniProt NPD GO	TBB1_ORYSA	Tubulin beta-1 chain (Beta-1 tubulin)	0.18	-	cyt	0					447
P29500 UniProt NPD GO	TBB1_PEA	Tubulin beta-1 chain (Beta-1 tubulin)	0.18	-	cyt	0					450
P83130 UniProt NPD GO	TBB2_DROER	Tubulin beta-2 chain (Beta-2 tubulin)	0.18	-	cyt	0					446
Q9ZPN9 UniProt NPD GO	TBB2_ELEIN	Tubulin beta-2 chain (Beta-2 tubulin)	0.18	-	cyt	0					448
P32882 UniProt NPD GO	TBB2_CHICK	Tubulin beta-2 chain (Beta-tubulin class-II)	0.18	-	cyt	0					445
Q9NFZ5 UniProt NPD GO	TBB3_ECHMU	Tubulin beta-3 chain (Beta-tubulin 3)	0.18	-	cyt	0					443
Q9BUF5 UniProt NPD GO	TBB6_HUMAN	Tubulin beta-6 chain	0.18	-	cyt	0					446
P30157 UniProt NPD GO	TBB6_ECTVR	Tubulin beta-6 chain (Beta-6 tubulin)	0.18	-	cyt	0					447
Q41783 UniProt NPD GO	TBB6_MAIZE	Tubulin beta-6 chain (Beta-6 tubulin)	0.18	-	cyt	0					446
Q76FS3 UniProt NPD GO	TBB6_ORYSA	Tubulin beta-6 chain (Beta-6 tubulin)	0.18	-	cyt	0					444
Q6VAF5 UniProt NPD GO	TBB7_GOSHI	Tubulin beta-7 chain (Beta-7 tubulin)	0.18	-	cyt	0					444
P29516 UniProt NPD GO	TBB8_ARATH	Tubulin beta-8 chain (Beta-8 tubulin)	0.18	-	cyt	0					449
Q76FS2 UniProt NPD GO	TBB8_ORYSA	Tubulin beta-8 chain (Beta-8 tubulin)	0.18	-	cyt	0					446
P54402 UniProt NPD GO	TBG_EUPAE	Tubulin gamma chain (Gamma tubulin)	0.18	-	cyt	0					461
P83626 UniProt NPD GO	TNR26_MOUSE	Tumor necrosis factor receptor superfamily member 26 precursor (TNF receptor homolog 3)	0.18	-	end	1	Membrane; single-pass type I membrane protein (Potential)				204

You are viewing entries 53751 to 53800 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.