Citrus Sinensis ID: 044317

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120---
Protein Sequence
MAARGGGKAAMAAMKGAGGLKLQAAASSSKAQAKAKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKTGSG
Secondary Structure (PSIPRED)
cccccccHHHHHHHHcccccccccccccHHHHHHHHcccccccccccccHHHHHHHccccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHccccccccHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHcccccccccccccccccccccccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHccccccccccEEEccHHHHHHHcccccccHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
MAARGGGKAAMAAMKGAGGLKLQAAASSSKAQAKAKAkgktksvapsstselgrflnipepprseTAKLITKFIKLnnrenpgmkkdllGEEKLKSLLsgkdrigiPEIAKLLsgqfvktgsg
Flexible Loop (DISEMBL)
MAARGGGKAAMAAMKGAGGLKLQAAASSSKAQAKAkakgktksvapsstselgrflnipepprsetAKLITKFIklnnrenpgmkkdllGEEKLKSLLsgkdrigipeiakllsgqfvktgsg
Low Complexity Region (SEG)
MaargggkaamaamkgagglklqaaassskaqakakakgkTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMkkdllgeeklksllsgkdRIGIPEIAKLLSGQFVKTGSG
Disordered region (IsUnstruct)
********************************************************************LITKFIK****************************IGIPEIAKLL**********
Disordered Region (DISOPRED)
**************************************************ELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV*****
Disordered Region (DISEMBL)
**************************************************ELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKTGSG
Disordered Region (DISPRO)
******************************************SVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAARGGGKAAMAAMKGAGGLKLQAAASSSKAQAKAKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKTGSG
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

No hits with e-value below 0.001 by BLAST

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	123
224083739	114	predicted protein [Populus trichocarpa]	0.902	0.973	0.533	2e-22
357484393	133	hypothetical protein MTR_5g025520 [Medic	0.829	0.766	0.461	4e-15
388504196	139	unknown [Lotus japonicus]	0.764	0.676	0.458	1e-14
356538435	132	PREDICTED: upstream activation factor su	0.626	0.583	0.5	4e-14
356496496	132	PREDICTED: upstream activation factor su	0.617	0.575	0.506	1e-13
357484389	134	Upstream activation factor subunit UAF30	0.585	0.537	0.472	5e-13
351726850	133	uncharacterized protein LOC100306154 [Gl	0.796	0.736	0.42	7e-13
225436221	128	PREDICTED: upstream activation factor su	0.764	0.734	0.447	1e-12
255554525	149	conserved hypothetical protein [Ricinus	0.609	0.503	0.539	2e-12
225427597	115	PREDICTED: upstream activation factor su	0.658	0.704	0.476	1e-10

>gi|224083739|ref|XP_002307106.1| predicted protein [Populus trichocarpa] gi|222856555|gb|EEE94102.1| predicted protein [Populus trichocarpa]

 Score =  109 bits (272), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 64/120 (53%), Positives = 84/120 (70%), Gaps = 9/120 (7%)

Query: 1   MAARGGGKAAMAAMKGAGGLKLQAAASS-SKAQAKAKAKGKTKSVAPSSTSELGRFLNIP 59
           MAA  GGKA+ +  K    +K  A AS  S   A+ KAK     + PSS   LG+FL I 
Sbjct: 1   MAA-AGGKASRSLKKAV--VKHPAYASWGSVVNAQVKAK-----LTPSSKCNLGKFLGIR 52

Query: 60  EPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK 119
           +PP S+ ++LIT+FIKLNNR+NPGMKKD+L EEKL+++L GK+R+G+ EIAKLL+ QF K
Sbjct: 53  DPPASDISQLITRFIKLNNRQNPGMKKDVLSEEKLRTMLEGKERVGVSEIAKLLAQQFPK 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357484393|ref|XP_003612484.1| hypothetical protein MTR_5g025520 [Medicago truncatula] gi|355513819|gb|AES95442.1| hypothetical protein MTR_5g025520 [Medicago truncatula]

 Score = 85.5 bits (210), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 48/104 (46%), Positives = 69/104 (66%), Gaps = 2/104 (1%)

Query: 14  MKGAGGLKLQAAASSSKAQAKAKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKF 73
           M  AG    ++ ++ SKA A+    GKTK+    +TSEL  F+ IP   RSE A +I+KF
Sbjct: 1   MNPAGLTGRRSMSTVSKAVAEIMGVGKTKT--RKATSELCTFMGIPHKSRSEIASIISKF 58

Query: 74  IKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQF 117
           IKL +  +PG+KKD L E+ L++LL G++ +G PEIAK+LS +F
Sbjct: 59  IKLYSFRSPGIKKDKLWEQNLQTLLRGRNSVGFPEIAKILSPEF 102

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388504196|gb|AFK40164.1| unknown [Lotus japonicus]

 Score = 84.0 bits (206), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 44/96 (45%), Positives = 63/96 (65%), Gaps = 2/96 (2%)

Query: 22  LQAAASSSKAQAKAKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNREN 81
            ++ ++ SKA A+    GKTK+   SS  EL  FL IP   RSE + +I+ FIKL N  +
Sbjct: 14  CRSMSTVSKAVAEIAGVGKTKTRKASS--ELCTFLGIPHHSRSEISLIISNFIKLYNARS 71

Query: 82  PGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQF 117
           PG+KKD + E+ L++LL G+  +G PEIAK+LS +F
Sbjct: 72  PGIKKDKIWEQNLQTLLRGRSSVGFPEIAKILSTEF 107

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538435|ref|XP_003537709.1| PREDICTED: upstream activation factor subunit UAF30-like [Glycine max]

 Score = 82.0 bits (201), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/78 (50%), Positives = 53/78 (67%), Gaps = 1/78 (1%)

Query: 44  VAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDR 103
           V P S SELG FL  P+  R++  K +  +IKL N +NP  KK++  +EKLK++  GKD+
Sbjct: 56  VVPVS-SELGDFLGAPQVSRTDAVKKVWAYIKLQNLQNPANKKEIFCDEKLKTIFEGKDK 114

Query: 104 IGIPEIAKLLSGQFVKTG 121
           +G  EIAKLLS  FVK+G
Sbjct: 115 VGFTEIAKLLSSHFVKSG 132

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496496|ref|XP_003517103.1| PREDICTED: upstream activation factor subunit UAF30-like [Glycine max]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 52/77 (67%), Gaps = 1/77 (1%)

Query: 44  VAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDR 103
           V P S SELG FL  P+  R+E  K +  +IKL N +NP  KK++  +EKLK++  GKD+
Sbjct: 56  VVPVS-SELGDFLGAPQVSRTEAVKKVWAYIKLQNLQNPANKKEIFCDEKLKTIFEGKDK 114

Query: 104 IGIPEIAKLLSGQFVKT 120
           +G  EIAKLLS  FVK+
Sbjct: 115 VGFTEIAKLLSNHFVKS 131

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357484389|ref|XP_003612482.1| Upstream activation factor subunit UAF30 [Medicago truncatula] gi|355513817|gb|AES95440.1| Upstream activation factor subunit UAF30 [Medicago truncatula] gi|388497934|gb|AFK37033.1| unknown [Medicago truncatula]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 34/72 (47%), Positives = 50/72 (69%)

Query: 49  TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPE 108
           TSELG F+  PE  R+E  K + ++IKL N +NP  KK++  ++KLK++  GKD++   E
Sbjct: 62  TSELGNFIGAPEVSRTEAVKKVWEYIKLQNLQNPNNKKEIFCDDKLKTIFDGKDKVVFTE 121

Query: 109 IAKLLSGQFVKT 120
           IAKLL+  FVK+
Sbjct: 122 IAKLLATHFVKS 133

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351726850|ref|NP_001238420.1| uncharacterized protein LOC100306154 [Glycine max] gi|255627701|gb|ACU14195.1| unknown [Glycine max]

 Score = 77.8 bits (190), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 42/100 (42%), Positives = 64/100 (64%), Gaps = 2/100 (2%)

Query: 18  GGLKLQAAASSSKAQAKAKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLN 77
           G    ++ ++ +KA  +    G TK     S+SEL  FL IP   RSE A +++KF KL 
Sbjct: 2   GSFGRRSMSTVAKAVEEITGTGNTK--IRKSSSELCTFLGIPRQSRSEIALILSKFTKLY 59

Query: 78  NRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQF 117
           N ++PG+KKD + E+ L++LL G++ +G PEIAK+LS +F
Sbjct: 60  NFKSPGIKKDKIWEQNLQTLLRGRNNVGFPEIAKILSPEF 99

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436221|ref|XP_002270166.1| PREDICTED: upstream activation factor subunit spp27 [Vitis vinifera] gi|147798865|emb|CAN68050.1| hypothetical protein VITISV_015104 [Vitis vinifera] gi|296090194|emb|CBI40013.3| unnamed protein product [Vitis vinifera]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/96 (44%), Positives = 60/96 (62%), Gaps = 2/96 (2%)

Query: 25  AASSSKAQAKAKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGM 84
           A   + A+   ++ G TK V  S    L +FL +PE  R+E  K I + IKLNN +NP  
Sbjct: 34  APPRTAAKGPPRSGGITKPVPVSPA--LRKFLGVPEASRAEAVKKIWEHIKLNNLQNPTN 91

Query: 85  KKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKT 120
           K+++L +EKLKS+  GKD++G  EI KLLS  F+KT
Sbjct: 92  KREILCDEKLKSVFEGKDKVGFLEIGKLLSHHFIKT 127

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255554525|ref|XP_002518301.1| conserved hypothetical protein [Ricinus communis] gi|223542521|gb|EEF44061.1| conserved hypothetical protein [Ricinus communis]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 41/76 (53%), Positives = 55/76 (72%), Gaps = 1/76 (1%)

Query: 40  KTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLS 99
           K+K V PS++S + +FL I EPP S+T+KLI  FIKL+NR+NP  +KD    + L +LLS
Sbjct: 75  KSKEV-PSTSSHICKFLGIVEPPGSDTSKLIANFIKLHNRQNPAKRKDRYFLDNLITLLS 133

Query: 100 GKDRIGIPEIAKLLSG 115
            + +IGI EIAKLLS 
Sbjct: 134 KEQKIGIGEIAKLLSN 149

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427597|ref|XP_002270707.1| PREDICTED: upstream activation factor subunit spp27 [Vitis vinifera] gi|296085458|emb|CBI29190.3| unnamed protein product [Vitis vinifera]

 Score = 70.9 bits (172), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 40/84 (47%), Positives = 55/84 (65%), Gaps = 3/84 (3%)

Query: 39  GKTKSVAPSSTSELGRFLN-IPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSL 97
           G TK V  S   +LG+FL  +P+  RS   K + + IKL+N +NP  KK++  +EKLK++
Sbjct: 34  GITKPVPVSP--QLGKFLGGVPQASRSLAIKKVWEHIKLHNLQNPTNKKEICCDEKLKTI 91

Query: 98  LSGKDRIGIPEIAKLLSGQFVKTG 121
             GKD++G  EIAKLLS  FVK G
Sbjct: 92  FDGKDKVGFLEIAKLLSPHFVKIG 115

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	123
smart00151	77	smart00151, SWIB, SWI complex, BAF60b domains	4e-09
pfam02201	76	pfam02201, SWIB, SWIB/MDM2 domain	2e-08
PRK06319	860	PRK06319, PRK06319, DNA topoisomerase I/SWI domain	9e-05
PRK14724	987	PRK14724, PRK14724, DNA topoisomerase III; Provisi	3e-04
COG5531	237	COG5531, COG5531, SWIB-domain-containing proteins	7e-04

>gnl|CDD|128456 smart00151, SWIB, SWI complex, BAF60b domains

 Score = 49.2 bits (118), Expect = 4e-09
 Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 3/79 (3%)

Query: 41  TKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSG 100
           TK V  S   EL + L  PE  R+E  K + ++IK +N ++P  K+++L + KL+ +  G
Sbjct: 2   TKKVTLSP--ELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIF-G 58

Query: 101 KDRIGIPEIAKLLSGQFVK 119
           KDR+ + E+ KLL+   +K
Sbjct: 59  KDRMDMFEMNKLLTPHLIK 77

Length = 77

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

 Score = 47.2 bits (113), Expect = 2e-08
 Identities = 28/69 (40%), Positives = 45/69 (65%), Gaps = 1/69 (1%)

Query: 50  SELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEI 109
            +L +FL   E  R+E  K + ++IK +N ++P  K+ +L +EKLKS+  G DR+G  E+
Sbjct: 9   PDLAKFLGAGELSRTEVVKKLWQYIKEHNLQDPKNKRIILCDEKLKSIF-GGDRVGFFEM 67

Query: 110 AKLLSGQFV 118
           +KLLS  F+
Sbjct: 68  SKLLSSHFI 76

This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2. Length = 76

>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein; Validated

 Score = 40.2 bits (94), Expect = 9e-05
 Identities = 27/108 (25%), Positives = 49/108 (45%), Gaps = 10/108 (9%)

Query: 21  KLQAAASSSKAQAKAKAKGKTKSVAPSST---------SELGRFLNIPEPPRSETAKLIT 71
           K ++A++  KA    K K K KS   +             L   +      R E  K + 
Sbjct: 754 KKKSASTKGKAAKTVKKKSKAKSKKTTKKRAGPLYTPSPALAAMIGAEPVGRGEATKKVW 813

Query: 72  KFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK 119
            +IK +  ++P  KK ++ + KL+ ++ G D I + +++K LS   +K
Sbjct: 814 DYIKEHGLQSPENKKLIIPDSKLQGVI-GPDPIDMFQLSKKLSQHLIK 860

Length = 860

>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 27/112 (24%), Positives = 49/112 (43%), Gaps = 1/112 (0%)

Query: 2   AARGGGKAAMAAMKGAGGLKLQAAASSSKAQAKAKAKGKTKSVAPSSTSELGRFLNIPEP 61
                 KAA  A K A        A++   +  AK K    +     ++ L   +     
Sbjct: 872 GGTVAVKAAKPAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGLKPSAALAAVIGAEPV 931

Query: 62  PRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLL 113
            R E  K +  +IK NN ++P  K+ +  + KL+ +  GKD++ + E+A ++
Sbjct: 932 ARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVF-GKDQVTMFELAGIV 982

Length = 987

>gnl|CDD|227818 COG5531, COG5531, SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]

 Score = 37.4 bits (87), Expect = 7e-04
 Identities = 27/99 (27%), Positives = 43/99 (43%), Gaps = 10/99 (10%)

Query: 25  AASSSKAQAKAKAKGKTKSVAPSSTSE---------LGRFLNIPEPPRSETAKLITKFIK 75
              +   + K   K K  S    ++           L   L +    R E  K + K+IK
Sbjct: 95  ETENGDTEGKETDKKKKSSTISKNSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIK 154

Query: 76  LNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLS 114
            +N ++P  K+ +L + KLK +L G D I + E+ K LS
Sbjct: 155 KHNLQDPNNKRLILCDSKLKKVL-GSDPIDMFELTKPLS 192

Length = 237

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	123
smart00151	77	SWIB SWI complex, BAF60b domains.	99.96
PF02201	76	SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SW	99.96
KOG1946	240	consensus RNA polymerase I transcription factor UA	99.95
PRK14724	987	DNA topoisomerase III; Provisional	99.9
COG5531	237	SWIB-domain-containing proteins implicated in chro	99.9
KOG2570	420	consensus SWI/SNF transcription activation complex	99.83
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	99.62
KOG2522	560	consensus Filamentous baseplate protein Ligatin, c	90.17
PRK05350	82	acyl carrier protein; Provisional	87.35
PRK05828	84	acyl carrier protein; Validated	84.73
CHL00124	82	acpP acyl carrier protein; Validated	81.59

>smart00151 SWIB SWI complex, BAF60b domains

Probab=99.96  E-value=3.6e-29  Score=168.84  Aligned_cols=76  Identities=36%  Similarity=0.596  Sum_probs=73.1

Q ss_pred             ccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCC
Q 044317           41 TKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK  119 (123)
Q Consensus        41 ~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k  119 (123)
                      +++  |.+|++|++|+|.+++||++|++.||+|||+||||||+||+.|+||+.|+++| |+++|.|++|+++|++||.+
T Consensus         2 ~~~--~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~-~~~~v~~~~~~~ll~~Hl~~   77 (77)
T smart00151        2 TKK--VTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIF-GKDRMDMFEMNKLLTPHLIK   77 (77)
T ss_pred             CCc--ccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHH-CcCeecHHHHHHHHHHHcCC
Confidence            455  99999999999999999999999999999999999999999999999999999 89999999999999999974

>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []

Probab=99.96  E-value=1.3e-30  Score=175.47  Aligned_cols=76  Identities=38%  Similarity=0.510  Sum_probs=69.9

Q ss_pred             CccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317           40 KTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV  118 (123)
Q Consensus        40 ~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~  118 (123)
                      |+++  |.||++|++|+|..++||++|++.||+||++||||||+|++.|+||++|+.|| +.++|++++|+++|++||.
T Consensus         1 ~~k~--~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf-~~~~v~~~~i~~~l~~hl~   76 (76)
T PF02201_consen    1 FPKR--FKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLF-GKDSVNFFEIPKLLKPHLI   76 (76)
T ss_dssp             -EEE--EHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHH-HTSECSEEETTHHHHHHHE
T ss_pred             CCCC--ccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHh-CCCeecHhhHHHHHHHhcC
Confidence            3455  88999999999999999999999999999999999999999999999999999 7899999999999999984

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

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

Probab=99.95  E-value=5.1e-29  Score=199.70  Aligned_cols=83  Identities=37%  Similarity=0.589  Sum_probs=79.3

Q ss_pred             CCCCccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhc
Q 044317           37 AKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQ  116 (123)
Q Consensus        37 ~~g~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~H  116 (123)
                      +.|++++  +.||++|++|+|.+++||.+|++.||+|||+||||||.||+.|+||++|+.|| +.++|++|+|++||.+|
T Consensus        97 ~~g~~kl--~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF-~~k~v~~fem~KLL~~H  173 (240)
T KOG1946|consen   97 SWGSTKL--IPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIF-GKKRVGMFEMLKLLTKH  173 (240)
T ss_pred             CcCcccc--cccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHh-ccCccceeeHHHHHHHh
Confidence            4699999  88999999999999999999999999999999999999999999999999999 88889999999999999


Q ss_pred             cCCCCC
Q 044317          117 FVKTGS  122 (123)
Q Consensus       117 l~k~~s  122 (123)
                      |++...
T Consensus       174 ~~~~~d  179 (240)
T KOG1946|consen  174 FLKNQD  179 (240)
T ss_pred             ccCccc
Confidence            998754

>PRK14724 DNA topoisomerase III; Provisional

Probab=99.90  E-value=2.3e-24  Score=198.47  Aligned_cols=76  Identities=22%  Similarity=0.406  Sum_probs=73.0

Q ss_pred             CccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317           40 KTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV  118 (123)
Q Consensus        40 ~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~  118 (123)
                      +..+  +.|||+|++|||..++||++|++.||+|||+||||||+|||.|+||++|+.|| |+++|.||+|+++|++||.
T Consensus       912 ~~~~--~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vf-g~~~~~~~~~~~~l~~hl~  987 (987)
T PRK14724        912 PAAG--LKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVF-GKDQVTMFELAGIVGKHLS  987 (987)
T ss_pred             cccc--cCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHh-CCCcccHHHHHHHHHHhcC
Confidence            5556  88999999999999999999999999999999999999999999999999999 9999999999999999984

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

Probab=99.90  E-value=2.7e-24  Score=172.19  Aligned_cols=74  Identities=32%  Similarity=0.469  Sum_probs=72.1

Q ss_pred             CCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCCC
Q 044317           46 PSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKT  120 (123)
Q Consensus        46 ~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k~  120 (123)
                      +.+|+.||.|||..++||++||+.||+|||.||||||+||+.|+||++|+.|| |.+.+.||+|.++|.+|+++-
T Consensus       125 ~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~-g~~p~~mf~~~k~l~~hl~~~  198 (237)
T COG5531         125 VKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVL-GSDPIDMFELTKPLSPHLIKY  198 (237)
T ss_pred             eecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHh-CCCchhhhhhhcccccceecC
Confidence            88899999999999999999999999999999999999999999999999999 699999999999999999983

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

Probab=99.83  E-value=4.2e-21  Score=163.17  Aligned_cols=95  Identities=19%  Similarity=0.302  Sum_probs=88.8

Q ss_pred             hcchhhhhccCCCC----------CccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHH
Q 044317           26 ASSSKAQAKAKAKG----------KTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLK   95 (123)
Q Consensus        26 a~~~~~~~kr~~~g----------~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk   95 (123)
                      ++..+++.||++.-          -..|+.|++||.|+++||+.+.||++||.+||+|||.|+||||+++.+|+||..|+
T Consensus       179 ~etdGf~VKR~Gd~~v~ctIll~l~~~P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~  258 (420)
T KOG2570|consen  179 NETDGFQVKRPGDRNVRCTILLLLDYQPEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALE  258 (420)
T ss_pred             CCcCceeeeccCCCccceEEEEeeccCCcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHH
Confidence            56778899998877          34888899999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCccCHHHHHHHHHhccCCCC
Q 044317           96 SLLSGKDRIGIPEIAKLLSGQFVKTG  121 (123)
Q Consensus        96 ~LF~g~d~i~~~~i~klL~~Hl~k~~  121 (123)
                      ++| |++++.|.+|+.+|++||...+
T Consensus       259 qif-~~~rl~F~elp~~l~~lL~P~d  283 (420)
T KOG2570|consen  259 QIF-GVDRLKFPELPQLLNPLLSPPD  283 (420)
T ss_pred             Hhh-cccccccccchhhhhhccCCCC
Confidence            999 9999999999999999998754

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

Probab=99.62  E-value=4.9e-16  Score=141.87  Aligned_cols=73  Identities=25%  Similarity=0.405  Sum_probs=71.1

Q ss_pred             CCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCC
Q 044317           46 PSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK  119 (123)
Q Consensus        46 ~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k  119 (123)
                      |.+|++|+.++|..+++|.++++.||+||+.|+||||+||+.|+||++|+.+| +++++.||+|+++|++||.+
T Consensus       788 ~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf-~~~~~~~~~~~k~l~~hl~~  860 (860)
T PRK06319        788 YTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVI-GPDPIDMFQLSKKLSQHLIK  860 (860)
T ss_pred             cccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhh-CcCccchhhhHHHHHhhhcC
Confidence            77899999999999999999999999999999999999999999999999999 89999999999999999875

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

Probab=90.17  E-value=0.35  Score=43.13  Aligned_cols=40  Identities=20%  Similarity=0.174  Sum_probs=35.7

Q ss_pred             CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhh
Q 044317           59 PEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLL   98 (123)
Q Consensus        59 ~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF   98 (123)
                      .-.+-+||...+.+||+.|||-|+.||..|+.|+-|-+..
T Consensus       380 ~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~  419 (560)
T KOG2522|consen  380 TLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMV  419 (560)
T ss_pred             ceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHH
Confidence            3478899999999999999999999999999888877766

>PRK05350 acyl carrier protein; Provisional

Probab=87.35  E-value=0.69  Score=30.67  Aligned_cols=54  Identities=19%  Similarity=0.073  Sum_probs=45.7

Q ss_pred             CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317           61 PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV  118 (123)
Q Consensus        61 ~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~  118 (123)
                      |+|.++...|+++|.+. +.-+.  ..|.+|..|..-+ |-|++.+-+|--.|..+|-
T Consensus         2 m~~~~i~~~v~~ii~~~-~~~~~--~~i~~d~~l~~dl-g~DSld~veli~~lE~~fg   55 (82)
T PRK05350          2 MTREEILERLRAILVEL-FEIDP--EDITPEANLYEDL-DLDSIDAVDLVVHLQKLTG   55 (82)
T ss_pred             CCHHHHHHHHHHHHHHH-hCCCH--HHCCCCccchhhc-CCCHHHHHHHHHHHHHHHC
Confidence            68999999999999987 53222  4799999998889 9999999999988888874

>PRK05828 acyl carrier protein; Validated

Probab=84.73  E-value=1.9  Score=29.37  Aligned_cols=54  Identities=17%  Similarity=0.085  Sum_probs=43.5

Q ss_pred             CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317           61 PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV  118 (123)
Q Consensus        61 ~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~  118 (123)
                      |+|.+|...|-+.|.+.++.-+  -..|.+|..|.+ + |-|++.+.+|--.|...|-
T Consensus         1 m~~~eI~~~i~~ii~e~~~~~~--~d~i~~~~~~~d-L-g~DSLd~velv~~lE~~f~   54 (84)
T PRK05828          1 MQEMEILLKIKEIAKKKNFAVT--LDESNINKPYRE-L-KIDSLDMFSIIVSLESEFN   54 (84)
T ss_pred             CCHHHHHHHHHHHHHHhccCCC--cccccCCCCHHh-c-CCCHHHHHHHHHHHHHHHC
Confidence            7899999999999988655322  245678889987 8 9999999999888887763

>CHL00124 acpP acyl carrier protein; Validated

Probab=81.59  E-value=1.7  Score=28.46  Aligned_cols=54  Identities=9%  Similarity=0.184  Sum_probs=44.3

Q ss_pred             CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317           61 PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV  118 (123)
Q Consensus        61 ~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~  118 (123)
                      |+|.+|...|-++|.+.-=.+|   ..|.+|..|..-+ |-|++.+.+|--.|...|-
T Consensus         1 M~~~~i~~~l~~ii~~~~~~~~---~~i~~d~~l~~dl-g~DSl~~~eli~~le~~f~   54 (82)
T CHL00124          1 MTKNDIFEKVQSIVAEQLGIEK---SEVTLDANFTRDL-GADSLDVVELVMAIEEKFD   54 (82)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhc-CCcHHHHHHHHHHHHHHHC
Confidence            6899999999999988742333   3599999999989 9999999999888877663

---

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	123
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	2e-10
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	3e-10
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	2e-09

>1v31_A Hypothetical protein RAFL11-05-P19; SWI/SNF complex subunit, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.42.1.1 Length = 93

 Score = 52.5 bits (126), Expect = 2e-10
 Identities = 13/86 (15%), Positives = 31/86 (36%), Gaps = 3/86 (3%)

Query: 34  KAKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEK 93
            + + G  +    S+   L   L I    R      I  ++K    +NP        +  
Sbjct: 2   SSGSSGVPEKFKLST--ALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAA 59

Query: 94  LKSLLSGKDRIGIPEIAKLLSGQFVK 119
           L+ +  G++++    +++ +S     
Sbjct: 60  LQKVF-GEEKLKFTMVSQKISHHLSP 84

>1v32_A AT5G08430, hypothetical protein RAFL09-47-K03; SWI/SNF complex subunit, structural genomics; NMR {Arabidopsis thaliana} SCOP: a.42.1.1 Length = 101

 Score = 52.1 bits (125), Expect = 3e-10
 Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 7/93 (7%)

Query: 33  AKAKAKGKTKSVAPSSTSELGRFLNI------PEPPRSETAKLITKFIKLNNRENPGMKK 86
             + + GK        + +L  FL+           R + +  I K+I      +P  KK
Sbjct: 1   GSSGSSGKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKK 60

Query: 87  DLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK 119
            ++ +++L  L  G   I   ++  LL   + +
Sbjct: 61  KVVCDKRLVLLF-GTRTIFRMKVYDLLEKHYKE 92

>1uhr_A SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily...; structural genomics, chromatin remodeling; NMR {Mus musculus} SCOP: a.42.1.1 Length = 93

 Score = 50.2 bits (120), Expect = 2e-09
 Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 34  KAKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEK 93
            + + G+           L R L I    R    + + ++IK +  ++P  ++ +L ++ 
Sbjct: 2   SSGSSGQPPQFKLDP--RLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKY 59

Query: 94  LKSLLSGKDRIGIPEIAKLLSGQFVK 119
           L+ +     R+   EI + L    + 
Sbjct: 60  LQQIF-ESQRMKFSEIPQRLHALLMP 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	123
1v31_A	93	Hypothetical protein RAFL11-05-P19; SWI/SNF comple	99.97
1uhr_A	93	SWI/SNF related, matrix associated, actin dependen	99.97
1v32_A	101	AT5G08430, hypothetical protein RAFL09-47-K03; SWI	99.97
3dac_M	130	MDM4 protein; MDMX, MDM4, HDMX, HDM4, MDM-4, MDM-X	97.65
3fea_A	100	MDM4 protein; HDMX, HDM4,human MDM4, human MDMX, p	97.44
1ycq_A	107	MDM2, MDM2; anti-oncogene, DNA-binding, transcript	97.4
1z1m_A	119	Ubiquitin-protein ligase E3 MDM2; peptide-binding	97.39
2z5s_M	140	MDM4 protein, zebrafish MDMX; MDMX, MDM4, acetylat	97.36
2axi_A	115	Ubiquitin-protein ligase E3 MDM2; drug design, pro	97.1
2kwl_A	84	ACP, acyl carrier protein; structural genomics, se	86.07

>1v31_A Hypothetical protein RAFL11-05-P19; SWI/SNF complex subunit, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.42.1.1

Probab=99.97  E-value=9.8e-33  Score=191.84  Aligned_cols=79  Identities=14%  Similarity=0.203  Sum_probs=75.8

Q ss_pred             cccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCCCC
Q 044317           42 KSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKTG  121 (123)
Q Consensus        42 kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k~~  121 (123)
                      .|++|.+|++|++|||.+++||++|++.||+|||+||||||+||+.|+||++|++|| |+++|.|++|+++|++||.+.+
T Consensus         8 ~p~~~~lS~~La~~lG~~~~sr~evvk~lW~YIK~n~Lqdp~~k~~I~cD~~L~~lf-g~~~v~~~~~~klL~~Hl~p~~   86 (93)
T 1v31_A            8 VPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVF-GEEKLKFTMVSQKISHHLSPPP   86 (93)
T ss_dssp             SCCCEECCHHHHHHSCCSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHS-CSSEEETTTTHHHHHHHCBCCC
T ss_pred             CCCccccCHHHHHHHCCCccCHHHHHHHHHHHHHHccCcCcccCceeehhHHHHHHh-CCCcccHHHHHHHHHHhcCCCC
Confidence            677799999999999999999999999999999999999999999999999999999 9999999999999999997653

>1uhr_A SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily...; structural genomics, chromatin remodeling; NMR {Mus musculus} SCOP: a.42.1.1

Probab=99.97  E-value=1.3e-32  Score=191.45  Aligned_cols=80  Identities=18%  Similarity=0.290  Sum_probs=76.1

Q ss_pred             ccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCCC
Q 044317           41 TKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKT  120 (123)
Q Consensus        41 ~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k~  120 (123)
                      +.|++|++|++|++|+|.+++||++|++.||+|||+||||||+||+.|+||++|++|| |+++|.|++|+++|++||...
T Consensus         7 ~~p~~~~lS~~La~~lG~~~~sr~evvk~lW~YIK~n~Lqdp~~k~~I~cD~~Lk~lf-g~~~v~~~~~~klL~~Hl~p~   85 (93)
T 1uhr_A            7 GQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIF-ESQRMKFSEIPQRLHALLMPP   85 (93)
T ss_dssp             SSCCEEEECTTHHHHTCCSEEEHHHHHHHHHHHHHHTTCBCSSCSSEECCCTTHHHHT-CCSSEEGGGSHHHHHHHEECS
T ss_pred             cCCCccCcCHHHHHHHCCCccCHHHHHHHHHHHHHhccCCCccccceeechHHHHHHh-CCCcccHHHHHHHHHHhcCCC
Confidence            3577799999999999999999999999999999999999999999999999999999 999999999999999999865


Q ss_pred             C
Q 044317          121 G  121 (123)
Q Consensus       121 ~  121 (123)
                      +
T Consensus        86 ~   86 (93)
T 1uhr_A           86 E   86 (93)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

Probab=99.97  E-value=2.4e-31  Score=188.09  Aligned_cols=79  Identities=20%  Similarity=0.262  Sum_probs=73.9

Q ss_pred             cccCCCCCHHHHhhh---CC---CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHh
Q 044317           42 KSVAPSSTSELGRFL---NI---PEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSG  115 (123)
Q Consensus        42 kp~~~~LS~eLa~fL---G~---~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~  115 (123)
                      .....|+|++|++||   |.   +++||++|++.||+|||+||||||+|||.|+||++|++|| |+++|.||+|+++|++
T Consensus        10 ~~~~~w~S~eLa~fl~~iG~~~~~~~sR~eVvk~lW~YIK~nnLQdp~~Kr~I~cD~kLk~lF-g~~~v~~~~m~klL~~   88 (101)
T 1v32_A           10 FEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLF-GTRTIFRMKVYDLLEK   88 (101)
T ss_dssp             CSSSSSSCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCTTEEECCSHHHHHT-CCSEEETTHHHHHHHH
T ss_pred             ceecccCCHHHHHHHHHcCCCCccccCHHHHHHHHHHHHHhhcCcCcccCCeeeccHHHHHHH-CCCcccHHHHHHHHHH
Confidence            344578999999999   87   5799999999999999999999999999999999999999 9999999999999999


Q ss_pred             ccCCCC
Q 044317          116 QFVKTG  121 (123)
Q Consensus       116 Hl~k~~  121 (123)
                      ||.+..
T Consensus        89 Hl~~~~   94 (101)
T 1v32_A           89 HYKENQ   94 (101)
T ss_dssp             HSCSCC
T ss_pred             HcCccc
Confidence            999853

>3dac_M MDM4 protein; MDMX, MDM4, HDMX, HDM4, MDM-4, MDM-X, MDM2, HDM2, nucleus, oncogene, apoptosis, cell cycle, disease mutation; 1.80A {Danio rerio}

Probab=97.65  E-value=4.1e-05  Score=55.88  Aligned_cols=71  Identities=13%  Similarity=0.158  Sum_probs=63.4

Q ss_pred             CHHHHhhh---CC--CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhhcCCCccCHHH---HHHHHHhccCC
Q 044317           49 TSELGRFL---NI--PEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLLSGKDRIGIPE---IAKLLSGQFVK  119 (123)
Q Consensus        49 S~eLa~fL---G~--~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF~g~d~i~~~~---i~klL~~Hl~k  119 (123)
                      -++|-.+|   |.  ...|..+|+..+-+||-.+.|.||.+..+|.|. +.|..+| |+++|++.+   +.+.|.++|+.
T Consensus        28 k~~lL~iLq~aGA~~dvfT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~ll-Gv~sFSVkdp~~L~~mL~~NLv~  106 (130)
T 3dac_M           28 RAPLLQILKVAGAQEEVFTVKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELL-EVGSFSVKNPSPLYEMLKRNLVI  106 (130)
T ss_dssp             CHHHHHHHHHTTCCCSSEEHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHH-TSSEEETTSCHHHHHHHHHHEEE
T ss_pred             cHHHHHHHHHhccCcceeehHHHHHHHHHhhhhhhccCccccceeEeCCccccccc-CCcceeecCcHHHHHHHHhheec
Confidence            67788887   43  568999999999999999999999999999996 7899999 999999998   99999999875


Q ss_pred             C
Q 044317          120 T  120 (123)
Q Consensus       120 ~  120 (123)
                      .
T Consensus       107 ~  107 (130)
T 3dac_M          107 L  107 (130)
T ss_dssp             C
T ss_pred             c
Confidence            3

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

Probab=97.44  E-value=0.0001  Score=51.74  Aligned_cols=72  Identities=14%  Similarity=0.202  Sum_probs=62.2

Q ss_pred             CHHHHhhh---CC--CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhhcCCCccCHH---HHHHHHHhccCC
Q 044317           49 TSELGRFL---NI--PEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLLSGKDRIGIP---EIAKLLSGQFVK  119 (123)
Q Consensus        49 S~eLa~fL---G~--~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF~g~d~i~~~---~i~klL~~Hl~k  119 (123)
                      -++|-.+|   |.  +..|..||+..+=+||-.+.|.||.+..+|.|. +.|-.+| |+++|++.   .+.+.|..||+.
T Consensus        19 k~~lL~iLq~aGA~~d~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~-G~~sFsvkdp~~l~~ml~~nLv~   97 (100)
T 3fea_A           19 KLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELL-GRQSFSVKDPSPLYDMLRKNLVT   97 (100)
T ss_dssp             CHHHHHHHHHTTCCSSCBCHHHHHHHHHHHHHHTTCEETTEEEEEECTTSHHHHHH-TCSEEETTCCHHHHHHHHHHEEC
T ss_pred             cHHHHHHHHHhccCcceeehHHHHHHHHHhhhhhhccCccccceEEeCCCcccccc-CCcceeecCchHHHHHHHhhcee
Confidence            67788887   43  568999999999999999999999999999997 7889999 99999987   688999999875


Q ss_pred             CC
Q 044317          120 TG  121 (123)
Q Consensus       120 ~~  121 (123)
                      ..
T Consensus        98 ~~   99 (100)
T 3fea_A           98 LA   99 (100)
T ss_dssp             --
T ss_pred             cC
Confidence            43

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

Probab=97.40  E-value=0.00025  Score=50.31  Aligned_cols=68  Identities=15%  Similarity=0.154  Sum_probs=57.0

Q ss_pred             CHHHHhhh---CC--CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhhcCCCccCHHHHH---HHHHhcc
Q 044317           49 TSELGRFL---NI--PEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLLSGKDRIGIPEIA---KLLSGQF  117 (123)
Q Consensus        49 S~eLa~fL---G~--~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF~g~d~i~~~~i~---klL~~Hl  117 (123)
                      .++|..+|   |-  ..-|+-+|+..+-+||-.+.|.|+.+..+|.|. +.|-.|| |+++|++.+..   +.|.+.+
T Consensus        15 k~~LLklL~~~GA~~~~fT~keVm~YLgqYI~~KqLyd~~~qhiV~C~~D~LG~l~-g~~~Fsvkdp~~l~~ml~~nL   91 (107)
T 1ycq_A           15 TPLLLSLLKSAGAQKETFTMKEVIYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELF-GVQEFSVKEPRRLYAMISRNL   91 (107)
T ss_dssp             CHHHHHHHHHTTCCCSCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHH-TCSEEETTCHHHHHHHHHTTE
T ss_pred             cHHHHHHHHHhccccceeeehhhhhhHHHHHhHHhhcccccCcEEeeCCccccccc-CccceeecCcHHHHHHHHHhc
Confidence            67787887   43  568999999999999999999999999999997 7779999 99999988765   4444444

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

Probab=97.39  E-value=0.00025  Score=51.06  Aligned_cols=68  Identities=13%  Similarity=0.144  Sum_probs=56.4

Q ss_pred             CHHHHhhh---CC--CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhhcCCCccCHHHHHHHHHhcc
Q 044317           49 TSELGRFL---NI--PEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLLSGKDRIGIPEIAKLLSGQF  117 (123)
Q Consensus        49 S~eLa~fL---G~--~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF~g~d~i~~~~i~klL~~Hl  117 (123)
                      .++|-.||   |-  ..-++-+|+..+-+||-.+.|.|+.+..+|.|. +.|-.|| |+++|++.+-..+...|+
T Consensus        31 k~~LLkiLq~aGA~~~vfT~keV~~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~-g~~~Fsvkdp~~l~~ml~  104 (119)
T 1z1m_A           31 KPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLF-GVPSFSVKEHRKIYTMIY  104 (119)
T ss_dssp             STTSHHHHHHHTCCCSCCCTTHHHHHHHHHHHTTTCSCSSSSCEECCTTSHHHHHS-CCSCEETTCHHHHHHHHS
T ss_pred             cHHHHHHHHHhccccceeechheeehhhhhhhHhhhcccccCcEEeeCCccccccc-CccceeecCcHHHHHHHH
Confidence            55666666   53  568999999999999999999999999999997 7779999 999999887655555443

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

Probab=97.36  E-value=0.00019  Score=52.88  Aligned_cols=69  Identities=13%  Similarity=0.168  Sum_probs=58.3

Q ss_pred             CHHHHhhh---CC--CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhhcCCCccCHHHHH---HHHHhccC
Q 044317           49 TSELGRFL---NI--PEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLLSGKDRIGIPEIA---KLLSGQFV  118 (123)
Q Consensus        49 S~eLa~fL---G~--~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF~g~d~i~~~~i~---klL~~Hl~  118 (123)
                      -++|-.||   |.  ..-|+-||+..+-+||-.+.|.|+.+..+|.|. +.|-.|| |+++|++.+..   +.|.+-++
T Consensus        27 k~~LLkiLq~aGA~~~~fT~keVm~YLGqYIm~KqLYD~~~qhiV~C~~D~LG~l~-Gv~sFSVKdp~~ly~ML~~NLv  104 (140)
T 2z5s_M           27 RAPLLQILKVAGAQEEVFTLKEVMHYLGQYIMMKQLYDKQRQHIVHCHDDPLGELL-EVGSFSVKNPSPVYEMLKRNLV  104 (140)
T ss_dssp             CHHHHHHHHHTTCCCSCBCHHHHHHHHHHHHHHHTCBCSSSTTEEECTTSHHHHHH-TSSEEETTBCHHHHHHHHHHEE
T ss_pred             cHHHHHHHHHhCcccceeeHHHHHHHHHHHHHHhhhcccccCcEEeeCCccccccc-CccceeecCcHHHHHHHHHhcc
Confidence            77888888   53  568999999999999999999999999999997 7789999 99999987644   55555444

>2axi_A Ubiquitin-protein ligase E3 MDM2; drug design, protein-protein interactions, ligase, LIGA inhibitor complex; HET: 6CW MPO; 1.40A {Homo sapiens} SCOP: a.42.1.1 PDB: 1ycr_A 2gv2_A* 1t4f_M* 3jzr_A 3g03_A 3tu1_A* 3jzk_A* 1t4e_A* 3lbl_A* 4dij_A* 3lbk_A* 3v3b_A* 3jzs_A 3eqs_A 3iux_A* 3iwy_A* 3lnj_A* 3lnz_A 1rv1_A* 1ttv_A*

Probab=97.10  E-value=0.00023  Score=51.04  Aligned_cols=66  Identities=14%  Similarity=0.132  Sum_probs=55.5

Q ss_pred             CHHHHhhh---CC--CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhhcCCCccCHHHHHHHHHh
Q 044317           49 TSELGRFL---NI--PEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLLSGKDRIGIPEIAKLLSG  115 (123)
Q Consensus        49 S~eLa~fL---G~--~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF~g~d~i~~~~i~klL~~  115 (123)
                      .++|..+|   |-  ..-|+-+|+-.+-+||-.+.|.||.+..+|.|. +.|-.|| |+++|++.+-..+...
T Consensus        15 k~~LLklLq~~GA~~~vfT~keVm~YLgqYIm~KqLyd~~~qhiV~C~~D~LG~l~-g~~~Fsvkdp~~l~~m   86 (115)
T 2axi_A           15 KPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLF-GVPSFSVKEHRKIYTM   86 (115)
T ss_dssp             CHHHHHHHHHTTCCCSCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHH-SSSEEETTCHHHHHHH
T ss_pred             cHHHHHHHHHhccccceeechhheehhhhhhhHhhhcccccCcEEeeCCccccccc-CccceeecCcHHHHHH
Confidence            67788887   43  567899999999999999999999999999997 7789999 9999998765544433

>2kwl_A ACP, acyl carrier protein; structural genomics, seattle structura genomics center for infectious disease, ssgcid, lipid bindi protein; NMR {Borrelia burgdorferi}

Probab=86.07  E-value=0.81  Score=28.62  Aligned_cols=58  Identities=16%  Similarity=0.181  Sum_probs=46.3

Q ss_pred             CCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317           57 NIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV  118 (123)
Q Consensus        57 G~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~  118 (123)
                      |-..|+|.++...|.++|.+.-=.+   ...|..|..|..-+ |-|++.+.+|...|..+|-
T Consensus         1 ~~~~m~~~~i~~~l~~~i~~~l~~~---~~~i~~~~~l~~dl-G~DSl~~vel~~~le~~fg   58 (84)
T 2kwl_A            1 GPGSMDNDEIFSKVRSIISEQLDKK---EDEITTDSRFVEDL-NADSLDIYELLYLLEEAFD   58 (84)
T ss_dssp             CCCCSTHHHHHHHHHHHHHHHHCCC---GGGCCTTTHHHHTS-SSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCC---cccCCCCCchhhhc-CCCHHHHHHHHHHHHHHHC
Confidence            4567999999999999998863223   24688999997778 8999999999988888764

---

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	123
d1v31a_	93	a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl	7e-11
d1v32a_	101	a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl	9e-10
d1uhra_	93	a.42.1.1 (A:) SWI/SNF related regulator of chromat	4e-09

>d1v31a_ a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl11-05-p19) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 93

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: Hypothetical protein AT5G14170 (rafl11-05-p19)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 52.5 bits (126), Expect = 7e-11
 Identities = 11/71 (15%), Positives = 27/71 (38%), Gaps = 1/71 (1%)

Query: 49  TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPE 108
           ++ L   L I    R      I  ++K    +NP        +  L+ +  G++++    
Sbjct: 15  STALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVF-GEEKLKFTM 73

Query: 109 IAKLLSGQFVK 119
           +++ +S     
Sbjct: 74  VSQKISHHLSP 84

>d1v32a_ a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl09-47-k03) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: Hypothetical protein AT5G08430 (rafl09-47-k03)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 49.8 bits (119), Expect = 9e-10
 Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 7/90 (7%)

Query: 37  AKGKTKSVAPSSTSELGRFLNIP------EPPRSETAKLITKFIKLNNRENPGMKKDLLG 90
           + GK        + +L  FL+           R + +  I K+I      +P  KK ++ 
Sbjct: 5   SSGKRFEFVGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVC 64

Query: 91  EEKLKSLLSGKDRIGIPEIAKLLSGQFVKT 120
           +++L  L  G   I   ++  LL   + + 
Sbjct: 65  DKRLVLLF-GTRTIFRMKVYDLLEKHYKEN 93

>d1uhra_ a.42.1.1 (A:) SWI/SNF related regulator of chromatin (BRG1-associated factor 60a) {Mouse (Mus musculus) [TaxId: 10090]} Length = 93

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: SWI/SNF related regulator of chromatin (BRG1-associated factor 60a)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.8 bits (114), Expect = 4e-09
 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 49  TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPE 108
              L R L I    R    + + ++IK +  ++P  ++ +L ++ L+ +     R+   E
Sbjct: 15  DPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIF-ESQRMKFSE 73

Query: 109 IAKLLSGQFVK 119
           I + L    + 
Sbjct: 74  IPQRLHALLMP 84

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	123
d1v31a_	93	Hypothetical protein AT5G14170 (rafl11-05-p19) {Th	99.98
d1uhra_	93	SWI/SNF related regulator of chromatin (BRG1-assoc	99.97
d1v32a_	101	Hypothetical protein AT5G08430 (rafl09-47-k03) {Th	99.96
d1ttva_	107	MDM2 {African clawed frog (Xenopus laevis) [TaxId:	98.06
d2axia1	85	MDM2 {Human (Homo sapiens) [TaxId: 9606]}	98.05
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	86.49

>d1v31a_ a.42.1.1 (A:) Hypothetical protein AT5G14170 (rafl11-05-p19) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: Hypothetical protein AT5G14170 (rafl11-05-p19)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.98  E-value=9.6e-34  Score=195.56  Aligned_cols=83  Identities=14%  Similarity=0.244  Sum_probs=79.9

Q ss_pred             cCCCCCccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHH
Q 044317           35 AKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLS  114 (123)
Q Consensus        35 r~~~g~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~  114 (123)
                      +..+||.++  |+||++|++|||++++||++|++.||+|||+||||||+||+.|+||++|+.|| |.++|+|++|+++|+
T Consensus         3 ~~~~G~~~~--~~lS~~La~~lg~~~~sR~~v~k~iw~YIk~n~Lqd~~nkr~I~~D~~L~~lf-g~~~v~~~~l~~~L~   79 (93)
T d1v31a_           3 SGSSGVPEK--FKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVF-GEEKLKFTMVSQKIS   79 (93)
T ss_dssp             SSCCSSCCC--EECCHHHHHHSCCSEECSHHHHHHHHHHHHHTTCBCSSCSSEEECCSHHHHHS-CSSEEETTTTHHHHH
T ss_pred             CCCCCCcCC--ccCCHHHHHHHCcCcCcHHHHHHHHHHHHHHhCCCCCCCCCEEecCHHHHHHh-CCCcccHHHHHHHHH
Confidence            458899999  99999999999999999999999999999999999999999999999999999 999999999999999


Q ss_pred             hccCCC
Q 044317          115 GQFVKT  120 (123)
Q Consensus       115 ~Hl~k~  120 (123)
                      +||.+.
T Consensus        80 ~Hl~p~   85 (93)
T d1v31a_          80 HHLSPP   85 (93)
T ss_dssp             HHCBCC
T ss_pred             HhCCCC
Confidence            999963

>d1uhra_ a.42.1.1 (A:) SWI/SNF related regulator of chromatin (BRG1-associated factor 60a) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: SWI/SNF related regulator of chromatin (BRG1-associated factor 60a)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.97  E-value=4e-33  Score=192.77  Aligned_cols=82  Identities=18%  Similarity=0.327  Sum_probs=77.5

Q ss_pred             cCCCCCccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHH
Q 044317           35 AKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLS  114 (123)
Q Consensus        35 r~~~g~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~  114 (123)
                      +..+|+..+  |+||++|++|||++++||++|++.||+|||+||||||+||++|+||++|++|| |+++|.|++|+++|+
T Consensus         3 ~~~sg~p~~--~~lS~~La~~lg~~~~sR~~v~k~iw~YIk~n~Lqdp~nkr~I~cD~~L~~lf-g~~~v~~~~l~~~L~   79 (93)
T d1uhra_           3 SGSSGQPPQ--FKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIF-ESQRMKFSEIPQRLH   79 (93)
T ss_dssp             CCCSSSCCE--EEECTTHHHHTCCSEEEHHHHHHHHHHHHHHTTCBCSSCSSEECCCTTHHHHT-CCSSEEGGGSHHHHH
T ss_pred             CCCCCCCCC--CCCCHHHHHHHCCCCcCHHHHHHHHHHHHHHhcCCCCCCCCEEecCHHHHHHh-CCCeecHHHHHHHHH
Confidence            345677666  99999999999999999999999999999999999999999999999999999 999999999999999


Q ss_pred             hccCC
Q 044317          115 GQFVK  119 (123)
Q Consensus       115 ~Hl~k  119 (123)
                      +||.+
T Consensus        80 ~Hl~p   84 (93)
T d1uhra_          80 ALLMP   84 (93)
T ss_dssp             HHEEC
T ss_pred             hhCCC
Confidence            99976

>d1v32a_ a.42.1.1 (A:) Hypothetical protein AT5G08430 (rafl09-47-k03) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: Hypothetical protein AT5G08430 (rafl09-47-k03)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.96  E-value=5.1e-30  Score=179.70  Aligned_cols=76  Identities=21%  Similarity=0.288  Sum_probs=71.1

Q ss_pred             CCCCCHHHHhhhC---C---CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317           45 APSSTSELGRFLN---I---PEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV  118 (123)
Q Consensus        45 ~~~LS~eLa~fLG---~---~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~  118 (123)
                      ..|.|+||++|||   .   +++||++|++.||+|||+||||||+|||.|+||++|+.|| |.++|+||+|+++|++||.
T Consensus        13 ~g~~S~eL~~FL~~~g~~~~~~~sR~eVtk~iw~YIK~nnLqdp~nkr~I~~D~~L~~Lf-g~~~v~~f~i~k~l~~H~~   91 (101)
T d1v32a_          13 VGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLF-GTRTIFRMKVYDLLEKHYK   91 (101)
T ss_dssp             SSSSCHHHHHHHHHHTCCCSSCCCHHHHHHHHHHHHHHHTCBCSSCTTEEECCSHHHHHT-CCSEEETTHHHHHHHHHSC
T ss_pred             cCcCCHHHHHHHHhcCCCCcccCCHHHHHHHHHHHHHHhcCCCCccCCEEccCHHHHHHh-CCCcccHHHHHHHHHHHcC
Confidence            4678999999984   3   5799999999999999999999999999999999999999 9999999999999999999


Q ss_pred             CCC
Q 044317          119 KTG  121 (123)
Q Consensus       119 k~~  121 (123)
                      +..
T Consensus        92 ~~~   94 (101)
T d1v32a_          92 ENQ   94 (101)
T ss_dssp             SCC
T ss_pred             Ccc
Confidence            764

>d1ttva_ a.42.1.1 (A:) MDM2 {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: MDM2
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.06  E-value=2.5e-06  Score=58.70  Aligned_cols=70  Identities=17%  Similarity=0.182  Sum_probs=62.5

Q ss_pred             CHHHHhhh---C--CCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhhcCCCccCHHH---HHHHHHhccCC
Q 044317           49 TSELGRFL---N--IPEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLLSGKDRIGIPE---IAKLLSGQFVK  119 (123)
Q Consensus        49 S~eLa~fL---G--~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF~g~d~i~~~~---i~klL~~Hl~k  119 (123)
                      .++|-.+|   |  .+.-|.-||+-.|-+||-.++|.||.+.++|.|- +.|-+|| |.++|+..+   +.+.|.+|+..
T Consensus        15 kp~LL~~L~~~GA~~~~fT~keVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~ll-gv~sFsVke~r~l~~ml~rnLv~   93 (107)
T d1ttva_          15 TPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELF-GVQEFSVKEHRRIYAMISRNLVS   93 (107)
T ss_dssp             CHHHHHHHHHTTCCSSCBCHHHHHHHHHHHHHHHTCBCSSCTTEECCSSCHHHHHH-TCSCEETTCHHHHHHHHHTTEEE
T ss_pred             CHHHHHHHHHcCCCcceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhc-CCCceeecCcHHHHHHHHhhhhc
Confidence            78899998   4  3678999999999999999999999999999995 7799999 999999877   77779999864

>d2axia1 a.42.1.1 (A:25-109) MDM2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SWIB/MDM2 domain
superfamily: SWIB/MDM2 domain
family: SWIB/MDM2 domain
domain: MDM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.05  E-value=7.8e-07  Score=59.16  Aligned_cols=69  Identities=14%  Similarity=0.166  Sum_probs=61.4

Q ss_pred             CHHHHhhh---C--CCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhhcCCCccCHHH---HHHHHHhccC
Q 044317           49 TSELGRFL---N--IPEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLLSGKDRIGIPE---IAKLLSGQFV  118 (123)
Q Consensus        49 S~eLa~fL---G--~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF~g~d~i~~~~---i~klL~~Hl~  118 (123)
                      .|+|-.+|   |  .++-|.-||+-.+-+||-.++|.||.+.++|.|- +.|-++| |.++|+..+   +...|.+||.
T Consensus         7 kp~Ll~~L~~~GA~~~~fT~kqVm~yLgqYIm~K~LyD~~~qhiV~C~~D~LG~l~-gv~sFsVk~~r~l~~ml~rnLv   84 (85)
T d2axia1           7 KPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLF-GVPSFSVKEHRKIYTMIYRNLV   84 (85)
T ss_dssp             CHHHHHHHHHTTCCCSCEEHHHHHHHHHHHHHHHTCEETTEEEEEECTTSHHHHHH-SSSEEETTCHHHHHHHHHTTEE
T ss_pred             cHHHHHHHHHcCCCcceeeHHHHHHHHHHHHHHHHhcCcccCceEecCCchHHhhc-CCCceeecCcHHHHHHHHhccc
Confidence            67888887   4  3668999999999999999999999999999996 6799999 999999887   8888888874

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=86.49  E-value=0.46  Score=28.69  Aligned_cols=43  Identities=12%  Similarity=0.166  Sum_probs=28.3

Q ss_pred             HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCC-CCCccccc-hhHHh
Q 044317           50 SELGRFLNIPEPPRSETAKLITKFIKLNNRENPG-MKKDLLGE-EKLKS   96 (123)
Q Consensus        50 ~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~-nKr~I~cD-ekLk~   96 (123)
                      .+||+++|+   ||..|...|-. .++.++-+-. ++.++++| ++|+.
T Consensus        34 ~eiA~~lG~---sretvsr~l~~-l~~~g~I~~~~~~~i~I~d~~~L~~   78 (80)
T d1ft9a1          34 EEIANLIGS---SRQTTSTALNS-LIKEGYISRQGRGHYTIPNLVRLKA   78 (80)
T ss_dssp             HHHHHHHCS---CHHHHHHHHHH-HHHTTSSEECSTTCEECSSHHHHHH
T ss_pred             HHHHHHHCC---CHHHHHHHHHH-HHHCCCEEECCCCeEEECCHHHHHh
Confidence            699999994   56666655554 4555555544 55688888 55554