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
O18748 UniProt NPD GO	HSP1_PLATE	Sperm protamine P1	0.81	+	mit	0	Nucleus				62
Q9GLP8 UniProt NPD GO	HSP1_POTLO	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
P67832 UniProt NPD GO	HSP1_PSEMD	Sperm protamine P1	0.81	+	mit	0	Nucleus				62
Q71VG5 UniProt NPD GO	HSP1_PSENI	Sperm protamine P1	0.81	+	mit	0	Nucleus (By similarity)				62
Q71VG4 UniProt NPD GO	HSP1_PSEWO	Sperm protamine P1	0.81	+	mit	0	Nucleus (By similarity)				62
Q8WNZ7 UniProt NPD GO	HSP1_RHIFE	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				51
P62486 UniProt NPD GO	HSP1_SARHA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67840 UniProt NPD GO	HSP1_SETBR	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
Q71UG9 UniProt NPD GO	HSP1_SMIAI	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UG8 UniProt NPD GO	HSP1_SMIAR	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
P67844 UniProt NPD GO	HSP1_SMICR	Sperm protamine P1	0.81	+	nuc	0	Nucleus				62
Q71UG7 UniProt NPD GO	HSP1_SMIDL	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UG6 UniProt NPD GO	HSP1_SMIDO	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UG4 UniProt NPD GO	HSP1_SMIGA	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UG5 UniProt NPD GO	HSP1_SMIGI	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q9TUC3 UniProt NPD GO	HSP1_SMIGR	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UG3 UniProt NPD GO	HSP1_SMIHI	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UG2 UniProt NPD GO	HSP1_SMILE	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q9TUC2 UniProt NPD GO	HSP1_SMILO	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				61
Q71VP8 UniProt NPD GO	HSP1_SMIMA	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71VP9 UniProt NPD GO	HSP1_SMIMU	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UG1 UniProt NPD GO	HSP1_SMIOO	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UG0 UniProt NPD GO	HSP1_SMIPS	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UF9 UniProt NPD GO	HSP1_SMIVI	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71UF8 UniProt NPD GO	HSP1_SMIYO	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
P35311 UniProt NPD GO	HSP1_TACAC	Sperm protamine P1	0.81	+	nuc	0	Nucleus				68
P67846 UniProt NPD GO	HSP1_THYCY	Sperm protamine P1	0.81	+	nuc	0	Nucleus				62
P42152 UniProt NPD GO	HSP1_TRIVU	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67843 UniProt NPD GO	HSP1_WALBI	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P35304 UniProt NPD GO	HSP1_CAVPO	Sperm protamine P1 (Cysteine-rich protamine)	0.81	+	nuc	0	Nucleus				47
P35303 UniProt NPD GO	HSP1_GORGO	Sperm protamine P1 (Cysteine-rich protamine)	0.81	+	mit	0	Nucleus	nucleoplasm [ISS]			50
P14309 UniProt NPD GO	PHI0_HOLTU	Sperm-specific protein Phi-0	0.81	+	mit	0	Nucleus				78
P17306 UniProt NPD GO	STP1_PIG	Spermatid nuclear transition protein 1 (STP-1) (TP-1)	0.81	-	nuc	0	Nucleus	nucleosome [ISS]			54
P47074 UniProt NPD GO	MAD3_YEAST	Spindle assembly checkpoint component MAD3 (Mitotic MAD3 protein)	0.81	-	nuc	0	Nucleus	nucleus [IDA]			515
Q95ZG3 UniProt NPD GO	SPC97_DICDI	Spindle pole body component 97 (Spc97) (DdSpc97)	0.81	-	nuc	0	Centrosome. Cytoplasm				1177
Q3MHR5 UniProt NPD GO	SFRS2_BOVIN	Splicing factor, arginine/serine-rich 2 (Splicing factor SC35) (SC-35) (Splicing component, 35 kDa)	0.81	+	nuc	0	Nucleus (By similarity)				220
Q6PDU1 UniProt NPD GO	SFRS2_RAT	Splicing factor, arginine/serine-rich 2 (Splicing factor SC35) (SC-35) (Splicing component, 35 kDa)	0.81	+	nuc	0	Nucleus (By similarity)				220
P30352 UniProt NPD GO	SFRS2_CHICK	Splicing factor, arginine/serine-rich 2 (Splicing factor SC35) (SC-35) (Splicing component, 35 kDa) ...	0.81	+	nuc	0	Nucleus				221
Q01130 UniProt NPD GO	SFRS2_HUMAN	Splicing factor, arginine/serine-rich 2 (Splicing factor SC35) (SC-35) (Splicing component, 35 kDa) ...	0.81	+	nuc	0	Nucleus	nucleus [IDA]	600813		220
Q62093 UniProt NPD GO	SFRS2_MOUSE	Splicing factor, arginine/serine-rich 2 (Splicing factor SC35) (SC-35) (Splicing component, 35 kDa) ...	0.81	+	nuc	0	Nucleus	nucleus [IDA] spliceosome complex [IDA]			220
P17123 UniProt NPD GO	SPO12_YEAST	Sporulation-specific protein 12	0.81	-	nuc	0		nucleolus [IDA] nucleus [IDA]			173
Q8LFW6 UniProt NPD GO	SPL13_ARATH	Squamosa promoter-binding-like protein 13	0.81	+	nuc	0	Nucleus (Probable)				359
Q09001 UniProt NPD GO	STM2A_XENLA	Stathmin-2-A (SCG10 protein homolog A)	0.81	-	nuc	0					178
Q15527 UniProt NPD GO	SURF2_HUMAN	Surfeit locus protein 2 (Surf-2)	0.81	-	nuc	0			185630		256
O43001 UniProt NPD GO	SYJ1_SCHPO	Synaptojanin homolog 1 (EC 3.1.3.36) (Inositol-1,4,5-trisphosphate 5-phosphatase 1)	0.81	-	nuc	0				1I9Z	1076
Q60547 UniProt NPD GO	SYCP3_MESAU	Synaptonemal complex protein 3 (SCP-3) (Synaptonemal complex protein COR1) (Meiotic chromosome core ...	0.81	-	nuc	0	Nucleus. It is present in early unpaired cores, in the lateral domains of the synaptonemal complex a ...				234
Q8WTV1 UniProt NPD GO	THAP3_HUMAN	THAP domain-containing protein 3	0.81	-	mit	0					239
P29549 UniProt NPD GO	TEBA_OXYNO	Telomere-binding protein alpha subunit (Telomere-binding protein 56 kDa subunit) (TEBP alpha)	0.81	-	nuc	0	Nucleus			1PHJ	495
P70371 UniProt NPD GO	TERF1_MOUSE	Telomeric repeat-binding factor 1 (TTAGGG repeat-binding factor 1)	0.81	-	nuc	0	Nucleus (By similarity). Colocalizes with telomeric DNA in interphase and metaphase cells and is loc ...				421
Q04205 UniProt NPD GO	TENS_CHICK	Tensin	0.81	-	nuc	0	Cell membrane; cell-cell junction; adherens junction			1WVH	1744

You are viewing entries 8651 to 8700 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.