Functional Clustering  


Cluster information

Cluster overview

Cluster id
CH_ath_2
Cluster type
GO
Species
Arabidopsis thaliana
Chromosome
chloroplast
E-value
4.13192e-57
GO label
GO:0044237
GO description
cellular metabolic process
 

Statistics

Gene family Num genes total Num genes species Num genes cluster Num species
HOM0002113609325
HOM00021535612625
HOM00039523411125
HOM0004622104324
HOM0004822025423
HOM0004911996225
HOM0005501823324
HOM0005751753323
HOM0006141656424
HOM0006191643323
HOM0007391463323
HOM0007701413225
HOM0007751404123
HOM0009611172223
HOM0010161113123
HOM0010811052223
HOM001150992123
HOM001193961124
HOM001197963321
HOM001436822222
HOM001599741117
HOM001724702220
HOM001874662125
HOM002419532223
HOM002716472219
HOM002742471119
HOM003137411122
HOM004406321119
HOM005581261119
HOM006202231113
HOM006438211117
HOM006468211118
HOM006756191119

Gene information

In cluster Gene id Description Gene type Gene family
V ATCG00010A chloroplast gene encoding a histidine-accepting tRNA.;rna_type=pre-trnaRNA gene
V ATCG00020Encodes chlorophyll binding protein D1, a part of the photosystem II reaction center core;photosystem II reaction center protein ACoding geneHOM000961 ORTHO001130
V ATCG00030Lysine tRNA;rna_type=pre-trnaRNA gene
V ATCG00040Encodes a maturase located in the trnK intron in the chloroplast genome.;maturase KCoding geneHOM000961 ORTHO007737
V ATCG00050Homologous to the bacterial ribosomal protein S16;ribosomal protein S16Coding geneHOM000395 ORTHO006335
V ATCG00060tRNA-Gln;rna_type=pre-trnaRNA gene
V ATCG00070PSII K protein;photosystem II reaction center protein K precursorCoding geneHOM002716 ORTHO005608
V ATCG00080PSII I protein;photosystem II reaction center protein ICoding geneHOM002716 ORTHO012703
V ATCG00090tRNA-Ser;rna_type=pre-trnaRNA gene
V ATCG00100tRNA-Gly;rna_type=pre-trnaRNA gene
V ATCG00110tRNA-Arg;rna_type=pre-trnaRNA gene
V ATCG00120Encodes the ATPase alpha subunit, which is a subunit of ATP synthase and part of the CF1 portion which catalyzes the conversion of ADP to ATP using the proton motive force. This complex is located in the thylakoid membrane of the chloroplast.;ATP synthase subunit alphaCoding geneHOM000215 ORTHO004312
V ATCG00130ATPase F subunit.;ATPase, F0 complex, subunit B/B', bacterial/chloroplastCoding geneHOM005581 ORTHO007020
V ATCG00140ATPase III subunit;ATP synthase subunit C family proteinCoding geneHOM000215 ORTHO001974
V ATCG00150Encodes a subunit of ATPase complex CF0, which is a proton channel that supplies the proton motive force to drive ATP synthesis by CF1 portion of the complex.;ATPase, F0 complex, subunit A proteinCoding geneHOM000215 ORTHO005607
V ATCG00160Chloroplast ribosomal protein S2;ribosomal protein S2Coding geneHOM000215 ORTHO002665
V ATCG00170RNA polymerase beta' subunit-2;DNA-directed RNA polymerase family proteinCoding geneHOM001193 ORTHO001668
V ATCG00180RNA polymerase beta' subunit-1;DNA-directed RNA polymerase family proteinCoding geneHOM000550 ORTHO002151
V ATCG00190Chloroplast DNA-dependent RNA polymerase B subunit. The transcription of this gene is regulated by a nuclear encoded RNA polymerase. This gene has been transferred to mitochondrial genome during crucifer evolution.;RNA polymerase subunit betaCoding geneHOM000550 ORTHO001338
V ATCG00200a chloroplast-encoded tRNA for cysteine;rna_type=pre-trnaRNA gene
X ATCG00210hypothetical protein;electron transporter, transferring electrons within cytochrome b6/f complex of photosystem IIsCoding geneHOM001026 ORTHO000110
V ATCG00220PSII low MW protein;photosystem II reaction center protein MCoding geneHOM000550 ORTHO013224
V ATCG00230tRNA-Asp;rna_type=pre-trnaRNA gene
V ATCG00240tRNA-Tyr;rna_type=pre-trnaRNA gene
V ATCG00250this chloroplast gene encodes a UUC tRNA whose expression is regulated by SIG2.;rna_type=pre-trnaRNA gene
V ATCG00260tRNA-Thr;rna_type=pre-trnaRNA gene
V ATCG00270PSII D2 protein;photosystem II reaction center protein DCoding geneHOM000619 ORTHO002969
V ATCG00280chloroplast gene encoding a CP43 subunit of the photosystem II reaction center. promoter contains a blue-light responsive element.;photosystem II reaction center protein CCoding geneHOM000619 ORTHO002407
V ATCG00290tRNA-Ser;rna_type=pre-trnaRNA gene
V ATCG00300encodes PsbZ, which is a subunit of photosystem II. In Chlamydomonas, this protein has been shown to be essential in the interaction between PS II and the light harvesting complex II.;YCF9Coding geneHOM000619 ORTHO004311
V ATCG00310tRNA-Gly;rna_type=pre-trnaRNA gene
V ATCG00320tRNA-Phe;rna_type=pre-trnaRNA gene
V ATCG0033030S chloroplast ribosomal protein S14;chloroplast ribosomal protein S14Coding geneHOM000575 ORTHO005606
V ATCG00340Encodes the D1 subunit of photosystem I and II reaction centers.;Photosystem I, PsaA/PsaB proteinCoding geneHOM000575 ORTHO001434
V ATCG00350Encodes psaA protein comprising the reaction center for photosystem I along with psaB protein; hydrophobic protein encoded by the chloroplast genome.;Photosystem I, PsaA/PsaB proteinCoding geneHOM000575 ORTHO002664
X ATCG00360Encodes a protein required for photosystem I assembly and stability. In Chlamydomonas reinhardtii, this protein seems to act as a PSI specific chaperone facilitating the assembly of the complex by interacting with PsaA and PsaD. A loss of function mutation in tobacco leads to a loss of photosystem I.;Tetratricopeptide repeat (TPR)-like superfamily proteinCoding geneHOM002384 ORTHO006334
V ATCG00370tRNA-Ser;rna_type=pre-trnaRNA gene
V ATCG00380Chloroplast encoded ribosomal protein S4;chloroplast ribosomal protein S4Coding geneHOM002742 ORTHO001806
V ATCG00390tRNA-Thr;rna_type=pre-trnaRNA gene
V ATCG00400tRNA-Leu;rna_type=pre-trnaRNA gene
V ATCG00410chloroplast TRNF;rna_type=pre-trnaRNA gene
X ATCG00420Encodes NADH dehydrogenase subunit J. Its transcription is increased upon sulfur depletion.;NADH dehydrogenase subunit JCoding geneHOM000211 ORTHO002150
X ATCG00430Encodes a protein which was originally thought to be part of photosystem II but its wheat homolog was later shown to encode for subunit K of NADH dehydrogenase.;photosystem II reaction center protein GCoding geneHOM000211 ORTHO005609
V ATCG00440Encodes NADH dehydrogenase D3 subunit of the chloroplast NAD(P)H dehydrogenase complex;NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 proteinCoding geneHOM000211 ORTHO007019
V ATCG00450tRNA-Val;rna_type=pre-trnaRNA gene
V ATCG00460Chloroplast encoded tRNA-Met gene.;rna_type=pre-trnaRNA gene
V ATCG00470ATPase epsilon subunit;ATP synthase epsilon chainCoding geneHOM000211 ORTHO007549
V ATCG00480chloroplast-encoded gene for beta subunit of ATP synthase;ATP synthase subunit betaCoding geneHOM000211 ORTHO001337
X ATCG00490large subunit of RUBISCO. Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.;ribulose-bisphosphate carboxylasesCoding geneHOM000775 ORTHO001077
V ATCG00500Encodes the carboxytransferase beta subunit of the Acetyl-CoA carboxylase (ACCase) complex in plastids. This complex catalyzes the carboxylation of acetyl-CoA to produce malonyl-CoA, the first committed step in fatty acid synthesis.;acetyl-CoA carboxylase carboxyl transferase subunit betaCoding geneHOM002419 ORTHO005610
V ATCG00510Encodes subunit I of photosystem I.;photsystem I subunit ICoding geneHOM002419 ORTHO016531
V ATCG00520Encodes a protein required for photosystem I assembly and stability. In cyanobacteria, loss of function mutation in this gene increases PSII/PSI ratio without any influence on photoautotrophic growth.;unfolded protein bindingCoding geneHOM003137 ORTHO002663
X ATCG00530hypothetical protein;CemA-like proton extrusion protein-relatedCoding geneHOM001150 ORTHO009935
V ATCG00540Encodes cytochrome f apoprotein; involved in photosynthetic electron transport chain; encoded by the chloroplast genome and is transcriptionally repressed by a nuclear gene HCF2.;photosynthetic electron transfer ACoding geneHOM001150 ORTHO002149
V ATCG00550PSII component;photosystem II reaction center protein JCoding geneHOM006202 ORTHO148450
V ATCG00560PSII L protein;photosystem II reaction center protein LCoding geneHOM001436 ORTHO006120
V ATCG00570PSII cytochrome b559;photosystem II reaction center protein FCoding geneHOM006756 ORTHO010425
V ATCG00580PSII cytochrome b559. There have been many speculations about the function of Cyt b559, but the most favored at present is that it plays a protective role by acting as an electron acceptor or electron donor under conditions when electron flow through PSII is not optimized.;photosystem II reaction center protein ECoding geneHOM001436 ORTHO001236
X ATCG00590hypothetical protein;electron carriersCoding genesingleton
V ATCG00600Cytochrome b6-f complex, subunit V. Disruption of homologous gene in Chlamydomonas results in disruption of cytochrome b6-f complex.;PETGCoding geneHOM006438 ORTHO010426
V ATCG00610tRNA-Trp;rna_type=pre-trnaRNA gene
V ATCG00620tRNA-Pro;rna_type=pre-trnaRNA gene
V ATCG00630Encodes subunit J of photosystem I.;PSAJCoding geneHOM000215 ORTHO013725
V ATCG00640encodes a chloroplast ribosomal protein L33, a constituent of the large subunit of the ribosomal complex;ribosomal protein L33Coding geneHOM000215 ORTHO002968
V ATCG00650chloroplast-encoded ribosomal protein S18;ribosomal protein S18Coding geneHOM004406 ORTHO004310
V ATCG00660encodes a chloroplast ribosomal protein L20, a constituent of the large subunit of the ribosomal complex;ribosomal protein L20Coding geneHOM001874 ORTHO009220
V ATCG00065chloroplast gene encoding ribosomal protein s12. The gene is located in three distinct loci on the chloroplast genome and is transpliced to make one transcript.;ribosomal protein S12ACoding genesingleton
X ATCG00670Encodes the only ClpP (caseinolytic protease) encoded within the plastid genome. Contains a highly conserved catalytic triad of Ser-type proteases (Ser-His-Asp). Part of the 350 kDa chloroplast Clp complex. The name reflects nomenclature described in Adam et. al (2001).;plastid-encoded CLP PCoding geneHOM000202 ORTHO007021
V ATCG00680encodes for CP47, subunit of the photosystem II reaction center.;photosystem II reaction center protein BCoding geneHOM000462 ORTHO002967
V ATCG00690Encodes photosystem II 5 kD protein subunit PSII-T. This is a plastid-encoded gene (PsbTc) which also has a nuclear-encoded paralog (PsbTn).;photosystem II reaction center protein TCoding genesingleton
V ATCG00700PSII low MW protein;photosystem II reaction center protein NCoding geneHOM006468 ORTHO012655
X ATCG00710Encodes a 8 kD phosphoprotein that is a component of the photosystem II oxygen evolving core. Its exact molecular function has not been determined but it may play a role in mediating electron transfer between the secondary quinone acceptors, QA and QB, associated with the acceptor side of PSII.;photosystem II reaction center protein HCoding geneHOM000462 ORTHO002966
V ATCG00720Encodes the cytochrome b(6) subunit of the cytochrome b6f complex.;photosynthetic electron transfer BCoding geneHOM000462 ORTHO004309
V ATCG00730A chloroplast gene encoding subunit IV of the cytochrome b6/f complex;photosynthetic electron transfer DCoding geneHOM000462 ORTHO002965
V ATCG00740RNA polymerase alpha subunit;RNA polymerase subunit alphaCoding geneHOM001081 ORTHO001805
V ATCG0075030S chloroplast ribosomal protein S11;ribosomal protein S11Coding geneHOM001081 ORTHO002662
V ATCG00760encodes a chloroplast ribosomal protein L36, a constituent of the large subunit of the ribosomal complex;ribosomal protein L36Coding geneHOM000614 ORTHO258390
V ATCG00770chloroplast 30S ribosomal protein S8;ribosomal protein S8Coding geneHOM000614 ORTHO003780
V ATCG00780encodes a chloroplast ribosomal protein L14, a constituent of the large subunit of the ribosomal complex;ribosomal protein L14Coding geneHOM000614 ORTHO002148
V ATCG00790chloroplast gene encoding a ribosomal protein L16, which is a constituent of 50S large ribosomal subunit;ribosomal protein L16Coding geneHOM000614 ORTHO001799
V ATCG00800encodes a chloroplast ribosomal protein S3, a constituent of the small subunit of the ribosomal complex;structural constituent of ribosomeCoding geneHOM000739 ORTHO001954
V ATCG00810encodes a chloroplast ribosomal protein L22, a constituent of the large subunit of the ribosomal complex;ribosomal protein L22Coding geneHOM000739 ORTHO004308
V ATCG00820Encodes a 6.8-kDa protein of the small ribosomal subunit.;ribosomal protein S19Coding geneHOM000739 ORTHO000923
V ATCG00830encodes a chloroplast ribosomal protein L2, a constituent of the large subunit of the ribosomal complex;ribosomal protein L2Coding geneHOM000770 ORTHO000561
V ATCG00840One of two chloroplast genes that encode chloroplast ribosomal protein L23, a constituent of the large subunit of the ribosomal complex;ribosomal protein L23.1Coding geneHOM001724 ORTHO000441
V ATCG00850tRNA-Ile;rna_type=pre-trnaRNA gene
X ATCG00860Encodes an unknown protein. This gene is regulated by AtSIG6 transcriptionally.;Chloroplast Ycf2;ATPase, AAA type, coreCoding geneHOM000666 ORTHO001129
X ATCG00870hypothetical protein;Protein precursor Ycf15, putative, chloroplastCoding geneHOM007653 ORTHO015132
V ATCG00880tRNA-Leu;rna_type=pre-trnaRNA gene
V ATCG00890NADH dehydrogenase ND2;NADH-Ubiquinone/plastoquinone (complex I) proteinCoding geneHOM000482 ORTHO001792
V ATCG00900encodes a chloroplast ribosomal protein S7, a constituent of the small subunit of the ribosomal complex;Ribosomal protein S7p/S5e family proteinCoding geneHOM000482 ORTHO000656
V ATCG00905chloroplast gene encoding ribosomal protein s12. The gene is located in three distinct loci on the chloroplast genome and is transpliced to make one transcript.;ribosomal protein S12CCoding genesingleton
V ATCG00910tRNA-Val;rna_type=pre-trnaRNA gene
V ATCG00920chloroplast-encoded 16S ribosomal RNA;rna_type=rrnaRNA gene
V ATCG00930tRNA-Ile;rna_type=pre-trnaRNA gene
V ATCG00940tRNA-Ala;rna_type=pre-trnaRNA gene
V ATCG00950chloroplast-encoded 23S ribosomal RNA;rna_type=rrnaRNA gene
V ATCG00960Chloroplast-encoded 4.5S ribosomal RNA, which is a constituent of the 50S large subunit of plastidic ribosome.;rna_type=rrnaRNA gene
V ATCG00970chloroplast-encoded 5S ribosomal RNA;rna_type=rrnaRNA gene
V ATCG00980tRNA-Arg;rna_type=pre-trnaRNA gene
V ATCG00990tRNA-Asn;rna_type=pre-trnaRNA gene
X ATCG01000hypothetical protein;Ycf1 proteinCoding geneHOM001370 ORTHO008905
V ATCG01010Chloroplast encoded NADH dehydrogenase unit.;NADH-Ubiquinone oxidoreductase (complex I), chain 5 proteinCoding geneHOM001016 ORTHO003686
V ATCG01020encodes a chloroplast ribosomal protein L32, a constituent of the large subunit of the ribosomal complex;ribosomal protein L32Coding genesingleton
V ATCG01030tRNA-Leu;rna_type=pre-trnaRNA gene
X ATCG01040hypothetical protein;Cytochrome C assembly proteinCoding geneHOM000431 ORTHO006162
V ATCG01050Represents a plastid-encoded subunit of a NAD(P)H dehydrogenase complex. Its mRNA is edited at four positions. Translation data is not available for this gene.;NADH-Ubiquinone/plastoquinone (complex I) proteinCoding geneHOM001599 ORTHO007550
V ATCG01060Encodes the PsaC subunit of photosystem I.;iron-sulfur cluster binding;electron carriers;4 iron, 4 sulfur cluster bindingCoding geneHOM001197 ORTHO006163
V ATCG01070NADH dehydrogenase ND4L;NADH-ubiquinone/plastoquinone oxidoreductase chain 4LCoding geneHOM001197 ORTHO008325
V ATCG01080NADH dehydrogenase ND6;NADH:ubiquinone/plastoquinone oxidoreductase, chain 6Coding geneHOM001197 ORTHO008326
V ATCG01090Encodes subunit of the chloroplast NAD(P)H dehydrogenase complex;NADPH dehydrogenasesCoding geneHOM000491 ORTHO010535
V ATCG01100NADH dehydrogenase ND1;NADH dehydrogenase family proteinCoding geneHOM000491 ORTHO002592
X ATCG01110Encodes the 49KDa plastid NAD(P)H dehydrogenase subunit H protein. Its transcription is regulated by an ndhF-specific plastid sigma factor, SIG4.;NAD(P)H dehydrogenase subunit HCoding geneHOM000491 ORTHO003254
V ATCG01120encodes a chloroplast ribosomal protein S15, a constituent of the small subunit of the ribosomal complex;chloroplast ribosomal protein S15Coding geneHOM000775 ORTHO002094
X ATCG01130hypothetical protein;Ycf1 proteinCoding geneHOM001370 ORTHO008905
V ATCG01140tRNA-Asn;rna_type=pre-trnaRNA gene
V ATCG01150tRNA-Arg;rna_type=pre-trnaRNA gene
V ATCG01160Chloroplast-encoded 5S ribosomal RNA, which is a component of the 50S large subunit of the plastidic ribosome.;rna_type=rrnaRNA gene
V ATCG01170chloroplast-encoded 4.5S ribosomal RNA, which is part of the 50S large ribosomal subunit in plastids;rna_type=rrnaRNA gene
V ATCG01180chloroplast-encoded 23S ribosomal RNA;rna_type=rrnaRNA gene
V ATCG01190tRNA-Ala;rna_type=pre-trnaRNA gene
V ATCG01200tRNA-Ile;rna_type=pre-trnaRNA gene
V ATCG01210chloroplast-encoded 16S ribosomal RNA;rna_type=rrnaRNA gene
V ATCG01220tRNA-Val;rna_type=pre-trnaRNA gene
V ATCG01230chloroplast gene encoding ribosomal protein s12. The gene is located in three distinct loci on the chloroplast genome and is transpliced to make one transcript.;ribosomal protein S12BCoding genesingleton
V ATCG0124030S chloroplast ribosomal protein S7;ribosomal protein S7Coding geneHOM000482 ORTHO000656
V ATCG01250NADH dehydrogenase ND2;NADH-Ubiquinone/plastoquinone (complex I) proteinCoding geneHOM000482 ORTHO001792
V ATCG01260tRNA-Leu;rna_type=pre-trnaRNA gene
X ATCG01270hypothetical protein;Protein precursor Ycf15, putative, chloroplastCoding geneHOM007653 ORTHO015132
X ATCG01280hypothetical protein;Chloroplast Ycf2;ATPase, AAA type, coreCoding geneHOM000666 ORTHO001129
V ATCG01290tRNA-Ile;rna_type=pre-trnaRNA gene
V ATCG01300One of two chloroplast genes that encode chloroplast ribosomal protein L23, a constituent of the large subunit of the ribosomal complex;ribosomal protein L23Coding geneHOM001724 ORTHO000441
V ATCG01310encodes a chloroplast ribosomal protein L2, a constituent of the large subunit of the ribosomal complex;ribosomal protein L2Coding geneHOM000770 ORTHO000561