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
Q9EQT6 UniProt NPD GO	SYT13_MOUSE	Synaptotagmin-13 (Synaptotagmin XIII) (SytXIII)	0.49	-	nuc	1 *	Membrane; single-pass membrane protein	integral to plasma membrane [IDA]			426
Q9H2B2 UniProt NPD GO	SYT4_HUMAN	Synaptotagmin-4 (Synaptotagmin IV) (SytIV)	0.49	+	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein	integral to membrane [ISS]	600103	1UGK	425
P50232 UniProt NPD GO	SYT4_RAT	Synaptotagmin-4 (Synaptotagmin IV) (SytIV)	0.49	+	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein	integral to membrane [ISS] synaptic vesicle [NAS]		1W16	425
Q8BVI5 UniProt NPD GO	STX16_MOUSE	Syntaxin-16	0.49	-	gol	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				326
Q9UNK0 UniProt NPD GO	STX8_HUMAN	Syntaxin-8	0.49	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity). Preferentially associated with the e ...	endoplasmic reticulum [TAS] integral to plasma membrane [TAS]	604203		236
Q13148 UniProt NPD GO	TADBP_HUMAN	TAR DNA-binding protein 43 (TDP-43)	0.49	-	nuc	0	Nucleus	nucleus [TAS]	605078	2CQG	414
Q8TAP9 UniProt NPD GO	TTDN1_HUMAN	TTD non-photosensitive 1 protein	0.49	-	nuc	0	Nucleus		609188		179
Q9D011 UniProt NPD GO	TTDN1_MOUSE	TTD non-photosensitive 1 protein homolog	0.49	-	nuc	0	Nucleus (By similarity)				178
Q9DAJ2 UniProt NPD GO	TEKT1_MOUSE	Tektin-1	0.49	-	nuc	0		microtubule [IDA]			418
Q9H0U9 UniProt NPD GO	TSYL1_HUMAN	Testis-specific Y-encoded-like protein 1 (TSPY-like 1)	0.49	-	cyt	0	Nucleus; nucleolus		608800		438
P16893 UniProt NPD GO	TRAP_PLAFA	Thrombospondin-related anonymous protein precursor	0.49	-	exc	0					559
P58605 UniProt NPD GO	TX325_SEGFL	Toxin SNX-325	0.49	-	nuc	0	Secreted protein				49
P13777 UniProt NPD GO	REP1_ZYGBI	Trans-acting factor B (REP1)	0.49	-	nuc	0					322
Q28772 UniProt NPD GO	HTF4_PAPHA	Transcription factor 12 (Transcription factor HTF-4) (E-box-binding protein) (DNA-binding protein HT ...	0.49	-	nuc	0	Nucleus				160
Q14186 UniProt NPD GO	TDP1_HUMAN	Transcription factor Dp-1 (E2F dimerization partner 1) (DRTF1-polypeptide 1) (DRTF1)	0.49	-	nuc	0	Nucleus		189902	2AZE	410
P70120 UniProt NPD GO	HES5_MOUSE	Transcription factor HES-5 (Hairy and enhancer of split 5)	0.49	-	nuc	0	Nucleus				167
Q9SZP1 UniProt NPD GO	MYB4_ARATH	Transcription repressor MYB4 (Myb-related protein 4) (AtMYB4)	0.49	-	nuc	0	Nucleus (Probable)				282
Q9BWW7 UniProt NPD GO	SCRT1_HUMAN	Transcriptional repressor scratch 1 (Scratch homolog 1 zinc finger protein) (Scratch 1) (SCRT) (hScr ...	0.49	-	nuc	0	Nucleus	nucleus [NAS]	605858		348
P50414 UniProt NPD GO	TGFB1_SHEEP	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.49	-	exc	0	Secreted protein				390
Q9WUD2 UniProt NPD GO	TRPV2_RAT	Transient receptor potential cation channel subfamily V member 2 (TrpV2) (osm-9-like TRP channel 2) ...	0.49	-	end	6	Cell membrane; multi-pass membrane protein (By similarity). Cytoplasm (By similarity). Translocates ...			2ETC	761
Q9XSM3 UniProt NPD GO	TRPV5_RABIT	Transient receptor potential cation channel subfamily V member 5 (TrpV5) (osm-9-like TRP channel 3) ...	0.49	-	end	5	Cell membrane; apical cell membrane; multi-pass membrane protein. Colocalized with S100A10 and ANAX2 ...	integral to plasma membrane [ISS]			730
O95140 UniProt NPD GO	MFN2_HUMAN	Transmembrane GTPase MFN2 (EC 3.6.5.-) (Mitofusin-2)	0.49	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein. Colocalizes with BAX durin ...	cytosol [ISS] intrinsic to mitochondrial outer membrane [ISS] mitochondrion [IDA]	609260		757
Q7M750 UniProt NPD GO	TMM10_MOUSE	Transmembrane protein TMP10	0.49	-	exc	1 *	Membrane; single-pass membrane protein (By similarity)				143
Q04202 UniProt NPD GO	TCB2_CAEBR	Transposable element Tcb2 transposase	0.49	-	mit	0	Nucleus				273
Q99PQ2 UniProt NPD GO	TRI11_MOUSE	Tripartite motif-containing protein 11 (EC 6.3.2.-)	0.49	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			467
O00635 UniProt NPD GO	TRI38_HUMAN	Tripartite motif-containing protein 38 (RING finger protein 15) (Zinc finger protein RoRet)	0.49	-	nuc	0					465
Q9NS80 UniProt NPD GO	TRI49_HUMAN	Tripartite motif-containing protein 49 (RING finger protein 18) (Testis-specific ring-finger protein ...	0.49	-	cyt	0			606124		452
Q9JHJ0 UniProt NPD GO	TMOD3_MOUSE	Tropomodulin-3 (Ubiquitous tropomodulin) (U-Tmod)	0.49	-	nuc	0					352
P09491 UniProt NPD GO	TPM2_DROME	Tropomyosin-2 (Tropomyosin I)	0.49	-	nuc	0					284
P27628 UniProt NPD GO	TUFT1_BOVIN	Tuftelin (Enamelin)	0.49	-	nuc	0	Secreted protein. Secreted at a very early stage of enamel formation, and tightly bound to the surfa ...	extracellular region [ISS]			390
P04177 UniProt NPD GO	TY3H_RAT	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH)	0.49	-	cyt	0				2TOH	498
Q7Y175 UniProt NPD GO	UBAX1_ARATH	UBA and UBX domain-containing protein At4g15410	0.49	-	nuc	0					421
Q9UT81 UniProt NPD GO	UBX3_SCHPO	UBX domain-containing protein 3	0.49	-	nuc	0					410
P54730 UniProt NPD GO	UBX4_YEAST	UBX domain-containing protein 4	0.49	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			416
Q12094 UniProt NPD GO	YO006_YEAST	UPF0293 protein YOR006C	0.49	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			313
Q9NQC8 UniProt NPD GO	U360_HUMAN	UPF0360 protein (Protein C11orf2)	0.49	-	nuc	0		nucleus [NAS]			304
O13525 UniProt NPD GO	COQ4_YEAST	Ubiquinone biosynthesis protein COQ4, mitochondrial precursor	0.49	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	mitochondrial inner membrane [IEP]			335
Q2NL34 UniProt NPD GO	COQ9_BOVIN	Ubiquinone biosynthesis protein COQ9, mitochondrial precursor	0.49	-	mit	0	Mitochondrion (By similarity)				319
Q86YT6 UniProt NPD GO	MIB1_HUMAN	Ubiquitin ligase protein MIB1 (EC 6.3.2.-) (Mind bomb homolog 1) (DAPK-interacting protein 1) (DIP-1 ...	0.49	-	cyt	0	Cytoplasm. Cell membrane (By similarity). Localizes to the plasma membrane (By similarity). Accordin ...		608677		1006
Q804S5 UniProt NPD GO	MIB1_BRARE	Ubiquitin ligase protein mib (EC 6.3.2.-) (Protein mind bomb)	0.49	-	cyt	0	Cytoplasm. Cell membrane. Localizes to the plasma membrane	cytoplasm [IGI] endocytic vesicle [IDA] ubiquitin ligase complex [IC]			1030
P22314 UniProt NPD GO	UBE1_HUMAN	Ubiquitin-activating enzyme E1 (A1S9 protein)	0.49	-	nuc	0			314370		1058
Q32M92 UniProt NPD GO	CO032_HUMAN	Uncharacterized protein C15orf32	0.49	-	nuc	0					178
Q6PI98 UniProt NPD GO	CR037_HUMAN	Uncharacterized protein C18orf37	0.49	-	nuc	0					192
Q8BHA0 UniProt NPD GO	CR037_MOUSE	Uncharacterized protein C18orf37 homolog	0.49	+	nuc	0					191
Q9H579 UniProt NPD GO	CT132_HUMAN	Uncharacterized protein C20orf132	0.49	-	nuc	0					483
Q8R184 UniProt NPD GO	CT055_MOUSE	Uncharacterized protein C20orf55 homolog	0.49	-	nuc	0					296
Q96K31 UniProt NPD GO	CH076_HUMAN	Uncharacterized protein C8orf76	0.49	-	nuc	0					380
P38180 UniProt NPD GO	YBI1_YEAST	Uncharacterized protein YBL081W	0.49	-	nuc	0					368
P53158 UniProt NPD GO	YGH9_YEAST	Uncharacterized protein YGL079W	0.49	-	nuc	0		endosome [IDA]			218
Q05867 UniProt NPD GO	YL283_YEAST	Uncharacterized protein YLR283W, mitochondrial precursor	0.49	-	nuc	0	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)	mitochondrion [IDA]			314

You are viewing entries 25951 to 26000 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.