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
Q9ZSS6 UniProt NPD GO	THD1_ARATH	Threonine dehydratase biosynthetic, chloroplast precursor (EC 4.3.1.19) (Threonine deaminase) (TD)	0.10	-	mit	0	Plastid; chloroplast (By similarity)				592
Q9S7B5 UniProt NPD GO	THRC_ARATH	Threonine synthase, chloroplast precursor (EC 4.2.3.1) (TS)	0.10	-	mit	0	Plastid; chloroplast			2C2G	526
Q95125 UniProt NPD GO	TA2R_BOVIN	Thromboxane A2 receptor (TXA2-R) (Prostanoid TP receptor)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				343
O81263 UniProt NPD GO	KITH_ORYSA	Thymidine kinase (EC 2.7.1.21)	0.10	-	mit	0					271
P23919 UniProt NPD GO	DTYMK_HUMAN	Thymidylate kinase (EC 2.7.4.9) (dTMP kinase)	0.10	-	cyt	0			188345	1NN5	212
P97930 UniProt NPD GO	DTYMK_MOUSE	Thymidylate kinase (EC 2.7.4.9) (dTMP kinase)	0.10	-	cyt	0					227
O62584 UniProt NPD GO	TYS1_ENCCU	Thymidylate synthase 1/2 (EC 2.1.1.45) (TS 1/2) (TSase 1/2)	0.10	-	cyt	0					294
P37240 UniProt NPD GO	TSHB_ONCMY	Thyrotropin beta chain precursor (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B)	0.10	-	nuc	0	Secreted protein				147
O73824 UniProt NPD GO	TSHB_SALSA	Thyrotropin beta chain precursor (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B)	0.10	-	nuc	0	Secreted protein				139
Q9TT36 UniProt NPD GO	THBG_BOVIN	Thyroxine-binding globulin precursor (T4-binding globulin) (Serpin A7)	0.10	-	exc	0	Secreted protein				411
P50450 UniProt NPD GO	THBG_SHEEP	Thyroxine-binding globulin precursor (T4-binding globulin) (Serpin A7)	0.10	-	exc	0	Secreted protein				412
P84510 UniProt NPD GO	TX3_PARSR	Toxin PaurTx3	0.10	-	nuc	0	Secreted protein	extracellular space [IDA]			34
Q06408 UniProt NPD GO	ARO10_YEAST	Transaminated amino acid decarboxylase (EC 4.1.1.-) (Transaminated branched-chain amino acid decarbo ...	0.10	-	mit	1	Cytoplasm	cytoplasm [IDA]			635
Q628A6 UniProt NPD GO	SPT4H_CAEBR	Transcription elongation factor SPT4 (DRB sensitivity-inducing factor small subunit) (DSIF small sub ...	0.10	-	nuc	0	Nucleus (By similarity)				120
Q05027 UniProt NPD GO	TAF9_YEAST	Transcription initiation factor TFIID subunit 9 (TBP-associated factor 9) (TBP-associated factor 17 ...	0.10	-	mit	0	Nucleus	SAGA complex [IDA] SLIK (SAGA-like) complex [IPI] transcription factor TFIID complex [IDA]			157
P22297 UniProt NPD GO	TRF_MANSE	Transferrin precursor	0.10	-	exc	0	Secreted protein				681
Q9MYZ3 UniProt NPD GO	TFR1_FELCA	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen)	0.10	-	cyt	1	Membrane; single-pass type II membrane protein (By similarity)				769
Q5RDH6 UniProt NPD GO	TFR1_PONPY	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen)	0.10	-	mit	1	Cell membrane; single-pass type II membrane (By similarity)				760
P55906 UniProt NPD GO	BGH3_BOVIN	Transforming growth factor-beta-induced protein ig-h3 (Beta ig-h3) (MP78) (MP70) (Fragments)	0.10	-	mit	0	Secreted protein; extracellular space. May be associated both with microfibrils and with the cell su ...				87
Q12630 UniProt NPD GO	TKT1_KLULA	Transketolase (EC 2.2.1.1) (TK)	0.10	-	cyt	0					679
O59683 UniProt NPD GO	IF2M_SCHPO	Translation initiation factor IF-2, mitochondrial precursor (IF-2Mt) (IF-2(Mt))	0.10	-	mit	0	Mitochondrion				686
Q9TLX8 UniProt NPD GO	IF3C_CYACA	Translation initiation factor IF-3, chloroplast	0.10	-	cyt	0	Plastid; chloroplast				185
Q12513 UniProt NPD GO	TMA17_YEAST	Translation machinery-associated protein 17	0.10	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			150
P23438 UniProt NPD GO	SSRB_CANFA	Translocon-associated protein subunit beta precursor (TRAP-beta) (Signal sequence receptor subunit b ...	0.10	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				183
Q9UNL2 UniProt NPD GO	SSRG_HUMAN	Translocon-associated protein subunit gamma (TRAP-gamma) (Signal sequence receptor subunit gamma) (S ...	0.10	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	microsome [TAS]	606213		185
Q9DCF9 UniProt NPD GO	SSRG_MOUSE	Translocon-associated protein subunit gamma (TRAP-gamma) (Signal sequence receptor subunit gamma) (S ...	0.10	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				185
Q5RCD7 UniProt NPD GO	SSRG_PONPY	Translocon-associated protein subunit gamma (TRAP-gamma) (Signal sequence receptor subunit gamma) (S ...	0.10	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				185
Q08013 UniProt NPD GO	SSRG_RAT	Translocon-associated protein subunit gamma (TRAP-gamma) (Signal sequence receptor subunit gamma) (S ...	0.10	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	translocon complex [NAS]			185
Q66HF2 UniProt NPD GO	TM9S1_RAT	Transmembrane 9 superfamily protein member 1 precursor	0.10	-	end	8	Membrane; multi-pass membrane protein (Probable)				589
Q4FZV7 UniProt NPD GO	TMUB2_RAT	Transmembrane and ubiquitin-like domain-containing protein 2	0.10	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				319
Q9CQG9 UniProt NPD GO	TM100_MOUSE	Transmembrane protein 100	0.10	-	end	2	Membrane; multi-pass membrane protein (Potential)				134
Q9WUH1 UniProt NPD GO	TM115_MOUSE	Transmembrane protein 115 (Protein PL6 homolog)	0.10	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				350
Q5ZJZ4 UniProt NPD GO	TMM22_CHICK	Transmembrane protein 22	0.10	-	end	10	Membrane; multi-pass membrane protein (Potential)				411
Q6ZUK4 UniProt NPD GO	TMM26_HUMAN	Transmembrane protein 26	0.10	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				368
Q22288 UniProt NPD GO	YNS5_CAEEL	Transthyretin-like protein T07C4.5 precursor	0.10	-	end	0	Secreted protein (Potential)				130
Q08423 UniProt NPD GO	TFF1_MOUSE	Trefoil factor 1 precursor (pS2 protein)	0.10	-	exc	1 *	Secreted protein	cytoplasm [TAS]			87
P01359 UniProt NPD GO	TFF2_PIG	Trefoil factor 2 precursor (Spasmolytic polypeptide) (SP) (Pancreatic spasmolytic polypeptide) (PSP) ...	0.10	-	nuc	0	Secreted protein			2PSP	127
P32358 UniProt NPD GO	TREA_BOMMO	Trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.10	-	end	0	Cell membrane; basolateral cell membrane				579
P83595 UniProt NPD GO	ITRY_BAUVA	Trypsin inhibitor BvTI	0.10	-	cyt	0	Secreted protein				174
P12788 UniProt NPD GO	TRY4_RAT	Trypsin-4 precursor (EC 3.4.21.4) (Trypsin IV) (Pretrypsinogen IV)	0.10	-	exc	0	Secreted protein; extracellular space				247
P31204 UniProt NPD GO	TRPA_ANTSP	Tryptophan synthase alpha chain (EC 4.2.1.20)	0.10	-	cyt	0	Plastid; chloroplast				263
P52273 UniProt NPD GO	TBA_BOMMO	Tubulin alpha chain	0.10	-	cyt	0					450
P32255 UniProt NPD GO	TBA_DICDI	Tubulin alpha chain	0.10	-	cyt	0					457
P12543 UniProt NPD GO	TBA_PLAYO	Tubulin alpha chain	0.10	-	cyt	0					453
Q27352 UniProt NPD GO	TBA_TRYCR	Tubulin alpha chain	0.10	-	cyt	0					451
P04105 UniProt NPD GO	TBAN_PHYPO	Tubulin alpha-1B chain (Tubulin alpha-N chain)	0.10	-	cyt	0	Spindle. Mitosis in the slime mold Plasmodium differs from the process in many eukaryotes. The tubul ...				449
P09642 UniProt NPD GO	TBA3_CHICK	Tubulin alpha-3 chain (Fragment)	0.10	-	cyt	0					322
P53373 UniProt NPD GO	TBB_BOTCI	Tubulin beta chain (Beta tubulin)	0.10	-	cyt	0					447
P10875 UniProt NPD GO	TBB_CANAL	Tubulin beta chain (Beta tubulin)	0.10	-	cyt	0					449
O04386 UniProt NPD GO	TBB_CHLIN	Tubulin beta chain (Beta tubulin)	0.10	-	cyt	0					443

You are viewing entries 65351 to 65400 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.