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
P83217 UniProt NPD GO	HSP5_OCTVU	Sperm protamine P5 (Po5)	0.76	+	nuc	0	Nucleus	nucleosome [NAS] nucleus [NAS]			30
P24056 UniProt NPD GO	SP4_XENLA	Sperm-specific basic nuclear protein SP4	0.76	+	mit	0					78
P47069 UniProt NPD GO	MPS3_YEAST	Spindle pole body assembly component MPS3 (Monopolar spindle protein 3) (98 kDa nuclear envelope pro ...	0.76	-	nuc	1	Nucleus; nuclear membrane; single-pass type II membrane protein. Localizes to the spindle pole body ...	half bridge of spindle pole body [IDA] integral to membrane [IDA]			682
Q01684 UniProt NPD GO	SPR6_YEAST	Sporulation-specific protein (SPR6)	0.76	+	nuc	0					191
Q93045 UniProt NPD GO	STMN2_HUMAN	Stathmin-2 (SCG10 protein) (Superior cervical ganglion-10 protein)	0.76	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Associated with punctate s ...	membrane fraction [NAS] soluble fraction [NAS]	600621		179
P55821 UniProt NPD GO	STMN2_MOUSE	Stathmin-2 (SCG10 protein) (Superior cervical ganglion-10 protein)	0.76	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region. Associated with punctate structures in the perinuclear cyt ...	growth cone [IDA]			179
Q6IDD9 UniProt NPD GO	SARM1_DROME	Sterile alpha and TIR motif-containing protein 1 (Tir-1 homolog)	0.76	-	nuc	0	Cytoplasm (By similarity)				1360
Q8CBY1 UniProt NPD GO	SAMD4_MOUSE	Sterile alpha motif domain-containing protein 4	0.76	-	nuc	0		synaptosome [IDA]			623
Q99593 UniProt NPD GO	TBX5_HUMAN	T-box transcription factor TBX5 (T-box protein 5)	0.76	-	nuc	0	Nucleus (Potential)		601620		518
P70326 UniProt NPD GO	TBX5_MOUSE	T-box transcription factor TBX5 (T-box protein 5)	0.76	-	nuc	0	Nucleus (Potential)				518
Q12799 UniProt NPD GO	TCP10_HUMAN	T-complex protein 10A homolog	0.76	-	nuc	0		cytosol [TAS]	187020		416
Q9QXG9 UniProt NPD GO	TINF2_MOUSE	TERF1-interacting nuclear factor 2 (TRF1-interacting nuclear protein 2)	0.76	-	nuc	0	Nucleus (By similarity). Associated with telomeres (By similarity)	chromosome, telomeric region [IDA]			341
Q13114 UniProt NPD GO	TRAF3_HUMAN	TNF receptor-associated factor 3 (CD40 receptor-associated factor 1) (CRAF1) (CD40-binding protein) ...	0.76	-	nuc	0	Cytoplasm (Probable)		601896	2GKW	568
P29548 UniProt NPD GO	TEBB_STYMY	Telomere-binding protein subunit beta	0.76	-	nuc	0	Nucleus				392
O19110 UniProt NPD GO	TSPY1_BOVIN	Testis-specific Y-encoded protein 1 (bTSPY)	0.76	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Also found in nucleus (By similar ...				317
P87061 UniProt NPD GO	TEA1_SCHPO	Tip elongation aberrant protein 1 (Cell polarity protein tea1)	0.76	-	nuc	0	Present at both poles of the cell throughout the cell cycle whether they are growing or not. Located ...	cell cortex of cell tip [IDA] microtubule [TAS] Tea1 cell-end complex [IDA]			1147
Q99NC0 UniProt NPD GO	VGLL1_MOUSE	Transcription cofactor vestigial-like protein 1 (Vgl-1) (Vestigial-related factor)	0.76	-	nuc	0	Nucleus (By similarity)				307
P15884 UniProt NPD GO	ITF2_HUMAN	Transcription factor 4 (Immunoglobulin transcription factor 2) (ITF-2) (SL3-3 enhancer factor 2) (SE ...	0.76	-	nuc	0	Nucleus (Probable)	nucleus [TAS]	602272		667
Q00417 UniProt NPD GO	TCF7_MOUSE	Transcription factor 7 (T-cell-specific transcription factor 1) (TCF-1) (T-cell factor 1)	0.76	+	nuc	0	Nucleus				419
O75461 UniProt NPD GO	E2F6_HUMAN	Transcription factor E2F6 (E2F-6)	0.76	-	nuc	0	Nucleus		602944		281
P43693 UniProt NPD GO	GATA6_CHICK	Transcription factor GATA-6 (GATA-binding factor 6)	0.76	-	nuc	0	Nucleus				387
O24646 UniProt NPD GO	HY5_ARATH	Transcription factor HY5 (Protein LONG HYPOCOL5) (AtbZIP56)	0.76	-	nuc	0	Nucleus				168
P27921 UniProt NPD GO	JUND_CHICK	Transcription factor jun-D	0.76	+	nuc	0	Nucleus				323
P15066 UniProt NPD GO	JUND_MOUSE	Transcription factor jun-D	0.76	+	nuc	0	Nucleus				341
P52909 UniProt NPD GO	JUND_RAT	Transcription factor jun-D	0.76	+	nuc	0	Nucleus				341
P23255 UniProt NPD GO	TAF2_YEAST	Transcription initiation factor TFIID subunit 2 (TBP-associated factor 2) (TBP-associated factor 150 ...	0.76	-	mit	0	Nucleus	transcription factor TFIID complex [IDA]			1407
P50105 UniProt NPD GO	TAF4_YEAST	Transcription initiation factor TFIID subunit 4 (TBP-associated factor 4) (TBP-associated factor 48 ...	0.76	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]			388
Q8VHR5 UniProt NPD GO	P66B_MOUSE	Transcriptional repressor p66 beta (p66/p68) (GATA zinc finger domain-containing protein 2B)	0.76	-	nuc	0	Nucleus (By similarity). Nuclear, in discrete foci (By similarity)				594
Q08122 UniProt NPD GO	TLE3_MOUSE	Transducin-like enhancer protein 3 (ESG) (Grg-3)	0.76	-	nuc	0	Nucleus				771
Q04726 UniProt NPD GO	TLE3_HUMAN	Transducin-like enhancer protein 3 (ESG3)	0.76	-	nuc	0	Nucleus	nucleus [TAS]	600190		772
Q6Y685 UniProt NPD GO	TACC1_MOUSE	Transforming acidic coiled-coil-containing protein 1	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Nucleus during interphase. Weakly concentrated a ...				774
Q9W0Y6 UniProt NPD GO	PAIN_DROME	Transient receptor potential cation channel protein painless	0.76	-	end	6	Membrane; multi-pass membrane protein (Probable)	integral to membrane [NAS]			913
P41111 UniProt NPD GO	EI2BD_RABIT	Translation initiation factor eIF-2B subunit delta (eIF-2B GDP-GTP exchange factor subunit delta)	0.76	-	nuc	0					523
Q63186 UniProt NPD GO	EI2BD_RAT	Translation initiation factor eIF-2B subunit delta (eIF-2B GDP-GTP exchange factor subunit delta)	0.76	-	nuc	0		eukaryotic translation initiation factor 2B... [NAS]			524
Q08687 UniProt NPD GO	TMA16_YEAST	Translation machinery-associated protein 16	0.76	+	nuc	0	Nucleus	nucleus [IDA]			178
P48553 UniProt NPD GO	TMEM1_HUMAN	Transmembrane protein 1 (Epilepsy holoprosencephaly candidate 1 protein) (EHOC-1) (GT334 protein)	0.76	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)	integral to membrane [TAS]	602103		1259
P14381 UniProt NPD GO	YTX2_XENLA	Transposon TX1 hypothetical 149 kDa protein (ORF 2)	0.76	-	cyt	0					1308
P31688 UniProt NPD GO	TPS2_YEAST	Trehalose-phosphatase (EC 3.1.3.12) (Trehalose 6-phosphate phosphatase) (TPP) (Trehalose synthase co ...	0.76	-	nuc	0	Cytoplasm	alpha,alpha-trehalose-phosphate synthase co... [IGI] mitochondrion [IDA]			896
P62603 UniProt NPD GO	TRI26_RAT	Tripartite motif-containing protein 26 (Zinc finger protein 173)	0.76	-	cyt	0					542
O13016 UniProt NPD GO	PTN1_CHICK	Tyrosine-protein phosphatase non-receptor type 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1B) (PT ...	0.76	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				434
Q05209 UniProt NPD GO	PTN12_HUMAN	Tyrosine-protein phosphatase non-receptor type 12 (EC 3.1.3.48) (Protein-tyrosine phosphatase G1) (P ...	0.76	-	nuc	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	600079		780
P34247 UniProt NPD GO	UTP11_YEAST	U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11)	0.76	+	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [NAS]			256
Q6NVP6 UniProt NPD GO	PRP31_XENTR	U4/U6 small nuclear ribonucleoprotein Prp31 (Pre-mRNA-processing factor 31)	0.76	-	nuc	0	Nucleus (By similarity)				498
Q9M2Q4 UniProt NPD GO	U202B_ARATH	UPF0202 protein At3g57940	0.76	+	mit	0	Nucleus (By similarity)				1024
P25037 UniProt NPD GO	UBP1_YEAST	Ubiquitin carboxyl-terminal hydrolase 1 (EC 3.1.2.15) (Ubiquitin thioesterase 1) (Ubiquitin-specific ...	0.76	-	nuc	1 *		cytoplasm [IDA] endoplasmic reticulum [IDA]			809
Q02863 UniProt NPD GO	UBP16_YEAST	Ubiquitin carboxyl-terminal hydrolase 16 (EC 3.1.2.15) (Ubiquitin thioesterase 16) (Ubiquitin-specif ...	0.76	-	nuc	1 *		cytoplasm [IC] mitochondrial outer membrane [IDA]			499
Q3ZBQ1 UniProt NPD GO	UBTD1_BOVIN	Ubiquitin domain-containing protein 1	0.76	+	nuc	0					227
Q14157 UniProt NPD GO	UBP2L_HUMAN	Ubiquitin-associated protein 2-like (Protein NICE-4)	0.76	+	nuc	0					1087
O15550 UniProt NPD GO	UTX_HUMAN	Ubiquitously transcribed X chromosome tetratricopeptide repeat protein (Ubiquitously transcribed TPR ...	0.76	-	nuc	0	Nucleus (Potential)		300128		1401
Q6DIB4 UniProt NPD GO	CT112_MOUSE	Uncharacterized protein C20orf112 homolog	0.76	-	nuc	0					494

You are viewing entries 11101 to 11150 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.