Citrus Sinensis ID: 034230

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
Protein Sequence
MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccHHHHHHHccccccHHHHHHHHHHHHHHccccccccccEEEccHHHHHHcccccEEccccHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccHHHHHHHccccccHHHHHHHHHHHHHHccccccccccEEEccHHHHHHHcccccccHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mlpqgvkktvidnPKKLANLIdlvnlpstlrEFVGQSRISRLGCFMRVWSYIKtnnlqdpnnknvvncDQKLRSILMGKSRVELAELPAliklhfpkdpk
Flexible Loop (DISEMBL)
mlpqgvkktvidnpkklaNLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKtnnlqdpnnknvVNCDQKLRSILMGKSRVELaelpaliklhfpkdpk
Low Complexity Region (SEG)
MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK
Disordered region (IsUnstruct)
**********IDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLH******
Disordered Region (DISOPRED)
***********************VNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFP****
Disordered Region (DISEMBL)
MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK
Disordered Region (DISPRO)
*******************LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFP****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK
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	100	2.2.26 [Sep-21-2011]
Q08747	228	Upstream activation facto	yes	no	0.74	0.324	0.363	4e-08
O74503	233	Upstream activation facto	yes	no	0.53	0.227	0.415	3e-07
Q05024	226	Protein TRI1 OS=Saccharom	no	no	0.68	0.300	0.294	0.0006
Q2TBN1	515	SWI/SNF-related matrix-as	yes	no	0.51	0.099	0.396	0.0007
Q6P9Z1	483	SWI/SNF-related matrix-as	yes	no	0.69	0.142	0.338	0.0008
Q6STE5	483	SWI/SNF-related matrix-as	yes	no	0.69	0.142	0.338	0.0008

>sp|Q08747|UAF30_YEAST Upstream activation factor subunit UAF30 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=UAF30 PE=1 SV=1

 Score = 56.6 bits (135), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 3/77 (3%)

Query: 24  VNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVE 83
           V L  +L   +G+  ++R     R+W+YIK +NLQ+PNNK  + CD+KL  +++GKS   
Sbjct: 124 VTLSKSLASLLGEHELTRTEVVRRLWAYIKAHNLQNPNNKKEILCDEKLE-LILGKS-TN 181

Query: 84  LAELPALIKLHFPKDPK 100
           + E+  ++  H   +PK
Sbjct: 182 MFEMHKILASHMT-EPK 197

Nonessential component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. Together with SPT15/TBP UAF seems to stimulate basal transcription to a fully activated level. UAF30 seems to play a role in silencing transcription by RNA polymerase II.
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|O74503|UAF30_SCHPO Upstream activation factor subunit spp27 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=spp27 PE=1 SV=1

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 24  VNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSIL 76
           + L   L EF+G  ++SR     ++W YIK ++LQDPN+K  + CD KL+S+ 
Sbjct: 121 MKLSPKLAEFLGLEQLSRPQTVKKLWEYIKAHDLQDPNDKRTILCDDKLKSVF 173

Component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. UAF seems to stimulate basal transcription to a fully activated level.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q05024|TRI1_YEAST Protein TRI1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TRI1 PE=1 SV=1

 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 37/68 (54%)

Query: 12  DNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQK 71
           D+P   +  +  V L + L++F+G   + R      +W YIK ++LQ+P ++  + CD+K
Sbjct: 112 DSPDSNSISVRKVLLSAPLQKFLGSEELPRTQVVKMIWQYIKEHDLQNPKDRREILCDEK 171

Query: 72  LRSILMGK 79
           +  I   K
Sbjct: 172 MEPIFGKK 179

May be involved in transcription regulation.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q2TBN1|SMRD1_BOVIN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 OS=Bos taurus GN=SMARCD1 PE=2 SV=1

 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 33/53 (62%), Gaps = 2/53 (3%)

Query: 48  VWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPA-LIKLHFPKDP 99
           +W YIKT+ LQDP+ +  V CD+ L+ I   + R++ +E+P  L  L  P +P
Sbjct: 319 LWQYIKTHKLQDPHEREFVICDKYLQQIFESQ-RMKFSEIPQRLHALLMPPEP 370

Involved in chromatin remodeling. Has a strong influence on the Vitamin D-mediated transcriptional activity from an enhancer Vitamin D receptor element (VDRE). May be a link between mammalian SWI-SNF-like chromatin remodeling complexes and the vitamin D receptor (VDR) heterodimer. Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for transactivation. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.

Bos taurus (taxid: 9913)

>sp|Q6P9Z1|SMRD3_MOUSE SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 OS=Mus musculus GN=Smarcd3 PE=1 SV=2

 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 30  LREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPA 89
           L   +G    SR      +W Y+KTN LQD ++K  +N D+  + I     R++ +E+P 
Sbjct: 269 LARLLGLHTQSRSAIVQALWQYVKTNRLQDSHDKEYINGDKYFQQIF-DCPRLKFSEIPQ 327

Query: 90  -LIKLHFPKDP 99
            L  L  P DP
Sbjct: 328 RLTALLLPPDP 338

Plays a role in ATP dependent nucleosome remodeling by SMARCA4 containing complexes. Stimulates nuclear receptor mediated transcription (By similarity). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.

Mus musculus (taxid: 10090)

>sp|Q6STE5|SMRD3_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 OS=Homo sapiens GN=SMARCD3 PE=1 SV=1

 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 30  LREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPA 89
           L   +G    SR      +W Y+KTN LQD ++K  +N D+  + I     R++ +E+P 
Sbjct: 269 LARLLGLHTQSRSAIVQALWQYVKTNRLQDSHDKEYINGDKYFQQIF-DCPRLKFSEIPQ 327

Query: 90  -LIKLHFPKDP 99
            L  L  P DP
Sbjct: 328 RLTALLLPPDP 338

Plays a role in ATP dependent nucleosome remodeling by SMARCA4 containing complexes. Stimulates nuclear receptor mediated transcription. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.

Homo sapiens (taxid: 9606)

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	100
388505468	100	unknown [Medicago truncatula]	1.0	1.0	0.84	2e-42
224136902	100	predicted protein [Populus trichocarpa]	1.0	1.0	0.83	3e-42
225460865	100	PREDICTED: upstream activation factor su	1.0	1.0	0.85	3e-42
351724909	100	uncharacterized protein LOC100527179 [Gl	1.0	1.0	0.83	8e-42
356567136	100	PREDICTED: upstream activation factor su	1.0	1.0	0.83	4e-41
297799312	320	hypothetical protein ARALYDRAFT_354113 [	0.95	0.296	0.842	7e-41
15236880	106	SWIB/MDM2 domain-containing protein [Ara	1.0	0.943	0.81	2e-40
91107221	100	SWIb domain-containing protein [Solanum	1.0	1.0	0.79	3e-40
449531627	100	PREDICTED: upstream activation factor su	1.0	1.0	0.78	1e-37
449457359	127	PREDICTED: protein TRI1-like [Cucumis sa	0.89	0.700	0.764	6e-32

>gi|388505468|gb|AFK40800.1| unknown [Medicago truncatula]

 Score =  176 bits (445), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 84/100 (84%), Positives = 93/100 (93%)

Query: 1   MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
           MLPQ +KK V DNPKKLANLIDLVNLPSTLR+FVGQS+ SRL CFMRVWSYIKTNNLQDP
Sbjct: 1   MLPQRMKKAVTDNPKKLANLIDLVNLPSTLRDFVGQSQTSRLSCFMRVWSYIKTNNLQDP 60

Query: 61  NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
           NNKNVVNCD+KL+ IL+GK +V+LAELPALIKLHFPK+PK
Sbjct: 61  NNKNVVNCDEKLKGILLGKPQVDLAELPALIKLHFPKEPK 100

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224136902|ref|XP_002322444.1| predicted protein [Populus trichocarpa] gi|222869440|gb|EEF06571.1| predicted protein [Populus trichocarpa]

 Score =  175 bits (444), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 83/100 (83%), Positives = 92/100 (92%)

Query: 1   MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
           MLPQ +KK + DNPK+LANLIDLVNLPSTLR+FVGQS+IS LGCFMRVWSYIKTNNLQDP
Sbjct: 1   MLPQKMKKAITDNPKQLANLIDLVNLPSTLRDFVGQSQISHLGCFMRVWSYIKTNNLQDP 60

Query: 61  NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
           NNKNVVNCD+KL+SIL+GK +VEL ELPALIKLHFPK  K
Sbjct: 61  NNKNVVNCDEKLKSILLGKQQVELVELPALIKLHFPKQKK 100

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225460865|ref|XP_002277738.1| PREDICTED: upstream activation factor subunit UAF30 [Vitis vinifera] gi|297737490|emb|CBI26691.3| unnamed protein product [Vitis vinifera]

 Score =  175 bits (443), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 85/100 (85%), Positives = 91/100 (91%)

Query: 1   MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
           MLPQ VK+ + +NPKKLANLIDL NLPSTLREFVGQS+ISRLGCFMRVWSYIK NNLQDP
Sbjct: 1   MLPQRVKRAITENPKKLANLIDLANLPSTLREFVGQSQISRLGCFMRVWSYIKANNLQDP 60

Query: 61  NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
           NNKNVV CD KLRSIL+GK RVELAELPALIKLHFPK+ K
Sbjct: 61  NNKNVVICDDKLRSILLGKPRVELAELPALIKLHFPKERK 100

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724909|ref|NP_001236050.1| uncharacterized protein LOC100527179 [Glycine max] gi|255631726|gb|ACU16230.1| unknown [Glycine max]

 Score =  174 bits (440), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 83/100 (83%), Positives = 93/100 (93%)

Query: 1   MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
           MLPQ +KK + DNPKKLANLIDLVNLPSTLREFVGQS+ISRLGCF  +WSYIKTNNLQD 
Sbjct: 1   MLPQRMKKAITDNPKKLANLIDLVNLPSTLREFVGQSQISRLGCFKCIWSYIKTNNLQDQ 60

Query: 61  NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
           NNKNVVNCD+KL+SIL+GK +VELAELPALIK+HFPK+PK
Sbjct: 61  NNKNVVNCDEKLKSILLGKPQVELAELPALIKMHFPKEPK 100

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567136|ref|XP_003551777.1| PREDICTED: upstream activation factor subunit spp27-like [Glycine max]

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 83/100 (83%), Positives = 92/100 (92%)

Query: 1   MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
           MLPQ +KK + DNPKKLANLIDLVNLPSTLREFVGQS+ISRLGCF  VW YIKTNNLQD 
Sbjct: 1   MLPQRMKKAITDNPKKLANLIDLVNLPSTLREFVGQSQISRLGCFKCVWFYIKTNNLQDQ 60

Query: 61  NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
           NNKNVVNCD+KL+SIL+GK +VELAELPALIK+HFPK+PK
Sbjct: 61  NNKNVVNCDEKLKSILLGKPQVELAELPALIKMHFPKEPK 100

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799312|ref|XP_002867540.1| hypothetical protein ARALYDRAFT_354113 [Arabidopsis lyrata subsp. lyrata] gi|297313376|gb|EFH43799.1| hypothetical protein ARALYDRAFT_354113 [Arabidopsis lyrata subsp. lyrata]

 Score =  171 bits (432), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 80/95 (84%), Positives = 88/95 (92%)

Query: 6   VKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNV 65
           +KK + DNPKKL NLIDLVNLPSTLREFVGQS+ISRLGCFMRVWSYIKTNNLQDP NKNV
Sbjct: 226 LKKAITDNPKKLGNLIDLVNLPSTLREFVGQSQISRLGCFMRVWSYIKTNNLQDPKNKNV 285

Query: 66  VNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
           V CD+KL+SIL+GK RVEL ELP+LIKLHFPK+PK
Sbjct: 286 VICDEKLKSILLGKQRVELVELPSLIKLHFPKEPK 320

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15236880|ref|NP_194411.1| SWIB/MDM2 domain-containing protein [Arabidopsis thaliana] gi|186513923|ref|NP_001119064.1| SWIB/MDM2 domain-containing protein [Arabidopsis thaliana] gi|4455204|emb|CAB36527.1| putative protein [Arabidopsis thaliana] gi|7269533|emb|CAB79536.1| putative protein [Arabidopsis thaliana] gi|38566544|gb|AAR24162.1| At4g26810 [Arabidopsis thaliana] gi|40823827|gb|AAR92306.1| At4g26810 [Arabidopsis thaliana] gi|332659855|gb|AEE85255.1| SWIB/MDM2 domain-containing protein [Arabidopsis thaliana] gi|332659856|gb|AEE85256.1| SWIB/MDM2 domain-containing protein [Arabidopsis thaliana]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 81/100 (81%), Positives = 90/100 (90%)

Query: 1   MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
           MLPQ +KK + DNPKKL NLIDLVNLPSTLR FVGQS+ISRLGCFMRVWSYIKTNNLQDP
Sbjct: 1   MLPQRLKKAITDNPKKLGNLIDLVNLPSTLRNFVGQSQISRLGCFMRVWSYIKTNNLQDP 60

Query: 61  NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
            NKNVV CD+KL+SIL+GK RVEL +LP+LIKLHFPK+ K
Sbjct: 61  KNKNVVICDEKLKSILLGKQRVELVDLPSLIKLHFPKEQK 100

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|91107221|gb|ABE11612.1| SWIb domain-containing protein [Solanum chacoense]

 Score =  168 bits (426), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 79/100 (79%), Positives = 90/100 (90%)

Query: 1   MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
           MLPQ +KK + DNPKKLANLIDLVNLPSTLREF+GQS+ SRLGCF RVWSYIK NNLQDP
Sbjct: 1   MLPQRMKKVMTDNPKKLANLIDLVNLPSTLREFMGQSQTSRLGCFKRVWSYIKENNLQDP 60

Query: 61  NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
           NNKN+VNCD+KL+S+L+GK +VEL ELP LIKLHFPK P+
Sbjct: 61  NNKNLVNCDEKLKSVLLGKPQVELTELPTLIKLHFPKQPR 100

Source: Solanum chacoense

Species: Solanum chacoense

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449531627|ref|XP_004172787.1| PREDICTED: upstream activation factor subunit spp27-like [Cucumis sativus]

 Score =  160 bits (404), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 78/100 (78%), Positives = 87/100 (87%)

Query: 1   MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
           M  + +K  + DNPKKLANLIDLVNLPSTLREFVG S+ISRLGCF  VWSYIKTNNLQDP
Sbjct: 1   MATKRMKMAITDNPKKLANLIDLVNLPSTLREFVGHSQISRLGCFKCVWSYIKTNNLQDP 60

Query: 61  NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
            NKNVV CD+KL+SIL+GK +VELAELPALIKLHFPK+ K
Sbjct: 61  TNKNVVICDEKLKSILLGKPKVELAELPALIKLHFPKNSK 100

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457359|ref|XP_004146416.1| PREDICTED: protein TRI1-like [Cucumis sativus]

 Score =  141 bits (355), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 68/89 (76%), Positives = 76/89 (85%)

Query: 1  MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
          M  + +K  + DNPKKLANLIDLVNLPSTLREFVG S+ISRLGCF  VWSYIKTNNLQDP
Sbjct: 1  MATKRMKMAITDNPKKLANLIDLVNLPSTLREFVGHSQISRLGCFKCVWSYIKTNNLQDP 60

Query: 61 NNKNVVNCDQKLRSILMGKSRVELAELPA 89
           NKNVV CD+KL+SIL+GK +VELAELP 
Sbjct: 61 TNKNVVICDEKLKSILLGKPKVELAELPT 89

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	100
TAIR|locus:2116302	106	AT4G26810 "AT4G26810" [Arabido	1.0	0.943	0.81	1.2e-40
TAIR|locus:505006294	109	AT2G35605 "AT2G35605" [Arabido	0.97	0.889	0.319	2.7e-13
TAIR|locus:2028671	112	AT1G31760 "AT1G31760" [Arabido	0.68	0.607	0.411	3.9e-12
TAIR|locus:2116189	144	AT4G34290 "AT4G34290" [Arabido	0.66	0.458	0.439	7.4e-11
TAIR|locus:2060469	141	AT2G14880 "AT2G14880" [Arabido	0.66	0.468	0.409	4.1e-10
SGD|S000005821	228	UAF30 "Subunit of UAF (upstrea	0.74	0.324	0.389	1.2e-09
TAIR|locus:2096404	143	AT3G03590 "AT3G03590" [Arabido	0.9	0.629	0.308	3.6e-09
UNIPROTKB|G4MMD0	285	MGG_01988 "Uncharacterized pro	0.73	0.256	0.346	8.6e-08
POMBASE|SPCC285.17	233	spp27 "RNA polymerase I upstre	0.52	0.223	0.423	1e-07
TAIR|locus:2010197	372	AT1G49520 "AT1G49520" [Arabido	0.64	0.172	0.369	3.3e-07

TAIR|locus:2116302 AT4G26810 "AT4G26810" [Arabidopsis thaliana (taxid:3702)]

 Score = 432 (157.1 bits), Expect = 1.2e-40, P = 1.2e-40
 Identities = 81/100 (81%), Positives = 90/100 (90%)

Query:     1 MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
             MLPQ +KK + DNPKKL NLIDLVNLPSTLR FVGQS+ISRLGCFMRVWSYIKTNNLQDP
Sbjct:     1 MLPQRLKKAITDNPKKLGNLIDLVNLPSTLRNFVGQSQISRLGCFMRVWSYIKTNNLQDP 60

Query:    61 NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDPK 100
              NKNVV CD+KL+SIL+GK RVEL +LP+LIKLHFPK+ K
Sbjct:    61 KNKNVVICDEKLKSILLGKQRVELVDLPSLIKLHFPKEQK 100

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:505006294 AT2G35605 "AT2G35605" [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 31/97 (31%), Positives = 54/97 (55%)

Query:     1 MLPQGVKKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60
             ++ +    T     ++   ++ +V +   L  F+G++ +SR     ++W YIK NNLQ+P
Sbjct:    11 LMAKAASSTGAKTGRQGTGILKVVPVSKPLANFIGENEVSRTTAVKKIWEYIKLNNLQNP 70

Query:    61 NNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK 97
              NK  + CD++L++I  GK  V   E+  L+  HFPK
Sbjct:    71 VNKREILCDEQLKTIFSGKDTVGFLEISKLLSQHFPK 107

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2028671 AT1G31760 "AT1G31760" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 28/68 (41%), Positives = 43/68 (63%)

Query:    30 LREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPA 89
             L  F G+  ++R     +VW Y+K +NLQ+P NK  ++CD KL++I  GK +V + E+  
Sbjct:    43 LASFAGERELTRGSALKKVWEYVKLHNLQNPANKKEIHCDDKLKTIFDGKDKVGITEIMK 102

Query:    90 LIKLHFPK 97
             L+  HFPK
Sbjct:   103 LLSPHFPK 110

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2116189 AT4G34290 "AT4G34290" [Arabidopsis thaliana (taxid:3702)]

 Score = 151 (58.2 bits), Expect = 7.4e-11, P = 7.4e-11
 Identities = 29/66 (43%), Positives = 40/66 (60%)

Query:    30 LREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPA 89
             +++ VG   I R     R+W+YIK ++LQDP NK  + CD+KL+ I  GK RV   E+  
Sbjct:    78 MQDVVGVPEIPRTQALKRIWAYIKEHDLQDPQNKRDILCDEKLKKIFEGKERVGFLEIAK 137

Query:    90 LIKLHF 95
             LI  HF
Sbjct:   138 LIGPHF 143

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2060469 AT2G14880 "AT2G14880" [Arabidopsis thaliana (taxid:3702)]

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 27/66 (40%), Positives = 40/66 (60%)

Query:    30 LREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPA 89
             +++ V    I+R     R+W+YIK ++LQDP NK  + CD+KL+ I  G+ RV   E+  
Sbjct:    75 MQDIVELPEIARTQALKRIWAYIKEHDLQDPQNKREILCDEKLKKIFEGRDRVGFLEIAK 134

Query:    90 LIKLHF 95
             LI  HF
Sbjct:   135 LIGPHF 140

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

SGD|S000005821 UAF30 "Subunit of UAF (upstream activation factor)" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 140 (54.3 bits), Expect = 1.2e-09, P = 1.2e-09
 Identities = 30/77 (38%), Positives = 46/77 (59%)

Query:    24 VNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVE 83
             V L  +L   +G+  ++R     R+W+YIK +NLQ+PNNK  + CD+KL  IL GKS   
Sbjct:   124 VTLSKSLASLLGEHELTRTEVVRRLWAYIKAHNLQNPNNKKEILCDEKLELIL-GKS-TN 181

Query:    84 LAELPALIKLHFPKDPK 100
             + E+  ++  H   +PK
Sbjct:   182 MFEMHKILASHMT-EPK 197

GO:0005730 "nucleolus" evidence=IEA;IDA

GO:0042790 "transcription of nuclear large rRNA transcript from RNA polymerase I promoter" evidence=IMP

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0001168 "RNA polymerase I upstream control element sequence-specific DNA binding transcription factor activity" evidence=IMP

GO:0001165 "RNA polymerase I upstream control element sequence-specific DNA binding" evidence=IDA

GO:0006325 "chromatin organization" evidence=IMP

GO:0005634 "nucleus" evidence=IEA

GO:0000500 "RNA polymerase I upstream activating factor complex" evidence=IDA

TAIR|locus:2096404 AT3G03590 "AT3G03590" [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 3.6e-09, P = 3.6e-09
 Identities = 29/94 (30%), Positives = 48/94 (51%)

Query:     8 KTVIDNPKKLA----NLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNK 63
             K   D+P K       +  +  +   L +F+G    SR      +W+YIK+++LQ+P +K
Sbjct:    48 KAKSDSPAKKTPRSTGIFKVTPVSPVLAQFLGTGETSRTDAIKGIWTYIKSHDLQNPADK 107

Query:    64 NVVNCDQKLRSILMGKSRVELAELPALIKLHFPK 97
               + CD+ L+ I  GK +V   E+  L+  HF K
Sbjct:   108 REIFCDETLKLIFEGKDKVGFLEISKLLSPHFVK 141

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006661 "phosphatidylinositol biosynthetic process" evidence=RCA

UNIPROTKB|G4MMD0 MGG_01988 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 127 (49.8 bits), Expect = 8.6e-08, P = 8.6e-08
 Identities = 26/75 (34%), Positives = 46/75 (61%)

Query:    25 NLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVEL 84
             +L ++L E  G+  +SR     ++W +IK NNLQDPN+K  + CD+K++++   +S + +
Sbjct:   210 HLSASLAEVCGEPTLSRPQVVKKLWEHIKGNNLQDPNDKRQILCDEKMQAVFK-QSSLNM 268

Query:    85 AELPALIKLH-FPKD 98
               +  LI  H +P D
Sbjct:   269 FAMNKLIGSHLYPVD 283

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

POMBASE|SPCC285.17 spp27 "RNA polymerase I upstream activation factor complex subunit Spp27" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 124 (48.7 bits), Expect = 1.0e-07, P = 1.0e-07
 Identities = 22/52 (42%), Positives = 34/52 (65%)

Query:    24 VNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSI 75
             + L   L EF+G  ++SR     ++W YIK ++LQDPN+K  + CD KL+S+
Sbjct:   121 MKLSPKLAEFLGLEQLSRPQTVKKLWEYIKAHDLQDPNDKRTILCDDKLKSV 172

GO:0000500 "RNA polymerase I upstream activating factor complex" evidence=NAS

GO:0003677 "DNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0045943 "positive regulation of transcription from RNA polymerase I promoter" evidence=TAS

GO:0001168 "RNA polymerase I upstream control element sequence-specific DNA binding transcription factor activity" evidence=TAS

TAIR|locus:2010197 AT1G49520 "AT1G49520" [Arabidopsis thaliana (taxid:3702)]

 Score = 124 (48.7 bits), Expect = 3.3e-07, P = 3.3e-07
 Identities = 24/65 (36%), Positives = 37/65 (56%)

Query:    12 DNPKKLAN-LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQ 70
             + PKK       + +L   L+ F G  +++R      +W YIK NNLQDP++K  + CD+
Sbjct:   242 EKPKKKGGGFTKVCSLSPELQAFTGTPQLARTEVVKMLWKYIKENNLQDPSDKRTIICDE 301

Query:    71 KLRSI 75
              LRS+
Sbjct:   302 SLRSL 306

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Your Input: eugene3.00151157 hypothetical protein (101 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	100
pfam02201	76	pfam02201, SWIB, SWIB/MDM2 domain	5e-21
smart00151	77	smart00151, SWIB, SWI complex, BAF60b domains	2e-13
PRK14724	987	PRK14724, PRK14724, DNA topoisomerase III; Provisi	1e-10
PRK06319	860	PRK06319, PRK06319, DNA topoisomerase I/SWI domain	3e-10
COG5531	237	COG5531, COG5531, SWIB-domain-containing proteins	2e-08

>gnl|CDD|145386 pfam02201, SWIB, SWIB/MDM2 domain

 Score = 78.8 bits (195), Expect = 5e-21
 Identities = 31/77 (40%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 20 LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGK 79
          L     L   L +F+G   +SR     ++W YIK +NLQDP NK ++ CD+KL+SI  G 
Sbjct: 1  LTKPFPLSPDLAKFLGAGELSRTEVVKKLWQYIKEHNLQDPKNKRIILCDEKLKSIF-GG 59

Query: 80 SRVELAELPALIKLHFP 96
           RV   E+  L+  HF 
Sbjct: 60 DRVGFFEMSKLLSSHFI 76

This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2. Length = 76

>gnl|CDD|128456 smart00151, SWIB, SWI complex, BAF60b domains

 Score = 59.6 bits (145), Expect = 2e-13
 Identities = 28/72 (38%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 24 VNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVE 83
          V L   L + +G   ++R     R+W YIK +NLQDP NK  + CD KL  I  GK R++
Sbjct: 5  VTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIF-GKDRMD 63

Query: 84 LAELPALIKLHF 95
          + E+  L+  H 
Sbjct: 64 MFEMNKLLTPHL 75

Length = 77

>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 27  PS-TLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELA 85
           PS  L   +G   ++R     ++W YIK NNLQDP +K  +N D KLR +  GK +V + 
Sbjct: 918 PSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVF-GKDQVTMF 976

Query: 86  ELPALIKLH 94
           EL  ++  H
Sbjct: 977 ELAGIVGKH 985

Length = 987

>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein; Validated

 Score = 54.8 bits (132), Expect = 3e-10
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 30  LREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPA 89
           L   +G   + R     +VW YIK + LQ P NK ++  D KL+ ++ G   +++ +L  
Sbjct: 794 LAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVI-GPDPIDMFQLSK 852

Query: 90  LIKLHFPK 97
            +  H  K
Sbjct: 853 KLSQHLIK 860

Length = 860

>gnl|CDD|227818 COG5531, COG5531, SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]

 Score = 49.0 bits (117), Expect = 2e-08
 Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 12  DNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQK 71
               K +   + V L   L   +G    +R     ++W YIK +NLQDPNNK ++ CD K
Sbjct: 113 STISKNSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSK 172

Query: 72  LRSILMGKSRVELAELPALIKLHFPKDPK 100
           L+ +L G   +++ EL   +  H  K   
Sbjct: 173 LKKVL-GSDPIDMFELTKPLSPHLIKYTI 200

Length = 237

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	100
smart00151	77	SWIB SWI complex, BAF60b domains.	99.96
PF02201	76	SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SW	99.96
KOG1946	240	consensus RNA polymerase I transcription factor UA	99.94
COG5531	237	SWIB-domain-containing proteins implicated in chro	99.9
PRK14724	987	DNA topoisomerase III; Provisional	99.88
KOG2570	420	consensus SWI/SNF transcription activation complex	99.8
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	99.59
KOG2522	560	consensus Filamentous baseplate protein Ligatin, c	95.15
PRK05350	82	acyl carrier protein; Provisional	87.92
PRK05828	84	acyl carrier protein; Validated	83.48
CHL00124	82	acpP acyl carrier protein; Validated	82.07
PRK12449	80	acyl carrier protein; Provisional	80.19

>smart00151 SWIB SWI complex, BAF60b domains

Probab=99.96  E-value=4.1e-29  Score=159.23  Aligned_cols=77  Identities=38%  Similarity=0.703  Sum_probs=74.4

Q ss_pred             ccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCC
Q 034230           20 LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK   97 (100)
Q Consensus        20 ~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~   97 (100)
                      ++++|.+|++|++|+|.+++||++|++++|+|||+||||||+|++.|+||+.|+++| |++++.|++|+++|++||.+
T Consensus         1 ~~~~~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~-~~~~v~~~~~~~ll~~Hl~~   77 (77)
T smart00151        1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIF-GKDRMDMFEMNKLLTPHLIK   77 (77)
T ss_pred             CCCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHH-CcCeecHHHHHHHHHHHcCC
Confidence            468899999999999999999999999999999999999999999999999999999 99999999999999999975

>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []

Probab=99.96  E-value=3.6e-30  Score=163.76  Aligned_cols=75  Identities=41%  Similarity=0.810  Sum_probs=70.3

Q ss_pred             ccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230           20 LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF   95 (100)
Q Consensus        20 ~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl   95 (100)
                      |.++|+||++|++++|.+++||++|+++||+||++||||||+|++.|+||+.|++|| |++++.+++|+++|++||
T Consensus         1 ~~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf-~~~~v~~~~i~~~l~~hl   75 (76)
T PF02201_consen    1 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLF-GKDSVNFFEIPKLLKPHL   75 (76)
T ss_dssp             -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHH-HTSECSEEETTHHHHHHH
T ss_pred             CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHh-CCCeecHhhHHHHHHHhc
Confidence            568899999999999999999999999999999999999999999999999999999 889999999999999997

The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....

>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]

Probab=99.94  E-value=3.2e-27  Score=177.95  Aligned_cols=81  Identities=43%  Similarity=0.749  Sum_probs=78.2

Q ss_pred             CCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCC
Q 034230           18 ANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK   97 (100)
Q Consensus        18 ~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~   97 (100)
                      +|+++.+.+|+.|+.|+|.+++||.+|++.||+|||+||||||.|++.|+||++|+.|| |..+|++++|.++|.+||.+
T Consensus        98 ~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF-~~k~v~~fem~KLL~~H~~~  176 (240)
T KOG1946|consen   98 WGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIF-GKKRVGMFEMLKLLTKHFLK  176 (240)
T ss_pred             cCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHh-ccCccceeeHHHHHHHhccC
Confidence            68999999999999999999999999999999999999999999999999999999999 88889999999999999987


Q ss_pred             CC
Q 034230           98 DP   99 (100)
Q Consensus        98 ~p   99 (100)
                      ..
T Consensus       177 ~~  178 (240)
T KOG1946|consen  177 NQ  178 (240)
T ss_pred             cc
Confidence            54

>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]

Probab=99.90  E-value=3.7e-24  Score=160.88  Aligned_cols=84  Identities=33%  Similarity=0.558  Sum_probs=79.7

Q ss_pred             CCCCCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhcc
Q 034230           15 KKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLH   94 (100)
Q Consensus        15 ~~~~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~H   94 (100)
                      .+++...+.|.+|+.||.|||..++||+|||+.||+|||.||||||+||+.|.||++|+.|| |.+.+.||+|.+.|.+|
T Consensus       116 ~~~~~~~~~~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~-g~~p~~mf~~~k~l~~h  194 (237)
T COG5531         116 SKNSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVL-GSDPIDMFELTKPLSPH  194 (237)
T ss_pred             ccccCCCCceecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHh-CCCchhhhhhhcccccc
Confidence            45677899999999999999999999999999999999999999999999999999999999 78999999999999999


Q ss_pred             CCCCC
Q 034230           95 FPKDP   99 (100)
Q Consensus        95 l~~~p   99 (100)
                      +.+-|
T Consensus       195 l~~~~  199 (237)
T COG5531         195 LIKYT  199 (237)
T ss_pred             eecCc
Confidence            98854

>PRK14724 DNA topoisomerase III; Provisional

Probab=99.88  E-value=3.1e-23  Score=179.60  Aligned_cols=80  Identities=34%  Similarity=0.613  Sum_probs=75.6

Q ss_pred             CCCCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230           16 KLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF   95 (100)
Q Consensus        16 ~~~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl   95 (100)
                      +...+...+.+|++|++|+|..++||++|++.||+|||+||||||.|++.|+||++|+.|| |++++.|++|+++|++||
T Consensus       908 ~~~~~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vf-g~~~~~~~~~~~~l~~hl  986 (987)
T PRK14724        908 KAAPPAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVF-GKDQVTMFELAGIVGKHL  986 (987)
T ss_pred             hccccccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHh-CCCcccHHHHHHHHHHhc
Confidence            3334677999999999999999999999999999999999999999999999999999999 999999999999999998


Q ss_pred             C
Q 034230           96 P   96 (100)
Q Consensus        96 ~   96 (100)
                      .
T Consensus       987 ~  987 (987)
T PRK14724        987 S  987 (987)
T ss_pred             C
Confidence            5

>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]

Probab=99.80  E-value=3.6e-20  Score=147.65  Aligned_cols=78  Identities=32%  Similarity=0.617  Sum_probs=75.2

Q ss_pred             cccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCCCC
Q 034230           21 IDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDP   99 (100)
Q Consensus        21 ~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~~p   99 (100)
                      ...|++||.||.+||+...||++|+.+||+|||.|+|||++++.+|+||..|+++| |++++.|.+|+.+|++||.+.|
T Consensus       206 P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif-~~~rl~F~elp~~l~~lL~P~d  283 (420)
T KOG2570|consen  206 PEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIF-GVDRLKFPELPQLLNPLLSPPD  283 (420)
T ss_pred             CcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhh-cccccccccchhhhhhccCCCC
Confidence            34589999999999999999999999999999999999999999999999999999 9999999999999999999876

>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated

Probab=99.59  E-value=1.2e-15  Score=131.09  Aligned_cols=77  Identities=27%  Similarity=0.498  Sum_probs=73.0

Q ss_pred             ccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCC
Q 034230           20 LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK   97 (100)
Q Consensus        20 ~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~   97 (100)
                      .+..|.+|++|+.++|..+++|.++++.+|+||++|+||||++++.|.||++|+++| |++++.+++|+++++.|+.+
T Consensus       784 ~~~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf-~~~~~~~~~~~k~l~~hl~~  860 (860)
T PRK06319        784 AGPLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVI-GPDPIDMFQLSKKLSQHLIK  860 (860)
T ss_pred             cccccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhh-CcCccchhhhHHHHHhhhcC
Confidence            445688999999999999999999999999999999999999999999999999999 89999999999999999865

>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]

Probab=95.15  E-value=0.055  Score=45.01  Aligned_cols=57  Identities=25%  Similarity=0.293  Sum_probs=46.1

Q ss_pred             ccccccCCHHHHHhh---CC---CcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhh
Q 034230           20 LIDLVNLPSTLREFV---GQ---SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSIL   76 (100)
Q Consensus        20 ~~~~~~lS~~La~~l---G~---~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf   76 (100)
                      +...|+.+.....++   |.   ...|-+||...+.+||+.|||-|+.||..|+.|.-|....
T Consensus       357 i~~lYk~~~~~~~Lf~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~  419 (560)
T KOG2522|consen  357 ILTLYKPFNLAKDLFKEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMV  419 (560)
T ss_pred             eeeeeccchHHHHHHHhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHH
Confidence            445566666555555   43   4677899999999999999999999999999999998865

>PRK05350 acyl carrier protein; Provisional

Probab=87.92  E-value=0.38  Score=30.09  Aligned_cols=53  Identities=9%  Similarity=0.118  Sum_probs=43.4

Q ss_pred             ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230           39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF   95 (100)
Q Consensus        39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl   95 (100)
                      |||.+|...+.++|.+. +.  .+...|.+|..|..-+ |-+++.+-+|.-.|..+|
T Consensus         2 m~~~~i~~~v~~ii~~~-~~--~~~~~i~~d~~l~~dl-g~DSld~veli~~lE~~f   54 (82)
T PRK05350          2 MTREEILERLRAILVEL-FE--IDPEDITPEANLYEDL-DLDSIDAVDLVVHLQKLT   54 (82)
T ss_pred             CCHHHHHHHHHHHHHHH-hC--CCHHHCCCCccchhhc-CCCHHHHHHHHHHHHHHH
Confidence            78999999999999987 42  1224699999997777 999999988888887776

>PRK05828 acyl carrier protein; Validated

Probab=83.48  E-value=1.5  Score=28.02  Aligned_cols=53  Identities=11%  Similarity=0.246  Sum_probs=41.4

Q ss_pred             ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230           39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF   95 (100)
Q Consensus        39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl   95 (100)
                      |||.+|...|-+.|.+.++.-  +-..|.+|..|.. + |-|++.+-++.-.|...|
T Consensus         1 m~~~eI~~~i~~ii~e~~~~~--~~d~i~~~~~~~d-L-g~DSLd~velv~~lE~~f   53 (84)
T PRK05828          1 MQEMEILLKIKEIAKKKNFAV--TLDESNINKPYRE-L-KIDSLDMFSIIVSLESEF   53 (84)
T ss_pred             CCHHHHHHHHHHHHHHhccCC--CcccccCCCCHHh-c-CCCHHHHHHHHHHHHHHH
Confidence            689999999999998865422  2235688899988 6 999998888888777665

>CHL00124 acpP acyl carrier protein; Validated

Probab=82.07  E-value=0.94  Score=27.98  Aligned_cols=53  Identities=21%  Similarity=0.278  Sum_probs=41.7

Q ss_pred             ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230           39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF   95 (100)
Q Consensus        39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl   95 (100)
                      |+|.+|...+-++|.+.-=.++.   .|.+|..|..-+ |-+++.+-+|...|...|
T Consensus         1 M~~~~i~~~l~~ii~~~~~~~~~---~i~~d~~l~~dl-g~DSl~~~eli~~le~~f   53 (82)
T CHL00124          1 MTKNDIFEKVQSIVAEQLGIEKS---EVTLDANFTRDL-GADSLDVVELVMAIEEKF   53 (82)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCHH---HCCCCcchhhhc-CCcHHHHHHHHHHHHHHH
Confidence            67899999999999887423333   599999999977 999998888887776655

>PRK12449 acyl carrier protein; Provisional

Probab=80.19  E-value=2.5  Score=25.92  Aligned_cols=53  Identities=19%  Similarity=0.236  Sum_probs=40.6

Q ss_pred             ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230           39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF   95 (100)
Q Consensus        39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl   95 (100)
                      |+|.+|...+-+++.+.-=.++.   .|.+|..|..-+ |-+++.+.+|.-.|...|
T Consensus         1 m~~~~i~~~l~~il~~~~~~~~~---~i~~~~~l~~dl-g~DSl~~~~li~~lE~~f   53 (80)
T PRK12449          1 MTREEIFERLINLIQKQRSYLSL---AITEQTHLKDDL-AVDSIELVEFIINVEDEF   53 (80)
T ss_pred             CCHHHHHHHHHHHHHHHhCCCcc---ccCCCCcHHHHc-CCcHHHHHHHHHHHHHHh
Confidence            57889999999998874323332   589999998887 999998888877776554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	100
1uhr_A	93	Solution Structure Of The Swib Domain Of Mouse Brg1		3e-05

>pdb|1UHR|A Chain A, Solution Structure Of The Swib Domain Of Mouse Brg1- Associated Factor 60a Length = 93

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 48 VWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPA-LIKLHFPKDP 99
          +W YIKT+ LQDP+ +  V CD+ L+ I   + R++ +E+P  L  L  P +P
Sbjct: 36 LWQYIKTHKLQDPHEREFVLCDKYLQQIFESQ-RMKFSEIPQRLHALLMPPEP 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	100
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	1e-19
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	2e-19
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	3e-19

>1v31_A Hypothetical protein RAFL11-05-P19; SWI/SNF complex subunit, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.42.1.1 Length = 93

 Score = 75.6 bits (186), Expect = 1e-19
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 24  VNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVE 83
             L + L + +G    +R      +W Y+K   LQ+PN+ +  NCD  L+ +  G+ +++
Sbjct: 12  FKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVF-GEEKLK 70

Query: 84  LAELPALIKLHF-PKDPK 100
              +   I  H  P  P 
Sbjct: 71  FTMVSQKISHHLSPPPPS 88

>1uhr_A SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily...; structural genomics, chromatin remodeling; NMR {Mus musculus} SCOP: a.42.1.1 Length = 93

 Score = 74.8 bits (184), Expect = 2e-19
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 24  VNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVE 83
             L   L   +G    +R      +W YIKT+ LQDP+ +  V CD+ L+ I     R++
Sbjct: 12  FKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIF-ESQRMK 70

Query: 84  LAELPALIKLHF-PKDPK 100
            +E+P  +     P +P 
Sbjct: 71  FSEIPQRLHALLMPPEPS 88

>1v32_A AT5G08430, hypothetical protein RAFL09-47-K03; SWI/SNF complex subunit, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.42.1.1 Length = 101

 Score = 74.5 bits (183), Expect = 3e-19
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 30 LREFVG------QSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVE 83
          L EF+          ISR      +  YI    L DP+NK  V CD++L  +  G   + 
Sbjct: 20 LIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLF-GTRTIF 78

Query: 84 LAELPALIKLHFPK 97
            ++  L++ H+ +
Sbjct: 79 RMKVYDLLEKHYKE 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	100
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	99.97
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	99.97
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	99.96
1z1m_A	119	Ubiquitin-protein ligase E3 MDM2; peptide-binding	97.75
3dac_M	130	MDM4 protein; MDMX, MDM4, HDMX, HDM4, MDM-4, MDM-X	97.71
2z5s_M	140	MDM4 protein, zebrafish MDMX; MDMX, MDM4, acetylat	97.58
1ycq_A	107	MDM2, MDM2; anti-oncogene, DNA-binding, transcript	97.51
3fea_A	100	MDM4 protein; HDMX, HDM4,human MDM4, human MDMX, p	97.45
2axi_A	115	Ubiquitin-protein ligase E3 MDM2; drug design, pro	97.27
2kwl_A	84	ACP, acyl carrier protein; structural genomics, se	85.02

>1v31_A Hypothetical protein RAFL11-05-P19; SWI/SNF complex subunit, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.42.1.1

Probab=99.97  E-value=7.9e-32  Score=176.61  Aligned_cols=81  Identities=23%  Similarity=0.554  Sum_probs=77.5

Q ss_pred             CCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCC
Q 034230           18 ANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK   97 (100)
Q Consensus        18 ~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~   97 (100)
                      ....++|++|++||+|+|.+++||++|++.||+|||+||||||+||+.|+||++|++|| |++++.|++|+++|++||.+
T Consensus         6 ~~~p~~~~lS~~La~~lG~~~~sr~evvk~lW~YIK~n~Lqdp~~k~~I~cD~~L~~lf-g~~~v~~~~~~klL~~Hl~p   84 (93)
T 1v31_A            6 SGVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVF-GEEKLKFTMVSQKISHHLSP   84 (93)
T ss_dssp             CSSCCCEECCHHHHHHSCCSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHS-CSSEEETTTTHHHHHHHCBC
T ss_pred             CCCCCccccCHHHHHHHCCCccCHHHHHHHHHHHHHHccCcCcccCceeehhHHHHHHh-CCCcccHHHHHHHHHHhcCC
Confidence            45678999999999999999999999999999999999999999999999999999999 99999999999999999977


Q ss_pred             CC
Q 034230           98 DP   99 (100)
Q Consensus        98 ~p   99 (100)
                      .+
T Consensus        85 ~~   86 (93)
T 1v31_A           85 PP   86 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>1uhr_A SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily...; structural genomics, chromatin remodeling; NMR {Mus musculus} SCOP: a.42.1.1

Probab=99.97  E-value=2.5e-31  Score=174.30  Aligned_cols=80  Identities=26%  Similarity=0.481  Sum_probs=76.5

Q ss_pred             CccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCCC
Q 034230           19 NLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKD   98 (100)
Q Consensus        19 ~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~~   98 (100)
                      ...++|++|++||+|+|.+++||++|++.||+|||+||||||+||+.|+||++|++|| |++++.|++|+++|++||.+.
T Consensus         7 ~~p~~~~lS~~La~~lG~~~~sr~evvk~lW~YIK~n~Lqdp~~k~~I~cD~~Lk~lf-g~~~v~~~~~~klL~~Hl~p~   85 (93)
T 1uhr_A            7 GQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIF-ESQRMKFSEIPQRLHALLMPP   85 (93)
T ss_dssp             SSCCEEEECTTHHHHTCCSEEEHHHHHHHHHHHHHHTTCBCSSCSSEECCCTTHHHHT-CCSSEEGGGSHHHHHHHEECS
T ss_pred             cCCCccCcCHHHHHHHCCCccCHHHHHHHHHHHHHhccCCCccccceeechHHHHHHh-CCCcccHHHHHHHHHHhcCCC
Confidence            3567899999999999999999999999999999999999999999999999999999 999999999999999999876


Q ss_pred             C
Q 034230           99 P   99 (100)
Q Consensus        99 p   99 (100)
                      +
T Consensus        86 ~   86 (93)
T 1uhr_A           86 E   86 (93)
T ss_dssp             S
T ss_pred             C
Confidence            5

>1v32_A AT5G08430, hypothetical protein RAFL09-47-K03; SWI/SNF complex subunit, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.42.1.1

Probab=99.96  E-value=2.1e-29  Score=167.58  Aligned_cols=75  Identities=28%  Similarity=0.442  Sum_probs=71.2

Q ss_pred             cccCCHHHHHhh---CC---CcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCC
Q 034230           23 LVNLPSTLREFV---GQ---SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFP   96 (100)
Q Consensus        23 ~~~lS~~La~~l---G~---~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~   96 (100)
                      .-.+|++||+||   |.   +++||++|++.||+|||+||||||+||+.|+||++|++|| |+++|.|++|+++|++||.
T Consensus        13 ~~w~S~eLa~fl~~iG~~~~~~~sR~eVvk~lW~YIK~nnLQdp~~Kr~I~cD~kLk~lF-g~~~v~~~~m~klL~~Hl~   91 (101)
T 1v32_A           13 VGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLF-GTRTIFRMKVYDLLEKHYK   91 (101)
T ss_dssp             SSSSCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCTTEEECCSHHHHHT-CCSEEETTHHHHHHHHHSC
T ss_pred             cccCCHHHHHHHHHcCCCCccccCHHHHHHHHHHHHHhhcCcCcccCCeeeccHHHHHHH-CCCcccHHHHHHHHHHHcC
Confidence            347899999999   87   5799999999999999999999999999999999999999 9999999999999999998


Q ss_pred             CC
Q 034230           97 KD   98 (100)
Q Consensus        97 ~~   98 (100)
                      +.
T Consensus        92 ~~   93 (101)
T 1v32_A           92 EN   93 (101)
T ss_dssp             SC
T ss_pred             cc
Confidence            75

>1z1m_A Ubiquitin-protein ligase E3 MDM2; peptide-binding groove, psudosymmetry, alpha-beta domains; NMR {Homo sapiens}

Probab=97.75  E-value=0.00011  Score=49.60  Aligned_cols=75  Identities=19%  Similarity=0.326  Sum_probs=59.7

Q ss_pred             ccccccCCHHHHHhh---CC--CcccHHHHHHHHHHHHhhcCCCCCCCCceeecc-hhHHhhhcCCCeeccccHHHHHhc
Q 034230           20 LIDLVNLPSTLREFV---GQ--SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCD-QKLRSILMGKSRVELAELPALIKL   93 (100)
Q Consensus        20 ~~~~~~lS~~La~~l---G~--~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cD-e~Lk~lf~g~~~i~~~el~~ll~~   93 (100)
                      ....++-.+.|-.+|   |-  ...|+-+|+..+-+||-.+.|.|+.+..+|.|. +.|.++| |++.+++-+-..+...
T Consensus        24 qe~~VrPk~~LLkiLq~aGA~~~vfT~keV~~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~-g~~~Fsvkdp~~l~~m  102 (119)
T 1z1m_A           24 QETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLF-GVPSFSVKEHRKIYTM  102 (119)
T ss_dssp             SCCCCCCSTTSHHHHHHHTCCCSCCCTTHHHHHHHHHHHTTTCSCSSSSCEECCTTSHHHHHS-CCSCEETTCHHHHHHH
T ss_pred             ccccccccHHHHHHHHHhccccceeechheeehhhhhhhHhhhcccccCcEEeeCCccccccc-CccceeecCcHHHHHH
Confidence            344666667777776   43  578889999999999999999999999999995 6679998 9999988765555544


Q ss_pred             cC
Q 034230           94 HF   95 (100)
Q Consensus        94 Hl   95 (100)
                      |.
T Consensus       103 l~  104 (119)
T 1z1m_A          103 IY  104 (119)
T ss_dssp             HS
T ss_pred             HH
Confidence            43

>3dac_M MDM4 protein; MDMX, MDM4, HDMX, HDM4, MDM-4, MDM-X, MDM2, HDM2, nucleus, oncogene, apoptosis, cell cycle, disease mutation; 1.80A {Danio rerio}

Probab=97.71  E-value=8.4e-05  Score=50.73  Aligned_cols=74  Identities=19%  Similarity=0.319  Sum_probs=63.1

Q ss_pred             cccCCHHHHHhh---C--CCcccHHHHHHHHHHHHhhcCCCCCCCCceeec-chhHHhhhcCCCeecccc---HHHHHhc
Q 034230           23 LVNLPSTLREFV---G--QSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNC-DQKLRSILMGKSRVELAE---LPALIKL   93 (100)
Q Consensus        23 ~~~lS~~La~~l---G--~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~c-De~Lk~lf~g~~~i~~~e---l~~ll~~   93 (100)
                      .++--++|-.+|   |  .+..|+.+|+..+=+||-.+.|.|+.+..+|.| ++.|.++| |++++++.+   +.+.|.+
T Consensus        24 ~Vrpk~~lL~iLq~aGA~~dvfT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~ll-Gv~sFSVkdp~~L~~mL~~  102 (130)
T 3dac_M           24 QVHPRAPLLQILKVAGAQEEVFTVKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELL-EVGSFSVKNPSPLYEMLKR  102 (130)
T ss_dssp             EEEECHHHHHHHHHTTCCCSSEEHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHH-TSSEEETTSCHHHHHHHHH
T ss_pred             ecCCcHHHHHHHHHhccCcceeehHHHHHHHHHhhhhhhccCccccceeEeCCccccccc-CCcceeecCcHHHHHHHHh
Confidence            455667777777   4  368999999999999999999999999999999 46788898 999999987   8888888


Q ss_pred             cCCC
Q 034230           94 HFPK   97 (100)
Q Consensus        94 Hl~~   97 (100)
                      ++..
T Consensus       103 NLv~  106 (130)
T 3dac_M          103 NLVI  106 (130)
T ss_dssp             HEEE
T ss_pred             heec
Confidence            7653

>2z5s_M MDM4 protein, zebrafish MDMX; MDMX, MDM4, acetylation, activator, anti-oncogene, apoptosis, cell cycle, cytoplasm, disease mutation, DNA- binding; 2.30A {Danio rerio} PDB: 2z5t_M

Probab=97.58  E-value=0.00029  Score=48.44  Aligned_cols=70  Identities=16%  Similarity=0.244  Sum_probs=58.5

Q ss_pred             CccccccCCHHHHHhh---C--CCcccHHHHHHHHHHHHhhcCCCCCCCCceeecc-hhHHhhhcCCCeeccccHHH
Q 034230           19 NLIDLVNLPSTLREFV---G--QSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCD-QKLRSILMGKSRVELAELPA   89 (100)
Q Consensus        19 ~~~~~~~lS~~La~~l---G--~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cD-e~Lk~lf~g~~~i~~~el~~   89 (100)
                      +-...++--+.|-.+|   |  .+..|+-||+..+-+||-.+.|.|+.+..+|.|. +.|.++| |++.+++-+...
T Consensus        19 ~e~~~VrPk~~LLkiLq~aGA~~~~fT~keVm~YLGqYIm~KqLYD~~~qhiV~C~~D~LG~l~-Gv~sFSVKdp~~   94 (140)
T 2z5s_M           19 GEGTQVHPRAPLLQILKVAGAQEEVFTLKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELL-EVGSFSVKNPSP   94 (140)
T ss_dssp             -CCCCBEECHHHHHHHHHTTCCCSCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHH-TSSEEETTBCHH
T ss_pred             cccceecCcHHHHHHHHHhCcccceeeHHHHHHHHHHHHHHhhhcccccCcEEeeCCccccccc-CccceeecCcHH
Confidence            3334777788898888   4  3688999999999999999999999999999995 6679999 999998866553

>1ycq_A MDM2, MDM2; anti-oncogene, DNA-binding, transcription regulation, nuclear protein, complex (oncogene protein/peptide), phosphorylation, activator; 2.30A {Xenopus laevis} SCOP: a.42.1.1

Probab=97.51  E-value=0.00041  Score=45.98  Aligned_cols=68  Identities=21%  Similarity=0.382  Sum_probs=56.5

Q ss_pred             cccCCHHHHHhh---C--CCcccHHHHHHHHHHHHhhcCCCCCCCCceeecc-hhHHhhhcCCCeeccccHHHHH
Q 034230           23 LVNLPSTLREFV---G--QSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCD-QKLRSILMGKSRVELAELPALI   91 (100)
Q Consensus        23 ~~~lS~~La~~l---G--~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cD-e~Lk~lf~g~~~i~~~el~~ll   91 (100)
                      .++-.+.|-.+|   |  ...-|+.+|+..+-+||-.+.|.|+.+..+|.|. +.|.++| |++++++-+-..+.
T Consensus        11 ~VrPk~~LLklL~~~GA~~~~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~-g~~~Fsvkdp~~l~   84 (107)
T 1ycq_A           11 LVQPTPLLLSLLKSAGAQKETFTMKEVIYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELF-GVQEFSVKEPRRLY   84 (107)
T ss_dssp             CBEECHHHHHHHHHTTCCCSCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHH-TCSEEETTCHHHHH
T ss_pred             ccCccHHHHHHHHHhccccceeeehhhhhhHHHHHhHHhhcccccCcEEeeCCccccccc-CccceeecCcHHHH
Confidence            556667777777   3  3578999999999999999999999999999995 6679999 99999887666433

>3fea_A MDM4 protein; HDMX, HDM4,human MDM4, human MDMX, protein-protein interaction, metal-binding; HET: PM3 6CW; 1.33A {Homo sapiens} SCOP: a.42.1.0 PDB: 3fe7_A* 3u15_A* 2vyr_A 3lbj_E* 3fdo_A 3dab_A 3jzp_A 3jzo_A 3jzq_A 3eqy_A

Probab=97.45  E-value=0.00021  Score=46.93  Aligned_cols=72  Identities=18%  Similarity=0.319  Sum_probs=60.6

Q ss_pred             ccCCHHHHHhh---C--CCcccHHHHHHHHHHHHhhcCCCCCCCCceeecc-hhHHhhhcCCCeeccc---cHHHHHhcc
Q 034230           24 VNLPSTLREFV---G--QSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCD-QKLRSILMGKSRVELA---ELPALIKLH   94 (100)
Q Consensus        24 ~~lS~~La~~l---G--~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cD-e~Lk~lf~g~~~i~~~---el~~ll~~H   94 (100)
                      ++--++|-.+|   |  .+..|+.+|+..+=+||-.+.|.||.+..+|.|. +.|-++| |++++++.   .+.+.|.++
T Consensus        16 Vrpk~~lL~iLq~aGA~~d~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~-G~~sFsvkdp~~l~~ml~~n   94 (100)
T 3fea_A           16 VRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELL-GRQSFSVKDPSPLYDMLRKN   94 (100)
T ss_dssp             BEECHHHHHHHHHTTCCSSCBCHHHHHHHHHHHHHHTTCEETTEEEEEECTTSHHHHHH-TCSEEETTCCHHHHHHHHHH
T ss_pred             cCCcHHHHHHHHHhccCcceeehHHHHHHHHHhhhhhhccCccccceEEeCCCcccccc-CCcceeecCchHHHHHHHhh
Confidence            45566777776   3  3689999999999999999999999999999994 6788898 99999885   788888887


Q ss_pred             CC
Q 034230           95 FP   96 (100)
Q Consensus        95 l~   96 (100)
                      +.
T Consensus        95 Lv   96 (100)
T 3fea_A           95 LV   96 (100)
T ss_dssp             EE
T ss_pred             ce
Confidence            64

>2axi_A Ubiquitin-protein ligase E3 MDM2; drug design, protein-protein interactions, ligase, LIGA inhibitor complex; HET: 6CW MPO; 1.40A {Homo sapiens} SCOP: a.42.1.1 PDB: 1ycr_A 2gv2_A* 1t4f_M* 3jzr_A 3g03_A 3tu1_A* 3jzk_A* 1t4e_A* 3lbl_A* 4dij_A* 3lbk_A* 3v3b_A* 3jzs_A 3eqs_A 3iux_A* 3iwy_A* 3lnj_A* 3lnz_A 1rv1_A* 1ttv_A*

Probab=97.27  E-value=0.00041  Score=46.46  Aligned_cols=71  Identities=20%  Similarity=0.333  Sum_probs=57.6

Q ss_pred             cccccCCHHHHHhh---C--CCcccHHHHHHHHHHHHhhcCCCCCCCCceeecc-hhHHhhhcCCCeeccccHHHHHh
Q 034230           21 IDLVNLPSTLREFV---G--QSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCD-QKLRSILMGKSRVELAELPALIK   92 (100)
Q Consensus        21 ~~~~~lS~~La~~l---G--~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cD-e~Lk~lf~g~~~i~~~el~~ll~   92 (100)
                      ...++-.+.|-.+|   |  ....|+.+|+..+-+||-.+.|.|+.+..+|.|. +.|.++| |++.+++-+-..+..
T Consensus         9 e~~VrPk~~LLklLq~~GA~~~vfT~keVm~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~-g~~~Fsvkdp~~l~~   85 (115)
T 2axi_A            9 ETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLF-GVPSFSVKEHRKIYT   85 (115)
T ss_dssp             CCEEEECHHHHHHHHHTTCCCSCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHH-SSSEEETTCHHHHHH
T ss_pred             ccccCccHHHHHHHHHhccccceeechhheehhhhhhhHhhhcccccCcEEeeCCccccccc-CccceeecCcHHHHH
Confidence            34566677777777   3  2578999999999999999999999999999995 6679999 999998866554443

>2kwl_A ACP, acyl carrier protein; structural genomics, seattle structura genomics center for infectious disease, ssgcid, lipid bindi protein; NMR {Borrelia burgdorferi}

Probab=85.02  E-value=0.48  Score=28.08  Aligned_cols=57  Identities=19%  Similarity=0.281  Sum_probs=42.9

Q ss_pred             CCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230           35 GQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF   95 (100)
Q Consensus        35 G~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl   95 (100)
                      |...|++.++...+.+.|.+.--.+   ...|..|..|..-+ |-|++.+-++...|..+|
T Consensus         1 ~~~~m~~~~i~~~l~~~i~~~l~~~---~~~i~~~~~l~~dl-G~DSl~~vel~~~le~~f   57 (84)
T 2kwl_A            1 GPGSMDNDEIFSKVRSIISEQLDKK---EDEITTDSRFVEDL-NADSLDIYELLYLLEEAF   57 (84)
T ss_dssp             CCCCSTHHHHHHHHHHHHHHHHCCC---GGGCCTTTHHHHTS-SSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCC---cccCCCCCchhhhc-CCCHHHHHHHHHHHHHHH
Confidence            4457899999999999998853223   34688999995555 889988888887777655

---

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	100
d1uhra_	93	a.42.1.1 (A:) SWI/SNF related regulator of chromat	8e-19
d1v32a_	101	a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl	2e-17
d1v31a_	93	a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl	4e-17

>d1uhra_ a.42.1.1 (A:) SWI/SNF related regulator of chromatin (BRG1-associated factor 60a) {Mouse (Mus musculus) [TaxId: 10090]} Length = 93

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: SWI/SNF related regulator of chromatin (BRG1-associated factor 60a)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 72.1 bits (177), Expect = 8e-19
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 25  NLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVEL 84
            L   L   +G    +R      +W YIKT+ LQDP+ +  V CD+ L+ I     R++ 
Sbjct: 13  KLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIF-ESQRMKF 71

Query: 85  AELPALIKLHF-PKDPK 100
           +E+P  +     P +P 
Sbjct: 72  SEIPQRLHALLMPPEPS 88

>d1v32a_ a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl09-47-k03) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: Hypothetical protein AT5G08430 (rafl09-47-k03)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 68.7 bits (168), Expect = 2e-17
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 30 LREFVGQ------SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVE 83
          L EF+          ISR      +  YI    L DP+NK  V CD++L  +  G   + 
Sbjct: 20 LIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLF-GTRTIF 78

Query: 84 LAELPALIKLHFPK 97
            ++  L++ H+ +
Sbjct: 79 RMKVYDLLEKHYKE 92

>d1v31a_ a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl11-05-p19) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 93

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: Hypothetical protein AT5G14170 (rafl11-05-p19)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 67.9 bits (166), Expect = 4e-17
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 25  NLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVEL 84
            L + L + +G    +R      +W Y+K   LQ+PN+ +  NCD  L+ +  G+ +++ 
Sbjct: 13  KLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVF-GEEKLKF 71

Query: 85  AELPALIKLHF-PKDPK 100
             +   I  H  P  P 
Sbjct: 72  TMVSQKISHHLSPPPPS 88

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	100
d1v31a_	93	Hypothetical protein AT5G14170 (rafl11-05-p19) {Th	100.0
d1uhra_	93	SWI/SNF related regulator of chromatin (BRG1-assoc	99.97
d1v32a_	101	Hypothetical protein AT5G08430 (rafl09-47-k03) {Th	99.94
d2axia1	85	MDM2 {Human (Homo sapiens) [TaxId: 9606]}	98.39
d1ttva_	107	MDM2 {African clawed frog (Xenopus laevis) [TaxId:	98.3

>d1v31a_ a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl11-05-p19) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: Hypothetical protein AT5G14170 (rafl11-05-p19)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=100.00  E-value=1.3e-33  Score=183.73  Aligned_cols=84  Identities=23%  Similarity=0.522  Sum_probs=80.8

Q ss_pred             CCCCCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhcc
Q 034230           15 KKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLH   94 (100)
Q Consensus        15 ~~~~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~H   94 (100)
                      +..+||.++|+||++||+|+|.+++||++|++.||+||++||||||+|++.|+||++|++|| |.+++.|++|+++|++|
T Consensus         3 ~~~~G~~~~~~lS~~La~~lg~~~~sR~~v~k~iw~YIk~n~Lqd~~nkr~I~~D~~L~~lf-g~~~v~~~~l~~~L~~H   81 (93)
T d1v31a_           3 SGSSGVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVF-GEEKLKFTMVSQKISHH   81 (93)
T ss_dssp             SSCCSSCCCEECCHHHHHHSCCSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHS-CSSEEETTTTHHHHHHH
T ss_pred             CCCCCCcCCccCCHHHHHHHCcCcCcHHHHHHHHHHHHHHhCCCCCCCCCEEecCHHHHHHh-CCCcccHHHHHHHHHHh
Confidence            45689999999999999999999999999999999999999999999999999999999999 99999999999999999


Q ss_pred             CCCCC
Q 034230           95 FPKDP   99 (100)
Q Consensus        95 l~~~p   99 (100)
                      |.+.+
T Consensus        82 l~p~~   86 (93)
T d1v31a_          82 LSPPP   86 (93)
T ss_dssp             CBCCC
T ss_pred             CCCCC
Confidence            99854

>d1uhra_ a.42.1.1 (A:) SWI/SNF related regulator of chromatin (BRG1-associated factor 60a) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: SWI/SNF related regulator of chromatin (BRG1-associated factor 60a)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.97  E-value=3.9e-33  Score=181.58  Aligned_cols=82  Identities=26%  Similarity=0.466  Sum_probs=79.2

Q ss_pred             CCCCCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhcc
Q 034230           15 KKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLH   94 (100)
Q Consensus        15 ~~~~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~H   94 (100)
                      ...+|+.++|+||++||+|+|.+++||++|+++||+|||+||||||+|++.|+||+.|++|| |++++.|++|+++|++|
T Consensus         3 ~~~sg~p~~~~lS~~La~~lg~~~~sR~~v~k~iw~YIk~n~Lqdp~nkr~I~cD~~L~~lf-g~~~v~~~~l~~~L~~H   81 (93)
T d1uhra_           3 SGSSGQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIF-ESQRMKFSEIPQRLHAL   81 (93)
T ss_dssp             CCCSSSCCEEEECTTHHHHTCCSEEEHHHHHHHHHHHHHHTTCBCSSCSSEECCCTTHHHHT-CCSSEEGGGSHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHCCCCcCHHHHHHHHHHHHHHhcCCCCCCCCEEecCHHHHHHh-CCCeecHHHHHHHHHhh
Confidence            44589999999999999999999999999999999999999999999999999999999999 99999999999999999


Q ss_pred             CCC
Q 034230           95 FPK   97 (100)
Q Consensus        95 l~~   97 (100)
                      |.+
T Consensus        82 l~p   84 (93)
T d1uhra_          82 LMP   84 (93)
T ss_dssp             EEC
T ss_pred             CCC
Confidence            976

>d1v32a_ a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl09-47-k03) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: Hypothetical protein AT5G08430 (rafl09-47-k03)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.94  E-value=5.2e-28  Score=159.29  Aligned_cols=72  Identities=28%  Similarity=0.447  Sum_probs=68.3

Q ss_pred             CCHHHHHhhC---C---CcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCCC
Q 034230           26 LPSTLREFVG---Q---SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKD   98 (100)
Q Consensus        26 lS~~La~~lG---~---~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~~   98 (100)
                      .|++|++|||   .   +++||.+|++.||+|||+||||||+|+|.|+||++|++|| |.+++++++|+++|++||.+.
T Consensus        16 ~S~eL~~FL~~~g~~~~~~~sR~eVtk~iw~YIK~nnLqdp~nkr~I~~D~~L~~Lf-g~~~v~~f~i~k~l~~H~~~~   93 (101)
T d1v32a_          16 GSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLF-GTRTIFRMKVYDLLEKHYKEN   93 (101)
T ss_dssp             SCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCTTEEECCSHHHHHT-CCSEEETTHHHHHHHHHSCSC
T ss_pred             CCHHHHHHHHhcCCCCcccCCHHHHHHHHHHHHHHhcCCCCccCCEEccCHHHHHHh-CCCcccHHHHHHHHHHHcCCc
Confidence            7999999985   2   6899999999999999999999999999999999999999 999999999999999999864

>d2axia1 a.42.1.1 (A:25-109) MDM2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: MDM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.39  E-value=1.9e-07  Score=58.09  Aligned_cols=72  Identities=21%  Similarity=0.381  Sum_probs=62.0

Q ss_pred             cccCCHHHHHhh---C--CCcccHHHHHHHHHHHHhhcCCCCCCCCceeec-chhHHhhhcCCCeecccc---HHHHHhc
Q 034230           23 LVNLPSTLREFV---G--QSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNC-DQKLRSILMGKSRVELAE---LPALIKL   93 (100)
Q Consensus        23 ~~~lS~~La~~l---G--~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~c-De~Lk~lf~g~~~i~~~e---l~~ll~~   93 (100)
                      .++..+.|-.+|   |  .+..|.-||+..+-+||..++|.|+.+.++|.| |+.|.++| |.++++.-+   +.+.|.+
T Consensus         3 lVrPkp~Ll~~L~~~GA~~~~fT~kqVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~l~-gv~sFsVk~~r~l~~ml~r   81 (85)
T d2axia1           3 LVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLF-GVPSFSVKEHRKIYTMIYR   81 (85)
T ss_dssp             EEEECHHHHHHHHHTTCCCSCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHH-SSSEEETTCHHHHHHHHHT
T ss_pred             cccCcHHHHHHHHHcCCCcceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhc-CCCceeecCcHHHHHHHHh
Confidence            345567788887   3  368999999999999999999999999999999 56699999 999998877   8888888


Q ss_pred             cC
Q 034230           94 HF   95 (100)
Q Consensus        94 Hl   95 (100)
                      |+
T Consensus        82 nL   83 (85)
T d2axia1          82 NL   83 (85)
T ss_dssp             TE
T ss_pred             cc
Confidence            75

>d1ttva_ a.42.1.1 (A:) MDM2 {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: MDM2
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.30  E-value=1.3e-06  Score=56.13  Aligned_cols=75  Identities=20%  Similarity=0.387  Sum_probs=64.6

Q ss_pred             cccccCCHHHHHhh---C--CCcccHHHHHHHHHHHHhhcCCCCCCCCceeec-chhHHhhhcCCCeecccc---HHHHH
Q 034230           21 IDLVNLPSTLREFV---G--QSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNC-DQKLRSILMGKSRVELAE---LPALI   91 (100)
Q Consensus        21 ~~~~~lS~~La~~l---G--~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~c-De~Lk~lf~g~~~i~~~e---l~~ll   91 (100)
                      ...++..+.|-.+|   |  .+..|.-+|+..|-+||..++|.|+.+.++|.| |+.|.++| |.++++.-+   +.+.|
T Consensus         9 ~~lVrPkp~LL~~L~~~GA~~~~fT~keVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~ll-gv~sFsVke~r~l~~ml   87 (107)
T d1ttva_           9 EKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELF-GVQEFSVKEHRRIYAMI   87 (107)
T ss_dssp             CCCEEECHHHHHHHHHTTCCSSCBCHHHHHHHHHHHHHHHTCBCSSCTTEECCSSCHHHHHH-TCSCEETTCHHHHHHHH
T ss_pred             ccccCCCHHHHHHHHHcCCCcceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhc-CCCceeecCcHHHHHHH
Confidence            45567788888888   3  368999999999999999999999999999999 56799999 999998876   77778


Q ss_pred             hccCC
Q 034230           92 KLHFP   96 (100)
Q Consensus        92 ~~Hl~   96 (100)
                      .+++.
T Consensus        88 ~rnLv   92 (107)
T d1ttva_          88 SRNLV   92 (107)
T ss_dssp             HTTEE
T ss_pred             Hhhhh
Confidence            88864