Citrus Sinensis ID: 032332

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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---
Protein Sequence
MNDELCNPTLWSTTTTTTTTSTSNGVVHADSTSDANNHHLDSSGGSGNSALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccHccccEEccccccccccHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
mndelcnptlwsttttttttstsngvvhadstsdannhhldssggsgnsaLDEARHRYKTSVAALRAVLTAipnshkaksfemvsspvdsvsrsdevEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDistwqspcsv
Flexible Loop (DISEMBL)
mndelcnptlwsttttttttstsngVVHADSTSDANNHHLDSSGGSGNSALDEARHRYKTSVAALRAVLTAipnshkaksfemvsspvdsvsrsdeveiDKLEERASLLRKELANKNKYLKRLIDQLRDLITdistwqspcsv
Low Complexity Region (SEG)
MNDELCNPTLWsttttttttstsNGVVHADSTSDANNHHLDSSGGSGNSALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMvsspvdsvsrsdeveIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV
Disordered region (IsUnstruct)
************************************************************SVAALRAVLTAI****************************************LANKNKYLKRLIDQLRDLITDISTW******
Disordered Region (DISOPRED)
***ELCNPTLW****************************************DEARHRYKTSVAALRAVLTAIP****************************************ANKNKYLKRLIDQLRDLITDISTWQSPC**
Disordered Region (DISEMBL)
MNDELCNPTLWSTTTTTTTTSTSNGVVHADSTSDANNHHLDSSGGSGNSALDEARHRYKTSVAALRAVLTAIPNSHKAKS***************EVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV
Disordered Region (DISPRO)
****LCN*******************************************LDEARHRYKTSVAALRAVLTAIPN*******E***********SDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDISTWQS*C**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNDELCNPTLWSTTTTTTTTSTSNGVVHADSTSDANNHHLDSSGGSGNSALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxITDISTWQSPCSV
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	143	2.2.26 [Sep-21-2011]
Q9FMV4	189	Mediator of RNA polymeras	yes	no	0.958	0.724	0.560	2e-35

>sp|Q9FMV4|MED30_ARATH Mediator of RNA polymerase II transcription subunit 30 OS=Arabidopsis thaliana GN=MED30 PE=1 SV=1

 Score =  147 bits (371), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 88/157 (56%), Positives = 107/157 (68%), Gaps = 20/157 (12%)

Query: 1   MNDELCNPTLWSTTTT-----TTTTSTSNGVVHADSTS-DANNHHLDSSGGSG-----NS 49
           MNDELCNP+LWST+ T     TTT S  + +V AD+ + D  +HH +S+GG G     NS
Sbjct: 39  MNDELCNPSLWSTSATPSSAATTTGSNGSALVSADAAAIDGTSHHSESAGGGGGGGSGNS 98

Query: 50  ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEM---VSSPVDSVSRSDEVEIDKLEERA 106
            LDEA  RYK SV +LRAVL AIPNS KAK+ EM   + SP        E EI+KLEE+A
Sbjct: 99  VLDEASLRYKNSVTSLRAVLAAIPNSQKAKASEMQNGLGSP------ESEDEIEKLEEQA 152

Query: 107 SLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV 143
             LR E+A KN ++K LID+LR+LI DISTWQSPCSV
Sbjct: 153 LSLRMEIAKKNVHVKELIDKLRELIADISTWQSPCSV 189

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.
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	143
255540207	196	conserved hypothetical protein [Ricinus	0.965	0.704	0.592	5e-39
224133984	177	predicted protein [Populus trichocarpa]	0.951	0.768	0.620	8e-36
225456359	174	PREDICTED: uncharacterized protein LOC10	0.972	0.798	0.641	2e-35
18424713	189	uncharacterized protein [Arabidopsis tha	0.958	0.724	0.560	1e-33
449440544	198	PREDICTED: mediator of RNA polymerase II	0.986	0.712	0.534	2e-33
224119684	185	predicted protein [Populus trichocarpa]	0.951	0.735	0.644	3e-33
356507364	164	PREDICTED: uncharacterized protein LOC10	0.909	0.792	0.583	8e-33
297793927	178	hypothetical protein ARALYDRAFT_496535 [	0.958	0.769	0.547	2e-32
51969384	184	unknown protein [Arabidopsis thaliana]	0.958	0.744	0.560	3e-32
356516539	168	PREDICTED: uncharacterized protein LOC10	0.923	0.785	0.562	1e-30

>gi|255540207|ref|XP_002511168.1| conserved hypothetical protein [Ricinus communis] gi|223550283|gb|EEF51770.1| conserved hypothetical protein [Ricinus communis]

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 96/162 (59%), Positives = 107/162 (66%), Gaps = 24/162 (14%)

Query: 1   MNDELCNPTLWS------------TTTTTTTTSTSNGVVHADSTSDAN-NHHLDSSGGSG 47
           MNDELCNPTLWS            +    + + + NGVV+ DS SDA   HH D +G   
Sbjct: 40  MNDELCNPTLWSTTSSSNNTTSPISAPANSNSLSQNGVVNGDSVSDAVVAHHFDGTGTGV 99

Query: 48  NS------ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDK 101
                   ALDEAR RYK SVAALR VL AIPNSHKA SFE  SS     S +DE +++K
Sbjct: 100 VGGGTGNGALDEARFRYKNSVAALREVLAAIPNSHKAISFETSSS-----SPADEADVEK 154

Query: 102 LEERASLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV 143
           LEE+AS LRKEL NKN YLK LIDQLRDLITDISTWQSPCSV
Sbjct: 155 LEEQASNLRKELFNKNAYLKLLIDQLRDLITDISTWQSPCSV 196

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133984|ref|XP_002321708.1| predicted protein [Populus trichocarpa] gi|222868704|gb|EEF05835.1| predicted protein [Populus trichocarpa]

 Score =  154 bits (390), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 98/158 (62%), Positives = 107/158 (67%), Gaps = 22/158 (13%)

Query: 1   MNDELCNPTLWSTTTTT--------TTTSTSNGVVHADSTSDANNHHLDSS-------GG 45
           MNDELCNPTLWSTT+T         T+ +  NG V      DAN    DS+       GG
Sbjct: 27  MNDELCNPTLWSTTSTATTAVTSPITSKNAQNGAVVITVNGDANAAVSDSTHELSGGGGG 86

Query: 46  SGNSALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEER 105
            GN ALDEAR RYK SVAALR VL AIPNSHKAK FE  SSP      +DE EI KLEER
Sbjct: 87  VGNGALDEARFRYKNSVAALRDVLAAIPNSHKAKPFE-TSSP------ADEAEIKKLEER 139

Query: 106 ASLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV 143
           AS LRKELA KN Y+K LIDQLR++ITDISTWQ+PCSV
Sbjct: 140 ASSLRKELAKKNTYVKLLIDQLREIITDISTWQTPCSV 177

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225456359|ref|XP_002283991.1| PREDICTED: uncharacterized protein LOC100264705 [Vitis vinifera] gi|147789866|emb|CAN73869.1| hypothetical protein VITISV_001275 [Vitis vinifera] gi|297734439|emb|CBI15686.3| unnamed protein product [Vitis vinifera]

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/145 (64%), Positives = 114/145 (78%), Gaps = 6/145 (4%)

Query: 1   MNDELCNPTLWSTTT--TTTTTSTSNGVVHADSTSDANNHHLDSSGGSGNSALDEARHRY 58
           MNDELCNPTLWST     T  +S S+  ++ D++SD + HH++ +GG    ALD+AR RY
Sbjct: 34  MNDELCNPTLWSTPPPPATAASSHSSASLNGDASSDFS-HHMEIAGGG---ALDDARLRY 89

Query: 59  KTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNK 118
           K+SVA+LRAVL AI +S KAK+FE  S+   S S++D+ EI+KLEERAS LRKELA+KNK
Sbjct: 90  KSSVASLRAVLNAIQSSQKAKAFEASSAASGSASQADQAEIEKLEERASNLRKELADKNK 149

Query: 119 YLKRLIDQLRDLITDISTWQSPCSV 143
           YLK LIDQLRDLITDISTWQSPCSV
Sbjct: 150 YLKLLIDQLRDLITDISTWQSPCSV 174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18424713|ref|NP_568973.1| uncharacterized protein [Arabidopsis thaliana] gi|75171739|sp|Q9FMV4.1|MED30_ARATH RecName: Full=Mediator of RNA polymerase II transcription subunit 30 gi|9758289|dbj|BAB08813.1| unnamed protein product [Arabidopsis thaliana] gi|190886513|gb|ACE95179.1| At1g17730 [Arabidopsis thaliana] gi|332010374|gb|AED97757.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 88/157 (56%), Positives = 107/157 (68%), Gaps = 20/157 (12%)

Query: 1   MNDELCNPTLWSTTTT-----TTTTSTSNGVVHADSTS-DANNHHLDSSGGSG-----NS 49
           MNDELCNP+LWST+ T     TTT S  + +V AD+ + D  +HH +S+GG G     NS
Sbjct: 39  MNDELCNPSLWSTSATPSSAATTTGSNGSALVSADAAAIDGTSHHSESAGGGGGGGSGNS 98

Query: 50  ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEM---VSSPVDSVSRSDEVEIDKLEERA 106
            LDEA  RYK SV +LRAVL AIPNS KAK+ EM   + SP        E EI+KLEE+A
Sbjct: 99  VLDEASLRYKNSVTSLRAVLAAIPNSQKAKASEMQNGLGSP------ESEDEIEKLEEQA 152

Query: 107 SLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV 143
             LR E+A KN ++K LID+LR+LI DISTWQSPCSV
Sbjct: 153 LSLRMEIAKKNVHVKELIDKLRELIADISTWQSPCSV 189

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440544|ref|XP_004138044.1| PREDICTED: mediator of RNA polymerase II transcription subunit 30-like [Cucumis sativus] gi|449532651|ref|XP_004173294.1| PREDICTED: mediator of RNA polymerase II transcription subunit 30-like [Cucumis sativus]

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 86/161 (53%), Positives = 111/161 (68%), Gaps = 20/161 (12%)

Query: 1   MNDELCNPTLWS---------------TTTTTTTTSTSNGVVHADSTSDANNHHLDSSGG 45
           MNDELCNPTLWS                + +  ++ ++NGVV+ D++S++ +HH DSSGG
Sbjct: 40  MNDELCNPTLWSTTSSTATTATSGLTIASPSGPSSHSANGVVNGDASSESTSHHTDSSGG 99

Query: 46  SGNS---ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKL 102
            G+    AL+EAR RYK SV ALRA+L AIPNS KAK++E  +S     S +D+ EIDKL
Sbjct: 100 GGSGSGGALEEARVRYKNSVLALRAILAAIPNSQKAKAYESGTS--GHASPADQSEIDKL 157

Query: 103 EERASLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV 143
           E+  S LRKEL  KN ++K LIDQLRDL+ D+STWQSPCSV
Sbjct: 158 EQHLSNLRKELVVKNLHIKLLIDQLRDLVADVSTWQSPCSV 198

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119684|ref|XP_002318134.1| predicted protein [Populus trichocarpa] gi|118486707|gb|ABK95190.1| unknown [Populus trichocarpa] gi|222858807|gb|EEE96354.1| predicted protein [Populus trichocarpa]

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 96/149 (64%), Positives = 105/149 (70%), Gaps = 13/149 (8%)

Query: 1   MNDELCNPTLWSTTTTTTTTSTSNGVVHADSTSDANNHHLDSS------GGSGNSALDEA 54
           MNDELCNPTLWSTT+T+T+T TS          DAN    DS+      GG GN ALDEA
Sbjct: 44  MNDELCNPTLWSTTSTSTSTVTSPITSSNAQNGDANAAVSDSTLELNGGGGVGNGALDEA 103

Query: 55  RHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELA 114
           R RYK SVAALR VL AIPNSHKAK FE  SSP      +D+ EI+KLEERAS LRKELA
Sbjct: 104 RFRYKNSVAALRDVLAAIPNSHKAKPFE-TSSP------ADQAEIEKLEERASNLRKELA 156

Query: 115 NKNKYLKRLIDQLRDLITDISTWQSPCSV 143
            KN Y+K LIDQLR+LI DISTWQ P SV
Sbjct: 157 KKNTYVKLLIDQLRELIADISTWQGPYSV 185

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507364|ref|XP_003522437.1| PREDICTED: uncharacterized protein LOC100788627 [Glycine max]

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 84/144 (58%), Positives = 100/144 (69%), Gaps = 14/144 (9%)

Query: 1   MNDELCNPTLWSTTTTTTTTSTSNGVVHADSTSDANNHHLDSSGGSGNSALDEA--RHRY 58
           MNDELCNP LWST+ +T+         +AD+TSD +NHH D+S  S  +       R RY
Sbjct: 32  MNDELCNPVLWSTSPSTSP--------NADATSDNSNHHADASAASAAAGGALEEARARY 83

Query: 59  KTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNK 118
           K +V ALR +LTAIP S K K+F+  S+     S +DE EIDKLEERAS LR+ELANKN 
Sbjct: 84  KKAVTALRTILTAIPTSQKEKTFDAGSA----ASPADEAEIDKLEERASSLRRELANKNL 139

Query: 119 YLKRLIDQLRDLITDISTWQSPCS 142
           +LK LIDQLRDLITDISTWQSP S
Sbjct: 140 HLKTLIDQLRDLITDISTWQSPFS 163

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297793927|ref|XP_002864848.1| hypothetical protein ARALYDRAFT_496535 [Arabidopsis lyrata subsp. lyrata] gi|297310683|gb|EFH41107.1| hypothetical protein ARALYDRAFT_496535 [Arabidopsis lyrata subsp. lyrata]

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 86/157 (54%), Positives = 106/157 (67%), Gaps = 20/157 (12%)

Query: 1   MNDELCNPTLWSTTTTTTTTSTSNG-----VVHADSTS-DANNHHLDSSGGSG-----NS 49
           MNDELCNP+LWST+ T ++ +T+ G     +V  D+ + D  +HH +S GG G     NS
Sbjct: 28  MNDELCNPSLWSTSATPSSAATATGSNGSALVSVDAAAIDGTSHHSESGGGGGGGGSGNS 87

Query: 50  ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEM---VSSPVDSVSRSDEVEIDKLEERA 106
            LDEA  RYK SV +LRAVL AIPNSHKAK+ EM     SP        E EI+KLEE+A
Sbjct: 88  VLDEASLRYKNSVTSLRAVLAAIPNSHKAKASEMENGFGSP------ESEDEIEKLEEQA 141

Query: 107 SLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV 143
             LR E+A KN ++K LID+LR+LI DISTWQSPCSV
Sbjct: 142 LSLRMEIAKKNVHVKELIDKLRELIADISTWQSPCSV 178

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51969384|dbj|BAD43384.1| unknown protein [Arabidopsis thaliana]

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 88/157 (56%), Positives = 106/157 (67%), Gaps = 20/157 (12%)

Query: 1   MNDELCNPTLWSTTTT-----TTTTSTSNGVVHADSTS-DANNHHLDSSGGSG-----NS 49
           MNDELCNP+LWST+ T     TTT S  + +V AD+ + D  +HH +S+GG G     NS
Sbjct: 34  MNDELCNPSLWSTSATPSSAATTTGSNGSALVSADAAAIDGTSHHSESAGGGGGEGSGNS 93

Query: 50  ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEM---VSSPVDSVSRSDEVEIDKLEERA 106
            LDEA  RYK SV +LRAVL AIPNS KAK+ EM   + SP        E EI+KLEE+A
Sbjct: 94  VLDEASLRYKNSVTSLRAVLAAIPNSQKAKASEMQNGLGSP------ESEDEIEKLEEQA 147

Query: 107 SLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV 143
             LR E+A KN ++K LID LR+LI DISTWQSPCSV
Sbjct: 148 LSLRMEIAKKNVHVKELIDILRELIADISTWQSPCSV 184

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516539|ref|XP_003526951.1| PREDICTED: uncharacterized protein LOC100816835 [Glycine max]

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 81/144 (56%), Positives = 103/144 (71%), Gaps = 12/144 (8%)

Query: 1   MNDELCNPTLWSTTTTTTTTSTSNGVVHADSTSDANNHHLDSSGGSGNSA--LDEARHRY 58
           MNDELCNP LWST+ + +++       +AD+TS+ +NHH D++  +      L++AR RY
Sbjct: 34  MNDELCNPVLWSTSPSASSSP------NADATSENSNHHADATTAAAGGGGALEQARSRY 87

Query: 59  KTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNK 118
           K +VAALR +LTAIPNS KA +     +   + S +DE EIDKLEERAS LR+ELANKN 
Sbjct: 88  KKAVAALRTILTAIPNSQKANA----FNASSAASPADEAEIDKLEERASSLRRELANKNL 143

Query: 119 YLKRLIDQLRDLITDISTWQSPCS 142
           +LK LIDQLRDLITDISTW SP S
Sbjct: 144 HLKTLIDQLRDLITDISTWHSPFS 167

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	143
TAIR|locus:2167321	189	AT5G63480 "AT5G63480" [Arabido	0.979	0.740	0.512	1.6e-31

TAIR|locus:2167321 AT5G63480 "AT5G63480" [Arabidopsis thaliana (taxid:3702)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 79/154 (51%), Positives = 95/154 (61%)

Query:     1 MNDELCNPTLWXXXXXXXXXXXXNG-----VVHADSTS-DANNHHLDSSGG-----SGNS 49
             MNDELCNP+LW             G     +V AD+ + D  +HH +S+GG     SGNS
Sbjct:    39 MNDELCNPSLWSTSATPSSAATTTGSNGSALVSADAAAIDGTSHHSESAGGGGGGGSGNS 98

Query:    50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMXXXXXXXXXXXXXXXIDKLEERASLL 109
              LDEA  RYK SV +LRAVL AIPNS KAK+ EM               I+KLEE+A  L
Sbjct:    99 VLDEASLRYKNSVTSLRAVLAAIPNSQKAKASEMQNGLGSPESEDE---IEKLEEQALSL 155

Query:   110 RKELANKNKYLKRLIDQLRDLITDISTWQSPCSV 143
             R E+A KN ++K LID+LR+LI DISTWQSPCSV
Sbjct:   156 RMEIAKKNVHVKELIDKLRELIADISTWQSPCSV 189


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.313   0.126   0.365    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      143       116   0.00091  102 3  11 23  0.38    31
                                                     29  0.45    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  575 (61 KB)
  Total size of DFA:  128 KB (2081 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  13.05u 0.10s 13.15t   Elapsed:  00:00:01
  Total cpu time:  13.05u 0.10s 13.15t   Elapsed:  00:00:01
  Start:  Sat May 11 01:54:29 2013   End:  Sat May 11 01:54:30 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0016592 "mediator complex" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9FMV4	MED30_ARATH	No assigned EC number	0.5605	0.9580	0.7248	yes	no

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

Your Input: gw1.XV.2160.1 hypothetical protein (177 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

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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	143
pfam11315	150	pfam11315, Med30, Mediator complex subunit 30	0.003

>gnl|CDD|221075 pfam11315, Med30, Mediator complex subunit 30

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 14/35 (40%), Positives = 24/35 (68%), Gaps = 1/35 (2%)

Query: 102 LEERASLLRKELANKNKYLKRLIDQLRDLITDIST 136
           L+ER  L+ K +  KN+ L+ +ID+LR  + +I+T
Sbjct: 110 LQERRELIEK-VKQKNQQLREIIDKLRITVWEINT 143

Med30 is a metazoan-specific subunit of Mediator, having no homologues in yeasts. Length = 150

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	143
PF11315	150	Med30: Mediator complex subunit 30; InterPro: IPR0	95.98
PF07544	83	Med9: RNA polymerase II transcription mediator com	90.56
PRK11546	143	zraP zinc resistance protein; Provisional	88.83
PF11221	144	Med21: Subunit 21 of Mediator complex; InterPro: I	86.95
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	85.51
KOG2829	326	consensus E2F-like protein [Transcription]	85.2
COG4387	139	Mu-like prophage protein gp36 [Function unknown]	85.19
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	85.05
PLN02678	448	seryl-tRNA synthetase	84.25
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	84.17
PLN02320	502	seryl-tRNA synthetase	84.1
smart00150	101	SPEC Spectrin repeats.	83.84
PF11831	231	Myb_Cef: pre-mRNA splicing factor component; Inter	83.62
PRK05431	425	seryl-tRNA synthetase; Provisional	83.48
PF11262	298	Tho2: Transcription factor/nuclear export subunit	82.91
PF01920	106	Prefoldin_2: Prefoldin subunit; InterPro: IPR00277	81.35
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	80.93

>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=95.98  E-value=0.018  Score=45.42  Aligned_cols=38  Identities=39%  Similarity=0.553  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhc
Q 032332           98 EIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDIS  135 (143)
Q Consensus        98 EIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~DiS  135 (143)
                      +...+.+.--.|=+-+..||.+||.+|||||.+|-||-
T Consensus       105 ~~~~~~~er~el~e~v~~KN~qLk~iid~lR~~iweIN  142 (150)
T PF11315_consen  105 EYRQLLEERKELIEQVKQKNQQLKEIIDQLRNIIWEIN  142 (150)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445554455666788999999999999999999984

Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.

>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=90.56  E-value=2  Score=30.00  Aligned_cols=52  Identities=23%  Similarity=0.478  Sum_probs=32.9

Q ss_pred             CchhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 032332           48 NSALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRL  123 (143)
Q Consensus        48 ggaLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~L  123 (143)
                      -.+.++-|||+++|-++++    .+|.        +..+            +|.-|++...||+++..|+..|+.|
T Consensus        27 ~~~~~~lk~Klq~ar~~i~----~lpg--------i~~s------------~eeq~~~i~~Le~~i~~k~~~L~~~   78 (83)
T PF07544_consen   27 DTATGSLKHKLQKARAAIR----ELPG--------IDRS------------VEEQEEEIEELEEQIRKKREVLQKF   78 (83)
T ss_pred             HHHHHHHHHHHHHHHHHHH----hCCC--------ccCC------------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467788999999866655    4443        2233            3445566666777777777666554

Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex

>PRK11546 zraP zinc resistance protein; Provisional

Probab=88.83  E-value=3.7  Score=32.31  Aligned_cols=60  Identities=17%  Similarity=0.269  Sum_probs=43.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNK  118 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~  118 (143)
                      .+|.-+.+|...++.||..|.+=-  ...++. +...      +.|++-|.+|.++.+.||..|..+-.
T Consensus        51 ~~q~I~~~f~~~t~~LRqqL~aKr--~ELnAL-l~~~------~pD~~kI~aL~kEI~~Lr~kL~e~r~  110 (143)
T PRK11546         51 AWQKIHNDFYAQTSALRQQLVSKR--YEYNAL-LTAN------PPDSSKINAVAKEMENLRQSLDELRV  110 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH--HHHHHH-HcCC------CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467788999999999999886521  111111 1333      78999999999999999988776543

>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=86.95  E-value=2.5  Score=31.87  Aligned_cols=39  Identities=31%  Similarity=0.443  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhc
Q 032332           97 VEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDIS  135 (143)
Q Consensus        97 aEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~DiS  135 (143)
                      ..|.+||+.--...+|+..+=+--..|+.+++++|.+|.
T Consensus       104 ~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~i~~ia  142 (144)
T PF11221_consen  104 KRIKELEEENEEAEEELQEAVKEAEELLKQVQELIREIA  142 (144)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            479999999999999999999999999999999999985

Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.

>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8

Probab=85.51  E-value=2.3  Score=32.65  Aligned_cols=38  Identities=34%  Similarity=0.309  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 032332           94 SDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLI  131 (143)
Q Consensus        94 ~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI  131 (143)
                      ....+.+++++....|++||..++..+..|-.|.-.|-
T Consensus       151 ~~~~~~~~~~~ei~~lk~el~~~~~~~~~LkkQ~~~l~  188 (192)
T PF05529_consen  151 LLKEENKKLSEEIEKLKKELEKKEKEIEALKKQSEGLQ  188 (192)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35577888999999999999999999999999987653

Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane

>KOG2829 consensus E2F-like protein [Transcription]

Probab=85.20  E-value=2  Score=38.16  Aligned_cols=35  Identities=23%  Similarity=0.380  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 032332           94 SDEVEIDKLEERASLLRKELANKNKYLKRLIDQLR  128 (143)
Q Consensus        94 ~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlr  128 (143)
                      .+-.||++||+....+|+-|..|+.+|+.||-|..
T Consensus       129 ~ss~dv~~le~Er~k~~erI~kK~a~lqEl~~q~~  163 (326)
T KOG2829|consen  129 TSSQDVSELEEERKKRMERIKKKAAQLQELIEQVS  163 (326)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45679999999999999999999999999988863

>COG4387 Mu-like prophage protein gp36 [Function unknown]

Probab=85.19  E-value=0.82  Score=36.46  Aligned_cols=21  Identities=43%  Similarity=0.616  Sum_probs=18.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLT   70 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~ia   70 (143)
                      +-|+||+||+.+|.=|+.+.+
T Consensus        82 ~Tdq~r~rYe~av~~L~~va~  102 (139)
T COG4387          82 ATDQARQRYEDAVRFLEKVAS  102 (139)
T ss_pred             hhHHHHHHHHHHHHHHHHHHc
Confidence            679999999999999888764

>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences

Probab=85.05  E-value=3  Score=31.51  Aligned_cols=42  Identities=29%  Similarity=0.340  Sum_probs=32.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhh
Q 032332           93 RSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDI  134 (143)
Q Consensus        93 ~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~Di  134 (143)
                      ..+.+|+..|..+...||+|+..-...+|.|-..|+.|.+-.
T Consensus        68 ~~s~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~  109 (169)
T PF07106_consen   68 VPSPEELAELDAEIKELREELAELKKEVKSLEAELASLSSEP  109 (169)
T ss_pred             CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            456778888888888888888888888888887777776543

TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].

>PLN02678 seryl-tRNA synthetase

Probab=84.25  E-value=2.5  Score=37.90  Aligned_cols=72  Identities=17%  Similarity=0.229  Sum_probs=54.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      .||+-|-.-+..+..||+-...|+..-+..             +.+..+.+.|-+++..|++||......++.+-++|.+
T Consensus        37 ~ld~~~r~l~~~~e~lr~erN~~sk~I~~~-------------k~~~~~~~~l~~~~~~Lk~ei~~le~~~~~~~~~l~~  103 (448)
T PLN02678         37 ALDKEWRQRQFELDSLRKEFNKLNKEVAKL-------------KIAKEDATELIAETKELKKEITEKEAEVQEAKAALDA  103 (448)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------hhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355666666777888999888888763221             1222456788889999999999999999999999998


Q ss_pred             HHhhh
Q 032332          130 LITDI  134 (143)
Q Consensus       130 lI~Di  134 (143)
                      +..-|
T Consensus       104 ~~~~i  108 (448)
T PLN02678        104 KLKTI  108 (448)
T ss_pred             HHHhC
Confidence            87654

>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6

Probab=84.17  E-value=1.6  Score=30.55  Aligned_cols=72  Identities=21%  Similarity=0.374  Sum_probs=54.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      .||+-|-..+..+..||+--..|+..       +...      .....+++.|-+++..|.++|......++.+-++|..
T Consensus        33 ~ld~~~r~l~~~~e~lr~~rN~~sk~-------I~~~------~~~~~~~~~l~~e~~~lk~~i~~le~~~~~~e~~l~~   99 (108)
T PF02403_consen   33 ELDQERRELQQELEELRAERNELSKE-------IGKL------KKAGEDAEELKAEVKELKEEIKELEEQLKELEEELNE   99 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHH------CHTTCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHH-------HHHH------hhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46777778888888999988888765       1000      0001467889999999999999999999999999988


Q ss_pred             HHhhh
Q 032332          130 LITDI  134 (143)
Q Consensus       130 lI~Di  134 (143)
                      +..-|
T Consensus       100 ~l~~i  104 (108)
T PF02403_consen  100 LLLSI  104 (108)
T ss_dssp             HHCTS
T ss_pred             HHHcC
Confidence            86543

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....

>PLN02320 seryl-tRNA synthetase

Probab=84.10  E-value=3  Score=38.29  Aligned_cols=70  Identities=27%  Similarity=0.277  Sum_probs=51.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 032332           51 LDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDL  130 (143)
Q Consensus        51 LDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdl  130 (143)
                      ||+-|..-+.-+..||+-..+|++.-+.              +....++++|-+++..|+++|......++.+-++|.++
T Consensus        98 ld~~~r~~~~~~~~lr~ern~~sk~i~~--------------~~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~~  163 (502)
T PLN02320         98 LYENMLALQKEVERLRAERNAVANKMKG--------------KLEPSERQALVEEGKNLKEGLVTLEEDLVKLTDELQLE  163 (502)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh--------------hhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444456678888888888776221              11124678899999999999999999999999999988


Q ss_pred             Hhhh
Q 032332          131 ITDI  134 (143)
Q Consensus       131 I~Di  134 (143)
                      +.-|
T Consensus       164 ~l~i  167 (502)
T PLN02320        164 AQSI  167 (502)
T ss_pred             HHhC
Confidence            7654

>smart00150 SPEC Spectrin repeats

Probab=83.84  E-value=6.5  Score=24.74  Aligned_cols=41  Identities=20%  Similarity=0.265  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhh
Q 032332           93 RSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITD  133 (143)
Q Consensus        93 ~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~D  133 (143)
                      +.|..+++.+-++-..|++||..+...++.++..-+.|+..
T Consensus        27 ~~d~~~~~~~~~~~~~~~~e~~~~~~~v~~~~~~~~~L~~~   67 (101)
T smart00150       27 GKDLESVEALLKKHEALEAELEAHEERVEALNELGEQLIEE   67 (101)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHc
Confidence            57899999999999999999999999999999988888764

>PF11831 Myb_Cef: pre-mRNA splicing factor component; InterPro: IPR021786 This domain is functionally uncharacterised

Probab=83.62  E-value=12  Score=30.52  Aligned_cols=71  Identities=20%  Similarity=0.320  Sum_probs=45.3

Q ss_pred             CchhHHHHHHHHHHHHHHHHHHHhcCCccccccccc--cCC------CCCCCCCCCHHHHHHHHHHHHHH--HHHHHhhh
Q 032332           48 NSALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEM--VSS------PVDSVSRSDEVEIDKLEERASLL--RKELANKN  117 (143)
Q Consensus        48 ggaLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~--~~s------~v~~v~~~DqaEIekLEe~As~L--RkEi~~KN  117 (143)
                      +..=.+.++|-+.+-..||+.|+.+|.-  -+.||.  .+.      ..+.....|++||++-+++.-.-  ++|+.+..
T Consensus        50 ~~tp~~~k~~~~~~k~~Lr~~LasLP~P--~Nd~EI~lPe~e~~e~~~~~~~~eeDaad~d~r~~~~~~~~e~~e~~rRS  127 (231)
T PF11831_consen   50 GDTPRDEKARQKAAKSQLRAGLASLPKP--KNDYEIVLPEEEEEEDEEAEEEMEEDAADRDARERAEREEEEEKELKRRS  127 (231)
T ss_pred             ccChHHHHHHHHHHHHHHHHHHhcCCCC--CCeeeeecCCcccccccccccccccCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4444667888888999999999999987  455654  111      11123467999998876654444  44444544


Q ss_pred             HHH
Q 032332          118 KYL  120 (143)
Q Consensus       118 ~~l  120 (143)
                      .+|
T Consensus       128 qvv  130 (231)
T PF11831_consen  128 QVV  130 (231)
T ss_pred             HHH
Confidence            444

This domain is found in bacteria. This presumed domain is typically between 73 to 279 amino acids in length.

>PRK05431 seryl-tRNA synthetase; Provisional

Probab=83.48  E-value=3.2  Score=36.37  Aligned_cols=72  Identities=22%  Similarity=0.290  Sum_probs=54.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      .||+-|-.-+..+..||+-...+++.-+....             +..+.+.|-+++..|+++|....+.++.+-+++.+
T Consensus        32 ~ld~~~r~l~~~~~~lr~~rn~~sk~i~~~~~-------------~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~   98 (425)
T PRK05431         32 ELDEERRELQTELEELQAERNALSKEIGQAKR-------------KGEDAEALIAEVKELKEEIKALEAELDELEAELEE   98 (425)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-------------cCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45666666677788999999888877322111             11246779999999999999999999999999998


Q ss_pred             HHhhh
Q 032332          130 LITDI  134 (143)
Q Consensus       130 lI~Di  134 (143)
                      ++.-|
T Consensus        99 ~~~~i  103 (425)
T PRK05431         99 LLLRI  103 (425)
T ss_pred             HHHhC
Confidence            87544

>PF11262 Tho2: Transcription factor/nuclear export subunit protein 2; InterPro: IPR021418 THO and TREX form a eukaryotic complex which functions in messenger ribonucleoprotein metabolism and plays a role in preventing the transcription-associated genetic instability [],[]

Probab=82.91  E-value=8.6  Score=32.19  Aligned_cols=64  Identities=13%  Similarity=0.297  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhh
Q 032332           55 RHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITD  133 (143)
Q Consensus        55 R~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~D  133 (143)
                      ..+|...++.|+..+...++.      .+         .--..|+++|++....|.+|...-.++.+....+|+..-.+
T Consensus        26 ~~~Y~~ei~~L~~~i~~~~~~------~~---------~~~~k~~~~l~~~i~~L~~E~~~h~~~~~~v~~~L~~~k~~   89 (298)
T PF11262_consen   26 KELYDEEIERLEKEISQMSRA------TI---------SKKKKEKERLKNLIDKLPEELKKHQEHVEKVKKRLQEEKDS   89 (298)
T ss_pred             HHHHHHHHHHHHHHHHHhccc------cc---------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            358999999999999981111      11         23467999999999999999999999999999998876443

Tho2, along with four other subunits forms THO []. This entry represents a conserved domain found towards the C terminus of these proteins.

>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea

Probab=81.35  E-value=3.7  Score=27.74  Aligned_cols=44  Identities=32%  Similarity=0.360  Sum_probs=26.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 032332           88 VDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLI  131 (143)
Q Consensus        88 v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI  131 (143)
                      ++.+.+.=+.+++.+++....|++++....+-++.+-.+|+.++
T Consensus        60 ~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~~~  103 (106)
T PF01920_consen   60 KEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYELF  103 (106)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33333444555666666666666666666666666666666554

Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.

>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins

Probab=80.93  E-value=14  Score=28.45  Aligned_cols=26  Identities=27%  Similarity=0.392  Sum_probs=20.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCc
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNS   75 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~   75 (143)
                      -++..++.+|.+.+.||.-+...-.+
T Consensus        48 d~e~~~~~~~a~~~eLr~el~~~~k~   73 (177)
T PF07798_consen   48 DLENQEYLFKAAIAELRSELQNSRKS   73 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36778888999999999888754433

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	143
2aze_A	155	Transcription factor DP-1; coiled coil, beta sandw	93.59
1gmj_A	84	ATPase inhibitor; coiled-coil structure, P depende	93.01
3lay_A	175	Zinc resistance-associated protein; salmonella typ	90.23
1ykh_B	132	RNA polymerase II holoenzyme component SRB7; gene	88.24
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	88.08
1yke_B	151	RNA polymerase II holoenzyme component SRB7; gene	87.28
1ses_A	421	Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A	86.28
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	85.9
2hzl_A	365	Trap-T family sorbitol/mannitol transporter, perip	85.65
2zzv_A	361	ABC transporter, solute-binding protein; periplasm	84.86
2p32_A	120	Heat shock 70 kDa protein A; three-helix bundle, c	84.44
1o5h_A	214	Formiminotetrahydrofolate cyclodeaminase; TM1560,	83.89
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	82.92
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	82.88
2dq0_A	455	Seryl-tRNA synthetase; coiled-coil, homodimer, str	81.35
1wle_A	501	Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bo	81.12
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	80.72
3qne_A	485	Seryl-tRNA synthetase, cytoplasmic; amino acid bio	80.2
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	80.17

>2aze_A Transcription factor DP-1; coiled coil, beta sandwich, cell cycle, transcription; 2.55A {Homo sapiens} SCOP: e.63.1.1

Probab=93.59  E-value=0.11  Score=40.31  Aligned_cols=35  Identities=23%  Similarity=0.184  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 032332           96 EVEIDKLEERASLLRKELANKNKYLKRLIDQLRDL  130 (143)
Q Consensus        96 qaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdl  130 (143)
                      -.||++||+.-..+++.|..|+.+|+.||.|...+
T Consensus         4 ~qe~~~Le~Ek~~~~~rI~~K~~~LqeL~~Q~vaf   38 (155)
T 2aze_A            4 AQECQNLEVERQRRLERIKQKQSQLQELILQQIAF   38 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46999999999999999999999999999997643

>1gmj_A ATPase inhibitor; coiled-coil structure, P dependent oligomerization, ATP hydrolysis; 2.2A {Bos taurus} SCOP: h.4.8.1 PDB: 1ohh_H* 1hf9_A

Probab=93.01  E-value=0.4  Score=34.17  Aligned_cols=15  Identities=40%  Similarity=0.412  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHHH
Q 032332           55 RHRYKTSVAALRAVL   69 (143)
Q Consensus        55 R~RYK~AvAALRa~i   69 (143)
                      |.+=|..+++||.-+
T Consensus        35 rqkekEqL~~LKkkl   49 (84)
T 1gmj_A           35 RARAKEQLAALKKHK   49 (84)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            444456667777665

>3lay_A Zinc resistance-associated protein; salmonella typhimurium L structural genomics, center for structural genomics of INFE diseases; 2.70A {Salmonella enterica subsp}

Probab=90.23  E-value=1.3  Score=34.16  Aligned_cols=59  Identities=19%  Similarity=0.244  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHH
Q 032332           52 DEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKY  119 (143)
Q Consensus        52 DeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~  119 (143)
                      ++-|..|+..+.+||.-+.+.-..  ..+ .+...      +.|++.|++|.++...||.++......
T Consensus        77 ~~I~~e~r~~~~~Lr~ql~akr~E--L~a-L~~a~------~~DeakI~aL~~Ei~~Lr~qL~~~R~k  135 (175)
T 3lay_A           77 QKIYDDYYTQTSALRQQLISKRYE--YNA-LLTAS------SPDTAKINAVAKEMESLGQKLDEQRVK  135 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH--HHH-HHTSS------SCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH--HHH-HHhCC------CCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666777777777665543211  111 11333      789999999999999999999875543

>1ykh_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.00A {Saccharomyces cerevisiae} SCOP: a.252.1.1

Probab=88.24  E-value=1.2  Score=32.59  Aligned_cols=40  Identities=20%  Similarity=0.277  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhc
Q 032332           96 EVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDIS  135 (143)
Q Consensus        96 qaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~DiS  135 (143)
                      .+.|.+||+.--...+|+..+=+--+.|+.+++++|.+|+
T Consensus        91 ~~ri~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~l~~i~  130 (132)
T 1ykh_B           91 LRKIDMLQKKLVEVEDEKIEAIKKKEKLMRHVDSMIEDFV  130 (132)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4579999999999999999999999999999999999986

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B

Probab=88.08  E-value=2.1  Score=28.35  Aligned_cols=57  Identities=16%  Similarity=0.307  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHH--------HHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 032332           55 RHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVE--------IDKLEERASLLRKELANKNKYLKRLIDQ  126 (143)
Q Consensus        55 R~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaE--------IekLEe~As~LRkEi~~KN~~lK~LIdq  126 (143)
                      |.+.+.+...||..|-.+++           .      +.+.++        |..|+++...|..|+..-......|-.+
T Consensus        14 R~~in~~f~~Lr~lvP~~~~-----------~------k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~~L~~~   76 (83)
T 1nkp_B           14 RDHIKDSFHSLRDSVPSLQG-----------E------KASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQ   76 (83)
T ss_dssp             HHHHHHHHHHHHTTSGGGTT-----------S------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCC-----------C------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44567888889887654432           1      344444        6777777777776665544444444444


Q ss_pred             HH
Q 032332          127 LR  128 (143)
Q Consensus       127 lr  128 (143)
                      |.
T Consensus        77 l~   78 (83)
T 1nkp_B           77 VR   78 (83)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>1yke_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.30A {Saccharomyces cerevisiae} SCOP: a.252.1.1

Probab=87.28  E-value=1.4  Score=33.17  Aligned_cols=41  Identities=22%  Similarity=0.283  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhcc
Q 032332           96 EVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDIST  136 (143)
Q Consensus        96 qaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~DiS~  136 (143)
                      .+.|.+||+.--...+|+..+=+--+.|+.+++++|.+|+-
T Consensus        91 ~~ri~~Le~E~~~~~~el~~~v~eae~ll~~v~~~l~~ia~  131 (151)
T 1yke_B           91 LRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHVDSLIEDFVD  131 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45799999999999999999999999999999999999973

>1ses_A Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A {Thermus thermophilus} SCOP: a.2.7.1 d.104.1.1 PDB: 1ser_A* 1set_A* 1sry_A

Probab=86.28  E-value=3.5  Score=34.73  Aligned_cols=70  Identities=17%  Similarity=0.232  Sum_probs=57.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      +||+.|..-+..+..||+-..++++.       +-.        .+..+.+.|-+++..|+++|......++.+-++|.+
T Consensus        32 ~~~~~~r~~~~~~~~l~~~~n~~sk~-------i~~--------~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (421)
T 1ses_A           32 ALDREVQELKKRLQEVQTERNQVAKR-------VPK--------APPEEKEALIARGKALGEEAKRLEEALREKEARLEA   96 (421)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH-------SSS--------SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHh--------hccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57888888888999999999988876       111        223578889999999999999999999999999988


Q ss_pred             HHhhh
Q 032332          130 LITDI  134 (143)
Q Consensus       130 lI~Di  134 (143)
                      ++.-|
T Consensus        97 ~~~~i  101 (421)
T 1ses_A           97 LLLQV  101 (421)
T ss_dssp             HHTTC
T ss_pred             HHHhC
Confidence            77544

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1

Probab=85.90  E-value=0.76  Score=31.54  Aligned_cols=66  Identities=26%  Similarity=0.331  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHH---HHhhhHHHHHHHHHHH
Q 032332           55 RHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKE---LANKNKYLKRLIDQLR  128 (143)
Q Consensus        55 R~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkE---i~~KN~~lK~LIdqlr  128 (143)
                      |...+.....||..|-.++.+.|+.-..+....        -+-|..|+++...|..+   +..+|..|+.=|.+|+
T Consensus        18 R~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A--------~~YI~~L~~~~~~l~~~~~~L~~~n~~L~~rl~~L~   86 (88)
T 1nkp_A           18 RNELKRSFFALRDQIPELENNEKAPKVVILKKA--------TAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQLG   86 (88)
T ss_dssp             HHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            344578889999988777766555444432221        23578888887777665   4455555555555543

>2hzl_A Trap-T family sorbitol/mannitol transporter, periplasmic binding protein, SMOM; trap transporter, periplasmic subunit, ligand binding; 1.40A {Rhodobacter sphaeroides 2} PDB: 2hzk_A

Probab=85.65  E-value=1  Score=35.51  Aligned_cols=46  Identities=17%  Similarity=0.256  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhcccc
Q 032332           93 RSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDISTWQ  138 (143)
Q Consensus        93 ~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~DiS~Wq  138 (143)
                      ..+.+|++.+.+.+..+++++..++..-+.+++++++.+.+..-|.
T Consensus       300 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~w~  345 (365)
T 2hzl_A          300 PFSPEILQACFEAANEVYAEMEASNPAFKKIWDSIKAFRSEHYTWA  345 (365)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             eCCHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhHHH
Confidence            4567889999999999999999888888999999999999998886

>2zzv_A ABC transporter, solute-binding protein; periplasmic substrate binding protein, calcium, lactate, trap transporter, transport protein; 1.40A {Thermus thermophilus} PDB: 2zzw_A 2zzx_A

Probab=84.86  E-value=1.3  Score=34.84  Aligned_cols=46  Identities=15%  Similarity=0.185  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhcccc
Q 032332           93 RSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDISTWQ  138 (143)
Q Consensus        93 ~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~DiS~Wq  138 (143)
                      ..+++|.+++.+.+..+++++..++..-+.+++++++++.+.--|.
T Consensus       307 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  352 (361)
T 2zzv_A          307 RLSNEDVRKFRRLAIPIWFKWAKMDKYSREAFASQLEYMKGIGYVT  352 (361)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTCSC
T ss_pred             ECCHHHHHHHHHHHHHHHHHHHhcCHhHHHHHHHHHHHHHHcCccc
Confidence            5667899999999999999998888889999999999999998886

>2p32_A Heat shock 70 kDa protein A; three-helix bundle, chaperone; 3.20A {Caenorhabditis elegans}

Probab=84.44  E-value=8  Score=26.69  Aligned_cols=71  Identities=11%  Similarity=0.149  Sum_probs=50.5

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhh----hHHHHHHH
Q 032332           49 SALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANK----NKYLKRLI  124 (143)
Q Consensus        49 gaLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~K----N~~lK~LI  124 (143)
                      -.+-|||-.-..-+-.+|..|.-   .       -...      +.+++|.+++++....||+-|...    -..++..+
T Consensus        14 re~iEarN~aEsliy~~e~~L~e---~-------~~~d------kl~~eek~~I~~~i~el~~~L~~~~~ad~e~ik~k~   77 (120)
T 2p32_A           14 LVPRGSHMGLESYAFNLKQTIED---E-------KLKD------KISPEDKKKIEDKCDEILKWLDSNQTAEKEEFEHQQ   77 (120)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHTC---T-------TTGG------GSCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhc---h-------hhhc------cCCHHHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHH
Confidence            34678888887777778776631   0       0122      678899999999999999888643    24577778


Q ss_pred             HHHHHHHhhhc
Q 032332          125 DQLRDLITDIS  135 (143)
Q Consensus       125 dqlrdlI~DiS  135 (143)
                      +.|..++..|.
T Consensus        78 ~eL~~~~~~i~   88 (120)
T 2p32_A           78 KDLEGLANPII   88 (120)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            88877776664

>1o5h_A Formiminotetrahydrofolate cyclodeaminase; TM1560, structural genomics, JCSG, PSI, protein structure initiative, joint CE structural genomics; 2.80A {Thermotoga maritima} SCOP: a.191.1.1

Probab=83.89  E-value=0.59  Score=37.10  Aligned_cols=20  Identities=25%  Similarity=0.257  Sum_probs=16.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q 032332           95 DEVEIDKLEERASLLRKELA  114 (143)
Q Consensus        95 DqaEIekLEe~As~LRkEi~  114 (143)
                      -+++++++-+++..||++|-
T Consensus        67 ~e~~~~~i~~~~~~l~~~ll   86 (214)
T 1o5h_A           67 VEPEMERIVEAMEEARLKLF   86 (214)
T ss_dssp             GHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            46789999999998888864

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1

Probab=82.92  E-value=3.4  Score=26.80  Aligned_cols=34  Identities=29%  Similarity=0.470  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhh
Q 032332           97 VEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDI  134 (143)
Q Consensus        97 aEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~Di  134 (143)
                      .+++.|+++-..|+.+|.    .|+.=+.+|++||.++
T Consensus        30 ~~~~~L~~~N~~L~~~i~----~L~~E~~~Lk~ll~e~   63 (63)
T 1ci6_A           30 GECKELEKKNEALKERAD----SLAKEIQYLKDLIEEV   63 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhhC
Confidence            455555555555555553    3344455666666653

>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 2.60A {Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A

Probab=81.35  E-value=1.1  Score=38.25  Aligned_cols=72  Identities=13%  Similarity=0.136  Sum_probs=55.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      +||+.|..-+..+..||+-..+|+..-+....    .      .   .+++.|-+++..|+++|......++.+-++|.+
T Consensus        35 ~l~~~~r~~~~~~~~l~~~~n~~sk~i~~~~~----~------~---~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (455)
T 2dq0_A           35 KLDTEWRTKLKEINRLRHERNKIAVEIGKRRK----K------G---EPVDELLAKSREIVKRIGELENEVEELKKKIDY  101 (455)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT----S------C---CCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc----c------c---ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57888888889999999999988876221100    1      1   235678889999999999999999999999988


Q ss_pred             HHhhh
Q 032332          130 LITDI  134 (143)
Q Consensus       130 lI~Di  134 (143)
                      ++.-|
T Consensus       102 ~~~~i  106 (455)
T 2dq0_A          102 YLWRL  106 (455)
T ss_dssp             HHTTS
T ss_pred             HHHhC
Confidence            87654

>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}

Probab=81.12  E-value=4.1  Score=35.56  Aligned_cols=80  Identities=14%  Similarity=0.113  Sum_probs=57.8

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      +||+.|...+..+..||+-..+|+..-+.........     +....++++.|-+++..|+++|......++.+-++|.+
T Consensus        74 ~ld~~~r~~~~~~~~l~~~rn~~sk~i~~~~~~~~~~-----~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~~~~~l~~  148 (501)
T 1wle_A           74 STWQELRQLREQIRSLEEEKEAVTEAVRALVVNQDNS-----QVQQDPQYQSLRARGREIRKQLTLLYPKEAQLEEQFYL  148 (501)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT-----TGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccc-----cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5788888888889999998888876632211110001     00111578899999999999999999999999999988


Q ss_pred             HHhhh
Q 032332          130 LITDI  134 (143)
Q Consensus       130 lI~Di  134 (143)
                      ++.-|
T Consensus       149 ~l~~i  153 (501)
T 1wle_A          149 RALRL  153 (501)
T ss_dssp             HHTTS
T ss_pred             HHHhC
Confidence            87654

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=80.72  E-value=3.7  Score=28.49  Aligned_cols=39  Identities=21%  Similarity=0.239  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHHHHHH--------HhhhHHHHHHHHHHHHHHhhh
Q 032332           96 EVEIDKLEERASLLRKEL--------ANKNKYLKRLIDQLRDLITDI  134 (143)
Q Consensus        96 qaEIekLEe~As~LRkEi--------~~KN~~lK~LIdqlrdlI~Di  134 (143)
                      +.||++|+.....++--|        ..++..+|..+.|+||+.-||
T Consensus        25 ~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~   71 (115)
T 3qfl_A           25 KKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVI   71 (115)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHH
Confidence            457777777766655433        225788999999999997765

>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis, CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA synthetase family; 2.00A {Candida albicans} PDB: 3qo7_A* 3qo8_A* 3qo5_A

Probab=80.20  E-value=0.98  Score=39.61  Aligned_cols=72  Identities=11%  Similarity=0.067  Sum_probs=54.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      +||+.|..-+..+..||+-..+++..-....   . .      .   .+++.|-+++..|+++|......++.+-++|.+
T Consensus        37 ~ld~~~r~~~~~~~~l~~~rn~~sk~i~~~k---~-~------~---~~~~~l~~~~~~l~~~i~~le~~~~~~~~~~~~  103 (485)
T 3qne_A           37 AEYKEWVKLRFDLDEHNKKLNSVQKEIGKRF---K-A------K---EDAKDLIAEKEKLSNEKKEIIEKEAEADKNLRS  103 (485)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---H-T------T---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---c-C------c---ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4788888888999999999988876521100   0 0      1   134678888999999999999999999999988


Q ss_pred             HHhhh
Q 032332          130 LITDI  134 (143)
Q Consensus       130 lI~Di  134 (143)
                      ++.-|
T Consensus       104 ~l~~i  108 (485)
T 3qne_A          104 KINQV  108 (485)
T ss_dssp             HHTTS
T ss_pred             HHHhC
Confidence            87654

>1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1

Probab=80.17  E-value=4  Score=27.57  Aligned_cols=43  Identities=14%  Similarity=0.315  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhccccCCCCC
Q 032332           97 VEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDISTWQSPCSV  143 (143)
Q Consensus        97 aEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~DiS~Wqspcs~  143 (143)
                      .+++.++++...||.++......++.|-..|..+=.|    ..||+|
T Consensus        10 ~~~~~~~~~l~~L~~~~~~l~~~i~~l~~~l~~l~~~----g~~CPv   52 (112)
T 1l8d_A           10 TKKTTIEEERNEITQRIGELKNKIGDLKTAIEELKKA----KGKCPV   52 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC----SEECTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC----CCCCCC
Confidence            3566677777777777666665555555555555333    557875

---

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	143
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	0.003

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.0 bits (75), Expect = 0.003
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 55  RHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELA 114
           R+  K S  ALR  +  + N+ KA    ++      +  S + E  KL     LLRK   
Sbjct: 18  RNELKRSFFALRDQIPELENNEKAPKVVILKKATAYI-LSVQAEEQKLISEEDLLRKR-- 74

Query: 115 NKNKYLKRLIDQLR 128
              + LK  ++QL 
Sbjct: 75  --REQLKHKLEQLG 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	143
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	91.92
d2azea1	148	Transcription factor DP-1 {Human (Homo sapiens) [T	91.17
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	90.92
d1ykhb1	129	RNA polymerase II holoenzyme component SRB7 (MED21	85.34
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	80.64

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=91.92  E-value=0.46  Score=31.05  Aligned_cols=70  Identities=17%  Similarity=0.245  Sum_probs=57.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           50 ALDEARHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        50 aLDeAR~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      .||+-|......+..||+--..++..       +.        +....+.+.|-+++..|+++|......++.+-+++.+
T Consensus        32 ~ld~~rr~l~~~~e~l~~~rN~~sk~-------i~--------k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~   96 (110)
T d1seta1          32 ALDREVQELKKRLQEVQTERNQVAKR-------VP--------KAPPEEKEALIARGKALGEEAKRLEEALREKEARLEA   96 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH-------GG--------GCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-------HH--------HhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57888888888889999888777644       11        3345678889999999999999999999999999999


Q ss_pred             HHhhh
Q 032332          130 LITDI  134 (143)
Q Consensus       130 lI~Di  134 (143)
                      ++..|
T Consensus        97 ~ll~i  101 (110)
T d1seta1          97 LLLQV  101 (110)
T ss_dssp             HHTTC
T ss_pred             HHHcC
Confidence            87655

>d2azea1 e.63.1.1 (A:199-346) Transcription factor DP-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Multi-domain proteins (alpha and beta)
fold: E2F-DP heterodimerization region
superfamily: E2F-DP heterodimerization region
family: DP dimerization segment
domain: Transcription factor DP-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.17  E-value=0.18  Score=37.22  Aligned_cols=34  Identities=24%  Similarity=0.189  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 032332           97 VEIDKLEERASLLRKELANKNKYLKRLIDQLRDL  130 (143)
Q Consensus        97 aEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdl  130 (143)
                      .|.++||+.-..+|+.|..|+.+|+.||.|...+
T Consensus         2 Qe~~~Le~E~~~~~erI~~K~~~LqeLi~Q~iaf   35 (148)
T d2azea1           2 QECQNLEVERQRRLERIKQKQSQLQELILQQIAF   35 (148)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999999999996543

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.92  E-value=0.11  Score=33.33  Aligned_cols=67  Identities=22%  Similarity=0.222  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032332           55 RHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKNKYLKRLIDQLRD  129 (143)
Q Consensus        55 R~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN~~lK~LIdqlrd  129 (143)
                      |.+-+.+...||..|--.+...|..-.++...        --+.|..|+++...|.+++..-......|..+|-.
T Consensus        18 R~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~--------A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~   84 (88)
T d1nkpa_          18 RNELKRSFFALRDQIPELENNEKAPKVVILKK--------ATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQ   84 (88)
T ss_dssp             HHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCCCCccCHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45567788889887754443333222222111        12457788888888877766655555555555433

>d1ykhb1 a.252.1.1 (B:2-130) RNA polymerase II holoenzyme component SRB7 (MED21) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Mediator hinge subcomplex-like
superfamily: Mediator hinge subcomplex-like
family: CSE2-like
domain: RNA polymerase II holoenzyme component SRB7 (MED21)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.34  E-value=0.82  Score=31.88  Aligned_cols=38  Identities=21%  Similarity=0.325  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhh
Q 032332           97 VEIDKLEERASLLRKELANKNKYLKRLIDQLRDLITDI  134 (143)
Q Consensus        97 aEIekLEe~As~LRkEi~~KN~~lK~LIdqlrdlI~Di  134 (143)
                      +-|.+||+.--...+|+..+=+.-+.|+.++..+|.||
T Consensus        91 ~~i~~Le~E~~~~~~el~~~v~e~e~ll~~i~~~i~~i  128 (129)
T d1ykhb1          91 RKIDMLQKKLVEVEDEKIEAIKKKEKLMRHVDSMIEDF  128 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45899999999999999999999999999999999998

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.64  E-value=0.56  Score=29.19  Aligned_cols=55  Identities=16%  Similarity=0.354  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHhcCCccccccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhh
Q 032332           55 RHRYKTSVAALRAVLTAIPNSHKAKSFEMVSSPVDSVSRSDEVEIDKLEERASLLRKELANKN  117 (143)
Q Consensus        55 R~RYK~AvAALRa~iaAI~~~~ka~~~e~~~s~v~~v~~~DqaEIekLEe~As~LRkEi~~KN  117 (143)
                      |.+-+.....||..|-..++..|+.-.++....        -.-|..|+++...|.+++..-.
T Consensus        13 R~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A--------~~yI~~L~~~~~~l~~~~~~L~   67 (79)
T d1nlwa_          13 RAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKA--------KLHIKKLEDSDRKAVHQIDQLQ   67 (79)
T ss_dssp             HHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHH
Confidence            455677888888887444444333222222111        1245666666555555544333