Citrus Sinensis ID: 048697

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
Protein Sequence
MAAKKTKGRQKIEMIITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAFMLGELDLLWKPQLSKYIIEPAI
Secondary Structure (PSIPRED)
ccccccccccccEEEEEEEccccHHHHHHHHHHHHHcccEEEEEEcccccccccccccHHHHHHHHHcccccccccccHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccccccEEEEHHHHHHHHHHHHHHHHHHHHHcccEEEEEEcccccEEEEEcHHHHHHHHcHHHHHccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
maakktkgrQKIEMIITFSKRRSWIYKNASELVTLTGSEIAIVVFsqsgkpytfghpsVEAVANRFlgmnqlpndnihSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILTQMRrgketqprmwetpvdehnLQEQLQMDSAFMLGELdllwkpqlskyiiepai
Flexible Loop (DISEMBL)
maakktkgrqkiemiitfskrrswIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELrrqldeekeqEKILTqmrrgketqprmwetpvdEHNLQEQLQMDSAFMLGELDLlwkpqlskyiiepai
Low Complexity Region (SEG)
MAAKKTKGRQKIEMIITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAFMLGELDLLWKPQLSKYIIEPAI
Disordered region (IsUnstruct)
***********IEMIITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRIN****************************************************DSAFMLGELDLLWKPQLSKYII****
Disordered Region (DISOPRED)
**************IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLG***********************LN********************************************************************YII*P**
Disordered Region (DISEMBL)
**********KIEMIITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAFMLGELDLLWKPQLSKYIIEPAI
Disordered Region (DISPRO)
*********QKIEMIITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAFMLGELDLLWKPQLSKYIIEPAI
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAKKTKGRQKIEMIITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRxxxxxxxxxxxxxxxxxxxxxxxxxxxxRRGKETQPRMWETPVDEHNLQEQLQMDSAFMLGELDLLWKPQLSKYIIEPAI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	168	2.2.26 [Sep-21-2011]
Q9FKK2	299	Agamous-like MADS-box pro	yes	no	0.779	0.438	0.422	3e-22
Q4PSU4	264	Agamous-like MADS-box pro	no	no	0.815	0.518	0.373	2e-20
Q9SZJ6	228	Agamous-like MADS-box pro	no	no	0.5	0.368	0.303	2e-07
Q9C633	266	Agamous-like MADS-box pro	no	no	0.351	0.221	0.484	2e-07
Q5K4R0	246	MADS-box transcription fa	no	no	0.303	0.207	0.431	3e-07
Q24535	449	Serum response factor hom	no	no	0.309	0.115	0.475	3e-07
Q39295	264	Agamous-like MADS-box pro	N/A	no	0.398	0.253	0.389	3e-07
O82743	219	Agamous-like MADS-box pro	no	no	0.523	0.401	0.327	4e-07
P29386	252	Agamous-like MADS-box pro	no	no	0.333	0.222	0.428	5e-07
Q9M2K8	256	Agamous-like MADS-box pro	no	no	0.339	0.222	0.409	5e-07

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

 Score =  104 bits (260), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 60/142 (42%), Positives = 85/142 (59%), Gaps = 11/142 (7%)

Query: 3   AKKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYT 53
            KK+KGRQKIEM+         +TFSKRRS ++K ASEL TL G+E+AIVVFS   K ++
Sbjct: 2   VKKSKGRQKIEMVKMKNESNLQVTFSKRRSGLFKKASELCTLCGAEVAIVVFSPGRKVFS 61

Query: 54  FGHPSVEAVANRFLGMNQLP--NDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEK 111
           FGHP+V++V +RF+  N LP    N   L    R   + +LN    ++  QL+ EK++  
Sbjct: 62  FGHPNVDSVIDRFINNNPLPPHQHNNMQLRETRRNSIVQDLNNHLTQVLSQLETEKKKYD 121

Query: 112 ILTQMRRGKETQPRMWETPVDE 133
            L ++R   +     WE PV+E
Sbjct: 122 ELKKIREKTKALGNWWEDPVEE 143

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

 Score = 98.2 bits (243), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 56/150 (37%), Positives = 88/150 (58%), Gaps = 13/150 (8%)

Query: 8   GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
           GRQKI M+         +TFSKRR+ ++K ASEL TL G+EI I+VFS + KP++FGHPS
Sbjct: 63  GRQKIPMVKIKKESHRQVTFSKRRAGLFKKASELCTLCGAEIGIIVFSPAKKPFSFGHPS 122

Query: 59  VEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILTQMRR 118
           VE+V +R++  N +      S  +        ELN Q   +  +++EEK++ + + +MR+
Sbjct: 123 VESVLDRYVSRNNM--SLAQSQQLQGSPAASCELNMQLTHILSEVEEEKKKGQAMEEMRK 180

Query: 119 G--KETQPRMWETPVDEHNLQEQLQMDSAF 146
              + +    WE PV+E N+ +  +M  A 
Sbjct: 181 ESVRRSMINWWEKPVEEMNMVQLQEMKYAL 210

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZJ6|AGL21_ARATH Agamous-like MADS-box protein AGL21 OS=Arabidopsis thaliana GN=AGL21 PE=1 SV=1

 Score = 55.5 bits (132), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 54/112 (48%), Gaps = 28/112 (25%)

Query: 16  ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRF----LGMNQ 71
           +TFSKRR  + K A EL  L  +E+ +++FS +GK Y F   S+++V +R+    +   Q
Sbjct: 19  VTFSKRRKGLIKKAKELAILCDAEVGLIIFSSTGKLYDFASSSMKSVIDRYNKSKIEQQQ 78

Query: 72  LPN----------------DNIHSLVVGHRQ--------VRINELNQQHNEL 99
           L N                  +H+L   HRQ        + +NELN   N++
Sbjct: 79  LLNPASEVKFWQREAAVLRQELHALQENHRQMMGEQLNGLSVNELNSLENQI 130

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 55.1 bits (131), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/64 (48%), Positives = 39/64 (60%), Gaps = 5/64 (7%)

Query: 16 ITFSKRRSWIYKNASELVTLTGSEIAIV---VFSQSGKP-YTFGHPSVEAVANRFLGMNQ 71
          ++FSKRR  +Y  ASEL  L+ +EIAI+   V S S    Y+FGH SV+ V   FL  NQ
Sbjct: 21 VSFSKRRKGLYSKASELCLLSDAEIAIIATPVSSNSNAAFYSFGHSSVDNVVAAFLA-NQ 79

Query: 72 LPND 75
           P D
Sbjct: 80 RPCD 83

Putative transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q5K4R0|MAD47_ORYSJ MADS-box transcription factor 47 OS=Oryza sativa subsp. japonica GN=MADS47 PE=1 SV=2

 Score = 54.7 bits (130), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 34/51 (66%)

Query: 16 ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRF 66
          +TFSKRR  ++K A EL  L  +E+ +VVFS +GK + F   S+E + +R+
Sbjct: 38 VTFSKRRRGLFKKAEELSILCDAEVGLVVFSATGKLFQFASTSMEQIIDRY 88

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q24535|SRF_DROME Serum response factor homolog OS=Drosophila melanogaster GN=bs PE=1 SV=2

 Score = 54.3 bits (129), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 39/61 (63%), Gaps = 9/61 (14%)

Query: 3   AKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYT 53
            KKTKGR KI+M           TFSKR++ I K A EL TLTG+++ ++V S++G  YT
Sbjct: 161 GKKTKGRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYT 220

Query: 54  F 54
           F
Sbjct: 221 F 221

Required for the formation of intervein tissue of the wing. Acts in a dosage-dependent manner to suppress wing vein formation and promote development of intervein cells. Might play a role in the proper formation and maintenance of the trachea.

Drosophila melanogaster (taxid: 7227)

>sp|Q39295|AGL15_BRANA Agamous-like MADS-box protein AGL15 OS=Brassica napus GN=AGL15 PE=3 SV=1

 Score = 54.3 bits (129), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 10/77 (12%)

Query: 8  GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR KIE+          +TFSKRR+ + K A EL  L  +E+A++VFS+SGK + F   S
Sbjct: 2  GRGKIEIKRIENANSRQVTFSKRRAGLLKKAHELSVLCDAEVAVIVFSKSGKLFEFSSTS 61

Query: 59 VEAVANRFLGMNQLPND 75
          ++    R+ G  Q+ +D
Sbjct: 62 MKKTLLRY-GNYQISSD 77

Probable transcription factor.

Brassica napus (taxid: 3708)

>sp|O82743|AGL19_ARATH Agamous-like MADS-box protein AGL19 OS=Arabidopsis thaliana GN=AGL19 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 38/116 (32%), Positives = 51/116 (43%), Gaps = 28/116 (24%)

Query: 16  ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRF------LGM 69
           +TFSKRR+ + K A EL  L  +E+A+V+FS   K Y F   S+ A   R+      +G 
Sbjct: 19  VTFSKRRNGLLKKAFELSVLCDAEVALVIFSPRSKLYEFSSSSIAATIERYQRRIKEIGN 78

Query: 70  NQLPNDN--------------IHSLVVGHRQ--------VRINELNQQHNELRRQL 103
           N   NDN              I  L +  R+          I EL Q  N+L R L
Sbjct: 79  NHKRNDNSQQARDETSGLTKKIEQLEISKRKLLGEGIDACSIEELQQLENQLDRSL 134

Probable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 53.9 bits (128), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 35/56 (62%)

Query: 11 KIEMIITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRF 66
          KI   +TFSKRR+ + K A EL  L  +E+A+++FS  GK Y FG   +E+   R+
Sbjct: 14 KINRQVTFSKRRNGLLKKAYELSVLCDAEVALIIFSSRGKLYEFGSVGIESTIERY 69

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|Q9M2K8|AGL18_ARATH Agamous-like MADS-box protein AGL18 OS=Arabidopsis thaliana GN=AGL18 PE=2 SV=1

 Score = 53.5 bits (127), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 39/61 (63%), Gaps = 4/61 (6%)

Query: 10 QKIEMI----ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANR 65
          +KIE I    +TFSKRR+ + K A EL  L  +E+A+++FS +GK Y F    +E + +R
Sbjct: 9  KKIENINSRQVTFSKRRNGLIKKAKELSILCDAEVALIIFSSTGKIYDFSSVCMEQILSR 68

Query: 66 F 66
          +
Sbjct: 69 Y 69

Probable transcription factor involved in the negative regulation of flowering, probably through the photoperiodic pathway. Prevents premature flowering. Downstream regulator of a subset of the MIKC* MADS-controlled genes required during pollen maturation.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	168
224077620	194	predicted protein [Populus trichocarpa]	0.845	0.731	0.559	2e-40
255557369	220	mads box protein, putative [Ricinus comm	0.863	0.659	0.551	2e-39
224054544	202	predicted protein [Populus trichocarpa]	0.910	0.757	0.530	2e-36
255557367	239	mads box protein, putative [Ricinus comm	0.851	0.598	0.529	4e-36
449434264	260	PREDICTED: agamous-like MADS-box protein	0.839	0.542	0.513	4e-35
449505973	269	PREDICTED: agamous-like MADS-box protein	0.851	0.531	0.515	2e-34
224104275	201	predicted protein [Populus trichocarpa]	0.857	0.716	0.483	3e-31
225462217	199	PREDICTED: agamous-like MADS-box protein	0.833	0.703	0.476	3e-29
225429161	214	PREDICTED: agamous-like MADS-box protein	0.976	0.766	0.414	8e-29
225429169	212	PREDICTED: agamous-like MADS-box protein	0.815	0.646	0.439	1e-26

>gi|224077620|ref|XP_002305331.1| predicted protein [Populus trichocarpa] gi|222848295|gb|EEE85842.1| predicted protein [Populus trichocarpa]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 85/152 (55%), Positives = 111/152 (73%), Gaps = 10/152 (6%)

Query: 1   MAAKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKP 51
           M  K+T+GRQKI +         +ITFSKRRS IYK ASELVTL G+E+A++VFS +GK 
Sbjct: 1   MEGKQTRGRQKIAIKRIENEDDRLITFSKRRSGIYKKASELVTLCGAEVAVLVFSPAGKA 60

Query: 52  YTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEK 111
           ++FGHPS+E+VANRFLG N  PNDN H LV  HR+VRINELNQQHNEL  +++ E+++ K
Sbjct: 61  FSFGHPSIESVANRFLGQNIAPNDNTHPLVEAHRKVRINELNQQHNELLSEMEAERDRGK 120

Query: 112 ILTQMRRGKETQPRMWETPVDEHNLQEQLQMD 143
           +L +    K +Q   WE P+DE +LQE  QM+
Sbjct: 121 VLKEGTSEKSSQG-WWEAPIDELSLQELKQMN 151

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255557369|ref|XP_002519715.1| mads box protein, putative [Ricinus communis] gi|223541132|gb|EEF42688.1| mads box protein, putative [Ricinus communis]

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 86/156 (55%), Positives = 112/156 (71%), Gaps = 11/156 (7%)

Query: 1   MAAKK-TKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGK 50
           MA KK TKGRQKI M         +ITFSKRRS IYK ASEL+TL G+E+ I+VFS +GK
Sbjct: 1   MAGKKQTKGRQKITMKRIENEEDRLITFSKRRSGIYKKASELITLCGAEVGILVFSPAGK 60

Query: 51  PYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQE 110
           P++FGHPS+E++ANRFLG N  P+DN H LV  HR++RINELN+Q+NEL  +L+ EKE+ 
Sbjct: 61  PFSFGHPSLESIANRFLGKNVPPSDNTHPLVEAHRKMRINELNKQYNELLNRLESEKERG 120

Query: 111 KILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAF 146
            +L +  RGK      WE P+D+ N+QE  Q+ + F
Sbjct: 121 SMLKKTIRGKGCN-NWWEAPIDDLNMQELEQIYAMF 155

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224054544|ref|XP_002298313.1| predicted protein [Populus trichocarpa] gi|222845571|gb|EEE83118.1| predicted protein [Populus trichocarpa]

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 88/166 (53%), Positives = 115/166 (69%), Gaps = 13/166 (7%)

Query: 1   MAAKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKP 51
           MA+KKTKGRQK+EM         +ITFSKRRS IYK ASEL TLTG+EIAI VFS +GKP
Sbjct: 1   MASKKTKGRQKVEMKRIENQDDRLITFSKRRSGIYKKASELATLTGAEIAIAVFSPAGKP 60

Query: 52  YTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEK 111
           ++FGHPSVE+V NRFL  + L  D+ + LV  HR++RI EL Q+HN+++ QLDEEK  EK
Sbjct: 61  FSFGHPSVESVINRFL-EDPLDMDSTYHLVEAHRRMRIEELTQKHNDMQHQLDEEK--EK 117

Query: 112 ILTQMRRGKETQPRM-WETPVDEHNLQEQLQMDSAFMLGELDLLWK 156
            L    + KE   +  W+T VDE N+QE ++++  F   ++ L  K
Sbjct: 118 GLKLKSKIKEMDSKGWWDTAVDELNIQELIELEKKFKELQMTLCSK 163

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255557367|ref|XP_002519714.1| mads box protein, putative [Ricinus communis] gi|223541131|gb|EEF42687.1| mads box protein, putative [Ricinus communis]

 Score =  156 bits (394), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 82/155 (52%), Positives = 106/155 (68%), Gaps = 12/155 (7%)

Query: 3   AKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYT 53
            KKTKGRQKIEM         +ITFSKRRS IYK ASELVTLTG+E+A +V+S +GKP++
Sbjct: 7   GKKTKGRQKIEMKKIENEDDRLITFSKRRSGIYKKASELVTLTGAELAFLVYSPAGKPFS 66

Query: 54  FGHPSVEAVANRFLGMNQLPNDN---IHSLVVGHRQVRINELNQQHNELRRQLDEEKEQE 110
           F HPS++A+ NRF G      +N    H L+  HR +RI ELNQQHNEL RQL+ EKE+ 
Sbjct: 67  FAHPSMDAITNRFFGQGSADRNNNPTTHPLIEAHRLMRIEELNQQHNELLRQLEIEKEKG 126

Query: 111 KILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSA 145
           K L Q  +    +   W+TP++E N+ E LQM++A
Sbjct: 127 KQLKQKHKKNNERKGWWDTPIEELNVPELLQMEAA 161

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434264|ref|XP_004134916.1| PREDICTED: agamous-like MADS-box protein AGL61-like [Cucumis sativus]

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 78/152 (51%), Positives = 103/152 (67%), Gaps = 11/152 (7%)

Query: 4   KKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTF 54
           K+TKGRQKIEM         +ITFSKRRS IYK ASEL TL G+E+ +VVFS +GKP++F
Sbjct: 15  KQTKGRQKIEMKKIVNEDDRLITFSKRRSGIYKKASELATLCGAEVGVVVFSPAGKPFSF 74

Query: 55  GHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILT 114
            HP +E +AN+FL  N         LV  HR+VRINELNQQHN+L  QLD EKE+ K L 
Sbjct: 75  AHPCIETIANKFL--NAAATTTTTPLVEAHRRVRINELNQQHNQLLSQLDAEKEKGKALE 132

Query: 115 QMRRGKETQPRMWETPVDEHNLQEQLQMDSAF 146
           +++R +      WETP +E  ++E  ++D++F
Sbjct: 133 KLKRVRGNGRGWWETPTEELGIEELQEVDASF 164

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449505973|ref|XP_004162618.1| PREDICTED: agamous-like MADS-box protein AGL61-like [Cucumis sativus]

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 82/159 (51%), Positives = 108/159 (67%), Gaps = 16/159 (10%)

Query: 4   KKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTF 54
           K+TKGRQKIEM         +ITFSKRRS IYK ASEL TL G+E+ +VVFS +GKP++F
Sbjct: 15  KQTKGRQKIEMKKIVNEDDRLITFSKRRSGIYKKASELATLCGAEVGVVVFSPAGKPFSF 74

Query: 55  GHPSVEAVANRFL-------GMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEK 107
            HP +E +AN+FL       G N   N+N H LV  HR+VRINELNQQHN+L  QLD EK
Sbjct: 75  AHPCIETIANKFLNGNKNNKGNNDDNNNNAHPLVEAHRRVRINELNQQHNQLLSQLDAEK 134

Query: 108 EQEKILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAF 146
           E+ K L +++R +      WETP +E  ++E  ++D++F
Sbjct: 135 EKGKALEKLKRVRGNGRGWWETPTEELGIEELQEVDASF 173

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224104275|ref|XP_002313380.1| predicted protein [Populus trichocarpa] gi|222849788|gb|EEE87335.1| predicted protein [Populus trichocarpa]

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 75/155 (48%), Positives = 104/155 (67%), Gaps = 11/155 (7%)

Query: 1   MAAKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKP 51
           M AKKT+GRQK+EM         ++TFSKRRS IYK  SEL+TLTG+E A +VFS  GKP
Sbjct: 1   MEAKKTRGRQKVEMKRIVNEDDRLVTFSKRRSGIYKKLSELITLTGTEAAFLVFSPGGKP 60

Query: 52  YTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEK 111
           ++FGHPS+E V +RFL  N    D  H LV  +R+ RI EL Q+++E+++QLD++KE+  
Sbjct: 61  FSFGHPSIENVLDRFL-ENPSNADGTHELVEEYRRARIEELTQKYDEMQQQLDDDKEKGS 119

Query: 112 ILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAF 146
            L    +G E +   W  PV+E NLQE ++++  F
Sbjct: 120 KLKDKIQGNE-RGDWWNAPVEELNLQELIELEKKF 153

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225462217|ref|XP_002269756.1| PREDICTED: agamous-like MADS-box protein AGL62-like [Vitis vinifera]

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 72/151 (47%), Positives = 99/151 (65%), Gaps = 11/151 (7%)

Query: 1   MAAKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKP 51
           M  K+TKGRQKIEM         +ITFSKRRS IYK ASEL TL G+E+ ++VFS +GK 
Sbjct: 1   MEKKQTKGRQKIEMKRIPNEEDRLITFSKRRSGIYKKASELSTLCGAEVGVLVFSPAGKA 60

Query: 52  YTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEK 111
           ++FG PS+E + N+ L  N  PNDN  +LV  HR+ R+NEL+Q+++EL  +++  KEQEK
Sbjct: 61  FSFGQPSIEKITNKVLYENPPPNDNTLNLVEAHRRFRLNELHQKYSELLSKMEVAKEQEK 120

Query: 112 ILTQMRRGKETQPRMWETPVDEHNLQEQLQM 142
           IL   ++        WE P+ E ++ E  QM
Sbjct: 121 ILR--KKVPNRSKGWWEEPISELSMHELEQM 149

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429161|ref|XP_002270964.1| PREDICTED: agamous-like MADS-box protein AGL62 [Vitis vinifera] gi|147772544|emb|CAN63001.1| hypothetical protein VITISV_024203 [Vitis vinifera]

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 73/176 (41%), Positives = 108/176 (61%), Gaps = 12/176 (6%)

Query: 1   MAAKKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKP 51
           M  K +KGRQKIE+          +TFSKRRS ++K ASEL TL G+ +AI+VFS +GK 
Sbjct: 1   MVKKPSKGRQKIEISKIPKKNHLQVTFSKRRSGLFKKASELCTLCGANVAIIVFSPAGKV 60

Query: 52  YTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEK 111
           ++FGHP VE++ +RF   N +P  N   L+  HR   + ELN Q  ++  QL+ EK++ +
Sbjct: 61  FSFGHPDVESIVDRFFTCNPIPEPNGLHLIEAHRNASVRELNLQLTQVLNQLEAEKKRGE 120

Query: 112 ILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAFMLGELDLLWKPQLSKYIIEPA 167
           IL+QMRR  +TQ   WE P++E ++ E  Q+  +  + EL  +   Q  K ++E A
Sbjct: 121 ILSQMRRASQTQ-CWWEAPINELSMPELEQLKVS--MEELKKVVLSQGDKLLMEAA 173

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429169|ref|XP_002271290.1| PREDICTED: agamous-like MADS-box protein AGL62-like [Vitis vinifera]

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 65/148 (43%), Positives = 94/148 (63%), Gaps = 11/148 (7%)

Query: 4   KKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTF 54
           +K+KGRQK+EM          +TFSKRRS ++K ASEL TL G+EIAI+VFS   K Y+F
Sbjct: 5   RKSKGRQKVEMTKMTKESNLQVTFSKRRSGLFKKASELCTLCGAEIAIIVFSPGKKMYSF 64

Query: 55  GHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILT 114
           GHP VE++ +RFL  N LP+     L   HR   + +LN Q  ++  QL+ EK++ + LT
Sbjct: 65  GHPGVESIIDRFLTGNPLPHSGALQLFEAHRSANVRDLNMQLTQVLNQLEGEKKRGEALT 124

Query: 115 QMRRGKETQPRMWETPVDEHNLQEQLQM 142
           QM++  + Q   W  P++E +  EQL++
Sbjct: 125 QMKKASQAQ-YWWAAPIEELSF-EQLEL 150

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	168
TAIR|locus:2175188	299	AGL62 "AGAMOUS-like 62" [Arabi	0.803	0.451	0.417	2.1e-22
TAIR|locus:2047304	264	AGL61 "AGAMOUS-like 61" [Arabi	0.875	0.556	0.392	3e-21
TAIR|locus:2025386	247	AGL28 "AGAMOUS-like 28" [Arabi	0.821	0.558	0.355	6.5e-19
TAIR|locus:2102990	207	AGL57 "AGAMOUS-like 57" [Arabi	0.857	0.695	0.346	8.3e-19
TAIR|locus:2115420	248	AT4G36590 [Arabidopsis thalian	0.845	0.572	0.365	7.5e-18
TAIR|locus:2032537	182	AGL59 "AGAMOUS-like 59" [Arabi	0.809	0.747	0.371	2e-17
TAIR|locus:2206320	226	AGL23 "AGAMOUS-like 23" [Arabi	0.815	0.606	0.310	5.3e-17
TAIR|locus:4010713489	185	AGL64 "AGAMOUS-like 64" [Arabi	0.845	0.767	0.352	2.3e-16
TAIR|locus:2040819	172	AGL29 "AGAMOUS-like 29" [Arabi	0.869	0.848	0.337	1.4e-14
TAIR|locus:2032543	185	AGL58 "AGAMOUS-like 58" [Arabi	0.755	0.686	0.345	7.9e-14

TAIR|locus:2175188 AGL62 "AGAMOUS-like 62" [Arabidopsis thaliana (taxid:3702)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 61/146 (41%), Positives = 87/146 (59%)

Query:     4 KKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTF 54
             KK+KGRQKIEM+         +TFSKRRS ++K ASEL TL G+E+AIVVFS   K ++F
Sbjct:     3 KKSKGRQKIEMVKMKNESNLQVTFSKRRSGLFKKASELCTLCGAEVAIVVFSPGRKVFSF 62

Query:    55 GHPSVEAVANRFLGMNQLP--NDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKI 112
             GHP+V++V +RF+  N LP    N   L    R   + +LN    ++  QL+ EK++   
Sbjct:    63 GHPNVDSVIDRFINNNPLPPHQHNNMQLRETRRNSIVQDLNNHLTQVLSQLETEKKKYDE 122

Query:   113 LTQMRRGKETQPRMWETPVDEHNLQE 138
             L ++R   +     WE PV+E  L +
Sbjct:   123 LKKIREKTKALGNWWEDPVEELALSQ 148

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:0009960 "endosperm development" evidence=IMP

TAIR|locus:2047304 AGL61 "AGAMOUS-like 61" [Arabidopsis thaliana (taxid:3702)]

 Score = 249 (92.7 bits), Expect = 3.0e-21, P = 3.0e-21
 Identities = 64/163 (39%), Positives = 96/163 (58%)

Query:     1 MAAKKTK-GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGK 50
             M+ KK   GRQKI M+         +TFSKRR+ ++K ASEL TL G+EI I+VFS + K
Sbjct:    55 MSKKKESIGRQKIPMVKIKKESHRQVTFSKRRAGLFKKASELCTLCGAEIGIIVFSPAKK 114

Query:    51 PYTFGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQE 110
             P++FGHPSVE+V +R++  N +       L  G       ELN Q   +  +++EEK++ 
Sbjct:   115 PFSFGHPSVESVLDRYVSRNNMSLAQSQQLQ-GSPAASC-ELNMQLTHILSEVEEEKKKG 172

Query:   111 KILTQMRRG--KETQPRMWETPVDEHNLQEQLQMDSAFMLGEL 151
             + + +MR+   + +    WE PV+E N+  QLQ +  + L EL
Sbjct:   173 QAMEEMRKESVRRSMINWWEKPVEEMNMV-QLQ-EMKYALEEL 213

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0009559 "embryo sac central cell differentiation" evidence=IMP

GO:0043078 "polar nucleus" evidence=IDA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0019722 "calcium-mediated signaling" evidence=RCA

TAIR|locus:2025386 AGL28 "AGAMOUS-like 28" [Arabidopsis thaliana (taxid:3702)]

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 53/149 (35%), Positives = 83/149 (55%)

Query:     3 AKKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYT 53
             A+K  GR+KIE++         +TFSKRRS ++K  SEL TL  +EIAI+VFS SGK Y+
Sbjct:     2 ARKNLGRRKIELVKMTNESNLQVTFSKRRSGLFKKGSELCTLCDAEIAIIVFSPSGKAYS 61

Query:    54 FGHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKIL 113
             FGHP+V  + +  LG  ++   N  +      ++RI  LN+   E+  + ++E+E ++ +
Sbjct:    62 FGHPNVNKLLDHSLG--RVIRHNNTNFAESRTKLRIQMLNESLTEVMAEKEKEQETKQSI 119

Query:   114 TQMRRGKETQPRMWETPVDEHNLQEQLQM 142
              Q  R  +   + W     E NL +   M
Sbjct:   120 VQNERENKDAEKWWRNSPTELNLAQSTSM 148

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

TAIR|locus:2102990 AGL57 "AGAMOUS-like 57" [Arabidopsis thaliana (taxid:3702)]

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 54/156 (34%), Positives = 89/156 (57%)

Query:     4 KKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTF 54
             +KTKG+QKIEM         +ITFSKR++ I+K  +ELV +   E+A ++FSQ  KPYTF
Sbjct:    10 RKTKGKQKIEMKKVENYGDRMITFSKRKTGIFKKMNELVAMCDVEVAFLIFSQPKKPYTF 69

Query:    55 GHPSVEAVANRFLGMNQ---LPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEK 111
              HPS++ VA+R    ++   L  D+   LV  +++ R+++L ++   L  +L  + E+ K
Sbjct:    70 AHPSMKKVADRLKNPSRQEPLERDDTRPLVEAYKKRRLHDLVKKMEALEEELAMDLEKLK 129

Query:   112 ILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAFM 147
             +L + R  K+     W  P +  + +E  Q   A +
Sbjct:   130 LLKESRNEKKLDKMWWNFPSEGLSAKELQQRYQAML 165

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:2115420 AT4G36590 [Arabidopsis thaliana (taxid:3702)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 57/156 (36%), Positives = 88/156 (56%)

Query:     4 KKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTF 54
             + TKGRQKIEM          +TFSKRR  ++K ASEL TL+G+EI ++VFS  GK ++F
Sbjct:     3 RSTKGRQKIEMKKMENESNLQVTFSKRRFGLFKKASELCTLSGAEILLIVFSPGGKVFSF 62

Query:    55 GHPSVEAVANRFLGMNQ----LPNDNIHSLVVGHRQVR-INELNQQHNELRRQLDEEKEQ 109
             GHPSV+ + +RF   N     + + N +  +V  R  R I  LN    E+    ++EK++
Sbjct:    63 GHPSVQELIHRFSNPNHNSAIVHHQNNNLQLVETRPDRNIQYLNNILTEVLANQEKEKQK 122

Query:   110 EKILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSA 145
               +L  ++  +E     +E  V + ++ E  Q+ SA
Sbjct:   123 RMVLDLLKESREQVGNWYEKDVKDLDMNETNQLISA 158

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

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2032537 AGL59 "AGAMOUS-like 59" [Arabidopsis thaliana (taxid:3702)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 55/148 (37%), Positives = 83/148 (56%)

Query:     1 MAAKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKP 51
             M  KKTKG+QKI +          +TFSKR + IY   SEL  L G E+A + +S SGKP
Sbjct:     1 MNPKKTKGKQKINIKKIEKDEGRSVTFSKRLNGIYTKISELSILCGVEVAFIGYSCSGKP 60

Query:    52 YTFGHPSVEAVANRFLGMNQLPNDNIHSLVVG-HRQVRINELNQQHNELRRQLDEEKEQE 110
             YTFG PS +AVA RFL      + +  SLV+  H+Q +I EL +++N L  +L  ++ + 
Sbjct:    61 YTFGSPSFQAVAERFLN-GDASSSSSSSLVMNAHKQAKIQELCKKYNRLVEELKVDEVKV 119

Query:   111 KILTQMRRGKETQPRMWETPVDEHNLQE 138
             K    +   +     +W   VD +++++
Sbjct:   120 KKAAALAETRVVNKDVW-WKVDPNDVKD 146

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

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

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 46/148 (31%), Positives = 85/148 (57%)

Query:     4 KKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTF 54
             KKT GR+K+E++         +TFSKR++ ++K ASE  TL  ++IA++VFS +GK ++F
Sbjct:     3 KKTLGRRKVEIVKMTKESNLQVTFSKRKAGLFKKASEFCTLCDAKIAMIVFSPAGKVFSF 62

Query:    55 GHPSVEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQEKILT 114
             GHP+V+ + + F G   +   N  +L   + ++ +  LN+ + E++ ++++E++ ++   
Sbjct:    63 GHPNVDVLLDHFRGC--VVGHNNTNLDESYTKLHVQMLNKSYTEVKAEVEKEQKNKQSRA 120

Query:   115 QMRRGKETQPRMWETPVDEHNLQEQLQM 142
             Q  R  E     W     E NL +   M
Sbjct:   121 QNERENENAEEWWSKSPLELNLSQSTCM 148

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:4010713489 AGL64 "AGAMOUS-like 64" [Arabidopsis thaliana (taxid:3702)]

 Score = 203 (76.5 bits), Expect = 2.3e-16, P = 2.3e-16
 Identities = 55/156 (35%), Positives = 85/156 (54%)

Query:     1 MAAKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKP 51
             M  KKTKG+Q+I +         ++T SKRR+ IY   SEL  L G+E+A + +S SGKP
Sbjct:     1 MKPKKTKGKQRINIKKIEKDEDRLVTLSKRRNGIYTKLSELSILCGAEVAFLGYSCSGKP 60

Query:    52 YTFGHPSVEAVANRFLG--MNQLPNDNIH-SLVVGHRQVRINELNQQHNELRRQLD-EEK 107
             YTFG PS +AVA RFL    +   + ++  S++  H+Q +I EL + +N L  ++  EE 
Sbjct:    61 YTFGSPSFQAVAERFLNGEASSSSSSSLQRSVMNAHQQAKIQELCKVYNRLVEEITVEEV 120

Query:   108 EQEKILTQMRRGKETQPRMWET-PVDEHNLQEQLQM 142
             + +K           +   W+  P D  + +E  +M
Sbjct:   121 KLKKTAALAEMMPMNEDAWWKVDPNDVKDREEVKKM 156

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0046983 "protein dimerization activity" evidence=IEA

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

TAIR|locus:2040819 AGL29 "AGAMOUS-like 29" [Arabidopsis thaliana (taxid:3702)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 54/160 (33%), Positives = 95/160 (59%)

Query:     8 GRQKI--EMI-------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
             GR+KI  EM+       +TFSKRR+ ++K ASEL TL  +E+ IVVFS  GKP+++G P+
Sbjct:     2 GRRKIKMEMVQDMNTRQVTFSKRRTGLFKKASELATLCNAELGIVVFSPGGKPFSYGKPN 61

Query:    59 VEAVANRFLGMNQLPNDNIHSLVVGHRQVRINELNQQHNELRRQLDEEKEQ-EKILTQMR 117
             +++VA RF+      +D+      G+ + ++  L+++ + L ++++ EKE+ EK   ++ 
Sbjct:    62 LDSVAERFMREYD-DSDSGDEEKSGNYRPKLKRLSERLDLLNQEVEAEKERGEKSQEKLE 120

Query:   118 R-GKETQPRMWET-PVDEHN-LQEQLQMDSAFMLGELDLL 154
               G E      ET  +DE N  +++LQ     + G+++ L
Sbjct:   121 SAGDERFKESIETLTLDELNEYKDRLQTVHGRIEGQVNHL 160

GO:0003677 "DNA binding" evidence=IEA

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:2032543 AGL58 "AGAMOUS-like 58" [Arabidopsis thaliana (taxid:3702)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 48/139 (34%), Positives = 72/139 (51%)

Query:     1 MAAKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKP 51
             M  KKTKG+QKI +          +T SKR + IY    EL  L G E+A + +S SGKP
Sbjct:     1 MNPKKTKGKQKINIKKIEKDEDRSVTLSKRLNAIYTMIIELSILCGVEVAFIGYSCSGKP 60

Query:    52 YTFGHPSVEAVANRFLG--MNQLPNDNIH-SLVVGHRQVRINELNQQHNELRRQLDEEKE 108
             YTFG PS +AV  RFL    +   + ++  S+   H+Q +I EL +++N L  +L  ++ 
Sbjct:    61 YTFGSPSFQAVVERFLNGEASSSSSSSLQRSVKNAHKQAKIQELCKRYNRLVEELKVDEV 120

Query:   109 QEKILTQMRRGKETQPRMW 127
             + K    +   +      W
Sbjct:   121 KVKKAAALAETRAVNKDAW 139

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_IV001019 hypothetical protein (194 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	168
cd00265	77	cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer fa	3e-19
cd00266	83	cd00266, MADS_SRF_like, SRF-like/Type I subfamily	7e-18
cd00120	59	cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and	1e-17
smart00432	59	smart00432, MADS, MADS domain	9e-16
pfam00319	51	pfam00319, SRF-TF, SRF-type transcription factor (	2e-09
COG5068	412	COG5068, ARG80, Regulator of arginine metabolism a	3e-06

>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 = 76.4 bits (189), Expect = 3e-19
 Identities = 30/69 (43%), Positives = 42/69 (60%), Gaps = 9/69 (13%)

Query: 8  GRQKIEM--I-------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR KIE+  I       +TFSKRR+ + K A EL  L  +E+A+++FS SGK Y F  PS
Sbjct: 1  GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPS 60

Query: 59 VEAVANRFL 67
          +E +  R+ 
Sbjct: 61 MEKIIERYQ 69

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|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 = 73.4 bits (181), Expect = 7e-18
 Identities = 33/78 (42%), Positives = 47/78 (60%), Gaps = 10/78 (12%)

Query: 8  GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGH-P 57
          GR+KI++          +TFSKRR  ++K ASEL TL G+E+A++V+S SGK Y F    
Sbjct: 1  GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSS 60

Query: 58 SVEAVANRFLGMNQLPND 75
           VE V +RF  ++ L   
Sbjct: 61 EVEGVISRFEVLSALERK 78

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 = 72.2 bits (178), Expect = 1e-17
 Identities = 27/59 (45%), Positives = 36/59 (61%), Gaps = 9/59 (15%)

Query: 8  GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHP 57
          GR KIE+          +TFSKRR+ ++K ASEL  L  +E+A++VFS SGK Y F   
Sbjct: 1  GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWSS 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|197721 smart00432, MADS, MADS domain

 Score = 67.2 bits (165), Expect = 9e-16
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 9/59 (15%)

Query: 8  GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHP 57
          GR+KIE+          +TFSKRR+ ++K A EL  L  +E+A++VFS +GK Y F  P
Sbjct: 1  GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP 59

Length = 59

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

 Score = 50.5 bits (121), Expect = 2e-09
 Identities = 19/39 (48%), Positives = 29/39 (74%)

Query: 16 ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTF 54
          +TFSKRR+ I+K A EL  L  +E+A+++FS +GK Y +
Sbjct: 11 VTFSKRRNGIFKKAHELSVLCDAEVAVIIFSSTGKLYEY 49

Length = 51

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

 Score = 45.4 bits (107), Expect = 3e-06
 Identities = 23/55 (41%), Positives = 35/55 (63%)

Query: 16  ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMN 70
           +TFSKR+  I K A EL  LTG+E+ ++V S++G  +TF  P +E+V     G +
Sbjct: 99  VTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVKSLEGKS 153

Length = 412

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	168
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	99.95
smart00432	59	MADS MADS domain.	99.93
cd00120	59	MADS MADS: MCM1, Agamous, Deficiens, and SRF (seru	99.93
PF00319	51	SRF-TF: SRF-type transcription factor (DNA-binding	99.91
KOG0015	338	consensus Regulator of arginine metabolism and rel	99.71
COG5068	412	ARG80 Regulator of arginine metabolism and related	99.21
PF01486	100	K-box: K-box region; InterPro: IPR002487 MADS gene	98.29
PF10491	214	Nrf1_DNA-bind: NLS-binding and DNA-binding and dim	88.24
PF10584	23	Proteasome_A_N: Proteasome subunit A N-terminal si	83.97

>KOG0014 consensus MADS box transcription factor [Transcription]

Probab=99.97  E-value=2.8e-32  Score=209.14  Aligned_cols=145  Identities=29%  Similarity=0.394  Sum_probs=96.2

Q ss_pred             CCccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCch--hHHHHHHhhcCCCCCCC
Q 048697            7 KGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS--VEAVANRFLGMNQLPND   75 (168)
Q Consensus         7 mgr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPs--v~~Vl~Ry~~~~~~~~~   75 (168)
                      |||+||+|         +|||+|||+||||||+||||||||+||||||||+|++|+|++|+  |++|++||...+.....
T Consensus         1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~   80 (195)
T KOG0014|consen    1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEPSRK   80 (195)
T ss_pred             CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhhhhc
Confidence            88999999         99999999999999999999999999999999999999999987  99999999997755444


Q ss_pred             ccccccccchhhh-hhHHHHHHHHH-------HHHHHHHHHHHHHHHH---HHhhccCCCCCCCCCCCCCCH-HHHHHHH
Q 048697           76 NIHSLVVGHRQVR-INELNQQHNEL-------RRQLDEEKEQEKILTQ---MRRGKETQPRMWETPVDEHNL-QEQLQMD  143 (168)
Q Consensus        76 ~~~~~~e~~~~~~-~~~l~~~~~~L-------~~~le~~k~~~~~l~~---~~~~~~~~~~~w~~~l~~Ls~-eeL~~L~  143 (168)
                      ......+...... +..+.......       ...........+.+..   ..+      ..-+.++.+++. .+|..++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~------~~~~~~l~~l~~~~~l~~~~  154 (195)
T KOG0014|consen   81 KKRVNLESFLRNKKLTELVEEEEKEELKLQLKKSLESSLKVDPEDLELLELEQR------KLTGEDLQSLSSLNELNSLE  154 (195)
T ss_pred             ccccchhhHhhhhhhhcccchhhhhhccchhhhhhhhhhhcchhhhhhhHHHHH------HHhccccccCCHHHHhcchh
Confidence            3322111110000 11110000000       0011111111122221   122      233458888888 9999999


Q ss_pred             HHHHHhhHhhhhhc
Q 048697          144 SAFMLGELDLLWKP  157 (168)
Q Consensus       144 ~~Le~~L~~v~~~~  157 (168)
                      ..|+..+..+....
T Consensus       155 ~~l~~~~~~~~~~~  168 (195)
T KOG0014|consen  155 SQLESSLHNSRSSK  168 (195)
T ss_pred             hHHHHhhcCCCCCC
Confidence            99999987666554

>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=3.6e-31  Score=174.74  Aligned_cols=63  Identities=46%  Similarity=0.760  Sum_probs=60.9

Q ss_pred             Cccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHhhcCC
Q 048697            8 GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMN   70 (168)
Q Consensus         8 gr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry~~~~   70 (168)
                      ||+||+|         ++||+|||.||||||+|||+||||+||+|||||+|++|+|++|++++||+||.+.+
T Consensus         1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~   72 (77)
T cd00265           1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTS   72 (77)
T ss_pred             CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhcc
Confidence            7888988         99999999999999999999999999999999999999999999999999999865

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=99.95  E-value=2.5e-28  Score=163.41  Aligned_cols=67  Identities=51%  Similarity=0.771  Sum_probs=61.7

Q ss_pred             Cccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCch-hHHHHHHhhcCCCCCC
Q 048697            8 GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS-VEAVANRFLGMNQLPN   74 (168)
Q Consensus         8 gr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPs-v~~Vl~Ry~~~~~~~~   74 (168)
                      ||+||+|         ++||+|||.||||||+||||||||+||+|||||+|+++.|++|+ +++++++|...++..+
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~~~   77 (83)
T cd00266           1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSALER   77 (83)
T ss_pred             CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHhhh
Confidence            6888888         99999999999999999999999999999999999999998877 9999999999875443

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=3.9e-27  Score=147.24  Aligned_cols=50  Identities=52%  Similarity=0.885  Sum_probs=48.4

Q ss_pred             Cccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCc
Q 048697            8 GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHP   57 (168)
Q Consensus         8 gr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sP   57 (168)
                      ||+||+|         ++||+|||.||||||+||||||||+||+|||||+|++++|++|
T Consensus         1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~p   59 (59)
T smart00432        1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP   59 (59)
T ss_pred             CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccCC
Confidence            7888888         9999999999999999999999999999999999999999987

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

Probab=99.93  E-value=1.5e-26  Score=144.69  Aligned_cols=50  Identities=54%  Similarity=0.814  Sum_probs=47.8

Q ss_pred             Cccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCc
Q 048697            8 GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHP   57 (168)
Q Consensus         8 gr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sP   57 (168)
                      ||+||+|         ++||+|||.||||||+||||||||+||+|||||+|+++.|++|
T Consensus         1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~~   59 (59)
T cd00120           1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWSS   59 (59)
T ss_pred             CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccCC
Confidence            6788888         9999999999999999999999999999999999999999876

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=99.91  E-value=6.5e-26  Score=137.39  Aligned_cols=42  Identities=52%  Similarity=0.826  Sum_probs=40.0

Q ss_pred             eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCC
Q 048697           15 IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGH   56 (168)
Q Consensus        15 ~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~s   56 (168)
                      ++||+|||.||||||+|||+||||+||+|||||+|++|+|+|
T Consensus        10 ~~tf~KRk~gL~KKa~ELs~LC~~~v~~iv~~~~g~~~~f~s   51 (51)
T PF00319_consen   10 KVTFSKRKKGLFKKASELSTLCGVDVALIVFSPDGKLYTFPS   51 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHT-EEEEEEEETTSEEEEEES
T ss_pred             HhHHHHHHhhhhhccceeeeecCCeEEEEEECCCCCEEEecC
Confidence            799999999999999999999999999999999999999986

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=99.71  E-value=3.9e-18  Score=135.36  Aligned_cols=70  Identities=44%  Similarity=0.665  Sum_probs=62.4

Q ss_pred             ccccCCccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchh---------HHHHH
Q 048697            3 AKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSV---------EAVAN   64 (168)
Q Consensus         3 ~~~~mgr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv---------~~Vl~   64 (168)
                      +|++.||+||+|         .|||||||.||||||+|||||+|.+|-|+|.|++|.+|+|++|..         +++|.
T Consensus        58 ~k~~~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i~s~~Gk~lIq  137 (338)
T KOG0015|consen   58 GKKTTGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMITSDEGKALIQ  137 (338)
T ss_pred             CccccceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccccccccccchhhHHHHH
Confidence            688899999999         999999999999999999999999999999999999999999863         46676


Q ss_pred             HhhcCCCC
Q 048697           65 RFLGMNQL   72 (168)
Q Consensus        65 Ry~~~~~~   72 (168)
                      --++.+..
T Consensus       138 ~cLn~pd~  145 (338)
T KOG0015|consen  138 ACLNAPDT  145 (338)
T ss_pred             HHhcCCCC
Confidence            66776543

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

Probab=99.21  E-value=5.2e-12  Score=104.68  Aligned_cols=59  Identities=41%  Similarity=0.573  Sum_probs=54.5

Q ss_pred             cCCccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHH
Q 048697            6 TKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVAN   64 (168)
Q Consensus         6 ~mgr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~   64 (168)
                      +|||+||.|         .|||+||+.||+|||.||++|.|.+|.++|.|.+|..+.|+.|....|+.
T Consensus        80 ~~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~~  147 (412)
T COG5068          80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVK  147 (412)
T ss_pred             ccccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCccccccc
Confidence            689999999         99999999999999999999999999999999999999999987555443

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

Probab=98.29  E-value=2.3e-06  Score=58.98  Aligned_cols=62  Identities=15%  Similarity=0.208  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCCCCCHHHHHHHHHHHHHhhHhhhhhcc
Q 048697           91 ELNQQHNELRRQLDEEKEQEKILTQMRRGKETQPRMWETPVDEHNLQEQLQMDSAFMLGELDLLWKPQ  158 (168)
Q Consensus        91 ~l~~~~~~L~~~le~~k~~~~~l~~~~~~~~~~~~~w~~~l~~Ls~eeL~~L~~~Le~~L~~v~~~~~  158 (168)
                      .+...+..+..+++..+..++.|+..++.+.|.      +|++||++||..|+..|+.+|.+|+.+..
T Consensus         9 ~~~~~~e~~~~e~~~L~~~~~~L~~~~R~~~Ge------dL~~Ls~~eL~~LE~~Le~aL~~VR~rK~   70 (100)
T PF01486_consen    9 LWDSQHEELQQEIAKLRKENESLQKELRHLMGE------DLESLSLKELQQLEQQLESALKRVRSRKD   70 (100)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHhccccc------cccccchHHHHHHHHhhhhhHHHHHHHHH
Confidence            334455666677777777778888899976664      99999999999999999999999998763

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

>PF10491 Nrf1_DNA-bind: NLS-binding and DNA-binding and dimerisation domains of Nrf1; InterPro: IPR019525 Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates

Probab=88.24  E-value=0.98  Score=34.99  Aligned_cols=50  Identities=20%  Similarity=0.310  Sum_probs=37.0

Q ss_pred             hhch-hhHHHHH----HHHhhhhcCcEEEEEecCCC---CCcccCCchhHHHHHHhhc
Q 048697           19 SKRR-SWIYKNA----SELVTLTGSEIAIVVFSQSG---KPYTFGHPSVEAVANRFLG   68 (168)
Q Consensus        19 ~KRr-~gL~KKa----~ELs~LC~v~vavIvfSp~g---k~~~f~sPsv~~Vl~Ry~~   68 (168)
                      .||. .-|+.|.    .|++|-+|-++.|+|.+|+.   ..-.||....+.|+..|+.
T Consensus        30 rkrq~~rllrkl~~~~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~   87 (214)
T PF10491_consen   30 RKRQQTRLLRKLRQTIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKP   87 (214)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHH
Confidence            4443 3466664    79999999999999999963   3457888777777777654

The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila []. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human []. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Q8C4C0 from SWISSPROT, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].

>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3

Probab=83.97  E-value=0.37  Score=24.12  Aligned_cols=12  Identities=33%  Similarity=0.742  Sum_probs=9.5

Q ss_pred             EEEEecCCCCCc
Q 048697           41 AIVVFSQSGKPY   52 (168)
Q Consensus        41 avIvfSp~gk~~   52 (168)
                      .+.+|||+|+++
T Consensus         4 ~~t~FSp~Grl~   15 (23)
T PF10584_consen    4 SITTFSPDGRLF   15 (23)
T ss_dssp             STTSBBTTSSBH
T ss_pred             CceeECCCCeEE
Confidence            345899999986

4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	168
1k6o_B	103	Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dn		2e-07
1srs_A	92	Serum Response Factor (Srf) Core Complexed With Spe		2e-07
1mnm_A	100	Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLE		1e-06
3kov_A	90	Structure Of Mef2a Bound To Dna Reveals A Completel		1e-04
1egw_A	77	Crystal Structure Of Mef2a Core Bound To Dna Length		1e-04
1c7u_A	85	Complex Of The Dna Binding Core Domain Of The Trans		2e-04
3mu6_A	71	Inhibiting The Binding Of Class Iia Histone Deacety		3e-04

>pdb|1K6O|B Chain B, Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dna Complex Length = 103

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 39/62 (62%), Gaps = 9/62 (14%)
Query: 3  AKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYT 53
           KKT+GR KI+M           TFSKR++ I K A EL TLTG+++ ++V S++G  YT
Sbjct: 5  GKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYT 64
Query: 54 FG 55
          F 
Sbjct: 65 FA 66

>pdb|1SRS|A Chain A, Serum Response Factor (Srf) Core Complexed With Specific Sre Dna Length = 92

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 39/61 (63%), Gaps = 9/61 (14%)
Query: 3  AKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYT 53
           KKT+GR KI+M           TFSKR++ I K A EL TLTG+++ ++V S++G  YT
Sbjct: 6  GKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYT 65
Query: 54 F 54
          F
Sbjct: 66 F 66

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 34/55 (61%)
Query: 16 ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMN 70
          +TFSKR+  I K A EL  LTG+++ ++V S++G  YTF  P  E +  +  G N
Sbjct: 34 VTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRN 88

>pdb|3KOV|A Chain A, Structure Of Mef2a Bound To Dna Reveals A Completely Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND RECRUITS Transcription Co-Factors Length = 90

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 9/73 (12%)
Query: 8  GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR+KI++          +TF+KR+  + K A EL  L   EIA+++F+ S K + +    
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 59 VEAVANRFLGMNQ 71
          ++ V  ++   N+
Sbjct: 61 MDKVLLKYTEYNE 73

>pdb|1EGW|A Chain A, Crystal Structure Of Mef2a Core Bound To Dna Length = 77

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 9/73 (12%)
Query: 8  GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR+KI++          +TF+KR+  + K A EL  L   EIA+++F+ S K + +    
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 59 VEAVANRFLGMNQ 71
          ++ V  ++   N+
Sbjct: 61 MDKVLLKYTEYNE 73

>pdb|1C7U|A Chain A, Complex Of The Dna Binding Core Domain Of The Transcription Factor Mef2a With A 20mer Oligonucleotide Length = 85

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 9/73 (12%)
Query: 8  GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR+KI++          +TF+KR+  + K A EL  L  +EIA+++F+ S K + +    
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTD 60
Query: 59 VEAVANRFLGMNQ 71
          ++ V  ++   N+
Sbjct: 61 MDKVLLKYTEYNE 73

>pdb|3MU6|A Chain A, Inhibiting The Binding Of Class Iia Histone Deacetylases To Myocyte Enhancer Factor-2 By Small Molecules Length = 71

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 9/64 (14%)
Query: 8  GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR+KI++          +TF+KR+  + K A EL  L   EIA+++F+ S K + +    
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 59 VEAV 62
          ++ V
Sbjct: 61 MDKV 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	168
1hbx_A	92	SRF, serum response factor; gene regulation, trans	3e-22
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	2e-21
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	2e-20
1egw_A	77	MADS box transcription enhancer factor 2, polypept	5e-12
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	2e-11

>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 = 84.5 bits (209), Expect = 3e-22
 Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 9/78 (11%)

Query: 2  AAKKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPY 52
            KKT+GR KI+M           TFSKR++ I K A EL TLTG+++ ++V S++G  Y
Sbjct: 5  PGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVY 64

Query: 53 TFGHPSVEAVANRFLGMN 70
          TF    ++ +     G  
Sbjct: 65 TFATRKLQPMITSETGKA 82

>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 = 83.0 bits (205), Expect = 2e-21
 Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 9/78 (11%)

Query: 2  AAKKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPY 52
            KKT+GR KI+M           TFSKR++ I K A EL TLTG+++ ++V S++G  Y
Sbjct: 4  PGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVY 63

Query: 53 TFGHPSVEAVANRFLGMN 70
          TF    ++ +     G  
Sbjct: 64 TFATRKLQPMITSETGKA 81

>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 = 80.3 bits (198), Expect = 2e-20
 Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 9/78 (11%)

Query: 2  AAKKTKGRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPY 52
             + K R+KIE+          +TFSKR+  I K A EL  LTG+++ ++V S++G  Y
Sbjct: 11 NNGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVY 70

Query: 53 TFGHPSVEAVANRFLGMN 70
          TF  P  E +  +  G N
Sbjct: 71 TFSTPKFEPIVTQQEGRN 88

>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 = 57.4 bits (139), Expect = 5e-12
 Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 9/68 (13%)

Query: 8  GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR+KI++          +TF+KR+  + K A EL  L   EIA+++F+ S K + +    
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60

Query: 59 VEAVANRF 66
          ++ V  ++
Sbjct: 61 MDKVLLKY 68

>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 = 56.3 bits (136), Expect = 2e-11
 Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 9/68 (13%)

Query: 8  GRQKIEMI---------ITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR+KI++          +TF+KR+  + K A EL  L   EIA+++F+ S K + +    
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60

Query: 59 VEAVANRF 66
          ++ V  ++
Sbjct: 61 MDKVLLKY 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	168
3p57_A	90	Myocyte-specific enhancer factor 2A; protein-DNA c	100.0
1egw_A	77	MADS box transcription enhancer factor 2, polypept	100.0
1hbx_A	92	SRF, serum response factor; gene regulation, trans	100.0
1mnm_A	100	Protein (MCM1 transcriptional regulator); transcri	100.0
1k6o_B	103	SRF, serum response factor; protein/DNA complex, t	99.98

>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=6.2e-35  Score=195.23  Aligned_cols=69  Identities=30%  Similarity=0.540  Sum_probs=64.9

Q ss_pred             Cccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHhhcCCCCCCCc
Q 048697            8 GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQLPNDN   76 (168)
Q Consensus         8 gr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry~~~~~~~~~~   76 (168)
                      ||+||+|         +|||+|||+||||||+||||||||+||||||||+|++|+|+||+++.||+||...+++....
T Consensus         1 GR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valiifs~~gk~~~f~s~~~~~il~rY~~~~~~~~~~   78 (90)
T 3p57_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEYNEPHESR   78 (90)
T ss_dssp             CCSCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEESSCHHHHHHHHHHCCSCCCEE
T ss_pred             CCCcceeEEecCchHHHHHHHHhhhhHHHHHHHHHhccCCceEEEEECCCCCEEEeCCCCHHHHHHHHHhcCcccccC
Confidence            8999999         99999999999999999999999999999999999999999999999999999987655544

>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=7e-35  Score=190.47  Aligned_cols=64  Identities=33%  Similarity=0.591  Sum_probs=60.5

Q ss_pred             Cccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHhhcCCC
Q 048697            8 GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGMNQ   71 (168)
Q Consensus         8 gr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry~~~~~   71 (168)
                      ||+||+|         +|||+|||+||||||+||||||||+||||||||+|++|+|+||+++.||+||...++
T Consensus         1 GR~Ki~ik~I~n~~~R~vTfsKRr~GL~KKA~ELsvLCdaeV~livfs~~gk~~~~~s~~~~~il~ry~~~~~   73 (77)
T 1egw_A            1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEYNE   73 (77)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTCCEEEEESSCHHHHHHHHHHC--
T ss_pred             CCceeeeEEecCchHHHHHHHHhHHHHHHHHHHHhcccCCeEEEEEECCCCCEeeCCCCCHHHHHHHHHhccC
Confidence            7899999         999999999999999999999999999999999999999999999999999998653

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

Probab=100.00  E-value=1.1e-34  Score=194.84  Aligned_cols=67  Identities=43%  Similarity=0.640  Sum_probs=63.4

Q ss_pred             CccccCCccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHhhc
Q 048697            2 AAKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLG   68 (168)
Q Consensus         2 ~~~~~mgr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry~~   68 (168)
                      .+|++|||+||+|         +|||+|||+||||||+||||||||+||||||||+|++|+|++|+++.||++|..
T Consensus         5 ~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~V~livfs~~gk~~~f~s~~~~~~i~~~~G   80 (92)
T 1hbx_A            5 PGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQPMITSETG   80 (92)
T ss_dssp             -CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTTSCEEEEECGGGGGGTSSHHH
T ss_pred             cCCCCCCcceEEEEEecChhHHHHHHHHhhhhHHHHHHHHHhhcCCceEEEEECCCCCEEEecCCCHHHHHhhhcc
Confidence            4789999999998         999999999999999999999999999999999999999999999999997754

>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=100.00  E-value=1.9e-34  Score=196.00  Aligned_cols=66  Identities=41%  Similarity=0.631  Sum_probs=61.8

Q ss_pred             ccccCCccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHhhc
Q 048697            3 AKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLG   68 (168)
Q Consensus         3 ~~~~mgr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry~~   68 (168)
                      ++++|||+||+|         +|||+|||+||||||+||||||||+||||||||+|++|+|+||++..|+++|..
T Consensus        12 ~~~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~gk~~~f~sps~~~il~r~~G   86 (100)
T 1mnm_A           12 NGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEG   86 (100)
T ss_dssp             ---CCCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEECTTTTHHHHSHHH
T ss_pred             CCCCCCccceeeEEecCcchhhhhhhHhhhhHHHHHHHHHHhcCCcEEEEEecCCCCcceecCCCHHHHHHHhhC
Confidence            578999999999         999999999999999999999999999999999999999999999999999975

>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=99.98  E-value=4.4e-34  Score=195.41  Aligned_cols=64  Identities=44%  Similarity=0.640  Sum_probs=62.0

Q ss_pred             ccccCCccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHh
Q 048697            3 AKKTKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRF   66 (168)
Q Consensus         3 ~~~~mgr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry   66 (168)
                      +|++|||+||+|         +|||+|||+||||||+||||||||+||||||||+|++|+|++|+++.||+++
T Consensus         5 ~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~gk~~~f~s~~~~~vi~~~   77 (103)
T 1k6o_B            5 GKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQPMITSE   77 (103)
T ss_dssp             CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECSSSCEEEEECGGGGGGTSSH
T ss_pred             CCCCCCcceeEEEEecCchHHHHhHhHhhHhHHHHHHHHHhhhCCceEEEEEeCCCCeeeecCccHHHHHHhh
Confidence            688999999998         9999999999999999999999999999999999999999999999999974

---

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	168
d1srsa_	84	d.88.1.1 (A:) Serum response factor (SRF) core {Hu	1e-20
d1mnma_	85	d.88.1.1 (A:) MCM1 transcriptional regulator {Bake	2e-20
d1egwa_	71	d.88.1.1 (A:) Myocyte enhancer factor Mef2a core {	2e-18

>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 = 78.6 bits (194), Expect = 1e-20
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 9/76 (11%)

Query: 6  TKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGH 56
          T+GR KI+M           TFSKR++ I K A EL TLTG+++ ++V S++G  YTF  
Sbjct: 1  TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 60

Query: 57 PSVEAVANRFLGMNQL 72
            ++ +     G   +
Sbjct: 61 RKLQPMITSETGKALI 76

>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 = 78.2 bits (193), Expect = 2e-20
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 9/75 (12%)

Query: 7  KGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHP 57
          K R+KIE+          +TFSKR+  I K A EL  LTG+++ ++V S++G  YTF  P
Sbjct: 2  KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTP 61

Query: 58 SVEAVANRFLGMNQL 72
            E +  +  G N +
Sbjct: 62 KFEPIVTQQEGRNLI 76

>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 = 73.1 bits (180), Expect = 2e-18
 Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 9/68 (13%)

Query: 8  GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPS 58
          GR+KI++          +TF+KR+  + K A EL  L   EIA+++F+ S K + +    
Sbjct: 1  GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60

Query: 59 VEAVANRF 66
          ++ V  ++
Sbjct: 61 MDKVLLKY 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	168
d1egwa_	71	Myocyte enhancer factor Mef2a core {Human (Homo sa	100.0
d1srsa_	84	Serum response factor (SRF) core {Human (Homo sapi	100.0
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=1.1e-35  Score=189.50  Aligned_cols=61  Identities=33%  Similarity=0.591  Sum_probs=59.3

Q ss_pred             Cccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHhhc
Q 048697            8 GRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLG   68 (168)
Q Consensus         8 gr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry~~   68 (168)
                      ||+||+|         +|||+|||+||||||+|||+||||+||||||||+|++|+|+||++++|++||..
T Consensus         1 GR~Ki~ik~Ie~~~~R~vTFsKRk~GL~KKa~ELs~LC~~~valiv~s~~gk~~~f~s~~~~~vl~ry~~   70 (71)
T d1egwa_           1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTE   70 (71)
T ss_dssp             CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTCCEEEEESSCHHHHHHHHHH
T ss_pred             CCccceEEeccCCchheeehhHhhhhHHHHHHHHhhccCCcEEEEEEcCCCCEEEeeCCCHHHHHHHHhc
Confidence            8999998         999999999999999999999999999999999999999999999999999975

>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=100.00  E-value=1.9e-34  Score=188.37  Aligned_cols=63  Identities=43%  Similarity=0.642  Sum_probs=61.1

Q ss_pred             cCCccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHhhc
Q 048697            6 TKGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLG   68 (168)
Q Consensus         6 ~mgr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry~~   68 (168)
                      ++||+||+|         +|||+|||.||||||+||||||||+||||||||+|++|+|+||++++|+++|..
T Consensus         1 ~~GR~Ki~i~~Ie~~~~R~vTFsKRr~GL~KKa~ELs~Lc~~~v~liv~s~~gk~~~f~s~~~~~vi~~~~~   72 (84)
T d1srsa_           1 TRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQPMITSETG   72 (84)
T ss_dssp             CCCCCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTTCCEEEEECGGGHHHHSSHHH
T ss_pred             CCCCceeeEEeecCcchhhhhhHHhhhhHHHHHHHHhcccCCcEEEEEEcCCCCEEEeeCCCHHHHHHHHHH
Confidence            579999999         899999999999999999999999999999999999999999999999999976

>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=8.1e-34  Score=186.54  Aligned_cols=63  Identities=43%  Similarity=0.652  Sum_probs=60.9

Q ss_pred             CCccceee---------eeeehhchhhHHHHHHHHhhhhcCcEEEEEecCCCCCcccCCchhHHHHHHhhcC
Q 048697            7 KGRQKIEM---------IITFSKRRSWIYKNASELVTLTGSEIAIVVFSQSGKPYTFGHPSVEAVANRFLGM   69 (168)
Q Consensus         7 mgr~ki~i---------~vTf~KRr~gL~KKa~ELs~LC~v~vavIvfSp~gk~~~f~sPsv~~Vl~Ry~~~   69 (168)
                      .||+||+|         +|||+|||+||||||+|||+||||+||||||||+|++|+|+||+|++|++||...
T Consensus         2 k~R~Ki~i~~I~~~~~R~vTFsKRr~GL~KKa~ELsvLc~a~vaviv~s~~gk~~~f~sp~v~~vl~r~~~~   73 (85)
T d1mnma_           2 KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGR   73 (85)
T ss_dssp             CCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTTCCEEEEECTTTTHHHHSHHHH
T ss_pred             CCccceEEEEecCCchhhhhhHHHHhhHHHHHHHHhccCCCcEEEEEEcCCCCEEeccCCCHHHHHHHHhcc
Confidence            38999999         9999999999999999999999999999999999999999999999999999874