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
Q00616 UniProt NPD GO	NOR1_CYLTO	Cytochrome P450 55A2 (EC 1.14.-.-) (Cytochrome P450NOR1)	0.14	-	nuc	0					403
Q9V674 UniProt NPD GO	CP6G1_DROME	Cytochrome P450 6g1 (EC 1.14.-.-) (CYPVIG1) (Cyp6-like protein)	0.14	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)	endoplasmic reticulum membrane [NAS]			524
P58046 UniProt NPD GO	C71AF_ARATH	Cytochrome P450 71A15 (EC 1.14.-.-)	0.14	-	end	0					496
Q9STL1 UniProt NPD GO	C71AM_ARATH	Cytochrome P450 71A22 (EC 1.14.-.-)	0.14	-	end	2 *					490
Q43135 UniProt NPD GO	C79A1_SORBI	Cytochrome P450 79A1 (EC 1.14.13.41) (Tyrosine N-monooxygenase) (Cytochrome P450Tyr)	0.14	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				557
Q9FG65 UniProt NPD GO	C81D1_ARATH	Cytochrome P450 81D1 (EC 1.14.-.-)	0.14	-	end	1 *					502
Q94ZK8 UniProt NPD GO	CYB_CEBAL	Cytochrome b	0.14	-	end	9 *					378
P92701 UniProt NPD GO	CYB_PONPA	Cytochrome b	0.14	-	end	9 *					380
O46521 UniProt NPD GO	CY24A_BOVIN	Cytochrome b-245 light chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 22 kDa polypeptid ...	0.14	-	end	3 *					190
Q5R9K2 UniProt NPD GO	COX7B_PONPY	Cytochrome c oxidase polypeptide VIIb, mitochondrial precursor (EC 1.9.3.1)	0.14	-	mit	0					80
P19536 UniProt NPD GO	COX5B_MOUSE	Cytochrome c oxidase polypeptide Vb, mitochondrial precursor (EC 1.9.3.1)	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			128
Q94WR7 UniProt NPD GO	COX1_BUTBU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.14	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
Q7GEN7 UniProt NPD GO	COX1_HYLLA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.14	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				513
Q34800 UniProt NPD GO	COX1_HYLSY	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.14	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				513
P14544 UniProt NPD GO	COX1_LEITA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.14	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				549
P98003 UniProt NPD GO	COX1_CRION	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.14	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				340
P84288 UniProt NPD GO	COX2_CHOFU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.14	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P84289 UniProt NPD GO	COX2_CHOOC	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.14	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P84290 UniProt NPD GO	COX2_CHOPI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.14	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q4ING3 UniProt NPD GO	CCPR_GIBZE	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.14	-	mit	1 *	Mitochondrion; mitochondrial matrix (By similarity)				358
Q7SDV9 UniProt NPD GO	CCPR_NEUCR	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.14	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				358
P83784 UniProt NPD GO	CAP6_CANAL	Cytoplasmic antigenic protein 6 (Fragment)	0.14	-		0	Cytoplasm				7
O43237 UniProt NPD GO	DC1L2_HUMAN	Cytoplasmic dynein 1 light intermediate chain 2 (Dynein light intermediate chain 2, cytosolic) (LIC5 ...	0.14	-	nuc	0		cytoplasmic dynein complex [TAS]			492
Q6BZA0 UniProt NPD GO	ALO_DEBHA	D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.14	-	cyt	0	Mitochondrion; mitochondrial membrane (By similarity). Membrane-embedded (By similarity)				557
P22031 UniProt NPD GO	LEG_ANTCR	D-galactoside-specific lectin (Sea urchin egg lectin) (SUEL)	0.14	-	nuc	0	Cytoplasm. Cytoplasmic in unfertilized eggs, and shifted to the peripheral regions after fertilizati ...				105
Q9ST48 UniProt NPD GO	DWRF8_MAIZE	DELLA protein DWARF8 (Protein dwarf-8)	0.14	-	cyt	0	Nucleus (By similarity)				630
Q5QJC3 UniProt NPD GO	DCR1B_CHICK	DNA cross-link repair 1B protein (chSNM1B)	0.14	-	mit	0	Nucleus (By similarity)				457
P33194 UniProt NPD GO	DDB1_CERAE	DNA damage-binding protein 1 (Damage-specific DNA-binding protein 1) (DDB p127 subunit) (DDBa) (UV-d ...	0.14	-	cyt	0	Nucleus				1140
Q16531 UniProt NPD GO	DDB1_HUMAN	DNA damage-binding protein 1 (Damage-specific DNA-binding protein 1) (UV-damaged DNA-binding factor) ...	0.14	-	cyt	0	Nucleus		600045	2B5N	1140
Q9LRE5 UniProt NPD GO	DPOD2_ORYSA	DNA polymerase delta small subunit (EC 2.7.7.7)	0.14	-	nuc	0	Nucleus (By similarity)				429
P70099 UniProt NPD GO	RAD51_CRIGR	DNA repair protein RAD51 homolog 1	0.14	-	cyt	0	Nucleus (Probable)	nucleus [ISS] synaptonemal complex [ISS]			339
Q08297 UniProt NPD GO	RAD51_MOUSE	DNA repair protein RAD51 homolog 1	0.14	-	cyt	0	Nucleus (By similarity). Colocalizes with RAD51AP1 to multiple nuclear foci upon induction of DNA da ...	nucleus [IDA] synaptonemal complex [TAS]			339
O77507 UniProt NPD GO	RAD51_RABIT	DNA repair protein RAD51 homolog 1	0.14	-	cyt	0	Nucleus (Probable)	nucleus [ISS] synaptonemal complex [ISS]			339
Q8MKI8 UniProt NPD GO	RAD51_CANFA	DNA repair protein RAD51 homolog 1 (cRad51)	0.14	-	cyt	0	Nucleus (Probable)	nucleus [ISS] synaptonemal complex [ISS]			339
Q06609 UniProt NPD GO	RAD51_HUMAN	DNA repair protein RAD51 homolog 1 (hRAD51) (HsRAD51)	0.14	-	cyt	0	Nucleus. Colocalizes with RAD51AP1 to multiple nuclear foci upon induction of DNA damage	nucleus [IDA] synaptonemal complex [ISS]	114480	1N0W	339
Q91918 UniProt NPD GO	RA51A_XENLA	DNA repair protein RAD51 homolog A (xRAD51.1)	0.14	-	cyt	0	Nucleus (Probable)				336
P20067 UniProt NPD GO	ID1_MOUSE	DNA-binding protein inhibitor ID-1 (Inhibitor of DNA binding 1)	0.14	-	cyt	0	Nucleus				168
Q00874 UniProt NPD GO	DR100_ARATH	DNA-damage-repair/toleration protein DRT100 precursor	0.14	-	mit	0					372
Q8L6J2 UniProt NPD GO	RPO2A_TOBAC	DNA-directed RNA polymerase 2A (EC 2.7.7.6) (T7 bacteriophage-type single subunit RNA polymerase 2A) ...	0.14	-	cyt	0					332
P32910 UniProt NPD GO	RPC6_YEAST	DNA-directed RNA polymerase III 36 kDa polypeptide (EC 2.7.7.6) (C34)	0.14	-	cyt	0	Nucleus	cytoplasm [IDA] DNA-directed RNA polymerase III complex [TAS] nucleus [IDA]			317
P22139 UniProt NPD GO	RPB10_YEAST	DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6) (DNA-directed RNA polymerases I, II, a ...	0.14	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase II, core complex [TAS] DNA-directed RNA polymerase III complex [TAS]		2B8K	70
Q2M2S7 UniProt NPD GO	RPC11_BOVIN	DNA-directed RNA polymerases III 12.5 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subunit K)	0.14	-	nuc	0	Nucleus (Potential)				108
Q9CQZ7 UniProt NPD GO	RPC11_MOUSE	DNA-directed RNA polymerases III 12.5 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subunit K) (R ...	0.14	-	nuc	0	Nucleus (Potential)				108
Q9Y2Y1 UniProt NPD GO	RPC11_HUMAN	DNA-directed RNA polymerases III 12.5 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subunit K) (R ...	0.14	-	nuc	0	Nucleus (Potential)	DNA-directed RNA polymerase III complex [TAS]	606007		108
P38727 UniProt NPD GO	YHE4_YEAST	DUP240 protein YHL044W	0.14	-	end	2 *	Cell membrane; multi-pass membrane protein	plasma membrane [IDA]			235
Q01129 UniProt NPD GO	PGS2_RAT	Decorin precursor (Bone proteoglycan II) (PG-S2) (PG40) (Dermatan sulfate proteoglycan-II) (DSPG)	0.14	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [IDA]			354
Q6FJR2 UniProt NPD GO	DCN1_CANGA	Defective in cullin neddylation protein 1	0.14	-	cyt	0					273
P81611 UniProt NPD GO	DEFB_MYTED	Defensin-B (Fragment)	0.14	-	nuc	0	Secreted protein				35
P82141 UniProt NPD GO	DLP3_ORNAN	Defensin-like peptide 3 (DLP-3)	0.14	-	nuc	0	Secreted protein	extracellular region [IDA]			38
P32296 UniProt NPD GO	P5CS_VIGAC	Delta 1-pyrroline-5-carboxylate synthetase (P5CS) [Includes: Glutamate 5-kinase (EC 2.7.2.11) (Gamma ...	0.14	-	nuc	0					671

You are viewing entries 58201 to 58250 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.