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
Q646D1 UniProt NPD GO	T2R16_PANPA	Taste receptor type 2 member 16 (T2R16)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				291
Q646B3 UniProt NPD GO	T2R16_PANTR	Taste receptor type 2 member 16 (T2R16)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				291
Q646E7 UniProt NPD GO	T2R16_PAPHA	Taste receptor type 2 member 16 (T2R16)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				291
Q645U1 UniProt NPD GO	T2R16_PONPY	Taste receptor type 2 member 16 (T2R16)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				291
Q646C7 UniProt NPD GO	T2R41_PANPA	Taste receptor type 2 member 41 (T2R41)	0.11	-	end	6 *	Membrane; multi-pass membrane protein				307
P59551 UniProt NPD GO	T2R60_HUMAN	Taste receptor type 2 member 60 (T2R60) (T2R56)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				318
Q6PN86 UniProt NPD GO	CX51A_CONMR	Tau conotoxin mr5.1a precursor	0.11	-	exc	0	Secreted protein (By similarity)				64
Q9FT37 UniProt NPD GO	TASY_TAXCH	Taxadiene synthase (EC 4.2.3.17) (Taxa-4(5),11(12)-diene synthase)	0.11	-	cyt	0					862
P61915 UniProt NPD GO	ACTPC_ACTTE	Tenebrosin-C	0.11	-	cyt	0	Secreted protein. Found in nematocyst				179
Q9EP64 UniProt NPD GO	TNMD_MOUSE	Tenomodulin (TeM) (mTeM) (Chondromodulin-I-like protein) (ChM1L) (mChM1L) (Myodulin) (Tendin)	0.11	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				317
P13858 UniProt NPD GO	THEM_MALSU	Thermomycolin (EC 3.4.21.65) (Thermomycolase) (Fragments)	0.11	-	nuc	0	Secreted protein				34
P30636 UniProt NPD GO	TPK1_CAEEL	Thiamin pyrophosphokinase 1 (EC 2.7.6.2) (Thiamine pyrophosphokinase 1) (TPK1)	0.11	-	cyt	0					243
Q01682 UniProt NPD GO	PPA2_SCHPO	Thiamine-repressible acid phosphatase precursor (EC 3.1.3.2)	0.11	-	vac	0	Cell wall				463
Q9BGW0 UniProt NPD GO	THTPA_MACFA	Thiamine-triphosphatase (EC 3.6.1.28) (ThTPase)	0.11	-	cyt	0	Cytoplasm (By similarity)	soluble fraction [ISS]			229
Q42596 UniProt NPD GO	THN21_ARATH	Thionin-2.1 precursor [Contains: Thionin-2.1; Acidic protein]	0.11	-	exc	0	Secreted protein (Potential)				134
Q9H1E5 UniProt NPD GO	TXD13_HUMAN	Thioredoxin domain-containing protein 13 precursor	0.11	-	end	1	Membrane; single-pass type I membrane protein (Potential)				349
Q5VZ03 UniProt NPD GO	CI121_HUMAN	Thioredoxin domain-containing protein C9orf121	0.11	-	cyt	0					156
P81778 UniProt NPD GO	TL17_SPIOL	Thylakoid lumenal 17.4 kDa protein (P17.4) (Fragment)	0.11	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				23
P33248 UniProt NPD GO	TYB12_LATJA	Thymosin beta-12	0.11	-	nuc	0	Cytoplasm				43
Q9UKU6 UniProt NPD GO	TRHDE_HUMAN	Thyrotropin-releasing hormone-degrading ectoenzyme (EC 3.4.19.6) (TRH-degrading ectoenzyme) (TRH-DE) ...	0.11	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	606950		1024
P84681 UniProt NPD GO	SC37_TITCA	Toxin Tc37 (Fragment)	0.11	-		0	Secreted protein	extracellular region [IDA]			10
P13779 UniProt NPD GO	REP2_KLULA	Trans-acting factor C (REP2)	0.11	-	cyt	0					212
P20061 UniProt NPD GO	TCO1_HUMAN	Transcobalamin-1 precursor (Transcobalamin I) (TCI) (TC I)	0.11	-	mit	0	Secreted protein		189905		433
Q5AK73 UniProt NPD GO	SPT4_CANAL	Transcription elongation factor SPT4 (Chromatin elongation factor SPT4)	0.11	-	nuc	0	Nucleus. Centromere and heterochromatin (By similarity)				112
Q8K0H5 UniProt NPD GO	TAF10_MOUSE	Transcription initiation factor TFIID subunit 10 (Transcription initiation factor TFIID 30 kDa subun ...	0.11	-	nuc	0	Nucleus (By similarity)	transcription factor TFIID complex [TAS]			218
Q9FKH1 UniProt NPD GO	SAP_ARATH	Transcriptional regulator STERILE APETALA	0.11	-	cyt	0	Nucleus (Probable)				446
P02786 UniProt NPD GO	TFR1_HUMAN	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen) (T9) (p90)	0.11	-	mit	1	Cell membrane; single-pass type II membrane protein. Processed sTfR form: Secreted protein	cytoplasmic membrane-bound vesicle [IDA] endosome [IDA] extracellular region [IDA] integral to plasma membrane [TAS] membrane [NAS]	190010	1SUV	760
P21214 UniProt NPD GO	TGFB2_BOVIN	Transforming growth factor beta-2 (TGF-beta-2) (Milk growth factor) (MGF)	0.11	-	nuc	0	Secreted protein				112
Q9TS87 UniProt NPD GO	TAGL_BOVIN	Transgelin (Smooth muscle protein 22-alpha) (SM22-alpha) (25 kDa F-actin-binding protein)	0.11	-	nuc	0	Cytoplasm (Probable)				200
Q01995 UniProt NPD GO	TAGL_HUMAN	Transgelin (Smooth muscle protein 22-alpha) (SM22-alpha) (WS3-10) (22 kDa actin-binding protein)	0.11	-	nuc	0	Cytoplasm (Probable)		600818		200
P40142 UniProt NPD GO	TKT_MOUSE	Transketolase (EC 2.2.1.1) (TK) (P68)	0.11	-	cyt	0					623
Q85C77 UniProt NPD GO	IF1C_ANTFO	Translation initiation factor IF-1, chloroplast	0.11	-	nuc	0	Plastid; chloroplast				78
Q85WZ7 UniProt NPD GO	IF1C_PINKO	Translation initiation factor IF-1, chloroplast	0.11	-	nuc	0	Plastid; chloroplast				75
O98459 UniProt NPD GO	IF1C_SPIMX	Translation initiation factor IF-1, chloroplast	0.11	-	nuc	0	Plastid; chloroplast				84
O15321 UniProt NPD GO	TM9S1_HUMAN	Transmembrane 9 superfamily protein member 1 precursor (hMP70)	0.11	-	end	9	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]			606
Q9Y3A6 UniProt NPD GO	TMED5_HUMAN	Transmembrane emp24 domain-containing protein 5 precursor	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	ER-Golgi intermediate compartment [IDA]			229
Q5R809 UniProt NPD GO	TMED5_PONPY	Transmembrane emp24 domain-containing protein 5 precursor	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				229
Q9Y3B3 UniProt NPD GO	TMED7_HUMAN	Transmembrane emp24 domain-containing protein 7 precursor	0.11	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				224
O15393 UniProt NPD GO	TMPS2_HUMAN	Transmembrane protease, serine 2 precursor (EC 3.4.21.-) [Contains: Transmembrane protease, serine 2 ...	0.11	-	nuc	1	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Activated by ...	integral to plasma membrane [TAS]	602060		492
Q9NRS4 UniProt NPD GO	TMPS4_HUMAN	Transmembrane protease, serine 4 (EC 3.4.21.-) (Membrane-type serine protease 2) (MT-SP2)	0.11	-	cyt	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to membrane [NAS]	606565		437
Q9ER04 UniProt NPD GO	TMPS5_MOUSE	Transmembrane protease, serine 5 (EC 3.4.21.-) (Spinesin)	0.11	-	cyt	1 *	Membrane; single-pass type II membrane protein (Potential)				455
Q2KIC8 UniProt NPD GO	TM100_BOVIN	Transmembrane protein 100	0.11	-	end	2	Membrane; multi-pass membrane protein (Potential)				134
Q9NV29 UniProt NPD GO	TM100_HUMAN	Transmembrane protein 100	0.11	-	end	2	Membrane; multi-pass membrane protein (Potential)				134
Q5EA90 UniProt NPD GO	T106A_BOVIN	Transmembrane protein 106A	0.11	-	mit	1	Membrane; single-pass membrane protein (Potential)				261
Q86TL2 UniProt NPD GO	TM110_HUMAN	Transmembrane protein 110	0.11	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				294
Q12893 UniProt NPD GO	TM115_HUMAN	Transmembrane protein 115 (Protein PL6) (Placental protein 6) (PP6)	0.11	-	end	6 *	Membrane; multi-pass membrane protein (Probable)		607069		351
Q9NWC5 UniProt NPD GO	TM45A_HUMAN	Transmembrane protein 45a (Dermal papilla-derived protein 7) (DNA polymerase-transactivated protein ...	0.11	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				275
Q9ESN3 UniProt NPD GO	TMEM8_MOUSE	Transmembrane protein 8 precursor (M83 protein)	0.11	-	end	3	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [NAS]			769
Q6QUN5 UniProt NPD GO	TREM1_BOVIN	Triggering receptor expressed on myeloid cells 1 precursor (TREM-1)	0.11	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				232
Q9JKE2 UniProt NPD GO	TREM1_MOUSE	Triggering receptor expressed on myeloid cells 1 precursor (TREM-1)	0.11	-	end	1	Membrane; single-pass type I membrane protein (By similarity)			1U9K	230

You are viewing entries 63601 to 63650 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.