Citrus Sinensis ID: 020764

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-
Protein Sequence
MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKGMAQRTP
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcccccccccccccccHHHHHHHccccccHHHHHHHHHHHccccccccccccccccHHHcccccHHHHHHccccccccccccccccccccccccccHHHccHHHHHHHHHcccccccEEEEEEEEEEEccccccccccEEEEEEEEEEEccccccccccEEEEEEcccccEEEEEcccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEEccccccccccccccccccccccEEEccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccccccccEEEEcHHHHHHHccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHcHHHHHHHHHHHHHHHcccHHcccEEEEEEEEEEccccccccccEEEEEEEEEEEcccccccccEEEEEEEcccccccEcEEccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
mgskadqesflwvpeydeplspqltnlkrrgrskkvkfdgwgsipLIEFLQSlgkdttqqisRYDVTDIINKYVNENKLVHSVkkkrvvsderllslfgkksfLRIKIYDLLEAHyaenqfesdddflfssdeennlfssekqksrkvplkklcletpkscwaaivpdniKLVYLKRSLVQDLLKDSETFECKVVGSfvrvksdpndylqknSHQLLQVIgtkkvpgtddksTEILLKVSNFVKDIRIatlsddnfseeECEDLRQRVKDgllkrptvvELQEKTQILHEDITKHWLVRELALLQKLIDRANvkgmaqrtp
Flexible Loop (DISEMBL)
mgskadqesflwvpeydeplspqltnlkrrgrskkvkfdgwgsiPLIEFLQSLGKDTTQQISRYDVTDIINKYVnenklvhsvkkkrvvsderllslfgkksflRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLfssekqksrkvplKKLCLetpkscwaaivpdnIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLqvigtkkvpgtddksteILLKVSNFVKDIRIAtlsddnfseeecEDLRQrvkdgllkrptvvelqektqilheditkHWLVRELALLQKLIdranvkgmaqrtp
Low Complexity Region (SEG)
MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQfesdddflfssdeeNNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKGMAQRTP
Disordered region (IsUnstruct)
*********FLWVP********************KVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF****************************LKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNF****C*DLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRA**********
Disordered Region (DISOPRED)
*****************************************GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAEN*********************************************IVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQ****************
Disordered Region (DISEMBL)
MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANV********
Disordered Region (DISPRO)
******QESFLWVPEYDEPLSPQLTNL******KKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAEN**************************************PKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVK*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGSKADQESFLWVPEYDEPLSPQLTNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKGMAQRTP
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	321	2.2.26 [Sep-21-2011]
Q9FT92	553	Uncharacterized protein A	yes	no	0.869	0.504	0.583	4e-89
Q9SIV5	1773	Zinc finger CCCH domain-c	no	no	0.859	0.155	0.300	8e-25
Q9SD34	1292	Zinc finger CCCH domain-c	no	no	0.819	0.203	0.302	4e-22

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

 Score =  328 bits (840), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 168/288 (58%), Positives = 218/288 (75%), Gaps = 9/288 (3%)

Query: 28  KRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKR 87
           KR+ R K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I KY+++  L+    KK+
Sbjct: 19  KRKARPKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKK 78

Query: 88  VVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLFSSEKQKSRK 147
           VV D+RL+ LFG ++  R+K+YDLLE HY ENQ +SD DFL+  DE   +  SEK   R 
Sbjct: 79  VVCDKRLVLLFGTRTIFRMKVYDLLEKHYKENQDDSDFDFLY-EDEPQIICHSEKIAKRT 137

Query: 148 VPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPND 207
             + K     P+  +AAIV DNIKL+YL++SLVQ+LLK  +TFE K++GSFVR+KSDPND
Sbjct: 138 SKVVK----KPRGTFAAIVSDNIKLLYLRKSLVQELLKSPDTFEGKMLGSFVRIKSDPND 193

Query: 208 YLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQR 267
           YLQK  +QL+QV G KK  GTDD     LL+V+N+VKD+ I+ LSDDNFS+EECEDL QR
Sbjct: 194 YLQKYPYQLVQVTGVKKEHGTDD----FLLQVTNYVKDVSISVLSDDNFSQEECEDLHQR 249

Query: 268 VKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKG 315
           +K+GLLK+PT+VE++EK + LH+D TKHWL RE+ LL++LIDRAN KG
Sbjct: 250 IKNGLLKKPTIVEMEEKAKKLHKDQTKHWLGREIELLKRLIDRANEKG 297

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 =  114 bits (286), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 91/303 (30%), Positives = 157/303 (51%), Gaps = 27/303 (8%)

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  EECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKGMAQ 318
            +EC+ L+Q +K GL+ R TV ++QEK   L E   K+ L  E+     L DRA+  G  +
Sbjct: 1042 DECKRLKQSIKCGLINRLTVGDIQEKAIALQEVRVKNLLEAEILRFSHLRDRASDMGRRK 1101

Query: 319  RTP 321
              P
Sbjct: 1102 EYP 1104

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 =  105 bits (262), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 89/294 (30%), Positives = 148/294 (50%), Gaps = 31/294 (10%)

Query: 41  WGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGK 100
           W +  L+EF+  +    T  +S++DV  ++  Y+ +  L   ++K +V+ D+ L+ LFGK
Sbjct: 319 WATKELLEFVSFMKNGDTSVLSQFDVQGLLLDYIKKKNLRDPLQKSQVLCDQMLVKLFGK 378

Query: 101 KSFLRIKIYDLLEAHY--------AENQFESDDDFLFSSDEENNLF---------SSEKQ 143
           +     ++  LLE+H         A+         + S  EE+++             ++
Sbjct: 379 QRVGHFEMLKLLESHVLIQEKPKGAKTTNGETTHAVPSQIEEDSVHDPMVRDRRRKMRRK 438

Query: 144 KSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKS 203
              +V  + L        +AAI   NI L+YL+R  ++ LL D    + KVVG+ +R+K 
Sbjct: 439 TDGRVQNENL------DAYAAIDVHNINLIYLRRKFLESLLDDINKVDEKVVGTILRIKV 492

Query: 204 DPNDYLQK-NSHQLLQVIGTKKVPGT---DDKSTEILLKVSNFVKD--IRIATLSDDNFS 257
             +D  QK + H+L+QV+GT K   +     K+T+++L++ N  K   I I  LSD N +
Sbjct: 493 SGSD--QKLDIHRLVQVVGTSKAIASYQLGAKTTDVMLEILNLDKREVISIDQLSDQNIT 550

Query: 258 EEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRA 311
           E+EC+ LRQ +K GL KR TVV++ +    L        L  E+  L  L DRA
Sbjct: 551 EDECKRLRQSIKCGLNKRLTVVDILKTAATLQAMRINEALEAEILKLNHLRDRA 604

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	321
255575782	502	protein binding protein, putative [Ricin	0.906	0.579	0.623	1e-103
449461126	543	PREDICTED: uncharacterized protein At5g0	0.956	0.565	0.578	5e-91
356529380	888	PREDICTED: uncharacterized protein At5g0	0.965	0.349	0.565	7e-91
30682386	553	SWIB/MDM2 and Plus-3 and GYF domain-cont	0.869	0.504	0.583	3e-87
356561784	734	PREDICTED: uncharacterized protein At5g0	0.859	0.376	0.577	7e-87
297806885	539	SWIB complex BAF60b domain-containing pr	0.875	0.521	0.558	2e-84
359480913	477	PREDICTED: uncharacterized protein At5g0	0.906	0.610	0.554	4e-79
449518039	376	PREDICTED: uncharacterized protein At5g0	0.841	0.718	0.568	1e-75
297739485	819	unnamed protein product [Vitis vinifera]	0.922	0.361	0.518	1e-74
359486219	785	PREDICTED: uncharacterized protein At5g0	0.903	0.369	0.525	3e-74

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

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 187/300 (62%), Positives = 244/300 (81%), Gaps = 9/300 (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 SNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVR 299
           SNF+KD+ I+ LSD+NFSEEEC+DLRQR++DGLLKRPT+VEL+EK Q+LHEDITKH+L R
Sbjct: 238 SNFMKDVSISMLSDENFSEEECQDLRQRIRDGLLKRPTLVELEEKVQVLHEDITKHYLER 297

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  340 bits (872), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 181/313 (57%), Positives = 239/313 (76%), Gaps = 6/313 (1%)

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 VKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELA 302
           +KD+ I+ LSD+NFSEEEC+DL  R+K+GL+KR T+ E+Q K ++LH DITKHWL RE++
Sbjct: 241 MKDVSISMLSDENFSEEECKDLDLRIKNGLVKRLTIAEVQRKVEVLHVDITKHWLSREIS 300

Query: 303 LLQKLIDRANVKG 315
           LLQ LID+AN KG
Sbjct: 301 LLQNLIDQANEKG 313

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  340 bits (871), Expect = 7e-91,   Method: Compositional matrix adjust.
 Identities = 181/320 (56%), Positives = 232/320 (72%), Gaps = 10/320 (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 LLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKH 295
            L+VS F+KDIRI  LSDDNFSEEECE+L QRVKDGL+KRP +V++++  ++LHED+ KH
Sbjct: 236 HLQVSGFIKDIRIQMLSDDNFSEEECENLHQRVKDGLVKRPMIVDMEQTARVLHEDMIKH 295

Query: 296 WLVRELALLQKLIDRANVKG 315
           WL RE  LLQ LIDRAN KG
Sbjct: 296 WLAREFILLQNLIDRANEKG 315

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  328 bits (840), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 168/288 (58%), Positives = 218/288 (75%), Gaps = 9/288 (3%)

Query: 28  KRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKR 87
           KR+ R K+ +F GWGS  LIEFL SLGKDT++ ISRYDV+D I KY+++  L+    KK+
Sbjct: 19  KRKARPKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKK 78

Query: 88  VVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDEENNLFSSEKQKSRK 147
           VV D+RL+ LFG ++  R+K+YDLLE HY ENQ +SD DFL+  DE   +  SEK   R 
Sbjct: 79  VVCDKRLVLLFGTRTIFRMKVYDLLEKHYKENQDDSDFDFLY-EDEPQIICHSEKIAKRT 137

Query: 148 VPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPND 207
             + K     P+  +AAIV DNIKL+YL++SLVQ+LLK  +TFE K++GSFVR+KSDPND
Sbjct: 138 SKVVK----KPRGTFAAIVSDNIKLLYLRKSLVQELLKSPDTFEGKMLGSFVRIKSDPND 193

Query: 208 YLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSEEECEDLRQR 267
           YLQK  +QL+QV G KK  GTDD     LL+V+N+VKD+ I+ LSDDNFS+EECEDL QR
Sbjct: 194 YLQKYPYQLVQVTGVKKEHGTDD----FLLQVTNYVKDVSISVLSDDNFSQEECEDLHQR 249

Query: 268 VKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKG 315
           +K+GLLK+PT+VE++EK + LH+D TKHWL RE+ LL++LIDRAN KG
Sbjct: 250 IKNGLLKKPTIVEMEEKAKKLHKDQTKHWLGREIELLKRLIDRANEKG 297

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 =  326 bits (836), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 164/284 (57%), Positives = 212/284 (74%), Gaps = 8/284 (2%)

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 LLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKG 315
           L+KRP +V++++  ++LHED+T+HWL REL LLQ LID+AN KG
Sbjct: 272 LVKRPMIVDMEQTARVLHEDMTRHWLARELILLQNLIDQANEKG 315

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 163/292 (55%), Positives = 215/292 (73%), Gaps = 11/292 (3%)

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 SDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELAL 303
           SDDNFS+EECEDL QR+K+GLLK+PT+VE++EK + LHED TKHWL RE+  
Sbjct: 235 SDDNFSQEECEDLHQRIKNGLLKKPTIVEMEEKARSLHEDQTKHWLGREIVF 286

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  300 bits (769), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 169/305 (55%), Positives = 219/305 (71%), Gaps = 14/305 (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 ILLKVSNFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITK 294
             + VS+F++   ++ L ++NFSEEEC+D +QR+KDGLLKR TVVEL++K Q LHEDITK
Sbjct: 235 --VHVSHFIRTSSLSILVEENFSEEECKDFQQRMKDGLLKRLTVVELKQKAQRLHEDITK 292

Query: 295 HWLVR 299
           H+L R
Sbjct: 293 HYLER 297

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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|297739485|emb|CBI29667.3| unnamed protein product [Vitis vinifera]

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 157/303 (51%), Positives = 213/303 (70%), Gaps = 7/303 (2%)

Query: 25  TNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVK 84
           +++K +    K +F GWGS  LIEFL S+G+DTTQ++S+YDVT II++YVN+N L+H  K
Sbjct: 209 SSVKGKATPLKREFIGWGSKVLIEFLASIGQDTTQKLSQYDVTSIISRYVNDNNLLHPQK 268

Query: 85  KKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDE---ENNLFSSE 141
           K++V+ DERL  + G+KS  + KIYD++E H AEN  ES+DD    S E   E  L + +
Sbjct: 269 KRKVLCDERLRPVLGRKSVNKNKIYDIVEGHLAENLEESEDDEARYSSEDKDETVLMACK 328

Query: 142 KQKSRKVP---LKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSF 198
           +Q+   +    +K+L    P+S +AAIVP NIKL+YLKRSL+ +LLK  +TFE KV GSF
Sbjct: 329 RQRKSNLETPQIKELTPLIPQSRFAAIVPKNIKLIYLKRSLMLELLKQPDTFESKVKGSF 388

Query: 199 VRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSE 258
           V+VK+D   Y Q  +HQL QV G KK   T + + EILL+V N  KDIRI  L++ + +E
Sbjct: 389 VKVKADSYWYSQNQTHQLFQVTGIKKTSETQEINAEILLQVPN-AKDIRINMLAELDLTE 447

Query: 259 EECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKGMAQ 318
            ECED RQ+VK+GL KR T+VEL+EK + LHEDITKHW+ +E++LLQ LIDRAN KG  +
Sbjct: 448 GECEDYRQKVKEGLYKRLTIVELEEKARSLHEDITKHWIEKEISLLQNLIDRANEKGWRR 507

Query: 319 RTP 321
             P
Sbjct: 508 EYP 510

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486219|ref|XP_003633415.1| PREDICTED: uncharacterized protein At5g08430-like [Vitis vinifera]

 Score =  285 bits (728), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 156/297 (52%), Positives = 211/297 (71%), Gaps = 7/297 (2%)

Query: 25  TNLKRRGRSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVK 84
           +++K +    K +F GWGS  LIEFL S+G+DTTQ++S+YDVT II++YVN+N L+H  K
Sbjct: 167 SSVKGKATPLKREFIGWGSKVLIEFLASIGQDTTQKLSQYDVTSIISRYVNDNNLLHPQK 226

Query: 85  KKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQFESDDDFLFSSDE---ENNLFSSE 141
           K++V+ DERL  + G+KS  + KIYD++E H AEN  ES+DD    S E   E  L + +
Sbjct: 227 KRKVLCDERLRPVLGRKSVNKNKIYDIVEGHLAENLEESEDDEARYSSEDKDETVLMACK 286

Query: 142 KQKSRKVP---LKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSF 198
           +Q+   +    +K+L    P+S +AAIVP NIKL+YLKRSL+ +LLK  +TFE KV GSF
Sbjct: 287 RQRKSNLETPQIKELTPLIPQSRFAAIVPKNIKLIYLKRSLMLELLKQPDTFESKVKGSF 346

Query: 199 VRVKSDPNDYLQKNSHQLLQVIGTKKVPGTDDKSTEILLKVSNFVKDIRIATLSDDNFSE 258
           V+VK+D   Y Q  +HQL QV G KK   T + + EILL+V N  KDIRI  L++ + +E
Sbjct: 347 VKVKADSYWYSQNQTHQLFQVTGIKKTSETQEINAEILLQVPN-AKDIRINMLAELDLTE 405

Query: 259 EECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKG 315
            ECED RQ+VK+GL KR T+VEL+EK + LHEDITKHW+ +E++LLQ LIDRAN KG
Sbjct: 406 GECEDYRQKVKEGLYKRLTIVELEEKARSLHEDITKHWIEKEISLLQNLIDRANEKG 462

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	321
TAIR|locus:2150828	553	AT5G08430 [Arabidopsis thalian	0.903	0.524	0.542	8.7e-79
TAIR|locus:2154473	570	AT5G23480 [Arabidopsis thalian	0.822	0.463	0.414	3.8e-46
TAIR|locus:2080863	1292	AT3G51120 [Arabidopsis thalian	0.894	0.222	0.311	9.3e-26
TAIR|locus:2827287	1773	NERD "Needed for RDR2-independ	0.554	0.100	0.376	8.4e-23
TAIR|locus:2060949	824	AT2G18090 "AT2G18090" [Arabido	0.242	0.094	0.269	0.0004

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

 Score = 792 (283.9 bits), Expect = 8.7e-79, P = 8.7e-79
 Identities = 166/306 (54%), Positives = 221/306 (72%)

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 TLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLID 309
              LSDDNFS+EECEDL QR+K+GLLK+PT+VE++EK + LH+D TKHWL RE+ LL++LID
Sbjct:   232 VLSDDNFSQEECEDLHQRIKNGLLKKPTIVEMEEKAKKLHKDQTKHWLGREIELLKRLID 291

Query:   310 RANVKG 315
             RAN KG
Sbjct:   292 RANEKG 297

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 = 484 (175.4 bits), Expect = 3.8e-46, P = 3.8e-46
 Identities = 122/294 (41%), Positives = 175/294 (59%)

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 SEEECEDLRQRVKDGLLKRPTVVELQEKTQILHED-ITKHWLVRELALLQKLID 309
             S+EECE+L QR+ +G  KR TVV+++EK + LHED + K  L++     ++L+D
Sbjct:   236 SQEECEELHQRINNGFAKRLTVVDMEEKARSLHEDYLEKRELLQNPDEQKRLVD 289

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 = 305 (112.4 bits), Expect = 9.3e-26, P = 9.3e-26
 Identities = 98/315 (31%), Positives = 158/315 (50%)

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--IRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHW 296
             + N  K   I I  LSD N +E+EC+ LRQ +K GL KR TVV++ +    L        
Sbjct:   530 ILNLDKREVISIDQLSDQNITEDECKRLRQSIKCGLNKRLTVVDILKTAATLQAMRINEA 589

Query:   297 LVRELALLQKLIDRA 311
             L  E+  L  L DRA
Sbjct:   590 LEAEILKLNHLRDRA 604

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 = 279 (103.3 bits), Expect = 8.4e-23, P = 8.4e-23
 Identities = 70/186 (37%), Positives = 113/186 (60%)

Query:   141 EKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVR 200
             +K+K+RK  ++K   ++    +AA+   NI L+YL+RSLV+DLL+DS  FE KV  +FVR
Sbjct:   922 KKRKTRKKNVRK-GRQSNLDDFAAVDMHNINLIYLRRSLVEDLLEDSTAFEEKVASAFVR 980

Query:   201 VKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKVSNFVKD--IRIATLSDDN 255
             ++   N   +++ ++L+QV+GT K P       K+T+ +L++ N  K   I I  +S+ +
Sbjct:   981 LRISGNQ--KQDLYRLVQVVGTSKAPEPYKVGKKTTDYVLEILNLDKTEVISIDIISNQD 1038

Query:   256 FSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANVKG 315
             F+E+EC+ L+Q +K GL+ R TV ++QEK   L E   K+ L  E+     L DRA+  G
Sbjct:  1039 FTEDECKRLKQSIKCGLINRLTVGDIQEKAIALQEVRVKNLLEAEILRFSHLRDRASDMG 1098

Query:   316 MAQRTP 321
               +  P
Sbjct:  1099 RRKEYP 1104

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 = 0.00040, P = 0.00040
 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        0.316   0.134   0.379    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      321       307    0.0010  115 3  11 22  0.42    34
                                                     33  0.45    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:  602 (64 KB)
  Total size of DFA:  205 KB (2116 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:  26.82u 0.10s 26.92t   Elapsed:  00:00:01
  Total cpu time:  26.82u 0.10s 26.92t   Elapsed:  00:00:01
  Start:  Fri May 10 07:36:26 2013   End:  Fri May 10 07:36:27 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	321
smart00719	109	smart00719, Plus3, Short conserved domain in trans	5e-30
pfam03126	105	pfam03126, Plus-3, Plus-3 domain	6e-26
pfam02201	76	pfam02201, SWIB, SWIB/MDM2 domain	4e-07

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

 Score =  109 bits (275), Expect = 5e-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 = 6e-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 = 46.4 bits (111), Expect = 4e-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	321
smart00719	109	Plus3 Short conserved domain in transcriptional re	100.0
PF03126	108	Plus-3: Plus-3 domain; InterPro: IPR004343 The yea	99.97
KOG2402	525	consensus Paf1/RNA polymerase II complex, RTF1 com	99.96
KOG1946	240	consensus RNA polymerase I transcription factor UA	99.96
COG5296	521	Transcription factor involved in TATA site selecti	99.92
PF02201	76	SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SW	99.87
smart00151	77	SWIB SWI complex, BAF60b domains.	99.87
COG5531	237	SWIB-domain-containing proteins implicated in chro	99.77
PRK14724	987	DNA topoisomerase III; Provisional	99.74
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	99.32
KOG2570	420	consensus SWI/SNF transcription activation complex	99.2

>smart00719 Plus3 Short conserved domain in transcriptional regulators

Probab=100.00  E-value=1.6e-33  Score=233.33  Aligned_cols=104  Identities=48%  Similarity=0.664  Sum_probs=96.2

Q ss_pred             ccCccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCccccceeEEEe
Q 020764          164 AIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKVS  240 (321)
Q Consensus       164 ai~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~L~v~  240 (321)
                      |++.+||++|||+|+.|++||+.| +|+++|+||||||+||++++++ ++||||||+||.++.+   .|+++||++|.+.
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            568999999999999999999999 8999999999999999999987 8999999999999655   5789999999994


Q ss_pred             C--CceeEEeeeecCCCCCHHHHHHHHHHHH
Q 020764          241 N--FVKDIRIATLSDDNFSEEECEDLRQRVK  269 (321)
Q Consensus       241 ~--~~k~~~i~~~Sd~~FTEeE~~r~~q~~~  269 (321)
                      +  ..+.|+|++|||+||||+||++|++.|+
T Consensus        79 ~g~~~~~~~i~~iSn~~fte~E~~~w~~~~~  109 (109)
T smart00719       79 NGDSEKVVQINFISNQDFTEEEFQRWKQAIK  109 (109)
T ss_pred             cCCceEEEEEEEecCCCCCHHHHHHHHHHhC
Confidence            3  4579999999999999999999999984

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=99.97  E-value=1.1e-31  Score=221.30  Aligned_cols=102  Identities=35%  Similarity=0.492  Sum_probs=86.1

Q ss_pred             cccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCccccceeEEEe-C-C
Q 020764          168 DNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKVS-N-F  242 (321)
Q Consensus       168 ~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~L~v~-~-~  242 (321)
                      +||++|||+||+|++||++| +|+++|+||||||+||++++++.++||||||+||.++++   .|++.||++|.+. | .
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 899999999999999999998877899999999999984   5899999999995 4 4


Q ss_pred             ceeEEeeeecCCCCCHHHHHHHHHHHHh
Q 020764          243 VKDIRIATLSDDNFSEEECEDLRQRVKD  270 (321)
Q Consensus       243 ~k~~~i~~~Sd~~FTEeE~~r~~q~~~~  270 (321)
                      .+.|+|++|||++|||+||++|++.|++
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            4799999999999999999999999986

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.

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

Probab=99.96  E-value=1.8e-29  Score=254.28  Aligned_cols=139  Identities=22%  Similarity=0.267  Sum_probs=127.5

Q ss_pred             cccCccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCccccceeEEE
Q 020764          163 AAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKV  239 (321)
Q Consensus       163 aai~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~L~v  239 (321)
                      ...+..++++++|+|+.|+.||+.| +|+++|+||||||+||..+  ++++||||+|+||.++..   .|.+.||.||.+
T Consensus       214 ~v~~~~dln~~rlsR~~vak~~~~P-~Fe~~V~gCfvRv~ig~~~--~~p~YRv~~I~gV~es~k~Y~l~~~~Tnk~l~~  290 (525)
T KOG2402|consen  214 RVPSISDLNALRLSRHKVAKWLFSP-FFESTVTGCFVRVGIGGEG--SKPVYRVAEIVGVLESDKPYKLEGVKTNKYLRV  290 (525)
T ss_pred             CCCCHHHHHHHHhhHHHHHHHHhhh-HHHHHhhhheEEeeecCcC--CCCceeEEEEeeecccCccccccceeecceeee
Confidence            3448899999999999999999999 9999999999999999994  468999999999999777   479999999999


Q ss_pred             -eC-CceeEEeeeecCCCCCHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHhccchHHHHHHH
Q 020764          240 -SN-FVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALL  304 (321)
Q Consensus       240 -~~-~~k~~~i~~~Sd~~FTEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~~i~~~w~e~El~rL  304 (321)
                       +| ..++|.|.+|||++|||+||++|+..|....+.+||++.|.+|..+|.+++++.+.++++..+
T Consensus       291 ~~G~s~r~f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~~a~~~~~sd~~v~~~  357 (525)
T KOG2402|consen  291 RHGRSERVFRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIVKALNYRLSDKEVDQM  357 (525)
T ss_pred             ecCcchhhcchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHhcCccCcccHHHH
Confidence             56 336999999999999999999999999999999999999999999999999999988888443

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

Probab=99.96  E-value=3.7e-30  Score=239.45  Aligned_cols=135  Identities=35%  Similarity=0.526  Sum_probs=100.8

Q ss_pred             cCCCCHHHHHHHhhcCCCC-CCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccc
Q 020764           39 DGWGSIPLIEFLQSLGKDT-TQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA  117 (321)
Q Consensus        39 ~~w~S~eL~~fl~~~g~~~-~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~  117 (321)
                      .+|||..|..|+.+|++++ +++|||++|+++||+|||+||||||.||+.|+||++|++|||+++|+||+|++||++||.
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            3499888888888888877 999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCC--------C-cccchhhhccccCchhhhccccccccccccCCcccccccCccccceeee
Q 020764          118 ENQFESDD--------D-FLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYL  175 (321)
Q Consensus       118 ~~~~~s~d--------~-~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aai~~~nI~~I~L  175 (321)
                      ++++...-        + ..+.++++.+...+...+.++...+.  .-.++..||++..++++++|+
T Consensus       176 ~~~d~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~e~~~k~~~~~--~~~~~~~~a~~~~~~~~l~~~  240 (240)
T KOG1946|consen  176 KNQDMVGTDLKQGEETETKEFKEEEDKSQDPCLSEKEAKETKKV--VKKPRGTFAAIVSDNIKLLYL  240 (240)
T ss_pred             CccccccchhhcCccccccccccccccccccchhhhhhhhhhhc--ccccccchhhhhccccccccC
Confidence            98864311        1 11111222222211112222222111  122233999999999999986

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

Probab=99.92  E-value=9.4e-25  Score=213.16  Aligned_cols=138  Identities=22%  Similarity=0.287  Sum_probs=125.2

Q ss_pred             ccccccCccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCcccccee
Q 020764          160 SCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEIL  236 (321)
Q Consensus       160 ~~~aai~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~  236 (321)
                      +.||.  .-|+|.++|+|+.++++|++| +|++.|+|||+||+||..+  |+-+||||+|.++.....   .|++.||.|
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-IFEDEVIGCFTRVRIGERG--GYLVYRIVGVGKGSTYSKPYGRKEVKTNRY  279 (521)
T ss_pred             chhhh--hhhhhhhhhhHHHHHHHhccc-chhhhhcceeeEEEecccC--CeeEEEEEEeccceeccccccccceeeeee
Confidence            56665  468999999999999999999 7999999999999999443  457999999999999665   479999999


Q ss_pred             EEEe-CCc-eeEEeeeecCCCCCHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHhccchHHHHH
Q 020764          237 LKVS-NFV-KDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELA  302 (321)
Q Consensus       237 L~v~-~~~-k~~~i~~~Sd~~FTEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~~i~~~w~e~El~  302 (321)
                      |.|+ |-. |+|+|..+||+||.++||+||...++.|.+.+|++.-|.+|...|-..+++..+++|+.
T Consensus       280 l~v~~Gr~~kvF~in~~Sn~pf~~~eyQr~~r~~~~~kl~~PS~~~v~~k~~~l~d~~~~~LSdkeis  347 (521)
T COG5296         280 LDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRRLSDKEIS  347 (521)
T ss_pred             EeeecCcceeeeEeecccCCcccHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHhCCcCchhHHH
Confidence            9995 544 59999999999999999999999999999999999999999999999999999999983

>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=99.87  E-value=2.3e-23  Score=162.56  Aligned_cols=70  Identities=36%  Similarity=0.511  Sum_probs=65.5

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccc
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA  117 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~  117 (321)
                      +|++|++|+|      ..++||++|++.||+|||+||||||+||+.|+||++|+.|||+++|++|+|+++|.+|+.
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            5899999998      467999999999999999999999999999999999999999999999999999999984

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

>smart00151 SWIB SWI complex, BAF60b domains

Probab=99.87  E-value=2.9e-22  Score=156.69  Aligned_cols=71  Identities=23%  Similarity=0.420  Sum_probs=68.3

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhcccc
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE  118 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~  118 (321)
                      .|++|++|+|      .+++||++|++.||+|||+||||||.||+.|+||+.|+.+||+++|.+++|+++|.+|+.+
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            6999999998      4899999999999999999999999999999999999999999999999999999999863

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

Probab=99.77  E-value=3.3e-19  Score=165.68  Aligned_cols=71  Identities=18%  Similarity=0.275  Sum_probs=69.2

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhcccc
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE  118 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~  118 (321)
                      +|+.|+.|||      ..++||+|||+.||+|||+||||||+|||.|+||++|+.|||.+.+.||+|+++|.+|+.+
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      5899999999999999999999999999999999999999998899999999999999997

>PRK14724 DNA topoisomerase III; Provisional

Probab=99.74  E-value=2.1e-18  Score=187.04  Aligned_cols=70  Identities=20%  Similarity=0.399  Sum_probs=67.8

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccc
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA  117 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~  117 (321)
                      +|++|++|||      ..++||++|++.||+|||+||||||.|||.|+||++|+.|||+++|.||+|+++|.+|+.
T Consensus       918 ls~~La~~lg------~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~  987 (987)
T PRK14724        918 PSAALAAVIG------AEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS  987 (987)
T ss_pred             CCHHHHHHhC------CCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence            7999999998      579999999999999999999999999999999999999999999999999999999983

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

Probab=99.32  E-value=8.6e-13  Score=142.06  Aligned_cols=71  Identities=20%  Similarity=0.332  Sum_probs=67.6

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhcccc
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE  118 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~  118 (321)
                      .|++|+.|+|      +.+++|.++++.||+|||+|+||||.+|+.|+||++|+++||++++.||.|+++|+.|+.+
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            6999999987      5899999999999999999999999999999999999999999999999999999999864

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

Probab=99.20  E-value=3e-12  Score=126.68  Aligned_cols=145  Identities=17%  Similarity=0.165  Sum_probs=104.1

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~  121 (321)
                      +||-|+..||      -..=+|++++..||.|||-|+||||.++..|.||.-|+.+||++++.+.+++.+|.+|+.+.+|
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            8999999998      3666899999999999999999999999999999999999999999999999999999998887


Q ss_pred             CC-CCCcccch--------hhhccccC-chhhhccccccccccccCCcccccc------cCccccceeeeeHHHHHHHhc
Q 020764          122 ES-DDDFLFSS--------DEENNLFS-SEKQKSRKVPLKKLCLETPKSCWAA------IVPDNIKLVYLKRSLVQDLLK  185 (321)
Q Consensus       122 ~s-~d~~~~~s--------~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~aa------i~~~nI~~I~L~Rs~l~~l~~  185 (321)
                      +- ++.|..|.        +|+++-+. |.+..-+.-    +.......+-+|      -..+.|+...-+|.+|.+|..
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            53 33343332        22222111 111100000    000001111111      134678889999999999999


Q ss_pred             Ccccccccccc
Q 020764          186 DSETFECKVVG  196 (321)
Q Consensus       186 ~P~~Fe~~VvG  196 (321)
                      +|..|-...+-
T Consensus       361 dPvefin~wi~  371 (420)
T KOG2570|consen  361 DPVEFINEWIE  371 (420)
T ss_pred             CHHHHHHHHHH
Confidence            99778766553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	321
1v32_A	101	Solution Structure Of The SwibMDM2 DOMAIN OF THE Hy		7e-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 (268), Expect = 7e-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	321
2bze_A	153	KIAA0252 protein; human RTF1 PLUS3 domain, transcr	3e-25
3u1u_A	137	RNA polymerase-associated protein RTF1 homolog; pl	1e-24
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	1e-23
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	6e-09
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>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 = 98.1 bits (244), Expect = 3e-25
 Identities = 26/140 (18%), Positives = 57/140 (40%), Gaps = 8/140 (5%)

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 GLLKRPTVVELQEKTQILHE 290
             ++ PT+ E+ +K   + E
Sbjct: 131 AGMQLPTLDEINKKELSIKE 150

>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 = 96.1 bits (239), Expect = 1e-24
 Identities = 28/138 (20%), Positives = 59/138 (42%), Gaps = 9/138 (6%)

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 LKRPTVVELQEKTQILHE 290
           ++ PT+ E+ +K   + E
Sbjct: 119 MQLPTLDEINKKELSIKE 136

>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 = 92.2 bits (229), Expect = 1e-23
 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

>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 = 6e-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 = 53.7 bits (128), Expect = 4e-08
 Identities = 52/333 (15%), Positives = 103/333 (30%), Gaps = 98/333 (29%)

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-LRQRVKDGLLKRPTVVELQEK 284
                  L V  F     I    LS    +  + +    + +  K  L+++    + +E 
Sbjct: 371 YRKMFDRLSV--FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK----QPKES 424

Query: 285 TQILHE---DITKHWLVRELALLQKLIDRANVK 314
           T  +     ++    L  E AL + ++D  N+ 
Sbjct: 425 TISIPSIYLELKVK-LENEYALHRSIVDHYNIP 456

>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 = 41.8 bits (97), Expect = 3e-04
 Identities = 55/318 (17%), Positives = 108/318 (33%), Gaps = 81/318 (25%)

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--HQLLQVIGTKKVPGTDDKSTEIL 236
            + +L+  +    ++  ++  R     N  L+ +S   +L +++ +K            L
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE-------NCL 247

Query: 237 LKVSNFVKDIRIATLSDDNFSEEECEDL---RQR-VKDGLL-KRPTVVELQEKTQILHED 291
           L + N V++ +      + F    C+ L   R + V D L     T + L   +  L  D
Sbjct: 248 LVLLN-VQNAKAW----NAF-NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301

Query: 292 ITKHWLVRELALLQKLID 309
                     +LL K +D
Sbjct: 302 EV-------KSLLLKYLD 312

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	321
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	99.92
1z1m_A	119	Ubiquitin-protein ligase E3 MDM2; peptide-binding	96.9
3dac_M	130	MDM4 protein; MDMX, MDM4, HDMX, HDM4, MDM-4, MDM-X	96.83
1ycq_A	107	MDM2, MDM2; anti-oncogene, DNA-binding, transcript	96.63
3fea_A	100	MDM4 protein; HDMX, HDM4,human MDM4, human MDMX, p	96.33
2z5s_M	140	MDM4 protein, zebrafish MDMX; MDMX, MDM4, acetylat	96.13
2axi_A	115	Ubiquitin-protein ligase E3 MDM2; drug design, pro	96.09

>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=2e-38  Score=275.97  Aligned_cols=128  Identities=19%  Similarity=0.296  Sum_probs=117.0

Q ss_pred             cccCccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCccccceeEEE
Q 020764          163 AAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKV  239 (321)
Q Consensus       163 aai~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~L~v  239 (321)
                      .+.+.+||++|||+|++|++||++| +|+++|+||||||+||++.  ++++||||||+|+.++.+   +|++.||++|.+
T Consensus        21 ~v~~l~di~~irL~Rs~l~~~~~~P-~Fe~~V~GcFVRV~ig~~~--~~~~YRl~qI~gv~~~~k~Y~l~~~~T~~~L~l   97 (153)
T 2bze_A           21 MVSLPEELNRVRLSRHKLERWCHMP-FFAKTVTGCFVRIGIGNHN--SKPVYRVAEITGVVETAKVYQLGGTRTNKGLQL   97 (153)
T ss_dssp             BCCCHHHHHHSEECHHHHHHHSSSS-SCHHHHTTCEEEEESSTTS--SSCCEEEEEEEEEEEEEEEEEETTEEEEEEEEE
T ss_pred             CcCCHHHhhheEEEHHHHHHHhcCC-chhHheEEEEEEEEeCCCC--CCccEEEEEEEeEEecCcccccCCcccceEEEE
Confidence            3448889999999999999999999 7999999999999999864  568999999999998776   578899999999


Q ss_pred             eC--CceeEEeeeecCCCCCHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHh
Q 020764          240 SN--FVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDIT  293 (321)
Q Consensus       240 ~~--~~k~~~i~~~Sd~~FTEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~~i~  293 (321)
                      .+  ..++|+|++|||++|||+||++|++.|+++++++||+++|++|+++|++++|
T Consensus        98 ~~g~~~r~~~m~~vSN~~fte~Ef~~w~~~~~~~~~~~PT~~~v~~K~~~i~~a~n  153 (153)
T 2bze_A           98 RHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEALN  153 (153)
T ss_dssp             ESSSCEEEECGGGBCCSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHHHHHC-
T ss_pred             EECCcceEEEeeEeeCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence            54  3469999999999999999999999999999999999999999999999975

>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=9.1e-39  Score=273.24  Aligned_cols=128  Identities=20%  Similarity=0.281  Sum_probs=113.9

Q ss_pred             ccccccCccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCcccccee
Q 020764          160 SCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEIL  236 (321)
Q Consensus       160 ~~~aai~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~  236 (321)
                      ..+.+ +.+||++|||+|++|++||++| +|+++|+||||||+||+++  ++++||||||+||.++.+   +|.+.||++
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            34555 8899999999999999999999 8999999999999999986  568999999999987655   588999999


Q ss_pred             EEEe-C-CceeEEeeeecCCCCCHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHH
Q 020764          237 LKVS-N-FVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHED  291 (321)
Q Consensus       237 L~v~-~-~~k~~~i~~~Sd~~FTEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~~  291 (321)
                      |.+. | ..++|+|++|||++|||+||++|++.|+++++++||+++|++|+++|+++
T Consensus        81 L~l~~g~~~r~~~~~~vSN~~fte~E~~~w~~~~~~~~~~~Pt~~~l~~K~~~i~~a  137 (137)
T 3u1u_A           81 LQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEA  137 (137)
T ss_dssp             EEEEETTEEEEEEGGGBCSSCCCHHHHHHHHHHHHHHTCCCCBHHHHHHHHHHTCCC
T ss_pred             EEEEeCCcceEEEeeeecCCCCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhhC
Confidence            9994 4 34799999999999999999999999999999999999999999999864

>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=7.7e-35  Score=238.14  Aligned_cols=93  Identities=54%  Similarity=0.922  Sum_probs=88.2

Q ss_pred             CCCcccccCCCCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHH
Q 020764           32 RSKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDL  111 (321)
Q Consensus        32 ~~k~~~~~~w~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~kl  111 (321)
                      .+|+.+|+||+|++|++||++||.+|++++||++|++.||+|||+||||||.|||.|+||++|++|||+++|+||+|+++
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            35677999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccCCCCCC
Q 020764          112 LEAHYAENQFESD  124 (321)
Q Consensus       112 L~~H~~~~~~~s~  124 (321)
                      |.+||.++++.++
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=2.4e-26  Score=185.01  Aligned_cols=75  Identities=19%  Similarity=0.212  Sum_probs=72.3

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~  121 (321)
                      +|++|++|||      ..++||++|++.||+|||+||||||.||+.|+||++|+.|||+++|.||+|+++|++||.+.+|
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      5799999999999999999999999999999999999999999999999999999999998887


Q ss_pred             C
Q 020764          122 E  122 (321)
Q Consensus       122 ~  122 (321)
                      .
T Consensus        88 i   88 (93)
T 1v31_A           88 S   88 (93)
T ss_dssp             S
T ss_pred             e
Confidence            5

>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=99.92  E-value=2.7e-26  Score=184.71  Aligned_cols=75  Identities=17%  Similarity=0.185  Sum_probs=72.3

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~  121 (321)
                      +|++|++|||      ..++||++|++.||+|||+||||||.||+.|+||++|+.|||+++|.||+|+++|++||...+|
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      5899999999999999999999999999999999999999999999999999999999998887


Q ss_pred             C
Q 020764          122 E  122 (321)
Q Consensus       122 ~  122 (321)
                      .
T Consensus        88 I   88 (93)
T 1uhr_A           88 S   88 (93)
T ss_dssp             C
T ss_pred             e
Confidence            5

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

Probab=96.90  E-value=0.0024  Score=53.18  Aligned_cols=81  Identities=19%  Similarity=0.258  Sum_probs=69.4

Q ss_pred             CHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchh-hhhhhCCCccchHhHHHHHHhccccCCC
Q 020764           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDER-LLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (321)
Q Consensus        43 S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDek-Lk~lFgk~~v~~f~m~klL~~H~~~~~~  121 (321)
                      .++|..+|...|... ...+..+|.-.+-.||=...|.||.+.+.|.|... |-.|||..++.+-+-..+...|......
T Consensus        31 k~~LLkiLq~aGA~~-~vfT~keV~~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml~~nLv~  109 (119)
T 1z1m_A           31 KPLLLKLLKSVGAQK-DTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVV  109 (119)
T ss_dssp             STTSHHHHHHHTCCC-SCCCTTHHHHHHHHHHHTTTCSCSSSSCEECCTTSHHHHHSCCSCEETTCHHHHHHHHSCSCCC
T ss_pred             cHHHHHHHHHhcccc-ceeechheeehhhhhhhHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHHhccc
Confidence            458999999888764 78999999999999999999999999999999654 5889999999999988888888765444


Q ss_pred             CCC
Q 020764          122 ESD  124 (321)
Q Consensus       122 ~s~  124 (321)
                      .++
T Consensus       110 ~~~  112 (119)
T 1z1m_A          110 VNQ  112 (119)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            433

>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=96.83  E-value=0.002  Score=54.28  Aligned_cols=76  Identities=18%  Similarity=0.327  Sum_probs=67.9

Q ss_pred             CHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecc-hhhhhhhCCCccchHh---HHHHHHhcccc
Q 020764           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSD-ERLLSLFGKKSFLRIK---IYDLLEAHYAE  118 (321)
Q Consensus        43 S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CD-ekLk~lFgk~~v~~f~---m~klL~~H~~~  118 (321)
                      -++|..+|.+.|.. ...++..+|.-.+=.||-.+.|.||.+...|-|- +-|..|||++++++-+   +...|.+++..
T Consensus        28 k~~lL~iLq~aGA~-~dvfT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~llGv~sFSVkdp~~L~~mL~~NLv~  106 (130)
T 3dac_M           28 RAPLLQILKVAGAQ-EEVFTVKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELLEVGSFSVKNPSPLYEMLKRNLVI  106 (130)
T ss_dssp             CHHHHHHHHHTTCC-CSSEEHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTSSEEETTSCHHHHHHHHHHEEE
T ss_pred             cHHHHHHHHHhccC-cceeehHHHHHHHHHhhhhhhccCccccceeEeCCcccccccCCcceeecCcHHHHHHHHhheec
Confidence            46899999988865 5789999999999999999999999999999995 5577799999999999   99999999886


Q ss_pred             C
Q 020764          119 N  119 (321)
Q Consensus       119 ~  119 (321)
                      -
T Consensus       107 ~  107 (130)
T 3dac_M          107 L  107 (130)
T ss_dssp             C
T ss_pred             c
Confidence            3

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

Probab=96.63  E-value=0.0039  Score=51.03  Aligned_cols=74  Identities=19%  Similarity=0.249  Sum_probs=64.6

Q ss_pred             CHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchh-hhhhhCCCccchHhHHHHHHhccc
Q 020764           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDER-LLSLFGKKSFLRIKIYDLLEAHYA  117 (321)
Q Consensus        43 S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDek-Lk~lFgk~~v~~f~m~klL~~H~~  117 (321)
                      .++|..+|...|... ...+..+|.-.|-.||=...|.||.+...|.|... |-.|||+.++++-+-..+...|..
T Consensus        15 k~~LLklL~~~GA~~-~~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml~~   89 (107)
T 1ycq_A           15 TPLLLSLLKSAGAQK-ETFTMKEVIYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEPRRLYAMISR   89 (107)
T ss_dssp             CHHHHHHHHHTTCCC-SCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTCSEEETTCHHHHHHHHHT
T ss_pred             cHHHHHHHHHhcccc-ceeeehhhhhhHHHHHhHHhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHH
Confidence            468999999988764 78999999999999999999999999999999655 588999999999888866666654

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

Probab=96.33  E-value=0.0057  Score=49.55  Aligned_cols=75  Identities=21%  Similarity=0.419  Sum_probs=65.7

Q ss_pred             CHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecch-hhhhhhCCCccchH---hHHHHHHhcccc
Q 020764           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE-RLLSLFGKKSFLRI---KIYDLLEAHYAE  118 (321)
Q Consensus        43 S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDe-kLk~lFgk~~v~~f---~m~klL~~H~~~  118 (321)
                      -++|..+|.+.|.. ...++..+|.-.+=.||-.+.|.||.+...|.|.. -|-.+||++++++-   .+...|.+|+..
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            46899999988865 57899999999999999999999999999999964 56679999999988   788888888764

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

Probab=96.13  E-value=0.0085  Score=50.86  Aligned_cols=74  Identities=18%  Similarity=0.241  Sum_probs=63.5

Q ss_pred             CHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchh-hhhhhCCCccchHhHHHHHHhccc
Q 020764           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDER-LLSLFGKKSFLRIKIYDLLEAHYA  117 (321)
Q Consensus        43 S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDek-Lk~lFgk~~v~~f~m~klL~~H~~  117 (321)
                      -++|..+|...|.- ...++..+|.-.|-.||=...|.||.+...|.|... |-.|||+.++++-+-..+...+..
T Consensus        27 k~~LLkiLq~aGA~-~~~fT~keVm~YLGqYIm~KqLYD~~~qhiV~C~~D~LG~l~Gv~sFSVKdp~~ly~ML~~  101 (140)
T 2z5s_M           27 RAPLLQILKVAGAQ-EEVFTLKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELLEVGSFSVKNPSPVYEMLKR  101 (140)
T ss_dssp             CHHHHHHHHHTTCC-CSCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHHTSSEEETTBCHHHHHHHHH
T ss_pred             cHHHHHHHHHhCcc-cceeeHHHHHHHHHHHHHHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHH
Confidence            36899999988764 568999999999999999999999999999999654 588999999999887766666554

>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=96.09  E-value=0.0054  Score=50.73  Aligned_cols=75  Identities=20%  Similarity=0.298  Sum_probs=65.5

Q ss_pred             CHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchh-hhhhhCCCccchHhHHHHHHhcccc
Q 020764           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDER-LLSLFGKKSFLRIKIYDLLEAHYAE  118 (321)
Q Consensus        43 S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDek-Lk~lFgk~~v~~f~m~klL~~H~~~  118 (321)
                      .++|..+|...|... ...+..+|.-.+-.||=...|.||.+...|.|... |-.|||+.++++-+-..+...|...
T Consensus        15 k~~LLklLq~~GA~~-~vfT~keVm~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~g~~~Fsvkdp~~l~~ml~~n   90 (115)
T 2axi_A           15 KPLLLKLLKSVGAQK-DTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRN   90 (115)
T ss_dssp             CHHHHHHHHHTTCCC-SCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHHSSSEEETTCHHHHHHHHHTT
T ss_pred             cHHHHHHHHHhcccc-ceeechhheehhhhhhhHhhhcccccCcEEeeCCcccccccCccceeecCcHHHHHHHHHh
Confidence            468999999988764 78999999999999999999999999999999654 5889999999998877777776653

---

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	321
d2bzea1	132	b.34.21.1 (A:345-476) RNA polymerase-associated pr	1e-26
d1v32a_	101	a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl	5e-23
d1uhra_	93	a.42.1.1 (A:) SWI/SNF related regulator of chromat	1e-08
d1v31a_	93	a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl	2e-08

>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 =  100 bits (250), Expect = 1e-26
 Identities = 25/129 (19%), Positives = 54/129 (41%), Gaps = 8/129 (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--NFVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVEL 281
                    T   L++   N  +  R+  +S+  F+E E    ++ +    ++ PT+ E+
Sbjct: 61  KVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEI 120

Query: 282 QEKTQILHE 290
            +K   + E
Sbjct: 121 NKKELSIKE 129

>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 = 89.1 bits (221), Expect = 5e-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

>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 = 1e-08
 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 = 49.0 bits (117), Expect = 2e-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	321
d2bzea1	132	RNA polymerase-associated protein RTF1 homolog {Hu	100.0
d1v32a_	101	Hypothetical protein AT5G08430 (rafl09-47-k03) {Th	99.98
d1v31a_	93	Hypothetical protein AT5G14170 (rafl11-05-p19) {Th	99.91
d1uhra_	93	SWI/SNF related regulator of chromatin (BRG1-assoc	99.91
d2axia1	85	MDM2 {Human (Homo sapiens) [TaxId: 9606]}	97.36
d1ttva_	107	MDM2 {African clawed frog (Xenopus laevis) [TaxId:	97.29

>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=4.5e-39  Score=271.41  Aligned_cols=125  Identities=19%  Similarity=0.309  Sum_probs=115.6

Q ss_pred             CccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCccccceeEEEeC-
Q 020764          166 VPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKVSN-  241 (321)
Q Consensus       166 ~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~L~v~~-  241 (321)
                      +++||++|||+|+.|++||++| +|+++|+||||||+||++.  ++++||||||+||.++.+   +|.+.||++|.+.+ 
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-FFAKTVTGCFVRIGIGNHN--SKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHG   79 (132)
T ss_dssp             CHHHHHHSEECHHHHHHHSSSS-SCHHHHTTCEEEEESSTTS--SSCCEEEEEEEEEEEEEEEEEETTEEEEEEEEEESS
T ss_pred             ChHHhhheEEeHHHHHHHHcCC-chHHhheeeEEEEEeCCCC--CCCceEEEEEEeeeecCcccccCCCcccEEEEEEEC
Confidence            6899999999999999999999 7999999999999999765  568999999999998766   47899999999953 


Q ss_pred             -CceeEEeeeecCCCCCHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHh
Q 020764          242 -FVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDIT  293 (321)
Q Consensus       242 -~~k~~~i~~~Sd~~FTEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~~i~  293 (321)
                       ..++|+|++|||+||||+||++|++.|+++++++||+.+|++|+++|++++|
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             4479999999999999999999999999999999999999999999999986

>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=99.98  E-value=2.9e-33  Score=226.87  Aligned_cols=90  Identities=56%  Similarity=0.955  Sum_probs=86.1

Q ss_pred             CCcccccCCCCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHH
Q 020764           33 SKKVKFDGWGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLL  112 (321)
Q Consensus        33 ~k~~~~~~w~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL  112 (321)
                      .|+.+|+||+|+||++||++||.|+.+++||++|++.||+|||+||||||.|||.|+||++|+.|||+++|++|+|+++|
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            45569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccccCCCC
Q 020764          113 EAHYAENQFE  122 (321)
Q Consensus       113 ~~H~~~~~~~  122 (321)
                      .+||.++++.
T Consensus        87 ~~H~~~~~~~   96 (101)
T d1v32a_          87 EKHYKENQDS   96 (101)
T ss_dssp             HHHSCSCCCC
T ss_pred             HHHcCCcccc
Confidence            9999998753

>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=99.91  E-value=2.3e-25  Score=177.47  Aligned_cols=76  Identities=18%  Similarity=0.194  Sum_probs=72.1

Q ss_pred             CCCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCC
Q 020764           41 WGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQ  120 (321)
Q Consensus        41 w~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~  120 (321)
                      -+|++|++|||      ..++||++|++.||+|||+||||||.||+.|+||++|+.|||+++|+||+|+++|.+|+.+.+
T Consensus        13 ~lS~~La~~lg------~~~~sR~~v~k~iw~YIk~n~Lqd~~nkr~I~~D~~L~~lfg~~~v~~~~l~~~L~~Hl~p~~   86 (93)
T d1v31a_          13 KLSTALMDVLG------IEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEKLKFTMVSQKISHHLSPPP   86 (93)
T ss_dssp             ECCHHHHHHSC------CSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHSCSSEEETTTTHHHHHHHCBCCC
T ss_pred             cCCHHHHHHHC------cCcCcHHHHHHHHHHHHHHhCCCCCCCCCEEecCHHHHHHhCCCcccHHHHHHHHHHhCCCCC
Confidence            37999999997      478999999999999999999999999999999999999999999999999999999999887


Q ss_pred             CC
Q 020764          121 FE  122 (321)
Q Consensus       121 ~~  122 (321)
                      |.
T Consensus        87 P~   88 (93)
T d1v31a_          87 PS   88 (93)
T ss_dssp             CS
T ss_pred             CC
Confidence            63

>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=99.91  E-value=1.7e-25  Score=178.47  Aligned_cols=75  Identities=17%  Similarity=0.185  Sum_probs=71.7

Q ss_pred             CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020764           42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF  121 (321)
Q Consensus        42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~  121 (321)
                      +|++|++|||      ..++||++|++.||+|||+||||||.|||.|+||++|+.|||+++|.+|+|+++|..||.+.+|
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            7999999997      4789999999999999999999999999999999999999999999999999999999998876


Q ss_pred             C
Q 020764          122 E  122 (321)
Q Consensus       122 ~  122 (321)
                      .
T Consensus        88 ~   88 (93)
T d1uhra_          88 S   88 (93)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=97.36  E-value=8.1e-05  Score=56.65  Aligned_cols=74  Identities=22%  Similarity=0.339  Sum_probs=64.9

Q ss_pred             CHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecch-hhhhhhCCCccchHh---HHHHHHhccc
Q 020764           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDE-RLLSLFGKKSFLRIK---IYDLLEAHYA  117 (321)
Q Consensus        43 S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDe-kLk~lFgk~~v~~f~---m~klL~~H~~  117 (321)
                      .++|..+|.+-|. ..+..+.-||.-.|-.||-...|.||++.+.|.|-. .|-.|||.++++.-+   +..+|.+|+.
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            4789999997775 457899999999999999999999999999999954 589999999999888   8888887763

>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=97.29  E-value=0.00023  Score=56.03  Aligned_cols=75  Identities=20%  Similarity=0.355  Sum_probs=66.5

Q ss_pred             CHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecc-hhhhhhhCCCccchHh---HHHHHHhcccc
Q 020764           43 SIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSD-ERLLSLFGKKSFLRIK---IYDLLEAHYAE  118 (321)
Q Consensus        43 S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CD-ekLk~lFgk~~v~~f~---m~klL~~H~~~  118 (321)
                      .++|..+|.+-|.. .+..+.-+|.-.|-.||-...|.||.+.+.|.|- +.|-.|||.++++.-+   +..+|.+|+..
T Consensus        15 kp~LL~~L~~~GA~-~~~fT~keVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~llgv~sFsVke~r~l~~ml~rnLv~   93 (107)
T d1ttva_          15 TPLLLSLLKSAGAQ-KETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLVS   93 (107)
T ss_dssp             CHHHHHHHHHTTCC-SSCBCHHHHHHHHHHHHHHHTCBCSSCTTEECCSSCHHHHHHTCSCEETTCHHHHHHHHHTTEEE
T ss_pred             CHHHHHHHHHcCCC-cceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhcCCCceeecCcHHHHHHHHhhhhc
Confidence            58999999987754 5789999999999999999999999999999995 5589999999999888   77779999864