Citrus Sinensis ID: 022354

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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-------30
Protein Sequence
MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSPYLF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccccccccEEEccHHHHHHHccccccHHHHHHHHHHHccccccccccccccccccccccccHHHHHHccccccccccccccccccEEEcccccHHHHHHHHHHHHHHcccccccEEEEEEEEEEEccccccccccEEEEEEEEEEcccccccccccEEEEEccccccEEccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEcccccccccccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccccccccEEEEcHHHHHHHccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHcHHHHHHHHHHHHHHHcccHHcccEEEEEEEEEEccccccccccEEEEEEEEEEEcccccccccEEEEEEEcccccccEcEEccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHcccccccccc
Coil and Loop (DISEMBL)
mgskadqesflwvpeydeplspqltnlkrrgrskkvkfdgwgsipLIEFLQSlgkdttqqisRYDVTDIINKYVNENKLVHSVkkkrvvsderllslfgkksfLRIKIYDLLEAHyaenqfesdddflfssdeennlfssekqksrkvplkklcletpkscwaaivpdniKLVYLKRSLVQDLLKDSETFECKVVGSfvrvksdpndylqknSHQLLQVIgtkkvpgtddksTEILLKVSNFVKDIRIatlsddnfseeECEDLRQRVKdgllkrptVVSSLLLFMRNyslfcspylf
Flexible Loop (DISEMBL)
mgskadqesflwvpeydeplspqltnlkrrgrskkvkfdgwgsiPLIEFLQSLGKDTTQQISRYDVTDIINKYVnenklvhsvkkkrvvsderllslfgkksflRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLfssekqksrkvplKKLCLetpkscwaaivpdnIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLqvigtkkvpgtddksteILLKVSNFVKDIRIAtlsddnfseeeCEDLRqrvkdgllkrpTVVSslllfmrnyslfcspylf
Low Complexity Region (SEG)
MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQfesdddflfssdeeNNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSPYLF
Disordered region (IsUnstruct)
*********FLWVP********************KVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF****************************LKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFS**ECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSPYL*
Disordered Region (DISOPRED)
******************************************SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE********************************************AAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSPYLF
Disordered Region (DISEMBL)
MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSPYLF
Disordered Region (DISPRO)
*******ESFLW*PE************************GWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE***************************************PKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSPYLF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSPYLF
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	298	2.2.26 [Sep-21-2011]
Q9FT92	553	Uncharacterized protein A	yes	no	0.859	0.462	0.552	1e-74
Q9SD34	1292	Zinc finger CCCH domain-c	no	no	0.808	0.186	0.311	1e-20
Q9SIV5	1773	Zinc finger CCCH domain-c	no	no	0.781	0.131	0.296	6e-20

>sp|Q9FT92|Y5843_ARATH Uncharacterized protein At5g08430 OS=Arabidopsis thaliana GN=At5g08430 PE=1 SV=2

 Score =  279 bits (714), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/268 (55%), Positives = 194/268 (72%), Gaps = 12/268 (4%)

Query: 12  WVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIIN 71
           WV E +       ++ KR+ R K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I 
Sbjct: 6   WVEEGN---GSATSSRKRKARPKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIA 62

Query: 72  KYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSS 131
           KY+++  L+    KK+VV D+RL+ LFG ++  R+K+YDLLE HY ENQ +SD DFL+  
Sbjct: 63  KYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDLLEKHYKENQDDSDFDFLY-E 121

Query: 132 DEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFE 191
           DE   +  SEK   R   + K     P+  +AAIV DNIKL+YL++SLVQ+LLK  +TFE
Sbjct: 122 DEPQIICHSEKIAKRTSKVVK----KPRGTFAAIVSDNIKLLYLRKSLVQELLKSPDTFE 177

Query: 192 CKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATL 251
            K++GSFVR+KSDPNDYLQK  +QL+QV G KK  GTDD     LL+V+N+VKD+ I+ L
Sbjct: 178 GKMLGSFVRIKSDPNDYLQKYPYQLVQVTGVKKEHGTDD----FLLQVTNYVKDVSISVL 233

Query: 252 SDDNFSEEECEDLRQRVKDGLLKRPTVV 279
           SDDNFS+EECEDL QR+K+GLLK+PT+V
Sbjct: 234 SDDNFSQEECEDLHQRIKNGLLKKPTIV 261

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SD34|C3H44_ARATH Zinc finger CCCH domain-containing protein 44 OS=Arabidopsis thaliana GN=At3g51120 PE=2 SV=3

 Score =  100 bits (249), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 140/273 (51%), Gaps = 32/273 (11%)

Query: 34  KKVKFD-GWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE 92
           KK   D  W +  L+EF+  +    T  +S++DV  ++  Y+ +  L   ++K +V+ D+
Sbjct: 311 KKAPGDTSWATKELLEFVSFMKNGDTSVLSQFDVQGLLLDYIKKKNLRDPLQKSQVLCDQ 370

Query: 93  RLLSLFGKKSFLRIKIYDLLEAHY--------AENQFESDDDFLFSSDEENNLF------ 138
            L+ LFGK+     ++  LLE+H         A+         + S  EE+++       
Sbjct: 371 MLVKLFGKQRVGHFEMLKLLESHVLIQEKPKGAKTTNGETTHAVPSQIEEDSVHDPMVRD 430

Query: 139 ---SSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVV 195
                 ++   +V  + L        +AAI   NI L+YL+R  ++ LL D    + KVV
Sbjct: 431 RRRKMRRKTDGRVQNENL------DAYAAIDVHNINLIYLRRKFLESLLDDINKVDEKVV 484

Query: 196 GSFVRVKSDPNDYLQK-NSHQLLQVIGTKKVPGT---DDKSTEILLKVSNFVKD--IRIA 249
           G+ +R+K   +D  QK + H+L+QV+GT K   +     K+T+++L++ N  K   I I 
Sbjct: 485 GTILRIKVSGSD--QKLDIHRLVQVVGTSKAIASYQLGAKTTDVMLEILNLDKREVISID 542

Query: 250 TLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSL 282
            LSD N +E+EC+ LRQ +K GL KR TVV  L
Sbjct: 543 QLSDQNITEDECKRLRQSIKCGLNKRLTVVDIL 575

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIV5|C3H19_ARATH Zinc finger CCCH domain-containing protein 19 OS=Arabidopsis thaliana GN=NERD PE=1 SV=3

 Score = 98.2 bits (243), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 77/260 (29%), Positives = 137/260 (52%), Gaps = 27/260 (10%)

Query: 41   WGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGK 100
            W S  L++ +  + +     +   +V  ++  Y+    L    +K +V+ D RL +LFGK
Sbjct: 807  WASKELLDLVVHMRRGDRSFLPMLEVQTLLLAYIKRYNLRDPRRKSQVICDSRLQNLFGK 866

Query: 101  KSFLRIKIYDLLEAHYAENQFESDDDF---LFSSDEENNLFSSEKQKSRKVPLKKLCLET 157
                  ++ +LL++H+ + +    DD    +  ++E N++   E       P+K    + 
Sbjct: 867  SHVGHFEMLNLLDSHFLKKEQNQADDIQGDIVDTEEPNHVDVDENLDH---PVKSGKDKK 923

Query: 158  PKSC--------------WAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKS 203
             K+               +AA+   NI L+YL+RSLV+DLL+DS  FE KV  +FVR++ 
Sbjct: 924  RKTRKKNVRKGRQSNLDDFAAVDMHNINLIYLRRSLVEDLLEDSTAFEEKVASAFVRLRI 983

Query: 204  DPNDYLQKNSHQLLQVIGTKKVP---GTDDKSTEILLKVSNFVKD--IRIATLSDDNFSE 258
              N   +++ ++L+QV+GT K P       K+T+ +L++ N  K   I I  +S+ +F+E
Sbjct: 984  SGNQ--KQDLYRLVQVVGTSKAPEPYKVGKKTTDYVLEILNLDKTEVISIDIISNQDFTE 1041

Query: 259  EECEDLRQRVKDGLLKRPTV 278
            +EC+ L+Q +K GL+ R TV
Sbjct: 1042 DECKRLKQSIKCGLINRLTV 1061

Arabidopsis thaliana (taxid: 3702)

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	298
255575782	502	protein binding protein, putative [Ricin	0.909	0.539	0.614	9e-94
356529380	888	PREDICTED: uncharacterized protein At5g0	0.919	0.308	0.563	4e-76
449461126	543	PREDICTED: uncharacterized protein At5g0	0.909	0.499	0.566	7e-76
449518039	376	PREDICTED: uncharacterized protein At5g0	0.906	0.718	0.568	1e-75
297806885	539	SWIB complex BAF60b domain-containing pr	0.862	0.476	0.555	1e-74
30682386	553	SWIB/MDM2 and Plus-3 and GYF domain-cont	0.859	0.462	0.552	9e-73
10178285	509	putative protein [Arabidopsis thaliana]	0.855	0.500	0.550	4e-72
356561784	734	PREDICTED: uncharacterized protein At5g0	0.805	0.326	0.576	5e-72
359480913	477	PREDICTED: uncharacterized protein At5g0	0.909	0.568	0.543	2e-70
224116464	603	predicted protein [Populus trichocarpa]	0.845	0.417	0.476	5e-59

>gi|255575782|ref|XP_002528790.1| protein binding protein, putative [Ricinus communis] gi|223531793|gb|EEF33612.1| protein binding protein, putative [Ricinus communis]

 Score =  349 bits (895), Expect = 9e-94,   Method: Compositional matrix adjust.
 Identities = 172/280 (61%), Positives = 226/280 (80%), Gaps = 9/280 (3%)

Query: 5   ADQESFLWVPEY-DEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISR 63
            + +SF WV E   E   P    +KR+ R++K++F GWGS PLIEFL+S+G DT+++IS+
Sbjct: 2   GEGDSFFWVEEITGEAYVP--VGMKRKARTRKMEFVGWGSRPLIEFLESIGVDTSKKISQ 59

Query: 64  YDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFES 123
           YDVTDI+NKY+ E+ L H  KKKR++SDERLLSLFG+K+  + K+Y+LL  H+AENQ ES
Sbjct: 60  YDVTDIVNKYIKEHNLHHPQKKKRILSDERLLSLFGRKTIAKNKVYELLGTHFAENQEES 119

Query: 124 DDDFLFSSDEENNLFSSEKQKS----RKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSL 179
           DDD LFSS+E+ N  +SE+QK+    RK  +KK  +ETPKSC+AAI+PDNIK +YL+R+L
Sbjct: 120 DDDLLFSSEEDGN--TSERQKNMTSERKTQIKKKVVETPKSCFAAIIPDNIKRIYLRRTL 177

Query: 180 VQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKV 239
           VQ+LLK+ E FE K++GSFVRVKSDP+DYLQKNSH L+QVIG KK   +D KS EI+L+V
Sbjct: 178 VQNLLKEPEAFERKIIGSFVRVKSDPHDYLQKNSHMLVQVIGWKKASDSDGKSGEIILQV 237

Query: 240 SNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVV 279
           SNF+KD+ I+ LSD+NFSEEEC+DLRQR++DGLLKRPT+V
Sbjct: 238 SNFMKDVSISMLSDENFSEEECQDLRQRIRDGLLKRPTLV 277

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356529380|ref|XP_003533272.1| PREDICTED: uncharacterized protein At5g08430-like [Glycine max]

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 160/284 (56%), Positives = 204/284 (71%), Gaps = 10/284 (3%)

Query: 1   MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQ 60
           MG +    SF W  E +E + P     KR+ R+KK ++ GWGS  LI FL+S+G+DT+ +
Sbjct: 1   MGDEPRAGSF-WTEEINEAV-PTPMRRKRKYRTKKKEYQGWGSTSLIWFLESIGRDTSTK 58

Query: 61  ISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQ 120
           I++ +V +I+ +YV ++ L H  KKKR+  DERL SLFG+K+  R+KI DLLE+H+ EN 
Sbjct: 59  IAQSEVANIVMEYVKQHNLFHKTKKKRIECDERLHSLFGRKTISRLKINDLLESHFKENC 118

Query: 121 FESDDDFLF-SSDEENNLFSSEKQKS----RKVPLKKLCLETPKSCWAAIVPDNIKLVYL 175
            ES D   F S D+EN L + E  ++    RK   KK   E P+SC+AAIVP NIKLVY+
Sbjct: 119 EESSDGVFFDSEDDENALTACETPRTAPSERKSQPKKPVFEKPRSCFAAIVPANIKLVYM 178

Query: 176 KRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEI 235
           KRSLV DLLKD ETFE KVVGSF+R++ DPNDYLQKNSHQLLQV GTKK   + + + EI
Sbjct: 179 KRSLVMDLLKDPETFETKVVGSFIRIRCDPNDYLQKNSHQLLQVTGTKK---SSEVNGEI 235

Query: 236 LLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVV 279
            L+VS F+KDIRI  LSDDNFSEEECE+L QRVKDGL+KRP +V
Sbjct: 236 HLQVSGFIKDIRIQMLSDDNFSEEECENLHQRVKDGLVKRPMIV 279

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461126|ref|XP_004148294.1| PREDICTED: uncharacterized protein At5g08430-like [Cucumis sativus]

 Score =  290 bits (741), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 157/277 (56%), Positives = 209/277 (75%), Gaps = 6/277 (2%)

Query: 8   ESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVT 67
           +SF W+    + +   +  +KR+ RSK+ +F GWGS PLIEFL+S+GKD  ++ISR+DVT
Sbjct: 2   DSFEWIESSGQQVCTPV-RMKRKIRSKRYEFVGWGSRPLIEFLESVGKDIKEKISRHDVT 60

Query: 68  DIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDF 127
            IIN+YVN N L+H  KKKR++ D+RL S+FG+K+  RIKI+D+LE H+AENQ ESDDDF
Sbjct: 61  SIINEYVNINNLLHPSKKKRILCDDRLHSIFGRKTIGRIKIHDMLEPHFAENQHESDDDF 120

Query: 128 LFSSDEENNLFSSEKQKSRKVPLKKLCLET-----PKSCWAAIVPDNIKLVYLKRSLVQD 182
            +SSDE  NLFS  K+ +   P +KL  +T     P S +AA+VP NI LVYL++SLV+D
Sbjct: 121 SYSSDETENLFSVLKRDNGITPGRKLSQKTRVHVNPNSSFAAVVPGNINLVYLRKSLVED 180

Query: 183 LLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNF 242
           LLKD ETFE K++GSFVR+KSDP+DYLQKN+HQL+QVIG KK+  + D     LL VSN 
Sbjct: 181 LLKDHETFESKLIGSFVRIKSDPHDYLQKNTHQLVQVIGLKKISISGDLGPGFLLHVSNV 240

Query: 243 VKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVV 279
           +KD+ I+ LSD+NFSEEEC+DL  R+K+GL+KR T+ 
Sbjct: 241 MKDVSISMLSDENFSEEECKDLDLRIKNGLVKRLTIA 277

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449518039|ref|XP_004166051.1| PREDICTED: uncharacterized protein At5g08430-like, partial [Cucumis sativus]

 Score =  289 bits (739), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 157/276 (56%), Positives = 209/276 (75%), Gaps = 6/276 (2%)

Query: 8   ESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVT 67
           +SF W+    + +   +  +KR+ RSK+ +F GWGS PLIEFL+S+GKD  ++ISR+DVT
Sbjct: 2   DSFEWIESSGQQVCTPV-RMKRKIRSKRYEFVGWGSRPLIEFLESVGKDIKEKISRHDVT 60

Query: 68  DIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDF 127
            IIN+YVN N L+H  KKKR++ D+RL S+FG+K+  RIKI+D+LE H+AENQ ESDDDF
Sbjct: 61  SIINEYVNINNLLHPSKKKRILCDDRLHSIFGRKTIGRIKIHDMLEPHFAENQHESDDDF 120

Query: 128 LFSSDEENNLFSSEKQKSRKVPLKKLCLET-----PKSCWAAIVPDNIKLVYLKRSLVQD 182
            +SSDE  NLFS  K+ +   P +KL  +T     P S +AA+VP NI LVYL++SLV+D
Sbjct: 121 SYSSDETENLFSVLKRDNGITPGRKLSQKTRVHVNPNSSFAAVVPGNINLVYLRKSLVED 180

Query: 183 LLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNF 242
           LLKD ETFE K++GSFVR+KSDP+DYLQKN+HQL+QVIG KK+  + D     LL VSN 
Sbjct: 181 LLKDHETFESKLIGSFVRIKSDPHDYLQKNTHQLVQVIGLKKISISGDLGPGFLLHVSNV 240

Query: 243 VKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTV 278
           +KD+ I+ LSD+NFSEEEC+DL  R+K+GL+KR T+
Sbjct: 241 MKDVSISMLSDENFSEEECKDLDLRIKNGLVKRLTI 276

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297806885|ref|XP_002871326.1| SWIB complex BAF60b domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297317163|gb|EFH47585.1| SWIB complex BAF60b domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  286 bits (731), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 149/268 (55%), Positives = 197/268 (73%), Gaps = 11/268 (4%)

Query: 12  WVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIIN 71
           WV E +      +++ KR+ R K+ +F GWGS  LIEFL+SLGKDT++ ISRYDV+D I 
Sbjct: 6   WVEEGNG--GSAISSRKRKARPKRFEFVGWGSKQLIEFLKSLGKDTSEMISRYDVSDTIA 63

Query: 72  KYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSS 131
           +Y+ +  L+    KK+VV D+RLLSLFG ++  R+K+YDLLE HY ENQ +SD DFL+  
Sbjct: 64  RYIAKEGLLDPSNKKKVVCDQRLLSLFGSRTIFRMKVYDLLEKHYKENQDDSDFDFLY-E 122

Query: 132 DEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFE 191
           DE   +  SEK   R   + K     P+  +AAIV DNIKL+YL++SLVQ+L+K  +TFE
Sbjct: 123 DEPQIISHSEKIAKRTSKVVK----KPRGTFAAIVSDNIKLLYLRKSLVQELVKSPDTFE 178

Query: 192 CKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATL 251
            K++GSFVR+KSDPNDYLQK  +QL+QV G KK PGTDD     LL+V+N+VKD+ I+ L
Sbjct: 179 SKMLGSFVRIKSDPNDYLQKYPYQLVQVTGVKKEPGTDD----FLLQVTNYVKDVSISVL 234

Query: 252 SDDNFSEEECEDLRQRVKDGLLKRPTVV 279
           SDDNFS+EECEDL QR+K+GLLK+PT+V
Sbjct: 235 SDDNFSQEECEDLHQRIKNGLLKKPTIV 262

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30682386|ref|NP_196460.2| SWIB/MDM2 and Plus-3 and GYF domain-containing protein [Arabidopsis thaliana] gi|73622094|sp|Q9FT92.2|Y5843_ARATH RecName: Full=Uncharacterized protein At5g08430 gi|192807344|gb|ACF06124.1| At5g08430 [Arabidopsis thaliana] gi|332003917|gb|AED91300.1| SWIB/MDM2 and Plus-3 and GYF domain-containing protein [Arabidopsis thaliana]

 Score =  279 bits (714), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 148/268 (55%), Positives = 194/268 (72%), Gaps = 12/268 (4%)

Query: 12  WVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIIN 71
           WV E +       ++ KR+ R K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I 
Sbjct: 6   WVEEGN---GSATSSRKRKARPKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIA 62

Query: 72  KYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSS 131
           KY+++  L+    KK+VV D+RL+ LFG ++  R+K+YDLLE HY ENQ +SD DFL+  
Sbjct: 63  KYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDLLEKHYKENQDDSDFDFLY-E 121

Query: 132 DEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFE 191
           DE   +  SEK   R   + K     P+  +AAIV DNIKL+YL++SLVQ+LLK  +TFE
Sbjct: 122 DEPQIICHSEKIAKRTSKVVK----KPRGTFAAIVSDNIKLLYLRKSLVQELLKSPDTFE 177

Query: 192 CKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATL 251
            K++GSFVR+KSDPNDYLQK  +QL+QV G KK  GTDD     LL+V+N+VKD+ I+ L
Sbjct: 178 GKMLGSFVRIKSDPNDYLQKYPYQLVQVTGVKKEHGTDD----FLLQVTNYVKDVSISVL 233

Query: 252 SDDNFSEEECEDLRQRVKDGLLKRPTVV 279
           SDDNFS+EECEDL QR+K+GLLK+PT+V
Sbjct: 234 SDDNFSQEECEDLHQRIKNGLLKKPTIV 261

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|10178285|emb|CAC08343.1| putative protein [Arabidopsis thaliana]

 Score =  277 bits (709), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 147/267 (55%), Positives = 193/267 (72%), Gaps = 12/267 (4%)

Query: 12  WVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIIN 71
           WV E +       ++ KR+ R K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I 
Sbjct: 6   WVEEGN---GSATSSRKRKARPKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIA 62

Query: 72  KYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSS 131
           KY+++  L+    KK+VV D+RL+ LFG ++  R+K+YDLLE HY ENQ +SD DFL+  
Sbjct: 63  KYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDLLEKHYKENQDDSDFDFLY-E 121

Query: 132 DEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFE 191
           DE   +  SEK   R   + K     P+  +AAIV DNIKL+YL++SLVQ+LLK  +TFE
Sbjct: 122 DEPQIICHSEKIAKRTSKVVK----KPRGTFAAIVSDNIKLLYLRKSLVQELLKSPDTFE 177

Query: 192 CKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATL 251
            K++GSFVR+KSDPNDYLQK  +QL+QV G KK  GTDD     LL+V+N+VKD+ I+ L
Sbjct: 178 GKMLGSFVRIKSDPNDYLQKYPYQLVQVTGVKKEHGTDD----FLLQVTNYVKDVSISVL 233

Query: 252 SDDNFSEEECEDLRQRVKDGLLKRPTV 278
           SDDNFS+EECEDL QR+K+GLLK+PT+
Sbjct: 234 SDDNFSQEECEDLHQRIKNGLLKKPTI 260

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356561784|ref|XP_003549158.1| PREDICTED: uncharacterized protein At5g08430-like [Glycine max]

 Score =  276 bits (707), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 143/248 (57%), Positives = 182/248 (73%), Gaps = 8/248 (3%)

Query: 37  KFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLS 96
           ++ GWGS  LI FL+S+G+DT+ +I++ +V +I+ +YV ++ L H  KKKR+  DE+L  
Sbjct: 35  EYQGWGSTSLIWFLESIGRDTSTEITQSEVANIVMEYVKQHNLFHKTKKKRIECDEKLHL 94

Query: 97  LFGKKSFLRIKIYDLLEAHYAENQFESDDDFLF-SSDEENNLFSSEKQKS----RKVPLK 151
           LFG+K+  R+KI DLLE+H+AEN  ES D   F S D+E+ L + E  ++    RK   K
Sbjct: 95  LFGRKTISRLKINDLLESHFAENCEESSDGIFFDSEDDESALTACETPRTAPSERKSQPK 154

Query: 152 KLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQK 211
           K   E P+SC+AAIVP NIKLVYLKRSLV+DLLKD ETFE KVVGSF+R++ DPNDYLQK
Sbjct: 155 KPAFEKPRSCFAAIVPANIKLVYLKRSLVEDLLKDPETFETKVVGSFIRIRCDPNDYLQK 214

Query: 212 NSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDG 271
           NSHQLLQV G KK   + +   EI L+ S F+KDIRI  LSDDNFS EECEDL QRVKD 
Sbjct: 215 NSHQLLQVTGMKK---SSEVKGEIHLQASGFIKDIRIQMLSDDNFSVEECEDLHQRVKDC 271

Query: 272 LLKRPTVV 279
           L+KRP +V
Sbjct: 272 LVKRPMIV 279

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480913|ref|XP_002267111.2| PREDICTED: uncharacterized protein At5g08430-like [Vitis vinifera]

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 155/285 (54%), Positives = 202/285 (70%), Gaps = 14/285 (4%)

Query: 1   MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQ 60
           M  K +   F+W+ E  E     + + ++  +SKK +F GWGS PLIEFLQS+GKDT+Q 
Sbjct: 1   MDKKVENVPFIWMEESKEQFYTPMKSKRKF-KSKKKEFVGWGSKPLIEFLQSIGKDTSQN 59

Query: 61  ISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQ 120
           +S YDVT IIN YVNEN L H  +KK VV DE+L SL G+KS  R KI+D+LE H+  NQ
Sbjct: 60  LSHYDVTAIINTYVNENSLFHPKRKKTVVCDEKLHSLLGRKSVSRFKIHDMLEPHFVGNQ 119

Query: 121 --FESDDDFLFSSD-EENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKR 177
              ES D+  +SSD EE+N+ ++ KQ S +   KK  +ETPKSC+AAIVP+NIKLVYL+R
Sbjct: 120 EEAESGDELFYSSDEEEDNVCATRKQHSLQ---KKKVVETPKSCFAAIVPENIKLVYLRR 176

Query: 178 SLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIG---TKKVPGTDDKSTE 234
           SLV++L+K  E FE KVVGS VRVK DPNDYLQKNSHQL++V G   + KV G   +   
Sbjct: 177 SLVENLIKKPEEFEDKVVGSIVRVKCDPNDYLQKNSHQLVRVAGFVTSFKVVGRSGER-- 234

Query: 235 ILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVV 279
             + VS+F++   ++ L ++NFSEEEC+D +QR+KDGLLKR TVV
Sbjct: 235 --VHVSHFIRTSSLSILVEENFSEEECKDFQQRMKDGLLKRLTVV 277

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224116464|ref|XP_002317307.1| predicted protein [Populus trichocarpa] gi|222860372|gb|EEE97919.1| predicted protein [Populus trichocarpa]

 Score =  234 bits (596), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 123/258 (47%), Positives = 183/258 (70%), Gaps = 6/258 (2%)

Query: 28  KRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKR 87
           KR+ RSK   F GWGS  L EFL S+G++T +++S++DVT II  Y  +N L+  +K+K 
Sbjct: 197 KRKERSKTKMFLGWGSKCLFEFLTSIGQETNKELSQHDVTIIIFGYCRDNNLLDPLKRKN 256

Query: 88  VVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFS--SDEENNLFSSEKQKS 145
           ++ DE+L SL G+K   +  IY LL  H+AEN  ES ++F+ S  ++ +N L   ++QK+
Sbjct: 257 ILCDEKLRSLLGRKFVNKNSIYKLLTKHFAENLEESRNEFVNSLEAEGQNALSPCKRQKN 316

Query: 146 R----KVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRV 201
                K   K++  +  +SC+A+++P NIKLVYL+RS +++L K  E F+  V+GSFVR 
Sbjct: 317 SSWEGKSQNKEVVSDMQRSCFASVIPRNIKLVYLRRSALEELSKQPEIFDAIVMGSFVRA 376

Query: 202 KSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEEC 261
           K+DPND++QKNSHQL+QVIG KK     + +++ILL++SN V D+ I+ +S+++FSEEEC
Sbjct: 377 KTDPNDWMQKNSHQLVQVIGIKKTSINGEVNSDILLQLSNRVSDVSISKVSENDFSEEEC 436

Query: 262 EDLRQRVKDGLLKRPTVV 279
           +DL QRVKDGLL+RPTV 
Sbjct: 437 QDLHQRVKDGLLRRPTVA 454

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	298
TAIR|locus:2150828	553	AT5G08430 [Arabidopsis thalian	0.852	0.459	0.529	9.4e-66
TAIR|locus:2154473	570	AT5G23480 [Arabidopsis thalian	0.785	0.410	0.425	1.7e-41
TAIR|locus:2080863	1292	AT3G51120 [Arabidopsis thalian	0.865	0.199	0.318	3.7e-24
TAIR|locus:2827287	1773	NERD "Needed for RDR2-independ	0.791	0.133	0.311	2.5e-23
TAIR|locus:2060949	824	AT2G18090 "AT2G18090" [Arabido	0.261	0.094	0.269	0.00034

TAIR|locus:2150828 AT5G08430 [Arabidopsis thaliana (taxid:3702)]

 Score = 669 (240.6 bits), Expect = 9.4e-66, P = 9.4e-66
 Identities = 143/270 (52%), Positives = 191/270 (70%)

Query:    12 WVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIIN 71
             WV E +   +   ++ KR+ R K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I 
Sbjct:     6 WVEEGNGSAT---SSRKRKARPKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIA 62

Query:    72 KYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQXXXXXXXXXXX 131
             KY+++  L+    KK+VV D+RL+ LFG ++  R+K+YDLLE HY ENQ           
Sbjct:    63 KYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDLLEKHYKENQDDSDFDFLYED 122

Query:   132 XXXNNLFSSEK--QKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSET 189
                  +  SEK  +++ KV +KK     P+  +AAIV DNIKL+YL++SLVQ+LLK  +T
Sbjct:   123 EP-QIICHSEKIAKRTSKV-VKK-----PRGTFAAIVSDNIKLLYLRKSLVQELLKSPDT 175

Query:   190 FECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIA 249
             FE K++GSFVR+KSDPNDYLQK  +QL+QV G KK  GTDD     LL+V+N+VKD+ I+
Sbjct:   176 FEGKMLGSFVRIKSDPNDYLQKYPYQLVQVTGVKKEHGTDD----FLLQVTNYVKDVSIS 231

Query:   250 TLSDDNFSEEECEDLRQRVKDGLLKRPTVV 279
              LSDDNFS+EECEDL QR+K+GLLK+PT+V
Sbjct:   232 VLSDDNFSQEECEDLHQRIKNGLLKKPTIV 261

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0016570 "histone modification" evidence=IEA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0009086 "methionine biosynthetic process" evidence=RCA

GO:0009616 "virus induced gene silencing" evidence=RCA

GO:0010050 "vegetative phase change" evidence=RCA

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2154473 AT5G23480 [Arabidopsis thaliana (taxid:3702)]

 Score = 440 (159.9 bits), Expect = 1.7e-41, P = 1.7e-41
 Identities = 112/263 (42%), Positives = 155/263 (58%)

Query:    28 KRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVK-KK 86
             KR  + K ++F GWGS  LIEFL+SLG+DTT +IS  DVT II  Y+ E      +K KK
Sbjct:    14 KRLRKPKSLEFVGWGSRNLIEFLESLGRDTTNKISENDVTAIIMNYIREKSRETPLKSKK 73

Query:    87 R---VVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQXXXXXXXXXXXXXXNNLFSSEKQ 143
             R   V  DE+L  LFG      IK+ DL+E HY ENQ              ++L++SE  
Sbjct:    74 RRKTVACDEKLRLLFGAGKINVIKVPDLVEKHYVENQEEDLFY--------DDLYASEDD 125

Query:   144 KSRKVPLK-KLCLET------PKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVG 196
             K +++ L  K+  +T      P+  +AAIV D +KL+YL++SLVQ+L K  ETFE KVV 
Sbjct:   126 KQQRLSLSDKVAKQTKQVVSKPRGTFAAIVRDTVKLLYLRKSLVQELAKTPETFESKVVR 185

Query:   197 SFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNF 256
             +FVR+K         N  QL+ V G K+    D    ++    S ++KD+  ++LSDD+F
Sbjct:   186 TFVRIK---------NPCQLVHVTGVKEGDPIDGNLFQVT-NYSYYLKDVTTSSLSDDDF 235

Query:   257 SEEECEDLRQRVKDGLLKRPTVV 279
             S+EECE+L QR+ +G  KR TVV
Sbjct:   236 SQEECEELHQRINNGFAKRLTVV 258

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0016570 "histone modification" evidence=IEA

TAIR|locus:2080863 AT3G51120 [Arabidopsis thaliana (taxid:3702)]

 Score = 290 (107.1 bits), Expect = 3.7e-24, P = 3.7e-24
 Identities = 91/286 (31%), Positives = 147/286 (51%)

Query:    21 SPQLTNLKRRGRS-----KKVKFD-GWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYV 74
             SP L N K  G++     KK   D  W +  L+EF+  +    T  +S++DV  ++  Y+
Sbjct:   294 SPTLPN-KLDGKNPSNILKKAPGDTSWATKELLEFVSFMKNGDTSVLSQFDVQGLLLDYI 352

Query:    75 NENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQXXXXXXXXXXXXXX 134
              +  L   ++K +V+ D+ L+ LFGK+     ++  LLE+H    Q              
Sbjct:   353 KKKNLRDPLQKSQVLCDQMLVKLFGKQRVGHFEMLKLLESHVLI-QEKPKGAKTTNGETT 411

Query:   135 NNLFSSEKQKSRKVPL-----KKLCLETPK-------SCWAAIVPDNIKLVYLKRSLVQD 182
             + + S  ++ S   P+     +K+  +T           +AAI   NI L+YL+R  ++ 
Sbjct:   412 HAVPSQIEEDSVHDPMVRDRRRKMRRKTDGRVQNENLDAYAAIDVHNINLIYLRRKFLES 471

Query:   183 LLKDSETFECKVVGSFVRVKSDPNDYLQK-NSHQLLQVIGTKKVPGTDD---KSTEILLK 238
             LL D    + KVVG+ +R+K   +D  QK + H+L+QV+GT K   +     K+T+++L+
Sbjct:   472 LLDDINKVDEKVVGTILRIKVSGSD--QKLDIHRLVQVVGTSKAIASYQLGAKTTDVMLE 529

Query:   239 VSNFVKD--IRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSL 282
             + N  K   I I  LSD N +E+EC+ LRQ +K GL KR TVV  L
Sbjct:   530 ILNLDKREVISIDQLSDQNITEDECKRLRQSIKCGLNKRLTVVDIL 575

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016570 "histone modification" evidence=IEA

GO:0007346 "regulation of mitotic cell cycle" evidence=RCA

TAIR|locus:2827287 NERD "Needed for RDR2-independent DNA methylation" [Arabidopsis thaliana (taxid:3702)]

 Score = 284 (105.0 bits), Expect = 2.5e-23, P = 2.5e-23
 Identities = 80/257 (31%), Positives = 133/257 (51%)

Query:    41 WGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGK 100
             W S  L++ +  + +     +   +V  ++  Y+    L    +K +V+ D RL +LFGK
Sbjct:   807 WASKELLDLVVHMRRGDRSFLPMLEVQTLLLAYIKRYNLRDPRRKSQVICDSRLQNLFGK 866

Query:   101 KSFLRIKIYDLLEAHYA---ENQXXXXXXXXXXXXXXN------NL---FSSEKQKSRKV 148
                   ++ +LL++H+    +NQ              N      NL     S K K RK 
Sbjct:   867 SHVGHFEMLNLLDSHFLKKEQNQADDIQGDIVDTEEPNHVDVDENLDHPVKSGKDKKRKT 926

Query:   149 PLKKLCLETPKSC--WAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPN 206
               K +      +   +AA+   NI L+YL+RSLV+DLL+DS  FE KV  +FVR++   N
Sbjct:   927 RKKNVRKGRQSNLDDFAAVDMHNINLIYLRRSLVEDLLEDSTAFEEKVASAFVRLRISGN 986

Query:   207 DYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKVSNFVKD--IRIATLSDDNFSEEEC 261
                +++ ++L+QV+GT K P       K+T+ +L++ N  K   I I  +S+ +F+E+EC
Sbjct:   987 Q--KQDLYRLVQVVGTSKAPEPYKVGKKTTDYVLEILNLDKTEVISIDIISNQDFTEDEC 1044

Query:   262 EDLRQRVKDGLLKRPTV 278
             + L+Q +K GL+ R TV
Sbjct:  1045 KRLKQSIKCGLINRLTV 1061

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0005829 "cytosol" evidence=IDA

GO:0031048 "chromatin silencing by small RNA" evidence=IMP

GO:0042393 "histone binding" evidence=IDA

TAIR|locus:2060949 AT2G18090 "AT2G18090" [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 0.00034, P = 0.00034
 Identities = 21/78 (26%), Positives = 45/78 (57%)

Query:    41 WGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGK 100
             W +  L++F+  +       +S+YDV  ++ +YV  N L +S +   ++ D +L+ LFGK
Sbjct:   295 WATNELLDFVGYMKNGDISVLSKYDVQTLVLEYVRRNNLQNSPQNSEIMCDSKLMRLFGK 354

Query:   101 KSFLRIKIYDLLEAHYAE 118
             +    +++  LL++H+ +
Sbjct:   355 ERVDNLEMLKLLDSHFID 372


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.135   0.386    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      298       284   0.00085  115 3  11 22  0.38    34
                                                     33  0.42    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  5
  No. of states in DFA:  596 (63 KB)
  Total size of DFA:  194 KB (2111 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  24.03u 0.08s 24.11t   Elapsed:  00:00:01
  Total cpu time:  24.03u 0.08s 24.11t   Elapsed:  00:00:01
  Start:  Thu May  9 18:05:46 2013   End:  Thu May  9 18:05:47 2013

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.IV.4519.1 annotation not avaliable (553 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	298
smart00719	109	smart00719, Plus3, Short conserved domain in trans	3e-30
pfam03126	105	pfam03126, Plus-3, Plus-3 domain	4e-26
pfam02201	76	pfam02201, SWIB, SWIB/MDM2 domain	3e-07

>gnl|CDD|197843 smart00719, Plus3, Short conserved domain in transcriptional regulators

 Score =  110 bits (276), Expect = 3e-30
 Identities = 49/111 (44%), Positives = 71/111 (63%), Gaps = 7/111 (6%)

Query: 164 AIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTK 223
           AIV DN+ L+ L+RSLV++LLK   TFE KVVG FVRVK  PND  Q   ++L+QV G K
Sbjct: 1   AIVFDNLNLLRLRRSLVEELLK-PPTFESKVVGCFVRVKIGPNDQKQ-PIYRLVQVTGVK 58

Query: 224 KVPGT---DDKSTEILLKV--SNFVKDIRIATLSDDNFSEEECEDLRQRVK 269
           +         K+T +LL+V   +  K ++I  +S+ +F+EEE +  +Q +K
Sbjct: 59  EADKPYSLGGKTTNVLLEVLNGDSEKVVQINFISNQDFTEEEFQRWKQAIK 109

Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1. Length = 109

>gnl|CDD|190531 pfam03126, Plus-3, Plus-3 domain

 Score = 98.9 bits (247), Expect = 4e-26
 Identities = 37/106 (34%), Positives = 54/106 (50%), Gaps = 6/106 (5%)

Query: 168 DNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG 227
           D+I  + L RSL+  LL     FE  VVG FVRV   P+    + S++L Q+ G K+   
Sbjct: 1   DDINRIRLGRSLLAKLLFYP-GFESTVVGCFVRVNIGPDKETGQQSYRLAQITGVKEGKK 59

Query: 228 T---DDKSTEILLKVS--NFVKDIRIATLSDDNFSEEECEDLRQRV 268
                 K+T+  LKV+     +  RI+ +S+  F+EEE E   Q  
Sbjct: 60  PYQLGGKTTDKYLKVTHGKSERVFRISFVSNSPFTEEEFERWLQSC 105

This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor. Length = 105

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

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 48  EFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIK 107
           +  + LG     ++SR +V   + +Y+ E+ L     K+ ++ DE+L S+FG       +
Sbjct: 10  DLAKFLG---AGELSRTEVVKKLWQYIKEHNLQDPKNKRIILCDEKLKSIFGGDRVGFFE 66

Query: 108 IYDLLEAHY 116
           +  LL +H+
Sbjct: 67  MSKLLSSHF 75

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	298
smart00719	109	Plus3 Short conserved domain in transcriptional re	99.98
PF03126	108	Plus-3: Plus-3 domain; InterPro: IPR004343 The yea	99.96
KOG1946	240	consensus RNA polymerase I transcription factor UA	99.95
KOG2402	525	consensus Paf1/RNA polymerase II complex, RTF1 com	99.93
PF02201	76	SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SW	99.86
COG5296	521	Transcription factor involved in TATA site selecti	99.86
smart00151	77	SWIB SWI complex, BAF60b domains.	99.86
COG5531	237	SWIB-domain-containing proteins implicated in chro	99.73
PRK14724	987	DNA topoisomerase III; Provisional	99.72
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	99.28
KOG2570	420	consensus SWI/SNF transcription activation complex	99.19
KOG2522	560	consensus Filamentous baseplate protein Ligatin, c	83.47

>smart00719 Plus3 Short conserved domain in transcriptional regulators

Probab=99.98  E-value=2.3e-32  Score=224.04  Aligned_cols=104  Identities=48%  Similarity=0.669  Sum_probs=97.1

Q ss_pred             cccccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCcCccceeEEEEEeeeecCCC---CCcccceEEEee
Q 022354          164 AIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGT---DDKSTEILLKVS  240 (298)
Q Consensus       164 ai~~~ninlIyL~Rslve~ll~~p~~F~~kVvG~FVRIki~~~~~~~k~~YRlvqV~gv~~~~e~---g~~~Tni~L~v~  240 (298)
                      |++.+||++|||+|+.+++||+.| +|+++|+||||||+||++++++ ++||||||+||.++++.   |++.||++|.|+
T Consensus         1 ~~~l~~l~~i~L~R~~l~~~~~~p-~Fe~~v~GcFVRv~ig~~~~~~-~~Yrl~qI~gv~~~~k~Y~~~~~~t~~~L~v~   78 (109)
T smart00719        1 AIVFDNLNLLRLRRSLVEELLKPP-TFESKVVGCFVRVKIGPNDQKQ-PIYRLVQVTGVKEADKPYELGGKTTNVLLEVL   78 (109)
T ss_pred             CCChHHhheEEEEHHHHHHHhcCC-chhHhceEeEEEEEECCCCCCC-CeEEEEEEeeEEecCcceecCCceeeEEEEEe
Confidence            468899999999999999999999 9999999999999999999987 89999999999997765   889999999998


Q ss_pred             C--CceeeEeecccCCCCCHHHHHHHHHHHH
Q 022354          241 N--FVKDIRIATLSDDNFSEEECEDLRQRVK  269 (298)
Q Consensus       241 ~--~~k~~~I~~iSn~dFTeeEc~rl~q~~~  269 (298)
                      +  ..+.|+|++|||++|||+||++|++.|+
T Consensus        79 ~g~~~~~~~i~~iSn~~fte~E~~~w~~~~~  109 (109)
T smart00719       79 NGDSEKVVQINFISNQDFTEEEFQRWKQAIK  109 (109)
T ss_pred             cCCceEEEEEEEecCCCCCHHHHHHHHHHhC
Confidence            6  4578999999999999999999999884

Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.

>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1

Probab=99.96  E-value=2.2e-30  Score=211.09  Aligned_cols=102  Identities=35%  Similarity=0.499  Sum_probs=86.8

Q ss_pred             cccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCcCccceeEEEEEeeeecCCC---CCcccceEEEeeC--C
Q 022354          168 DNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGT---DDKSTEILLKVSN--F  242 (298)
Q Consensus       168 ~ninlIyL~Rslve~ll~~p~~F~~kVvG~FVRIki~~~~~~~k~~YRlvqV~gv~~~~e~---g~~~Tni~L~v~~--~  242 (298)
                      +||++|||+|++|++||++| +|+++|+||||||+||++++++.++|||+||+||.+.++.   |++.||++|.|.+  .
T Consensus         1 e~i~~i~l~Rs~l~~~~~~P-~Fe~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~v~~~~k~Y~~~~~~t~~~L~l~~g~~   79 (108)
T PF03126_consen    1 EDIKRIRLSRSQLEKWLFKP-FFEDAVVGCFVRVNIGPNDYTQNPVYRLCQIVGVKEGKKPYKLGSKKTNKYLVLRHGNS   79 (108)
T ss_dssp             HHHHHTBE-HHHHHHHTTST-THHHHHTT-EEEEEEETTSSS-E--EEEEEEEEEEEEEEEEEETTEEEEEEEEEEETTE
T ss_pred             CchHeEEEEHHHHHHHHcCC-ChhHheeEEEEEEEecCCCCCCceeEEEEEEEEEecccccEecCCeEEEEEEEEEECCc
Confidence            58999999999999999999 9999999999999999999988678999999999998843   8999999999997  4


Q ss_pred             ceeeEeecccCCCCCHHHHHHHHHHHHc
Q 022354          243 VKDIRIATLSDDNFSEEECEDLRQRVKD  270 (298)
Q Consensus       243 ~k~~~I~~iSn~dFTeeEc~rl~q~~~~  270 (298)
                      .+.|+|++|||++|||+||++|++.|++
T Consensus        80 ~r~~~i~~vSn~~~te~E~~~w~~~~~~  107 (108)
T PF03126_consen   80 ERDFPIDMVSNSPFTEEEFERWKQSCEK  107 (108)
T ss_dssp             EEEEEGGGBBSS---HHHHHHHHHHH--
T ss_pred             eeEEEeEeeECCCCCHHHHHHHHHHhcc
Confidence            5799999999999999999999999986

The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.

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

Probab=99.95  E-value=2e-29  Score=232.35  Aligned_cols=134  Identities=34%  Similarity=0.511  Sum_probs=100.3

Q ss_pred             cCCCCHHHHHHHHhcCCCC-CCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhccc
Q 022354           39 DGWGSIPLIEFLQSLGKDT-TQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA  117 (298)
Q Consensus        39 ~~w~S~eL~efl~~~g~~~-~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~  117 (298)
                      .+|||..|..|+.+|++++ +++|||++|++.||+|||+||||||.||+.|+||++|++|||+++|+||+|++||.+||.
T Consensus        96 ~~~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H~~  175 (240)
T KOG1946|consen   96 ASWGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKHFL  175 (240)
T ss_pred             cCcCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHhcc
Confidence            4499999998888888887 999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCC------C--CCccC-ccccccccChhh-hhccccccccccccCCccccccccccccceeee
Q 022354          118 ENQFESD------D--DFLFS-SDEENNLFSSEK-QKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYL  175 (298)
Q Consensus       118 ~~~~~~~------d--~~~~~-sedd~~~~~~~k-~~~r~~~~k~~~~~~~~~~~aai~~~ninlIyL  175 (298)
                      ++++.++      +  +.... .+.+.. ..++. .+.++...++  .-.+...||++..+|++++||
T Consensus       176 ~~~d~~~~~~~~~~~~e~~~~~~~~~~~-~~~~~~e~~~k~~~~~--~~~~~~~~a~~~~~~~~l~~~  240 (240)
T KOG1946|consen  176 KNQDMVGTDLKQGEETETKEFKEEEDKS-QDPCLSEKEAKETKKV--VKKPRGTFAAIVSDNIKLLYL  240 (240)
T ss_pred             CccccccchhhcCccccccccccccccc-cccchhhhhhhhhhhc--ccccccchhhhhccccccccC
Confidence            9877531      0  11111 111221 12221 1122221111  111223999999999999996

>KOG2402 consensus Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription]

Probab=99.93  E-value=3.7e-26  Score=228.29  Aligned_cols=132  Identities=21%  Similarity=0.220  Sum_probs=121.6

Q ss_pred             ccccccccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCcCccceeEEEEEeeeecCCC---CCcccceEE
Q 022354          161 CWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGT---DDKSTEILL  237 (298)
Q Consensus       161 ~~aai~~~ninlIyL~Rslve~ll~~p~~F~~kVvG~FVRIki~~~~~~~k~~YRlvqV~gv~~~~e~---g~~~Tni~L  237 (298)
                      .+.. +..++|+++|+|+.|+.||+.| +|+++|+||||||+||+.+.  +++|||++|+||.++.+.   |.+.||.+|
T Consensus       213 ~~v~-~~~dln~~rlsR~~vak~~~~P-~Fe~~V~gCfvRv~ig~~~~--~p~YRv~~I~gV~es~k~Y~l~~~~Tnk~l  288 (525)
T KOG2402|consen  213 ARVP-SISDLNALRLSRHKVAKWLFSP-FFESTVTGCFVRVGIGGEGS--KPVYRVAEIVGVLESDKPYKLEGVKTNKYL  288 (525)
T ss_pred             cCCC-CHHHHHHHHhhHHHHHHHHhhh-HHHHHhhhheEEeeecCcCC--CCceeEEEEeeecccCccccccceeeccee
Confidence            3444 7889999999999999999999 99999999999999999955  589999999999998776   899999999


Q ss_pred             EeeCC--ceeeEeecccCCCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHhhhhccCCC
Q 022354          238 KVSNF--VKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSPY  296 (298)
Q Consensus       238 ~v~~~--~k~~~I~~iSn~dFTeeEc~rl~q~~~~g~~~rpTv~di~~~~~~~~~~~~~~~  296 (298)
                      .|++-  .++|+|++|||++||++||++|+..|+..++..||+..|..|.+.++.+.+-+|
T Consensus       289 ~~~~G~s~r~f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~~a~~~~~  349 (525)
T KOG2402|consen  289 RVRHGRSERVFRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIVKALNYRL  349 (525)
T ss_pred             eeecCcchhhcchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHhcCcc
Confidence            99973  368999999999999999999999999999999999999999999999887655

>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=99.86  E-value=7.1e-23  Score=158.17  Aligned_cols=70  Identities=36%  Similarity=0.511  Sum_probs=65.3

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhccc
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA  117 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~  117 (298)
                      .|++|++|+|      ..++||++|++.||+|||+||||||++|+.|+||++|+.|||+++|.+++|+++|.+|+.
T Consensus         7 ls~~L~~~lg------~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl~   76 (76)
T PF02201_consen    7 LSPELAEFLG------EDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHLI   76 (76)
T ss_dssp             HHHHHHHHTT-------SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHHE
T ss_pred             CCHHHHHHhC------CCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhcC
Confidence            5899999997      566999999999999999999999999999999999999999999999999999999974

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 ....

>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]

Probab=99.86  E-value=1.2e-21  Score=190.34  Aligned_cols=131  Identities=20%  Similarity=0.216  Sum_probs=120.0

Q ss_pred             cccccccccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCcCccceeEEEEEeeeecCCC---CCcccceE
Q 022354          160 SCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGT---DDKSTEIL  236 (298)
Q Consensus       160 ~~~aai~~~ninlIyL~Rslve~ll~~p~~F~~kVvG~FVRIki~~~~~~~k~~YRlvqV~gv~~~~e~---g~~~Tni~  236 (298)
                      ++||.  --++|.++++|++|+++|++| .|++.|+|||+||+||..++  +-+||||+|-++....+.   |+..||.+
T Consensus       205 d~~a~--l~Dfn~~rvgR~~VA~~~f~P-~Fed~v~Gcf~Rv~Ig~R~g--~~vyRiv~V~~~~~~~kpy~~~~v~Tn~y  279 (521)
T COG5296         205 DDFAE--LYDFNQCRVGRDMVARNVFKP-IFEDEVIGCFTRVRIGERGG--YLVYRIVGVGKGSTYSKPYGRKEVKTNRY  279 (521)
T ss_pred             chhhh--hhhhhhhhhhHHHHHHHhccc-chhhhhcceeeEEEecccCC--eeEEEEEEeccceeccccccccceeeeee
Confidence            66666  367899999999999999999 99999999999999996554  469999999999997775   89999999


Q ss_pred             EEeeC-Cc-eeeEeecccCCCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHhhhhccCC
Q 022354          237 LKVSN-FV-KDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFCSP  295 (298)
Q Consensus       237 L~v~~-~~-k~~~I~~iSn~dFTeeEc~rl~q~~~~g~~~rpTv~di~~~~~~~~~~~~~~  295 (298)
                      |.|++ .. ++|+|+.|||++|.++||+||+.+++.|.+..|++.-+++|++.+-.|++.|
T Consensus       280 l~v~~Gr~~kvF~in~~Sn~pf~~~eyQr~~r~~~~~kl~~PS~~~v~~k~~~l~d~~~~~  340 (521)
T COG5296         280 LDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRR  340 (521)
T ss_pred             EeeecCcceeeeEeecccCCcccHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHhCCc
Confidence            99997 44 6899999999999999999999999999999999999999999999998876

>smart00151 SWIB SWI complex, BAF60b domains

Probab=99.86  E-value=6.5e-22  Score=153.17  Aligned_cols=71  Identities=23%  Similarity=0.420  Sum_probs=68.2

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhcccc
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE  118 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~~  118 (298)
                      .|++|++|+|      .+++||.+|++.||+|||+||||||++|+.|.||+.|+.+||++++.+++|+++|.+|+.+
T Consensus         7 ls~~L~~~lg------~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl~~   77 (77)
T smart00151        7 LSPELAKVLG------APEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK   77 (77)
T ss_pred             CCHHHHHHhC------CCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence            6999999997      5889999999999999999999999999999999999999999999999999999999864

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

Probab=99.73  E-value=2.3e-18  Score=158.64  Aligned_cols=71  Identities=18%  Similarity=0.275  Sum_probs=69.1

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhcccc
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE  118 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~~  118 (298)
                      .|+.||.|||      ..++||++||+.||+|||+||||||.+||.|+||++|+.|||.+.+.||+|+++|.+|+.+
T Consensus       127 lS~~La~ilG------~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl~~  197 (237)
T COG5531         127 LSPKLAAILG------LEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPLSPHLIK  197 (237)
T ss_pred             cCHHHHHHhC------CCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhcccccceec
Confidence            7999999998      6899999999999999999999999999999999999999999999999999999999997

>PRK14724 DNA topoisomerase III; Provisional

Probab=99.72  E-value=5.4e-18  Score=181.76  Aligned_cols=71  Identities=20%  Similarity=0.377  Sum_probs=68.1

Q ss_pred             CCCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhccc
Q 022354           41 WGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA  117 (298)
Q Consensus        41 w~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~  117 (298)
                      -.|++|++|||      ..++||++|++.||+|||+||||||.|||.|+||++|+.|||+++|.||+|+++|++|+.
T Consensus       917 ~ls~~La~~lg------~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~  987 (987)
T PRK14724        917 KPSAALAAVIG------AEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS  987 (987)
T ss_pred             CCCHHHHHHhC------CCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence            37999999997      678999999999999999999999999999999999999999999999999999999984

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

Probab=99.28  E-value=2.2e-12  Score=137.23  Aligned_cols=71  Identities=20%  Similarity=0.332  Sum_probs=67.5

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhcccc
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE  118 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~~  118 (298)
                      .|++|+.+++      +.+++|.++++.||+|||+|+||||.+|+.|+||++|+.+||++++.+|+|+++|+.|+.+
T Consensus       790 ~S~~La~~~g------~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~~  860 (860)
T PRK06319        790 PSPALAAMIG------AEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLIK  860 (860)
T ss_pred             cccccccccC------cCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhcC
Confidence            6999999986      6789999999999999999999999999999999999999999999999999999999863

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

Probab=99.19  E-value=6.6e-12  Score=123.26  Aligned_cols=146  Identities=18%  Similarity=0.158  Sum_probs=104.4

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhccccCCC
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~~~~~  121 (298)
                      .||.|+..||      ...-||++|+..||.|||.|+||||.++..|.||.-|+.+||++++.+.+++.+|.+|+.+.++
T Consensus       211 lsp~La~lLG------i~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~dP  284 (420)
T KOG2570|consen  211 LSPRLANLLG------IHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPDP  284 (420)
T ss_pred             cCHHHHHHhh------hccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCCC
Confidence            7999999998      5667999999999999999999999999999999999999999999999999999999998877


Q ss_pred             CCCCCCc-------cCc--ccccc-ccChhhhhccccccccccccCCcccccc------ccccccceeeeeHHHHHHHhc
Q 022354          122 ESDDDFL-------FSS--DEENN-LFSSEKQKSRKVPLKKLCLETPKSCWAA------IVPDNIKLVYLKRSLVQDLLK  185 (298)
Q Consensus       122 ~~~d~~~-------~~s--edd~~-~~~~~k~~~r~~~~k~~~~~~~~~~~aa------i~~~ninlIyL~Rslve~ll~  185 (298)
                      .-=+-.+       ..+  -|.++ .-.+.+..-+..    ..+.....+-+|      -+.++||...-||.++.+|..
T Consensus       285 Ivi~h~I~v~~~~~~~tacyDIdV~v~~p~~~q~~nf----l~~~~~~~eI~alD~kI~~li~~ine~~~rr~Ff~~Fs~  360 (420)
T KOG2570|consen  285 IVIDHTISVDGNDTKVTACYDIDVEVEDPRKSQMSNF----LASTESQKEIAALDRKITELIQQINESKERRDFFLEFSK  360 (420)
T ss_pred             eeecceeccCCCcccceeEEeeeeccCCccchhhhhh----hcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            5211011       011  01111 011221111000    001111112222      245788999999999999999


Q ss_pred             Cccccccccccc
Q 022354          186 DSETFECKVVGS  197 (298)
Q Consensus       186 ~p~~F~~kVvG~  197 (298)
                      +|-.|...++-|
T Consensus       361 dPvefin~wi~S  372 (420)
T KOG2570|consen  361 DPVEFINEWIES  372 (420)
T ss_pred             CHHHHHHHHHHh
Confidence            998898877643

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

Probab=83.47  E-value=1.4  Score=45.18  Aligned_cols=54  Identities=17%  Similarity=0.343  Sum_probs=46.5

Q ss_pred             HHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhh
Q 022354           45 PLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLF   98 (298)
Q Consensus        45 eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LF   98 (298)
                      -..+++.+.|.+-.+-++-.||...+-.||+.|||-|+.||..++.|+-|-...
T Consensus       366 ~~~~Lf~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~  419 (560)
T KOG2522|consen  366 LAKDLFKEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMV  419 (560)
T ss_pred             HHHHHHHhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHH
Confidence            345666777777788899999999999999999999999999999999887643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	298
1v32_A	101	Solution Structure Of The SwibMDM2 DOMAIN OF THE Hy		8e-24

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

Iteration: 1
 Score =  107 bits (267), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 50/88 (56%), Positives = 66/88 (75%)
Query: 33  SKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE 92
            K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I KY+++  L+    KK+VV D+
Sbjct: 7   GKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDK 66
Query: 93  RLLSLFGKKSFLRIKIYDLLEAHYAENQ 120
           RL+ LFG ++  R+K+YDLLE HY ENQ
Sbjct: 67  RLVLLFGTRTIFRMKVYDLLEKHYKENQ 94

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	298
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	4e-24
2bze_A	153	KIAA0252 protein; human RTF1 PLUS3 domain, transcr	1e-21
3u1u_A	137	RNA polymerase-associated protein RTF1 homolog; pl	5e-21
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	5e-09
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>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 = 93.0 bits (231), Expect = 4e-24
 Identities = 50/95 (52%), Positives = 66/95 (69%)

Query: 32  RSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSD 91
             K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I KY+++  L+    KK+VV D
Sbjct: 6   SGKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCD 65

Query: 92  ERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDD 126
           +RL+ LFG ++  R+K+YDLLE HY ENQ      
Sbjct: 66  KRLVLLFGTRTIFRMKVYDLLEKHYKENQDSGPSS 100

>2bze_A KIAA0252 protein; human RTF1 PLUS3 domain, transcription, elongation, PAF1 complex, histone H3 methylation, H2B ubiquitination, CDC73, LEO1, CTR9; NMR {Homo sapiens} SCOP: b.34.21.1 Length = 153

 Score = 87.7 bits (217), Expect = 1e-21
 Identities = 23/129 (17%), Positives = 51/129 (39%), Gaps = 8/129 (6%)

Query: 156 ETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQ 215
             P+      +P+ +  V L R  ++        F   V G FVR+    ++   K  ++
Sbjct: 14  LVPRGSHMVSLPEELNRVRLSRHKLERWC-HMPFFAKTVTGCFVRIGIGNHN--SKPVYR 70

Query: 216 LLQVIGTKKVP---GTDDKSTEILLKVS--NFVKDIRIATLSDDNFSEEECEDLRQRVKD 270
           + ++ G  +           T   L++   N  +  R+  +S+  F+E E    ++ +  
Sbjct: 71  VAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFS 130

Query: 271 GLLKRPTVV 279
             ++ PT+ 
Sbjct: 131 AGMQLPTLD 139

>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3, transcription elongation, structural genomics, struc genomics consortium, SGC; 1.80A {Homo sapiens} PDB: 2db9_A Length = 137

 Score = 86.1 bits (213), Expect = 5e-21
 Identities = 25/127 (19%), Positives = 53/127 (41%), Gaps = 9/127 (7%)

Query: 158 PKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLL 217
           PKS   ++ P+ +  V L R  ++        F   V G FVR+    ++   K  +++ 
Sbjct: 3   PKSQPVSL-PEELNRVRLSRHKLERWC-HMPFFAKTVTGCFVRIGIGNHN--SKPVYRVA 58

Query: 218 QVIGTKKVP---GTDDKSTEILLKVS--NFVKDIRIATLSDDNFSEEECEDLRQRVKDGL 272
           ++ G  +           T   L++   N  +  R+  +S+  F+E E    ++ +    
Sbjct: 59  EITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAG 118

Query: 273 LKRPTVV 279
           ++ PT+ 
Sbjct: 119 MQLPTLD 125

>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 = 51.7 bits (124), Expect = 5e-09
 Identities = 14/73 (19%), Positives = 25/73 (34%), Gaps = 6/73 (8%)

Query: 43  SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKS 102
           S  L++ L        +  +R  +   I  YV   KL +         D  L  +FG++ 
Sbjct: 15  STALMDVLG------IEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEK 68

Query: 103 FLRIKIYDLLEAH 115
                +   +  H
Sbjct: 69  LKFTMVSQKISHH 81

>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 = 50.2 bits (120), Expect = 2e-08
 Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 6/73 (8%)

Query: 43  SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKS 102
              L   L           +R  +   + +Y+  +KL    +++ V+ D+ L  +F  + 
Sbjct: 15  DPRLARLLG------IHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQR 68

Query: 103 FLRIKIYDLLEAH 115
               +I   L A 
Sbjct: 69  MKFSEIPQRLHAL 81

>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 = 46.0 bits (108), Expect = 1e-05
 Identities = 44/291 (15%), Positives = 86/291 (29%), Gaps = 90/291 (30%)

Query: 32  RSKKV--KFDG---WGSI-------PLIEFLQSLGKDTTQQ-ISRYDVTDIINKYVNE-- 76
            S KV  K D    W ++        ++E LQ L         SR D +  I   ++   
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231

Query: 77  ---NKLVHSVKKKRV------VSDERLLSLFGKKSFLRI-------KIYDLLEAHYAENQ 120
               +L+ S   +        V + +  + F      +I       ++ D L A    + 
Sbjct: 232 AELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC--KILLTTRFKQVTDFLSAATTTHI 289

Query: 121 FESDDDFLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLV 180
                    + DE  +L      K      + L  E          P        + S++
Sbjct: 290 SLDHHSMTLTPDEVKSLLL----KYLDCRPQDLPREVLT-----TNP-------RRLSII 333

Query: 181 QDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEIL---- 236
            + ++D                +  +++   N  +L  +I         + S  +L    
Sbjct: 334 AESIRDG--------------LATWDNWKHVNCDKLTTII---------ESSLNVLEPAE 370

Query: 237 -------LKVSNFVKDIRI--ATLSD--DNFSEEECED-LRQRVKDGLLKR 275
                  L V  F     I    LS    +  + +    + +  K  L+++
Sbjct: 371 YRKMFDRLSV--FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK 419

>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 = 42.1 bits (98), Expect = 2e-04
 Identities = 49/329 (14%), Positives = 108/329 (32%), Gaps = 95/329 (28%)

Query: 46  LIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGK----- 100
           L  F  +   +        DV D+    +++ ++ H +  K  V     L LF       
Sbjct: 22  LSVFEDAFVDN----FDCKDVQDMPKSILSKEEIDHIIMSKDAV--SGTLRLFWTLLSKQ 75

Query: 101 ----KSFLRIKI---YD-LLEAHYAENQFESDDDFLFSSDEENNLFS-----SEKQKSRK 147
               + F+   +   Y  L+     E +  S    ++   + + L++     ++   SR 
Sbjct: 76  EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIE-QRDRLYNDNQVFAKYNVSRL 134

Query: 148 VPLKKL--CLE--TP-------------KSCWAAIVPDNIKLV--------YL---KRSL 179
            P  KL   L    P             K+  A  V  + K+         +L     + 
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNS 194

Query: 180 VQDLLKDSETFECKVVGSFV-RVKSDPNDYLQKNS--HQLLQVIGTKKVPGT----DD-K 231
            + +L+  +    ++  ++  R     N  L+ +S   +L +++ +K          + +
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254

Query: 232 STE----------ILL-----KVSNFVKDIRIATLS----DDNFSEEE------------ 260
           + +          ILL     +V++F+       +S        + +E            
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314

Query: 261 CEDLRQRVKDGLLKRPTVVSSLLLFMRNY 289
            +DL + V       P  +S +   +R+ 
Sbjct: 315 PQDLPREVLTTN---PRRLSIIAESIRDG 340

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	298
2bze_A	153	KIAA0252 protein; human RTF1 PLUS3 domain, transcr	100.0
3u1u_A	137	RNA polymerase-associated protein RTF1 homolog; pl	100.0
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	100.0
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	99.92
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	99.91
3dac_M	130	MDM4 protein; MDMX, MDM4, HDMX, HDM4, MDM-4, MDM-X	96.38
1z1m_A	119	Ubiquitin-protein ligase E3 MDM2; peptide-binding	96.17
3fea_A	100	MDM4 protein; HDMX, HDM4,human MDM4, human MDMX, p	95.72
1ycq_A	107	MDM2, MDM2; anti-oncogene, DNA-binding, transcript	95.62
2axi_A	115	Ubiquitin-protein ligase E3 MDM2; drug design, pro	94.87
2z5s_M	140	MDM4 protein, zebrafish MDMX; MDMX, MDM4, acetylat	94.79

>2bze_A KIAA0252 protein; human RTF1 PLUS3 domain, transcription, elongation, PAF1 complex, histone H3 methylation, H2B ubiquitination, CDC73, LEO1, CTR9; NMR {Homo sapiens} SCOP: b.34.21.1

Probab=100.00  E-value=1e-35  Score=256.18  Aligned_cols=130  Identities=17%  Similarity=0.210  Sum_probs=118.5

Q ss_pred             cccccccccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCcCccceeEEEEEeeeecCCC---CCcccceE
Q 022354          160 SCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGT---DDKSTEIL  236 (298)
Q Consensus       160 ~~~aai~~~ninlIyL~Rslve~ll~~p~~F~~kVvG~FVRIki~~~~~~~k~~YRlvqV~gv~~~~e~---g~~~Tni~  236 (298)
                      ..+++ +.+||++|||+|++|++||+.| .|+++|+||||||+||++++  +++||||||+||.++++.   |++.||++
T Consensus        19 ~~~v~-~l~di~~irL~Rs~l~~~~~~P-~Fe~~V~GcFVRV~ig~~~~--~~~YRl~qI~gv~~~~k~Y~l~~~~T~~~   94 (153)
T 2bze_A           19 SHMVS-LPEELNRVRLSRHKLERWCHMP-FFAKTVTGCFVRIGIGNHNS--KPVYRVAEITGVVETAKVYQLGGTRTNKG   94 (153)
T ss_dssp             CSBCC-CHHHHHHSEECHHHHHHHSSSS-SCHHHHTTCEEEEESSTTSS--SCCEEEEEEEEEEEEEEEEEETTEEEEEE
T ss_pred             CCCcC-CHHHhhheEEEHHHHHHHhcCC-chhHheEEEEEEEEeCCCCC--CccEEEEEEEeEEecCcccccCCcccceE
Confidence            33444 7889999999999999999999 89999999999999998654  589999999999998774   89999999


Q ss_pred             EEeeCC--ceeeEeecccCCCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHhhhhcc
Q 022354          237 LKVSNF--VKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFC  293 (298)
Q Consensus       237 L~v~~~--~k~~~I~~iSn~dFTeeEc~rl~q~~~~g~~~rpTv~di~~~~~~~~~~~~  293 (298)
                      |.|++.  .++|+|++|||++|||+||++|++.|+++++++||+.+|++|..+++.+++
T Consensus        95 L~l~~g~~~r~~~m~~vSN~~fte~Ef~~w~~~~~~~~~~~PT~~~v~~K~~~i~~a~n  153 (153)
T 2bze_A           95 LQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEALN  153 (153)
T ss_dssp             EEEESSSCEEEECGGGBCCSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHHHHHC-
T ss_pred             EEEEECCcceEEEeeEeeCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence            999973  468999999999999999999999999999999999999999999998764

>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3, transcription elongation, structural genomics, struc genomics consortium, SGC; 1.80A {Homo sapiens} PDB: 2db9_A

Probab=100.00  E-value=1.5e-35  Score=250.65  Aligned_cols=127  Identities=17%  Similarity=0.209  Sum_probs=114.3

Q ss_pred             cccccccccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCcCccceeEEEEEeeeecCCC---CCcccceE
Q 022354          160 SCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGT---DDKSTEIL  236 (298)
Q Consensus       160 ~~~aai~~~ninlIyL~Rslve~ll~~p~~F~~kVvG~FVRIki~~~~~~~k~~YRlvqV~gv~~~~e~---g~~~Tni~  236 (298)
                      ..+.+ +.+||++|||+|++|++||++| +|+++|+||||||+||+++  ++++|||+||+||.++++.   |++.||++
T Consensus         5 ~~~v~-~l~dl~~i~L~R~~l~~~~~~P-~Fe~~V~GcFVRv~ig~~~--~~~~Yrl~qI~gv~~~~k~Y~l~~~~T~~~   80 (137)
T 3u1u_A            5 SQPVS-LPEELNRVRLSRHKLERWCHMP-FFAKTVTGCFVRIGIGNHN--SKPVYRVAEITGVVETAKVYQLGGTRTNKG   80 (137)
T ss_dssp             TSBCC-SHHHHHTTBCCHHHHHHHTTST-THHHHHTTCEEEEEEEC------CEEEEEEEEEEEEEEEEEEETTEEEEEE
T ss_pred             cCCCC-CHHHhcceEEEHHHHHHHhcCC-ChhHheEEEEEEEEeCCCC--CCccEEEEEEEEEEecCcccccCCceeeEE
Confidence            45566 8899999999999999999999 9999999999999999987  3589999999999987764   88999999


Q ss_pred             EEeeCC--ceeeEeecccCCCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHhhh
Q 022354          237 LKVSNF--VKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYS  290 (298)
Q Consensus       237 L~v~~~--~k~~~I~~iSn~dFTeeEc~rl~q~~~~g~~~rpTv~di~~~~~~~~~  290 (298)
                      |.|++.  .++|+|++|||++|||+||++|++.|+++++++||+.+|++|+..+..
T Consensus        81 L~l~~g~~~r~~~~~~vSN~~fte~E~~~w~~~~~~~~~~~Pt~~~l~~K~~~i~~  136 (137)
T 3u1u_A           81 LQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKE  136 (137)
T ss_dssp             EEEEETTEEEEEEGGGBCSSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHTCC
T ss_pred             EEEEeCCcceEEEeeeecCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhh
Confidence            999973  468999999999999999999999999999999999999999998753

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

Probab=100.00  E-value=2.3e-34  Score=233.32  Aligned_cols=93  Identities=54%  Similarity=0.922  Sum_probs=88.6

Q ss_pred             CCCcccccCCCCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHH
Q 022354           32 RSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDL  111 (298)
Q Consensus        32 ~~k~~~~~~w~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~kl  111 (298)
                      .+|+.+|+||+|++|++||++||.+|++++||++|++.||+|||+||||||.+||.|+||++|++|||+++|.||+|+++
T Consensus         6 ~~~~~~~~~w~S~eLa~fl~~iG~~~~~~~sR~eVvk~lW~YIK~nnLQdp~~Kr~I~cD~kLk~lFg~~~v~~~~m~kl   85 (101)
T 1v32_A            6 SGKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDL   85 (101)
T ss_dssp             CSSCCSSSSSSCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCTTEEECCSHHHHHTCCSEEETTHHHHH
T ss_pred             CCCcceecccCCHHHHHHHHHcCCCCccccCHHHHHHHHHHHHHhhcCcCcccCCeeeccHHHHHHHCCCcccHHHHHHH
Confidence            36788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccCCCCCC
Q 022354          112 LEAHYAENQFESD  124 (298)
Q Consensus       112 L~~H~~~~~~~~~  124 (298)
                      |++||.++++.+.
T Consensus        86 L~~Hl~~~~e~~~   98 (101)
T 1v32_A           86 LEKHYKENQDSGP   98 (101)
T ss_dssp             HHHHSCSCCCCCS
T ss_pred             HHHHcCcccccCC
Confidence            9999999876543

>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=99.92  E-value=9.8e-26  Score=179.66  Aligned_cols=75  Identities=19%  Similarity=0.212  Sum_probs=71.9

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhccccCCC
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~~~~~  121 (298)
                      .|++|++|||      ..++||++|++.||+|||+||||||.+|+.|+||++|+.|||+++|.||+|+++|++|+.+.++
T Consensus        14 lS~~La~~lG------~~~~sr~evvk~lW~YIK~n~Lqdp~~k~~I~cD~~L~~lfg~~~v~~~~~~klL~~Hl~p~~P   87 (93)
T 1v31_A           14 LSTALMDVLG------IEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEKLKFTMVSQKISHHLSPPPP   87 (93)
T ss_dssp             CCHHHHHHSC------CSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHSCSSEEETTTTHHHHHHHCBCCCC
T ss_pred             cCHHHHHHHC------CCccCHHHHHHHHHHHHHHccCcCcccCceeehhHHHHHHhCCCcccHHHHHHHHHHhcCCCCC
Confidence            8999999997      6789999999999999999999999999999999999999999999999999999999998876


Q ss_pred             C
Q 022354          122 E  122 (298)
Q Consensus       122 ~  122 (298)
                      .
T Consensus        88 i   88 (93)
T 1v31_A           88 S   88 (93)
T ss_dssp             S
T ss_pred             e
Confidence            4

>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=99.91  E-value=1.4e-25  Score=178.80  Aligned_cols=75  Identities=17%  Similarity=0.185  Sum_probs=71.9

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhccccCCC
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~~~~~  121 (298)
                      .|++|++|||      ..++||++|++.||+|||+||||||.+|+.|+||++|+.|||+++|.||+|+++|++|+.+.++
T Consensus        14 lS~~La~~lG------~~~~sr~evvk~lW~YIK~n~Lqdp~~k~~I~cD~~Lk~lfg~~~v~~~~~~klL~~Hl~p~~P   87 (93)
T 1uhr_A           14 LDPRLARLLG------IHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSEIPQRLHALLMPPEP   87 (93)
T ss_dssp             ECTTHHHHTC------CSEEEHHHHHHHHHHHHHHTTCBCSSCSSEECCCTTHHHHTCCSSEEGGGSHHHHHHHEECSSC
T ss_pred             cCHHHHHHHC------CCccCHHHHHHHHHHHHHhccCCCccccceeechHHHHHHhCCCcccHHHHHHHHHHhcCCCCC
Confidence            6999999997      6799999999999999999999999999999999999999999999999999999999998876


Q ss_pred             C
Q 022354          122 E  122 (298)
Q Consensus       122 ~  122 (298)
                      .
T Consensus        88 I   88 (93)
T 1uhr_A           88 S   88 (93)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=96.38  E-value=0.0053  Score=51.41  Aligned_cols=77  Identities=18%  Similarity=0.316  Sum_probs=67.5

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccc-hhhhhhhCCCccchHH---HHHHHHhccc
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSD-ERLLSLFGKKSFLRIK---IYDLLEAHYA  117 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCD-ekL~~LFgk~~v~~f~---m~klL~~H~~  117 (298)
                      .-++|..+|.+.|.. ...++..+|.-.+=.||-.+.|.||.+...|.|- +.|-.+||++++.+-+   +..+|.+++.
T Consensus        27 pk~~lL~iLq~aGA~-~dvfT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~llGv~sFSVkdp~~L~~mL~~NLv  105 (130)
T 3dac_M           27 PRAPLLQILKVAGAQ-EEVFTVKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELLEVGSFSVKNPSPLYEMLKRNLV  105 (130)
T ss_dssp             ECHHHHHHHHHTTCC-CSSEEHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTSSEEETTSCHHHHHHHHHHEE
T ss_pred             CcHHHHHHHHHhccC-cceeehHHHHHHHHHhhhhhhccCccccceeEeCCcccccccCCcceeecCcHHHHHHHHhhee
Confidence            357899999988864 5578999999999999999999999999999995 5567899999999987   9999999988


Q ss_pred             cC
Q 022354          118 EN  119 (298)
Q Consensus       118 ~~  119 (298)
                      .-
T Consensus       106 ~~  107 (130)
T 3dac_M          106 IL  107 (130)
T ss_dssp             EC
T ss_pred             cc
Confidence            63

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

Probab=96.17  E-value=0.013  Score=48.41  Aligned_cols=76  Identities=20%  Similarity=0.279  Sum_probs=64.4

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccch-hhhhhhCCCccchHHHHHHHHhcccc
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE-RLLSLFGKKSFLRIKIYDLLEAHYAE  118 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDe-kL~~LFgk~~v~~f~m~klL~~H~~~  118 (298)
                      ..++|..+|...|... ...+..+|.-.+-.||=.+.|.||.+...|.|.. .|-.|||..++.+-+-..+...|...
T Consensus        30 Pk~~LLkiLq~aGA~~-~vfT~keV~~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml~~n  106 (119)
T 1z1m_A           30 PKPLLLKLLKSVGAQK-DTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRN  106 (119)
T ss_dssp             CSTTSHHHHHHHTCCC-SCCCTTHHHHHHHHHHHTTTCSCSSSSCEECCTTSHHHHHSCCSCEETTCHHHHHHHHSCS
T ss_pred             ccHHHHHHHHHhcccc-ceeechheeehhhhhhhHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHHh
Confidence            3468999999888754 6789999999999999999999999999999964 55799999999988777777666553

>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=95.72  E-value=0.014  Score=46.97  Aligned_cols=75  Identities=21%  Similarity=0.419  Sum_probs=64.9

Q ss_pred             CHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccch-hhhhhhCCCccchH---HHHHHHHhcccc
Q 022354           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE-RLLSLFGKKSFLRI---KIYDLLEAHYAE  118 (298)
Q Consensus        43 S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDe-kL~~LFgk~~v~~f---~m~klL~~H~~~  118 (298)
                      -++|..+|.+.|.. ...++..+|.-.+=.||-.+.|.||.+...|.|.. .|-.+||++++.+-   .+..+|..|+..
T Consensus        19 k~~lL~iLq~aGA~-~d~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~G~~sFsvkdp~~l~~ml~~nLv~   97 (100)
T 3fea_A           19 KLPLLKILHAAGAQ-GEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVT   97 (100)
T ss_dssp             CHHHHHHHHHTTCC-SSCBCHHHHHHHHHHHHHHTTCEETTEEEEEECTTSHHHHHHTCSEEETTCCHHHHHHHHHHEEC
T ss_pred             cHHHHHHHHHhccC-cceeehHHHHHHHHHhhhhhhccCccccceEEeCCCccccccCCcceeecCchHHHHHHHhhcee
Confidence            46899999988864 55789999999999999999999999999999964 56689999999887   788889888763

>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=95.62  E-value=0.024  Score=46.09  Aligned_cols=72  Identities=19%  Similarity=0.264  Sum_probs=61.0

Q ss_pred             CHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccch-hhhhhhCCCccchHHHHHHHHhc
Q 022354           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE-RLLSLFGKKSFLRIKIYDLLEAH  115 (298)
Q Consensus        43 S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDe-kL~~LFgk~~v~~f~m~klL~~H  115 (298)
                      .++|..+|...|... ...+..+|+-.+-.||=.+.|.||.+...|.|.. .|-.|||..++.+-+-..+...|
T Consensus        15 k~~LLklL~~~GA~~-~~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml   87 (107)
T 1ycq_A           15 TPLLLSLLKSAGAQK-ETFTMKEVIYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEPRRLYAMI   87 (107)
T ss_dssp             CHHHHHHHHHTTCCC-SCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTCSEEETTCHHHHHHHH
T ss_pred             cHHHHHHHHHhcccc-ceeeehhhhhhHHHHHhHHhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHH
Confidence            468999999988754 6789999999999999999999999999999965 55799999999888665444444

>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=94.87  E-value=0.024  Score=46.60  Aligned_cols=73  Identities=21%  Similarity=0.296  Sum_probs=61.5

Q ss_pred             CHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccch-hhhhhhCCCccchHHHHHHHHhcc
Q 022354           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE-RLLSLFGKKSFLRIKIYDLLEAHY  116 (298)
Q Consensus        43 S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDe-kL~~LFgk~~v~~f~m~klL~~H~  116 (298)
                      .++|..+|...|... ...+..+|+-.+-.||=.+.|.||.+...|.|.. .|-.|||..++.+-+-..+...|.
T Consensus        15 k~~LLklLq~~GA~~-~vfT~keVm~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml~   88 (115)
T 2axi_A           15 KPLLLKLLKSVGAQK-DTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIY   88 (115)
T ss_dssp             CHHHHHHHHHTTCCC-SCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHHSSSEEETTCHHHHHHHHH
T ss_pred             cHHHHHHHHHhcccc-ceeechhheehhhhhhhHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHH
Confidence            468999999988754 6789999999999999999999999999999964 557999999998886555555443

>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=94.79  E-value=0.039  Score=46.58  Aligned_cols=75  Identities=19%  Similarity=0.316  Sum_probs=61.6

Q ss_pred             CHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccch-hhhhhhCCCccchHHH---HHHHHhcccc
Q 022354           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE-RLLSLFGKKSFLRIKI---YDLLEAHYAE  118 (298)
Q Consensus        43 S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDe-kL~~LFgk~~v~~f~m---~klL~~H~~~  118 (298)
                      -++|..+|..-|. ....++.-+|.-.|-.||=.+.|.||.+...|.|.. .|-.|||..++.+-+-   .++|.+-+..
T Consensus        27 k~~LLkiLq~aGA-~~~~fT~keVm~YLGqYIm~KqLYD~~~qhiV~C~~D~LG~l~Gv~sFSVKdp~~ly~ML~~NLv~  105 (140)
T 2z5s_M           27 RAPLLQILKVAGA-QEEVFTLKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELLEVGSFSVKNPSPVYEMLKRNLVI  105 (140)
T ss_dssp             CHHHHHHHHHTTC-CCSCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTSSEEETTBCHHHHHHHHHHEEC
T ss_pred             cHHHHHHHHHhCc-ccceeeHHHHHHHHHHHHHHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHHhccc
Confidence            3689999998775 355789999999999999999999999999999964 5579999999988754   4555555443

---

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	298
d1v32a_	101	a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl	3e-23
d2bzea1	132	b.34.21.1 (A:345-476) RNA polymerase-associated pr	3e-23
d1uhra_	93	a.42.1.1 (A:) SWI/SNF related regulator of chromat	9e-09
d1v31a_	93	a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl	1e-08

>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 = 89.5 bits (222), Expect = 3e-23
 Identities = 50/92 (54%), Positives = 66/92 (71%)

Query: 33  SKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE 92
            K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I KY+++  L+    KK+VV D+
Sbjct: 7   GKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDK 66

Query: 93  RLLSLFGKKSFLRIKIYDLLEAHYAENQFESD 124
           RL+ LFG ++  R+K+YDLLE HY ENQ    
Sbjct: 67  RLVLLFGTRTIFRMKVYDLLEKHYKENQDSGP 98

>d2bzea1 b.34.21.1 (A:345-476) RNA polymerase-associated protein RTF1 homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 132

class: All beta proteins
fold: SH3-like barrel
superfamily: Plus3-like
family: Plus3
domain: RNA polymerase-associated protein RTF1 homolog
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 90.6 bits (225), Expect = 3e-23
 Identities = 22/118 (18%), Positives = 48/118 (40%), Gaps = 8/118 (6%)

Query: 167 PDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVP 226
           P+ +  V L R  ++        F   V G FVR+    ++   K  +++ ++ G  +  
Sbjct: 4   PEELNRVRLSRHKLERWC-HMPFFAKTVTGCFVRIGIGNHN--SKPVYRVAEITGVVETA 60

Query: 227 GT---DDKSTEILLKVS--NFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVV 279
                    T   L++   N  +  R+  +S+  F+E E    ++ +    ++ PT+ 
Sbjct: 61  KVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLD 118

>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 = 49.7 bits (119), Expect = 9e-09
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 43  SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKS 102
              L   L   G  T    +R  +   + +Y+  +KL    +++ V+ D+ L  +F  + 
Sbjct: 15  DPRLARLL---GIHT---QTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQR 68

Query: 103 FLRIKIYDLLEAHY 116
               +I   L A  
Sbjct: 69  MKFSEIPQRLHALL 82

>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 = 49.4 bits (118), Expect = 1e-08
 Identities = 14/73 (19%), Positives = 25/73 (34%), Gaps = 6/73 (8%)

Query: 43  SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKS 102
           S  L++ L        +  +R  +   I  YV   KL +         D  L  +FG++ 
Sbjct: 15  STALMDVLG------IEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEK 68

Query: 103 FLRIKIYDLLEAH 115
                +   +  H
Sbjct: 69  LKFTMVSQKISHH 81

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	298
d2bzea1	132	RNA polymerase-associated protein RTF1 homolog {Hu	100.0
d1v32a_	101	Hypothetical protein AT5G08430 (rafl09-47-k03) {Th	99.97
d1uhra_	93	SWI/SNF related regulator of chromatin (BRG1-assoc	99.9
d1v31a_	93	Hypothetical protein AT5G14170 (rafl11-05-p19) {Th	99.9
d2axia1	85	MDM2 {Human (Homo sapiens) [TaxId: 9606]}	97.28
d1ttva_	107	MDM2 {African clawed frog (Xenopus laevis) [TaxId:	97.23

>d2bzea1 b.34.21.1 (A:345-476) RNA polymerase-associated protein RTF1 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Plus3-like
family: Plus3
domain: RNA polymerase-associated protein RTF1 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.4e-36  Score=250.92  Aligned_cols=125  Identities=17%  Similarity=0.217  Sum_probs=116.2

Q ss_pred             cccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCcCccceeEEEEEeeeecCCC---CCcccceEEEeeC-
Q 022354          166 VPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGT---DDKSTEILLKVSN-  241 (298)
Q Consensus       166 ~~~ninlIyL~Rslve~ll~~p~~F~~kVvG~FVRIki~~~~~~~k~~YRlvqV~gv~~~~e~---g~~~Tni~L~v~~-  241 (298)
                      ++++|++|+|+|+.|++||++| .|+++|+||||||+||++++  +++|||+||+||.++++.   |+++||++|.|.+ 
T Consensus         3 ~~e~l~~irL~R~~l~~~~~~P-~Fe~~v~GcFVRv~ig~~~~--~~~Yrl~~I~gv~~~~k~Y~~~~~~T~~~L~l~~g   79 (132)
T d2bzea1           3 LPEELNRVRLSRHKLERWCHMP-FFAKTVTGCFVRIGIGNHNS--KPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHG   79 (132)
T ss_dssp             CHHHHHHSEECHHHHHHHSSSS-SCHHHHTTCEEEEESSTTSS--SCCEEEEEEEEEEEEEEEEEETTEEEEEEEEEESS
T ss_pred             ChHHhhheEEeHHHHHHHHcCC-chHHhheeeEEEEEeCCCCC--CCceEEEEEEeeeecCcccccCCCcccEEEEEEEC
Confidence            6899999999999999999999 89999999999999997654  589999999999987764   8999999999996 


Q ss_pred             -CceeeEeecccCCCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHhhhhcc
Q 022354          242 -FVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVSSLLLFMRNYSLFC  293 (298)
Q Consensus       242 -~~k~~~I~~iSn~dFTeeEc~rl~q~~~~g~~~rpTv~di~~~~~~~~~~~~  293 (298)
                       ..++|+|++|||++|||+||++|++.|++++.++||+.+|++|..+++..+|
T Consensus        80 ~~~~~~~l~~vSn~~fte~E~~~w~~~~~~~~~~~Pt~~~l~~K~~~i~~a~n  132 (132)
T d2bzea1          80 NDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEALN  132 (132)
T ss_dssp             SCEEEECGGGBCCSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHHHHHC-
T ss_pred             CceeEEEeEEEeCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence             3468999999999999999999999999999999999999999999998764

>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=99.97  E-value=8.8e-33  Score=222.14  Aligned_cols=90  Identities=56%  Similarity=0.955  Sum_probs=86.2

Q ss_pred             CCcccccCCCCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHH
Q 022354           33 SKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLL  112 (298)
Q Consensus        33 ~k~~~~~~w~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL  112 (298)
                      .|+.+|+||+|+||++||++||.|+.+++||++|++.||+|||+||||||.+||.|+||++|+.|||+++|++|+|+++|
T Consensus         7 ~k~~~~~g~~S~eL~~FL~~~g~~~~~~~sR~eVtk~iw~YIK~nnLqdp~nkr~I~~D~~L~~Lfg~~~v~~f~i~k~l   86 (101)
T d1v32a_           7 GKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLFGTRTIFRMKVYDLL   86 (101)
T ss_dssp             SSCCSSSSSSCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCTTEEECCSHHHHHTCCSEEETTHHHHHH
T ss_pred             CCcccccCcCCHHHHHHHHhcCCCCcccCCHHHHHHHHHHHHHHhcCCCCccCCEEccCHHHHHHhCCCcccHHHHHHHH
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccccCCCC
Q 022354          113 EAHYAENQFE  122 (298)
Q Consensus       113 ~~H~~~~~~~  122 (298)
                      .+||.++++.
T Consensus        87 ~~H~~~~~~~   96 (101)
T d1v32a_          87 EKHYKENQDS   96 (101)
T ss_dssp             HHHSCSCCCC
T ss_pred             HHHcCCcccc
Confidence            9999998753

>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=99.90  E-value=5.7e-25  Score=173.76  Aligned_cols=74  Identities=18%  Similarity=0.187  Sum_probs=71.0

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHhccccCCC
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~H~~~~~~  121 (298)
                      .|++|++|||      ..++||++|++.||+|||+||||||+|||.|+||++|+.|||+++|.+|+|+++|.+||.+.++
T Consensus        14 lS~~La~~lg------~~~~sR~~v~k~iw~YIk~n~Lqdp~nkr~I~cD~~L~~lfg~~~v~~~~l~~~L~~Hl~p~eP   87 (93)
T d1uhra_          14 LDPRLARLLG------IHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSEIPQRLHALLMPPEP   87 (93)
T ss_dssp             ECTTHHHHTC------CSEEEHHHHHHHHHHHHHHTTCBCSSCSSEECCCTTHHHHTCCSSEEGGGSHHHHHHHEECSSC
T ss_pred             CCHHHHHHHC------CCCcCHHHHHHHHHHHHHHhcCCCCCCCCEEecCHHHHHHhCCCeecHHHHHHHHHhhCCCCCC
Confidence            7999999996      5689999999999999999999999999999999999999999999999999999999998765

>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=99.90  E-value=7.7e-25  Score=172.78  Aligned_cols=81  Identities=19%  Similarity=0.153  Sum_probs=73.7

Q ss_pred             cccccCCCCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCcccccchhhhhhhCCCccchHHHHHHHHh
Q 022354           35 KVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEA  114 (298)
Q Consensus        35 ~~~~~~w~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiCDekL~~LFgk~~v~~f~m~klL~~  114 (298)
                      +....--.|++|++|||      ..++||++|++.||+|||+||||||+||+.|+||++|+.|||+++|.|++|+++|.+
T Consensus         7 G~~~~~~lS~~La~~lg------~~~~sR~~v~k~iw~YIk~n~Lqd~~nkr~I~~D~~L~~lfg~~~v~~~~l~~~L~~   80 (93)
T d1v31a_           7 GVPEKFKLSTALMDVLG------IEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEKLKFTMVSQKISH   80 (93)
T ss_dssp             SSCCCEECCHHHHHHSC------CSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHSCSSEEETTTTHHHHHH
T ss_pred             CCcCCccCCHHHHHHHC------cCcCcHHHHHHHHHHHHHHhCCCCCCCCCEEecCHHHHHHhCCCcccHHHHHHHHHH
Confidence            33333347999999997      568999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCC
Q 022354          115 HYAENQF  121 (298)
Q Consensus       115 H~~~~~~  121 (298)
                      |+.+.++
T Consensus        81 Hl~p~~P   87 (93)
T d1v31a_          81 HLSPPPP   87 (93)
T ss_dssp             HCBCCCC
T ss_pred             hCCCCCC
Confidence            9998765

>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=97.28  E-value=0.0001  Score=55.80  Aligned_cols=74  Identities=22%  Similarity=0.354  Sum_probs=64.1

Q ss_pred             CHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCccccc-chhhhhhhCCCccchHH---HHHHHHhccc
Q 022354           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVS-DERLLSLFGKKSFLRIK---IYDLLEAHYA  117 (298)
Q Consensus        43 S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiC-DekL~~LFgk~~v~~f~---m~klL~~H~~  117 (298)
                      .|+|..+|.+-|- .....+.-+|+-.|-.||-...|.||++.+.|.| |+.|-.+||.+++..-+   +..+|.+|+.
T Consensus         7 kp~Ll~~L~~~GA-~~~~fT~kqVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~l~gv~sFsVk~~r~l~~ml~rnLv   84 (85)
T d2axia1           7 KPLLLKLLKSVGA-QKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLV   84 (85)
T ss_dssp             CHHHHHHHHHTTC-CCSCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHHSSSEEETTCHHHHHHHHHTTEE
T ss_pred             cHHHHHHHHHcCC-CcceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhcCCCceeecCcHHHHHHHHhccc
Confidence            5789999987664 4567899999999999999999999999999999 45588999999988876   8888888763

>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=97.23  E-value=0.00027  Score=55.42  Aligned_cols=76  Identities=20%  Similarity=0.347  Sum_probs=66.2

Q ss_pred             CCHHHHHHHHhcCCCCCCccCHHHHHHHHHHHHHhcCCCCCcCCccccc-chhhhhhhCCCccchHH---HHHHHHhccc
Q 022354           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVS-DERLLSLFGKKSFLRIK---IYDLLEAHYA  117 (298)
Q Consensus        42 ~S~eL~efl~~~g~~~~~~lsr~~Vvk~lW~YIK~nnLqDP~~Kr~IiC-DekL~~LFgk~~v~~f~---m~klL~~H~~  117 (298)
                      ..++|..+|.+-|- .....+.-+|+-.|-.||-.+.|.||.+.+.|.| ++.|-.|||..++..-+   +..+|.+|+.
T Consensus        14 Pkp~LL~~L~~~GA-~~~~fT~keVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~llgv~sFsVke~r~l~~ml~rnLv   92 (107)
T d1ttva_          14 PTPLLLSLLKSAGA-QKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLV   92 (107)
T ss_dssp             ECHHHHHHHHHTTC-CSSCBCHHHHHHHHHHHHHHHTCBCSSCTTEECCSSCHHHHHHTCSCEETTCHHHHHHHHHTTEE
T ss_pred             CCHHHHHHHHHcCC-CcceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhcCCCceeecCcHHHHHHHHhhhh
Confidence            35899999987775 4567899999999999999999999999999999 55688999999988876   7888999986


Q ss_pred             c
Q 022354          118 E  118 (298)
Q Consensus       118 ~  118 (298)
                      .
T Consensus        93 ~   93 (107)
T d1ttva_          93 S   93 (107)
T ss_dssp             E
T ss_pred             c
Confidence            5