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
Q9P7Y9 UniProt NPD GO	SIN1_SCHPO	Stress-activated map kinase-interacting protein 1 (SAPK-interacting protein 1)	0.69	-	nuc	0					665
O35814 UniProt NPD GO	STIP1_RAT	Stress-induced-phosphoprotein 1 (STI1) (Hsc70/Hsp90-organizing protein) (Hop)	0.69	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				543
Q9ER00 UniProt NPD GO	STX12_MOUSE	Syntaxin-12	0.69	-	nuc	1	Intracytoplasmic membrane; single-pass type IV membrane protein; cytoplasmic side (Potential)				274
Q8K1E0 UniProt NPD GO	STX5_MOUSE	Syntaxin-5	0.69	-	nuc	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...	Golgi membrane [TAS]			301
Q5DQR4 UniProt NPD GO	STB5L_MOUSE	Syntaxin-binding protein 5-like (Tomosyn-2) (Lethal(2) giant larvae protein homolog 4)	0.69	-	nuc	0	Cytoplasm (Potential). Cell membrane; peripheral membrane protein (Potential). Membrane; peripheral ...				1185
O02073 UniProt NPD GO	TBX18_CAEEL	T-box transcription factor 18 (Signal element on autosome protein 1)	0.69	-	nuc	0	Nucleus				376
O15119 UniProt NPD GO	TBX3_HUMAN	T-box transcription factor TBX3 (T-box protein 3)	0.69	-	exc	0	Nucleus (Potential)		181450	1H6F	743
P70325 UniProt NPD GO	TBX4_MOUSE	T-box transcription factor TBX4 (T-box protein 4)	0.69	-	nuc	0	Nucleus (Potential)				552
Q99J36 UniProt NPD GO	THUM1_MOUSE	THUMP domain-containing protein 1	0.69	-	nuc	0					350
O00463 UniProt NPD GO	TRAF5_HUMAN	TNF receptor-associated factor 5 (RING finger protein 84)	0.69	-	nuc	0	Cytoplasm (Probable)		602356		557
Q9BXF9 UniProt NPD GO	TEKT3_HUMAN	Tektin-3	0.69	-	nuc	0					490
Q6X6Z7 UniProt NPD GO	TEKT3_MOUSE	Tektin-3	0.69	-	nuc	0					490
Q91VL8 UniProt NPD GO	TE2IP_MOUSE	Telomeric repeat-binding factor 2-interacting protein 1 (TRF2-interacting telomeric protein Rap1)	0.69	-	nuc	0	Nucleus (By similarity). Colocalizes with telomeric DNA in interphase and metaphase cells (By simila ...				393
Q9H147 UniProt NPD GO	TDIF1_HUMAN	Terminal deoxynucleotidyltransferase-interacting factor 1 (TdT-interacting factor 1) (TdIF1)	0.69	+	nuc	0	Nucleus				329
Q95LZ5 UniProt NPD GO	TTC16_MACFA	Tetratricopeptide repeat protein 16 (TPR repeat protein 16)	0.69	-	nuc	0					872
O08710 UniProt NPD GO	THYG_MOUSE	Thyroglobulin precursor	0.69	-	end	0	Secreted protein				2766
Q02445 UniProt NPD GO	TFPI1_RAT	Tissue factor pathway inhibitor precursor (TFPI) (Lipoprotein-associated coagulation inhibitor) (LAC ...	0.69	+	exc	0	Secreted protein				302
Q9I7U4 UniProt NPD GO	TITIN_DROME	Titin (D-Titin) (Kettin)	0.69	+	nuc	0	Cytoplasm. Nucleus. Uniformly distributed along condensed mitotic chromosomes				18074
P23772 UniProt NPD GO	GATA3_MOUSE	Trans-acting T-cell-specific transcription factor GATA-3 (GATA-binding factor 3)	0.69	-	nuc	0	Nucleus	nucleus [IDA]			443
P20232 UniProt NPD GO	TFS2_DROME	Transcription elongation factor S-II (RNA polymerase II elongation factor DMS-II) (TFIIS)	0.69	-	nuc	0	Nucleus				313
Q9TSV4 UniProt NPD GO	TCF19_PIG	Transcription factor 19 (Transcription factor SC1)	0.69	+	nuc	0	Nucleus (Potential)				346
Q9NZI6 UniProt NPD GO	TF2L1_HUMAN	Transcription factor CP2-like protein 1 (CP2-related transcriptional repressor 1) (CRTR-1) (Transcri ...	0.69	-	nuc	0	Nucleus		609785		479
P98180 UniProt NPD GO	TFE2_MESAU	Transcription factor E2-alpha (Immunoglobulin-enhancer-binding factor E12/E47) (Transcription factor ...	0.69	-	nuc	0	Nucleus				649
Q01978 UniProt NPD GO	TFE2_XENLA	Transcription factor E2-alpha (Transcription factor XE12/XE47)	0.69	-	nuc	0	Nucleus (Potential)				658
P34695 UniProt NPD GO	TF3A_RANPI	Transcription factor IIIA (Factor A) (TFIIIA)	0.69	+	nuc	0	Nucleus				335
Q9VLA2 UniProt NPD GO	GCM2_DROME	Transcription factor glial cells missing 2 (Protein glide-2)	0.69	+	nuc	0	Nucleus (By similarity)	nucleus [NAS]			613
Q09824 UniProt NPD GO	REP2_SCHPO	Transcriptional activator protein rep2	0.69	+	nuc	0		MBF transcription complex [IDA]			219
P30051 UniProt NPD GO	TEAD1_MOUSE	Transcriptional enhancer factor TEF-1 (TEA domain family member 1) (TEAD-1) (Protein GT-IIC) (Transc ...	0.69	-	nuc	0	Nucleus	transcription factor complex [IDA]			426
Q62296 UniProt NPD GO	TEAD4_MOUSE	Transcriptional enhancer factor TEF-3 (TEA domain family member 4) (TEAD-4) (ETF-related factor 2) ( ...	0.69	-	nuc	0	Nucleus	transcription factor complex [IDA]			427
P48984 UniProt NPD GO	TEAD4_CHICK	Transcriptional enhancer factor TEF-3 (TEA domain family member 4) (TEAD-4) (TEF-1) (M-CAT-binding f ...	0.69	-	nuc	0	Nucleus				438
Q7Z020 UniProt NPD GO	TRPA1_DROME	Transient receptor potential cation channel subfamily A member 1 (Ankyrin-like with transmembrane do ...	0.69	+	end	8	Membrane; multi-pass membrane protein (Probable)	integral to membrane [IC]			1197
Q03660 UniProt NPD GO	TR130_YEAST	Transport protein particle 130 kDa subunit (TRAPP 130 kDa subunit) (Trafficking protein particle com ...	0.69	-	cyt	0		TRAPP complex [IDA]			1102
P08771 UniProt NPD GO	YAC1_MAIZE	Transposable element activator hypothetical 12 kDa protein (AC 12 kDa protein)	0.69	-	nuc	0					102
Q04215 UniProt NPD GO	YMT6_YEAST	Transposon Ty1 protein A	0.69	-	nuc	0					440
P08057 UniProt NPD GO	TNNI3_BOVIN	Troponin I, cardiac muscle (Cardiac troponin I)	0.69	-	nuc	0					211
P42271 UniProt NPD GO	TBG2_DROME	Tubulin gamma-2 chain (Gamma-2 tubulin)	0.69	+	cyt	0	Embryonic mitotic spindle, female meiotic spindle: Centrosome				457
Q9NRH3 UniProt NPD GO	TBG2_HUMAN	Tubulin gamma-2 chain (Gamma-2 tubulin)	0.69	+	cyt	0		microtubule cytoskeleton [TAS]	605785		451
P11982 UniProt NPD GO	TY3H_PHASP	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH)	0.69	-	cyt	0					491
P42684 UniProt NPD GO	ABL2_HUMAN	Tyrosine-protein kinase ABL2 (EC 2.7.10.2) (Abelson murine leukemia viral oncogene homolog 2) (Tyros ...	0.69	-	nuc	0	Cytoplasm		164690		1182
Q6P5G6 UniProt NPD GO	UBXD7_MOUSE	UBX domain-containing protein 7	0.69	-	nuc	0					467
Q3T1I3 UniProt NPD GO	USBP1_RAT	USH1C-binding protein 1 (Usher syndrome type-1C protein-binding protein 1)	0.69	-	nuc	0					680
O88623 UniProt NPD GO	UBP2_MOUSE	Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15) (Ubiquitin thioesterase 2) (Ubiquitin-specific ...	0.69	-	nuc	0					353
Q8NB14 UniProt NPD GO	UBP38_HUMAN	Ubiquitin carboxyl-terminal hydrolase 38 (EC 3.1.2.15) (Ubiquitin thioesterase 38) (Ubiquitin-specif ...	0.69	-	nuc	0					1042
Q9H611 UniProt NPD GO	CO020_HUMAN	Uncharacterized protein C15orf20	0.69	-	nuc	0					266
Q9JJB9 UniProt NPD GO	CA037_MOUSE	Uncharacterized protein C1orf37 homolog	0.69	-	nuc	1					375
P25573 UniProt NPD GO	YCE4_YEAST	Uncharacterized protein YCL044C	0.69	-	nuc	0		i-AAA complex [IDA] mitochondrion [IDA]			417
P36137 UniProt NPD GO	YK24_YEAST	Uncharacterized protein YKR044W	0.69	-	end	2 *		nuclear envelope [IDA]			443
Q12110 UniProt NPD GO	YL049_YEAST	Uncharacterized protein YLR049C	0.69	-	nuc	0					428
P53960 UniProt NPD GO	YNE0_YEAST	Uncharacterized protein YNL040W	0.69	-	nuc	0		cytoplasm [IDA]			456
P53890 UniProt NPD GO	YNQ6_YEAST	Uncharacterized protein YNL166C	0.69	-	nuc	0		bud neck [IDA] septin ring (sensu Saccharomyces) [IDA]			448

You are viewing entries 14501 to 14550 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.