AppleGFDB:The Apple Gene Function & Gene Family DataBase v1.0
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Gene family

A gene family is a group of genes that share important characteristics. In many cases, genes in a family share a similar sequence of DNA building blocks (nucleotides). These genes provide instructions for making products (such as proteins) that have a similar structure or function. In other cases, dissimilar genes are grouped together in a family because proteins produced from these genes work together as a unit or participate in the same process.

Classifying individual genes into families helps researchers describe how genes are related to each other. Researchers can use gene families to predict the function of newly identified genes based on their similarity to known genes. Similarities among genes in a family can also be used to predict where and when a specific gene is active (expressed). Additionally, gene families may provide clues for identifying genes that are involved in particular diseases.

This part collected the gene families based on alignment to Arabidopsis genome. The Arabidopsis classification collection criteron was considered. Most genes in the same gene family have the similar protein structure and same functional domains. For these genes, we used MUSCLE (Edgar et al. 2004.) to generate a multiple sequence alignment for each Arabidopsis gene family. The multiple sequence alignment was then input into SAM 3.5 to build a hidden Markov model (HMM) for each family. Every gene sequence was aligned with each of these HMMs, and output an e-value. The lower the e-value is, the better fitness between the gene family sequence and a hidden Markov model. Thus, the gene was assigned into the family whose HMM produces the lowest e-value.

 

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Transcription Factor Families
ABI3VP1 CAMTA LIM TAZ
Alfin-like CCAAT LOB TCP
AP2-EREBP CSD MADS Tify
ARF DBP mTERF Trihelix
ARR-B E2F-DP MYB TUB
BBR-BPC EIL MYB-related ULT
BES1 FAR1 NAC VOZ
bHLH FHA OFP WRKY
BSD G2-like PBF-2-like zf-HD
bZIP GeBP PLATZ
C2C2-CO-like GRAS RWP-RK
C2C2-Dof GRF S1Fa-like
C2C2-GATA HB SAP
C2C2-YABBY HRT SBP
C2H2 HSF Sigma70-like
C3H LFY SRS
Other Transcriptional Regulators
ARID IWS1 PHD SWI-SNF-BAF60b
AUX-IAA Jumonji Pseudo ARR-B SWI-SNF-SWI3
Coactivator p15 LUG RB TRAF
DDT MBF1 Rcd1-like
GNAT MED6 SET
HMG MED7 SNF2
Protein Kinases Gene families
LysM ATN1-like Protein Kinase
RLCK VIII Light-Sensory Kinase
RLCK VII Ankyrin Repeat Domain Protein Kinase
CRPK1L-1 CTR1-EDR1-like Protein Kinase
LRR VIII-1 GmPK6-AtMRK1-like Protein Kinase
LRR I and URK I ATN1-like Protein Kinase
Crinkly 4_Like C-terminal Ankyrin Repeat Domain Kinase
Wall Associated Kinase-Like Casein Kinase I
LRK10L-1 Non-Transmembrane Protein Kinases
RLCK IV MAP3K
LRR IX STE20-PAK1-like Protein Kinase (MAP4K)
PERK-Like MAPKK
RLCK V Possible MAPKK
RKF-Like3 WNK like kinase with no lysine kinase
S-Domain Kinase (Type 1) APG1-like Protein Kinase
DUF26 Kinase Calcium Dependent Protein Kinase (CPK)
LRR I Phosphoenolpyruvate Carboxylase Kinase (PPCK)
CRPK1l-1, CRPK1L-2, Thaumatin, and LRK10L-2 Calcium-Calmodulin Dependent Protein Kinase (CCamK)
S-Domain Kinase (Type 2) SNF1-related Protein Kinase (SnRK)
RLCK VI IRE-NPH-Phosphoinositide dependent-Ribosomal Protein S6 Kinase
Legume Lectin Domain Kinase ELM1-PAK1-TOS3-like Protein Kinase
LRR X Mitogen Activated Protein Kinase (MAPK)
LRR II and LRR X Male grem cell-associated kinase (mak)
LRR VII CDC2 Kinase (CDC2 Like Kinase Family)
LRR XI and LRR XII Casein Kinase II
LRR IV GSK3-Shaggy Like Protein Kinase
LRR III LAMMER Protein Kinase
Crinkly 4-Like
RLCK IX
RLCK I
LRR VI
RLCK II
Wall Associated Kinase
Other Families
14-3-3 family Nin-like Gene Family
ABC Superfamily NLP Transcription Factor Family
Acyl Lipid Metabolism Gene Families Nodulin-like Gene Family
AGC Kinase Gene Family Non-SMC Element family
Aldehyde Dehydrogenase Gene Family Nucleobase Ascorbate Transporter Gene Family
Amino Acid-Auxin Permease AAAP Family Organic Solute Cotransporters Gene Family
Antiporter super family Orphan Transcription Factor Family
Antiporters Pectate lyase family
Aquaporins Pectin acetylesterase family protein
ARIADNE Family Pectin lyase-like superfamily protein
AS2 family Pectin methylesterase inhibitor superfamily
B3 DNA Binding Superfamily Pectin methylesterase inhibitor superfamily protein
BES1 Gene Family PHD Gene Family
Calcium Dependent Protein Kinase Phospholipase D Gene Family
Calmodulin-binding Proteins Gene Family Phytocyanin Superfamily
Carbohydrate Esterase Gene Families Plant Defensins Gene Families
CBL-interacting protein kinase Pollen Coat Proteome Gene Family
CBL-interacting serine-threonine protein kinases Polysaccharide Lyase
Cell Wall Biosynthesis Gene Families PP2C-type Phosphatase Gene Family
Chloroplast and Mitochondria Gene Families Primary Pumps ATPases Gene Family
COBRA Gene Family Protein tyrosine phosphatase (PTP) family
Core Cell Cycle Gene Family PRT Gene Family
Core DNA Replication Machinery Family Purine permease Gene Family
Cytochrome b5 RAD5-RAD16-like Gene Family
Cytochrome P450 Rapid Response to Elicitors Gene Family
Cytoplasmic Ribosomal Protein Gene Family RAV Transcription Factor Family
Cytoskeleton Gene Families RCI2 Gene Family
DBB Gene Family Receptor kinase-like Gene Family
EF-hand containing proteins Response Regulator Gene Family
Equilibrative Nucleoside Transporter Gene Family (ENT) RING finger gene family
ERF Gene Family RKD Transcription Factor Family
Eukaryotic Initiation Factors Gene Family S1Fa-like Gene Family
EXO70 exocyst subunit family SAP Gene Family
Expansin Gene Family SBP Transcription Factor Family
F-Box Gene Family SNARE and Associated Proteins Gene Family
FH2 protein Gene Family SRS Gene Family
FRS (FAR1 Related) transcription factor family STAT Gene Family
FtsH Gene Family Strubbelig Receptor Gene Family
Glutamine Dumper (GDU) Family Structural Maintenance of Chromosomes family
Glutathione S-transferase Gene Family Subtilisin-like Serine Gene Family
Glycoside Hydrolase Sucrose Transporter Gene Family
Glycosyltransferase Gene Family Sulfurtransferasese-Rhodanese
Histidine Kinase Gene Family TALE Gene Family
Histidine Phosphotransfer Proteins Tify Gene Family
IAA Gene Family Trehalose Biosynthesis Gene Families
IDZ Gene Family V-Type ATPase Gene Family
Inorganic Solute Cotransporter Gene Families Wox Gene Family
Ion Channels Gene Family Xyloglucan Fucosyltransferase
IQD Protein Family
JAZ Gene Family
JUMONJI Transcription Factor Family
Kinesins gene family
Lateral Organ Boundaries Gene Family
LBD Gene Family
Leucine-rich Repeat extensin Gene Families
LFY Gene Family
Lipid Metabolism Gene Family
LSD Gene Family
Major Intrinsic Protein MIP
Mechanosensitive Ion Channel Family
Miscellaneous Gene Family
MLO family
Monolignol Biosynthesis Gene Families
Monosaccharide Transporter(-like) Gene Family
MRS2 Gene Family
M-type Gene Family
Myosins gene family
NADPH P450 reductases Gene Family
NF-X1 Gene Family
NF-YA Gene Family
NF-YB Gene Family
NF-YC Gene Family
Nicotianamine Synthase Gene Family
 

 

Submit Your Gene Family
Submit by ***Input Your Name, Necessary
URL Input Your Lab or your pubilication URL. Not Necessary
Publication PMID Not Necessary
Gene Family ***Input Your Gene Family Name, Necessary
Related MDPIDs ( ONE per row, without no other characters)
After your submission, please contact us by Email to gfdb@sdau.edu.cn. After the confirmation of the webmaster, the gene family will be online later.

 


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