Citrus Sinensis ID: 042235

---

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-----
Protein Sequence
MVAVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLASPQVSNSGSCSASASASASNVGCASDEQFKFGNNYACGERFKFGNNHIHEDDNKKEFIKFGT
Secondary Structure (PSIPRED)
ccccccccccEEEccccccccEEcccccccHHHHHHHHHHHccccEEEEEEcccccccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHcHHHHcccHHcHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEcccccEEEEEcccccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHEEHccc
Coil and Loop (DISEMBL)
mvavgkrriplkrrdtkeQRAVSFSKRRHGLLNKAAEYCLRTRSQLALlvsspvsdttfytfghSSVDAVLDAFvnnrapeaadKELVRLGISMFNEVKDLELYDKKISKAIksdgnleregFWEDYeklgnsdesiGELGVIVDKLAKAKEKAILRLTDllaspqvsnsgscsasasasasnvgcasdeqfkfgnnyacgerfkfgnnhiheddnkkefikfgt
Flexible Loop (DISEMBL)
mvavgkrriplkrrdtkeqravsfskrrhgllnkAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISkaiksdgnlereGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLASPQVSNSGSCSASASASASNVGCASDEQFKFGNNYACGERFKFgnnhiheddnkkefikfgt
Low Complexity Region (SEG)
MVAVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLASPQvsnsgscsasasasasnvgcasDEQFKFGNNYACGERFKFGNNHIHEDDNKKEFIKFGT
Disordered region (IsUnstruct)
****************************HGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLL***************************EQFKFGNNYACGERFKFGNNHI**************
Disordered Region (DISOPRED)
****GKR*IPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFV********************************************************************************************************************FKFGNNYACGERFKFGNNHIHEDDNKK*FIKFG*
Disordered Region (DISEMBL)
MVAVGKRRIPLK************SKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLASP*********************ASDEQFKFGNNYACGERFKFGNNHIHEDDNKKEFIKFGT
Disordered Region (DISPRO)
********IPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLAS*******************VGCASDEQFKFGNNYACGERFKFGNNHIHEDDNKKEFIKFGT
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVAVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLASPQVSNSGSCSASASASASNVGCASDEQFKFGNNYACGERFKFGNNHIHEDDNKKEFIKFGT
Positional Conservation
no confident homologs detected

---

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	225	2.2.26 [Sep-21-2011]
Q9C633	266	Agamous-like MADS-box pro	yes	no	0.328	0.278	0.487	1e-13
Q4PSU4	264	Agamous-like MADS-box pro	no	no	0.32	0.272	0.378	9e-10
Q9FKK2	299	Agamous-like MADS-box pro	no	no	0.511	0.384	0.314	1e-08
P29386	252	Agamous-like MADS-box pro	no	no	0.737	0.658	0.235	6e-07
Q7XUN2	249	MADS-box transcription fa	yes	no	0.306	0.277	0.380	8e-06
Q6EU39	250	MADS-box transcription fa	no	no	0.306	0.276	0.380	2e-05
Q6Z6W2	241	MADS-box transcription fa	no	no	0.315	0.294	0.356	3e-05
Q6VAM4	159	MADS-box transcription fa	no	no	0.306	0.433	0.366	9e-05
Q2QQA3	233	MADS-box transcription fa	no	no	0.822	0.793	0.233	0.0001
Q8RVL4	247	MADS-box protein defh21 O	N/A	no	0.448	0.408	0.313	0.0001

>sp|Q9C633|AGL97_ARATH Agamous-like MADS-box protein AGL97 OS=Arabidopsis thaliana GN=AGL97 PE=1 SV=1

 Score = 76.6 bits (187), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 57/78 (73%), Gaps = 4/78 (5%)

Query: 6  KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPV---SDTTFYTF 62
          KR+I +++   K  RAVSFSKRR GL +KA+E CL + +++A ++++PV   S+  FY+F
Sbjct: 5  KRKIAIEKIQNKNPRAVSFSKRRKGLYSKASELCLLSDAEIA-IIATPVSSNSNAAFYSF 63

Query: 63 GHSSVDAVLDAFVNNRAP 80
          GHSSVD V+ AF+ N+ P
Sbjct: 64 GHSSVDNVVAAFLANQRP 81

Putative transcription factor.
Arabidopsis thaliana (taxid: 3702)

>sp|Q4PSU4|AGL61_ARATH Agamous-like MADS-box protein AGL61 OS=Arabidopsis thaliana GN=AGL61 PE=1 SV=1

 Score = 63.9 bits (154), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 49/74 (66%), Gaps = 2/74 (2%)

Query: 3   AVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTF 62
           ++G+++IP+ +   +  R V+FSKRR GL  KA+E C    +++ ++V SP      ++F
Sbjct: 61  SIGRQKIPMVKIKKESHRQVTFSKRRAGLFKKASELCTLCGAEIGIIVFSPAKKP--FSF 118

Query: 63  GHSSVDAVLDAFVN 76
           GH SV++VLD +V+
Sbjct: 119 GHPSVESVLDRYVS 132

Probable transcription factor. Controls central cell differentiation during female gametophyte development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKK2|AGL62_ARATH Agamous-like MADS-box protein AGL62 OS=Arabidopsis thaliana GN=AGL62 PE=1 SV=1

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 44/140 (31%), Positives = 71/140 (50%), Gaps = 25/140 (17%)

Query: 5   GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
           G+++I + +   +    V+FSKRR GL  KA+E C    +++A++V SP      ++FGH
Sbjct: 7   GRQKIEMVKMKNESNLQVTFSKRRSGLFKKASELCTLCGAEVAIVVFSP--GRKVFSFGH 64

Query: 65  SSVDAVLDAFVNNRAPEAADKELVRLGISMFNE-VKDL---------------ELYD--K 106
            +VD+V+D F+NN          ++L  +  N  V+DL               + YD  K
Sbjct: 65  PNVDSVIDRFINNNPLPPHQHNNMQLRETRRNSIVQDLNNHLTQVLSQLETEKKKYDELK 124

Query: 107 KISKAIKSDGNLEREGFWED 126
           KI +  K+ GN     +WED
Sbjct: 125 KIREKTKALGN-----WWED 139

Probable transcription factor. Required for suppression of cellularization and promotion of nuclear proliferation during early endosperm development. The FERTILIZATION-INDEPENDENT SEED (FIS) polycomb complex is required for suppression of ALG62 expression at the end of the syncytial phase of endosperm development.

Arabidopsis thaliana (taxid: 3702)

>sp|P29386|AGL6_ARATH Agamous-like MADS-box protein AGL6 OS=Arabidopsis thaliana GN=AGL6 PE=1 SV=2

 Score = 54.7 bits (130), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 46/195 (23%), Positives = 90/195 (46%), Gaps = 29/195 (14%)

Query: 4   VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
           +G+ R+ +KR + K  R V+FSKRR+GLL KA E  +   +++AL++ S  S    Y FG
Sbjct: 1   MGRGRVEMKRIENKINRQVTFSKRRNGLLKKAYELSVLCDAEVALIIFS--SRGKLYEFG 58

Query: 64  HSSVDAVLDAF-------VNNRAPEAADK--------------ELVRLGISMFNE----- 97
              +++ ++ +       ++N  PE   +               LVR   ++  E     
Sbjct: 59  SVGIESTIERYNRCYNCSLSNNKPEETTQSWCQEVTKLKSKYESLVRTNRNLLGEDLGEM 118

Query: 98  -VKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAIL 156
            VK+L+  ++++  A+ +    + +   E+ E L   +  +G++   +    + +  A  
Sbjct: 119 GVKELQALERQLEAALTATRQRKTQVMMEEMEDLRKKERQLGDINKQLKIKFETEGHAFK 178

Query: 157 RLTDLLASPQVSNSG 171
              DL A+   S +G
Sbjct: 179 TFQDLWANSAASVAG 193

Probable transcription factor. Forms an heterodimer via the K-box domain with AG, that could be involved in genes regulation during floral meristem development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XUN2|MAD17_ORYSJ MADS-box transcription factor 17 OS=Oryza sativa subsp. japonica GN=MADS17 PE=1 SV=2

 Score = 50.4 bits (119), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 44/71 (61%), Gaps = 2/71 (2%)

Query: 4  VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
          +G+ R+ LKR + K  R V+FSKRR+GLL KA E  +   +++AL++ S  S    Y FG
Sbjct: 1  MGRGRVELKRIENKINRQVTFSKRRNGLLKKAYELSVLCDAEVALIIFS--SRGKLYEFG 58

Query: 64 HSSVDAVLDAF 74
           + ++  L+ +
Sbjct: 59 SAGINKTLEKY 69

Probable transcription factor. Plays minor but redundant roles with MADS6 in floral development.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6EU39|MADS6_ORYSJ MADS-box transcription factor 6 OS=Oryza sativa subsp. japonica GN=MADS6 PE=1 SV=1

 Score = 49.3 bits (116), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 2/71 (2%)

Query: 4  VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
          +G+ R+ LKR + K  R V+FSKRR+GLL KA E  +   +++AL++ S  S    Y FG
Sbjct: 1  MGRGRVELKRIENKINRQVTFSKRRNGLLKKAYELSVLCDAEVALIIFS--SRGKLYEFG 58

Query: 64 HSSVDAVLDAF 74
           + +   L+ +
Sbjct: 59 SAGITKTLERY 69

Probable transcription factor. Regulates floral organ identity and floral meristem determinacy. May be involved in the control of flowering time.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6Z6W2|MAD57_ORYSJ MADS-box transcription factor 57 OS=Oryza sativa subsp. japonica GN=MADS57 PE=2 SV=2

 Score = 48.5 bits (114), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 4  VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
          +G+ +I ++R D    R V+FSKRR+GLL KA E  +   +++ L+V S  S    Y F 
Sbjct: 1  MGRGKIVIRRIDNSTSRQVTFSKRRNGLLKKAKELSILCDAEVGLVVFS--STGRLYEFS 58

Query: 64 HSSVDAVLDAFVN 76
           +++  V+D + N
Sbjct: 59 STNMKTVIDRYTN 71

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6VAM4|MAD23_ORYSJ MADS-box transcription factor 23 OS=Oryza sativa subsp. japonica GN=MADS23 PE=2 SV=1

 Score = 47.4 bits (111), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 4  VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
          +G+ +I +KR D    R V+FSKRR GL  KA E  +   +++ LLV S  S    Y F 
Sbjct: 1  MGRGKIEIKRIDNATSRQVTFSKRRSGLFKKARELSILCDAEVGLLVFSSTS--RLYDFA 58

Query: 64 HSSVDAVLDAF 74
           SS+ ++++ +
Sbjct: 59 SSSMKSIIERY 69

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2QQA3|MAD20_ORYSJ MADS-box transcription factor 20 OS=Oryza sativa subsp. japonica GN=MADS20 PE=2 SV=2

 Score = 47.0 bits (110), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 50/214 (23%), Positives = 97/214 (45%), Gaps = 29/214 (13%)

Query: 4   VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
           +G+ ++ ++R + +  R V+FSKRR GLL KA E  +     +A +V S   +   Y   
Sbjct: 1   MGRGKVQVRRIENEVSRQVTFSKRRPGLLKKAHEIAVLCDVDVAAIVFSAKGNLFHYASS 60

Query: 64  HSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLE---LYDK-----KISKAIKSD 115
           H++++ +L+ +  +        EL+  G ++  E  +LE    YD      +I    KS 
Sbjct: 61  HTTMERILEKYDRH--------ELLSEGNNVIEEFPELEGSMSYDHIKLRGRIEALKKSQ 112

Query: 116 GNLEREGF----WEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLAS--PQVSN 169
            NL  +       +D ++L N      ++   ++ +   KEK ++    +L     ++  
Sbjct: 113 RNLMGQELDSLTLQDIQQLEN------QIDTSLNNIRSRKEKLLMEKNTILEKKITELET 166

Query: 170 SGSC-SASASASASNVGCASDEQFKFGNNYACGE 202
             +C  AS + +A+   C + + F    N  CG+
Sbjct: 167 LHTCIRASPTKAAAPPACNTADAFVPNLNICCGD 200

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8RVL4|DEF21_ANTMA MADS-box protein defh21 OS=Antirrhinum majus GN=DEFH21 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 54/115 (46%), Gaps = 14/115 (12%)

Query: 4   VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
           +G+ +I +KR +    R V+FSKRR GL+ K  E  +   +Q+ L+V S     T Y   
Sbjct: 1   MGRGKIEVKRIENNTSRQVTFSKRRSGLMKKTHELSVLCDAQIGLIVFSTKGKLTEYCTP 60

Query: 64  HSSVDAVLDAFV---------NNRAPEAAD-----KELVRLGISMFNEVKDLELY 104
             S+  ++D +V          NRA   AD     KEL R+     N   +L+ Y
Sbjct: 61  PFSMKQIIDRYVKAKGILPEMENRAGPHADNDQVIKELTRMKEETLNLQLNLQRY 115

Probable transcription factor.

Antirrhinum majus (taxid: 4151)

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	225
255582376	328	mads box protein, putative [Ricinus comm	0.64	0.439	0.466	1e-24
255582804	349	mads box protein, putative [Ricinus comm	0.68	0.438	0.391	1e-19
224150125	304	predicted protein [Populus trichocarpa]	0.684	0.506	0.387	2e-19
224065194	304	predicted protein [Populus trichocarpa]	0.684	0.506	0.381	3e-19
224146919	375	predicted protein [Populus trichocarpa]	0.613	0.368	0.406	4e-19
224089304	316	predicted protein [Populus trichocarpa]	0.613	0.436	0.4	2e-18
224119870	347	predicted protein [Populus trichocarpa]	0.613	0.397	0.4	6e-18
15220103	266	agamous-like MADS-box protein AGL97 [Ara	0.328	0.278	0.487	7e-12
15238246	322	protein agamous-like 99 [Arabidopsis tha	0.328	0.229	0.474	1e-11
15240962	349	MADS-box protein AGL73 [Arabidopsis thal	0.591	0.381	0.316	1e-11

>gi|255582376|ref|XP_002531977.1| mads box protein, putative [Ricinus communis] gi|223528374|gb|EEF30413.1| mads box protein, putative [Ricinus communis]

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 70/150 (46%), Positives = 100/150 (66%), Gaps = 6/150 (4%)

Query: 7   RRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSS 66
           R++P+K+R+TK+QR+VSF+KRR+GL NKAAE  +   +QLALLVSSP S    Y+FGH S
Sbjct: 5   RKLPMKKRETKKQRSVSFTKRRYGLFNKAAELFMLCDAQLALLVSSPCS-RKVYSFGHPS 63

Query: 67  VDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLER--EGFW 124
           VD +LDAF+ N  P A+D ++ +  +S+ NE+K LE   K  S + + + NLE    GF 
Sbjct: 64  VDVILDAFLENHLPIASDGKVKQRALSLLNEIKGLERDIK--SSSTQRNKNLENVASGFS 121

Query: 125 EDYEKLGNSDESIGELGVIVDKLAKAKEKA 154
             +E   NS +SI EL  +V+ L K  ++A
Sbjct: 122 SVFECFENS-QSIEELRPVVNALEKLVDEA 150

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582804|ref|XP_002532176.1| mads box protein, putative [Ricinus communis] gi|223528144|gb|EEF30213.1| mads box protein, putative [Ricinus communis]

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 63/161 (39%), Positives = 98/161 (60%), Gaps = 8/161 (4%)

Query: 7   RRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDT--TFYTFGH 64
           R+ P+K+ ++++QR+VSF+KRR+GL NKAAE  +   +QLA+LV+SP S      Y+FGH
Sbjct: 5   RKRPMKKLESQKQRSVSFTKRRNGLFNKAAELFMLCDAQLAVLVASPCSKPKRKVYSFGH 64

Query: 65  SSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLER--EG 122
            S D VLDAF+NN AP   D    +  +S+  E+K LE    +I+   + +  L    +G
Sbjct: 65  PSADVVLDAFLNNCAPVPVDNGARQSALSLLGEIKGLE---SEINSLSQRNARLTNVGDG 121

Query: 123 FWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLA 163
           F   ++   NS +SI EL  +VD L K   +A  R+++ ++
Sbjct: 122 FSSAFQYFENS-KSIEELQAVVDVLEKLIVEAKSRVSNSIS 161

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224150125|ref|XP_002336908.1| predicted protein [Populus trichocarpa] gi|222837108|gb|EEE75487.1| predicted protein [Populus trichocarpa]

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 64/165 (38%), Positives = 95/165 (57%), Gaps = 11/165 (6%)

Query: 7   RRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSS 66
           R+IP+ +R+T EQR+V+F+KRR GL NKAA+ C    +Q+A++VSS  S    YTFGHSS
Sbjct: 5   RKIPMAKRETAEQRSVTFTKRRQGLFNKAADLCRICDAQIAIMVSSTGSKEKVYTFGHSS 64

Query: 67  VDAVLDAFVNN--RAPEAADKE--LVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREG 122
           VDAV D F++N   APEA   E  +     S++ E+K LE     ++  +++        
Sbjct: 65  VDAVFDRFLDNFTAAPEAVAYEAGIKSASNSLYEEIKALE---GDVNTLMQNKKRNVGGV 121

Query: 123 FWEDYEKLGNSDESIGELGVIVDK----LAKAKEKAILRLTDLLA 163
            W+  E++  S  S+ EL  +VD     L +AK K +   T+ L 
Sbjct: 122 LWDSLEEIEQSSTSVEELQDVVDTLESLLGQAKNKLMNNATENLG 166

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224065194|ref|XP_002301710.1| predicted protein [Populus trichocarpa] gi|222843436|gb|EEE80983.1| predicted protein [Populus trichocarpa]

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 63/165 (38%), Positives = 95/165 (57%), Gaps = 11/165 (6%)

Query: 7   RRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSS 66
           R+IP+ +R+T EQR+V+F+KRR GL NKAA+ C    +Q+A++VSS  S    YTFGHSS
Sbjct: 5   RKIPMAKRETAEQRSVTFTKRRQGLFNKAADLCRICDAQIAIMVSSTGSKEKVYTFGHSS 64

Query: 67  VDAVLDAFVNN--RAPEAADKE--LVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREG 122
           +DAV D F++N   APEA   E  +     S++ E+K LE     ++  +++        
Sbjct: 65  IDAVFDRFLDNFTAAPEAVAYEAGIKSASNSLYEEIKALE---GDVNTLMQNKKRNVGGV 121

Query: 123 FWEDYEKLGNSDESIGELGVIVDK----LAKAKEKAILRLTDLLA 163
            W+  E++  S  S+ EL  +VD     L +AK K +   T+ L 
Sbjct: 122 LWDSLEEIEQSSTSVEELQDVVDTLESLLGQAKNKLMNNATENLG 166

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146919|ref|XP_002336367.1| predicted protein [Populus trichocarpa] gi|222834817|gb|EEE73266.1| predicted protein [Populus trichocarpa]

 Score =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 59/145 (40%), Positives = 88/145 (60%), Gaps = 7/145 (4%)

Query: 7   RRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSS 66
           R+IP+ +R+T EQR+V+F+KRR GL NKAA+ C    +Q+A++VSS  S    YTFGHSS
Sbjct: 5   RKIPMAKRETAEQRSVTFTKRRQGLFNKAADLCRICDAQIAIMVSSTGSKEKVYTFGHSS 64

Query: 67  VDAVLDAFVNN--RAPEAADKE--LVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREG 122
           VDAV D F++N   APEA   E  +     S++ E+K LE     ++  +++        
Sbjct: 65  VDAVFDRFLDNFTAAPEAVAYEAGIKSASNSLYEEIKALE---GDVNTLMQNKKRNVGGV 121

Query: 123 FWEDYEKLGNSDESIGELGVIVDKL 147
            W+  E++  S+ S+ EL  +VD L
Sbjct: 122 LWDALEEIEQSNTSVEELQDVVDIL 146

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224089304|ref|XP_002308682.1| predicted protein [Populus trichocarpa] gi|222854658|gb|EEE92205.1| predicted protein [Populus trichocarpa]

 Score = 98.6 bits (244), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 58/145 (40%), Positives = 88/145 (60%), Gaps = 7/145 (4%)

Query: 7   RRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSS 66
           R+IP+ +R+T EQR+V+F+KRR GL NKAA+ C    +Q+A++VSS  S    Y+FGHSS
Sbjct: 5   RKIPMAKRETAEQRSVTFTKRRQGLFNKAADLCRICDAQIAIMVSSTGSKDKVYSFGHSS 64

Query: 67  VDAVLDAFVNN--RAPEAADKE--LVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREG 122
           VDAV D F++N   APEA   E  +     S++ E+K LE     ++  +++        
Sbjct: 65  VDAVFDRFLDNFTAAPEAVAYEAGIKSASNSLYEEIKALE---GDVNTLMQNKKRNVGGV 121

Query: 123 FWEDYEKLGNSDESIGELGVIVDKL 147
            W+  E++  S+ S+ EL  +VD L
Sbjct: 122 LWDALEEIEQSNTSVEELHDVVDIL 146

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119870|ref|XP_002318183.1| predicted protein [Populus trichocarpa] gi|222858856|gb|EEE96403.1| predicted protein [Populus trichocarpa]

 Score = 96.7 bits (239), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 58/145 (40%), Positives = 86/145 (59%), Gaps = 7/145 (4%)

Query: 7   RRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSS 66
           R+IP+ +R+T EQR+V+F+KRR GL NKAA+ C    +Q+A++VSS  S    YTFGHSS
Sbjct: 5   RKIPMLKRETAEQRSVTFTKRRQGLFNKAADLCRICDAQIAIMVSSTGSKEKVYTFGHSS 64

Query: 67  VDAVLDAFVNN--RAPEAADKE--LVRLGISMFNEVKDLELYDKKISKAIKSDGNLEREG 122
           VDAV D F+ N   APEA   E  +     S++ E+K LE     ++  +++        
Sbjct: 65  VDAVFDRFLYNFTAAPEAVAYEAGIKSASNSLYEEIKALE---GDVNTLMQNKKRNVGGV 121

Query: 123 FWEDYEKLGNSDESIGELGVIVDKL 147
            W+  E++  S  S+ EL  +V+ L
Sbjct: 122 LWDSLEEIEQSSTSVDELQDVVNIL 146

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15220103|ref|NP_175144.1| agamous-like MADS-box protein AGL97 [Arabidopsis thaliana] gi|75308798|sp|Q9C633.1|AGL97_ARATH RecName: Full=Agamous-like MADS-box protein AGL97 gi|12320999|gb|AAG50617.1|AC083835_2 hypothetical protein [Arabidopsis thaliana] gi|225898012|dbj|BAH30338.1| hypothetical protein [Arabidopsis thaliana] gi|332194005|gb|AEE32126.1| agamous-like MADS-box protein AGL97 [Arabidopsis thaliana]

 Score = 76.6 bits (187), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 57/78 (73%), Gaps = 4/78 (5%)

Query: 6  KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPV---SDTTFYTF 62
          KR+I +++   K  RAVSFSKRR GL +KA+E CL + +++A ++++PV   S+  FY+F
Sbjct: 5  KRKIAIEKIQNKNPRAVSFSKRRKGLYSKASELCLLSDAEIA-IIATPVSSNSNAAFYSF 63

Query: 63 GHSSVDAVLDAFVNNRAP 80
          GHSSVD V+ AF+ N+ P
Sbjct: 64 GHSSVDNVVAAFLANQRP 81

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15238246|ref|NP_196084.1| protein agamous-like 99 [Arabidopsis thaliana] gi|7406468|emb|CAB85570.1| MADS-box protein-like [Arabidopsis thaliana] gi|67633782|gb|AAY78815.1| MADS-box family protein [Arabidopsis thaliana] gi|332003385|gb|AED90768.1| protein agamous-like 99 [Arabidopsis thaliana]

 Score = 76.3 bits (186), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 37/78 (47%), Positives = 58/78 (74%), Gaps = 4/78 (5%)

Query: 6  KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPV---SDTTFYTF 62
          KR+I ++  + K+ RAV+FSKR  GL +KA++ CL + +Q+A ++++PV   S+ +FYTF
Sbjct: 5  KRKISIELIEKKDSRAVAFSKRSRGLYSKASDLCLLSDAQIA-IIATPVSSKSNVSFYTF 63

Query: 63 GHSSVDAVLDAFVNNRAP 80
          GHSSVD V+ AF+ N+ P
Sbjct: 64 GHSSVDNVVAAFLTNQRP 81

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15240962|ref|NP_198678.1| MADS-box protein AGL73 [Arabidopsis thaliana] gi|10176830|dbj|BAB10152.1| MADS-box protein-like [Arabidopsis thaliana] gi|32402438|gb|AAN52801.1| MADS-box protein AGL73 [Arabidopsis thaliana] gi|332006959|gb|AED94342.1| MADS-box protein AGL73 [Arabidopsis thaliana]

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 85/161 (52%), Gaps = 28/161 (17%)

Query: 1   MVAVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVS--DTT 58
           MV   KR+I ++    ++   V+ +KRR GL +KA++ CL + +Q+A+L + P S  D +
Sbjct: 1   MVKGTKRKIAIETIQKRDSLRVTCTKRRKGLYSKASQLCLLSDAQIAILATPPSSESDVS 60

Query: 59  FYTFGHSSVDAVLDAFVNNRAPEAA--DKELVRLGISMFNEVKDLELYDKKISKAIKSDG 116
           FY+FGHSSVDAV+ AF++ + P +A  D +  R  + +    K+L L             
Sbjct: 61  FYSFGHSSVDAVVSAFLSGKRPVSAPKDNKETREDVGICLTRKNLGL------------- 107

Query: 117 NLEREGFWEDYEKLGNSD------ESIGELGVIVDKLAKAK 151
                GFW + E L  S+      E+IG +  ++  L + +
Sbjct: 108 -----GFWWNDESLVRSENPQEISEAIGSMWTLLSNLKELR 143

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	225
TAIR|locus:2825756	266	AGL97 "AGAMOUS-like 97" [Arabi	0.328	0.278	0.487	2.5e-16
TAIR|locus:2158039	334	AT5G49420 [Arabidopsis thalian	0.417	0.281	0.39	7.5e-15
TAIR|locus:2184427	322	AGL99 "AGAMOUS-like 99" [Arabi	0.555	0.388	0.360	6.5e-14
TAIR|locus:2159848	349	AT5G38620 [Arabidopsis thalian	0.382	0.246	0.420	2.5e-13
TAIR|locus:2206016	191	AGL55 "AGAMOUS-like 55" [Arabi	0.408	0.481	0.410	3.4e-13
TAIR|locus:2181226	306	AGL39 "AGAMOUS-like 39" [Arabi	0.333	0.245	0.441	1e-11
TAIR|locus:2206320	226	AGL23 "AGAMOUS-like 23" [Arabi	0.666	0.663	0.304	1e-11
TAIR|locus:2157874	285	AGL83 "AGAMOUS-like 83" [Arabi	0.417	0.329	0.36	3.7e-11
TAIR|locus:2023741	323	AT1G48150 [Arabidopsis thalian	0.333	0.232	0.402	7.2e-11
TAIR|locus:2206081	201	AGL56 "AGAMOUS-like-56" [Arabi	0.471	0.527	0.321	1.2e-10

TAIR|locus:2825756 AGL97 "AGAMOUS-like 97" [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 2.5e-16, Sum P(2) = 2.5e-16
 Identities = 38/78 (48%), Positives = 57/78 (73%)

Query:     6 KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTT---FYTF 62
             KR+I +++   K  RAVSFSKRR GL +KA+E CL + +++A+ +++PVS  +   FY+F
Sbjct:     5 KRKIAIEKIQNKNPRAVSFSKRRKGLYSKASELCLLSDAEIAI-IATPVSSNSNAAFYSF 63

Query:    63 GHSSVDAVLDAFVNNRAP 80
             GHSSVD V+ AF+ N+ P
Sbjct:    64 GHSSVDNVVAAFLANQRP 81

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2158039 AT5G49420 [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 7.5e-15, Sum P(2) = 7.5e-15
 Identities = 39/100 (39%), Positives = 65/100 (65%)

Query:     1 MVAVG--KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDT- 57
             MV  G  KR+I ++    ++   V+ +KRR GL +KA++ CL + +Q+A+L + P S++ 
Sbjct:     1 MVKKGGTKRKIAIETIQKRDSLRVTCTKRREGLYSKASQLCLLSDAQIAILATPPSSESN 60

Query:    58 -TFYTFGHSSVDAVLDAFVNNRAPEAADKELVR--LGISM 94
              +FY+FGHSSVDAV+ AF++ + P   D +  R  +GI +
Sbjct:    61 VSFYSFGHSSVDAVVSAFLSGQRPVPKDNKETREDVGICL 100

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2184427 AGL99 "AGAMOUS-like 99" [Arabidopsis thaliana (taxid:3702)]

 Score = 183 (69.5 bits), Expect = 6.5e-14, P = 6.5e-14
 Identities = 48/133 (36%), Positives = 80/133 (60%)

Query:     6 KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVS---DTTFYTF 62
             KR+I ++  + K+ RAV+FSKR  GL +KA++ CL + +Q+A+ +++PVS   + +FYTF
Sbjct:     5 KRKISIELIEKKDSRAVAFSKRSRGLYSKASDLCLLSDAQIAI-IATPVSSKSNVSFYTF 63

Query:    63 GHSSVDAVLDAFVNNRAPEAA---DKELVRLGISMFNEVKDLELYDKKISKAIKSDGNLE 119
             GHSSVD V+ AF+ N+ P      D       +S   ++++L      +SK +K   +L+
Sbjct:    64 GHSSVDNVVAAFLTNQRPREGLGLDYWWEDERLSKSEDLEELRDAMDSMSKMLKDLKDLQ 123

Query:   120 RE-GFWEDYEKLG 131
              +    ED +K G
Sbjct:   124 NQRDCEEDVKKKG 136

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2159848 AT5G38620 [Arabidopsis thaliana (taxid:3702)]

 Score = 179 (68.1 bits), Expect = 2.5e-13, P = 2.5e-13
 Identities = 37/88 (42%), Positives = 60/88 (68%)

Query:     1 MVAVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVS--DTT 58
             MV   KR+I ++    ++   V+ +KRR GL +KA++ CL + +Q+A+L + P S  D +
Sbjct:     1 MVKGTKRKIAIETIQKRDSLRVTCTKRRKGLYSKASQLCLLSDAQIAILATPPSSESDVS 60

Query:    59 FYTFGHSSVDAVLDAFVNNRAPEAADKE 86
             FY+FGHSSVDAV+ AF++ + P +A K+
Sbjct:    61 FYSFGHSSVDAVVSAFLSGKRPVSAPKD 88

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2206016 AGL55 "AGAMOUS-like 55" [Arabidopsis thaliana (taxid:3702)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 39/95 (41%), Positives = 62/95 (65%)

Query:     6 KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTR-SQLALLVS--SPVSDTTFYTF 62
             KR+I +KR + K  RAV+F+KR+ GL +KA+E CL +  +Q+A+L +  S  S  +FY+F
Sbjct:     5 KRKIEMKRIEDKNVRAVAFTKRKSGLFHKASELCLLSPGTQIAILATPLSSHSHASFYSF 64

Query:    63 GHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNE 97
             GHSSVD V+ + ++N+ P     +  R G+  + E
Sbjct:    65 GHSSVDHVVSSLLHNQHPSLPTNQDNRSGLGFWWE 99

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2181226 AGL39 "AGAMOUS-like 39" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 34/77 (44%), Positives = 53/77 (68%)

Query:     6 KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPV-SDTTFYTF-G 63
             KR+I +K+R+TKEQRAV+ SKRR  + +KAA+ CL + + +A+ V+SP  S    Y+F G
Sbjct:    14 KRKIEIKKRETKEQRAVTCSKRRQTVFSKAADLCLISGANIAVFVTSPSDSSDVVYSFSG 73

Query:    64 HSSVDAVLDAFVNNRAP 80
             +SS   + D ++N + P
Sbjct:    74 YSSAYEIADCYLNRKPP 90

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2206320 AGL23 "AGAMOUS-like 23" [Arabidopsis thaliana (taxid:3702)]

 Score = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 49/161 (30%), Positives = 79/161 (49%)

Query:     4 VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFG 63
             +G+R++ + +   +    V+FSKR+ GL  KA+E+C    +++A++V SP      ++FG
Sbjct:     6 LGRRKVEIVKMTKESNLQVTFSKRKAGLFKKASEFCTLCDAKIAMIVFSPAGKV--FSFG 63

Query:    64 HSSVDAVLDAF---VNNRAPEAADKELVRLGISMFN----EVK-DLELYDK-KISKAIKS 114
             H +VD +LD F   V        D+   +L + M N    EVK ++E   K K S+A   
Sbjct:    64 HPNVDVLLDHFRGCVVGHNNTNLDESYTKLHVQMLNKSYTEVKAEVEKEQKNKQSRAQNE 123

Query:   115 DGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAI 155
               N   E +W       N  +S   + V+ D      EKAI
Sbjct:   124 RENENAEEWWSKSPLELNLSQSTCMIRVLKDLKKIVDEKAI 164

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0009553 "embryo sac development" evidence=IMP

GO:0009658 "chloroplast organization" evidence=IMP

TAIR|locus:2157874 AGL83 "AGAMOUS-like 83" [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 3.7e-11, P = 3.7e-11
 Identities = 36/100 (36%), Positives = 64/100 (64%)

Query:     1 MVAVG--KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDT- 57
             MV  G  KR+I ++     +   V+ +KRR GL +KA++ CL + +Q+A+L + P S++ 
Sbjct:    39 MVKKGGTKRKIAIETIQKSDYLRVTCTKRREGLFSKASQLCLLSDAQIAILATPPTSESN 98

Query:    58 -TFYTFGHSSVDAVLDAFVNNR--APEAADKELVRLGISM 94
              +FY+FGHSSVDAV+ +F++ +   P   D + +R  +++
Sbjct:    99 ISFYSFGHSSVDAVVSSFLSGQRCVPLQEDTKEMREDVAI 138

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2023741 AT1G48150 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 7.2e-11, P = 7.2e-11
 Identities = 31/77 (40%), Positives = 55/77 (71%)

Query:     6 KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDT-TFYTF-G 63
             KR+I +++R TK+QR+V+ SKRR  L +KAA+ CL + + +A+ V+SP  ++   Y+F G
Sbjct:    17 KRKIEIEKRMTKQQRSVACSKRRPTLFSKAADLCLLSGANIAVFVTSPDENSDVVYSFSG 76

Query:    64 HSSVDAVLDAFVNNRAP 80
             +S    ++D ++NN++P
Sbjct:    77 YSHASEIVDCYLNNKSP 93

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2206081 AGL56 "AGAMOUS-like-56" [Arabidopsis thaliana (taxid:3702)]

 Score = 149 (57.5 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 36/112 (32%), Positives = 69/112 (61%)

Query:     6 KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRT-RSQLALLVSSPVSDT--TFYTF 62
             K +I +K+   K  + V+F+KRR GL  KA++ CL +  +Q+A+L +   S +  +FY+F
Sbjct:     5 KTKIEIKKIINKPAKTVAFTKRREGLFRKASQLCLLSPATQIAILAAPMTSKSHASFYSF 64

Query:    63 GHSSVDAVLDAFVNNRAPEAADKELVRLGISMFNEVKDLELYD--KKISKAI 112
             GHSSVD V+ + + +  P  A+++  R G+  + E K  ++ +  +++ +A+
Sbjct:    65 GHSSVDNVVSSLLYDHPPLTANQDN-RSGLGFWWEDKRFDVSENVEELKEAV 115

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	225
cd00266	83	cd00266, MADS_SRF_like, SRF-like/Type I subfamily	3e-12
smart00432	59	smart00432, MADS, MADS domain	7e-12
cd00120	59	cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and	6e-11
cd00265	77	cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer fa	2e-10
pfam00319	51	pfam00319, SRF-TF, SRF-type transcription factor (	2e-06
COG5068	412	COG5068, ARG80, Regulator of arginine metabolism a	0.003

>gnl|CDD|238166 cd00266, MADS_SRF_like, SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators

 Score = 60.4 bits (147), Expect = 3e-12
 Identities = 32/82 (39%), Positives = 48/82 (58%), Gaps = 3/82 (3%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+++I +KR + K++RAV+FSKRR GL  KA+E      +++A++V SP      Y F  
Sbjct: 1  GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSP--SGKLYVFWP 58

Query: 65 SS-VDAVLDAFVNNRAPEAADK 85
          SS V+ V+  F    A E   K
Sbjct: 59 SSEVEGVISRFEVLSALERKKK 80

Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. Length = 83

>gnl|CDD|197721 smart00432, MADS, MADS domain

 Score = 58.3 bits (142), Expect = 7e-12
 Identities = 23/49 (46%), Positives = 34/49 (69%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSP 53
          G+R+I +KR + K  R V+FSKRR+GL  KA E  +   +++AL+V SP
Sbjct: 1  GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSP 49

Length = 59

>gnl|CDD|238067 cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators

 Score = 55.6 bits (135), Expect = 6e-11
 Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 2/61 (3%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+ +I +KR + K  R V+FSKRR+GL  KA+E  +   +++A++V SP      Y F  
Sbjct: 1  GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSP--SGKLYEFWS 58

Query: 65 S 65
          S
Sbjct: 59 S 59

Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. Length = 59

>gnl|CDD|238165 cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators

 Score = 54.9 bits (133), Expect = 2e-10
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+ +I +KR +    R V+FSKRR+GLL KA E  +   +++AL++ S       Y F  
Sbjct: 1  GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSG--KLYEFSS 58

Query: 65 SSVDAVLDAFVNN 77
           S++ +++ +   
Sbjct: 59 PSMEKIIERYQKT 71

Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. Length = 77

>gnl|CDD|109379 pfam00319, SRF-TF, SRF-type transcription factor (DNA-binding and dimerisation domain)

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 12 KRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTF 62
          KR + K  R V+FSKRR+G+  KA E  +   +++A+++ S       Y +
Sbjct: 1  KRIENKSNRQVTFSKRRNGIFKKAHELSVLCDAEVAVIIFSS--TGKLYEY 49

Length = 51

>gnl|CDD|227400 COG5068, ARG80, Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]

 Score = 37.7 bits (87), Expect = 0.003
 Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 4   VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDT-TFYTF 62
           V  R+I +     K +R+V+FSKR+HG+  KA E  + T +++ LLV S      TF T 
Sbjct: 81  VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTP 140

Query: 63  GHSSV 67
              SV
Sbjct: 141 KLESV 145

Length = 412

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	225
cd00265	77	MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-li	99.96
KOG0014	195	consensus MADS box transcription factor [Transcrip	99.96
cd00266	83	MADS_SRF_like SRF-like/Type I subfamily of MADS (M	99.94
smart00432	59	MADS MADS domain.	99.93
cd00120	59	MADS MADS: MCM1, Agamous, Deficiens, and SRF (seru	99.92
PF00319	51	SRF-TF: SRF-type transcription factor (DNA-binding	99.88
KOG0015	338	consensus Regulator of arginine metabolism and rel	99.74
COG5068	412	ARG80 Regulator of arginine metabolism and related	99.35
PF01486	100	K-box: K-box region; InterPro: IPR002487 MADS gene	97.3
PF01486	100	K-box: K-box region; InterPro: IPR002487 MADS gene	90.72

>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators

Probab=99.96  E-value=1.1e-30  Score=187.12  Aligned_cols=73  Identities=32%  Similarity=0.608  Sum_probs=70.6

Q ss_pred             CccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHHhhcCc
Q 042235            5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRA   79 (225)
Q Consensus         5 gr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry~~~~~   79 (225)
                      ||+||+|++|+|+.+|++||+||+.||||||+|||+||||+||+|||||.  |++|+|++|++++||+||...+.
T Consensus         1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~--gk~~~f~s~s~~~vl~ry~~~~~   73 (77)
T cd00265           1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSS--GKLYEFSSPSMEKIIERYQKTSG   73 (77)
T ss_pred             CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCC--CceEEecCCCHHHHHHHHHhccc
Confidence            89999999999999999999999999999999999999999999999998  58999999999999999998864

Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.

>KOG0014 consensus MADS box transcription factor [Transcription]

Probab=99.96  E-value=3e-30  Score=214.32  Aligned_cols=76  Identities=42%  Similarity=0.737  Sum_probs=72.1

Q ss_pred             CCccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCc--hhhHHHHHhhcCccc
Q 042235            4 VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSS--VDAVLDAFVNNRAPE   81 (225)
Q Consensus         4 mgr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~sps--v~~Vl~Ry~~~~~~e   81 (225)
                      |||+||+|++|+|+++|+|||+|||.||||||+||||||||+||||||||.  |++|+|++++  |+.|++||.....+.
T Consensus         1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~--~~~~~~~~~~~~~~~v~~~~~~~~~~~   78 (195)
T KOG0014|consen    1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPS--GKLYEFGSSDESVDAVVDRFLNLTEPS   78 (195)
T ss_pred             CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCC--CCccccCCcchhHHHHHHHHHhhhhhh
Confidence            899999999999999999999999999999999999999999999999999  5999999986  999999999886543

>cd00266 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators

Probab=99.94  E-value=5.3e-28  Score=175.58  Aligned_cols=75  Identities=41%  Similarity=0.640  Sum_probs=69.6

Q ss_pred             CccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCc-hhhHHHHHhhcCccc
Q 042235            5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSS-VDAVLDAFVNNRAPE   81 (225)
Q Consensus         5 gr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~sps-v~~Vl~Ry~~~~~~e   81 (225)
                      ||+||+|++|+|+.+|++||+|||.||||||+||||||||+||+|||||.+  +++.|++++ ++.+|++|...+..+
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~--~~~~~~~~~~~~~~l~~~~~~~~~~   76 (83)
T cd00266           1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSG--KLYVFWPSSEVEGVISRFEVLSALE   76 (83)
T ss_pred             CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCC--CcceecCcHHHHHHHHHHhhcCHhh
Confidence            799999999999999999999999999999999999999999999999984  688887765 999999999987543

Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.

>smart00432 MADS MADS domain

Probab=99.93  E-value=3.5e-27  Score=160.07  Aligned_cols=59  Identities=42%  Similarity=0.730  Sum_probs=57.0

Q ss_pred             CccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCC
Q 042235            5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHS   65 (225)
Q Consensus         5 gr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~sp   65 (225)
                      ||+||+|++|+|+..|++||+||+.||+|||+|||+||||+||+|||||+  |+++.|++|
T Consensus         1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~--g~~~~~~~p   59 (59)
T smart00432        1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPT--GKLYEFASP   59 (59)
T ss_pred             CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCC--CCeeeccCC
Confidence            89999999999999999999999999999999999999999999999998  589999886

>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators

Probab=99.92  E-value=1.6e-26  Score=156.90  Aligned_cols=59  Identities=41%  Similarity=0.673  Sum_probs=56.5

Q ss_pred             CccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCC
Q 042235            5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHS   65 (225)
Q Consensus         5 gr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~sp   65 (225)
                      ||+||+|++|+|+..|++||+||+.||+|||+|||+||||+||+|||||+  |+++.|++|
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~--g~~~~~~~~   59 (59)
T cd00120           1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPS--GKLYEFWSS   59 (59)
T ss_pred             CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCC--CCcccccCC
Confidence            79999999999999999999999999999999999999999999999998  489998875

Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.

>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation

Probab=99.88  E-value=1.6e-24  Score=142.60  Aligned_cols=51  Identities=43%  Similarity=0.634  Sum_probs=46.1

Q ss_pred             eecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCC
Q 042235           12 KRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH   64 (225)
Q Consensus        12 ~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~s   64 (225)
                      ++|+|+..|++||+||+.||+|||+|||+||||+||+|||||.  |++|+|+|
T Consensus         1 K~I~n~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~~iv~~~~--g~~~~f~s   51 (51)
T PF00319_consen    1 KRIENKSRRKVTFSKRKKGLFKKASELSTLCGVDVALIVFSPD--GKLYTFPS   51 (51)
T ss_dssp             S--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEEETT--SEEEEEES
T ss_pred             CCccchhHhHhHHHHHHhhhhhccceeeeecCCeEEEEEECCC--CCEEEecC
Confidence            5899999999999999999999999999999999999999998  59999976

SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....

>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]

Probab=99.74  E-value=5.8e-19  Score=152.17  Aligned_cols=67  Identities=33%  Similarity=0.539  Sum_probs=62.2

Q ss_pred             CCccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHH
Q 042235            4 VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLD   72 (225)
Q Consensus         4 mgr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~   72 (225)
                      -||+||+|+||+|+..|.+||||||.||||||+||+||+|.+|-|+|.|..  |.+|+|++|..+.||.
T Consensus        62 ~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEt--GhVyTFaTpKLep~i~  128 (338)
T KOG0015|consen   62 TGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATPKLEPMIT  128 (338)
T ss_pred             cceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecC--cceEEecccccccccc
Confidence            369999999999999999999999999999999999999999999999998  5899999987666553

>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]

Probab=99.35  E-value=3.6e-13  Score=121.21  Aligned_cols=68  Identities=34%  Similarity=0.471  Sum_probs=63.4

Q ss_pred             CCccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHH
Q 042235            4 VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDA   73 (225)
Q Consensus         4 mgr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~R   73 (225)
                      |||+||.|.+|+|+.+|.|||+||+.||+|||.||++|+|.+|.++|.|..  |.++.|++|..+.|+.-
T Consensus        81 ~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~--g~v~tf~tp~~e~v~~~  148 (412)
T COG5068          81 VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISEN--GLVHTFTTPKLESVVKS  148 (412)
T ss_pred             cccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCC--CceeeecCCcccccccc
Confidence            789999999999999999999999999999999999999999999999987  58999999987766643

>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development

Probab=97.30  E-value=0.0016  Score=48.59  Aligned_cols=64  Identities=23%  Similarity=0.269  Sum_probs=50.1

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHhcCccccCchhhhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Q 042235           88 VRLGISMFNEVKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNSDESIGELGVIVDKLAKAKEKAILRLTDLLA  163 (225)
Q Consensus        88 ~~~~~~l~kEl~~Le~qle~l~k~~r~~k~l~~~~~~~~i~~Lq~~~lsl~EL~~l~~~Le~~l~~i~~R~~~l~~  163 (225)
                      ....+.+..|+..|..+++.+....|.   ++|+    +++     +++++||..|+..|+..+..|+.|+.++..
T Consensus        11 ~~~~e~~~~e~~~L~~~~~~L~~~~R~---~~Ge----dL~-----~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~   74 (100)
T PF01486_consen   11 DSQHEELQQEIAKLRKENESLQKELRH---LMGE----DLE-----SLSLKELQQLEQQLESALKRVRSRKDQLLM   74 (100)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhc---cccc----ccc-----ccchHHHHHHHHhhhhhHHHHHHHHHHHHH
Confidence            345577888899999888888544432   2454    444     599999999999999999999999998754

The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development

Probab=90.72  E-value=0.11  Score=38.65  Aligned_cols=37  Identities=22%  Similarity=0.249  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCccccCchhhhhhhcCCC
Q 042235           94 MFNEVKDLELYDKKISKAIKSDGNLEREGFWEDYEKLGNS  133 (225)
Q Consensus        94 l~kEl~~Le~qle~l~k~~r~~k~l~~~~~~~~i~~Lq~~  133 (225)
                      ..++|+.||++++..+.+||.+|   .+.|.+.+..|+++
T Consensus        47 s~~eL~~LE~~Le~aL~~VR~rK---~~~l~~~i~~l~~k   83 (100)
T PF01486_consen   47 SLKELQQLEQQLESALKRVRSRK---DQLLMEQIEELKKK   83 (100)
T ss_pred             chHHHHHHHHhhhhhHHHHHHHH---HHHHHHHHHHHHHH
Confidence            57999999999999999999998   67776666655543

The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	225
1mnm_A	100	Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLE		2e-05

>pdb|1MNM|A Chain A, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX Crystal Structure Length = 100

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 42/67 (62%), Gaps = 4/67 (5%)
Query: 6  KRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTF-YTFGH 64
          +R+I +K  + K +R V+FSKR+HG++ KA E  + T +Q+ LLV   VS+T   YTF  
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLV---VSETGLVYTFST 74
Query: 65 SSVDAVL 71
             + ++
Sbjct: 75 PKFEPIV 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	225
1hbx_A	92	SRF, serum response factor; gene regulation, trans	2e-13
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	2e-13
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	2e-12
1egw_A	77	MADS box transcription enhancer factor 2, polypept	1e-08
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	1e-08

>1hbx_A SRF, serum response factor; gene regulation, transcription complex; 3.15A {Homo sapiens} SCOP: d.88.1.1 PDB: 1srs_A* Length = 92

 Score = 62.9 bits (153), Expect = 2e-13
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+ +I ++  D K +R  +FSKR+ G++ KA E    T +Q+ LLV+S       YTF  
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETG--HVYTFAT 68

Query: 65 SSVDAVLDAFVNNRAPEAA 83
            +  ++ +       +  
Sbjct: 69 RKLQPMITSETGKALIQTC 87

>1k6o_B SRF, serum response factor; protein/DNA complex, transcription factor, combinatorial gene regulation, ETS proteins, MADS-box proteins; 3.19A {Homo sapiens} SCOP: d.88.1.1 Length = 103

 Score = 63.0 bits (153), Expect = 2e-13
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+ +I ++  D K +R  +FSKR+ G++ KA E    T +Q+ LLV+S       YTF  
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETG--HVYTFAT 67

Query: 65 SSVDAVLDAFVNNRAPEAA 83
            +  ++ +       +  
Sbjct: 68 RKLQPMITSETGKALIQTC 86

>1mnm_A Protein (MCM1 transcriptional regulator); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: d.88.1.1 Length = 100

 Score = 60.6 bits (147), Expect = 2e-12
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
           +R+I +K  + K +R V+FSKR+HG++ KA E  + T +Q+ LLV S       YTF  
Sbjct: 17 ERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETG--LVYTFST 74

Query: 65 SSVDAVLDAF 74
             + ++   
Sbjct: 75 PKFEPIVTQQ 84

>1egw_A MADS box transcription enhancer factor 2, polypeptide A; MADS-box transcription factor, DNA/protein complex, transcription/DNA; HET: DNA; 1.50A {Homo sapiens} SCOP: d.88.1.1 PDB: 1c7u_A 3mu6_A* Length = 77

 Score = 49.7 bits (119), Expect = 1e-08
 Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+++I + R   +  R V+F+KR+ GL+ KA E  +    ++AL++ +  S    + +  
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFN--SSNKLFQYAS 58

Query: 65 SSVDAVLD 72
          + +D VL 
Sbjct: 59 TDMDKVLL 66

>3p57_A Myocyte-specific enhancer factor 2A; protein-DNA complex, transcription factor, transcriptional activation, zinc finger; HET: DNA; 2.19A {Homo sapiens} PDB: 3kov_A* 1tqe_P 1n6j_A Length = 90

 Score = 49.7 bits (119), Expect = 1e-08
 Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+++I + R   +  R V+F+KR+ GL+ KA E  +    ++AL++ +  S    + +  
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFN--SSNKLFQYAS 58

Query: 65 SSVDAVLDAFVNNRAPE 81
          + +D VL  +     P 
Sbjct: 59 TDMDKVLLKYTEYNEPH 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	225
1egw_A	77	MADS box transcription enhancer factor 2, polypept	100.0
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	100.0
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	99.97
1hbx_A	92	SRF, serum response factor; gene regulation, trans	99.97
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	99.97
3twe_A	27	Alpha4H; unknown function; HET: PGE; 1.36A {Synthe	89.31

>1egw_A MADS box transcription enhancer factor 2, polypeptide A; MADS-box transcription factor, DNA/protein complex, transcription/DNA; HET: DNA; 1.50A {Homo sapiens} SCOP: d.88.1.1 PDB: 1c7u_A 3mu6_A*

Probab=100.00  E-value=5.9e-35  Score=207.21  Aligned_cols=74  Identities=26%  Similarity=0.552  Sum_probs=69.6

Q ss_pred             CccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHHhhcCcc
Q 042235            5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAP   80 (225)
Q Consensus         5 gr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry~~~~~~   80 (225)
                      ||+||+|++|+|+++|+|||+|||.||||||+||||||||+||||||||.  |++|+|+||+|+.||+||...+.+
T Consensus         1 GR~Ki~ik~I~n~~~R~vTfsKRr~GL~KKA~ELsvLCdaeV~livfs~~--gk~~~~~s~~~~~il~ry~~~~~~   74 (77)
T 1egw_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYASTDMDKVLLKYTEYNEP   74 (77)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTT--CCEEEEESSCHHHHHHHHHHC---
T ss_pred             CCceeeeEEecCchHHHHHHHHhHHHHHHHHHHHhcccCCeEEEEEECCC--CCEeeCCCCCHHHHHHHHHhccCC
Confidence            89999999999999999999999999999999999999999999999998  599999999999999999988643

>3p57_A Myocyte-specific enhancer factor 2A; protein-DNA complex, transcription factor, transcriptional activation, zinc finger; HET: DNA; 2.19A {Homo sapiens} PDB: 3kov_A* 1tqe_P 1n6j_A

Probab=100.00  E-value=1.2e-34  Score=210.55  Aligned_cols=76  Identities=25%  Similarity=0.539  Sum_probs=72.8

Q ss_pred             CccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHHhhcCccch
Q 042235            5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNRAPEA   82 (225)
Q Consensus         5 gr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry~~~~~~e~   82 (225)
                      ||+||+|++|+|+.+|+|||+|||.||||||+||||||||+||||||||.  |++|+|+||+|+.||+||...+.+..
T Consensus         1 GR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valiifs~~--gk~~~f~s~~~~~il~rY~~~~~~~~   76 (90)
T 3p57_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYASTDMDKVLLKYTEYNEPHE   76 (90)
T ss_dssp             CCSCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTT--CCEEEEESSCHHHHHHHHHHCCSCCC
T ss_pred             CCCcceeEEecCchHHHHHHHHhhhhHHHHHHHHHhccCCceEEEEECCC--CCEEEeCCCCHHHHHHHHHhcCcccc
Confidence            89999999999999999999999999999999999999999999999998  58999999999999999999886654

>1mnm_A Protein (MCM1 transcriptional regulator); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: d.88.1.1

Probab=99.97  E-value=3.9e-33  Score=206.02  Aligned_cols=73  Identities=33%  Similarity=0.509  Sum_probs=69.9

Q ss_pred             CCCccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHHhhc
Q 042235            3 AVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNN   77 (225)
Q Consensus         3 ~mgr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry~~~   77 (225)
                      .|||+||+|++|+|+.+|+|||+|||.||||||+||||||||+||||||||.  |++|+|+||++..||++|...
T Consensus        15 ~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~--gk~~~f~sps~~~il~r~~G~   87 (100)
T 1mnm_A           15 QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSET--GLVYTFSTPKFEPIVTQQEGR   87 (100)
T ss_dssp             CCCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTT--CCEEEEECTTTTHHHHSHHHH
T ss_pred             CCCccceeeEEecCcchhhhhhhHhhhhHHHHHHHHHHhcCCcEEEEEecCC--CCcceecCCCHHHHHHHhhCC
Confidence            4999999999999999999999999999999999999999999999999998  599999999999999998654

>1hbx_A SRF, serum response factor; gene regulation, transcription complex; 3.15A {Homo sapiens} SCOP: d.88.1.1 PDB: 1srs_A*

Probab=99.97  E-value=5.5e-33  Score=202.65  Aligned_cols=72  Identities=31%  Similarity=0.460  Sum_probs=68.5

Q ss_pred             CCCccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHHhh
Q 042235            3 AVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVN   76 (225)
Q Consensus         3 ~mgr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry~~   76 (225)
                      .|||+||+|++|+|+.+|+|||+|||.||||||+||||||||+||||||||.  |++|+|+||+|+.+|++|..
T Consensus         9 ~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~V~livfs~~--gk~~~f~s~~~~~~i~~~~G   80 (92)
T 1hbx_A            9 TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATRKLQPMITSETG   80 (92)
T ss_dssp             SCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTT--SCEEEEECGGGGGGTSSHHH
T ss_pred             CCCcceEEEEEecChhHHHHHHHHhhhhHHHHHHHHHhhcCCceEEEEECCC--CCEEEecCCCHHHHHhhhcc
Confidence            3999999999999999999999999999999999999999999999999998  59999999999999996643

>1k6o_B SRF, serum response factor; protein/DNA complex, transcription factor, combinatorial gene regulation, ETS proteins, MADS-box proteins; 3.19A {Homo sapiens} SCOP: d.88.1.1

Probab=99.97  E-value=2.1e-32  Score=203.26  Aligned_cols=70  Identities=31%  Similarity=0.471  Sum_probs=67.5

Q ss_pred             CCCccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHH
Q 042235            3 AVGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAF   74 (225)
Q Consensus         3 ~mgr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry   74 (225)
                      .|||+||+|++|+|+.+|+|||+|||.||||||+||||||||+||||||||.  |++|+|++|+|+.||+++
T Consensus         8 ~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~--gk~~~f~s~~~~~vi~~~   77 (103)
T 1k6o_B            8 TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATRKLQPMITSE   77 (103)
T ss_dssp             SCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECSS--SCEEEEECGGGGGGTSSH
T ss_pred             CCCcceeEEEEecCchHHHHhHhHhhHhHHHHHHHHHhhhCCceEEEEEeCC--CCeeeecCccHHHHHHhh
Confidence            3999999999999999999999999999999999999999999999999998  599999999999999874

>3twe_A Alpha4H; unknown function; HET: PGE; 1.36A {Synthetic} PDB: 3twf_A* 4g4m_A*

Probab=89.31  E-value=0.65  Score=24.67  Aligned_cols=23  Identities=26%  Similarity=0.472  Sum_probs=19.3

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHh
Q 042235           92 ISMFNEVKDLELYDKKISKAIKS  114 (225)
Q Consensus        92 ~~l~kEl~~Le~qle~l~k~~r~  114 (225)
                      ..+.+|++.|++.+.++++..|+
T Consensus         4 delykeledlqerlrklrkklrs   26 (27)
T 3twe_A            4 DELYKELEDLQERLRKLRKKLRS   26 (27)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcC
Confidence            45789999999999999888765

---

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	225
d1egwa_	71	d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {	2e-15
d1mnma_	85	d.88.1.1 (A:) MCM1 transcriptional regulator {Bake	9e-15
d1srsa_	84	d.88.1.1 (A:) Serum response factor (SRF) core {Hu	1e-14

>d1egwa_ d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: Myocyte enhancer factor Mef2a core
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.2 bits (162), Expect = 2e-15
 Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+++I + R   +  R V+F+KR+ GL+ KA E  +    ++AL++ +  +    + +  
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSN--KLFQYAS 58

Query: 65 SSVDAVLDAF 74
          + +D VL  +
Sbjct: 59 TDMDKVLLKY 68

>d1mnma_ d.88.1.1 (A:) MCM1 transcriptional regulator {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 85

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: MCM1 transcriptional regulator
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 65.1 bits (159), Expect = 9e-15
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
           +R+I +K  + K +R V+FSKR+HG++ KA E  + T +Q+ LLV S       YTF  
Sbjct: 3  ERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETG--LVYTFST 60

Query: 65 SSVDAVLDAF 74
             + ++   
Sbjct: 61 PKFEPIVTQQ 70

>d1srsa_ d.88.1.1 (A:) Serum response factor (SRF) core {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: Serum response factor (SRF) core
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.8 bits (158), Expect = 1e-14
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 5  GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGH 64
          G+ +I ++  D K +R  +FSKR+ G++ KA E    T +Q+ LLV+S       YTF  
Sbjct: 3  GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASE--TGHVYTFAT 60

Query: 65 SSVDAVLD 72
            +  ++ 
Sbjct: 61 RKLQPMIT 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	225
d1egwa_	71	Myocyte enhancer factor Mef2a core {Human (Homo sa	100.0
d1srsa_	84	Serum response factor (SRF) core {Human (Homo sapi	99.97
d1mnma_	85	MCM1 transcriptional regulator {Baker's yeast (Sac	99.97

>d1egwa_ d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: Myocyte enhancer factor Mef2a core
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.1e-35  Score=203.56  Aligned_cols=71  Identities=25%  Similarity=0.538  Sum_probs=68.6

Q ss_pred             CccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHHhhc
Q 042235            5 GKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNN   77 (225)
Q Consensus         5 gr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry~~~   77 (225)
                      ||+||+|++|+|+..|+|||+|||.||||||+|||+||||+||||||||.  |++|+|+||++++||+||..+
T Consensus         1 GR~Ki~ik~Ie~~~~R~vTFsKRk~GL~KKa~ELs~LC~~~valiv~s~~--gk~~~f~s~~~~~vl~ry~~~   71 (71)
T d1egwa_           1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYASTDMDKVLLKYTEY   71 (71)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTT--CCEEEEESSCHHHHHHHHHHC
T ss_pred             CCccceEEeccCCchheeehhHhhhhHHHHHHHHhhccCCcEEEEEEcCC--CCEEEeeCCCHHHHHHHHhcC
Confidence            89999999999999999999999999999999999999999999999998  589999999999999999763

>d1srsa_ d.88.1.1 (A:) Serum response factor (SRF) core {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: Serum response factor (SRF) core
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.9e-33  Score=198.63  Aligned_cols=72  Identities=31%  Similarity=0.461  Sum_probs=69.2

Q ss_pred             CCccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHHhhc
Q 042235            4 VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNN   77 (225)
Q Consensus         4 mgr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry~~~   77 (225)
                      +||+||+|++|+|+..|+|||+|||.||||||+|||+||||+||||||||.  |++|+|+||+++.||++|...
T Consensus         2 ~GR~Ki~i~~Ie~~~~R~vTFsKRr~GL~KKa~ELs~Lc~~~v~liv~s~~--gk~~~f~s~~~~~vi~~~~~~   73 (84)
T d1srsa_           2 RGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATRKLQPMITSETGK   73 (84)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTT--CCEEEEECGGGHHHHSSHHHH
T ss_pred             CCCceeeEEeecCcchhhhhhHHhhhhHHHHHHHHhcccCCcEEEEEEcCC--CCEEEeeCCCHHHHHHHHHHH
Confidence            699999999999999999999999999999999999999999999999998  589999999999999999754

>d1mnma_ d.88.1.1 (A:) MCM1 transcriptional regulator {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: SRF-like
superfamily: SRF-like
family: SRF-like
domain: MCM1 transcriptional regulator
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.97  E-value=5.2e-33  Score=198.41  Aligned_cols=73  Identities=33%  Similarity=0.511  Sum_probs=70.1

Q ss_pred             CCccccceeecCCCCCcccchhccccchhhhhhhhhcccCcceeeeeccCCCCCceeeeCCCchhhHHHHHhhcC
Q 042235            4 VGKRRIPLKRRDTKEQRAVSFSKRRHGLLNKAAEYCLRTRSQLALLVSSPVSDTTFYTFGHSSVDAVLDAFVNNR   78 (225)
Q Consensus         4 mgr~ki~i~~I~~~~~R~~tf~kRr~gl~KKa~ELs~LC~~~valIvfs~~~~gk~~~f~spsv~~Vl~Ry~~~~   78 (225)
                      -||+||+|++|+|+..|+|||+|||.||||||+|||+||||+||||||||.  |++|+|+||+|+.||+||...+
T Consensus         2 k~R~Ki~i~~I~~~~~R~vTFsKRr~GL~KKa~ELsvLc~a~vaviv~s~~--gk~~~f~sp~v~~vl~r~~~~~   74 (85)
T d1mnma_           2 KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSET--GLVYTFSTPKFEPIVTQQEGRN   74 (85)
T ss_dssp             CCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTT--CCEEEEECTTTTHHHHSHHHHH
T ss_pred             CCccceEEEEecCCchhhhhhHHHHhhHHHHHHHHhccCCCcEEEEEEcCC--CCEEeccCCCHHHHHHHHhccc
Confidence            589999999999999999999999999999999999999999999999998  5899999999999999998764