Citrus Sinensis ID: 040948

---

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------
Protein Sequence
MDAETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILETKIDEASSVEELGVVYNKVESKLASMRETIELAIIEEQKNQQFAAPPIRPPVYGNNLLLSDYVSSSSNNNNNNNDFGRHESFLFPPSQNHQINGGENGNIGDNVMLPDNNFLPSEIGNNFMLPDNSLLPGYVHANKGAWAQENFSGLIGGPCCNCGRGPSS
Secondary Structure (PSIPRED)
cccccccccccEEEEEEcccccccccHHcHHccccHHHHHHHHHHHHHccEEEEEEcccccEEEEccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEcccEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHcccEEEEEEEccccccccccccHHHHHHHHHHHHHcccHccHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccEEEEEcccccHHHHcccccccccccccccccc
Coil and Loop (DISEMBL)
mdaettqvKRKRSVKLIEehggnsrqgnfEKRKETLKNKAHELETLCDVMVCLVcygpdgkvetwpedktkVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILETKIDEASSVEELGVVYNKVESKLASMRETIELAIIEEQknqqfaappirppvygnnlLLSDYVSsssnnnnnnndfgrhesflfppsqnhqinggengnigdnvmlpdnnflpseignnfmlpdnsllpgyvhankgawaqenfsgliggpccncgrgpss
Flexible Loop (DISEMBL)
mdaettqvkrkrsvklieehggnsrqgnfekRKETLKNKAHELETLCDVMVCLVCYGPdgkvetwpedktkvNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILetkideassveeLGVVYNKVESKLASMRETIELAIIEEQKNQQFAAPPIRPPVYGNNLLLSDYVSSSSNNNNNNNDFGRHESFLFPPSQNHQINGGENGNIGDNVMLPDNNFLPSEIGNNFMLPDNSLLPGYVHANKGAWAQENFSGLIGGPCCNCGRGPSS
Low Complexity Region (SEG)
MDAETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESkkqklmekkkAFVEKMFSILETKIDEASSVEELGVVYNKVESKLASMRETIELAIIEEQKNQQFAAPPIRPPVYGnnlllsdyvssssnnnnnnnDFGRHESFLFPPSQNHQinggengnigdnVMLPDNNFLPSEIGNNFMLPDNSLLPGYVHANKGAWAQENFSGLIGGPCCNCGRGPSS
Disordered region (IsUnstruct)
*****************************************ELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELF**********KKAFVEKMFSILETKIDEASSVEELGVVYNKVESKLASMRETIELAIIEE*****FA***IRPPVYGNNLLLS*******************************************VMLPDNNFLPSEIGNNFMLPDNSLLPGYVHANKGAWAQENFSGLIGGPCCNCG*****
Disordered Region (DISOPRED)
*****TQ**RKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKY*****************************************************SVEELGVVYNKVESKLASMRETIE******************************************************************************NFLPSEIGNNFMLPDNSLLPGYVHANKGAWAQENFSGLIGGPCC*CGR****
Disordered Region (DISEMBL)
*************VKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILETKIDEASSVEELGVVYNKVESKLASMRETIELAIIEEQKNQQFAAPPIRPPVYGNNLLLSDYVSSSSNNNNNNNDFGRHESFLFPPSQNHQINGGENGNIGDNVMLPDNNFLPSEIGNNFMLPDNSLLPGYVHANKGAWAQENFSGLIGGPCCNCGRGPSS
Disordered Region (DISPRO)
*****TQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILETKIDEASSVEELGVVYNKVESKLASMRETIELAIIEEQKNQQFAAPPIRPPVYGNNLLLSDYVSSSSNNNNNNNDFGRHESFLFPPSQNHQINGGENGNIGDNVMLPDNNFLPSEIGNNFMLPDNSLLPGYVHANKGAWAQENFSGLIGGPCCNCG*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDAETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKKAEQRLDLxxxxxxxxxxxxxxxxxxxxxMFSILETKIDEASSVEELGVVYNKVESKLASMRETIELAIIEEQKNQQFAAPPIRPPVYGNNLLLSDYVSSSSNNNNNNNDFGRHESFLFPPSQNHQINGGENGNIGDNVMLPDNNFLPSEIGNNFMLPDNSLLPGYVHANKGAWAQENFSGLIGGPCCNCGRGPSS
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	286	2.2.26 [Sep-21-2011]
Q7X9H9	289	Agamous-like MADS-box pro	no	no	0.199	0.197	0.465	7e-10
Q7XJK8	278	MADS-box transcription fa	no	no	0.346	0.356	0.339	2e-06
Q9XJ66	228	MADS-box transcription fa	yes	no	0.237	0.298	0.361	8e-06
Q9XJ60	230	MADS-box transcription fa	no	no	0.479	0.595	0.317	8e-06
P35632	232	Floral homeotic protein A	no	no	0.465	0.573	0.251	3e-05
Q7XJK5	320	Agamous-like MADS-box pro	no	no	0.412	0.368	0.304	4e-05
Q9C6V4	464	Agamous-like MADS-box pro	no	no	0.244	0.150	0.323	4e-05
Q7XJK6	366	Agamous-like MADS-box pro	no	no	0.503	0.393	0.277	7e-05
Q9FJK3	321	Agamous-like MADS-box pro	no	no	0.395	0.352	0.308	9e-05
Q69TG5	245	MADS-box transcription fa	no	no	0.188	0.220	0.410	0.0001

>sp|Q7X9H9|AGL93_ARATH Agamous-like MADS-box protein AGL93 OS=Arabidopsis thaliana GN=AGL93 PE=1 SV=1

 Score = 64.7 bits (156), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 42/58 (72%), Gaps = 1/58 (1%)

Query: 28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGK-VETWPEDKTKVNDMIDKYKELRE 84
          N   R++T+  KA EL TLC++ VC++ YG DGK ++TWP+D++KV DM +++  L E
Sbjct: 37 NLSMREQTMFKKALELSTLCNIDVCVIYYGRDGKLIKTWPDDQSKVRDMAERFSRLHE 94

Probable transcription factor.
Arabidopsis thaliana (taxid: 3702)

>sp|Q7XJK8|PHE2_ARATH MADS-box transcription factor PHERES 2 OS=Arabidopsis thaliana GN=PHE2 PE=1 SV=1

 Score = 53.5 bits (127), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 52/103 (50%), Gaps = 4/103 (3%)

Query: 8   VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKV-ETWP 66
           +KRK  + LIE     SR+  F KRK+ +  K  EL TLC V  C V Y P   + E WP
Sbjct: 1   MKRKMKLSLIE--NSVSRKTTFTKRKKGMTKKLTELVTLCGVEACAVVYSPFNSIPEAWP 58

Query: 67  EDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKL 109
             +  V D++ K+ EL  +    K  +Q   + +    +K++L
Sbjct: 59  S-REGVEDVVSKFMELSVLDRTKKMVDQETFISQRIAKEKEQL 100

Probable transcription factor involved in the development of gametophytes and seeds.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XJ66|MAD22_ORYSJ MADS-box transcription factor 22 OS=Oryza sativa subsp. japonica GN=MADS22 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 8  VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPE 67
           + +R +K IE     +RQ  F KR+  L  KA EL  LCD  V L+ +   GK+  +  
Sbjct: 2  ARERREIKRIE--SAAARQVTFSKRRRGLFKKAEELSVLCDADVALIVFSSTGKLSHFA- 58

Query: 68 DKTKVNDMIDKY 79
            + +N++IDKY
Sbjct: 59 -SSSMNEIIDKY 69

Probable transcription factor. May be required for spikelet (rice flower) development.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9XJ60|MAD50_ORYSJ MADS-box transcription factor 50 OS=Oryza sativa subsp. japonica GN=MADS50 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 71/145 (48%), Gaps = 8/145 (5%)

Query: 8   VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPE 67
           V+ K  +K IE     SRQ  F KR+  L  KA EL  LCD  V L+ + P GK+  +  
Sbjct: 2   VRGKTQMKRIE--NPTSRQVTFSKRRNGLLKKAFELSVLCDAEVALIVFSPRGKLYEFAS 59

Query: 68  DKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILETK 127
             T+    I++Y+   +  +  K  +Q    +E  ++    L +K +A       +L  K
Sbjct: 60  ASTQ--KTIERYRTYTKENIGNKTVQQD---IEQVKADADGLAKKLEALETYKRKLLGEK 114

Query: 128 IDEASSVEELGVVYNKVESKLASMR 152
           +DE  S+EEL  +  K+E  L S+R
Sbjct: 115 LDEC-SIEELHSLEVKLERSLISIR 138

Probable transcription factor active in flowering time control. May control internode elongation and promote floral transition phase. May act upstream of the floral regulators MADS1, MADS14, MADS15 and MADS18 in the floral induction pathway.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P35632|AP3_ARATH Floral homeotic protein APETALA 3 OS=Arabidopsis thaliana GN=AP3 PE=1 SV=1

 Score = 49.3 bits (116), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 36/143 (25%), Positives = 69/143 (48%), Gaps = 10/143 (6%)

Query: 11  KRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKT 70
           K  +K IE     +RQ  + KR+  L  KAHEL  LCD  V ++ +    K+  +    T
Sbjct: 5   KIQIKRIE--NQTNRQVTYSKRRNGLFKKAHELTVLCDARVSIIMFSSSNKLHEYISPNT 62

Query: 71  KVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILETKIDE 130
              +++D Y+ + ++ V   + E+        +  K+KL+E  +    ++   L   +DE
Sbjct: 63  TTKEIVDLYQTISDVDVWATQYER-------MQETKRKLLETNRNLRTQIKQRLGECLDE 115

Query: 131 ASSVEELGVVYNKVESKLASMRE 153
              ++EL  + +++E+    +RE
Sbjct: 116 L-DIQELRRLEDEMENTFKLVRE 137

Probable transcription factor involved in the genetic control of flower development. Is required for normal development of petals and stamens in the wild-type flower. Forms an heterodimer with PISTILLATA that is required for autoregulation of both AP3 and PI genes. AP3/PI heterodimer interacts with APETALA1 or SEPALLATA3 to form a ternary complex that could be responsible for the regulation of the genes involved in the flower development. AP3/PI heterodimer activates the expression of NAP.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XJK5|AGL90_ARATH Agamous-like MADS-box protein AGL90 OS=Arabidopsis thaliana GN=AGL90 PE=1 SV=2

 Score = 48.9 bits (115), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 58/125 (46%), Gaps = 7/125 (5%)

Query: 12  RSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKV-ETWPEDKT 70
           + VKL       SR+ +F KRK  +  K HEL TLC V  C + Y P   V E+WP  + 
Sbjct: 2   KKVKLSLIANERSRKTSFMKRKNGIFKKLHELSTLCGVQACALIYSPFIPVPESWPS-RE 60

Query: 71  KVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKL----MEKKKAFVEK-MFSILE 125
               +  K+ E+       K  +Q   L+E     K++L     E ++  V + MF  +E
Sbjct: 61  GAKKVASKFLEMPRTARTRKMMDQETHLMERITKAKEQLKNLAAENRELQVRRFMFDCVE 120

Query: 126 TKIDE 130
            K+ +
Sbjct: 121 GKMSQ 125

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C6V4|AGL92_ARATH Agamous-like MADS-box protein AGL92 OS=Arabidopsis thaliana GN=AGL92 PE=1 SV=1

 Score = 48.9 bits (115), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 11 KRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKT 70
          +   KL+     + R+  F KR   ++ K HEL TLCD+  C V Y P      WP  + 
Sbjct: 2  RTKTKLVLIPDRHFRRATFRKRNAGIRKKLHELTTLCDIKACAVIYSPFENPTVWPSTE- 60

Query: 71 KVNDMIDKYKE 81
           V ++I ++ E
Sbjct: 61 GVQEVISEFME 71

Putative transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XJK6|AGL36_ARATH Agamous-like MADS-box protein AGL36 OS=Arabidopsis thaliana GN=AGL36 PE=1 SV=1

 Score = 48.1 bits (113), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 71/155 (45%), Gaps = 11/155 (7%)

Query: 12  RSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKV-ETWPEDKT 70
           + VKL       SR+ +F KRK+ +  K HEL TLC V  C + Y P   V E+WP  + 
Sbjct: 2   KKVKLSLIANERSRKTSFIKRKDGIFKKLHELSTLCGVQACALIYSPFIPVPESWPS-RE 60

Query: 71  KVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKL----MEKKKAFVEK-MFSILE 125
               +  ++ E+       K  +Q   L+E     K++L     E ++  V + MF  +E
Sbjct: 61  GAKKVASRFLEMPPTARTKKMMDQETYLMERITKAKEQLKNLAAENRELQVRRFMFDCVE 120

Query: 126 TKIDE----ASSVEELGVVYNKVESKLASMRETIE 156
            K+ +    A  +++L    N    +L    E+I+
Sbjct: 121 GKMSQYHYDAKDLQDLQSCINLYLDQLNGRIESIK 155

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJK3|AGL80_ARATH Agamous-like MADS-box protein AGL80 OS=Arabidopsis thaliana GN=AGL80 PE=1 SV=1

 Score = 47.8 bits (112), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 57/120 (47%), Gaps = 7/120 (5%)

Query: 11  KRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGP-DGKVETWPEDK 69
           ++ VKL      +SR+  F+KRK+ L  K HEL TLC +  C + Y P D   E WP + 
Sbjct: 3   RKKVKLAYISNDSSRKATFKKRKKGLMKKVHELSTLCGITACAIIYSPYDTNPEVWPSN- 61

Query: 70  TKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKK-----AFVEKMFSIL 124
           + V  ++ +++ L EM    K  +Q   L +      + L  ++K        E MF  L
Sbjct: 62  SGVQRVVSEFRTLPEMDQHKKMVDQEGFLKQRIAKATETLRRQRKDSRELEMTEVMFQCL 121

Probable transcription factor. Controls central cell differentiation during female gametophyte development. Required for the expression of DEMETER and DD46, but not for the expression of FIS2.

Arabidopsis thaliana (taxid: 3702)

>sp|Q69TG5|MAD55_ORYSJ MADS-box transcription factor 55 OS=Oryza sativa subsp. japonica GN=MADS55 PE=2 SV=2

 Score = 47.8 bits (112), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 24 SRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKY 79
          +RQ  F KR+  L  KA EL  LCD  V LV +   GK+  +    + +N++IDKY
Sbjct: 16 ARQVTFSKRRRGLFKKAEELAVLCDADVALVVFSSTGKLSQFA--SSNMNEIIDKY 69

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

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	286
224129366	253	predicted protein [Populus trichocarpa]	0.625	0.707	0.341	8e-14
255581207	330	mads box protein, putative [Ricinus comm	0.685	0.593	0.300	9e-13
224133558	237	predicted protein [Populus trichocarpa]	0.552	0.666	0.339	2e-12
297801628	336	hypothetical protein ARALYDRAFT_916318 [	0.454	0.386	0.316	1e-11
297805684	297	hypothetical protein ARALYDRAFT_493979 [	0.454	0.437	0.323	8e-11
297801634	395	predicted protein [Arabidopsis lyrata su	0.444	0.321	0.330	1e-10
255547504	237	mads box protein, putative [Ricinus comm	0.178	0.215	0.607	1e-10
15230155	386	protein agamous-like 103 [Arabidopsis th	0.265	0.196	0.412	3e-10
224113445	210	predicted protein [Populus trichocarpa]	0.185	0.252	0.584	4e-10
15242468	355	protein agamous-like 81 [Arabidopsis tha	0.454	0.366	0.317	5e-10

>gi|224129366|ref|XP_002328699.1| predicted protein [Populus trichocarpa] gi|222838997|gb|EEE77348.1| predicted protein [Populus trichocarpa]

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 69/202 (34%), Positives = 97/202 (48%), Gaps = 23/202 (11%)

Query: 24  SRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELR 83
           S   +F KR +TLK KAHEL+TLCDV +C+VC+GPD  V+TWPE   +V D I  YK L 
Sbjct: 24  SHAMSFSKRTKTLKKKAHELQTLCDVKICMVCFGPDSTVQTWPEGAVEVKDAIMSYKGLG 83

Query: 84  EMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILETKIDEASSVEELG----- 138
           +     KK E    LL     KK KL E KK  V K     E  +  +  V+ L      
Sbjct: 84  D----RKKYESS--LLGYLHDKKMKL-EVKKRKVMKKKVNKELIVKWSDHVDGLSDDALR 136

Query: 139 VVYNKVESKLASMRETIELAI-------IEEQKNQQFAAPPIRPP--VYGNNLLLSDYVS 189
              N +ES+L  ++E I+L +       I++  + +F       P    G     +D + 
Sbjct: 137 DTVNTLESRLFDLKEKIKLCMQRDKVEAIQDHVDMEFEMDGSSVPSSAAGATAWPADVMD 196

Query: 190 SSSNNNNNNNDFGRHESFLFPP 211
           + +  NN+ +      SF  PP
Sbjct: 197 TYTVGNNDKD--AASTSFEMPP 216

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581207|ref|XP_002531416.1| mads box protein, putative [Ricinus communis] gi|223528966|gb|EEF30958.1| mads box protein, putative [Ricinus communis]

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 112/223 (50%), Gaps = 27/223 (12%)

Query: 7   QVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWP 66
           + +++  ++ I +    ++  +F KRK TLK KA EL TLCDV VC+VC+GP+G V+ WP
Sbjct: 25  EARKQNFIRKILDDDKATKTASFYKRKPTLKKKAQELHTLCDVPVCVVCFGPNGSVDVWP 84

Query: 67  EDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFE-SKKQKLMEKKKAFVEKMFSILE 125
           E++    +++  YK         KK  +  ++LEL +  KK+   +K++  +  + S L 
Sbjct: 85  EEEQCAKELMMSYKRSD------KKERKESNVLELMQCKKKKLEKKKQEVKINALVSTLS 138

Query: 126 TKIDEASSVEELGVVYNKVESKLASMRETIELAIIEEQKNQQFAAPP--IRPPVY----- 178
             +D  S +  +  V N+++ KL   +E IEL  + E+K ++   P   I P V      
Sbjct: 139 KCLDGLSGIPLIDRV-NELQDKLKIFKERIELLSM-EKKRKRIETPDEEISPIVSILSSP 196

Query: 179 ----GNNLLLSDYVSSSSNNNNNNNDFGRHESFLFPPSQNHQI 217
                +N+LL    +S SN         R E F    + NH +
Sbjct: 197 KNQEFDNILLWPTSTSCSN-------LARPEGFDMAGTNNHSV 232

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133558|ref|XP_002321604.1| predicted protein [Populus trichocarpa] gi|222868600|gb|EEF05731.1| predicted protein [Populus trichocarpa]

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 57/168 (33%), Positives = 83/168 (49%), Gaps = 10/168 (5%)

Query: 3   AETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKV 62
           ++ T  +R++ +K I E    ++  +F KRK TLK K  EL+TLC V +C+VC+GPDG V
Sbjct: 5   SQKTATRREKFMKKINEGNKETQAVSFSKRKPTLKKKVEELKTLCAVTICMVCFGPDGTV 64

Query: 63  ETWPEDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFS 122
           ET+PE+  +V   I  YK L  M       ++  +LL   E+ K KL  K++    K   
Sbjct: 65  ETYPENAAEVKREIGFYKGLHAM------QKREFNLLGYLENVKGKLGLKRQKVKRKKLE 118

Query: 123 ILETKID---EASSVEELGVVYNKVESKLASMRETI-ELAIIEEQKNQ 166
            L        E  S +        +E KL  +R  I +L  I   K Q
Sbjct: 119 ALAESFSNQIEGLSGDAFLHFIETLEKKLMGLRGKIGDLLSIRGDKGQ 166

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297801628|ref|XP_002868698.1| hypothetical protein ARALYDRAFT_916318 [Arabidopsis lyrata subsp. lyrata] gi|297314534|gb|EFH44957.1| hypothetical protein ARALYDRAFT_916318 [Arabidopsis lyrata subsp. lyrata]

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 84/139 (60%), Gaps = 9/139 (6%)

Query: 32  RKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKK 91
           R ET+  KA EL TLCD+  C++ YGPDG+++TWP+++ KV D+  +Y +L E   L +K
Sbjct: 33  RLETIFKKASELCTLCDIEACVIYYGPDGELKTWPKEREKVRDIALRYSQLNE--ALRRK 90

Query: 92  AEQRLDLLELFESKKQKLME---KKKAFVEKMFSILETKIDEASSVEELGVVYNKVESKL 148
             +R++L +    KK+K ++   K++    K  ++L+  I +  S +++  +   +E  +
Sbjct: 91  --KRVNLYDFLNKKKEKGLKNPNKRRKTSLKKVNVLKYPISDHYSPDQISKLIQSLELNV 148

Query: 149 ASMRETIELAIIEEQKNQQ 167
           + ++E   L  +E QK+++
Sbjct: 149 SKVQE--RLRFVESQKHKE 165

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297805684|ref|XP_002870726.1| hypothetical protein ARALYDRAFT_493979 [Arabidopsis lyrata subsp. lyrata] gi|297316562|gb|EFH46985.1| hypothetical protein ARALYDRAFT_493979 [Arabidopsis lyrata subsp. lyrata]

 Score = 73.6 bits (179), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 45/139 (32%), Positives = 83/139 (59%), Gaps = 9/139 (6%)

Query: 32  RKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKK 91
           R ET+  KA EL TLCD+  C++ YGPDG+++TWP+++ KV D+  +Y +L E   L +K
Sbjct: 14  RLETIFKKASELCTLCDIKACVIYYGPDGELKTWPKEREKVRDIALRYSQLNE--ALRRK 71

Query: 92  AEQRLDLLELFESKKQKLME---KKKAFVEKMFSILETKIDEASSVEELGVVYNKVESKL 148
             +R++L +    KK+K ++   KK+    K  + L+  I +  S +++  +   +E  +
Sbjct: 72  --KRVNLYDFLNKKKEKGLKNPNKKRKTSLKKVNELKYPISDHYSPDQISKLIQSLELNV 129

Query: 149 ASMRETIELAIIEEQKNQQ 167
           + ++E   L  +E QK+++
Sbjct: 130 SKVQE--RLRFVESQKHKE 146

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297801634|ref|XP_002868701.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297314537|gb|EFH44960.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 45/136 (33%), Positives = 80/136 (58%), Gaps = 9/136 (6%)

Query: 32  RKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKK 91
           R ET+  KA EL TLCD+  C++ YGPDG+++TWP+++ KV D+  +Y +L E   L +K
Sbjct: 25  RLETIFKKASELCTLCDIEACVIYYGPDGELKTWPKEREKVRDIALRYSQLNE--ALRRK 82

Query: 92  AEQRLDLLELFESKKQKLME---KKKAFVEKMFSILETKIDEASSVEELGVVYNKVESKL 148
             +R++L +    KK+K ++   KK+    K  + L+  I +  S +++  +   +E  +
Sbjct: 83  --KRVNLYDFLNKKKEKGLKNPNKKRKTSLKKVNELKYPISDHYSPDQISKLIQSLELNV 140

Query: 149 ASMRETIELAIIEEQK 164
           + ++E   L  +E QK
Sbjct: 141 SKVQE--RLRFVESQK 154

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547504|ref|XP_002514809.1| mads box protein, putative [Ricinus communis] gi|223545860|gb|EEF47363.1| mads box protein, putative [Ricinus communis]

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/51 (60%), Positives = 41/51 (80%)

Query: 29 FEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKY 79
          ++ RK TLK KA EL  LCDV V LVCY PDGKV+TWPEDK+KV++++ ++
Sbjct: 8  YKNRKATLKKKAEELSILCDVPVALVCYDPDGKVDTWPEDKSKVDEILTEF 58

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15230155|ref|NP_188495.1| protein agamous-like 103 [Arabidopsis thaliana] gi|9293888|dbj|BAB01791.1| unnamed protein product [Arabidopsis thaliana] gi|119360153|gb|ABL66805.1| At3g18650 [Arabidopsis thaliana] gi|332642605|gb|AEE76126.1| protein agamous-like 103 [Arabidopsis thaliana]

 Score = 71.6 bits (174), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/80 (41%), Positives = 51/80 (63%), Gaps = 4/80 (5%)

Query: 24  SRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELR 83
           SR  +  KR++T+  KA EL  LCD+ VC++CYG +G+++TWPE++ KV  +  +Y EL 
Sbjct: 31  SRATSLIKRQQTVFKKAKELSILCDIDVCVICYGSNGELKTWPEEREKVKAIARRYGELS 90

Query: 84  EMPVLMKKAEQRLDLLELFE 103
           E     K+ +  +DL E  E
Sbjct: 91  E----TKRRKGSVDLHEFLE 106

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224113445|ref|XP_002316498.1| predicted protein [Populus trichocarpa] gi|222865538|gb|EEF02669.1| predicted protein [Populus trichocarpa]

 Score = 71.2 bits (173), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 31/53 (58%), Positives = 40/53 (75%)

Query: 28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYK 80
          ++E+RK+ LK KA EL TLCDV VCLVC  PDG  ETWPE++ +V D++  YK
Sbjct: 16 SYEERKQNLKKKASELATLCDVPVCLVCVNPDGSTETWPEEEERVVDVLMAYK 68

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15242468|ref|NP_198791.1| protein agamous-like 81 [Arabidopsis thaliana] gi|10177975|dbj|BAB11381.1| unnamed protein product [Arabidopsis thaliana] gi|32402414|gb|AAN52789.1| MADS-box protein AGL81 [Arabidopsis thaliana] gi|332007088|gb|AED94471.1| protein agamous-like 81 [Arabidopsis thaliana]

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 80/145 (55%), Gaps = 15/145 (10%)

Query: 32  RKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPVLMKK 91
           R ET+  KA EL TLCD+  C++ YGPDG+++TWP ++ KV D+  +Y +L E   L +K
Sbjct: 31  RLETIFKKASELCTLCDIEACVIYYGPDGELKTWPPEREKVEDIALRYSQLNE--ALRRK 88

Query: 92  AEQRLDLLELFESKKQKLMEKKKAFVE---------KMFSILETKIDEASSVEELGVVYN 142
             + + L +    KK K   +KKA +          K  +IL+  + +  S +++  +  
Sbjct: 89  --KSVTLYDFLNKKKDKTNLEKKAKITDNDDLKTCLKNVNILKYPLADHYSPDQVSQLIQ 146

Query: 143 KVESKLASMRETIELAIIEEQKNQQ 167
            +E  ++ +RE I    +E QK+++
Sbjct: 147 SLEPHVSKVRERIRF--VESQKHKE 169

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	286
TAIR|locus:2144377	187	AGL54 "AGAMOUS-like 54" [Arabi	0.248	0.379	0.444	1.2e-12
TAIR|locus:2143646	223	AGL89 "AGAMOUS-like 89" [Arabi	0.479	0.614	0.315	1.2e-12
TAIR|locus:4515103623	224	AT5G27944 [Arabidopsis thalian	0.482	0.616	0.322	1.9e-12
TAIR|locus:2167047	355	AGL81 "AGAMOUS-like 81" [Arabi	0.479	0.385	0.287	2.1e-12
TAIR|locus:2144387	120	AGL101 "AGAMOUS-like 101" [Ara	0.209	0.5	0.442	1.2e-11
TAIR|locus:2093979	386	AGL103 "AGAMOUS-like 103" [Ara	0.332	0.246	0.373	3.1e-11
TAIR|locus:2167027	329	AGL98 "AGAMOUS-like 98" [Arabi	0.248	0.215	0.416	3.6e-11
TAIR|locus:1006230382	196	AGL51 "AGAMOUS-like 51" [Arabi	0.272	0.397	0.370	4.9e-11
TAIR|locus:2144397	287	AGL53 "AGAMOUS-like 53" [Arabi	0.493	0.491	0.3	1.8e-10
TAIR|locus:2148468	289	AGL93 "AGAMOUS-like 93" [Arabi	0.248	0.245	0.416	6.4e-10

TAIR|locus:2144377 AGL54 "AGAMOUS-like 54" [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 32/72 (44%), Positives = 46/72 (63%)

Query:    28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGK-VETWPEDKTKVNDMIDKYKELREMP 86
             N   R++T+  KA EL TLCD+ VC++ YG DGK ++TWPED++KV DM +++  L E  
Sbjct:    36 NLSMREQTMFKKALELSTLCDIEVCVIYYGRDGKLIKTWPEDQSKVRDMAERFSRLHERE 95

Query:    87 VLMKKAEQRLDL 98
                K+    L L
Sbjct:    96 RCKKRTNLSLFL 107

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2143646 AGL89 "AGAMOUS-like 89" [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 47/149 (31%), Positives = 77/149 (51%)

Query:    28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGK-VETWPEDKTKVNDMIDKYKELREMP 86
             N   R+ET+  KA EL TLCD+ VC++ YG DG+ ++TWPED++KV DM +++ +L E  
Sbjct:    37 NLSMREETMFKKALELSTLCDIEVCVIYYGRDGELIKTWPEDQSKVRDMAERFSKLHERE 96

Query:    87 VLMKKAEQRLDLLE--LFESXXXXXXXXXXAFVEKMFSILETKID--EASSVEELGVVYN 142
                K+    L L +  L ++            +E    +L+ K+   +  +  ELG    
Sbjct:    97 RRKKRTNLSLFLRKKILDDNKLSEKVLEMKDSLESGLRVLQDKLLLLQPENQTELG---- 152

Query:   143 KVESKLASMRETIELAIIEEQKNQQFAAP 171
               +S+  S   T  L+  E+  +QQ+  P
Sbjct:   153 --QSRAVSST-TNPLSSPEDHHHQQWTEP 178

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:4515103623 AT5G27944 [Arabidopsis thaliana (taxid:3702)]

 Score = 166 (63.5 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 48/149 (32%), Positives = 77/149 (51%)

Query:    28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGK-VETWPEDKTKVNDMIDKYKELREMP 86
             N   R++T+  KA EL TLCD+ VC++ YG DG+ ++TWPED++KV DM +++  L E  
Sbjct:    37 NLSMREQTMFKKALELSTLCDIEVCVILYGRDGELIKTWPEDQSKVRDMAERFSRLHER- 95

Query:    87 VLMKKAEQRLDLLELFESXXXXXXXXXXAFVEKMFSILETKIDEASSVEELGVVYNKVES 146
                ++ ++R +L  LF              V +M   LE+ +    + + L +   K ++
Sbjct:    96 ---ERCKKRTNL-SLFLRKKILDDNKLSEKVLEMEDSLESGLRVLQN-KLLLLQPEKNQT 150

Query:   147 KLASMRE----TIELAIIEEQKNQQFAAP 171
             KL   R     T  L+  E   NQQ+  P
Sbjct:   151 KLGQSRAVSSTTNLLSSPENHHNQQWTEP 179

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2167047 AGL81 "AGAMOUS-like 81" [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 2.1e-12, Sum P(2) = 2.1e-12
 Identities = 42/146 (28%), Positives = 73/146 (50%)

Query:    28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPV 87
             +   R ET+  KA EL TLCD+  C++ YGPDG+++TWP ++ KV D+  +Y +L E  +
Sbjct:    27 SLSNRLETIFKKASELCTLCDIEACVIYYGPDGELKTWPPEREKVEDIALRYSQLNEA-L 85

Query:    88 LMKKAEQRLDLLEL------FESXXXXXXXXXXAFVEKMFSILETKIDEASSVEELGVVY 141
               KK+    D L         E               K  +IL+  + +  S +++  + 
Sbjct:    86 RRKKSVTLYDFLNKKKDKTNLEKKAKITDNDDLKTCLKNVNILKYPLADHYSPDQVSQLI 145

Query:   142 NKVESKLASMRETIELAIIEEQKNQQ 167
               +E  ++ +RE I    +E QK+++
Sbjct:   146 QSLEPHVSKVRERIRF--VESQKHKE 169

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2144387 AGL101 "AGAMOUS-like 101" [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 1.2e-11, Sum P(2) = 1.2e-11
 Identities = 27/61 (44%), Positives = 41/61 (67%)

Query:    39 KAHELETLCDVMVCLVCYGPDGKV-ETWPEDKTKVNDMIDKYKELREMPVLMKKAEQRLD 97
             KA EL TLC++ VC++ YG DG++ +TWPED++KV DM +++ +L E     K+    L 
Sbjct:     4 KALELSTLCNIEVCVIYYGRDGELFKTWPEDESKVRDMAERFTKLNERERRKKRTNLSLF 63

Query:    98 L 98
             L
Sbjct:    64 L 64

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2093979 AGL103 "AGAMOUS-like 103" [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 3.1e-11, P = 3.1e-11
 Identities = 37/99 (37%), Positives = 57/99 (57%)

Query:     5 TTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVET 64
             +T  K K   K       +SR  +  KR++T+  KA EL  LCD+ VC++CYG +G+++T
Sbjct:    12 STSKKNKTFFKKPNSAFSSSRATSLIKRQQTVFKKAKELSILCDIDVCVICYGSNGELKT 71

Query:    65 WPEDKTKVNDMIDKYKELREMPVLMKKAEQRLDLLELFE 103
             WPE++ KV  +  +Y EL E     K+ +  +DL E  E
Sbjct:    72 WPEEREKVKAIARRYGELSET----KRRKGSVDLHEFLE 106

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2167027 AGL98 "AGAMOUS-like 98" [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 3.6e-11, Sum P(2) = 3.6e-11
 Identities = 30/72 (41%), Positives = 45/72 (62%)

Query:    28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPV 87
             +   R ET+  KA EL TLCD+  C++ YGPDG+++TWP ++ KV D+  +Y +L E  +
Sbjct:    27 SLSNRLETIFRKASELCTLCDIEACVIYYGPDGELKTWPPEREKVEDIALRYSQLNEA-L 85

Query:    88 LMKKAEQRLDLL 99
               KK+    D L
Sbjct:    86 RRKKSVTLYDFL 97

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:1006230382 AGL51 "AGAMOUS-like 51" [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 4.9e-11, P = 4.9e-11
 Identities = 30/81 (37%), Positives = 49/81 (60%)

Query:    23 NSRQG-NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKE 81
             +SR   +   R +T+  KA EL  LC + VC++ YGPDG++ TWP+++  V DM  +YKE
Sbjct:    11 SSRNSTSLTNRLKTIFKKAEELSILCAIDVCVIYYGPDGELRTWPKERNTVKDMASRYKE 70

Query:    82 L--REMPVLMKKAEQRLDLLE 100
                R+    +   ++RL ++E
Sbjct:    71 ATKRKKKRTLSTLQERLRIVE 91

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0046983 "protein dimerization activity" evidence=IEA

TAIR|locus:2144397 AGL53 "AGAMOUS-like 53" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 1.8e-10, P = 1.8e-10
 Identities = 45/150 (30%), Positives = 73/150 (48%)

Query:    28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGK-VETWPEDKTKVNDMIDKYKELREMP 86
             N   R++T+  KA EL TLC++ VC++ YG DGK ++TWPED++KV DM +++  L E  
Sbjct:    37 NLSMREQTMFKKALELSTLCNIDVCVIYYGRDGKLIKTWPEDQSKVRDMAERFSRLHERE 96

Query:    87 VLMKKAEQRLDLLE--LFESXXXXXXXXXXAFVEKMFSILETKI---DEASSVEELGVVY 141
                K+    L L +  L ++            +E    +L+ K+       +  E G   
Sbjct:    97 RCKKRTNLSLFLRKKILDDTKLSEKVLEMEDSLESGLRVLQDKLLLLQPEKNQTEFGQT- 155

Query:   142 NKVESKLASMRETIELAIIEEQKNQQFAAP 171
               V S    +     L  IE+ ++QQ+  P
Sbjct:   156 RAVSSTTNPLSPPPSL--IEDHRHQQWTEP 183

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2148468 AGL93 "AGAMOUS-like 93" [Arabidopsis thaliana (taxid:3702)]

 Score = 159 (61.0 bits), Expect = 6.4e-10, P = 6.4e-10
 Identities = 30/72 (41%), Positives = 46/72 (63%)

Query:    28 NFEKRKETLKNKAHELETLCDVMVCLVCYGPDGK-VETWPEDKTKVNDMIDKYKELREMP 86
             N   R++T+  KA EL TLC++ VC++ YG DGK ++TWP+D++KV DM +++  L E  
Sbjct:    37 NLSMREQTMFKKALELSTLCNIDVCVIYYGRDGKLIKTWPDDQSKVRDMAERFSRLHERE 96

Query:    87 VLMKKAEQRLDL 98
                K+    L L
Sbjct:    97 RCKKRTNLSLFL 108

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

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	286
cd00266	83	cd00266, MADS_SRF_like, SRF-like/Type I subfamily	9e-17
cd00120	59	cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and	1e-15
pfam00319	51	pfam00319, SRF-TF, SRF-type transcription factor (	6e-12
smart00432	59	smart00432, MADS, MADS domain	2e-11
cd00265	77	cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer fa	9e-09

>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 = 73.1 bits (180), Expect = 9e-17
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED 68
          ++K  +K IE      R   F KR++ L  KA EL TLC   V ++ Y P GK+  +   
Sbjct: 2  RKKIKIKRIENK--KKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPS 59

Query: 69 KTKVNDMIDKYKELREMP 86
             V  +I +++ L  + 
Sbjct: 60 SE-VEGVISRFEVLSALE 76

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

 Score = 69.5 bits (171), Expect = 1e-15
 Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWP 66
          + K  +K IE     SRQ  F KR+  L  KA EL  LCD  V ++ + P GK+  + 
Sbjct: 2  RGKIEIKRIENK--TSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFW 57

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

 Score = 58.9 bits (143), Expect = 6e-12
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 25 RQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWP 66
          RQ  F KR+  +  KAHEL  LCD  V ++ +   GK+  + 
Sbjct: 9  RQVTFSKRRNGIFKKAHELSVLCDAEVAVIIFSSTGKLYEYS 50

Length = 51

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

 Score = 58.0 bits (141), Expect = 2e-11
 Identities = 25/59 (42%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKV-ETWP 66
          +RK  +K IE     +RQ  F KR+  L  KAHEL  LCD  V L+ + P GK+ E   
Sbjct: 2  RRKIEIKRIEN--KTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFAS 58

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 = 51.0 bits (123), Expect = 9e-09
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED 68
          + K  +K IE     +RQ  F KR+  L  KAHEL  LCD  V L+ +   GK+  +   
Sbjct: 2  RGKIEIKRIEN--STNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSS- 58

Query: 69 KTKVNDMIDKYKE 81
             +  +I++Y++
Sbjct: 59 -PSMEKIIERYQK 70

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	286
KOG0014	195	consensus MADS box transcription factor [Transcrip	99.97
cd00265	77	MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-li	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	99.9
KOG0015	338	consensus Regulator of arginine metabolism and rel	99.7
COG5068	412	ARG80 Regulator of arginine metabolism and related	99.28
PF01486	100	K-box: K-box region; InterPro: IPR002487 MADS gene	98.33
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	82.92

>KOG0014 consensus MADS box transcription factor [Transcription]

Probab=99.97  E-value=1.3e-32  Score=240.80  Aligned_cols=146  Identities=25%  Similarity=0.320  Sum_probs=106.9

Q ss_pred             CCccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhcccch
Q 040948            7 QVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMP   86 (286)
Q Consensus         7 MgRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~~e~~   86 (286)
                      |||+||+|++|+|  +++|+|||+|||.||||||+||||||||+||||||||+|++|.|+++..+|+.|++||....+.+
T Consensus         1 M~R~ki~i~~Ien--~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~~   78 (195)
T KOG0014|consen    1 MGRGKIEIKRIEN--ESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEPS   78 (195)
T ss_pred             CCCCccceeeccc--cchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhhh
Confidence            9999999999999  99999999999999999999999999999999999999999877775345999999999987765


Q ss_pred             hhhhhhHHHHHHHHH------------------HHHHHHHHHHHHHHHHH---HHHhcccCCCCCCCH-HHHhcchHHHH
Q 040948           87 VLMKKAEQRLDLLEL------------------FESKKQKLMEKKKAFVE---KMFSILETKIDEASS-VEELGVVYNKV  144 (286)
Q Consensus        87 ~skk~~~qe~~l~e~------------------l~~e~~KL~Kk~kel~~---~~~~~~g~~Ld~LS~-eEL~eL~e~~L  144 (286)
                      ..++...++.++...                  ...+...+++..+.+..   ..+++.+.++.+++. .+|..+ +..|
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~l~~~~~l~~~-~~~l  157 (195)
T KOG0014|consen   79 RKKKRVNLESFLRNKKLTELVEEEEKEELKLQLKKSLESSLKVDPEDLELLELEQRKLTGEDLQSLSSLNELNSL-ESQL  157 (195)
T ss_pred             hcccccchhhHhhhhhhhcccchhhhhhccchhhhhhhhhhhcchhhhhhhHHHHHHHhccccccCCHHHHhcch-hhHH
Confidence            544444444433211                  01111111121112211   144566788888888 888888 7777


Q ss_pred             HHHHHHHHHHH
Q 040948          145 ESKLASMRETI  155 (286)
Q Consensus       145 E~kL~~Ir~Rk  155 (286)
                      +..+..++.+.
T Consensus       158 ~~~~~~~~~~~  168 (195)
T KOG0014|consen  158 ESSLHNSRSSK  168 (195)
T ss_pred             HHhhcCCCCCC
Confidence            77666555544

>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-29  Score=194.50  Aligned_cols=73  Identities=33%  Similarity=0.586  Sum_probs=70.6

Q ss_pred             CccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhccc
Q 040948            8 VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELRE   84 (286)
Q Consensus         8 gRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~~e   84 (286)
                      ||+||+|++|++  +.+|++||+|||.||||||+||||||||+||+|||||+|++++|++|  ++++||+||++.+.
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 GRGKIEIKRIEN--STNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSP--SMEKIIERYQKTSG   73 (77)
T ss_pred             CCCcceeEEecC--ccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCC--CHHHHHHHHHhccc
Confidence            899999999999  99999999999999999999999999999999999999999999997  78999999998854

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.

>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=8.2e-28  Score=186.60  Aligned_cols=77  Identities=31%  Similarity=0.535  Sum_probs=70.3

Q ss_pred             CccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhcccchh
Q 040948            8 VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPV   87 (286)
Q Consensus         8 gRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~~e~~~   87 (286)
                      ||+||+|++|++  +.+|++||+|||.||||||+||||||||+||+|||||+|++++|+++ ..++.+|++|...++.++
T Consensus         1 gr~Ki~i~~I~~--~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~-~~~~~~l~~~~~~~~~~~   77 (83)
T cd00266           1 GRKKIKIKRIEN--KKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPS-SEVEGVISRFEVLSALER   77 (83)
T ss_pred             CCccceeEEeec--cchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCc-HHHHHHHHHHhhcCHhhh
Confidence            799999999999  99999999999999999999999999999999999999987776665 239999999999876543

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=1.8e-26  Score=168.28  Aligned_cols=59  Identities=41%  Similarity=0.654  Sum_probs=57.0

Q ss_pred             CccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCC
Q 040948            8 VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED   68 (286)
Q Consensus         8 gRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp   68 (286)
                      ||+||+|++|++  +++|++||+|||.||+|||+||||||||+||+|||||+|++++|.+|
T Consensus         1 gR~Ki~i~~I~~--~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~p   59 (59)
T smart00432        1 GRRKIEIKRIEN--KTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP   59 (59)
T ss_pred             CCCcceeEEeeC--cchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccCC
Confidence            899999999999  99999999999999999999999999999999999999999988764

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

Probab=99.92  E-value=2.4e-26  Score=167.67  Aligned_cols=59  Identities=37%  Similarity=0.562  Sum_probs=57.3

Q ss_pred             CccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCC
Q 040948            8 VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED   68 (286)
Q Consensus         8 gRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp   68 (286)
                      ||+||+|++|++  +..|++||+|||.||+|||+||||||||+||+|||||+|++++|+++
T Consensus         1 gr~Ki~i~~I~~--~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~~   59 (59)
T cd00120           1 GRGKIEIKRIEN--KTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWSS   59 (59)
T ss_pred             CCccceeEEeeC--cchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccCC
Confidence            799999999999  99999999999999999999999999999999999999999999874

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=99.90  E-value=3.5e-25  Score=156.98  Aligned_cols=51  Identities=49%  Similarity=0.756  Sum_probs=47.0

Q ss_pred             EEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCC
Q 040948           15 KLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPE   67 (286)
Q Consensus        15 K~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpS   67 (286)
                      |+|+|  ++.|++||+|||.||||||+||||||||+||+|||+|+|++++|||
T Consensus         1 K~I~n--~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~~iv~~~~g~~~~f~s   51 (51)
T PF00319_consen    1 KRIEN--KSRRKVTFSKRKKGLFKKASELSTLCGVDVALIVFSPDGKLYTFPS   51 (51)
T ss_dssp             S--SS--HHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEEETTSEEEEEES
T ss_pred             CCccc--hhHhHhHHHHHHhhhhhccceeeeecCCeEEEEEECCCCCEEEecC
Confidence            58999  9999999999999999999999999999999999999999999997

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=99.70  E-value=4.4e-18  Score=157.52  Aligned_cols=69  Identities=33%  Similarity=0.375  Sum_probs=63.3

Q ss_pred             cccCCccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhH
Q 040948            4 ETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMI   76 (286)
Q Consensus         4 ~~~MgRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VI   76 (286)
                      +++-||+||+|++|+|  +..|.+||+|||.|+||||+|||||+|.+|-|+|.|+.|-+|+|..|  ..+.||
T Consensus        59 k~~~gr~kik~eyIen--K~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTp--KLep~i  127 (338)
T KOG0015|consen   59 KKTTGRVKIKMEYIEN--KLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATP--KLEPMI  127 (338)
T ss_pred             ccccceeeccchhhcc--cceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccc--cccccc
Confidence            3455899999999999  99999999999999999999999999999999999999999999997  555554

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

Probab=99.28  E-value=2.2e-12  Score=124.35  Aligned_cols=67  Identities=28%  Similarity=0.425  Sum_probs=62.6

Q ss_pred             cCCccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhH
Q 040948            6 TQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMI   76 (286)
Q Consensus         6 ~MgRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VI   76 (286)
                      .|||+|+.|.+|++  +.+|.|||+|||.||+|||.||++|.|.+|.++|.+..|++++|..|  ..+.|+
T Consensus        80 ~~~~~~~~is~i~n--k~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp--~~e~v~  146 (412)
T COG5068          80 SVTGRKIGISYITN--KTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTP--KLESVV  146 (412)
T ss_pred             ccccccCCcccccC--cccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCC--cccccc
Confidence            58999999999999  99999999999999999999999999999999999999999999997  444444

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

Probab=98.33  E-value=1.5e-06  Score=69.33  Aligned_cols=64  Identities=16%  Similarity=0.237  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCCCCHHHHhcchHHHHHHHHHHHHHHHHHHHHh
Q 040948           97 DLLELFESKKQKLMEKKKAFVEKMFSILETKIDEASSVEELGVVYNKVESKLASMRETIELAIIE  161 (286)
Q Consensus        97 ~l~e~l~~e~~KL~Kk~kel~~~~~~~~g~~Ld~LS~eEL~eL~e~~LE~kL~~Ir~Rk~~L~~~  161 (286)
                      .-.+.+..+..+|+++++.++..++++.|++|++|+++||..| +..|+.+|..||+|+..+..+
T Consensus        12 ~~~e~~~~e~~~L~~~~~~L~~~~R~~~GedL~~Ls~~eL~~L-E~~Le~aL~~VR~rK~~~l~~   75 (100)
T PF01486_consen   12 SQHEELQQEIAKLRKENESLQKELRHLMGEDLESLSLKELQQL-EQQLESALKRVRSRKDQLLME   75 (100)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccccccccccchHHHHHH-HHhhhhhHHHHHHHHHHHHHH
Confidence            4466788899999999999999999999999999999999999 999999999999999998765

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

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=82.92  E-value=39  Score=34.43  Aligned_cols=25  Identities=20%  Similarity=0.226  Sum_probs=19.1

Q ss_pred             ccccCCCCCCce----eecCCcchhhhcc
Q 040948          245 FMLPDNSLLPGY----VHANKGAWAQENF  269 (286)
Q Consensus       245 ~~~~~~~~~~~~----~~~~~~~~~~~~~  269 (286)
                      .+||.+|...++    +.||-|-.||.|-
T Consensus       212 ~YiPsgSf~~avll~G~DA~tg~~aq~nP  240 (475)
T PRK13729        212 PYIPSGSFAKAMLIEGADANASVTGNEST  240 (475)
T ss_pred             ceeCCCCeEEEEEecccccCccccccCCC
Confidence            588999984433    6889998888874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	286
1egw_A	77	MADS box transcription enhancer factor 2, polypept	5e-09
1hbx_A	92	SRF, serum response factor; gene regulation, trans	1e-08
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	2e-08
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	2e-08
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05

>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 = 51.2 bits (123), Expect = 5e-09
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED 68
          ++K  +  I +    +RQ  F KRK  L  KA+EL  LCD  + L+ +    K+  +   
Sbjct: 2  RKKIQITRIMD--ERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAS- 58

Query: 69 KTKVNDMIDKYKELRE 84
           T ++ ++ KY E  E
Sbjct: 59 -TDMDKVLLKYTEYNE 73

>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 = 50.6 bits (121), Expect = 1e-08
 Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 3  AETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKV 62
           + T+ + K  ++ I+      R   F KRK  +  KA+EL TL    V L+     G V
Sbjct: 6  GKKTRGRVKIKMEFIDN--KLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHV 63

Query: 63 ETWPEDKTKVNDMIDKYK 80
           T+     K+  MI    
Sbjct: 64 YTFATR--KLQPMITSET 79

>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 = 50.2 bits (120), Expect = 2e-08
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 4/72 (5%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED 68
          +RK  +K IE      R   F KRK  +  KA EL  L    V L+     G V T+   
Sbjct: 18 RRKIEIKFIEN--KTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTP 75

Query: 69 KTKVNDMIDKYK 80
          K +   ++ + +
Sbjct: 76 KFE--PIVTQQE 85

>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 = 50.3 bits (120), Expect = 2e-08
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 3  AETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKV 62
           + T+ + K  ++ I+      R   F KRK  +  KA+EL TL    V L+     G V
Sbjct: 5  GKKTRGRVKIKMEFIDN--KLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHV 62

Query: 63 ETWPEDKTKVNDMIDKYKE 81
           T+     K+  MI     
Sbjct: 63 YTFAT--RKLQPMITSETG 79

>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 = 2e-08
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED 68
          ++K  +  I +    +RQ  F KRK  L  KA+EL  LCD  + L+ +    K+  +   
Sbjct: 2  RKKIQITRIMD--ERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYA-- 57

Query: 69 KTKVNDMIDKYKELRE 84
           T ++ ++ KY E  E
Sbjct: 58 STDMDKVLLKYTEYNE 73

>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 = 43.3 bits (101), Expect = 6e-05
 Identities = 22/137 (16%), Positives = 51/137 (37%), Gaps = 18/137 (13%)

Query: 70  TKVNDMIDKYKELREMPVLMKKAEQRLDLLELFESKKQKLMEKKKAFVEKMFSILETKID 129
            +  +   +YK++  + V         D  ++ +  K  L    K  ++ +       I 
Sbjct: 9   FETGEHQYQYKDI--LSVFEDAFVDNFDCKDVQDMPKSIL---SKEEIDHI-------IM 56

Query: 130 EASSVEELGVVYNKVESKLASMRETIELAIIEE--QKNQQFAAPPIRPPVYGNNLLLSDY 187
              +V     ++  + SK    +E +    +EE  + N +F   PI+      +++   Y
Sbjct: 57  SKDAVSGTLRLFWTLLSK----QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMY 112

Query: 188 VSSSSNNNNNNNDFGRH 204
           +       N+N  F ++
Sbjct: 113 IEQRDRLYNDNQVFAKY 129

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	286
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	99.98
1egw_A	77	MADS box transcription enhancer factor 2, polypept	99.98
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

>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=99.98  E-value=1.4e-33  Score=220.27  Aligned_cols=77  Identities=29%  Similarity=0.425  Sum_probs=73.6

Q ss_pred             CccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhcccchh
Q 040948            8 VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREMPV   87 (286)
Q Consensus         8 gRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~~e~~~   87 (286)
                      ||+||+|++|+|  +++|+|||+|||.||||||+||||||||+||||||||+|++|+|+|+  +|+.||+||+..++.++
T Consensus         1 GR~Ki~ik~Ien--~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valiifs~~gk~~~f~s~--~~~~il~rY~~~~~~~~   76 (90)
T 3p57_A            1 GRKKIQITRIMD--ERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST--DMDKVLLKYTEYNEPHE   76 (90)
T ss_dssp             CCSCCCSSCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEESS--CHHHHHHHHHHCCSCCC
T ss_pred             CCCcceeEEecC--chHHHHHHHHhhhhHHHHHHHHHhccCCceEEEEECCCCCEEEeCCC--CHHHHHHHHHhcCcccc
Confidence            899999999999  99999999999999999999999999999999999999999999996  89999999999877654


Q ss_pred             h
Q 040948           88 L   88 (286)
Q Consensus        88 s   88 (286)
                      +
T Consensus        77 ~   77 (90)
T 3p57_A           77 S   77 (90)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=99.98  E-value=1.1e-33  Score=215.36  Aligned_cols=74  Identities=30%  Similarity=0.465  Sum_probs=69.7

Q ss_pred             CccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhcccc
Q 040948            8 VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELREM   85 (286)
Q Consensus         8 gRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~~e~   85 (286)
                      ||+||+|++|+|  +++|+|||+|||.||||||+||||||||+||||||||+|++|+|+|+  +|+.||+||+...++
T Consensus         1 GR~Ki~ik~I~n--~~~R~vTfsKRr~GL~KKA~ELsvLCdaeV~livfs~~gk~~~~~s~--~~~~il~ry~~~~~~   74 (77)
T 1egw_A            1 GRKKIQITRIMD--ERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST--DMDKVLLKYTEYNEP   74 (77)
T ss_dssp             CCSCCCSSCCCS--HHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTCCEEEEESS--CHHHHHHHHHHC---
T ss_pred             CCceeeeEEecC--chHHHHHHHHhHHHHHHHHHHHhcccCCeEEEEEECCCCCEeeCCCC--CHHHHHHHHHhccCC
Confidence            899999999999  99999999999999999999999999999999999999999999996  899999999988653

>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=1.3e-32  Score=218.43  Aligned_cols=76  Identities=28%  Similarity=0.379  Sum_probs=70.7

Q ss_pred             ccccCCccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhc
Q 040948            3 AETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKEL   82 (286)
Q Consensus         3 ~~~~MgRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~   82 (286)
                      +.++|||+||+|++|+|  +.+|+|||+|||.||||||+||||||||+||||||||+|++|+|+||  +++.||++|...
T Consensus        12 ~~~~mgR~Ki~ik~Ien--~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~gk~~~f~sp--s~~~il~r~~G~   87 (100)
T 1mnm_A           12 NGQQKERRKIEIKFIEN--KTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTP--KFEPIVTQQEGR   87 (100)
T ss_dssp             ---CCCCCCCCSSCCCS--HHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEECT--TTTHHHHSHHHH
T ss_pred             CCCCCCccceeeEEecC--cchhhhhhhHhhhhHHHHHHHHHHhcCCcEEEEEecCCCCcceecCC--CHHHHHHHhhCC
Confidence            56899999999999999  99999999999999999999999999999999999999999999998  899999998654

>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=1.3e-32  Score=215.65  Aligned_cols=75  Identities=29%  Similarity=0.355  Sum_probs=71.5

Q ss_pred             ccccCCccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhh
Q 040948            3 AETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKE   81 (286)
Q Consensus         3 ~~~~MgRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~   81 (286)
                      ++++|||+||+|++|+|  +.+|+|||+|||.||||||+||||||||+||||||||+|++|+|++|  +|+.||++|..
T Consensus         6 ~k~~mgR~Ki~ik~Ien--~~~R~vTFsKRr~GL~KKA~ELsvLCda~V~livfs~~gk~~~f~s~--~~~~~i~~~~G   80 (92)
T 1hbx_A            6 GKKTRGRVKIKMEFIDN--KLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATR--KLQPMITSETG   80 (92)
T ss_dssp             CCSSCCSCCCCSSCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTTSCEEEEECG--GGGGGTSSHHH
T ss_pred             CCCCCCcceEEEEEecC--hhHHHHHHHHhhhhHHHHHHHHHhhcCCceEEEEECCCCCEEEecCC--CHHHHHhhhcc
Confidence            57789999999999999  99999999999999999999999999999999999999999999997  89999997654

>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=6.7e-32  Score=215.49  Aligned_cols=74  Identities=30%  Similarity=0.363  Sum_probs=70.5

Q ss_pred             ccccCCccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhh
Q 040948            3 AETTQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYK   80 (286)
Q Consensus         3 ~~~~MgRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~   80 (286)
                      .+++|||+||+|++|+|  +.+|+|||+|||.||||||+||||||||+||||||||+|++|+|+++  +|+.||+++.
T Consensus         5 ~k~~mgR~Ki~ik~Ien--~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~gk~~~f~s~--~~~~vi~~~~   78 (103)
T 1k6o_B            5 GKKTRGRVKIKMEFIDN--KLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATR--KLQPMITSET   78 (103)
T ss_dssp             CCSSCCSCCCCSSCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECSSSCEEEEECG--GGGGGTSSHH
T ss_pred             CCCCCCcceeEEEEecC--chHHHHhHhHhhHhHHHHHHHHHhhhCCceEEEEEeCCCCeeeecCc--cHHHHHHhhh
Confidence            46789999999999999  99999999999999999999999999999999999999999999997  8999998753

---

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	286
d1egwa_	71	d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {	9e-14
d1mnma_	85	d.88.1.1 (A:) MCM1 transcriptional regulator {Bake	8e-12
d1srsa_	84	d.88.1.1 (A:) Serum response factor (SRF) core {Hu	1e-11

>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 = 62.7 bits (153), Expect = 9e-14
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED 68
          ++K  +  I +    +RQ  F KRK  L  KA+EL  LCD  + L+ +    K+  +   
Sbjct: 2  RKKIQITRIMD--ERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAS- 58

Query: 69 KTKVNDMIDKYKE 81
           T ++ ++ KY E
Sbjct: 59 -TDMDKVLLKYTE 70

>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 = 57.8 bits (140), Expect = 8e-12
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED 68
          +RK  +K IE      R   F KRK  +  KA EL  L    V L+     G V T+   
Sbjct: 4  RRKIEIKFIEN--KTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFS-- 59

Query: 69 KTKVNDMIDKYK 80
            K   ++ + +
Sbjct: 60 TPKFEPIVTQQE 71

>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 = 57.4 bits (139), Expect = 1e-11
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 9  KRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPED 68
          + K  ++ I+      R   F KRK  +  KA+EL TL    V L+     G V T+   
Sbjct: 4  RVKIKMEFIDN--KLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFA-- 59

Query: 69 KTKVNDMIDKYK 80
            K+  MI    
Sbjct: 60 TRKLQPMITSET 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	286
d1egwa_	71	Myocyte enhancer factor Mef2a core {Human (Homo sa	99.98
d1srsa_	84	Serum response factor (SRF) core {Human (Homo sapi	99.97
d1mnma_	85	MCM1 transcriptional regulator {Baker's yeast (Sac	99.96

>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=99.98  E-value=4.9e-34  Score=212.28  Aligned_cols=71  Identities=30%  Similarity=0.478  Sum_probs=69.0

Q ss_pred             CccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhc
Q 040948            8 VKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKEL   82 (286)
Q Consensus         8 gRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~   82 (286)
                      ||+||+|++|+|  +..|+|||+|||.||||||+||||||||+||||||||+|++++|+||  ++++||+||+++
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 GRKKIQITRIMD--ERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST--DMDKVLLKYTEY   71 (71)
T ss_dssp             CCSCCCSSCCCS--HHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTCCEEEEESS--CHHHHHHHHHHC
T ss_pred             CCccceEEeccC--CchheeehhHhhhhHHHHHHHHhhccCCcEEEEEEcCCCCEEEeeCC--CHHHHHHHHhcC
Confidence            899999999999  99999999999999999999999999999999999999999999997  899999999863

>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=3.1e-32  Score=208.00  Aligned_cols=73  Identities=30%  Similarity=0.347  Sum_probs=70.5

Q ss_pred             cCCccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhc
Q 040948            6 TQVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKEL   82 (286)
Q Consensus         6 ~MgRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~   82 (286)
                      ++||+||+|++|++  +..|+|||+|||.||||||+||||||||+||||||||+|++|+|+||  +|+.||++|...
T Consensus         1 ~~GR~Ki~i~~Ie~--~~~R~vTFsKRr~GL~KKa~ELs~Lc~~~v~liv~s~~gk~~~f~s~--~~~~vi~~~~~~   73 (84)
T d1srsa_           1 TRGRVKIKMEFIDN--KLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATR--KLQPMITSETGK   73 (84)
T ss_dssp             CCCCCCCCSSCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTTCCEEEEECG--GGHHHHSSHHHH
T ss_pred             CCCCceeeEEeecC--cchhhhhhHHhhhhHHHHHHHHhcccCCcEEEEEEcCCCCEEEeeCC--CHHHHHHHHHHH
Confidence            57999999999999  99999999999999999999999999999999999999999999997  999999999765

>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=99.96  E-value=1.6e-31  Score=204.83  Aligned_cols=73  Identities=29%  Similarity=0.401  Sum_probs=70.5

Q ss_pred             CCccceeeEEeccCCCCccchhhhhhhhhHHHHHHHHhhhccCcEEEEEecCCCCeeecCCCcchhhhhHHHhhhcc
Q 040948            7 QVKRKRSVKLIEEHGGNSRQGNFEKRKETLKNKAHELETLCDVMVCLVCYGPDGKVETWPEDKTKVNDMIDKYKELR   83 (286)
Q Consensus         7 MgRrKi~iK~Ien~~~~sRqvTFsKRR~GL~KKA~ELStLCdveV~lIVfSp~Gk~~~wpSp~~sVe~VIdRY~~~~   83 (286)
                      .||+||+|++|++  +..|+|||+|||.||||||+||||||||+||||||||+|++|+|+||  +|+.||+||....
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 KERRKIEIKFIEN--KTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTP--KFEPIVTQQEGRN   74 (85)
T ss_dssp             CCCCCCCSSCCCS--HHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEECT--TTTHHHHSHHHHH
T ss_pred             CCccceEEEEecC--CchhhhhhHHHHhhHHHHHHHHhccCCCcEEEEEEcCCCCEEeccCC--CHHHHHHHHhccc
Confidence            4899999999999  99999999999999999999999999999999999999999999997  8999999998763