Citrus Sinensis ID: 027848

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------22
Protein Sequence
MSQSSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGKFEFLLVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWNIPRKGLMIIRIHILKVRF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccEEccEEcHHHHHHHHHHHcccHHHHHccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHcccccccccccccccccccEEEEEEccEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccHHcccccccHHHHHHHHHHHHHHcccccEEEEEcccEEcHHHHHHHHHHccccHHHHcHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHEEEccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEEEc
Coil and Loop (DISEMBL)
msqssaaktkgrsvvedklypaplsshedvskdpivFWDTLRRFHFImgtkfmipviggkeLDLHVLYVEATTRGGYEKVVAEKKWrevgavfkfsptttsasFVLRKHYLTLLYHYEQVHFfkmqgppcvpsgkfEFLLVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWniprkglmIIRIHILKVRF
Flexible Loop (DISEMBL)
msqssaaktkgrsvvedklypaplsshedvskdpiVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEAttrggyekvvAEKKWREVGAvfkfsptttsasfVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGKFEFLLVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWNIPRKGLMIIRIHILKVRF
Low Complexity Region (SEG)
MSQSSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGKFEFLLVQQYLRVTCSEFFVFYHQiltrlclllfglfvglilfitlQQLHFLFTALRAGLAWLLWNIPRKGLMIIRIHILKVRF
Disordered region (IsUnstruct)
********************************DPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGKFEFLLVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWNIPRKGLMIIRIHILKV**
Disordered Region (DISOPRED)
***********************************VFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHF******************************************LLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWNIPRKGLMIIRIHILKVRF
Disordered Region (DISEMBL)
*************VVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGKFEFLLVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWNIPRKGLMIIRIHILKVRF
Disordered Region (DISPRO)
*******************YPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQG************LVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWNIPRKGLMIIRIHILKVRF
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiHHHHHHHHHHHHHHHHooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSQSSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGKFEFLLVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWNIPRKGLMIIRIHILKVRF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	218	2.2.26 [Sep-21-2011]
Q9SGS2	338	High mobility group B pro	yes	no	0.509	0.328	0.801	2e-46
Q9MAT6	448	High mobility group B pro	no	no	0.688	0.334	0.404	2e-30
Q9LG02	337	Putative high mobility gr	no	no	0.458	0.296	0.450	5e-22
Q9LTT3	319	High mobility group B pro	no	no	0.486	0.332	0.422	7e-20
Q68CP9	1835	AT-rich interactive domai	yes	no	0.435	0.051	0.437	3e-17
P29375	1690	Lysine-specific demethyla	no	no	0.431	0.055	0.357	9e-10
Q3UXZ9	1690	Lysine-specific demethyla	no	no	0.431	0.055	0.357	1e-09
Q9VMJ7	1838	Lysine-specific demethyla	yes	no	0.536	0.063	0.286	1e-07
Q5XGD9	541	AT-rich interactive domai	no	no	0.376	0.151	0.397	1e-07
Q6GQD7	539	AT-rich interactive domai	N/A	no	0.376	0.152	0.397	1e-07

>sp|Q9SGS2|HMGB9_ARATH High mobility group B protein 9 OS=Arabidopsis thaliana GN=HMGB9 PE=2 SV=1

 Score =  185 bits (469), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 89/111 (80%), Positives = 93/111 (83%)

Query: 18  KLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGY 77
           K YP PL+ HE V KD  VFWDTLRRFH IM TKFMIPVIGGKELDLHVLYVE T RGGY
Sbjct: 25  KEYPEPLALHEVVVKDSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGY 84

Query: 78  EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGP 128
           EKVV EKKWREVG VF+FS TTTSASFVLRKHYL LL+HYEQVH F  +GP
Sbjct: 85  EKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYEQVHLFTARGP 135

Binds preferentially DNA with A/T-rich content.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9MAT6|HMG15_ARATH High mobility group B protein 15 OS=Arabidopsis thaliana GN=HMGB15 PE=2 SV=1

 Score =  132 bits (331), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 68/168 (40%), Positives = 104/168 (61%), Gaps = 18/168 (10%)

Query: 4   SSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELD 63
           +S++  K  SV  + +   P +++E V  DP +F  +L R H ++GTKFM+P+IGG++LD
Sbjct: 2   ASSSCLKQGSVPMNNVCVTPEATYEAVVADPRLFMTSLERLHSLLGTKFMVPIIGGRDLD 61

Query: 64  LHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
           LH L+VE T+RGG  K++ E++W+EV A F F PT T+AS+VLRK+Y +LL +YEQ++FF
Sbjct: 62  LHKLFVEVTSRGGINKILNERRWKEVTATFVFPPTATNASYVLRKYYFSLLNNYEQIYFF 121

Query: 124 K---------MQGP---PCV------PSGKFEFLLVQQYLRVTCSEFF 153
           +         MQ P   PC       PS + + L      ++  +EF 
Sbjct: 122 RSNGQIPPDSMQSPSARPCFIQGAIRPSQELQALTFTPQPKINTAEFL 169

Binds preferentially DNA with A/T-rich content.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LG02|HMG11_ARATH Putative high mobility group B protein 11 OS=Arabidopsis thaliana GN=HMGB11 PE=3 SV=2

 Score =  104 bits (259), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 46/102 (45%), Positives = 71/102 (69%), Gaps = 2/102 (1%)

Query: 27  HEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKW 86
           ++D+ ++P +FW+ LR FH     KF IP++GGK LDLH L+ E T+RGG EKV+ +++ 
Sbjct: 30  YQDIVRNPELFWEMLRDFHESSDKKFKIPIVGGKSLDLHRLFNEVTSRGGLEKVIKDRRC 89

Query: 87  REVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGP 128
           +EV   F F  T T+++FVLRK YL +L+ +E +++F  Q P
Sbjct: 90  KEVIDAFNFKTTITNSAFVLRKSYLKMLFEFEHLYYF--QAP 129

Binds preferentially DNA with A/T-rich content.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LTT3|HMG10_ARATH High mobility group B protein 10 OS=Arabidopsis thaliana GN=HMGB10 PE=2 SV=1

 Score = 97.4 bits (241), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 46/109 (42%), Positives = 69/109 (63%), Gaps = 3/109 (2%)

Query: 16  EDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRG 75
           +D   PA    ++D+ ++  +FW+ LR F  +      +P +GG  LDLH L++E T+RG
Sbjct: 28  DDSSVPA---KYDDLVRNSALFWEKLRAFLGLTSKTLKVPTVGGNTLDLHRLFIEVTSRG 84

Query: 76  GYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFK 124
           G E+VV ++KW+EV   F F  T TSASFVLRK+YL  L+  E V++ +
Sbjct: 85  GIERVVKDRKWKEVIGAFSFPTTITSASFVLRKYYLKFLFQLEHVYYLE 133

Binds preferentially DNA with A/T-rich content.

Arabidopsis thaliana (taxid: 3702)

>sp|Q68CP9|ARID2_HUMAN AT-rich interactive domain-containing protein 2 OS=Homo sapiens GN=ARID2 PE=1 SV=2

 Score = 88.6 bits (218), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 42/96 (43%), Positives = 59/96 (61%), Gaps = 1/96 (1%)

Query: 29  DVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWR 87
           D  +  + F D LR+FH   G+ F  IP +GGKELDLH LY   TT GG+ KV  + +W 
Sbjct: 11  DERRKGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWG 70

Query: 88  EVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
           E+   F F  + ++A+F L+++YL  L  YE+VH F
Sbjct: 71  EIVEEFNFPRSCSNAAFALKQYYLRYLEKYEKVHHF 106

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Required for the stability of the SWI/SNF chromatin remodeling complex SWI/SNF-B (PBAF). May be involved in targeting the complex to different genes. May be involved in regulating transcriptional activation of cardiac genes.

Homo sapiens (taxid: 9606)

>sp|P29375|KDM5A_HUMAN Lysine-specific demethylase 5A OS=Homo sapiens GN=KDM5A PE=1 SV=3

 Score = 63.9 bits (154), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 1/95 (1%)

Query: 24  LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
           L+  E +++  + F D L +F  + G+   IPV+  K LDL+ L     ++GG+E V  E
Sbjct: 77  LNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKE 136

Query: 84  KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
           KKW +VG+   + P   + S +L+ HY  +LY YE
Sbjct: 137 KKWSKVGSRLGYLPGKGTGS-LLKSHYERILYPYE 170

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May stimulate transcription mediated by nuclear receptors. May be involved in transcriptional regulation of Hox proteins during cell differentiation. May participate in transcriptional repression of cytokines such as CXCL12.

Homo sapiens (taxid: 9606)

EC: 1

EC: .

EC: 1

EC: 4

EC: .

EC: 1

EC: 1

EC: .

EC: -

>sp|Q3UXZ9|KDM5A_MOUSE Lysine-specific demethylase 5A OS=Mus musculus GN=Kdm5a PE=1 SV=2

 Score = 63.2 bits (152), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 1/95 (1%)

Query: 24  LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
           L+  E +++  + F D L +F  + G+   IPV+  K LDL+ L     ++GG+E V  E
Sbjct: 77  LNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEIVTKE 136

Query: 84  KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
           KKW +VG+   + P   + S +L+ HY  +LY YE
Sbjct: 137 KKWSKVGSRLGYLPGKGTGS-LLKSHYERILYPYE 170

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May stimulate transcription mediated by nuclear receptors. Involved in transcriptional regulation of Hox proteins during cell differentiation. May participate in transcriptional repression of cytokines such as CXCL12.

Mus musculus (taxid: 10090)

EC: 1

EC: .

EC: 1

EC: 4

EC: .

EC: 1

EC: 1

EC: .

EC: -

>sp|Q9VMJ7|KDM5_DROME Lysine-specific demethylase lid OS=Drosophila melanogaster GN=lid PE=1 SV=1

 Score = 56.6 bits (135), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/122 (28%), Positives = 60/122 (49%), Gaps = 5/122 (4%)

Query: 17  DKLYPAP----LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEAT 72
           DKL   P    L+  E  ++  + F D + +F  + G+   IP++  K LDL+ L+    
Sbjct: 208 DKLRFVPRVQRLNELEAKTRVKLNFLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQ 267

Query: 73  TRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVP 132
             GG E+   ++KW +V    ++ P++ S    L+ HY  +L+ +E     K+ GP    
Sbjct: 268 EEGGMEQTTKDRKWAKVANRMQY-PSSKSVGATLKAHYERILHPFEVYTSGKVLGPTPTS 326

Query: 133 SG 134
           SG
Sbjct: 327 SG 328

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Specifically demethylates trimethylated H3 'Lys-4'. Required for the correct regulation of homeotic genes during development.

Drosophila melanogaster (taxid: 7227)

EC: 1

EC: .

EC: 1

EC: 4

EC: .

EC: 1

EC: 1

EC: .

EC: -

>sp|Q5XGD9|ARI3A_XENTR AT-rich interactive domain-containing protein 3A OS=Xenopus tropicalis GN=arid3a PE=2 SV=1

 Score = 56.6 bits (135), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 37  FWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D L  F    GT    IP++  + LDL++LYV  T +GG  +V+ +K WRE+      
Sbjct: 218 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYMLYVLVTEKGGLVEVINKKLWREITKGLNL 277

Query: 96  SPTTTSASFVLRKHYLTLLYHYE 118
             + TSA+F LR  Y+  LY YE
Sbjct: 278 PTSITSAAFTLRTQYMKYLYPYE 300

Transcription factor required for smad1 and smad2-mediated responses to TGFbeta during mesoderm induction.

Xenopus tropicalis (taxid: 8364)

>sp|Q6GQD7|ARI3A_XENLA AT-rich interactive domain-containing protein 3A OS=Xenopus laevis GN=arid3a PE=2 SV=1

 Score = 56.6 bits (135), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 37  FWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D L  F    GT    IP++  + LDL++LYV  T +GG  +V+ +K WRE+      
Sbjct: 215 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYMLYVLVTEKGGLVEVINKKLWREITKGLNL 274

Query: 96  SPTTTSASFVLRKHYLTLLYHYE 118
             + TSA+F LR  Y+  LY YE
Sbjct: 275 PTSITSAAFTLRTQYMKYLYPYE 297

Transcription factor required for smad1 and smad2-mediated responses to TGFbeta during mesoderm induction.

Xenopus laevis (taxid: 8355)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	218
224085968	329	high mobility group family [Populus tric	0.637	0.422	0.709	6e-53
307136305	324	high mobility group family [Cucumis melo	0.619	0.416	0.748	4e-52
118487139	317	unknown [Populus trichocarpa]	0.587	0.403	0.744	9e-52
449455571	324	PREDICTED: high mobility group B protein	0.619	0.416	0.740	6e-51
356508987	322	PREDICTED: high mobility group B protein	0.591	0.400	0.770	2e-50
255539100	338	transcription factor, putative [Ricinus	0.587	0.378	0.726	3e-49
297842355	338	high mobility group family protein [Arab	0.545	0.352	0.781	9e-47
15222957	338	high mobility group-box and ARID domain-	0.509	0.328	0.801	1e-44
32490476	306	glutathione S-transferase GST 16 - like	0.633	0.450	0.572	4e-38
298205254	483	unnamed protein product [Vitis vinifera]	0.577	0.260	0.558	2e-35

>gi|224085968|ref|XP_002307758.1| high mobility group family [Populus trichocarpa] gi|222857207|gb|EEE94754.1| high mobility group family [Populus trichocarpa]

 Score =  213 bits (541), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 105/148 (70%), Positives = 119/148 (80%), Gaps = 9/148 (6%)

Query: 4   SSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELD 63
           S  +K K ++ +E+K YPAPL+SHEDV  DP VFWDTLRRFHF+MGTKFMIPVIGGKELD
Sbjct: 2   SPGSKRKLKAGMENKHYPAPLASHEDVVNDPSVFWDTLRRFHFVMGTKFMIPVIGGKELD 61

Query: 64  LHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
           L VLYVE T RGGY+KVVAEKKWREVG+VF FS TTTSASFVL+KHY +LLYHYEQVHFF
Sbjct: 62  LQVLYVETTNRGGYDKVVAEKKWREVGSVFCFSATTTSASFVLKKHYFSLLYHYEQVHFF 121

Query: 124 KMQGP---PCV------PSGKFEFLLVQ 142
           K+QGP   P V      PS K E  +V+
Sbjct: 122 KIQGPVSTPAVAFPLGSPSSKTELAIVE 149

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136305|gb|ADN34129.1| high mobility group family [Cucumis melo subsp. melo]

 Score =  210 bits (534), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 101/135 (74%), Positives = 112/135 (82%)

Query: 4   SSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELD 63
           S  A+TK  +   DK YP PL++H++V  DPIVFWDTLRRFHF+M TKFMIPVIGGKELD
Sbjct: 2   SPPARTKTWNGGLDKHYPPPLATHDEVISDPIVFWDTLRRFHFMMNTKFMIPVIGGKELD 61

Query: 64  LHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
           LHVLY E T RGG+EKVVAEKKWREVG+VFKFSPTTTSASFVLRKHYL+LLYHYEQV+ F
Sbjct: 62  LHVLYSEVTRRGGHEKVVAEKKWREVGSVFKFSPTTTSASFVLRKHYLSLLYHYEQVYLF 121

Query: 124 KMQGPPCVPSGKFEF 138
             QGP CVP   F F
Sbjct: 122 GRQGPICVPQAPFSF 136

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118487139|gb|ABK95398.1| unknown [Populus trichocarpa]

 Score =  209 bits (531), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 102/137 (74%), Positives = 113/137 (82%), Gaps = 9/137 (6%)

Query: 15  VEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTR 74
           +E+K YPAPL+SHEDV  DP VFWDTLRRFHF+MGTKFMIPVIGGKELDL VLYVE T R
Sbjct: 1   MENKHYPAPLASHEDVVNDPSVFWDTLRRFHFVMGTKFMIPVIGGKELDLQVLYVETTNR 60

Query: 75  GGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGP---PCV 131
           GGY+KVVAEKKWREVG+VF FS TTTSASFVL+KHY +LLYHYEQVHFFK+QGP   P V
Sbjct: 61  GGYDKVVAEKKWREVGSVFCFSATTTSASFVLKKHYFSLLYHYEQVHFFKIQGPVSTPAV 120

Query: 132 ------PSGKFEFLLVQ 142
                 PS K E  +V+
Sbjct: 121 AFPLGSPSSKTELAIVE 137

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455571|ref|XP_004145526.1| PREDICTED: high mobility group B protein 9-like [Cucumis sativus] gi|449519744|ref|XP_004166894.1| PREDICTED: high mobility group B protein 9-like [Cucumis sativus]

 Score =  206 bits (524), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 100/135 (74%), Positives = 111/135 (82%)

Query: 4   SSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELD 63
           S  A+TK  +   DK YP  L++H++V  DPIVFWDTLRRFHF+M TKFMIPVIGGKELD
Sbjct: 2   SPPARTKTWNGGLDKHYPPSLATHDEVISDPIVFWDTLRRFHFMMNTKFMIPVIGGKELD 61

Query: 64  LHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
           LHVLY E T RGG+EKVVAEKKWREVG+VFKFSPTTTSASFVLRKHYL+LLYHYEQV+ F
Sbjct: 62  LHVLYSEVTRRGGHEKVVAEKKWREVGSVFKFSPTTTSASFVLRKHYLSLLYHYEQVYLF 121

Query: 124 KMQGPPCVPSGKFEF 138
             QGP CVP   F F
Sbjct: 122 GRQGPICVPQAPFPF 136

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508987|ref|XP_003523234.1| PREDICTED: high mobility group B protein 9-like [Glycine max]

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 101/131 (77%), Positives = 109/131 (83%), Gaps = 2/131 (1%)

Query: 4   SSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELD 63
           SSAA+T G    E K YPAPL+ HE V KD  +FWDTLRRFHF+MGTKFMIPVIGGKELD
Sbjct: 2   SSAARTPGGE--EGKHYPAPLAPHEGVVKDSTLFWDTLRRFHFVMGTKFMIPVIGGKELD 59

Query: 64  LHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
           LHVLYVE T R GYEKVVAEKKWREVG+VFKF+ TTTSASFVLRKHY +LLYHYEQVHFF
Sbjct: 60  LHVLYVEVTRRSGYEKVVAEKKWREVGSVFKFAATTTSASFVLRKHYFSLLYHYEQVHFF 119

Query: 124 KMQGPPCVPSG 134
           K +GP   PS 
Sbjct: 120 KARGPIYTPSA 130

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539100|ref|XP_002510615.1| transcription factor, putative [Ricinus communis] gi|223551316|gb|EEF52802.1| transcription factor, putative [Ricinus communis]

 Score =  200 bits (509), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 93/128 (72%), Positives = 107/128 (83%)

Query: 1   MSQSSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGK 60
           MS ++        V + + YP PL+SH+ + +DPI FWDTLRRFH +M TKFMIPVIGG+
Sbjct: 1   MSPATKKIALDHEVEKTRHYPTPLASHDKIVEDPITFWDTLRRFHSLMSTKFMIPVIGGR 60

Query: 61  ELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQV 120
           ELDLH+LYVEAT RGGYEKVVA+KKWREVG+VFKFSPTTTSASFVLRKHY  LLYHYEQV
Sbjct: 61  ELDLHILYVEATKRGGYEKVVADKKWREVGSVFKFSPTTTSASFVLRKHYFGLLYHYEQV 120

Query: 121 HFFKMQGP 128
           HFFK+QGP
Sbjct: 121 HFFKVQGP 128

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297842355|ref|XP_002889059.1| high mobility group family protein [Arabidopsis lyrata subsp. lyrata] gi|297334900|gb|EFH65318.1| high mobility group family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  192 bits (487), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 93/119 (78%), Positives = 98/119 (82%)

Query: 18  KLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGY 77
           K YP PL+SHE V KD  VFWDTLRRFH IM TKFMIPVIGGKELDLHVLYVE T RGGY
Sbjct: 25  KEYPEPLASHEVVVKDSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGY 84

Query: 78  EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGKF 136
           EKVVAEKKWREVG VF+FS TTTSASFVLRKHYL LL+HYEQVH F  +GP   P+  F
Sbjct: 85  EKVVAEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYEQVHLFTARGPLLHPTATF 143

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15222957|ref|NP_177738.1| high mobility group-box and ARID domain-binding domain-containing protein [Arabidopsis thaliana] gi|75265821|sp|Q9SGS2.1|HMGB9_ARATH RecName: Full=High mobility group B protein 9; AltName: Full=Nucleosome/chromatin assembly factor group D 09; Short=Nucleosome/chromatin assembly factor group D 9 gi|6573729|gb|AAF17649.1|AC009978_25 T23E18.4 [Arabidopsis thaliana] gi|20466328|gb|AAM20481.1| unknown protein [Arabidopsis thaliana] gi|31711812|gb|AAP68262.1| At1g76110 [Arabidopsis thaliana] gi|332197676|gb|AEE35797.1| high mobility group-box and ARID domain-binding domain-containing protein [Arabidopsis thaliana]

 Score =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 89/111 (80%), Positives = 93/111 (83%)

Query: 18  KLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGY 77
           K YP PL+ HE V KD  VFWDTLRRFH IM TKFMIPVIGGKELDLHVLYVE T RGGY
Sbjct: 25  KEYPEPLALHEVVVKDSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGY 84

Query: 78  EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGP 128
           EKVV EKKWREVG VF+FS TTTSASFVLRKHYL LL+HYEQVH F  +GP
Sbjct: 85  EKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYEQVHLFTARGP 135

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|32490476|dbj|BAC79159.1| glutathione S-transferase GST 16 - like protein [Oryza sativa Japonica Group] gi|125564567|gb|EAZ09947.1| hypothetical protein OsI_32246 [Oryza sativa Indica Group] gi|125606508|gb|EAZ45544.1| hypothetical protein OsJ_30204 [Oryza sativa Japonica Group]

 Score =  163 bits (413), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 79/138 (57%), Positives = 99/138 (71%)

Query: 14  VVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATT 73
           + E  LYP PL SHE+V+ D   F DTLRRFH +MGTKFMIPVIGGKE+DLH LYVE T+
Sbjct: 1   MAEKLLYPPPLLSHEEVANDRAAFMDTLRRFHSLMGTKFMIPVIGGKEMDLHALYVEVTS 60

Query: 74  RGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPS 133
           RGG  KV+ E+KWREV A F F  TTTSAS+VLR++YL+LL+HYEQV+FF+  G    P+
Sbjct: 61  RGGLAKVMEERKWREVMARFSFPATTTSASYVLRRYYLSLLHHYEQVYFFRAHGALLRPA 120

Query: 134 GKFEFLLVQQYLRVTCSE 151
                   ++ +R T  +
Sbjct: 121 ASALTKTPRRKMRGTSDQ 138

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298205254|emb|CBI17313.3| unnamed protein product [Vitis vinifera]

 Score =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/129 (55%), Positives = 97/129 (75%), Gaps = 3/129 (2%)

Query: 2   SQSSAAKT---KGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIG 58
           SQSSA ++   +  +V     YP PL+ +ED+   P +F  TL + H +MGTKFMIP+IG
Sbjct: 25  SQSSANQSPSLRNETVSNYHPYPPPLAKYEDIVSSPKLFMGTLEKLHAVMGTKFMIPIIG 84

Query: 59  GKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
           GKELDLH L+VE T+RGG EK++ E++W+EV AVF F  T T+ASFVLRK+Y++LL+HYE
Sbjct: 85  GKELDLHRLFVEVTSRGGLEKIIRERRWKEVTAVFSFPSTATNASFVLRKYYVSLLHHYE 144

Query: 119 QVHFFKMQG 127
           Q++FFK QG
Sbjct: 145 QIYFFKAQG 153

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	218
TAIR|locus:2199824	338	AT1G76110 [Arabidopsis thalian	0.545	0.352	0.764	7.1e-45
TAIR|locus:2010587	448	AT1G04880 [Arabidopsis thalian	0.582	0.283	0.488	6.2e-30
TAIR|locus:2020517	337	AT1G55650 [Arabidopsis thalian	0.449	0.290	0.448	7e-22
TAIR|locus:2088160	319	AT3G13350 [Arabidopsis thalian	0.486	0.332	0.422	4.9e-21
UNIPROTKB|E1C9H0	1831	ARID2 "Uncharacterized protein	0.449	0.053	0.444	3e-17
UNIPROTKB|Q68CP9	1835	ARID2 "AT-rich interactive dom	0.435	0.051	0.437	9.2e-16
ZFIN|ZDB-GENE-030131-6311	1573	arid2 "AT rich interactive dom	0.399	0.055	0.454	1.8e-14
UNIPROTKB|E2RFL8	1836	ARID2 "Uncharacterized protein	0.435	0.051	0.375	2.7e-11
DICTYBASE|DDB_G0275333	478	DDB_G0275333 "ARID/BRIGHT DNA	0.380	0.173	0.406	1.1e-10
UNIPROTKB|F5H1F7	1636	KDM5A "Lysine-specific demethy	0.431	0.057	0.357	3.2e-09

TAIR|locus:2199824 AT1G76110 [Arabidopsis thaliana (taxid:3702)]

 Score = 472 (171.2 bits), Expect = 7.1e-45, P = 7.1e-45
 Identities = 91/119 (76%), Positives = 95/119 (79%)

Query:    18 KLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGY 77
             K YP PL+ HE V KD  VFWDTLRRFH IM TKFMIPVIGGKELDLHVLYVE T RGGY
Sbjct:    25 KEYPEPLALHEVVVKDSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGY 84

Query:    78 EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGKF 136
             EKVV EKKWREVG VF+FS TTTSASFVLRKHYL LL+HYEQVH F  +GP   P   F
Sbjct:    85 EKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYEQVHLFTARGPLLHPIATF 143

GO:0003677 "DNA binding" evidence=IEA;IDA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA;TAS

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2010587 AT1G04880 [Arabidopsis thaliana (taxid:3702)]

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 64/131 (48%), Positives = 94/131 (71%)

Query:     1 MSQSSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGK 60
             M+ SS  K +G SV  + +   P +++E V  DP +F  +L R H ++GTKFM+P+IGG+
Sbjct:     1 MASSSCLK-QG-SVPMNNVCVTPEATYEAVVADPRLFMTSLERLHSLLGTKFMVPIIGGR 58

Query:    61 ELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQV 120
             +LDLH L+VE T+RGG  K++ E++W+EV A F F PT T+AS+VLRK+Y +LL +YEQ+
Sbjct:    59 DLDLHKLFVEVTSRGGINKILNERRWKEVTATFVFPPTATNASYVLRKYYFSLLNNYEQI 118

Query:   121 HFFKMQG--PP 129
             +FF+  G  PP
Sbjct:   119 YFFRSNGQIPP 129

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

TAIR|locus:2020517 AT1G55650 [Arabidopsis thaliana (taxid:3702)]

 Score = 255 (94.8 bits), Expect = 7.0e-22, P = 7.0e-22
 Identities = 44/98 (44%), Positives = 70/98 (71%)

Query:    27 HEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKW 86
             ++D+ ++P +FW+ LR FH     KF IP++GGK LDLH L+ E T+RGG EKV+ +++ 
Sbjct:    30 YQDIVRNPELFWEMLRDFHESSDKKFKIPIVGGKSLDLHRLFNEVTSRGGLEKVIKDRRC 89

Query:    87 REVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFK 124
             +EV   F F  T T+++FVLRK YL +L+ +E +++F+
Sbjct:    90 KEVIDAFNFKTTITNSAFVLRKSYLKMLFEFEHLYYFQ 127

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2088160 AT3G13350 [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/109 (42%), Positives = 69/109 (63%)

Query:    16 EDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRG 75
             +D   PA    ++D+ ++  +FW+ LR F  +      +P +GG  LDLH L++E T+RG
Sbjct:    28 DDSSVPA---KYDDLVRNSALFWEKLRAFLGLTSKTLKVPTVGGNTLDLHRLFIEVTSRG 84

Query:    76 GYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFK 124
             G E+VV ++KW+EV   F F  T TSASFVLRK+YL  L+  E V++ +
Sbjct:    85 GIERVVKDRKWKEVIGAFSFPTTITSASFVLRKYYLKFLFQLEHVYYLE 133

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

UNIPROTKB|E1C9H0 ARID2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 227 (85.0 bits), Expect = 3.0e-17, P = 3.0e-17
 Identities = 44/99 (44%), Positives = 62/99 (62%)

Query:    26 SHEDVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEK 84
             +H D  +  + F D LR+FH   G+ F  IPV+GGKELDLH LY   TT GG+ KV  + 
Sbjct:     8 NHADQRRKGLAFLDELRQFHHSRGSPFKKIPVVGGKELDLHALYTRVTTLGGFGKVSEKN 67

Query:    85 KWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
             +W E+   F F  + ++A+F L+++YL  L  YE+VH F
Sbjct:    68 QWGEIVEEFNFPRSCSNAAFALKQYYLRYLEKYEKVHHF 106

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006337 "nucleosome disassembly" evidence=IEA

UNIPROTKB|Q68CP9 ARID2 "AT-rich interactive domain-containing protein 2" [Homo sapiens (taxid:9606)]

 Score = 213 (80.0 bits), Expect = 9.2e-16, P = 9.2e-16
 Identities = 42/96 (43%), Positives = 59/96 (61%)

Query:    29 DVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWR 87
             D  +  + F D LR+FH   G+ F  IP +GGKELDLH LY   TT GG+ KV  + +W 
Sbjct:    11 DERRKGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWG 70

Query:    88 EVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
             E+   F F  + ++A+F L+++YL  L  YE+VH F
Sbjct:    71 EIVEEFNFPRSCSNAAFALKQYYLRYLEKYEKVHHF 106

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0006337 "nucleosome disassembly" evidence=IDA

ZFIN|ZDB-GENE-030131-6311 arid2 "AT rich interactive domain 2 (ARID, RFX-like)" [Danio rerio (taxid:7955)]

 Score = 200 (75.5 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 40/88 (45%), Positives = 58/88 (65%)

Query:    37 FWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
             F D LR+FH   G+ F  +PV+GGKELDL  LYV   + GG+ KV  + +W E+   F+F
Sbjct:    19 FLDELRQFHHSRGSPFKKVPVVGGKELDLGALYVRVVSLGGFAKVSDKNQWVELVEDFQF 78

Query:    96 SPTTTSASFVLRKHYLTLLYHYEQVHFF 123
               + ++A+FVL+++YL  L  YE+VH F
Sbjct:    79 PRSCSNAAFVLKQYYLRYLEKYEKVHHF 106

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2RFL8 ARID2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 171 (65.3 bits), Expect = 2.7e-11, P = 2.7e-11
 Identities = 36/96 (37%), Positives = 55/96 (57%)

Query:    29 DVSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWR 87
             D  +  + F D LR+FH   G+   +IP +GG   DLH L  E+   GG+ KV  + +W 
Sbjct:    11 DERRKGLAFLDELRQFHHSRGSPCQIIPAVGGNPPDLHGLKPESPPVGGFAKVSEKNQWG 70

Query:    88 EVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
             E+   F F  + ++A+F L+++YL  L  YE+VH F
Sbjct:    71 EIVEEFNFPRSCSNAAFALKQYYLRYLEKYEKVHHF 106

GO:0006337 "nucleosome disassembly" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

DICTYBASE|DDB_G0275333 DDB_G0275333 "ARID/BRIGHT DNA binding domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 158 (60.7 bits), Expect = 1.1e-10, P = 1.1e-10
 Identities = 35/86 (40%), Positives = 48/86 (55%)

Query:    44 FHFIM--GTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTT 100
             F+F+   GT    IP+   KEL+L+ LY    +RGG E V+  K WR++       P  T
Sbjct:    53 FYFMTQRGTPIEKIPIFDHKELNLYKLYNCVISRGGLEAVIDNKLWRQITTDLAVDPERT 112

Query:   101 SASFVLRKHYLTLLYHYEQVHFFKMQ 126
              A F LR HYL  LY YE+ H+ K++
Sbjct:   113 DAGFRLRIHYLKYLYPYERKHYLKIE 138

GO:0005622 "intracellular" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISS

UNIPROTKB|F5H1F7 KDM5A "Lysine-specific demethylase 5A" [Homo sapiens (taxid:9606)]

 Score = 151 (58.2 bits), Expect = 3.2e-09, P = 3.2e-09
 Identities = 34/95 (35%), Positives = 54/95 (56%)

Query:    24 LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
             L+  E +++  + F D L +F  + G+   IPV+  K LDL+ L     ++GG+E V  E
Sbjct:    77 LNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKE 136

Query:    84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
             KKW +VG+   + P   + S +L+ HY  +LY YE
Sbjct:   137 KKWSKVGSRLGYLPGKGTGS-LLKSHYERILYPYE 170

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016706 "oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SGS2	HMGB9_ARATH	No assigned EC number	0.8018	0.5091	0.3284	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	218
smart00501	93	smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interac	1e-29
smart01014	88	smart01014, ARID, ARID/BRIGHT DNA binding domain	5e-27
pfam01388	90	pfam01388, ARID, ARID/BRIGHT DNA binding domain	9e-22

>gnl|CDD|128777 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interaction domain) domain

 Score =  105 bits (265), Expect = 1e-29
 Identities = 38/93 (40%), Positives = 53/93 (56%), Gaps = 1/93 (1%)

Query: 32  KDPIVFWDTLRRFHFIMGTK-FMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVG 90
           ++ ++F D L +F    G+    IPVIGGK LDL+ LY     RGGY++V  +KKW+E+ 
Sbjct: 1   RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIA 60

Query: 91  AVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
                  T+TSA+  LRKHY   L  YE+    
Sbjct: 61  RELGIPDTSTSAASSLRKHYERYLLPYERFLRG 93

DNA-binding domain containing a helix-turn-helix structure. Length = 93

>gnl|CDD|198082 smart01014, ARID, ARID/BRIGHT DNA binding domain

 Score = 98.5 bits (246), Expect = 5e-27
 Identities = 40/83 (48%), Positives = 48/83 (57%), Gaps = 1/83 (1%)

Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D LR+F    GT    IPVIGGK LDL+ LY     RGG++KV  +KKW++V      
Sbjct: 6   FLDRLRKFMEKRGTPLDKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGI 65

Query: 96  SPTTTSASFVLRKHYLTLLYHYE 118
            P+ TSA   LRKHY   L  YE
Sbjct: 66  PPSATSAGTSLRKHYEKYLLPYE 88

Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. Length = 88

>gnl|CDD|216473 pfam01388, ARID, ARID/BRIGHT DNA binding domain

 Score = 84.9 bits (211), Expect = 9e-22
 Identities = 41/83 (49%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 37  FWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D L +F    GT    IPVIGGK LDL+ LY      GG+EKV   KKWREV      
Sbjct: 8   FLDRLAKFMERRGTPLDKIPVIGGKPLDLYKLYRLVQKLGGFEKVTKSKKWREVAQKLGI 67

Query: 96  SPTTTSASFVLRKHYLTLLYHYE 118
            PT TSAS  LR  Y   L  YE
Sbjct: 68  PPTITSASQELRSIYEKYLLPYE 90

This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain. Length = 90

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	218
smart00501	93	BRIGHT BRIGHT, ARID (A/T-rich interaction domain)	99.95
PF01388	92	ARID: ARID/BRIGHT DNA binding domain; InterPro: IP	99.94
KOG2744	512	consensus DNA-binding proteins Bright/BRCAA1/RBP1	99.76
KOG2510	532	consensus SWI-SNF chromatin-remodeling complex pro	99.14
PF00249	48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	86.47

>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain

Probab=99.95  E-value=7.9e-28  Score=182.33  Aligned_cols=90  Identities=41%  Similarity=0.699  Sum_probs=86.6

Q ss_pred             CChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHH
Q 027848           32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY  110 (218)
Q Consensus        32 ~er~~Fl~~L~~F~~~rG~pl-~~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y  110 (218)
                      ++++.|+++|.+||+++|+|+ ++|.|+|++||||+||.+|+++|||++||++++|.+||++||+|+++++++..||++|
T Consensus         1 ~~~~~F~~~L~~F~~~~g~~~~~~P~i~g~~vdL~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y   80 (93)
T smart00501        1 RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHY   80 (93)
T ss_pred             CcHHHHHHHHHHHHHHcCCcCCcCCeECCEeCcHHHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHH
Confidence            478999999999999999998 7999999999999999999999999999999999999999999998899999999999


Q ss_pred             HHhhHHHHhhh
Q 027848          111 LTLLYHYEQVH  121 (218)
Q Consensus       111 ~kyLl~YE~~~  121 (218)
                      .+||+|||+++
T Consensus        81 ~k~L~~yE~~~   91 (93)
T smart00501       81 ERYLLPFERFL   91 (93)
T ss_pred             HHHhHHHHHHh
Confidence            99999999974

DNA-binding domain containing a helix-turn-helix structure

>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans

Probab=99.94  E-value=1e-26  Score=174.73  Aligned_cols=90  Identities=43%  Similarity=0.721  Sum_probs=82.8

Q ss_pred             cccCChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHH
Q 027848           29 DVSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLR  107 (218)
Q Consensus        29 ~~~~er~~Fl~~L~~F~~~rG~pl-~~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK  107 (218)
                      ..+++++.|+++|++||+++|+++ ++|.++|++||||+||.+|+++|||++|+++++|.+||++||+++.+++.+..|+
T Consensus         2 ~~~~~~~~F~~~L~~f~~~~g~~~~~~P~i~g~~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~   81 (92)
T PF01388_consen    2 ANTREREQFLEQLREFHESRGTPIDRPPVIGGKPVDLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLR   81 (92)
T ss_dssp             SSCHHHHHHHHHHHHHHHHTTSSSSS-SEETTSE-SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHHHcCCCCCCCCcCCCEeCcHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHH
Confidence            345789999999999999999997 7999999999999999999999999999999999999999999998888888999


Q ss_pred             HHHHHhhHHHH
Q 027848          108 KHYLTLLYHYE  118 (218)
Q Consensus       108 ~~Y~kyLl~YE  118 (218)
                      ++|++||++||
T Consensus        82 ~~Y~~~L~~fE   92 (92)
T PF01388_consen   82 QHYEKYLLPFE   92 (92)
T ss_dssp             HHHHHHTHHHH
T ss_pred             HHHHHHhHhhC
Confidence            99999999998

ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....

>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]

Probab=99.76  E-value=1.2e-18  Score=167.58  Aligned_cols=108  Identities=46%  Similarity=0.684  Sum_probs=97.7

Q ss_pred             CCCCCCcccCChhHHHHHHHHHHhhcCCCCC-CCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCC-CCC
Q 027848           23 PLSSHEDVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSP-TTT  100 (218)
Q Consensus        23 p~~~~e~~~~er~~Fl~~L~~F~~~rG~pl~-~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~-~~t  100 (218)
                      |....+....+++.|+++|+.||+++|++++ +|+|+|+++|||+||.+|+++||+++|+..+.|++|...+.+|. +++
T Consensus       153 ~~~~~e~~~~~~eeF~~dl~~f~~~~~~~~~~iPii~~~~ldL~~Ly~lV~s~GG~~~V~~~k~Wrev~~~l~~pt~tiT  232 (512)
T KOG2744|consen  153 PLYETEGVPKSSEEFMEDLRRFMKKRGTKVKSIPIIGGQPLDLHWLYALVTSRGGLDEVTNKKLWREVIDGLNFPTPTIT  232 (512)
T ss_pred             cccccccccccHHHHHHHHHHHHHHhCCcceeccccCCCcchHHHHHHHHhcCCchhHhhhhhhHHHHhccccCCCcccc
Confidence            3344455566999999999999999999995 99999999999999999999999999999999999999999999 999


Q ss_pred             cHHHHHHHHHHHhhHHHHhhhhhhccCCCC
Q 027848          101 SASFVLRKHYLTLLYHYEQVHFFKMQGPPC  130 (218)
Q Consensus       101 ~as~~LK~~Y~kyLl~YE~~~~~~e~~~~~  130 (218)
                      ++++.|++.|.|+|++||+.+.+....+.+
T Consensus       233 saaf~lr~~y~K~L~~ye~~~~~~~~~pln  262 (512)
T KOG2744|consen  233 SAAFTLRKQYLKLLFEYECEFEKNRHVPLN  262 (512)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence            999999999999999999998876553333

>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]

Probab=99.14  E-value=6.3e-11  Score=113.28  Aligned_cols=91  Identities=29%  Similarity=0.437  Sum_probs=82.5

Q ss_pred             cCChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHH
Q 027848           31 SKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKH  109 (218)
Q Consensus        31 ~~er~~Fl~~L~~F~~~rG~pl-~~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~  109 (218)
                      ..+++..+++|+.|++.+.+++ ..|.++.++||||+||..|.+.||+..|+++|  +++|.-||     .++++.||++
T Consensus       291 qp~r~~wvDR~raF~ee~~Sp~t~~p~~gakPldl~rlYvsvke~gg~~~v~knk--rd~a~~lg-----ssaa~~l~k~  363 (532)
T KOG2510|consen  291 QPERKEWVDRLRAFTEERASPMTNLPAVGAKPLDLYRLYVSVKEIGGLTQVNKNK--RDLATNLG-----SSAASSLKKQ  363 (532)
T ss_pred             CcchhhHHHHHHHHHHhhcCcccccccccccchhHHHHHHHHHHhccceeeccch--hhhhhccc-----hHHHHHHHHH
Confidence            5689999999999999999999 58999999999999999999999999999999  99999888     5578899999


Q ss_pred             HHHhhHHHHhhhhhhccCC
Q 027848          110 YLTLLYHYEQVHFFKMQGP  128 (218)
Q Consensus       110 Y~kyLl~YE~~~~~~e~~~  128 (218)
                      |.+||+.||++...+++++
T Consensus       364 y~~~lf~fec~f~Rg~e~p  382 (532)
T KOG2510|consen  364 YIQYLFAFECKFERGEEPP  382 (532)
T ss_pred             HHHHHHhhceeeeccCCCC
Confidence            9999999999866555543

>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins

Probab=86.47  E-value=1.5  Score=28.87  Aligned_cols=39  Identities=18%  Similarity=0.307  Sum_probs=28.0

Q ss_pred             hhhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027848           65 HVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL  114 (218)
Q Consensus        65 y~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y~kyL  114 (218)
                      -.|..+|...|.-       .|..||..++  .+  -.+.+++..|.++|
T Consensus        10 ~~l~~~v~~~g~~-------~W~~Ia~~~~--~~--Rt~~qc~~~~~~~~   48 (48)
T PF00249_consen   10 EKLLEAVKKYGKD-------NWKKIAKRMP--GG--RTAKQCRSRYQNLL   48 (48)
T ss_dssp             HHHHHHHHHSTTT-------HHHHHHHHHS--SS--STHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCc-------HHHHHHHHcC--CC--CCHHHHHHHHHhhC
Confidence            3466677766644       6999999999  21  23448999999886

These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	218
2jxj_A	96	Nmr Structure Of The Arid Domain From The Histone H		9e-10
2kk0_A	145	Solution Structure Of Dead Ringer-Like Protein 1 (A		5e-09
1c20_A	128	Solution Structure Of The Dna-Binding Domain From T		2e-07
2lm1_A	107	Solution Nmr Structure Of Lysine-Specific Demethyla		5e-07
2yqe_A	100	Solution Structure Of The Arid Domain Of Jarid1d Pr		7e-07
2jrz_A	117	Solution Structure Of The BrightARID DOMAIN FROM TH		7e-07
1ig6_A	107	Human Mrf-2 Domain, Nmr, 11 Structures Length = 107		1e-06
1kqq_A	139	Solution Structure Of The Dead Ringer Arid-Dna Comp		2e-06
1ryu_A	120	Solution Structure Of The Swi1 Arid Length = 120		1e-05
2eqy_A	122	Solution Structure Of The Arid Domain Of Jarid1b Pr		2e-04
2cxy_A	125	Crystal Structure Of The Hbaf250b At-Rich Interacti		5e-04

>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4 Demethylase Rbp2 Length = 96

Iteration: 1
 Score = 60.1 bits (144), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 32/82 (39%), Positives = 47/82 (57%), Gaps = 1/82 (1%)
Query: 37  FWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFS 96
           F D L +F  + G+   IPV+  K LDL+ L     ++GG+E V  EKKW +VG+   + 
Sbjct: 11  FLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYL 70
Query: 97  PTTTSASFVLRKHYLTLLYHYE 118
           P   + S +L+ HY  +LY YE
Sbjct: 71  PGKGTGS-LLKSHYERILYPYE 91

>pdb|2KK0|A Chain A, Solution Structure Of Dead Ringer-Like Protein 1 (At-Rich Interactive Domain-Containing Protein 3a) From Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4394c Length = 145

Iteration: 1
 Score = 57.8 bits (138), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 37  FWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D L  F    GT    IP++  + LDL +LYV  T +GG  +V+ +K WRE+      
Sbjct: 38  FLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNL 97
Query: 96  SPTTTSASFVLRKHYLTLLYHYE 118
             + TSA+F LR  Y+  LY YE
Sbjct: 98  PTSITSAAFTLRTQYMKYLYPYE 120

>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead Ringer Protein Length = 128

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 46/93 (49%), Gaps = 3/93 (3%)
Query: 29  DVSKDPI--VFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKK 85
           +++ DP    F D L  F    GT    +P++    LDL+ LY     RGG   V+ +K 
Sbjct: 16  EINDDPKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKL 75
Query: 86  WREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
           W+E+        + TSA+F LR  Y+  LY YE
Sbjct: 76  WQEIIKGLHLPSSITSAAFTLRTQYMKYLYPYE 108

>pdb|2LM1|A Chain A, Solution Nmr Structure Of Lysine-Specific Demethylase Lid From Drosophila Melanogaster, Northeast Structural Genomics Consortium Target Fr824d Length = 107

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 26/95 (27%), Positives = 50/95 (52%), Gaps = 1/95 (1%)
Query: 24  LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
           L+  E  ++  + F D + +F  + G+   IP++  K LDL+ L+      GG E+   +
Sbjct: 6   LNELEAKTRVKLNFLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKD 65
Query: 84  KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
           +KW +V    ++ P++ S    L+ HY  +L+ +E
Sbjct: 66  RKWAKVANRMQY-PSSKSVGATLKAHYERILHPFE 99

>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein Length = 100

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 1/94 (1%)
Query: 25  SSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEK 84
           SS    ++  + + D + +F  I G+   IP +  K LDL+ L       GGYE +  ++
Sbjct: 2   SSGSSGTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDR 61
Query: 85  KWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
           +W  V     + P     S +LR HY  ++Y YE
Sbjct: 62  RWARVAQRLHYPPGKNIGS-LLRSHYERIIYPYE 94

>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN Jarid1c Protein Length = 117

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 37  FWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFS 96
           + D + +F  I G+   IP +  + LDL+ L       GGYE +  +++W  V     + 
Sbjct: 15  YLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKDRRWARVAQRLNYP 74
Query: 97  PTTTSASFVLRKHYLTLLYHYE 118
           P     S  LR HY  ++Y YE
Sbjct: 75  PGKNIGSL-LRSHYERIVYPYE 95

>pdb|1IG6|A Chain A, Human Mrf-2 Domain, Nmr, 11 Structures Length = 107

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 39/66 (59%)
Query: 54  IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
           IP +G K+++L  ++  A   GGYE + A ++W+ +      +P +TSA+   R+HY  L
Sbjct: 25  IPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERL 84
Query: 114 LYHYEQ 119
           +  YE+
Sbjct: 85  ILPYER 90

>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex Length = 139

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 45/93 (48%), Gaps = 3/93 (3%)
Query: 29  DVSKDPI--VFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKK 85
           +++ DP    F D L  F    GT    +P++    LDL+ LY     RGG   V+ +K 
Sbjct: 18  EINDDPKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKL 77
Query: 86  WREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
           W+E+        + TSA+  LR  Y+  LY YE
Sbjct: 78  WQEIIKGLHLPSSITSAALTLRTQYMKYLYPYE 110

>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid Length = 120

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 54  IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
           +P +G K LDL+ LYV     GG  +V   KKWRE+        T++SA+  L+K Y+  
Sbjct: 42  LPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVG-TSSSAASSLKKQYIQC 100
Query: 114 LYHYEQVHFFKMQGPP 129
           LY +E     + + PP
Sbjct: 101 LYAFE-CKIERGEDPP 115

>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein Length = 122

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 1/94 (1%)
Query: 25  SSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEK 84
           SS E  ++  + F D + ++  + G+   IP +  K LDL  L       GG+  V  ++
Sbjct: 5   SSGEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDR 64
Query: 85  KWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
           KW ++     F+P     S + R HY  +L  Y 
Sbjct: 65  KWTKIATKMGFAPGKAVGSHI-RGHYERILNPYN 97

>pdb|2CXY|A Chain A, Crystal Structure Of The Hbaf250b At-Rich Interaction Domain (Arid) Length = 125

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 54  IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
           +P +G K LDL  LYV     GG  +V   KKWRE+        T++SA+  L+K Y+  
Sbjct: 43  LPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVG-TSSSAASSLKKQYIQY 101
Query: 114 LYHYEQVHFFKMQGPP 129
           L+ +E     + + PP
Sbjct: 102 LFAFE-CKIERGEEPP 116

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	218
2rq5_A	121	Protein jumonji; developmental protein, nucleus, r	4e-30
2eqy_A	122	RBP2 like, jumonji, at rich interactive domain 1B;	1e-29
2jrz_A	117	Histone demethylase jarid1C; bright/ARID domain, h	5e-28
1ig6_A	107	MRF-2, modulator recognition factor 2; DNA binding	3e-27
2lm1_A	107	Lysine-specific demethylase LID; structural genomi	1e-26
2cxy_A	125	BAF250B subunit, HBAF250B; DNA-binding domain, str	7e-26
2jxj_A	96	Histone demethylase jarid1A; ARID domain, chromati	2e-24
2li6_A	116	SWI/SNF chromatin-remodeling complex subunit SWI1;	4e-22
1c20_A	128	DEAD ringer protein; DNA-binding domain, ARID, AT-	2e-21
2kk0_A	145	AT-rich interactive domain-containing protein 3A;	3e-21
1kkx_A	123	Transcription regulatory protein ADR6; ARID, DNA-b	4e-21

>2rq5_A Protein jumonji; developmental protein, nucleus, repressor, transcription, transcription regulation; NMR {Mus musculus} Length = 121

 Score =  106 bits (267), Expect = 4e-30
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 1/101 (0%)

Query: 22  APLSSHEDVSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKV 80
            PL S        +     +++     G     +P+IGG ELDL   +      GG ++V
Sbjct: 1   GPLGSLGRRWGPNVQRLACIKKHLRSQGITMDELPLIGGCELDLACFFRLINEMGGMQQV 60

Query: 81  VAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVH 121
              KKW ++  + +   T       L++ Y   L  Y+ + 
Sbjct: 61  TDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQYLLSYDSLS 101

>2eqy_A RBP2 like, jumonji, at rich interactive domain 1B; ARID domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 122

 Score =  105 bits (264), Expect = 1e-29
 Identities = 27/115 (23%), Positives = 45/115 (39%), Gaps = 5/115 (4%)

Query: 25  SSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEK 84
           SS E  ++  + F D + ++  + G+   IP +  K LDL  L       GG+  V  ++
Sbjct: 5   SSGEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDR 64

Query: 85  KWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFK----MQGPPCVPSGK 135
           KW ++     F     +    +R HY  +L  Y           +Q P      K
Sbjct: 65  KWTKIATKMGF-APGKAVGSHIRGHYERILNPYNLFLSGDSLRCLQKPNLTSDTK 118

>2jrz_A Histone demethylase jarid1C; bright/ARID domain, helical, structural genomics, structural genomics consortium, SGC, oxidoreductase; NMR {Homo sapiens} PDB: 2yqe_A Length = 117

 Score =  101 bits (253), Expect = 5e-28
 Identities = 26/112 (23%), Positives = 48/112 (42%), Gaps = 3/112 (2%)

Query: 24  LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
           ++  E  ++  + + D + +F  I G+   IP +  + LDL+ L       GGYE +  +
Sbjct: 2   MNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKD 61

Query: 84  KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSGK 135
           ++W  V     + P   +   +LR HY  ++Y YE   +       C     
Sbjct: 62  RRWARVAQRLNY-PPGKNIGSLLRSHYERIVYPYEM--YQSGANLVCNTRPF 110

>1ig6_A MRF-2, modulator recognition factor 2; DNA binding protein, DNA-binding motif, protein-DNA interaction; NMR {Homo sapiens} SCOP: a.4.3.1 PDB: 2oeh_A Length = 107

 Score = 99.2 bits (247), Expect = 3e-27
 Identities = 27/99 (27%), Positives = 47/99 (47%), Gaps = 1/99 (1%)

Query: 32  KDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVG 90
            D   F   L ++     T    IP +G K+++L  ++  A   GGYE + A ++W+ + 
Sbjct: 2   ADEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIY 61

Query: 91  AVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPP 129
                +P +TSA+   R+HY  L+  YE+    +   P 
Sbjct: 62  DELGGNPGSTSAATCTRRHYERLILPYERFIKGEEDKPL 100

>2lm1_A Lysine-specific demethylase LID; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Drosophila melanogaster} Length = 107

 Score = 97.6 bits (243), Expect = 1e-26
 Identities = 26/96 (27%), Positives = 50/96 (52%), Gaps = 1/96 (1%)

Query: 24  LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
           L+  E  ++  + F D + +F  + G+   IP++  K LDL+ L+      GG E+   +
Sbjct: 6   LNELEAKTRVKLNFLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKD 65

Query: 84  KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQ 119
           +KW +V    ++ P++ S    L+ HY  +L+ +E 
Sbjct: 66  RKWAKVANRMQY-PSSKSVGATLKAHYERILHPFEV 100

>2cxy_A BAF250B subunit, HBAF250B; DNA-binding domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.60A {Homo sapiens} PDB: 2eh9_A 1ryu_A Length = 125

 Score = 96.3 bits (239), Expect = 7e-26
 Identities = 30/94 (31%), Positives = 44/94 (46%), Gaps = 2/94 (2%)

Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           + D    F    G+    +P +G K LDL  LYV     GG  +V   KKWRE+      
Sbjct: 25  WVDRYLTFMEERGSPVSSLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNV 84

Query: 96  SPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPP 129
             T++SA+  L+K Y+  L+ +E       + PP
Sbjct: 85  -GTSSSAASSLKKQYIQYLFAFECKIERGEEPPP 117

>2jxj_A Histone demethylase jarid1A; ARID domain, chromatin regulator, developmental protein, dioxygenase, iron, metal-binding, nucleus, oxidoreductase; NMR {Homo sapiens} Length = 96

 Score = 91.8 bits (228), Expect = 2e-24
 Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 1/85 (1%)

Query: 37  FWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFS 96
           F D L +F  + G+   IPV+  K LDL+ L     ++GG+E V  EKKW +VG+   + 
Sbjct: 11  FLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGY- 69

Query: 97  PTTTSASFVLRKHYLTLLYHYEQVH 121
                   +L+ HY  +LY YE   
Sbjct: 70  LPGKGTGSLLKSHYERILYPYELFQ 94

>2li6_A SWI/SNF chromatin-remodeling complex subunit SWI1; ligand binding, DNA binding protein; NMR {Saccharomyces cerevisiae} Length = 116

 Score = 86.6 bits (214), Expect = 4e-22
 Identities = 25/106 (23%), Positives = 41/106 (38%), Gaps = 7/106 (6%)

Query: 24  LSSHEDVSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVA 82
             S E  +K   +F  +L             IP IG ++++L  LY+     GG ++V  
Sbjct: 10  KISTELNNKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTR 69

Query: 83  EKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGP 128
            ++W  V    + S         L   Y  +L  YE+ H    +G 
Sbjct: 70  TQQWSMVAQRLQISDYQQ-----LESIYFRILLPYER-HMISQEGI 109

>1c20_A DEAD ringer protein; DNA-binding domain, ARID, AT-rich interaction domain, DNA- binding protein; NMR {Drosophila melanogaster} SCOP: a.4.3.1 PDB: 1kqq_A Length = 128

 Score = 84.8 bits (209), Expect = 2e-21
 Identities = 30/86 (34%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D L  F    GT    +P++    LDL+ LY     RGG   V+ +K W+E+      
Sbjct: 26  FLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHL 85

Query: 96  SPTTTSASFVLRKHYLTLLYHYEQVH 121
             + TSA+F LR  Y+  LY YE   
Sbjct: 86  PSSITSAAFTLRTQYMKYLYPYECEK 111

>2kk0_A AT-rich interactive domain-containing protein 3A; DEAD ringer, AT-rich interaction domain, NESG, ARID, cytopla binding, nucleus, phosphoprotein; NMR {Homo sapiens} Length = 145

 Score = 84.8 bits (209), Expect = 3e-21
 Identities = 33/94 (35%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D L  F    GT    IP++  + LDL +LYV  T +GG  +V+ +K WRE+      
Sbjct: 38  FLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNL 97

Query: 96  SPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPP 129
             + TSA+F LR  Y+  LY YE           
Sbjct: 98  PTSITSAAFTLRTQYMKYLYPYECEKRGLSNPNE 131

>1kkx_A Transcription regulatory protein ADR6; ARID, DNA-binding domain, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.4.3.1 PDB: 1kn5_A Length = 123

 Score = 83.9 bits (207), Expect = 4e-21
 Identities = 25/112 (22%), Positives = 40/112 (35%), Gaps = 9/112 (8%)

Query: 20  YPAPLSSHEDVS--KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGG 76
                  H   S  K   +F  +L             IP IG ++++L  LY+     GG
Sbjct: 3   GSGSHHHHHHGSNNKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGG 62

Query: 77  YEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGP 128
            ++V   ++W  V    + S         L   Y  +L  YE+ H    +G 
Sbjct: 63  ADQVTRTQQWSMVAQRLQISDYQQ-----LESIYFRILLPYER-HMISQEGI 108

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	218
d1ryua_	120	a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1	3e-29
d1c20a_	128	a.4.3.1 (A:) DNA-binding domain from the dead ring	6e-28
d1ig6a_	107	a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo	3e-27
d1kkxa_	102	a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {	6e-22

>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 120

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: SWI-SNF complex protein p270, SMARCF1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  103 bits (259), Expect = 3e-29
 Identities = 30/96 (31%), Positives = 43/96 (44%), Gaps = 2/96 (2%)

Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           + D    F          +P +G K LDL+ LYV     GG  +V   KKWRE+      
Sbjct: 24  WVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNV 83

Query: 96  SPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCV 131
             T++SA+  L+K Y+  LY +E         PP +
Sbjct: 84  -GTSSSAASSLKKQYIQCLYAFECKIERGEDPPPDI 118

>d1c20a_ a.4.3.1 (A:) DNA-binding domain from the dead ringer protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 128

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: DNA-binding domain from the dead ringer protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score =  100 bits (250), Expect = 6e-28
 Identities = 31/94 (32%), Positives = 43/94 (45%), Gaps = 2/94 (2%)

Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D L  F    GT    +P++    LDL+ LY     RGG   V+ +K W+E+      
Sbjct: 26  FLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHL 85

Query: 96  SPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPP 129
             + TSA+F LR  Y+  LY YE      +  P 
Sbjct: 86  PSSITSAAFTLRTQYMKYLYPYEC-EKKNLSTPA 118

>d1ig6a_ a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 107

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: MRF-2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 98.0 bits (244), Expect = 3e-27
 Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 1/98 (1%)

Query: 33  DPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGA 91
           D   F   L ++     T    IP +G K+++L  ++  A   GGYE + A ++W+ +  
Sbjct: 3   DEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYD 62

Query: 92  VFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPP 129
               +P +TSA+   R+HY  L+  YE+    +   P 
Sbjct: 63  ELGGNPGSTSAATCTRRHYERLILPYERFIKGEEDKPL 100

>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 102

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: Transcription regulator Adr6 (Swi1)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 84.1 bits (208), Expect = 6e-22
 Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 7/93 (7%)

Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F  +L             IP IG ++++L  LY+     GG ++V   ++W  V    + 
Sbjct: 8   FMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQI 67

Query: 96  SPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGP 128
           S         L   Y  +L  YE+ H    +G 
Sbjct: 68  SDYQQ-----LESIYFRILLPYER-HMISQEGI 94

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	218
d1ig6a_	107	MRF-2 DNA-binding domain {Human (Homo sapiens) [Ta	99.93
d1ryua_	120	SWI-SNF complex protein p270, SMARCF1 {Human (Homo	99.93
d1c20a_	128	DNA-binding domain from the dead ringer protein {F	99.92
d1kkxa_	102	Transcription regulator Adr6 (Swi1) {Baker's yeast	99.89

>d1ig6a_ a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: MRF-2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=5.5e-27  Score=175.27  Aligned_cols=103  Identities=27%  Similarity=0.447  Sum_probs=92.8

Q ss_pred             CCHHHHHHHHHHHHHHCCCCC-CCCEECCEECCHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             784689999999996319988-8871499450444369998732861220236776888866178999873789999999
Q 027848           32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY  110 (218)
Q Consensus        32 ~er~~Fl~~L~~F~~~rG~pl-k~P~i~Gk~VDLy~Ly~~V~~~GGy~kVt~~k~W~eVa~~LGlp~~~tsas~~LK~~Y  110 (218)
                      .+++.|+++|.+||+++|+|+ ++|.++|++||||+||.+|+++|||++||++++|.+|++.||+|+++++++.+||++|
T Consensus         2 ~e~~~Fl~~L~~F~~~rg~~~~~~P~i~gk~vDL~~Ly~~V~~~GG~~~V~~~~~W~~ia~~lg~~~~~~~~~~~Lk~~Y   81 (107)
T d1ig6a_           2 ADEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHY   81 (107)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCGGGCCCSSSSSCCHHHHHHHHHHTTHHHHHHHHTTHHHHHHHHTCCTTCTTTTTTHHHHH
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHHHHCCHHHCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf             54999999999999985998875882898254199999999996770533650619999998688987787999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             9824887855652015999999997
Q 027848          111 LTLLYHYEQVHFFKMQGPPCVPSGK  135 (218)
Q Consensus       111 ~kyLlpYE~~~~~ge~d~~~~p~~~  135 (218)
                      ++||++||++.. +.++++.+|+.+
T Consensus        82 ~~~L~~yE~~~~-~~~~~~~p~~~~  105 (107)
T d1ig6a_          82 ERLILPYERFIK-GEEDKPLPPIKP  105 (107)
T ss_dssp             HHHTTTTHHHHH-HHTSSSSCTTCS
T ss_pred             HHHHHHHHHHHH-CCCCCCCCCCCC
T ss_conf             999999998870-688788999988

>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: SWI-SNF complex protein p270, SMARCF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=2.1e-26  Score=171.89  Aligned_cols=97  Identities=30%  Similarity=0.468  Sum_probs=89.9

Q ss_pred             CCHHHHHHHHHHHHHHCCCCC-CCCEECCEECCHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             784689999999996319988-8871499450444369998732861220236776888866178999873789999999
Q 027848           32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY  110 (218)
Q Consensus        32 ~er~~Fl~~L~~F~~~rG~pl-k~P~i~Gk~VDLy~Ly~~V~~~GGy~kVt~~k~W~eVa~~LGlp~~~tsas~~LK~~Y  110 (218)
                      .+++.|++.|.+||+++|+|+ ++|.|+|++||||+||.+|+++|||++||++++|.+|++.||++. +++++.+||++|
T Consensus        19 ~e~~~Fl~~L~~F~~~rg~~~~~~P~i~gr~vDL~~Ly~~V~~~GG~~~V~~~~~W~~Va~~l~~~~-~~~~~~~Lk~~Y   97 (120)
T d1ryua_          19 PERKMWVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGT-SSSAASSLKKQY   97 (120)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCSSCCSCCSSSSCCHHHHHHHHHHHTCTTGGGTSSHHHHHHHHTTSCC-SSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEECCEECCHHHHHHHHHHHCCHHHHCCCCHHHHHHHHHCCCC-CCCHHHHHHHHH
T ss_conf             7799999999999997799787688189844569999999998158876064050999999849998-787999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCC
Q ss_conf             9824887855652015999
Q 027848          111 LTLLYHYEQVHFFKMQGPP  129 (218)
Q Consensus       111 ~kyLlpYE~~~~~ge~d~~  129 (218)
                      ++||++||+++.+++++++
T Consensus        98 ~r~L~~yE~~~~~~~~~p~  116 (120)
T d1ryua_          98 IQCLYAFECKIERGEDPPP  116 (120)
T ss_dssp             HHHTTTTTTTTTTTTSCCC
T ss_pred             HHHHHHHHHHHHCCCCCCC
T ss_conf             9999999999874799970

>d1c20a_ a.4.3.1 (A:) DNA-binding domain from the dead ringer protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: DNA-binding domain from the dead ringer protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.92  E-value=2.1e-25  Score=165.99  Aligned_cols=91  Identities=33%  Similarity=0.511  Sum_probs=86.6

Q ss_pred             CCHHHHHHHHHHHHHHCCCCC-CCCEECCEECCHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             784689999999996319988-8871499450444369998732861220236776888866178999873789999999
Q 027848           32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY  110 (218)
Q Consensus        32 ~er~~Fl~~L~~F~~~rG~pl-k~P~i~Gk~VDLy~Ly~~V~~~GGy~kVt~~k~W~eVa~~LGlp~~~tsas~~LK~~Y  110 (218)
                      ++++.|++.|.+||+.+|+|+ ++|.|+|++||||+||.+|+++|||++|+.+++|.+|++.||+|+++++++++|+++|
T Consensus        21 ~er~~F~~~L~~f~~~rg~~~~~~P~i~gk~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y  100 (128)
T d1c20a_          21 PKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAAFTLRTQY  100 (128)
T ss_dssp             HHHHHHHHHHHHHHTTTSSCSSCCCEETTEECCHHHHHHHHHHHTCHHHHHHHTTHHHHHHHTCCCSSCCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEECCEECCHHHHHHHHHHHCCHHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf             77999999999999984885676881898316599999999993677872521529999999689988886999999999


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             982488785565
Q 027848          111 LTLLYHYEQVHF  122 (218)
Q Consensus       111 ~kyLlpYE~~~~  122 (218)
                      .+||++||++..
T Consensus       101 ~k~L~~fE~~~~  112 (128)
T d1c20a_         101 MKYLYPYECEKK  112 (128)
T ss_dssp             HHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999982

>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: Transcription regulator Adr6 (Swi1)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.89  E-value=1.3e-23  Score=155.48  Aligned_cols=90  Identities=23%  Similarity=0.367  Sum_probs=82.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCC-CCCEECCEECCHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf             6784689999999996319988-887149945044436999873286122023677688886617899987378999999
Q 027848           31 SKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKH  109 (218)
Q Consensus        31 ~~er~~Fl~~L~~F~~~rG~pl-k~P~i~Gk~VDLy~Ly~~V~~~GGy~kVt~~k~W~eVa~~LGlp~~~tsas~~LK~~  109 (218)
                      +++.+.|++.|..||+++|+|+ ++|.++|++||||+||.+|+++|||++||+++.|.+|+++||++.     +.+++++
T Consensus         2 ~~~~e~F~~~L~~f~~~rg~~~~~~P~i~gk~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~-----~~~lr~~   76 (102)
T d1kkxa_           2 NKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISD-----YQQLESI   76 (102)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCSSSSCCCCSSSSCCTTHHHHHHTTTSCHHHHTTSHHHHHHHHHHTCCC-----HHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEECCEEEEHHHHHHHHHHHCCHHHHCCCCCHHHHHHHHCCCH-----HHHHHHH
T ss_conf             63899999999999998699887698399954009999999999768688625275999999978885-----8999999


Q ss_pred             HHHHHHHHHHHHHHHC
Q ss_conf             9982488785565201
Q 027848          110 YLTLLYHYEQVHFFKM  125 (218)
Q Consensus       110 Y~kyLlpYE~~~~~ge  125 (218)
                      |++||+|||++..-.+
T Consensus        77 Y~~~L~~yE~~~~~~e   92 (102)
T d1kkxa_          77 YFRILLPYERHMISQE   92 (102)
T ss_dssp             HHHHHHHHHHHSCTTC
T ss_pred             HHHHHHHHHHHHHCCC
T ss_conf             9999999999872814