Citrus Sinensis ID: 022018

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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-------220-------230-------240-------250-------260-------270-------280-------290-------300----
Protein Sequence
MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHccccccccccHHHHccccccccccccccHHHHHcccccccccccccHHHHcccccccccccccHHHHHHHHcccccHHHHHHHHHHHHHHcccccccccccEEccHHHHHHHccccccHHHHHHHHHHcccccccccccccccccHHHHHccccccccccHHHHHHHcccccccccccccccHHHHHHHccccccccHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccHcHHHcHHHHHHccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccHHHHHHHHHHHHHHccccccccccEEEccHHHHHHHccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEccHHHHHHHccccccccHHHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
MVSDSELIARLQEFLknsdlntttTGIVRRQLekdfgvdltdkkiFIREQVDLFLQSQfendqndggneeqqeeddgeddqmakvksdetdgsddaaveegdddnndendnddeaneakgpakrrsrKLNNEVKkrgggfsklcalspqlqefigVTELARTEVVKQLWAYIREKdlqdpnnrrnivcdeRLRALFGVDTINMFQMNKALskhiwpldsddvisvkstpkekqrkqertedldeptrkekrqkggksgflapLQLSDALIKFLGtgesalprsDVIKRMWDYIKEKNLQVSLRK
Flexible Loop (DISEMBL)
MVSDSELIARLQeflknsdlnttttgivrrqlekdfgvdltdkKIFIREQVDLFLQSQFendqndggneeqqeeddgeddQMAKVksdetdgsddaaveegdddnndendnddeaneakgpakrrsrklnnevkkrgggfsklcalsPQLQEFIGVTELARTEVVKQLWAYIrekdlqdpnnrrnivcDERLRALFGVDTINMFQMNKALSkhiwpldsddvisvkstpkekqrkqertedldeptrkekrqkggksgflapLQLSDALIKFLGtgesalprsdVIKRMWDYikeknlqvslrk
Low Complexity Region (SEG)
MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFendqndggneeqqeeddgeddqMAKVKSDETDGSddaaveegdddnndendnddeaneaKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK
Disordered region (IsUnstruct)
*********RLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQ**********************************************************************************GFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDV************************************FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKE*********
Disordered Region (DISOPRED)
**S*SELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQF*******************************************************************************GFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKE**L******
Disordered Region (DISEMBL)
MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFEN******************************************************************KLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVK******************************SGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK
Disordered Region (DISPRO)
***DSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE*******************************************************************************FSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDS*************************************SGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNL******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK
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	304	2.2.26 [Sep-21-2011]
O74503	233	Upstream activation facto	yes	no	0.421	0.549	0.398	7e-20
Q08747	228	Upstream activation facto	yes	no	0.555	0.741	0.325	2e-17
Q05024	226	Protein TRI1 OS=Saccharom	no	no	0.312	0.420	0.418	1e-16
Q2TBN1	515	SWI/SNF-related matrix-as	yes	no	0.263	0.155	0.289	4e-06
Q96GM5	515	SWI/SNF-related matrix-as	no	no	0.263	0.155	0.289	5e-06
Q61466	515	SWI/SNF-related matrix-as	yes	no	0.263	0.155	0.289	8e-06
Q9P7S3	425	SWI/SNF and RSC complexes	no	no	0.398	0.284	0.266	2e-05
Q92925	531	SWI/SNF-related matrix-as	no	no	0.361	0.207	0.277	4e-05
E1BJD1	531	SWI/SNF-related matrix-as	no	no	0.361	0.207	0.277	4e-05
O54772	531	SWI/SNF-related matrix-as	no	no	0.361	0.207	0.268	5e-05

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

 Score = 98.2 bits (243), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 57/143 (39%), Positives = 87/143 (60%), Gaps = 15/143 (10%)

Query: 117 EAKGPAKR-RSRKLNNE---VKKRG-----GGFSKLCALSPQLQEFIGVTELARTEVVKQ 167
           E K PAKR R RK + E    +KR         +K   LSP+L EF+G+ +L+R + VK+
Sbjct: 85  EGKKPAKRTRKRKEDGEEGGKRKRNQDPANNPLNKPMKLSPKLAEFLGLEQLSRPQTVKK 144

Query: 168 LWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKS 227
           LW YI+  DLQDPN++R I+CD++L+++F VDT++MF MNK L+  +  +  D +     
Sbjct: 145 LWEYIKAHDLQDPNDKRTILCDDKLKSVFEVDTLHMFTMNKYLTNLMTKIPDDQL----- 199

Query: 228 TPKEKQRKQERTEDLDEPTRKEK 250
            PK + + +E     D P ++EK
Sbjct: 200 -PKPQPKNEEPAAPNDLPKQEEK 221

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

 Score = 90.1 bits (222), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/212 (32%), Positives = 103/212 (48%), Gaps = 43/212 (20%)

Query: 14  FLKNSDLNTTTTGIVRRQLEKDFGVDLTD--KKI--FIREQVDLFLQ-SQFENDQNDGGN 68
            L + DL T TT  VR  L++ + +D+    K I   IR+ +DL  +  +FE    D   
Sbjct: 14  LLSDMDLETVTTKKVRMALKEVYAIDVESQGKAINKLIRKHLDLVKERPRFERSLEDLLK 73

Query: 69  EEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRSRK 128
           E         +  +A   + E   S  ++ EE +D            +E KG        
Sbjct: 74  E---------NATLAIELTKEITVSKRSSGEEKND------------SETKG-------- 104

Query: 129 LNNEVKKRGGGFSKL------CALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNN 182
               V+K+ G  SK         LS  L   +G  EL RTEVV++LWAYI+  +LQ+PNN
Sbjct: 105 --THVEKKKGTVSKSPISTRKVTLSKSLASLLGEHELTRTEVVRRLWAYIKAHNLQNPNN 162

Query: 183 RRNIVCDERLRALFGVDTINMFQMNKALSKHI 214
           ++ I+CDE+L  + G  T NMF+M+K L+ H+
Sbjct: 163 KKEILCDEKLELILGKST-NMFEMHKILASHM 193

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

 Score = 87.4 bits (215), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/98 (41%), Positives = 65/98 (66%), Gaps = 3/98 (3%)

Query: 144 CALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINM 203
             LS  LQ+F+G  EL RT+VVK +W YI+E DLQ+P +RR I+CDE++  +FG   + M
Sbjct: 124 VLLSAPLQKFLGSEELPRTQVVKMIWQYIKEHDLQNPKDRREILCDEKMEPIFG-KKMTM 182

Query: 204 FQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTED 241
           F MNK L+KH++  + D+++  +   K+   K+ + E+
Sbjct: 183 FSMNKLLTKHLF--NPDEIVKHEEEQKQTPEKEIKLEN 218

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 = 52.4 bits (124), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 3/83 (3%)

Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           L P+L   +G+    R  +++ LW YI+   LQDP+ R  ++CD+ L+ +F    +   +
Sbjct: 297 LDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVICDKYLQQIFESQRMKFSE 356

Query: 206 MNKALSKHIWPLDS---DDVISV 225
           + + L   + P +    + VISV
Sbjct: 357 IPQRLHALLMPPEPIIINHVISV 379

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|Q96GM5|SMRD1_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 OS=Homo sapiens GN=SMARCD1 PE=1 SV=2

 Score = 52.0 bits (123), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 3/83 (3%)

Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           L P+L   +G+    R  +++ LW YI+   LQDP+ R  ++CD+ L+ +F    +   +
Sbjct: 297 LDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVICDKYLQQIFESQRMKFSE 356

Query: 206 MNKALSKHIWPLDS---DDVISV 225
           + + L   + P +    + VISV
Sbjct: 357 IPQRLHALLMPPEPIIINHVISV 379

Involved in chromatin remodeling. 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 (By similarity). 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.

Homo sapiens (taxid: 9606)

>sp|Q61466|SMRD1_MOUSE SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 OS=Mus musculus GN=Smarcd1 PE=1 SV=3

 Score = 51.6 bits (122), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 3/83 (3%)

Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           L P+L   +G+    R  +++ LW YI+   LQDP+ R  ++CD+ L+ +F    +   +
Sbjct: 297 LDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSE 356

Query: 206 MNKALSKHIWPLDS---DDVISV 225
           + + L   + P +    + VISV
Sbjct: 357 IPQRLHALLMPPEPIIINHVISV 379

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 (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|Q9P7S3|SSR3_SCHPO SWI/SNF and RSC complexes subunit ssr3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ssr3 PE=1 SV=1

 Score = 50.4 bits (119), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/124 (26%), Positives = 55/124 (44%), Gaps = 3/124 (2%)

Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           LS      +G+ E  R ++V  LW YI+   LQD   +R I CD+ LR LF  D +   +
Sbjct: 208 LSKAFANILGIREGTRPDIVSYLWQYIKFHRLQDMEEKRLINCDKALRDLFEADRLYFPR 267

Query: 206 MNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLAPLQL 265
           + + +++ + P+D    I +  T    +   E+    D     E  +      FLA +  
Sbjct: 268 IPELMNRFLEPIDP---IVIPYTINVSEHTVEKVTIFDIRINTEDPRHSQIRSFLATMMS 324

Query: 266 SDAL 269
            D +
Sbjct: 325 QDKI 328

Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. Controls particularly membrane and organelle development genes. Part of the SWI/SNF complex, an ATP-dependent chromatin remodeling complex, required for the positive and negative regulation of gene expression of a large number of genes. It changes chromatin structure by altering DNA-histone contacts within a nucleosome, leading eventually to a change in nucleosome position, thus facilitating or repressing binding of gene-specific transcription factors.

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

>sp|Q92925|SMRD2_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 OS=Homo sapiens GN=SMARCD2 PE=1 SV=3

 Score = 48.9 bits (115), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 55/119 (46%), Gaps = 9/119 (7%)

Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           L P+L   +GV    R  +++ LW YI+   LQD + R  I C+   R +F    +   +
Sbjct: 313 LDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSE 372

Query: 206 MNKALS---KHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLA 261
           +   L+   +H  P+  + VISV    ++K    +   ++D+P       K   S FLA
Sbjct: 373 IPMKLAGLLQHPDPIVINHVISVDPNDQKKTACYDIDVEVDDPL------KAQMSNFLA 425

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).

Homo sapiens (taxid: 9606)

>sp|E1BJD1|SMRD2_BOVIN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 OS=Bos taurus GN=SMARCD2 PE=3 SV=1

 Score = 48.9 bits (115), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 55/119 (46%), Gaps = 9/119 (7%)

Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           L P+L   +GV    R  +++ LW YI+   LQD + R  I C+   R +F    +   +
Sbjct: 313 LDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSE 372

Query: 206 MNKALS---KHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLA 261
           +   L+   +H  P+  + VISV    ++K    +   ++D+P       K   S FLA
Sbjct: 373 IPMKLAGLLQHPDPIVINHVISVDPNDQKKTACYDIDVEVDDPL------KAQMSNFLA 425

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).

Bos taurus (taxid: 9913)

>sp|O54772|SMRD2_RAT SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 OS=Rattus norvegicus GN=Smarcd2 PE=2 SV=3

 Score = 48.9 bits (115), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 56/119 (47%), Gaps = 9/119 (7%)

Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           L P+L   +GV    R  +++ LW YI+   LQD + R  I C+   R +F    +   +
Sbjct: 313 LDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSE 372

Query: 206 MNKALS---KHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLA 261
           +   L+   +H  P+  + VISV    ++K    +   ++D+P + +       S FLA
Sbjct: 373 IPMKLAGLLQHPDPIVINHVISVDPNDQKKTACYDIDVEVDDPLKAQ------MSNFLA 425

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).

Rattus norvegicus (taxid: 10116)

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	304
255562647	322	Upstream activation factor subunit UAF30	0.930	0.878	0.705	1e-105
302144157	303	unnamed protein product [Vitis vinifera]	0.963	0.966	0.667	1e-102
356496858	337	PREDICTED: upstream activation factor su	0.967	0.872	0.664	1e-102
359480441	296	PREDICTED: upstream activation factor su	0.960	0.986	0.666	1e-102
147860060	332	hypothetical protein VITISV_044372 [Viti	0.957	0.876	0.668	1e-102
356496860	331	PREDICTED: upstream activation factor su	0.950	0.873	0.653	1e-101
356537694	346	PREDICTED: uncharacterized protein LOC10	0.967	0.849	0.654	1e-100
449461413	332	PREDICTED: upstream activation factor su	0.904	0.828	0.584	3e-92
224081550	313	predicted protein [Populus trichocarpa]	0.848	0.824	0.572	3e-91
357483029	361	Upstream activation factor subunit spp27	0.937	0.789	0.608	2e-85

>gi|255562647|ref|XP_002522329.1| Upstream activation factor subunit UAF30, putative [Ricinus communis] gi|223538407|gb|EEF40013.1| Upstream activation factor subunit UAF30, putative [Ricinus communis]

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 211/299 (70%), Positives = 242/299 (80%), Gaps = 16/299 (5%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVSDSELI RL+EFLKNSDLNTTTTGIVRRQLE+DFG+DL+DKK FIREQVDLFLQSQFE
Sbjct: 1   MVSDSELIERLREFLKNSDLNTTTTGIVRRQLEEDFGIDLSDKKAFIREQVDLFLQSQFE 60

Query: 61  NDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKG 120
            +      + ++EE + +DDQ A VKS++TDG +D   EE    +N  ++          
Sbjct: 61  END-----QNEEEEQEDDDDQRANVKSEQTDGDNDDDEEEESTASNGTSN---------- 105

Query: 121 PAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDP 180
            AKRRS +  NE KKRGGGFSKLC+LSPQLQE  GV +LARTEVVKQLW++IREK LQDP
Sbjct: 106 -AKRRSNEQKNEGKKRGGGFSKLCSLSPQLQELTGVPQLARTEVVKQLWSHIREKKLQDP 164

Query: 181 NNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTE 240
           NNRRNI+CDE  RALFGVD+I+MFQMNK LSKHIWPLDSD V+  KS PKEKQRKQER E
Sbjct: 165 NNRRNIICDEPFRALFGVDSIDMFQMNKVLSKHIWPLDSDGVVPAKSEPKEKQRKQEREE 224

Query: 241 DLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299
           + DEP RKEKR+KG KSGFLAPLQLSDALIKF GTGE+AL R+DVIKRMW+YIK+ NLQ
Sbjct: 225 EPDEPKRKEKRRKGEKSGFLAPLQLSDALIKFFGTGENALSRADVIKRMWEYIKQNNLQ 283

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302144157|emb|CBI23284.3| unnamed protein product [Vitis vinifera]

 Score =  379 bits (973), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 201/301 (66%), Positives = 243/301 (80%), Gaps = 8/301 (2%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVSDSEL+ARL EFL++SDLNTTTT IVRR+LE+DFG+DL+ KK FIRE VDLFLQSQ E
Sbjct: 1   MVSDSELVARLHEFLRSSDLNTTTTAIVRRKLEEDFGIDLSGKKAFIREHVDLFLQSQLE 60

Query: 61  NDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKG 120
                   +E    ++ E++  + VKS+   GS+ +  ++ +DD++DE +  +E++  KG
Sbjct: 61  K----AEEDEGDGGEEEEEEHKSNVKSE---GSNGSDSKDENDDDDDEEEEVEESSNGKG 113

Query: 121 PAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDP 180
             KR S+K N EVKKRGGGF KLC+LSP+LQ+FIGV ELARTEVVKQLW +IREKDLQDP
Sbjct: 114 AKKRGSKKSNKEVKKRGGGFCKLCSLSPELQKFIGVPELARTEVVKQLWVHIREKDLQDP 173

Query: 181 NNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTE 240
           NNRRNI+CDE LRALFGVD+INMFQMNKALSKHIWPLDSDD   VK TPKEKQRKQER +
Sbjct: 174 NNRRNIICDETLRALFGVDSINMFQMNKALSKHIWPLDSDDAAPVKPTPKEKQRKQER-D 232

Query: 241 DLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQV 300
           D DEP RK+KRQKGG SGFLAPL LSDAL+KFL   ESAL R++V+K++W+YIK+ NLQV
Sbjct: 233 DSDEPKRKQKRQKGGNSGFLAPLPLSDALVKFLNIEESALSRAEVVKKIWEYIKQNNLQV 292

Query: 301 S 301
            
Sbjct: 293 C 293

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496858|ref|XP_003517282.1| PREDICTED: upstream activation factor subunit spp27-like isoform 1 [Glycine max]

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 200/301 (66%), Positives = 239/301 (79%), Gaps = 7/301 (2%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVS+SELI RL+EFL++SDLNTTTT  VRRQLE DFG+DL+D+K FIREQVDLFLQ++  
Sbjct: 1   MVSESELIGRLREFLRSSDLNTTTTATVRRQLEADFGIDLSDRKAFIREQVDLFLQTE-- 58

Query: 61  NDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKG 120
              N    EE+Q +D  E ++ A    +++  SD     + +++  +E D  ++A  AK 
Sbjct: 59  --HNQPQQEERQNDDVEEQEEDAPNNPEQSQPSDSKEETDEEEEGEEEEDKPEQAKNAKK 116

Query: 121 PAKRRSRKLNNEV-KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQD 179
             K RS KL +EV KKRGGGF KLC+LSPQLQEF+   E+ARTEVVKQLW YIREK+LQD
Sbjct: 117 -NKGRSNKLGDEVVKKRGGGFCKLCSLSPQLQEFMEAPEMARTEVVKQLWVYIREKNLQD 175

Query: 180 PNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERT 239
           PNNRRNI+CDERLR+LF V++INMFQMNKALSKHIWPL+SDDV+ VKSTPKEKQ+KQER 
Sbjct: 176 PNNRRNIICDERLRSLFNVNSINMFQMNKALSKHIWPLESDDVVQVKSTPKEKQKKQERD 235

Query: 240 EDLDEPTRKEKRQK-GGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNL 298
           +D DE  +KEKRQK GGKSGFLAPLQLSDAL+ FLGTGES L R+DVIKRMWDYIK  NL
Sbjct: 236 DDSDEAKKKEKRQKGGGKSGFLAPLQLSDALVNFLGTGESELARTDVIKRMWDYIKGNNL 295

Query: 299 Q 299
           Q
Sbjct: 296 Q 296

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480441|ref|XP_003632462.1| PREDICTED: upstream activation factor subunit spp27-like [Vitis vinifera]

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 200/300 (66%), Positives = 243/300 (81%), Gaps = 8/300 (2%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVSDSEL+ARL EFL++SDLNTTTT IVRR+LE+DFG+DL+ KK FIRE VDLFLQSQ E
Sbjct: 1   MVSDSELVARLHEFLRSSDLNTTTTAIVRRKLEEDFGIDLSGKKAFIREHVDLFLQSQLE 60

Query: 61  NDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKG 120
                   +E    ++ E++  + VKS+   GS+ +  ++ +DD++DE +  +E++  KG
Sbjct: 61  K----AEEDEGDGGEEEEEEHKSNVKSE---GSNGSDSKDENDDDDDEEEEVEESSNGKG 113

Query: 121 PAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDP 180
             KR S+K N EVKKRGGGF KLC+LSP+LQ+FIGV ELARTEVVKQLW +IREKDLQDP
Sbjct: 114 AKKRGSKKSNKEVKKRGGGFCKLCSLSPELQKFIGVPELARTEVVKQLWVHIREKDLQDP 173

Query: 181 NNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTE 240
           NNRRNI+CDE LRALFGVD+INMFQMNKALSKHIWPLDSDD   VK TPKEKQRKQER +
Sbjct: 174 NNRRNIICDETLRALFGVDSINMFQMNKALSKHIWPLDSDDAAPVKPTPKEKQRKQER-D 232

Query: 241 DLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQV 300
           D DEP RK+KRQKGG SGFLAPL LSDAL+KFL   ESAL R++V+K++W+YIK+ NLQ+
Sbjct: 233 DSDEPKRKQKRQKGGNSGFLAPLPLSDALVKFLNIEESALSRAEVVKKIWEYIKQNNLQL 292

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860060|emb|CAN83123.1| hypothetical protein VITISV_044372 [Vitis vinifera]

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 200/299 (66%), Positives = 241/299 (80%), Gaps = 8/299 (2%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVSDSEL+ARL EFL++SDLNTTTT IVRR+LE+DFG+DL+ KK FIRE VDLFLQSQ E
Sbjct: 1   MVSDSELVARLHEFLRSSDLNTTTTAIVRRKLEEDFGIDLSGKKAFIREHVDLFLQSQLE 60

Query: 61  NDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKG 120
                   +E    ++ E++  + VKS+   GS+ +  ++ +DD++DE +  +E++  KG
Sbjct: 61  K----AEEDEGDGGEEEEEEHKSNVKSE---GSNGSDSKDENDDDDDEEEEVEESSNGKG 113

Query: 121 PAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDP 180
             KR S+K N EVKKRGGGF KLC+LSP+LQ+FIGV ELARTEVVKQLW +IREKDLQDP
Sbjct: 114 AKKRGSKKSNKEVKKRGGGFCKLCSLSPELQKFIGVPELARTEVVKQLWVHIREKDLQDP 173

Query: 181 NNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTE 240
           NNRRNI+CDE LRALFGVD+INMFQMNKALSKHIWPLDSDD   VK TPKEKQRKQER  
Sbjct: 174 NNRRNIICDETLRALFGVDSINMFQMNKALSKHIWPLDSDDAAPVKPTPKEKQRKQERX- 232

Query: 241 DLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299
           D DEP RK+KRQKGG SGFLAPL LSDAL+KFL   ESAL R++V+K++W+YIK+ NLQ
Sbjct: 233 DSDEPKRKQKRQKGGNSGFLAPLPLSDALVKFLNIEESALSRAEVVKKIWEYIKQNNLQ 291

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496860|ref|XP_003517283.1| PREDICTED: upstream activation factor subunit spp27-like isoform 2 [Glycine max]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 196/300 (65%), Positives = 236/300 (78%), Gaps = 11/300 (3%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVS+SELI RL+EFL++SDLNTTTT  VRRQLE DFG+DL+D+K FIREQVDLFLQ+   
Sbjct: 1   MVSESELIGRLREFLRSSDLNTTTTATVRRQLEADFGIDLSDRKAFIREQVDLFLQT--- 57

Query: 61  NDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKG 120
            + N    EE+Q +D  E ++ A    +++  SD     + +++  +E D  ++A  AK 
Sbjct: 58  -EHNQPQQEERQNDDVEEQEEDAPNNPEQSQPSDSKEETDEEEEGEEEEDKPEQAKNAK- 115

Query: 121 PAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDP 180
             K + R +   VKKRGGGF KLC+LSPQLQEF+   E+ARTEVVKQLW YIREK+LQDP
Sbjct: 116 --KNKGRLV---VKKRGGGFCKLCSLSPQLQEFMEAPEMARTEVVKQLWVYIREKNLQDP 170

Query: 181 NNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTE 240
           NNRRNI+CDERLR+LF V++INMFQMNKALSKHIWPL+SDDV+ VKSTPKEKQ+KQER +
Sbjct: 171 NNRRNIICDERLRSLFNVNSINMFQMNKALSKHIWPLESDDVVQVKSTPKEKQKKQERDD 230

Query: 241 DLDEPTRKEKRQK-GGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299
           D DE  +KEKRQK GGKSGFLAPLQLSDAL+ FLGTGES L R+DVIKRMWDYIK  NLQ
Sbjct: 231 DSDEAKKKEKRQKGGGKSGFLAPLQLSDALVNFLGTGESELARTDVIKRMWDYIKGNNLQ 290

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537694|ref|XP_003537360.1| PREDICTED: uncharacterized protein LOC100786835 [Glycine max]

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 203/310 (65%), Positives = 244/310 (78%), Gaps = 16/310 (5%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVS+SELI RL+EFL++SDLNTTTT  VRRQLE DFG+DL+D+K FIREQVDLFLQ++  
Sbjct: 1   MVSESELIGRLREFLRSSDLNTTTTATVRRQLEADFGIDLSDRKAFIREQVDLFLQTEHN 60

Query: 61  NDQNDGG---------NEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDN 111
             Q +           + E+QEED   + + ++  SD  + +D+   EE +++  D+  +
Sbjct: 61  QSQQEEEEKEEKHQNDHVEEQEEDAPNNPEQSQ-PSDSKEVTDEDEEEEDEEEEEDKPKH 119

Query: 112 DDEANEAKGPAKRRSRKLNNEV-KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWA 170
             +A + KG    RS  L +EV KKRGGGF KLC+LSPQLQEF+G  E+ARTEVVKQLWA
Sbjct: 120 AKKAKKNKG----RSNTLGDEVVKKRGGGFCKLCSLSPQLQEFMGAPEMARTEVVKQLWA 175

Query: 171 YIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPK 230
           YIREK+LQDPNNRRNI+CDERLR+LF V++INMFQMNKALSKHIWPLDSDDV+ VKSTPK
Sbjct: 176 YIREKNLQDPNNRRNIICDERLRSLFNVNSINMFQMNKALSKHIWPLDSDDVVQVKSTPK 235

Query: 231 EKQRKQERTEDLDEPTRKEKRQK-GGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRM 289
           EKQ+KQER +D DEP +KEKRQK GGKSGFLAPLQLSDAL+ FLGTGES L R+DVIKRM
Sbjct: 236 EKQKKQERDDDSDEPKKKEKRQKGGGKSGFLAPLQLSDALVNFLGTGESELARTDVIKRM 295

Query: 290 WDYIKEKNLQ 299
           WDYIK  NLQ
Sbjct: 296 WDYIKGNNLQ 305

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461413|ref|XP_004148436.1| PREDICTED: upstream activation factor subunit UAF30-like [Cucumis sativus]

 Score =  344 bits (882), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 184/315 (58%), Positives = 230/315 (73%), Gaps = 40/315 (12%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVSDSELI+RL++FL+NSDLNTTTT IVRR+LE+DFG+DL+DKK+FIREQVDLFLQ++ E
Sbjct: 1   MVSDSELISRLRDFLRNSDLNTTTTAIVRRKLEEDFGIDLSDKKLFIREQVDLFLQTEHE 60

Query: 61  NDQNDG--GNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEA 118
               +G    EE  +ED  E+ +M      ET+                  D D E  + 
Sbjct: 61  KAVQEGYAHCEEVHQEDGDENLKM------ETE------------------DGDSEDGDN 96

Query: 119 KGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQ 178
                 + +  + +VKKRGGGF+KLC+LSPQLQEFIG  E+ARTEVVKQLW +IRE +LQ
Sbjct: 97  DNEDDEKGKTSSEKVKKRGGGFTKLCSLSPQLQEFIGAPEMARTEVVKQLWNHIRENNLQ 156

Query: 179 DPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKST---------- 228
           DP+NRRNI+CDE L+ALFGV++INMFQMNKALSKHIWPL+S+DVI  KS+          
Sbjct: 157 DPSNRRNILCDEPLKALFGVNSINMFQMNKALSKHIWPLESNDVIPAKSSQKEKPQKEKQ 216

Query: 229 ----PKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSD 284
               P++K++KQ + ED D+  R++KRQK GKSGFLAPL LS+AL+ FLGTGE ALPRSD
Sbjct: 217 PKEKPQKKRQKQGKEEDSDDSAREDKRQKKGKSGFLAPLPLSNALVAFLGTGEDALPRSD 276

Query: 285 VIKRMWDYIKEKNLQ 299
           V+KRMWDYIK+ NLQ
Sbjct: 277 VVKRMWDYIKQNNLQ 291

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224081550|ref|XP_002306454.1| predicted protein [Populus trichocarpa] gi|222855903|gb|EEE93450.1| predicted protein [Populus trichocarpa]

 Score =  341 bits (874), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 182/318 (57%), Positives = 216/318 (67%), Gaps = 60/318 (18%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVSDSEL  RL+EFL+N+DL+ TTTG VRR+LE+DF +DL+DKK+FIREQVDLFLQ++ +
Sbjct: 1   MVSDSELTERLKEFLRNADLDKTTTGTVRRKLEEDFAIDLSDKKVFIREQVDLFLQNELD 60

Query: 61  NDQNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKG 120
           + Q +G NE   E                            D   N END  D   E +G
Sbjct: 61  DGQKNGDNEYTHE----------------------------DQKVNVENDGCDLQEEVQG 92

Query: 121 PAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDP 180
                        +KRGGGFSKLC+LSPQLQEFIGV  LARTEVV+QLW YIREK+LQDP
Sbjct: 93  -------------RKRGGGFSKLCSLSPQLQEFIGVPHLARTEVVRQLWTYIREKNLQDP 139

Query: 181 NNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTE 240
           ++RRNI CDE L+ALFGVD+INMFQMNKALS+HIWPLDS+DV+S+ S   EKQ K+ER E
Sbjct: 140 SDRRNINCDEPLQALFGVDSINMFQMNKALSRHIWPLDSEDVVSINSKQHEKQHKREREE 199

Query: 241 D-------------------LDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALP 281
                                +E  +KEK+QKGG SGFLAPLQLSDAL KFLGTGES L 
Sbjct: 200 GNESNYDAILPRMLYLYVKYGNESNKKEKKQKGGNSGFLAPLQLSDALKKFLGTGESTLS 259

Query: 282 RSDVIKRMWDYIKEKNLQ 299
           RSDV+KRMW+YIK+ NLQ
Sbjct: 260 RSDVVKRMWEYIKQNNLQ 277

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357483029|ref|XP_003611801.1| Upstream activation factor subunit spp27 [Medicago truncatula] gi|355513136|gb|AES94759.1| Upstream activation factor subunit spp27 [Medicago truncatula]

 Score =  322 bits (824), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 193/317 (60%), Positives = 222/317 (70%), Gaps = 32/317 (10%)

Query: 1   MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60
           MVS+SELI RL+EFL+NSDLNTTTT  VRRQLE DFG+DL+D+K FIREQVDLFLQ+  +
Sbjct: 1   MVSESELIDRLREFLRNSDLNTTTTSTVRRQLESDFGIDLSDRKSFIREQVDLFLQTVQQ 60

Query: 61  ND--QNDGGNEEQQEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEA 118
           +D  QND   EE  ++   +  + ++ + D  +  +      G               + 
Sbjct: 61  DDEPQNDAVEEEDADDKPEQSQEGSEEEDDNNEEEETPKRTRG------------SVKKT 108

Query: 119 KGPAKRRSRKLNNEV--KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKD 176
           K   K RS K  +EV  KK GGGF K+C+LSPQLQEF+G  E+ARTEVVKQLWAYIREKD
Sbjct: 109 KNKKKERSNKSGDEVVKKKGGGGFCKICSLSPQLQEFVGAPEMARTEVVKQLWAYIREKD 168

Query: 177 LQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQ 236
           LQDPNNRRNI+CDE LRALFGVDTINMFQMNK L+KHIWPLDSDDVI VKS PKEK   +
Sbjct: 169 LQDPNNRRNIICDEPLRALFGVDTINMFQMNKVLAKHIWPLDSDDVIQVKSAPKEKPAPK 228

Query: 237 ERT-------------EDLDEPTRKEKRQK-GGKSGFLAPLQLSDALIKFLGTGESALPR 282
           E+              +DLDEP  KEKRQK G   GFLAPLQLSDAL KFL  GES L R
Sbjct: 229 EKPARKEKKKKQEREDDDLDEPKGKEKRQKVGSGKGFLAPLQLSDALAKFL--GESELSR 286

Query: 283 SDVIKRMWDYIKEKNLQ 299
           SDVIKRMWDYIK  NLQ
Sbjct: 287 SDVIKRMWDYIKGNNLQ 303

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	304
TAIR|locus:2085894	462	AT3G19080 [Arabidopsis thalian	0.585	0.385	0.560	4.2e-69
TAIR|locus:2010197	372	AT1G49520 "AT1G49520" [Arabido	0.417	0.341	0.561	1.4e-52
TAIR|locus:2132055	385	AT4G22360 "AT4G22360" [Arabido	0.506	0.4	0.426	3.2e-41
POMBASE|SPCC285.17	233	spp27 "RNA polymerase I upstre	0.414	0.540	0.397	6.9e-23
ASPGD|ASPL0000053508	279	AN0360 [Emericella nidulans (t	0.309	0.336	0.44	2.3e-22
UNIPROTKB|G4MMD0	285	MGG_01988 "Uncharacterized pro	0.286	0.305	0.459	1.6e-21
SGD|S000004846	226	TRI1 "Non-essential sumoylated	0.407	0.548	0.362	8.3e-19
SGD|S000005821	228	UAF30 "Subunit of UAF (upstrea	0.309	0.412	0.425	1.3e-15
TAIR|locus:2060469	141	AT2G14880 "AT2G14880" [Arabido	0.246	0.531	0.421	8.8e-15
TAIR|locus:505006294	109	AT2G35605 "AT2G35605" [Arabido	0.259	0.724	0.425	1.8e-14

TAIR|locus:2085894 AT3G19080 [Arabidopsis thaliana (taxid:3702)]

 Score = 526 (190.2 bits), Expect = 4.2e-69, Sum P(2) = 4.2e-69
 Identities = 102/182 (56%), Positives = 137/182 (75%)

Query:   119 KGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQ 178
             K   K+ ++ +    +K GGGF+K+C+LSP+LQ F GVTELARTEVVK LW YI+E +LQ
Sbjct:   243 KRKRKKPAKSVEKPKRKGGGGFAKVCSLSPELQAFTGVTELARTEVVKLLWKYIKENNLQ 302

Query:   179 DPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKS-TPKEKQRKQE 237
             DPN++R+I+CDE  R+LF V++INMFQMNK L+KHIWPL+ +   SV S +PK  ++K E
Sbjct:   303 DPNDKRSIICDESFRSLFPVESINMFQMNKQLTKHIWPLEDNAGESVSSKSPKNGKQKME 362

Query:   238 RTEDLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKN 297
                D +EP  K+K+QK  K   LAPL LSDAL+KFLG GE++L R+DV+KR+W+YI   +
Sbjct:   363 SDGDSEEPNEKDKKQK--KE-VLAPLPLSDALVKFLGDGENSLSRADVVKRLWEYINHND 419

Query:   298 LQ 299
             LQ
Sbjct:   420 LQ 421

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009506 "plasmodesma" evidence=IDA

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

 Score = 373 (136.4 bits), Expect = 1.4e-52, Sum P(2) = 1.4e-52
 Identities = 73/130 (56%), Positives = 96/130 (73%)

Query:   123 KRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNN 182
             KR+  K   + KK+GGGF+K+C+LSP+LQ F G  +LARTEVVK LW YI+E +LQDP++
Sbjct:   234 KRKPAKSEEKPKKKGGGFTKVCSLSPELQAFTGTPQLARTEVVKMLWKYIKENNLQDPSD 293

Query:   183 RRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTP-KEKQR-KQERTE 240
             +R I+CDE LR+LF V++INMFQMNK L+KHIWPL  +D     + P K KQ+ K E  E
Sbjct:   294 KRTIICDESLRSLFPVESINMFQMNKQLAKHIWPLVQEDEAGTTNDPEKGKQKMKMETDE 353

Query:   241 DLDEPTRKEK 250
             D DE + +EK
Sbjct:   354 DNDE-SNEEK 362

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2132055 AT4G22360 "AT4G22360" [Arabidopsis thaliana (taxid:3702)]

 Score = 348 (127.6 bits), Expect = 3.2e-41, Sum P(2) = 3.2e-41
 Identities = 72/169 (42%), Positives = 106/169 (62%)

Query:   134 KKRGG--GFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDER 191
             K++GG  G +K+C +SP+L+  +G   L RTE+V+QLWAYIR+ +LQDP+N+R I+CD+ 
Sbjct:   189 KRKGGPGGLNKVCRVSPELEVVVGEPALPRTEIVRQLWAYIRKNNLQDPSNKRKIICDDA 248

Query:   192 LRALFGVDTINMFQMNKALSKHIWPLD-SDDVISVKSTPKEKQRKQERTEDLDEPTRKEK 250
             LR +F  D  +MF+MNK L+KHI PLD S D    K    E + K E TE +        
Sbjct:   249 LRVVFETDCTDMFKMNKLLAKHILPLDPSKDSGQAKKAKTEVETKTETTEPISS------ 302

Query:   251 RQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299
                   +   + + LS+ L KF GTGE+ +   ++I+R+W+YIK  NL+
Sbjct:   303 ------TAISSTVTLSEPLGKFFGTGETEMADEEIIRRVWEYIKLNNLE 345

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 241 (89.9 bits), Expect = 6.9e-23, Sum P(2) = 6.9e-23
 Identities = 56/141 (39%), Positives = 86/141 (60%)

Query:   119 KGPAKR-RSRKLNNEV---KKRG-----GGFSKLCALSPQLQEFIGVTELARTEVVKQLW 169
             K PAKR R RK + E    +KR         +K   LSP+L EF+G+ +L+R + VK+LW
Sbjct:    87 KKPAKRTRKRKEDGEEGGKRKRNQDPANNPLNKPMKLSPKLAEFLGLEQLSRPQTVKKLW 146

Query:   170 AYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTP 229
              YI+  DLQDPN++R I+CD++L+++F VDT++MF MNK L+  +  +  D +      P
Sbjct:   147 EYIKAHDLQDPNDKRTILCDDKLKSVFEVDTLHMFTMNKYLTNLMTKIPDDQL------P 200

Query:   230 KEKQRKQERTEDLDEPTRKEK 250
             K + + +E     D P ++EK
Sbjct:   201 KPQPKNEEPAAPNDLPKQEEK 221

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

ASPGD|ASPL0000053508 AN0360 [Emericella nidulans (taxid:162425)]

 Score = 202 (76.2 bits), Expect = 2.3e-22, Sum P(2) = 2.3e-22
 Identities = 44/100 (44%), Positives = 60/100 (60%)

Query:   120 GPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIG-VTELARTEVVKQLWAYIREKDLQ 178
             G      +K+N     R GGF K   LSP L   +G    L+R + VK+LW YI E DLQ
Sbjct:   184 GSGSESGKKVN-----RSGGFHKPLNLSPALSALLGGAATLSRPQTVKKLWEYIHEHDLQ 238

Query:   179 DPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLD 218
             DP++RR I CD+ +RA+F  D I+MF M K LS++++  D
Sbjct:   239 DPSDRRQIRCDDPMRAVFKQDRIHMFTMTKILSQNLYSPD 278

GO:0008150 "biological_process" evidence=ND

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

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

 Score = 226 (84.6 bits), Expect = 1.6e-21, Sum P(2) = 1.6e-21
 Identities = 40/87 (45%), Positives = 61/87 (70%)

Query:   134 KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLR 193
             +K GGGF K   LS  L E  G   L+R +VVK+LW +I+  +LQDPN++R I+CDE+++
Sbjct:   199 RKAGGGFQKPFHLSASLAEVCGEPTLSRPQVVKKLWEHIKGNNLQDPNDKRQILCDEKMQ 258

Query:   194 ALFGVDTINMFQMNKALSKHIWPLDSD 220
             A+F   ++NMF MNK +  H++P+D +
Sbjct:   259 AVFKQSSLNMFAMNKLIGSHLYPVDEE 285

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

SGD|S000004846 TRI1 "Non-essential sumoylated protein of unknown function" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 46/127 (36%), Positives = 75/127 (59%)

Query:   119 KGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQ 178
             K  +K + +K  N+         +   LS  LQ+F+G  EL RT+VVK +W YI+E DLQ
Sbjct:    99 KSESKSKRKKKKNDSPDSNSISVRKVLLSAPLQKFLGSEELPRTQVVKMIWQYIKEHDLQ 158

Query:   179 DPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQER 238
             +P +RR I+CDE++  +FG   + MF MNK L+KH++  + D+++  +   K+   K+ +
Sbjct:   159 NPKDRREILCDEKMEPIFG-KKMTMFSMNKLLTKHLF--NPDEIVKHEEEQKQTPEKEIK 215

Query:   239 TEDLDEP 245
              E+   P
Sbjct:   216 LENESLP 222

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;IDA

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

GO:0005737 "cytoplasm" evidence=IEA;IDA

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

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005730 "nucleolus" evidence=IEA;IDA

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

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 43/101 (42%), Positives = 60/101 (59%)

Query:   120 GPAKRRSRKLNNEVKKRGGGFSKL------CALSPQLQEFIGVTELARTEVVKQLWAYIR 173
             G  K  S      V+K+ G  SK         LS  L   +G  EL RTEVV++LWAYI+
Sbjct:    94 GEEKNDSETKGTHVEKKKGTVSKSPISTRKVTLSKSLASLLGEHELTRTEVVRRLWAYIK 153

Query:   174 EKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHI 214
               +LQ+PNN++ I+CDE+L  + G  T NMF+M+K L+ H+
Sbjct:   154 AHNLQNPNNKKEILCDEKLELILGKST-NMFEMHKILASHM 193

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

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 32/76 (42%), Positives = 53/76 (69%)

Query:   139 GFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALF-G 197
             G  K   +SP++Q+ + + E+ART+ +K++WAYI+E DLQDP N+R I+CDE+L+ +F G
Sbjct:    64 GIMKPRPVSPEMQDIVELPEIARTQALKRIWAYIKEHDLQDPQNKREILCDEKLKKIFEG 123

Query:   198 VDTINMFQMNKALSKH 213
              D +   ++ K +  H
Sbjct:   124 RDRVGFLEIAKLIGPH 139

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 = 185 (70.2 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 34/80 (42%), Positives = 55/80 (68%)

Query:   135 KRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRA 194
             ++G G  K+  +S  L  FIG  E++RT  VK++W YI+  +LQ+P N+R I+CDE+L+ 
Sbjct:    25 RQGTGILKVVPVSKPLANFIGENEVSRTTAVKKIWEYIKLNNLQNPVNKREILCDEQLKT 84

Query:   195 LF-GVDTINMFQMNKALSKH 213
             +F G DT+   +++K LS+H
Sbjct:    85 IFSGKDTVGFLEISKLLSQH 104

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

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	304
pfam02201	76	pfam02201, SWIB, SWIB/MDM2 domain	5e-32
smart00151	77	smart00151, SWIB, SWI complex, BAF60b domains	8e-32
COG5531	237	COG5531, COG5531, SWIB-domain-containing proteins	3e-24
PRK06319	860	PRK06319, PRK06319, DNA topoisomerase I/SWI domain	3e-20
PRK14724	987	PRK14724, PRK14724, DNA topoisomerase III; Provisi	4e-15
pfam08766	54	pfam08766, DEK_C, DEK C terminal domain	2e-11
pfam02201	76	pfam02201, SWIB, SWIB/MDM2 domain	2e-09
smart00151	77	smart00151, SWIB, SWI complex, BAF60b domains	7e-08
COG5531	237	COG5531, COG5531, SWIB-domain-containing proteins	4e-04
PRK06319	860	PRK06319, PRK06319, DNA topoisomerase I/SWI domain	5e-04
PRK14724	987	PRK14724, PRK14724, DNA topoisomerase III; Provisi	5e-04

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

 Score =  113 bits (285), Expect = 5e-32
 Identities = 40/76 (52%), Positives = 56/76 (73%)

Query: 140 FSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVD 199
            +K   LSP L +F+G  EL+RTEVVK+LW YI+E +LQDP N+R I+CDE+L+++FG D
Sbjct: 1   LTKPFPLSPDLAKFLGAGELSRTEVVKKLWQYIKEHNLQDPKNKRIILCDEKLKSIFGGD 60

Query: 200 TINMFQMNKALSKHIW 215
            +  F+M+K LS H  
Sbjct: 61  RVGFFEMSKLLSSHFI 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 =  113 bits (284), Expect = 8e-32
 Identities = 36/77 (46%), Positives = 55/77 (71%)

Query: 140 FSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVD 199
            +K   LSP+L + +G  E+ RTE++K+LW YI+E +LQDP N+R I+CD +L  +FG D
Sbjct: 1   ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKD 60

Query: 200 TINMFQMNKALSKHIWP 216
            ++MF+MNK L+ H+  
Sbjct: 61  RMDMFEMNKLLTPHLIK 77

Length = 77

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

 Score = 97.9 bits (244), Expect = 3e-24
 Identities = 55/242 (22%), Positives = 94/242 (38%), Gaps = 21/242 (8%)

Query: 12  QEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQ 71
             +L+  + +T     V + L  ++ V L  +     + +     S  E  +     +  
Sbjct: 12  DSWLQLDERDTNNEKDVGKLLFSEWTVRLEGRFKDNNDLIRDKFDSLAEEPRVLRKEKYN 71

Query: 72  QEEDDGEDDQMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRSRKLNN 131
                         K+D     D +     + +N D         E K   K++     +
Sbjct: 72  ITRKT-------TGKNDLPKEEDSSLPSSKETENGDT--------EGKETDKKKKSSTIS 116

Query: 132 EVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDER 191
           +    G        LSP+L   +G+    R E VK+LW YI++ +LQDPNN+R I+CD +
Sbjct: 117 KNSPSGEKVK----LSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSK 172

Query: 192 LRALFGVDTINMFQMNKALSKHIWPLDSDDVISVKSTPKEKQRKQERTEDLDEPTRKEKR 251
           L+ + G D I+MF++ K LS H+     D  +S   T        E   + D   +    
Sbjct: 173 LKKVLGSDPIDMFELTKPLSPHLIKYTID--VSKAPTYGGTTLDIEIPLENDSLQQLPTL 230

Query: 252 QK 253
             
Sbjct: 231 YT 232

Length = 237

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

 Score = 90.7 bits (225), Expect = 3e-20
 Identities = 38/97 (39%), Positives = 54/97 (55%), Gaps = 3/97 (3%)

Query: 118 AKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDL 177
           AK   K+   K     KKR G    L   SP L   IG   + R E  K++W YI+E  L
Sbjct: 765 AKTVKKKSKAKSKKTTKKRAG---PLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGL 821

Query: 178 QDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHI 214
           Q P N++ I+ D +L+ + G D I+MFQ++K LS+H+
Sbjct: 822 QSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHL 858

Length = 860

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

 Score = 75.4 bits (185), Expect = 4e-15
 Identities = 32/97 (32%), Positives = 48/97 (49%), Gaps = 4/97 (4%)

Query: 118 AKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDL 177
               AK   +    +      G       S  L   IG   +AR EV+K+LW YI+  +L
Sbjct: 894 KTAAAKTPRKAAKKKAAPPAAGLKP----SAALAAVIGAEPVARPEVIKKLWDYIKANNL 949

Query: 178 QDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHI 214
           QDP ++R I  D +LR +FG D + MF++   + KH+
Sbjct: 950 QDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHL 986

Length = 987

>gnl|CDD|204056 pfam08766, DEK_C, DEK C terminal domain

 Score = 57.9 bits (141), Expect = 2e-11
 Identities = 20/53 (37%), Positives = 36/53 (67%)

Query: 3  SDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFL 55
          +D E+   ++E L+ +DL T T   +R++LE   GVDL+++K FI++ ++ FL
Sbjct: 1  TDEEIKEEIREILREADLETVTKKQIRKELEARLGVDLSERKAFIKDLIEEFL 53

DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family. This domain is also found in chitin synthase proteins and in protein phosphatases. Length = 54

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 22/41 (53%), Positives = 27/41 (65%), Gaps = 2/41 (4%)

Query: 259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299
              P  LS  L KFLG GE  L R++V+K++W YIKE NLQ
Sbjct: 1   LTKPFPLSPDLAKFLGAGE--LSRTEVVKKLWQYIKEHNLQ 39

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 = 48.5 bits (116), Expect = 7e-08
 Identities = 19/39 (48%), Positives = 26/39 (66%), Gaps = 2/39 (5%)

Query: 262 PLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQV 300
            + LS  L K LG  E  + R+++IKR+W+YIKE NLQ 
Sbjct: 4   KVTLSPELAKVLGAPE--MTRTEIIKRLWEYIKEHNLQD 40

Length = 77

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

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 226 KSTPKEKQRKQE---RTEDLDEPTRKEKRQKGGKSGFLA-----PLQLSDALIKFLGTGE 277
              PKE+         TE+ D   ++  ++K   +          ++LS  L   LG   
Sbjct: 80  NDLPKEEDSSLPSSKETENGDTEGKETDKKKKSSTISKNSPSGEKVKLSPKLAAILGLEP 139

Query: 278 SALPRSDVIKRMWDYIKEKNLQ 299
               R + +K++W YIK+ NLQ
Sbjct: 140 --GTRPEAVKKLWKYIKKHNLQ 159

Length = 237

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

 Score = 41.3 bits (97), Expect = 5e-04
 Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 225 VKSTPKEKQR--KQERTEDLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPR 282
            K T  +K+    + +     +   K K +K  K         S AL   +G       R
Sbjct: 748 EKKTKAKKKSASTKGKAAKTVKKKSKAKSKKTTKKRAGPLYTPSPALAAMIGAEPVG--R 805

Query: 283 SDVIKRMWDYIKEKNLQ 299
            +  K++WDYIKE  LQ
Sbjct: 806 GEATKKVWDYIKEHGLQ 822

Length = 860

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

 Score = 41.5 bits (97), Expect = 5e-04
 Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 5/55 (9%)

Query: 245 PTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299
           P +  K++    +  L P   S AL   +G    A  R +VIK++WDYIK  NLQ
Sbjct: 901 PRKAAKKKAAPPAAGLKP---SAALAAVIGAEPVA--RPEVIKKLWDYIKANNLQ 950

Length = 987

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	304
KOG1946	240	consensus RNA polymerase I transcription factor UA	99.97
COG5531	237	SWIB-domain-containing proteins implicated in chro	99.93
PF02201	76	SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SW	99.92
smart00151	77	SWIB SWI complex, BAF60b domains.	99.91
PRK14724	987	DNA topoisomerase III; Provisional	99.81
KOG2570	420	consensus SWI/SNF transcription activation complex	99.73
PF08766	54	DEK_C: DEK C terminal domain; InterPro: IPR014876	99.58
KOG1946	240	consensus RNA polymerase I transcription factor UA	99.45
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	99.39
PF02201	76	SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SW	99.38
smart00151	77	SWIB SWI complex, BAF60b domains.	99.37
COG5531	237	SWIB-domain-containing proteins implicated in chro	99.21
PRK14724	987	DNA topoisomerase III; Provisional	98.97
KOG2266	594	consensus Chromatin-associated protein Dek and rel	98.86
KOG2570	420	consensus SWI/SNF transcription activation complex	98.15
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	97.9

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

Probab=99.97  E-value=1.6e-31  Score=245.57  Aligned_cols=181  Identities=35%  Similarity=0.497  Sum_probs=136.7

Q ss_pred             CCCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHhhhhhcccCCCCCCcccccccCchh
Q 022018            1 MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQQEEDDGEDD   80 (304)
Q Consensus         1 m~sd~ei~~~I~~IL~~aDl~~vT~k~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   80 (304)
                      |.+...+...+..||...+++++|...||++++..||++++..+..++.+|...+..-......     +...       
T Consensus         1 ~~~~~~~~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~~~k~~~~~~~~~~~~~~~~~~~k-----~~~~-------   68 (240)
T KOG1946|consen    1 MDSLSWEYLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGTAQKSLLAKAIDESSDEDSALPVK-----GSKK-------   68 (240)
T ss_pred             CcchhhhhhhhHHHhcccccccCCHHHHHHHhccccCCCCcchhhhhhhhhhcccccccccccc-----cccc-------
Confidence            5677889999999999999999999999999999999999999999988886665432110000     0000       


Q ss_pred             hhhhccCCCCCCCCcccccCCCCCCCCCCCCchhhhhcCCchhhhhcccccccccCCCCCCccccCCHHHHhhhCCCCcc
Q 022018           81 QMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELA  160 (304)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~k~~~~~~~~~~g~~k~~~LS~~La~~lG~~~~s  160 (304)
                      .  + .+     ...      ...            .+.+...  +.....+.+..++|+++.|.||+.|+.|+|.+++|
T Consensus        69 k--~-~~-----~~~------~~~------------~~~~~~~--~~~~~~~~~~~~~g~~kl~~ls~~L~~~~G~~~ls  120 (240)
T KOG1946|consen   69 K--K-RG-----SKT------RSR------------KPKSLES--SGEKNKKKKKASWGSTKLIPLSPSLARFVGTSELS  120 (240)
T ss_pred             c--c-cc-----ccc------ccc------------cCccccc--ccccchhccccCcCcccccccCHHHHhhccccccc
Confidence            0  0 00     000      000            0000000  00000111124689999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCCCCcc
Q 022018          161 RTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDD  221 (304)
Q Consensus       161 R~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~pl~p~~  221 (304)
                      |++|++.||+|||+||||||.|++.|+||++|+.|||..+|+||+|+++|.+||++.....
T Consensus       121 R~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H~~~~~d~~  181 (240)
T KOG1946|consen  121 RTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKHFLKNQDMV  181 (240)
T ss_pred             HHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHhccCccccc
Confidence            9999999999999999999999999999999999999999999999999999998877654

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

Probab=99.93  E-value=3.6e-26  Score=208.99  Aligned_cols=193  Identities=24%  Similarity=0.380  Sum_probs=128.9

Q ss_pred             HHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHhhhhhcccCCCCCCcccccccCchhhhhhcc
Q 022018            7 LIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQQEEDDGEDDQMAKVK   86 (304)
Q Consensus         7 i~~~I~~IL~~aDl~~vT~k~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (304)
                      +..++..+|+..+..+++.+.|++.+...++++|..+..++++.+...+.+................+       .    
T Consensus         7 ~~~~~~~~~~~~e~~~~~ek~v~~~~~~~~~~~l~~r~k~~~~~~~~~~~s~~~~~~~~~~~k~~~~r-------~----   75 (237)
T COG5531           7 YGTMNDSWLQLDERDTNNEKDVGKLLFSEWTVRLEGRFKDNNDLIRDKFDSLAEEPRVLRKEKYNITR-------K----   75 (237)
T ss_pred             cccccceeeecccccccChhhcccccchhhheehhhhhhhccchhhhhhhhhcccchhhhhhhhccCc-------c----
Confidence            34467788999999999999999999999999999999999988877766543211000000000000       0    


Q ss_pred             CCCCCCCCcccccCCCCCCCCCCCCchhh-hhcCCchhhhhcccccccccCCCCCCccccCCHHHHhhhCCCCccHHHHH
Q 022018           87 SDETDGSDDAAVEEGDDDNNDENDNDDEA-NEAKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVV  165 (304)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~-~~~~~~~~~~~~k~~~~~~~~~~g~~k~~~LS~~La~~lG~~~~sR~evv  165 (304)
                         ++....    ..+..  ++......+ +.+..-.+....++..+....++-+...|.||+.||+|||..++||++||
T Consensus        76 ---~~~~~~----~~~~~--~~~~~s~k~~~n~~te~k~~~~~k~~~~~~~~~~~~~~~~lS~~La~ilG~~~~tr~~~v  146 (237)
T COG5531          76 ---TTGKND----LPKEE--DSSLPSSKETENGDTEGKETDKKKKSSTISKNSPSGEKVKLSPKLAAILGLEPGTRPEAV  146 (237)
T ss_pred             ---cccccc----ccccc--ccccCcchhhhcCccccccccccccccccccccCCCCceecCHHHHHHhCCCCCCccHHH
Confidence               000000    00000  000000000 00000000000011111112356677899999999999999999999999


Q ss_pred             HHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCCCC
Q 022018          166 KQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDS  219 (304)
Q Consensus       166 k~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~pl~p  219 (304)
                      +.||+||+.||||||.|++.|+||++|+.|||.+.|.||+|++.|++|+.+++-
T Consensus       147 ~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl~~~~~  200 (237)
T COG5531         147 KKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPLSPHLIKYTI  200 (237)
T ss_pred             HHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhcccccceecCcc
Confidence            999999999999999999999999999999999999999999999999987543

>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=99.92  E-value=1.7e-26  Score=177.99  Aligned_cols=75  Identities=53%  Similarity=1.027  Sum_probs=70.8

Q ss_pred             CCccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccC
Q 022018          140 FSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHI  214 (304)
Q Consensus       140 ~~k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl  214 (304)
                      |+++|+|||+|++|+|..++||++|+++||+||++||||||+|++.|+||+.|+.|||+++|+||+|+++|++||
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 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHL   75 (76)
T ss_dssp             -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHH
T ss_pred             CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhc
Confidence            578899999999999999999999999999999999999999999999999999999999999999999999997

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 ....

>smart00151 SWIB SWI complex, BAF60b domains

Probab=99.91  E-value=6.7e-25  Score=169.57  Aligned_cols=76  Identities=47%  Similarity=0.966  Sum_probs=74.0

Q ss_pred             CccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCC
Q 022018          141 SKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWP  216 (304)
Q Consensus       141 ~k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~p  216 (304)
                      +++|.||++|++|+|..++||++|+++||+||+.||||||+|++.|+||+.|+.|||+++|.|++|+++|++||.|
T Consensus         2 ~~~~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl~~   77 (77)
T smart00151        2 TKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK   77 (77)
T ss_pred             CCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999999975

>PRK14724 DNA topoisomerase III; Provisional

Probab=99.81  E-value=2.7e-20  Score=200.03  Aligned_cols=77  Identities=38%  Similarity=0.673  Sum_probs=74.7

Q ss_pred             CCCccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 022018          139 GFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW  215 (304)
Q Consensus       139 g~~k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~  215 (304)
                      .|...+.|||+|++|||..++||++||++||+|||.||||||.|++.|+||++|+.|||+++|.||+|+++|++||.
T Consensus       911 ~~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~  987 (987)
T PRK14724        911 PPAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS  987 (987)
T ss_pred             ccccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence            37788999999999999999999999999999999999999999999999999999999999999999999999984

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

Probab=99.73  E-value=2.6e-18  Score=166.83  Aligned_cols=82  Identities=32%  Similarity=0.614  Sum_probs=79.4

Q ss_pred             ccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCCCCcc
Q 022018          142 KLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDD  221 (304)
Q Consensus       142 k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~pl~p~~  221 (304)
                      ..|+|||.||.+||+...||+.||.+||.||+.|+||||.++.+|+||..|+.+||++++.|.+|+.+|++||.|++||.
T Consensus       207 ~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~dPIv  286 (420)
T KOG2570|consen  207 EEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPDPIV  286 (420)
T ss_pred             cccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCCCee
Confidence            44789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cc
Q 022018          222 VI  223 (304)
Q Consensus       222 ~~  223 (304)
                      +.
T Consensus       287 i~  288 (420)
T KOG2570|consen  287 ID  288 (420)
T ss_pred             ec
Confidence            65

>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease

Probab=99.58  E-value=2.7e-15  Score=108.55  Aligned_cols=54  Identities=46%  Similarity=0.762  Sum_probs=45.7

Q ss_pred             CHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHh
Q 022018            3 SDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQ   56 (304)
Q Consensus         3 sd~ei~~~I~~IL~~aDl~~vT~k~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~   56 (304)
                      ||++|...|++||+++||+++|.|+||++|+++||+||+++|.||+++|+.+|.
T Consensus         1 td~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~~K~~I~~~I~~~l~   54 (54)
T PF08766_consen    1 TDEEIREAIREILREADLDTVTKKQVREQLEERFGVDLSSRKKFIKELIDEFLS   54 (54)
T ss_dssp             -HHHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhC
Confidence            799999999999999999999999999999999999999999999999999884

This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.

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

Probab=99.45  E-value=1e-13  Score=128.07  Aligned_cols=48  Identities=44%  Similarity=0.717  Sum_probs=45.7

Q ss_pred             CCCCCCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          255 GKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       255 ~~~g~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      .++|+++++.||+.|+.|+|..  +|||++|+++||+|||+||||||.||
T Consensus        96 ~~~g~~kl~~ls~~L~~~~G~~--~lsR~~vvk~iw~YIke~nLqDP~nk  143 (240)
T KOG1946|consen   96 ASWGSTKLIPLSPSLARFVGTS--ELSRTDVVKKIWAYIKEHNLQDPKNK  143 (240)
T ss_pred             cCcCcccccccCHHHHhhcccc--cccHHHHHHHHHHHHHHhccCCcccc
Confidence            4579999999999999999977  99999999999999999999999997

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

Probab=99.39  E-value=2.5e-13  Score=145.04  Aligned_cols=74  Identities=41%  Similarity=0.759  Sum_probs=71.2

Q ss_pred             ccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 022018          142 KLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW  215 (304)
Q Consensus       142 k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~  215 (304)
                      .+|.+|+.|+.|+|...++|+++++.||+||+.|+||||.|++.|+||++|+++||++.+.||.|+++|++||.
T Consensus       786 ~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~  859 (860)
T PRK06319        786 PLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLI  859 (860)
T ss_pred             cccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhc
Confidence            44779999999999999999999999999999999999999999999999999999999999999999999985

>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=99.38  E-value=1.1e-13  Score=106.75  Aligned_cols=44  Identities=50%  Similarity=0.825  Sum_probs=40.0

Q ss_pred             CCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       259 ~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      |+++|.||++|++|+|..  ++||++|+++||+||++|+||||.||
T Consensus         1 ~~k~~~ls~~L~~~lg~~--~~sr~~v~~~lw~YIk~~~L~dp~~k   44 (76)
T PF02201_consen    1 FPKRFKLSPELAEFLGED--ELSRSEVVKRLWQYIKENNLQDPKDK   44 (76)
T ss_dssp             -EEEEHHHHHHHHHTT-S--CEEHHHHHHHHHHHHHHTTSBESSST
T ss_pred             CCCCccCCHHHHHHhCCC--CCCHHHHHHHHHHHHHHhcCCCcccC
Confidence            467899999999999987  89999999999999999999999986

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 ....

>smart00151 SWIB SWI complex, BAF60b domains

Probab=99.37  E-value=6.3e-13  Score=102.70  Aligned_cols=44  Identities=43%  Similarity=0.740  Sum_probs=41.4

Q ss_pred             CCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       259 ~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      ++.+|.||++|+.|+|..  ++||++|++.||+|||.||||||.||
T Consensus         1 ~~~~~~ls~~L~~~lg~~--~~tr~ev~~~lw~YIk~n~L~d~~~k   44 (77)
T smart00151        1 ITKKVTLSPELAKVLGAP--EMTRTEIIKRLWEYIKEHNLQDPQNK   44 (77)
T ss_pred             CCCcccCCHHHHHHhCCC--cCcHHHHHHHHHHHHHHhcccCCccC
Confidence            367899999999999976  99999999999999999999999986

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

Probab=99.21  E-value=1.1e-11  Score=114.07  Aligned_cols=47  Identities=34%  Similarity=0.497  Sum_probs=44.4

Q ss_pred             CCCCCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          256 KSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       256 ~~g~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      .+.+..+|.+|+.||.|||.+  ++||++||+.||+|||.||||||.||
T Consensus       118 ~~~~~~~~~lS~~La~ilG~~--~~tr~~~v~~lw~YIk~h~lq~~~nk  164 (237)
T COG5531         118 NSPSGEKVKLSPKLAAILGLE--PGTRPEAVKKLWKYIKKHNLQDPNNK  164 (237)
T ss_pred             ccCCCCceecCHHHHHHhCCC--CCCccHHHHHHHHHHHHhcCCCcccc
Confidence            456789999999999999988  99999999999999999999999997

>PRK14724 DNA topoisomerase III; Provisional

Probab=98.97  E-value=4.6e-10  Score=121.64  Aligned_cols=44  Identities=43%  Similarity=0.653  Sum_probs=42.3

Q ss_pred             CCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       259 ~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      +..++.|||+||.|||++  ++||++||++||+|||.|+||||.||
T Consensus       912 ~~~~~~ls~~La~~lg~~--~~~r~~v~~~lW~YIK~~~Lqdp~~k  955 (987)
T PRK14724        912 PAAGLKPSAALAAVIGAE--PVARPEVIKKLWDYIKANNLQDPADK  955 (987)
T ss_pred             cccccCCCHHHHHHhCCC--cCCHHHHHHHHHHHHHHccCCCcccC
Confidence            678999999999999988  99999999999999999999999996

>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]

Probab=98.86  E-value=3e-09  Score=105.53  Aligned_cols=60  Identities=28%  Similarity=0.447  Sum_probs=58.1

Q ss_pred             CCCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHhhhhh
Q 022018            1 MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE   60 (304)
Q Consensus         1 m~sd~ei~~~I~~IL~~aDl~~vT~k~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~~~~~   60 (304)
                      .|||++|...|..||..+||+++|.+.|.++|..+|++||++||.||.++|..+|..+.+
T Consensus       519 ePTdeelk~~V~kILk~vdfntaTm~dIlKkl~~~f~~dLt~rK~~IK~~Ike~I~~~~d  578 (594)
T KOG2266|consen  519 EPTDEELKEVVKKILKEVDFNTATMKDILKKLYAKFPIDLTHRKDFIKDTIKELINKMAD  578 (594)
T ss_pred             CCcHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHhcc
Confidence            499999999999999999999999999999999999999999999999999999998865

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

Probab=98.15  E-value=1.5e-06  Score=85.38  Aligned_cols=41  Identities=32%  Similarity=0.569  Sum_probs=38.5

Q ss_pred             CCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          262 PLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       262 ~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      .|.+||.||.+||..  +-||++||-.||.|||.|+||||.++
T Consensus       208 ~fklsp~La~lLGi~--t~Trp~iI~alWqYIk~n~Lqd~~e~  248 (420)
T KOG2570|consen  208 EFKLSPRLANLLGIH--TGTRPDIVTALWQYIKTNKLQDPEDS  248 (420)
T ss_pred             ccccCHHHHHHhhhc--cCcchHHHHHHHHHHHHhccCCcccc
Confidence            477999999999998  99999999999999999999999874

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

Probab=97.90  E-value=5.8e-06  Score=89.10  Aligned_cols=44  Identities=34%  Similarity=0.509  Sum_probs=40.9

Q ss_pred             CCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       259 ~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      .+.+|.+|++|+.|+|+.  +++|+++++.||+|||.|+||||+||
T Consensus       784 ~~~~~~~S~~La~~~g~~--~~sr~~~~~~lw~yIk~~~lqdp~~K  827 (860)
T PRK06319        784 AGPLYTPSPALAAMIGAE--PVGRGEATKKVWDYIKEHGLQSPENK  827 (860)
T ss_pred             cccccccccccccccCcC--ccCchHHHHHHHHHHHHhcccCcccc
Confidence            356788999999999987  99999999999999999999999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	304
1v31_A	93	Solution Structure Of The SwibMDM2 DOMAIN OF THE Hy		1e-05
1v32_A	101	Solution Structure Of The SwibMDM2 DOMAIN OF THE Hy		1e-05
1uhr_A	93	Solution Structure Of The Swib Domain Of Mouse Brg1		1e-05

>pdb|1V31|A Chain A, Solution Structure Of The SwibMDM2 DOMAIN OF THE Hypothetical Protein At5g14170 From Arabidopsis Thaliana Length = 93

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/69 (26%), Positives = 38/69 (55%)
Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           LS  L + +G+    R  ++  +W Y++ + LQ+PN+     CD  L+ +FG + +    
Sbjct: 14  LSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEKLKFTM 73
Query: 206 MNKALSKHI 214
           +++ +S H+
Sbjct: 74  VSQKISHHL 82

>pdb|1V32|A Chain A, Solution Structure Of The SwibMDM2 DOMAIN OF THE Hypothetical Protein At5g08430 From Arabidopsis Thaliana Length = 101

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKH 213
           ++R +V   +  YI ++ L DP+N++ +VCD+RL  LFG  TI   ++   L KH
Sbjct: 35  ISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDLLEKH 89

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/71 (28%), Positives = 38/71 (53%)
Query: 146 LSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQ 205
           L P+L   +G+    R  +++ LW YI+   LQDP+ R  ++CD+ L+ +F    +   +
Sbjct: 14  LDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSE 73
Query: 206 MNKALSKHIWP 216
           + + L   + P
Sbjct: 74  IPQRLHALLMP 84
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	304
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	2e-35
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	1e-09
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	5e-35
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	1e-09
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	2e-27
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-10
1q1v_A	70	DEK protein; winged-helix motif, DNA binding prote	6e-07
1ycq_A	107	MDM2, MDM2; anti-oncogene, DNA-binding, transcript	9e-06

>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 =  122 bits (308), Expect = 2e-35
 Identities = 20/85 (23%), Positives = 41/85 (48%)

Query: 134 KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLR 193
                G  +   LS  L + +G+    R  ++  +W Y++ + LQ+PN+     CD  L+
Sbjct: 2   SSGSSGVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQ 61

Query: 194 ALFGVDTINMFQMNKALSKHIWPLD 218
            +FG + +    +++ +S H+ P  
Sbjct: 62  KVFGEEKLKFTMVSQKISHHLSPPP 86

>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 = 53.2 bits (128), Expect = 1e-09
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 253 KGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299
             G SG     +LS AL+  LG       R  +I  +W Y+K + LQ
Sbjct: 2   SSGSSGVPEKFKLSTALMDVLGIEV--ETRPRIIAAIWHYVKARKLQ 46

>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 =  121 bits (305), Expect = 5e-35
 Identities = 21/85 (24%), Positives = 40/85 (47%)

Query: 134 KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLR 193
                G      L P+L   +G+    R  +++ LW YI+   LQDP+ R  ++CD+ L+
Sbjct: 2   SSGSSGQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQ 61

Query: 194 ALFGVDTINMFQMNKALSKHIWPLD 218
            +F    +   ++ + L   + P +
Sbjct: 62  QIFESQRMKFSEIPQRLHALLMPPE 86

>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 = 53.2 bits (128), Expect = 1e-09
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 2/47 (4%)

Query: 253 KGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299
             G SG     +L   L + LG       R  +I+ +W YIK   LQ
Sbjct: 2   SSGSSGQPPQFKLDPRLARLLGIHT--QTRPVIIQALWQYIKTHKLQ 46

>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 =  101 bits (254), Expect = 2e-27
 Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 147 SPQLQEFIGV------TELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDT 200
           S QL EF+          ++R +V   +  YI ++ L DP+N++ +VCD+RL  LFG  T
Sbjct: 17  SRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLFGTRT 76

Query: 201 INMFQMNKALSKHIWPLDSDD 221
           I   ++   L KH        
Sbjct: 77  IFRMKVYDLLEKHYKENQDSG 97

>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 = 44.4 bits (105), Expect = 3e-06
 Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 4/38 (10%)

Query: 266 SDALIKFLGT----GESALPRSDVIKRMWDYIKEKNLQ 299
           S  LI+FL +        + R DV   +  YI ++ L 
Sbjct: 17  SRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLL 54

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 59.9 bits (144), Expect = 4e-10
 Identities = 57/346 (16%), Positives = 106/346 (30%), Gaps = 90/346 (26%)

Query: 34  KDFGV-DLTD--KKIFIREQVDLFLQSQFENDQND---GGNEEQQEE------DDGEDDQ 81
            +F   D+ D  K I  +E++D  + S+               +QEE      ++     
Sbjct: 31  DNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN 90

Query: 82  ----MAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRS--RKLNNEVKK 135
               M+ +K+++   S    +   +  +   NDN      AK    R     KL   + +
Sbjct: 91  YKFLMSPIKTEQRQPSMMTRMYI-EQRDRLYNDNQ---VFAKYNVSRLQPYLKLRQALLE 146

Query: 136 ---------RG-GGFSK------LCALSPQLQEF------IGVTELARTE-VVKQLWAYI 172
                     G  G  K      +C       +       + +      E V++ L   +
Sbjct: 147 LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL 206

Query: 173 REKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDV---------- 222
            + D  +  +R +   + +LR       +     +K     +  L   +V          
Sbjct: 207 YQID-PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL--LVLLNVQNAKAWNAFN 263

Query: 223 ISVK---STPKEKQRKQERTEDLDEPTRKEKRQKGGKSGFLAPLQLSDALIKFLGTGESA 279
           +S K   +T     R ++ T+ L   T               P ++   L+K+L      
Sbjct: 264 LSCKILLTT-----RFKQVTDFLSAATTTHISLDHHSMTL-TPDEVKSLLLKYLDCRPQD 317

Query: 280 LPRS---------DVIKRM-------WDYIKEKN-------LQVSL 302
           LPR           +I          WD  K  N       ++ SL
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363

>1q1v_A DEK protein; winged-helix motif, DNA binding protein; NMR {Homo sapiens} SCOP: a.159.4.1 Length = 70

 Score = 45.2 bits (107), Expect = 6e-07
 Identities = 13/57 (22%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 3  SDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDF-GVDLTDKKIFIREQVDLFLQSQ 58
          +D EL   +++ L +++L   T   + +++ +++   DLT++K FI+  V   +  +
Sbjct: 13 TDEELKETIKKLLASANLEEVTMKQICKKVYENYPTYDLTERKDFIKTTVKELISLE 69

>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 Length = 107

 Score = 43.0 bits (100), Expect = 9e-06
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 145 ALSPQLQEFIGVTE--LARTEVVKQLWAYIREKDLQDPNNRRNIVC-DERLRALFGVDTI 201
            L   L +  G  +      EV+  L  YI  K L D   +  + C ++ L  LFGV   
Sbjct: 16  PLLLSLLKSAGAQKETFTMKEVIYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEF 75

Query: 202 NMFQMNK---ALSKHIWPLDSDDVIS 224
           ++ +  +    +S+++   +  +   
Sbjct: 76  SVKEPRRLYAMISRNLVSANVKESSE 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	304
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	99.96
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	99.95
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	99.93
1q1v_A	70	DEK protein; winged-helix motif, DNA binding prote	99.71
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	99.51
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	99.4
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	99.34
3dac_M	130	MDM4 protein; MDMX, MDM4, HDMX, HDM4, MDM-4, MDM-X	96.95
3fea_A	100	MDM4 protein; HDMX, HDM4,human MDM4, human MDMX, p	96.52
1z1m_A	119	Ubiquitin-protein ligase E3 MDM2; peptide-binding	96.51
2z5s_M	140	MDM4 protein, zebrafish MDMX; MDMX, MDM4, acetylat	96.29
1ycq_A	107	MDM2, MDM2; anti-oncogene, DNA-binding, transcript	96.23
2axi_A	115	Ubiquitin-protein ligase E3 MDM2; drug design, pro	95.76

>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=99.96  E-value=1.6e-30  Score=206.81  Aligned_cols=87  Identities=23%  Similarity=0.547  Sum_probs=83.5

Q ss_pred             CCCCCccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCC
Q 022018          137 GGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWP  216 (304)
Q Consensus       137 ~~g~~k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~p  216 (304)
                      ..+++.+|.||++||+|||..++||++||++||+|||.||||||.||+.|+||++|+.|||+++|.||+|+++|++||.|
T Consensus         5 ~~~~p~~~~lS~~La~~lG~~~~sr~evvk~lW~YIK~n~Lqdp~~k~~I~cD~~L~~lfg~~~v~~~~~~klL~~Hl~p   84 (93)
T 1v31_A            5 SSGVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEKLKFTMVSQKISHHLSP   84 (93)
T ss_dssp             CCSSCCCEECCHHHHHHSCCSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHSCSSEEETTTTHHHHHHHCBC
T ss_pred             CCCCCCccccCHHHHHHHCCCccCHHHHHHHHHHHHHHccCcCcccCceeehhHHHHHHhCCCcccHHHHHHHHHHhcCC
Confidence            45677999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccc
Q 022018          217 LDSDDVI  223 (304)
Q Consensus       217 l~p~~~~  223 (304)
                      ++|+...
T Consensus        85 ~~Pi~~~   91 (93)
T 1v31_A           85 PPPSGPS   91 (93)
T ss_dssp             CCCSSCC
T ss_pred             CCCeeCC
Confidence            9998764

>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=99.95  E-value=8.9e-30  Score=202.51  Aligned_cols=84  Identities=24%  Similarity=0.563  Sum_probs=80.9

Q ss_pred             CCccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCCCC
Q 022018          140 FSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDS  219 (304)
Q Consensus       140 ~~k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~pl~p  219 (304)
                      .+.+|+||++||+|||..++||++||++||+|||.||||||.||+.|+||++|+.|||+++|.||+|+++|++||.|++|
T Consensus         8 ~p~~~~lS~~La~~lG~~~~sr~evvk~lW~YIK~n~Lqdp~~k~~I~cD~~Lk~lfg~~~v~~~~~~klL~~Hl~p~~P   87 (93)
T 1uhr_A            8 QPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSEIPQRLHALLMPPEP   87 (93)
T ss_dssp             SCCEEEECTTHHHHTCCSEEEHHHHHHHHHHHHHHTTCBCSSCSSEECCCTTHHHHTCCSSEEGGGSHHHHHHHEECSSC
T ss_pred             CCCccCcCHHHHHHHCCCccCHHHHHHHHHHHHHhccCCCccccceeechHHHHHHhCCCcccHHHHHHHHHHhcCCCCC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 022018          220 DDVI  223 (304)
Q Consensus       220 ~~~~  223 (304)
                      +...
T Consensus        88 I~i~   91 (93)
T 1uhr_A           88 SGPS   91 (93)
T ss_dssp             CCSS
T ss_pred             eeCC
Confidence            9764

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

Probab=99.93  E-value=1.5e-26  Score=186.41  Aligned_cols=73  Identities=37%  Similarity=0.557  Sum_probs=69.9

Q ss_pred             cCCHHHHhhh---CC---CCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCC
Q 022018          145 ALSPQLQEFI---GV---TELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPL  217 (304)
Q Consensus       145 ~LS~~La~~l---G~---~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~pl  217 (304)
                      .+|++||+||   |.   .++||++||++||+|||+||||||.||+.|+||++|+.|||+++|.||+|+++|++||.+.
T Consensus        15 w~S~eLa~fl~~iG~~~~~~~sR~eVvk~lW~YIK~nnLQdp~~Kr~I~cD~kLk~lFg~~~v~~~~m~klL~~Hl~~~   93 (101)
T 1v32_A           15 WGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDLLEKHYKEN   93 (101)
T ss_dssp             SSCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCTTEEECCSHHHHHTCCSEEETTHHHHHHHHHSCSC
T ss_pred             cCCHHHHHHHHHcCCCCccccCHHHHHHHHHHHHHhhcCcCcccCCeeeccHHHHHHHCCCcccHHHHHHHHHHHcCcc
Confidence            5899999999   98   5799999999999999999999999999999999999999999999999999999999753

>1q1v_A DEK protein; winged-helix motif, DNA binding protein; NMR {Homo sapiens} SCOP: a.159.4.1

Probab=99.71  E-value=1.3e-17  Score=125.82  Aligned_cols=57  Identities=23%  Similarity=0.414  Sum_probs=55.5

Q ss_pred             CCCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHh-CCCCchhhHHHHHHHHHHHhh
Q 022018            1 MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDF-GVDLTDKKIFIREQVDLFLQS   57 (304)
Q Consensus         1 m~sd~ei~~~I~~IL~~aDl~~vT~k~VR~~Le~~f-gvDLs~kK~~I~~~I~~~l~~   57 (304)
                      +|||++|...|++||++|||++||.|+||++|+++| |+||++||+||+++|+.+|+.
T Consensus        11 ~Psd~ei~~~I~~IL~~aDL~tvT~K~VR~~Le~~~pg~dLs~kK~~I~~~I~~~L~~   68 (70)
T 1q1v_A           11 PPTDEELKETIKKLLASANLEEVTMKQICKKVYENYPTYDLTERKDFIKTTVKELISL   68 (70)
T ss_dssp             CCCHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHCSSSCCSHHHHHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHHHHHHHhCCHHHHhHHHHHHHHHHHccCCCChHHHHHHHHHHHHHHhc
Confidence            699999999999999999999999999999999999 999999999999999999964

>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=99.51  E-value=7.7e-15  Score=116.33  Aligned_cols=47  Identities=32%  Similarity=0.557  Sum_probs=43.6

Q ss_pred             CCCCCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          256 KSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       256 ~~g~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      ...+...|.+|++||+|+|..  ++||++||++||+|||.|+||||.||
T Consensus         5 ~~~~p~~~~lS~~La~~lG~~--~~sr~evvk~lW~YIK~n~Lqdp~~k   51 (93)
T 1v31_A            5 SSGVPEKFKLSTALMDVLGIE--VETRPRIIAAIWHYVKARKLQNPNDP   51 (93)
T ss_dssp             CCSSCCCEECCHHHHHHSCCS--EECSHHHHHHHHHHHHHTTCBCSSCS
T ss_pred             CCCCCCccccCHHHHHHHCCC--ccCHHHHHHHHHHHHHHccCcCcccC
Confidence            345678999999999999987  99999999999999999999999986

>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=99.40  E-value=5.8e-14  Score=111.30  Aligned_cols=43  Identities=28%  Similarity=0.543  Sum_probs=40.3

Q ss_pred             CCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          260 LAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       260 ~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      ...|.+|++||+|+|..  ++||++||++||+|||.||||||.||
T Consensus         9 p~~~~lS~~La~~lG~~--~~sr~evvk~lW~YIK~n~Lqdp~~k   51 (93)
T 1uhr_A            9 PPQFKLDPRLARLLGIH--TQTRPVIIQALWQYIKTHKLQDPHER   51 (93)
T ss_dssp             CCEEEECTTHHHHTCCS--EEEHHHHHHHHHHHHHHTTCBCSSCS
T ss_pred             CCccCcCHHHHHHHCCC--ccCHHHHHHHHHHHHHhccCCCcccc
Confidence            35789999999999987  99999999999999999999999987

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

Probab=99.34  E-value=1.2e-12  Score=105.16  Aligned_cols=44  Identities=30%  Similarity=0.308  Sum_probs=39.0

Q ss_pred             CCCCCcHHHHHhh---CCCC-CCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          261 APLQLSDALIKFL---GTGE-SALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       261 ~~~~lS~~L~~~~---g~~~-~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      ..--+|++||+||   |.+. .++||++||++||+|||+||||||.||
T Consensus        12 ~~~w~S~eLa~fl~~iG~~~~~~~sR~eVvk~lW~YIK~nnLQdp~~K   59 (101)
T 1v32_A           12 FVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNK   59 (101)
T ss_dssp             SSSSSCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCT
T ss_pred             ecccCCHHHHHHHHHcCCCCccccCHHHHHHHHHHHHHhhcCcCcccC
Confidence            4457999999999   8742 479999999999999999999999997

>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=96.95  E-value=0.00081  Score=55.53  Aligned_cols=76  Identities=21%  Similarity=0.351  Sum_probs=65.2

Q ss_pred             ccCCHHHHhhh---CC--CCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHHhhhCCCccChhh---HHHHHHccC
Q 022018          144 CALSPQLQEFI---GV--TELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRALFGVDTINMFQ---MNKALSKHI  214 (304)
Q Consensus       144 ~~LS~~La~~l---G~--~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD-~~Lk~lfg~~~i~~f~---m~k~L~~hl  214 (304)
                      ++--++|-.||   |.  +..|..+|+--+=+||-.+.|+||.+..+|.|- +.|-.|||+++|++-+   +...|.++|
T Consensus        25 Vrpk~~lL~iLq~aGA~~dvfT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~llGv~sFSVkdp~~L~~mL~~NL  104 (130)
T 3dac_M           25 VHPRAPLLQILKVAGAQEEVFTVKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELLEVGSFSVKNPSPLYEMLKRNL  104 (130)
T ss_dssp             EEECHHHHHHHHHTTCCCSSEEHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTSSEEETTSCHHHHHHHHHHE
T ss_pred             cCCcHHHHHHHHHhccCcceeehHHHHHHHHHhhhhhhccCccccceeEeCCcccccccCCcceeecCcHHHHHHHHhhe
Confidence            44456677776   54  578999999999999999999999999999996 7899999999999998   999999999


Q ss_pred             CCCCC
Q 022018          215 WPLDS  219 (304)
Q Consensus       215 ~pl~p  219 (304)
                      .++..
T Consensus       105 v~~~~  109 (130)
T 3dac_M          105 VILNN  109 (130)
T ss_dssp             EEC--
T ss_pred             ecccC
Confidence            87764

>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=96.52  E-value=0.0017  Score=51.57  Aligned_cols=74  Identities=23%  Similarity=0.358  Sum_probs=62.2

Q ss_pred             ccCCHHHHhhh---CC--CCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHHhhhCCCccChh---hHHHHHHccC
Q 022018          144 CALSPQLQEFI---GV--TELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRALFGVDTINMF---QMNKALSKHI  214 (304)
Q Consensus       144 ~~LS~~La~~l---G~--~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD-~~Lk~lfg~~~i~~f---~m~k~L~~hl  214 (304)
                      ++--++|-.+|   |.  +..|..+|+.-+=+||-.+.|+||.+...|.|- +.|-.|||+++|.+-   -+...|.+||
T Consensus        16 Vrpk~~lL~iLq~aGA~~d~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~G~~sFsvkdp~~l~~ml~~nL   95 (100)
T 3fea_A           16 VRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNL   95 (100)
T ss_dssp             BEECHHHHHHHHHTTCCSSCBCHHHHHHHHHHHHHHTTCEETTEEEEEECTTSHHHHHHTCSEEETTCCHHHHHHHHHHE
T ss_pred             cCCcHHHHHHHHHhccCcceeehHHHHHHHHHhhhhhhccCccccceEEeCCCccccccCCcceeecCchHHHHHHHhhc
Confidence            34456677666   54  579999999999999999999999999999996 788999999999987   7888898888


Q ss_pred             CCC
Q 022018          215 WPL  217 (304)
Q Consensus       215 ~pl  217 (304)
                      ..+
T Consensus        96 v~~   98 (100)
T 3fea_A           96 VTL   98 (100)
T ss_dssp             EC-
T ss_pred             eec
Confidence            654

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

Probab=96.51  E-value=0.0047  Score=50.36  Aligned_cols=74  Identities=26%  Similarity=0.371  Sum_probs=59.1

Q ss_pred             ccCCHHHHhhh---CC--CCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHHhhhCCCccChhhHHHHHHccCCCC
Q 022018          144 CALSPQLQEFI---GV--TELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRALFGVDTINMFQMNKALSKHIWPL  217 (304)
Q Consensus       144 ~~LS~~La~~l---G~--~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD-~~Lk~lfg~~~i~~f~m~k~L~~hl~pl  217 (304)
                      ++-.+.|-.||   |.  ...|+.+|+.-|=+||-.+.|+||.+..+|.|. +.|-.|||+..|.+-+-..+...|...+
T Consensus        28 VrPk~~LLkiLq~aGA~~~vfT~keV~~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml~~nL  107 (119)
T 1z1m_A           28 VRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNL  107 (119)
T ss_dssp             CCCSTTSHHHHHHHTCCCSCCCTTHHHHHHHHHHHTTTCSCSSSSCEECCTTSHHHHHSCCSCEETTCHHHHHHHHSCSC
T ss_pred             ccccHHHHHHHHHhccccceeechheeehhhhhhhHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHHhc
Confidence            34444555555   54  578999999999999999999999999999997 7779999999999887766665555443

>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=96.29  E-value=0.0056  Score=50.87  Aligned_cols=76  Identities=21%  Similarity=0.327  Sum_probs=63.3

Q ss_pred             cccCCHHHHhhh---CC--CCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHHhhhCCCccChhhHH---HHHHcc
Q 022018          143 LCALSPQLQEFI---GV--TELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRALFGVDTINMFQMN---KALSKH  213 (304)
Q Consensus       143 ~~~LS~~La~~l---G~--~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD-~~Lk~lfg~~~i~~f~m~---k~L~~h  213 (304)
                      .++--+.|-.||   |.  ...|+.+|+--|=+||-...|+||.+..+|.|. +.|-.|||+..|++-+..   +.|.+.
T Consensus        23 ~VrPk~~LLkiLq~aGA~~~~fT~keVm~YLGqYIm~KqLYD~~~qhiV~C~~D~LG~l~Gv~sFSVKdp~~ly~ML~~N  102 (140)
T 2z5s_M           23 QVHPRAPLLQILKVAGAQEEVFTLKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELLEVGSFSVKNPSPVYEMLKRN  102 (140)
T ss_dssp             CBEECHHHHHHHHHTTCCCSCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTSSEEETTBCHHHHHHHHHH
T ss_pred             eecCcHHHHHHHHHhCcccceeeHHHHHHHHHHHHHHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHHh
Confidence            456677888887   54  579999999999999999999999999999997 777999999999987654   667777


Q ss_pred             CCCCC
Q 022018          214 IWPLD  218 (304)
Q Consensus       214 l~pl~  218 (304)
                      +.+..
T Consensus       103 Lv~~~  107 (140)
T 2z5s_M          103 LVILN  107 (140)
T ss_dssp             EECC-
T ss_pred             ccccc
Confidence            76554

>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=96.23  E-value=0.0064  Score=48.73  Aligned_cols=72  Identities=25%  Similarity=0.454  Sum_probs=58.8

Q ss_pred             ccCCHHHHhhh---CC--CCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHHhhhCCCccChhhHH---HHHHccC
Q 022018          144 CALSPQLQEFI---GV--TELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRALFGVDTINMFQMN---KALSKHI  214 (304)
Q Consensus       144 ~~LS~~La~~l---G~--~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD-~~Lk~lfg~~~i~~f~m~---k~L~~hl  214 (304)
                      ++-.+.|-.+|   |.  ...|+.+|+.-|=+||-...|+||.+..+|.|. +.|-.|||+..|++-+..   +.|.+.+
T Consensus        12 VrPk~~LLklL~~~GA~~~~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml~~nL   91 (107)
T 1ycq_A           12 VQPTPLLLSLLKSAGAQKETFTMKEVIYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEPRRLYAMISRNL   91 (107)
T ss_dssp             BEECHHHHHHHHHTTCCCSCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTCSEEETTCHHHHHHHHHTTE
T ss_pred             cCccHHHHHHHHHhccccceeeehhhhhhHHHHHhHHhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHHhc
Confidence            44456666666   53  578999999999999999999999999999997 777999999999988776   4455554


Q ss_pred             C
Q 022018          215 W  215 (304)
Q Consensus       215 ~  215 (304)
                      .
T Consensus        92 v   92 (107)
T 1ycq_A           92 V   92 (107)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=95.76  E-value=0.0052  Score=49.76  Aligned_cols=71  Identities=25%  Similarity=0.379  Sum_probs=57.8

Q ss_pred             ccCCHHHHhhh---CC--CCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHHhhhCCCccChhhHHHHHHccC
Q 022018          144 CALSPQLQEFI---GV--TELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRALFGVDTINMFQMNKALSKHI  214 (304)
Q Consensus       144 ~~LS~~La~~l---G~--~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD-~~Lk~lfg~~~i~~f~m~k~L~~hl  214 (304)
                      ++-.+.|-.||   |.  ...|+.+|+--+=+||-...|+||.+..+|.|. +.|-.|||+..|++-+-..+...+.
T Consensus        12 VrPk~~LLklLq~~GA~~~vfT~keVm~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml~   88 (115)
T 2axi_A           12 VRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIY   88 (115)
T ss_dssp             EEECHHHHHHHHHTTCCCSCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHHSSSEEETTCHHHHHHHHH
T ss_pred             cCccHHHHHHHHHhccccceeechhheehhhhhhhHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHH
Confidence            44456666666   53  578999999999999999999999999999997 7779999999999887655544443

---

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	304
d1uhra_	93	a.42.1.1 (A:) SWI/SNF related regulator of chromat	3e-32
d1uhra_	93	a.42.1.1 (A:) SWI/SNF related regulator of chromat	2e-11
d1v31a_	93	a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl	7e-32
d1v31a_	93	a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl	8e-11
d1v32a_	101	a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl	8e-25
d1v32a_	101	a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl	8e-07
d1q1va_	70	a.159.4.1 (A:) DEK C-terminal domain {Human (Homo	2e-12

>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 =  112 bits (283), Expect = 3e-32
 Identities = 21/85 (24%), Positives = 40/85 (47%)

Query: 134 KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLR 193
                G      L P+L   +G+    R  +++ LW YI+   LQDP+ R  ++CD+ L+
Sbjct: 2   SSGSSGQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQ 61

Query: 194 ALFGVDTINMFQMNKALSKHIWPLD 218
            +F    +   ++ + L   + P +
Sbjct: 62  QIFESQRMKFSEIPQRLHALLMPPE 86

>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 = 57.4 bits (139), Expect = 2e-11
 Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 253 KGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK 304
             G SG     +L   L + LG       R  +I+ +W YIK   LQ    +
Sbjct: 2   SSGSSGQPPQFKLDPRLARLLGIHT--QTRPVIIQALWQYIKTHKLQDPHER 51

>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 =  112 bits (281), Expect = 7e-32
 Identities = 20/85 (23%), Positives = 41/85 (48%)

Query: 134 KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLR 193
                G  +   LS  L + +G+    R  ++  +W Y++ + LQ+PN+     CD  L+
Sbjct: 2   SSGSSGVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQ 61

Query: 194 ALFGVDTINMFQMNKALSKHIWPLD 218
            +FG + +    +++ +S H+ P  
Sbjct: 62  KVFGEEKLKFTMVSQKISHHLSPPP 86

>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 = 55.5 bits (134), Expect = 8e-11
 Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 255 GKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK 304
           G SG     +LS AL+  LG       R  +I  +W Y+K + LQ     
Sbjct: 4   GSSGVPEKFKLSTALMDVLGIEV--ETRPRIIAAIWHYVKARKLQNPNDP 51

>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 = 93.7 bits (233), Expect = 8e-25
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 147 SPQLQEFIGV------TELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDT 200
           S QL EF+          ++R +V   +  YI ++ L DP+N++ +VCD+RL  LFG  T
Sbjct: 17  SRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLFGTRT 76

Query: 201 INMFQMNKALSKHIWP 216
           I   ++   L KH   
Sbjct: 77  IFRMKVYDLLEKHYKE 92

>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 = 44.4 bits (105), Expect = 8e-07
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 4/43 (9%)

Query: 266 SDALIKFLGT----GESALPRSDVIKRMWDYIKEKNLQVSLRK 304
           S  LI+FL +        + R DV   +  YI ++ L     K
Sbjct: 17  SRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNK 59

>d1q1va_ a.159.4.1 (A:) DEK C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: All alpha proteins
fold: Another 3-helical bundle
superfamily: DEK C-terminal domain
family: DEK C-terminal domain
domain: DEK C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (145), Expect = 2e-12
 Identities = 13/59 (22%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 1  MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDF-GVDLTDKKIFIREQVDLFLQSQ 58
            +D EL   +++ L +++L   T   + +++ +++   DLT++K FI+  V   +  +
Sbjct: 11 PPTDEELKETIKKLLASANLEEVTMKQICKKVYENYPTYDLTERKDFIKTTVKELISLE 69

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	304
d1v31a_	93	Hypothetical protein AT5G14170 (rafl11-05-p19) {Th	99.97
d1uhra_	93	SWI/SNF related regulator of chromatin (BRG1-assoc	99.96
d1v32a_	101	Hypothetical protein AT5G08430 (rafl09-47-k03) {Th	99.9
d1q1va_	70	DEK C-terminal domain {Human (Homo sapiens) [TaxId	99.68
d1v31a_	93	Hypothetical protein AT5G14170 (rafl11-05-p19) {Th	99.6
d1uhra_	93	SWI/SNF related regulator of chromatin (BRG1-assoc	99.56
d1v32a_	101	Hypothetical protein AT5G08430 (rafl09-47-k03) {Th	99.23
d2axia1	85	MDM2 {Human (Homo sapiens) [TaxId: 9606]}	97.64
d1ttva_	107	MDM2 {African clawed frog (Xenopus laevis) [TaxId:	97.64

>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=99.97  E-value=1.5e-31  Score=210.90  Aligned_cols=89  Identities=22%  Similarity=0.539  Sum_probs=85.4

Q ss_pred             ccCCCCCCccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHcc
Q 022018          134 KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKH  213 (304)
Q Consensus       134 ~~~~~g~~k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~h  213 (304)
                      .++++||+++|.||++||+|||.+++||++|+++||+||++||||||+|++.|+||+.|+.|||+++|+||+|+++|++|
T Consensus         2 ~~~~~G~~~~~~lS~~La~~lg~~~~sR~~v~k~iw~YIk~n~Lqd~~nkr~I~~D~~L~~lfg~~~v~~~~l~~~L~~H   81 (93)
T d1v31a_           2 SSGSSGVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEKLKFTMVSQKISHH   81 (93)
T ss_dssp             CSSCCSSCCCEECCHHHHHHSCCSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHSCSSEEETTTTHHHHHHH
T ss_pred             CCCCCCCcCCccCCHHHHHHHCcCcCcHHHHHHHHHHHHHHhCCCCCCCCCEEecCHHHHHHhCCCcccHHHHHHHHHHh
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCccc
Q 022018          214 IWPLDSDDV  222 (304)
Q Consensus       214 l~pl~p~~~  222 (304)
                      |.|++|...
T Consensus        82 l~p~~P~~~   90 (93)
T d1v31a_          82 LSPPPPSGP   90 (93)
T ss_dssp             CBCCCCSSC
T ss_pred             CCCCCCCCC
Confidence            999999644

>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=99.96  E-value=3e-31  Score=209.12  Aligned_cols=88  Identities=24%  Similarity=0.576  Sum_probs=84.3

Q ss_pred             ccCCCCCCccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHcc
Q 022018          134 KKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKH  213 (304)
Q Consensus       134 ~~~~~g~~k~~~LS~~La~~lG~~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~h  213 (304)
                      ..+.+||+.+|+||++||+|||.+++||++|+++||+||++||||||+|+++|+||+.|+.|||+++|.||+|+++|++|
T Consensus         2 ~~~~sg~p~~~~lS~~La~~lg~~~~sR~~v~k~iw~YIk~n~Lqdp~nkr~I~cD~~L~~lfg~~~v~~~~l~~~L~~H   81 (93)
T d1uhra_           2 SSGSSGQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSEIPQRLHAL   81 (93)
T ss_dssp             CCCCSSSCCEEEECTTHHHHTCCSEEEHHHHHHHHHHHHHHTTCBCSSCSSEECCCTTHHHHTCCSSEEGGGSHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHCCCCcCHHHHHHHHHHHHHHhcCCCCCCCCEEecCHHHHHHhCCCeecHHHHHHHHHhh
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcc
Q 022018          214 IWPLDSDD  221 (304)
Q Consensus       214 l~pl~p~~  221 (304)
                      |.|++|-.
T Consensus        82 l~p~eP~~   89 (93)
T d1uhra_          82 LMPPEPSG   89 (93)
T ss_dssp             EECSSCCC
T ss_pred             CCCCCCCC
Confidence            99999853

>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=99.90  E-value=9.5e-25  Score=173.90  Aligned_cols=72  Identities=36%  Similarity=0.544  Sum_probs=67.9

Q ss_pred             CCHHHHhhhC---C---CCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCC
Q 022018          146 LSPQLQEFIG---V---TELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPL  217 (304)
Q Consensus       146 LS~~La~~lG---~---~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD~~Lk~lfg~~~i~~f~m~k~L~~hl~pl  217 (304)
                      .|++|++|||   .   ..+||++|++.||+|||+||||||.|||.|+||++|+.|||+++|+||+|+++|++||..-
T Consensus        16 ~S~eL~~FL~~~g~~~~~~~sR~eVtk~iw~YIK~nnLqdp~nkr~I~~D~~L~~Lfg~~~v~~f~i~k~l~~H~~~~   93 (101)
T d1v32a_          16 GSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDLLEKHYKEN   93 (101)
T ss_dssp             SCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCTTEEECCSHHHHHTCCSEEETTHHHHHHHHHSCSC
T ss_pred             CCHHHHHHHHhcCCCCcccCCHHHHHHHHHHHHHHhcCCCCccCCEEccCHHHHHHhCCCcccHHHHHHHHHHHcCCc
Confidence            5999999984   3   5799999999999999999999999999999999999999999999999999999999653

>d1q1va_ a.159.4.1 (A:) DEK C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Another 3-helical bundle
superfamily: DEK C-terminal domain
family: DEK C-terminal domain
domain: DEK C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.1e-17  Score=122.86  Aligned_cols=57  Identities=23%  Similarity=0.414  Sum_probs=55.3

Q ss_pred             CCCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHh-CCCCchhhHHHHHHHHHHHhh
Q 022018            1 MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDF-GVDLTDKKIFIREQVDLFLQS   57 (304)
Q Consensus         1 m~sd~ei~~~I~~IL~~aDl~~vT~k~VR~~Le~~f-gvDLs~kK~~I~~~I~~~l~~   57 (304)
                      +|||++|...|++||++|||++||.|+||++||+.| |+||++||.||+++|+.||..
T Consensus        11 ~ptd~ei~~~i~~IL~~aDL~tvT~K~IR~~LE~~~~g~dL~~rK~~I~~~I~~~Ls~   68 (70)
T d1q1va_          11 PPTDEELKETIKKLLASANLEEVTMKQICKKVYENYPTYDLTERKDFIKTTVKELISL   68 (70)
T ss_dssp             CCCHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHCSSSCCSHHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHhhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHhc
Confidence            699999999999999999999999999999999999 999999999999999999963

>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=99.60  E-value=2.3e-16  Score=123.32  Aligned_cols=49  Identities=33%  Similarity=0.582  Sum_probs=46.4

Q ss_pred             CCCCCCCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          254 GGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       254 ~~~~g~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      .+.+||..+|.||++||+|||..  ++||++|+++||+|||+||||||.||
T Consensus         3 ~~~~G~~~~~~lS~~La~~lg~~--~~sR~~v~k~iw~YIk~n~Lqd~~nk   51 (93)
T d1v31a_           3 SGSSGVPEKFKLSTALMDVLGIE--VETRPRIIAAIWHYVKARKLQNPNDP   51 (93)
T ss_dssp             SSCCSSCCCEECCHHHHHHSCCS--EECSHHHHHHHHHHHHHTTCBCSSCS
T ss_pred             CCCCCCcCCccCCHHHHHHHCcC--cCcHHHHHHHHHHHHHHhCCCCCCCC
Confidence            45789999999999999999987  99999999999999999999999986

>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=99.56  E-value=4e-16  Score=121.91  Aligned_cols=50  Identities=30%  Similarity=0.556  Sum_probs=46.9

Q ss_pred             cCCCCCCCCCCCCcHHHHHhhCCCCCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          253 KGGKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       253 ~~~~~g~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      +++.+||...|.||++||+|||..  ++||++|+++||+|||+||||||.||
T Consensus         2 ~~~~sg~p~~~~lS~~La~~lg~~--~~sR~~v~k~iw~YIk~n~Lqdp~nk   51 (93)
T d1uhra_           2 SSGSSGQPPQFKLDPRLARLLGIH--TQTRPVIIQALWQYIKTHKLQDPHER   51 (93)
T ss_dssp             CCCCSSSCCEEEECTTHHHHTCCS--EEEHHHHHHHHHHHHHHTTCBCSSCS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHCCC--CcCHHHHHHHHHHHHHHhcCCCCCCC
Confidence            345789999999999999999987  99999999999999999999999986

>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=99.23  E-value=4.5e-12  Score=99.94  Aligned_cols=40  Identities=30%  Similarity=0.368  Sum_probs=35.6

Q ss_pred             CcHHHHHhhC---CC-CCCcCHHHHHHHHHHHHHhcCCCCCCCC
Q 022018          265 LSDALIKFLG---TG-ESALPRSDVIKRMWDYIKEKNLQVSLRK  304 (304)
Q Consensus       265 lS~~L~~~~g---~~-~~~~~r~~v~k~~W~YIk~~~Lqdp~nk  304 (304)
                      .|++|++|||   .+ ..+|||++|+++||+|||+||||||.||
T Consensus        16 ~S~eL~~FL~~~g~~~~~~~sR~eVtk~iw~YIK~nnLqdp~nk   59 (101)
T d1v32a_          16 GSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNK   59 (101)
T ss_dssp             SCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCT
T ss_pred             CCHHHHHHHHhcCCCCcccCCHHHHHHHHHHHHHHhcCCCCccC
Confidence            7999999984   22 2479999999999999999999999997

>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=97.64  E-value=1.4e-05  Score=59.64  Aligned_cols=71  Identities=24%  Similarity=0.424  Sum_probs=61.6

Q ss_pred             ccCCHHHHhhh---CC--CCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHHhhhCCCccChhh---HHHHHHccC
Q 022018          144 CALSPQLQEFI---GV--TELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRALFGVDTINMFQ---MNKALSKHI  214 (304)
Q Consensus       144 ~~LS~~La~~l---G~--~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD-~~Lk~lfg~~~i~~f~---m~k~L~~hl  214 (304)
                      ++.-|.|-.+|   |.  +..|.-+|+--|=+||....|.||.+...|.|- +.|-.|||+.+|++-+   +...|.+|+
T Consensus         4 VrPkp~Ll~~L~~~GA~~~~fT~kqVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~l~gv~sFsVk~~r~l~~ml~rnL   83 (85)
T d2axia1           4 VRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNL   83 (85)
T ss_dssp             EEECHHHHHHHHHTTCCCSCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHHSSSEEETTCHHHHHHHHHTTE
T ss_pred             ccCcHHHHHHHHHcCCCcceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhcCCCceeecCcHHHHHHHHhcc
Confidence            34467777776   53  689999999999999999999999999999995 6799999999999887   788888876

>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=97.64  E-value=4.1e-05  Score=59.17  Aligned_cols=77  Identities=25%  Similarity=0.452  Sum_probs=66.0

Q ss_pred             cccCCHHHHhhh---CC--CCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHHhhhCCCccChhh---HHHHHHcc
Q 022018          143 LCALSPQLQEFI---GV--TELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRALFGVDTINMFQ---MNKALSKH  213 (304)
Q Consensus       143 ~~~LS~~La~~l---G~--~~~sR~evvk~lW~YIK~~nLqdP~~kr~I~cD-~~Lk~lfg~~~i~~f~---m~k~L~~h  213 (304)
                      .++.-|.|-.+|   |.  +..|.-+|+--|-+||....|+||.+..+|.|- +.|-.|||+.+|++-+   +...|.+|
T Consensus        11 lVrPkp~LL~~L~~~GA~~~~fT~keVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~llgv~sFsVke~r~l~~ml~rn   90 (107)
T d1ttva_          11 LVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRN   90 (107)
T ss_dssp             CEEECHHHHHHHHHTTCCSSCBCHHHHHHHHHHHHHHHTCBCSSCTTEECCSSCHHHHHHTCSCEETTCHHHHHHHHHTT
T ss_pred             ccCCCHHHHHHHHHcCCCcceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhcCCCceeecCcHHHHHHHHhh
Confidence            355678888887   53  689999999999999999999999999999995 7799999999999887   67779999


Q ss_pred             CCCCCC
Q 022018          214 IWPLDS  219 (304)
Q Consensus       214 l~pl~p  219 (304)
                      +.|...
T Consensus        91 Lv~v~~   96 (107)
T d1ttva_          91 LVSANV   96 (107)
T ss_dssp             EEEECC
T ss_pred             hhcccc
Confidence            965443