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
P11499 UniProt NPD GO	HS90B_MOUSE	Heat shock protein HSP 90-beta (HSP 84) (Tumor-specific transplantation 84 kDa antigen) (TSTA)	0.63	-	nuc	0	Cytoplasm	mitochondrion [IDA]			723
Q43468 UniProt NPD GO	STIP_SOYBN	Heat shock protein STI (Stress-inducible protein) (GmSTI)	0.63	-	nuc	0					569
Q9USI5 UniProt NPD GO	STI1_SCHPO	Heat shock protein sti1 homolog	0.63	-	nuc	0	Cytoplasm (By similarity)				591
P49710 UniProt NPD GO	HCLS1_MOUSE	Hematopoietic lineage cell-specific protein (Hematopoietic cell-specific LYN substrate 1) (LckBP1)	0.63	+	nuc	0	Mitochondrion (By similarity)	cytoplasm [IDA] nucleus [IDA]			486
Q14541 UniProt NPD GO	HNF4G_HUMAN	Hepatocyte nuclear factor 4-gamma (HNF-4-gamma)	0.63	-	nuc	0	Nucleus (By similarity)		605966	1LV2	408
Q9DCB1 UniProt NPD GO	HMGN3_MOUSE	High mobility group nucleosome-binding domain-containing protein 3	0.63	-	nuc	0	Nucleus (By similarity)				99
Q66H40 UniProt NPD GO	HMGN3_RAT	High mobility group nucleosome-binding domain-containing protein 3	0.63	-	nuc	0	Nucleus (By similarity)				95
P26584 UniProt NPD GO	HMGB2_CHICK	High mobility group protein B2 (High mobility group protein 2) (HMG-2)	0.63	-	nuc	0	Nucleus	condensed chromosome [ISS] cytoplasm [ISS] nucleus [ISS] perinuclear region [ISS]			206
Q6URC2 UniProt NPD GO	HMGA1_CANFA	High mobility group protein HMG-I/HMG-Y (HMG-I(Y)) (High mobility group AT-hook protein 1) (High mob ...	0.63	+	nuc	0	Nucleus (By similarity)				106
P17096 UniProt NPD GO	HMGA1_HUMAN	High mobility group protein HMG-I/HMG-Y (HMG-I(Y)) (High mobility group AT-hook protein 1) (High mob ...	0.63	+	nuc	0	Nucleus	transcription factor complex [TAS]	600701	2EZG	106
Q06943 UniProt NPD GO	HMGZ_DROME	High mobility group protein Z (HMG-Z)	0.63	+	nuc	0	Nucleus (Probable)				111
P02284 UniProt NPD GO	H2B_PATGR	Histone H2B, gonadal	0.63	+	nuc	0	Nucleus				121
Q6BSQ1 UniProt NPD GO	HAT1_DEBHA	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.63	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				409
P13544 UniProt NPD GO	HM1_CHICK	Homeobox protein CHOX-1 (Fragment)	0.63	+	nuc	0	Nucleus (Potential)				67
Q91975 UniProt NPD GO	HOXE_CHICK	Homeobox protein CHOX-E (CHOX E) (Fragment)	0.63	+	nuc	0	Nucleus (Potential)				157
P52950 UniProt NPD GO	DBX1_MOUSE	Homeobox protein DBX1	0.63	+	nuc	0	Nucleus				335
P54655 UniProt NPD GO	DLL3_XENLA	Homeobox protein DLL-3 (XDLL-3)	0.63	+	nuc	0	Nucleus (Potential)				289
P56178 UniProt NPD GO	DLX5_HUMAN	Homeobox protein DLX-5	0.63	+	nuc	0	Nucleus (Potential)		600028		289
P56179 UniProt NPD GO	DLX6_HUMAN	Homeobox protein DLX-6	0.63	+	nuc	0	Nucleus (Potential)		600030		175
P70397 UniProt NPD GO	DLX6_MOUSE	Homeobox protein DLX-6 (Fragment)	0.63	+	nuc	0	Nucleus (Potential)				158
Q98877 UniProt NPD GO	DLX6A_BRARE	Homeobox protein Dlx6a (DLX-6) (Distal-less homeobox protein 6a)	0.63	+	nuc	0	Nucleus (Potential)				247
P13545 UniProt NPD GO	HMB1_STRPU	Homeobox protein HB1 (SPHBOX1)	0.63	+	nuc	0	Nucleus (Probable)				308
P09080 UniProt NPD GO	HMB1_TRIGR	Homeobox protein HB1 (TGHBOX1) (Fragment)	0.63	+	nuc	0	Nucleus (Probable)				307
O08656 UniProt NPD GO	HXA1_RAT	Homeobox protein Hox-A1	0.63	+	nuc	0	Nucleus (By similarity)				333
Q90X25 UniProt NPD GO	HXA13_CHICK	Homeobox protein Hox-A13	0.63	+	nuc	0	Nucleus				290
P09021 UniProt NPD GO	HXA5_MOUSE	Homeobox protein Hox-A5 (Hox-1.3) (M2)	0.63	+	nuc	0	Nucleus				270
O42366 UniProt NPD GO	HXB1A_BRARE	Homeobox protein Hox-B1a (Hox-B1)	0.63	+	nuc	0	Nucleus (By similarity)				311
P14838 UniProt NPD GO	HXB5_CHICK	Homeobox protein Hox-B5 (Ghox-2.1) (Fragment)	0.63	+	nuc	0	Nucleus				82
P02832 UniProt NPD GO	HXC6_XENLA	Homeobox protein Hox-C6 (XlHbox-1) (AC1) [Contains: Homeobox protein Hox-C6 PRII; Homeobox protein H ...	0.63	+	nuc	0	Nucleus				234
P31277 UniProt NPD GO	HXD11_HUMAN	Homeobox protein Hox-D11 (Hox-4F)	0.63	+	nuc	0	Nucleus	nucleus [NAS]	142986		338
P17487 UniProt NPD GO	HM12_CAEEL	Homeobox protein ceh-12	0.63	+	nuc	0	Nucleus (Probable)				180
P56660 UniProt NPD GO	KNOX2_MAIZE	Homeobox protein knotted-1-like 2 (Fragment)	0.63	-	nuc	0	Nucleus (Probable)				88
P09085 UniProt NPD GO	CAD_DROME	Homeotic protein caudal	0.63	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			427
Q5ZLF0 UniProt NPD GO	F10A1_CHICK	Hsc70-interacting protein (Hip) (Protein ST13 homolog) (Protein FAM10A1)	0.63	-	nuc	0	Cytoplasm (By similarity)				361
O57476 UniProt NPD GO	CDC37_CHICK	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (p50Cdc37)	0.63	+	nuc	0	Cytoplasm (By similarity)				393
P38194 UniProt NPD GO	YBE4_YEAST	Hypothetical 13.9 kDa protein in QCR1-FUI1 intergenic region	0.63	-	nuc	0					122
O20118 UniProt NPD GO	YCX1_CHLVU	Hypothetical 16.5 kDa protein in psaC-atpA intergenic region (ORF138)	0.63	+	nuc	1	Plastid; chloroplast				138
P36138 UniProt NPD GO	YK25_YEAST	Hypothetical 21.1 kDa protein in GAP1-NAP1 intergenic region	0.63	-	mit	0		cytoplasm [IDA]			191
P36052 UniProt NPD GO	YKQ2_YEAST	Hypothetical 46.5 kDa protein in PIR3-APE2 intergenic region	0.63	-	nuc	0		mitochondrion [IDA]			402
Q04263 UniProt NPD GO	YMA2_YEAST	Hypothetical 84.6 kDa protein in GLO1-YPT7 intergenic region	0.63	-	nuc	0					737
Q9FZA4 UniProt NPD GO	DOF14_ARATH	Hypothetical Dof zinc finger protein DOF1.4 (AtDOF1.4)	0.63	-	nuc	0	Nucleus (Probable)				311
O13699 UniProt NPD GO	YEN6_SCHPO	Hypothetical UPF0300 protein C11G7.06c in chromosome I	0.63	-	cyt	0					430
P92537 UniProt NPD GO	M1030_ARATH	Hypothetical mitochondrial protein AtMg01030 (ORF106e)	0.63	-	nuc	0	Mitochondrion (Potential)				106
P92566 UniProt NPD GO	M1400_ARATH	Hypothetical mitochondrial protein AtMg01400 (ORF105b)	0.63	-	nuc	0	Mitochondrion (Potential)				105
Q09223 UniProt NPD GO	YP76_CAEEL	Hypothetical protein B0228.6	0.63	-	nuc	1					153
P34304 UniProt NPD GO	YKQ9_CAEEL	Hypothetical protein C06E1.9	0.63	-	nuc	0					643
P34325 UniProt NPD GO	YKV4_CAEEL	Hypothetical protein C08C3.4	0.63	-	nuc	0					262
O14318 UniProt NPD GO	YB71_SCHPO	Hypothetical protein C16E9.01c in chromosome II	0.63	-	nuc	0					295
Q09705 UniProt NPD GO	YA2F_SCHPO	Hypothetical protein C2F7.15 in chromosome I	0.63	-	nuc	0					258
O14177 UniProt NPD GO	YDS1_SCHPO	Hypothetical protein C4F8.01 in chromosome I	0.63	-	nuc	0					210

You are viewing entries 17401 to 17450 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.