Psyllid ID: psy1953

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------38

LNSCQFQNGTSRQLQANCYGQSIGGCSKIPQCNENNFSEYEKNLKAYHNSPQYLAYMAAKAKGKQAQQAAEEREAQAQGFSGKNADRRIDIQPAEDEDEQEDGYSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKPGMGPEGYLNRLSASPVLTAPVSAQGPPPGPSVPPMHGGQTGPVATVHHPPPSQGGHGAMLPPHPRPGSPSGYPGAGGPYPPPQQYPGASQPLAPRPPHGQYPYPYPQYPTHPYYGNAYPYPQHMNAGRPPHYPPHPGSQHPHQNCAHPETGQLVFQEGVLAKAMRLGYWIILDELNLAPLPFLLYLLC

ccccccccccccccHHHHHccccccccccccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHcc

cccccccccccHHHHHcccccEEccccccccccHHcHHHHHHHHHHHcccHHHHHHHHHHHHcHHHHHHHcHHHcccccccccccccEEEEEEccccccccccccHHHHHHHHHHHHcHHHHHHHccccccccccEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHEHHHccccccHHHHHHcc

lnscqfqngtsrqlqancygqsiggcskipqcnennfSEYEKNLKAYHNSPQYLAYMAAKAKGKQAQQAAEEREAQaqgfsgknadrridiqpaededeqedgysvkHVAYARYLRNHRLINeifsdsvvpdvrsVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEElkkpgmgpegylnrlsaspvltapvsaqgpppgpsvppmhggqtgpvatvhhpppsqgghgamlpphprpgspsgypgaggpypppqqypgasqplaprpphgqypypypqypthpyygnaypypqhmnagrpphypphpgsqhphqncahpetgqlVFQEGVLAKAMRLGYWIILdelnlaplpfLLYLLC

lnscqfqnGTSRQLQANCYGQSIGGCSKIPQCNENNFSEYEKNLKAYHNSPQYLAYMAAKAKGKQAQQAAEEREAqaqgfsgknadrrIDIQpaededeqedgysVKHVAYARYLRNHRLINeifsdsvvpdvrSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFqeelkkpgmgpEGYLNRLSASPVLTAPVSAQGPPPGPSVPPMHGGQTGPVATVHHPPPSQGGHGAMLPPHPRPGSPSGYPGAGGPYPPPQQYPGASQPLAPRPPHGQYPYPYPQYPTHPYYGNAYPYPQHMNAGRPPHYPPHPGSQHPHQNCAHPETGQLVFQEGVLAKAMRLGYWIILDELNLAPLPFLLYLLC

LNSCQFQNGTSRQLQANCYGQSIGGCSKIPQCNENNFSEYEKNLKAYHNSPQYLAYMaakakgkqaqqaaeereaqaqGFSGKNADRRIDIQPAEDEDEQEDGYSVKHVAYARYLRNHRLINEIFsdsvvpdvrsvvTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKPGMGPEGYLNRLSASPVLTapvsaqgpppgpsvppMHGGQTGPVATVHHPPPSQGGHGAMLpphprpgspsgypgaggpypppqqypgasqpLAPRpphgqypypypqypthpyygNAYPYPQHMNAGRPPHYPPHPGSQHPHQNCAHPETGQLVFQEGVLAKAMRLGYWIIldelnlaplpfllyllC

***************ANCYGQSIGGCSKIPQCNENNFSEYEKNLKAYHNSPQYLAYM**********************************************YSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQVLKR**************************************************************************************************************************************************YPYPQYPTHPYYGNAYPY******************************GQLVFQEGVLAKAMRLGYWIILDELNLAPLPFLLYLL*

*********TSRQLQANCYGQSIGGCSKI***********EKNLKAYHNSPQYLAYM*********************************************************LRNHRLINEIFSDSVVPDVRSVVTTNRMQVL*******************************************************************************************************************************************************************************************************VFQEGVLAKAMRLGYWIILDELNLAPLPFLLYLLC

LNSCQFQNGTSRQLQANCYGQSIGGCSKIPQCNENNFSEYEKNLKAYHNSPQYLAYMA***********************GKNADRRIDIQPA*********YSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRK*************KPGMGPEGYLNRLSASPVLTAP**********SVPPMHGGQTGPVATVHHPPPSQGGHGAMLPPHPRPGSPSGYPGAGGPYPPPQQYPGASQPLAPRPPHGQYPYPYPQYPTHPYYGNAYPYPQHMNAGRPPHYP***********CAHPETGQLVFQEGVLAKAMRLGYWIILDELNLAPLPFLLYLLC

*NSCQFQNGTSRQLQANCYGQSIGGCSKIPQCNENNFSEYEKNLKAYHNSPQYLAYMAAKAKGKQAQQA****************DRRIDIQPAEDEDEQEDGYSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKPGMGPEGYLNRLSAS**********************************************PPHP***S*SG**G**GPYPPPQQYPGASQPLAPRPPHGQYPYPYPQYPTHPYYGNAYPYPQHMNAGRPPHYP**PGSQ*P******PETGQLVFQEGVLAKAMRLGYWIILDELNLAPLPFLLYLLC

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LNSCQFQNGTSRQLQANCYGQSIGGCSKIPQCNENNFSEYEKNLKAYHNSPQYLAYMAAKAKGKQAQQAAEEREAQAQGFSGKNADRRIDIQPAEDEDEQEDGYSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxFQEELKKPGMGPEGYLNRLSASPVLTAPVSAQGPPPGPSVPPMHGGQTGPVATVHHPPPSQGGHGAMLPPHPRPGSPSGYPGAGGPYPPPQQYPGASQPLAPRPPHGQYPYPYPQYPTHPYYGNAYPYPQHMNAGRPPHYPPHPGSQHPHQNCAHPETGQLVFQEGVLAKAMRLGYWIILDELNLAPLPFLLYLLC

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		379	2.2.26 [Sep-21-2011]
O54941		411	SWI/SNF-related matrix-as	yes	N/A	0.427	0.394	0.556	8e-44
Q969G3		411	SWI/SNF-related matrix-as	yes	N/A	0.427	0.394	0.556	9e-44
Q56A18		376	SWI/SNF-related matrix-as	yes	N/A	0.427	0.430	0.556	1e-43
Q9NU22		5596	Midasin OS=Homo sapiens G	no	N/A	0.087	0.005	0.735	2e-07

>sp\|O54941\|SMCE1_MOUSE SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 OS=Mus musculus GN=Smarce1 PE=1 SV=1	Back alignment and function desciption

 Score =  177 bits (450), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 93/167 (55%), Positives = 126/167 (75%), Gaps = 5/167 (2%)

Query: 39  EYEKNLKAYHNSPQYLAYMAAKAKGKQAQQAAEEREAQAQGFSGKNADRRIDIQPAEDED 98
           EY +++KAYHNSP YLAY+ AK++     +AA E E++ +    +  +  + IQPAED D
Sbjct: 125 EYNESMKAYHNSPAYLAYINAKSRA----EAALEEESRQRQSRMEKGEPYMSIQPAEDPD 180

Query: 99  EQEDGYSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQVLKRQVQSLTMHQKK 158
           + +DG+S+KH A AR+ RNHRLI+EI S+SVVPDVRSVVTT RMQVLKRQVQSL +HQ+K
Sbjct: 181 DYDDGFSMKHTATARFQRNHRLISEILSESVVPDVRSVVTTARMQVLKRQVQSLMVHQRK 240

Query: 159 LEAELQQIEEKFEAKKRKFVESSEQFQEELKKP-GMGPEGYLNRLSA 204
           LEAEL QIEE+ + KKRKF+ES++ F  ELK+  G+  E  + +++A
Sbjct: 241 LEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVEVDMEKIAA 287

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Required for the coactivation of estrogen responsive promoters by Swi/Snf complexes and the SRC/p160 family of histone acetyltransferases (HATs). Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene (By similarity). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.
Mus musculus (taxid: 10090)

>sp\|Q969G3\|SMCE1_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 OS=Homo sapiens GN=SMARCE1 PE=1 SV=2	Back alignment and function description

>sp\|Q56A18\|SMCE1_RAT SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 OS=Rattus norvegicus GN=Smarce1 PE=1 SV=1	Back alignment and function description

>sp\|Q9NU22\|MDN1_HUMAN Midasin OS=Homo sapiens GN=MDN1 PE=1 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		379
357620405		619	hypothetical protein KGM_12870 [Danaus p	0.411	0.252	0.745	5e-59
345481107		897	PREDICTED: hypothetical protein LOC10012	0.401	0.169	0.743	6e-59
242005029		592	hypothetical protein Phum_PHUM055050 [Pe	0.445	0.285	0.715	2e-56
307187667		741	SWI/SNF-related matrix-associated actin-	0.401	0.205	0.756	3e-56
328780490		718	PREDICTED: hypothetical protein LOC41207	0.401	0.211	0.756	6e-56
380014712		716	PREDICTED: uncharacterized protein LOC10	0.401	0.212	0.756	6e-56
332026217		756	SWI/SNF-related matrix-associated actin-	0.414	0.207	0.739	9e-56
307195541		777	SWI/SNF-related matrix-associated actin-	0.401	0.195	0.756	1e-55
383862615		767	PREDICTED: uncharacterized protein LOC10	0.401	0.198	0.75	1e-55
340710108		747	PREDICTED: hypothetical protein LOC10065	0.401	0.203	0.75	3e-55

>gi\|357620405\|gb\|EHJ72609.1\| hypothetical protein KGM_12870 [Danaus plexippus]	Back alignment and taxonomy information

 Score =  234 bits (597), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 120/161 (74%), Positives = 134/161 (83%), Gaps = 5/161 (3%)

Query: 33  NENNFSEYEKNLKAYHNSPQYLAYMAAKAKGKQAQQAAEEREAQAQGFSGKNA---DRRI 89
           N+ + SEYEK+LK YHNSP YLAY+AAK K        EE  +  +G S K +   DRRI
Sbjct: 190 NKGDLSEYEKSLKTYHNSPAYLAYIAAKNKAVVGN--LEEESSSKKGGSQKESQQQDRRI 247

Query: 90  DIQPAEDEDEQEDGYSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQVLKRQV 149
           DIQPAEDED+Q++G SVKHVAYARYLRNHRLINEIFSD+VVPDVRSVVTT RMQ+LK+QV
Sbjct: 248 DIQPAEDEDDQDEGLSVKHVAYARYLRNHRLINEIFSDTVVPDVRSVVTTARMQILKKQV 307

Query: 150 QSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKK 190
           QSLTMHQKKLE ELQQIEEKFEAKKRKF+ESSE FQEELKK
Sbjct: 308 QSLTMHQKKLEDELQQIEEKFEAKKRKFIESSESFQEELKK 348

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|345481107\|ref\|XP_001606235.2\| PREDICTED: hypothetical protein LOC100122623 [Nasonia vitripennis]	Back alignment and taxonomy information

>gi\|242005029\|ref\|XP_002423377.1\| hypothetical protein Phum_PHUM055050 [Pediculus humanus corporis] gi\|212506421\|gb\|EEB10639.1\| hypothetical protein Phum_PHUM055050 [Pediculus humanus corporis]	Back alignment and taxonomy information

>gi\|307187667\|gb\|EFN72639.1\| SWI/SNF-related matrix-associated actin-dependent regulator chromatin subfamily E member 1 [Camponotus floridanus]	Back alignment and taxonomy information

>gi\|328780490\|ref\|XP_395543.4\| PREDICTED: hypothetical protein LOC412077 [Apis mellifera]	Back alignment and taxonomy information

>gi\|380014712\|ref\|XP_003691364.1\| PREDICTED: uncharacterized protein LOC100865252 [Apis florea]	Back alignment and taxonomy information

>gi\|332026217\|gb\|EGI66359.1\| SWI/SNF-related matrix-associated actin-dependent regulator chromatin subfamily E member 1 [Acromyrmex echinatior]	Back alignment and taxonomy information

>gi\|307195541\|gb\|EFN77427.1\| SWI/SNF-related matrix-associated actin-dependent regulator chromatin subfamily E member 1 [Harpegnathos saltator]	Back alignment and taxonomy information

>gi\|383862615\|ref\|XP_003706779.1\| PREDICTED: uncharacterized protein LOC100879979 [Megachile rotundata]	Back alignment and taxonomy information

>gi\|340710108\|ref\|XP_003393638.1\| PREDICTED: hypothetical protein LOC100651274 [Bombus terrestris]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		379
FB\|FBgn0030093		749	dalao "dalao" [Drosophila mela	0.416	0.210	0.582	1.1e-44
UNIPROTKB\|F1NCC9		412	SMARCE1 "Uncharacterized prote	0.390	0.359	0.486	2.3e-32
UNIPROTKB\|A5PKF6		415	SMARCE1 "SMARCE1 protein" [Bos	0.427	0.390	0.455	2.9e-32
UNIPROTKB\|E2QX86		393	SMARCE1 "Uncharacterized prote	0.427	0.412	0.455	2.9e-32
UNIPROTKB\|B4DFR4		341	SMARCE1 "Smarce1 variant 5" [H	0.427	0.475	0.455	2.9e-32
UNIPROTKB\|B4DGM3		393	SMARCE1 "cDNA FLJ55202, highly	0.427	0.412	0.455	2.9e-32
UNIPROTKB\|Q969G3		411	SMARCE1 "SWI/SNF-related matri	0.427	0.394	0.455	2.9e-32
MGI\|MGI:1927347		411	Smarce1 "SWI/SNF related, matr	0.427	0.394	0.455	2.9e-32
RGD\|1304726		376	Smarce1 "SWI/SNF related, matr	0.427	0.430	0.455	2.9e-32
WB\|WBGene00022182		338	swsn-3 [Caenorhabditis elegans	0.261	0.292	0.4	1.1e-12

FB\|FBgn0030093 dalao "dalao" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 447 (162.4 bits), Expect = 1.1e-44, Sum P(2) = 1.1e-44
 Identities = 95/163 (58%), Positives = 108/163 (66%)

Query:    39 EYEKNLKAYHNSPQYLAYMXXXXXXXXXXXXXXXXXXXXXGFSGKNADRRIDIQPAEDED 98
             EYEK+LKAYH +P Y AYM                     G S    +RRIDIQPAEDED
Sbjct:   148 EYEKSLKAYHQTPAYQAYMSAKSKVKTDVDMHETPSRG--GGSKSQHERRIDIQPAEDED 205

Query:    99 EQEDGYSVKHVAYARYLRNHRLINEIFXXXXXXXXXXXXTTNRMQVLKRQVQSLTMHQKK 158
             +Q++GY+ KH+AYARYL NHRLINEIF            TT RMQVLKRQV SLTMHQ K
Sbjct:   206 DQDEGYTTKHLAYARYLHNHRLINEIFSEAVVPDVRSVVTTTRMQVLKRQVSSLTMHQTK 265

Query:   159 LEAELQQIEEKFEAKKRKFVESSEQFQEELK---KPGMGPEGY 198
             LEAELQQ+EEKFEAKK++ VESSE FQEELK   KP +  E +
Sbjct:   266 LEAELQQMEEKFEAKKQRMVESSEAFQEELKRHCKPAVDEETF 308

GO:0003713 "transcription coactivator activity" evidence=IC

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0035060 "brahma complex" evidence=NAS;IDA;IPI

GO:0005515 "protein binding" evidence=IPI

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0006338 "chromatin remodeling" evidence=IGI;IPI

UNIPROTKB\|F1NCC9 SMARCE1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|A5PKF6 SMARCE1 "SMARCE1 protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QX86 SMARCE1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|B4DFR4 SMARCE1 "Smarce1 variant 5" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|B4DGM3 SMARCE1 "cDNA FLJ55202, highly similar to SWI/SNF-related matrix-associatedactin-dependent regulator of chromatin subfamily E member 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q969G3 SMARCE1 "SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:1927347 Smarce1 "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1304726 Smarce1 "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

WB\|WBGene00022182 swsn-3 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

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)
Q969G3	SMCE1_HUMAN	No assigned EC number	0.5568	0.4274	0.3941	yes	N/A
Q56A18	SMCE1_RAT	No assigned EC number	0.5568	0.4274	0.4308	yes	N/A
O54941	SMCE1_MOUSE	No assigned EC number	0.5568	0.4274	0.3941	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		379
COG5271		4600	COG5271, MDN1, AAA ATPase containing von Willebran	3e-09
pfam09770		804	pfam09770, PAT1, Topoisomerase II-associated prote	3e-07
PHA03377		1000	PHA03377, PHA03377, EBNA-3C; Provisional	5e-07
pfam09770		804	pfam09770, PAT1, Topoisomerase II-associated prote	3e-06
PHA03378		991	PHA03378, PHA03378, EBNA-3B; Provisional	2e-05
pfam09770		804	pfam09770, PAT1, Topoisomerase II-associated prote	4e-05
PRK14086		617	PRK14086, dnaA, chromosomal replication initiation	9e-05
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-04
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-04
pfam04652		315	pfam04652, DUF605, Vta1 like	2e-04
PRK10263		1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	3e-04
COG5271		4600	COG5271, MDN1, AAA ATPase containing von Willebran	4e-04
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-04
COG5271		4600	COG5271, MDN1, AAA ATPase containing von Willebran	6e-04
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.001
pfam04368		183	pfam04368, DUF507, Protein of unknown function (DU	0.001
pfam04652		315	pfam04652, DUF605, Vta1 like	0.002
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
pfam07415		489	pfam07415, Herpes_LMP2, Gammaherpesvirus latent me	0.002
PHA03378		991	PHA03378, PHA03378, EBNA-3B; Provisional	0.003
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.003
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	0.003
pfam04959		211	pfam04959, ARS2, Arsenite-resistance protein 2	0.003
PRK03918		880	PRK03918, PRK03918, chromosome segregation protein	0.003
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.004
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	0.004
pfam03763		112	pfam03763, Remorin_C, Remorin, C-terminal region	0.004

>gnl\|CDD\|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

 Score = 58.5 bits (141), Expect = 3e-09
 Identities = 21/31 (67%), Positives = 26/31 (83%)

Query: 340 ETGQLVFQEGVLAKAMRLGYWIILDELNLAP 370
           + G L F+EGVL +A+R GYWI+LDELNLAP
Sbjct: 938 DDGSLSFKEGVLVEALRRGYWIVLDELNLAP 968

Length = 4600

>gnl\|CDD\|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1	Back alignment and domain information

>gnl\|CDD\|177614 PHA03377, PHA03377, EBNA-3C; Provisional	Back alignment and domain information

>gnl\|CDD\|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1	Back alignment and domain information

>gnl\|CDD\|223065 PHA03378, PHA03378, EBNA-3B; Provisional	Back alignment and domain information

>gnl\|CDD\|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1	Back alignment and domain information

>gnl\|CDD\|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|218191 pfam04652, DUF605, Vta1 like	Back alignment and domain information

>gnl\|CDD\|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional	Back alignment and domain information

>gnl\|CDD\|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|146815 pfam04368, DUF507, Protein of unknown function (DUF507)	Back alignment and domain information

>gnl\|CDD\|218191 pfam04652, DUF605, Vta1 like	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein (LMP2) protein	Back alignment and domain information

>gnl\|CDD\|223065 PHA03378, PHA03378, EBNA-3B; Provisional	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|218350 pfam04959, ARS2, Arsenite-resistance protein 2	Back alignment and domain information

>gnl\|CDD\|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|190741 pfam03763, Remorin_C, Remorin, C-terminal region	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		379
KOG4715\|consensus		410		100.0
KOG1924\|consensus		1102		99.74
COG5271		4600	MDN1 AAA ATPase containing von Willebrand factor t	99.43
KOG1924\|consensus		1102		99.28
KOG1808\|consensus		1856		98.91
COG5271		4600	MDN1 AAA ATPase containing von Willebrand factor t	98.69
PF07728		139	AAA_5: AAA domain (dynein-related subfamily); Inte	98.16
TIGR01650		327	PD_CobS cobaltochelatase, CobS subunit. This model	97.9
KOG3671\|consensus		569		97.44
TIGR02640		262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.25
KOG0381\|consensus		96		97.14
PTZ00199		94	high mobility group protein; Provisional	97.05
KOG1923\|consensus		830		96.96
PF00505		69	HMG_box: HMG (high mobility group) box; InterPro:	96.89
KOG3671\|consensus		569		96.66
cd01389		77	MATA_HMG-box MATA_HMG-box, class I member of the H	96.56
PHA02244		383	ATPase-like protein	96.49
cd01390		66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	96.27
KOG1923\|consensus		830		96.17
smart00398		70	HMG high mobility group.	96.11
KOG1830\|consensus		518		96.04
PF07726		131	AAA_3: ATPase family associated with various cellu	95.47
PHA03247		3151	large tegument protein UL36; Provisional	95.21
cd01388		72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	95.2
COG0714		329	MoxR-like ATPases [General function prediction onl	94.79
KOG1808\|consensus		1856		94.78
COG5648		211	NHP6B Chromatin-associated proteins containing the	94.58
cd00084		66	HMG-box High Mobility Group (HMG)-box is found in	94.25
KOG4672\|consensus		487		94.2
PHA03247		3151	large tegument protein UL36; Provisional	93.78
PF09011		73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	93.27
PRK13407		334	bchI magnesium chelatase subunit I; Provisional	93.25
PF08549		669	SWI-SNF_Ssr4: Fungal domain of unknown function (D	93.22
KOG4849\|consensus		498		93.08
TIGR02030		337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	91.07
KOG1830\|consensus		518		88.24
KOG0132\|consensus		894		87.36
CHL00081		350	chlI Mg-protoporyphyrin IX chelatase	87.18
PRK13729		475	conjugal transfer pilus assembly protein TraB; Pro	86.52
PF06346		160	Drf_FH1: Formin Homology Region 1; InterPro: IPR00	86.48
PF12774		231	AAA_6: Hydrolytic ATP binding site of dynein motor	85.99
PF06346		160	Drf_FH1: Formin Homology Region 1; InterPro: IPR00	84.67
KOG0527\|consensus		331		83.97
PRK13406		584	bchD magnesium chelatase subunit D; Provisional	83.49
TIGR02031		589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	82.95
cd09235		339	V_Alix Middle V-domain of mammalian Alix and relat	82.9
KOG2893\|consensus		341		82.61
KOG4672\|consensus		487		82.13
KOG4849\|consensus		498		81.08

>KOG4715\|consensus	Back alignment and domain information

Probab=100.00  E-value=1.6e-63  Score=481.71  Aligned_cols=195  Identities=50%  Similarity=0.757  Sum_probs=186.6

Q ss_pred             cccCCCCCchhhhhhhhhccc-cCCCcccccchh--------hHHHHHHHhhCCHHHHHHHHHHHHhHHhHHHHHHHHHH
Q psy1953           6 FQNGTSRQLQANCYGQSIGGC-SKIPQCNENNFS--------EYEKNLKAYHNSPQYLAYMAAKAKGKQAQQAAEEREAQ   76 (379)
Q Consensus         6 f~~~~n~dl~lweigKiig~m-~~l~d~ek~~~~--------eY~~~~k~yhnSpay~ayi~aK~ra~~~~~~~~~~~~~   76 (379)
                      -++..||||||||||||||+| +||+|+||++|+        ||||+||+|||||+|++||+||+||+++ +|+++|+++
T Consensus        82 ~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y~ayinaKsra~a~-le~~sr~~~  160 (410)
T KOG4715|consen   82 QVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAA-LEEESRQRQ  160 (410)
T ss_pred             hhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchHHHHhhhhhhhhhh-hcccccccc
Confidence            467899999999999999999 999999999998        8999999999999999999999999998 588888877


Q ss_pred             hhcCCCCCCCCcceecccCCCCccCCCccccccccccccchHHHHHHHhcCCCCCCccchhhhhHHHHHHHHHHHHHHHH
Q psy1953          77 AQGFSGKNADRRIDIQPAEDEDEQEDGYSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQVLKRQVQSLTMHQ  156 (379)
Q Consensus        77 ~~~~~~~~~~~~~~iqpaeD~dD~dd~~S~k~laaarfdRNhrLmsELfsd~vVpd~rS~vt~dRiq~LkkQVqsL~~eQ  156 (379)
                         ++++++++|||||||+|+||+|||||+||++.+||+||||||++||+.+||+|+||+|+..||++|++||++|..||
T Consensus       161 ---sr~~~ge~~~~IQPaeDeDD~ddg~stkhla~arf~rN~rLIsei~SesvVpDvrsVVtt~RMqvlkrQv~SL~~HQ  237 (410)
T KOG4715|consen  161 ---SRMEKGEPYMSIQPAEDEDDYDDGFSTKHLATARFQRNHRLISEILSESVVPDVRSVVTTARMQVLKRQVQSLMVHQ  237 (410)
T ss_pred             ---chhhcCCcceecccccCccccccccchhhhhhhhhhhhhHHHHHHhccccccchhhhhhHHHHHHHHHHHHHHHHHH
Confidence               47899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHhcC-----CCCCchhhhhhhcc
Q psy1953         157 KKLEAELQQIEEKFEAKKRKFVESSEQFQEELKK-----PGMGPEGYLNRLSA  204 (379)
Q Consensus       157 eKLeaELqqlEeefqeKKrK~~E~sEkf~~ELKK-----~~vdeE~~~~~l~~  204 (379)
                      .||++||.++|++|+++|++|++++|.|++||||     +.||+|+|+.+|+.
T Consensus       238 ~KLEaEL~q~Ee~hq~kKrk~~estdsf~~eLKr~c~~kvevd~eK~~~~i~q  290 (410)
T KOG4715|consen  238 RKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVEVDMEKMAAEIAQ  290 (410)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHhcCCcccccHHHHHHHHHH
Confidence            9999999999999999999999999999999999     88999998876644

>KOG1924\|consensus	Back alignment and domain information

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>KOG1924\|consensus	Back alignment and domain information

>KOG1808\|consensus	Back alignment and domain information

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []	Back alignment and domain information

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit	Back alignment and domain information

>KOG3671\|consensus	Back alignment and domain information

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN	Back alignment and domain information

>KOG0381\|consensus	Back alignment and domain information

>PTZ00199 high mobility group protein; Provisional	Back alignment and domain information

>KOG1923\|consensus	Back alignment and domain information

>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin	Back alignment and domain information

>KOG3671\|consensus	Back alignment and domain information

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins	Back alignment and domain information

>PHA02244 ATPase-like protein	Back alignment and domain information

>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins	Back alignment and domain information

>KOG1923\|consensus	Back alignment and domain information

>smart00398 HMG high mobility group	Back alignment and domain information

>KOG1830\|consensus	Back alignment and domain information

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model	Back alignment and domain information

>PHA03247 large tegument protein UL36; Provisional	Back alignment and domain information

>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins	Back alignment and domain information

>COG0714 MoxR-like ATPases [General function prediction only]	Back alignment and domain information

>KOG1808\|consensus	Back alignment and domain information

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]	Back alignment and domain information

>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors	Back alignment and domain information

>KOG4672\|consensus	Back alignment and domain information

>PHA03247 large tegument protein UL36; Provisional	Back alignment and domain information

>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins	Back alignment and domain information

>PRK13407 bchI magnesium chelatase subunit I; Provisional	Back alignment and domain information

>PF08549 SWI-SNF_Ssr4: Fungal domain of unknown function (DUF1750); InterPro: IPR013859 This is a fungal protein of unknown function	Back alignment and domain information

>KOG4849\|consensus	Back alignment and domain information

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I	Back alignment and domain information

>KOG1830\|consensus	Back alignment and domain information

>KOG0132\|consensus	Back alignment and domain information

>CHL00081 chlI Mg-protoporyphyrin IX chelatase	Back alignment and domain information

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional	Back alignment and domain information

>PF06346 Drf_FH1: Formin Homology Region 1; InterPro: IPR009408 This domain is found in some of the Diaphanous related formins (Drfs) []	Back alignment and domain information

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A	Back alignment and domain information

>PF06346 Drf_FH1: Formin Homology Region 1; InterPro: IPR009408 This domain is found in some of the Diaphanous related formins (Drfs) []	Back alignment and domain information

>KOG0527\|consensus	Back alignment and domain information

>PRK13406 bchD magnesium chelatase subunit D; Provisional	Back alignment and domain information

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D	Back alignment and domain information

>cd09235 V_Alix Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules	Back alignment and domain information

>KOG2893\|consensus	Back alignment and domain information

>KOG4672\|consensus	Back alignment and domain information

>KOG4849\|consensus	Back alignment and domain information

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	Alignment Graph	Length	Definition	E-value
Query		379
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	7e-12
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-10
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	7e-10
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-09
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-06
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-05
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-04
3v1v_A		433	2-MIB synthase, 2-methylisoborneol synthase; class	7e-09
3pgw_B		231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-07
1twf_A		1733	B220, DNA-directed RNA polymerase II largest subun	6e-06
1twf_A		1733	B220, DNA-directed RNA polymerase II largest subun	1e-04
1twf_A		1733	B220, DNA-directed RNA polymerase II largest subun	3e-04
1twf_A		1733	B220, DNA-directed RNA polymerase II largest subun	7e-04
1deq_A		390	Fibrinogen (alpha chain); coiled-coil, blood clott	1e-05
1deq_A		390	Fibrinogen (alpha chain); coiled-coil, blood clott	7e-05
3dzy_A		467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	5e-05
3dzy_A		467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	7e-05
2z73_A		448	Rhodopsin; visual pigment, GQ-type, G-protein coup	5e-05
3h0g_A		1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-04
3tx7_B		352	Nuclear receptor subfamily 5 group A member 2; LRH	2e-04

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

 Score = 66.0 bits (160), Expect = 7e-12
 Identities = 21/137 (15%), Positives = 28/137 (20%), Gaps = 3/137 (2%)

Query: 213 SAQGPPPGPSVPPMHGGQTGPVATVHHPPPSQGGHGAMLPPHPRPGSPSGYPGAGGPYPP 272
            AQ      + P     Q  P         S G  G   P    P               
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMP-PQGAVPSMGQQQFLTPAQEQL 69

Query: 273 PQQYPGASQPLAPRPPHGQYPYPYPQY--PTHPYYGNAYPYPQHMNAGRPPHYPPHPGSQ 330
            QQ   A+  +     H         Y  P  P         Q      P +  P     
Sbjct: 70  HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129

Query: 331 HPHQNCAHPETGQLVFQ 347
              +         L+ +
Sbjct: 130 QNMRPMNQLYPIDLLTE 146

PyMOL of 1m2v

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433	Back alignment and structure

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231	Back alignment and structure

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733	Back alignment and structure

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733	Back alignment and structure

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733	Back alignment and structure

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733	Back alignment and structure

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467	Back alignment and structure

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467	Back alignment and structure

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448	Back alignment and structure

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752	Back alignment and structure

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		379
2crj_A		92	SWI/SNF-related matrix-associated actin- dependent	98.11
2cs1_A		92	PMS1 protein homolog 1; DNA mismatch repair protei	97.44
1aab_A		83	High mobility group protein; HMG-BOX, DNA-binding;	97.43
2lhj_A		97	High mobility group protein homolog NHP1; structur	97.37
1v63_A		101	Nucleolar transcription factor 1; DNA binding, str	97.35
1ckt_A		71	High mobility group 1 protein; high-mobility group	97.34
1k99_A		99	Upstream binding factor 1; alpha-helix, L-shape, D	97.33
1gt0_D		80	Transcription factor SOX-2; POU factors, SOX prote	97.3
2lef_A		86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	97.26
2co9_A		102	Thymus high mobility group box protein TOX; TOX pr	97.25
1hme_A		77	High mobility group protein fragment-B; DNA-bindin	97.24
1cg7_A		93	Protein (NON histone protein 6 A); HMG BOX, DNA be	97.22
1j46_A		85	SRY, sex-determining region Y protein; MALE sex de	97.15
2eqz_A		86	High mobility group protein B3; HMG-box domain, mo	97.1
1wxl_A		73	Single-strand recognition protein; FACT, SSRP1, HM	97.08
1wz6_A		82	HMG-box transcription factor BBX; bobby SOX homolo	96.99
3nm9_A		73	HMG-D, high mobility group protein D; DNA bending,	96.95
3f27_D		83	Transcription factor SOX-17; protein-DNA complex,	96.88
1hry_A		76	Human SRY; DNA, DNA-binding protein, DNA binding p	96.82
3u2b_C		79	Transcription factor SOX-4; HMG domain, transcript	96.8
4a3n_A		71	Transcription factor SOX-17; 2.40A {Homo sapiens}	96.73
4euw_A		106	Transcription factor SOX-9; protein-DNA complex, H	96.67
1i11_A		81	Transcription factor SOX-5; HMG BOX, DNA bending,	96.57
3fgh_A		67	Transcription factor A, mitochondrial; HMG domain,	96.4
1l8y_A		91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	96.16
1wgf_A		90	Upstream binding factor 1; transcription factor, D	96.06
1v64_A		108	Nucleolar transcription factor 1; DNA binding, str	95.97
2yrq_A		173	High mobility group protein B1; HMG box domain, DN	95.66
2e6o_A		87	HMG box-containing protein 1; HMG-box domain, HMG-	95.53
3tq6_A		214	Transcription factor A, mitochondrial; transcripti	94.94
3tmm_A		238	Transcription factor A, mitochondrial; HMG, high m	94.84
2gzk_A		159	Sex-determining region on Y / HMGB1; protein-DNA c	94.79
2yrq_A		173	High mobility group protein B1; HMG box domain, DN	94.56
2gzk_A		159	Sex-determining region on Y / HMGB1; protein-DNA c	94.53
2v8f_C		26	MDIA1, profilin IIA; alternative splicing, protein	94.24
2d7l_A		81	WD repeat and HMG-box DNA binding protein 1; high	94.09
3tmm_A		238	Transcription factor A, mitochondrial; HMG, high m	93.96
3tq6_A		214	Transcription factor A, mitochondrial; transcripti	93.77
4akg_A		2695	Glutathione S-transferase class-MU 26 kDa isozyme	89.06
1kd8_B		36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	87.82
4akg_A		2695	Glutathione S-transferase class-MU 26 kDa isozyme	84.95
2cto_A		93	Novel protein; high mobility group box domain, hel	81.93
3c3g_A		33	Alpha/beta peptide with the GCN4-PLI SIDE chain S	80.85

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus}	Back alignment and structure

Probab=98.11  E-value=3.8e-07  Score=73.41  Aligned_cols=50  Identities=22%  Similarity=0.306  Sum_probs=46.4

Q ss_pred             cCCCCCchhhhhhhhhccc-cCCCcccccchh--------hHHHHHHHhhCCHHHHHHH
Q psy1953           8 NGTSRQLQANCYGQSIGGC-SKIPQCNENNFS--------EYEKNLKAYHNSPQYLAYM   57 (379)
Q Consensus         8 ~~~n~dl~lweigKiig~m-~~l~d~ek~~~~--------eY~~~~k~yhnSpay~ayi   57 (379)
                      ...||++...||+|+||.| ++|++++|+.|.        +|++.|.+|+.+++|++|.
T Consensus        27 ~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~~~   85 (92)
T 2crj_A           27 RTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYKVCT   85 (92)
T ss_dssp             HHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHCSS
T ss_pred             HHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHH
Confidence            3578999999999999999 999999999998        7999999999999998864

PyMOL of 2crj

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1	Back alignment and structure

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis}	Back alignment and structure

>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1	Back alignment and structure

>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A	Back alignment and structure

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1	Back alignment and structure

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B	Back alignment and structure

>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1	Back alignment and structure

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A	Back alignment and structure

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A	Back alignment and structure

>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A	Back alignment and structure

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster}	Back alignment and structure

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus}	Back alignment and structure

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*	Back alignment and structure

>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A	Back alignment and structure

>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A*	Back alignment and structure

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1	Back alignment and structure

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0	Back alignment and structure

>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens}	Back alignment and structure

>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1	Back alignment and structure

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens}	Back alignment and structure

>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A	Back alignment and structure

>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1	Back alignment and structure

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1	Back alignment and structure

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens}	Back alignment and structure

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}	Back alignment and structure

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}	Back alignment and structure

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1	Back alignment and structure

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1	Back alignment and structure

>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}	Back alignment and structure

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}	Back alignment and structure

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A	Back alignment and structure

>1kd8_B GABH BLL, GCN4 acid base heterodimer base-D12LA16L; coiled coil heterodimer, de novo protein; 1.90A {Synthetic} SCOP: h.1.3.1 PDB: 1kd9_B 1kdd_B	Back alignment and structure

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A	Back alignment and structure

>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3c3g_A Alpha/beta peptide with the GCN4-PLI SIDE chain S AN (alpha-alpha-beta) backbone; helix bundle, foldamer, unknown function protein; HET: HMR B3Q B3D B3E B3L BIL B3K BAL GOL; 1.80A {Synthetic} PDB: 3heu_A* 3het_A* 3hev_A* 3hew_A* 3hey_A* 3hex_A* 3c3h_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		379
d1j46a_		85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.21
d1hsma_		79	High mobility group protein 1, HMG1 {Hamster (Cric	97.09
d1gt0d_		80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	97.05
d1i11a_		70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	97.03
d1ckta_		71	High mobility group protein 1, HMG1 {Rat (Rattus n	96.92
d1lwma_		93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	96.82
d1k99a_		91	Nucleolar transcription factor 1 (Upstream binding	96.61
d2lefa_		86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	96.57
d1v63a_		101	Nucleolar transcription factor 1 (Upstream binding	96.48
d1qrva_		73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	96.26
d1v64a_		108	Nucleolar transcription factor 1 (Upstream binding	94.86
d1wgfa_		90	Nucleolar transcription factor 1 (Upstream binding	94.49
d1g8pa_		333	ATPase subunit of magnesium chelatase, BchI {Rhodo	85.07

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.21  E-value=1.1e-05  Score=62.30  Aligned_cols=44  Identities=9%  Similarity=0.156  Sum_probs=38.1

Q ss_pred             cCCCCCchhhhhhhhhccc-cCCCcccccchh--------hHHHHHHHhhCCH
Q psy1953           8 NGTSRQLQANCYGQSIGGC-SKIPQCNENNFS--------EYEKNLKAYHNSP   51 (379)
Q Consensus         8 ~~~n~dl~lweigKiig~m-~~l~d~ek~~~~--------eY~~~~k~yhnSp   51 (379)
                      ...||++...||+|+||.+ ++|++++|+.|.        +|.+.|..|+-.|
T Consensus        24 ~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~p   76 (85)
T d1j46a_          24 ALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (85)
T ss_dssp             HHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccCC
Confidence            4579999999999999999 999999999998        6777777776554

PyMOL of d1j46a_

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]}	Back information, alignment and structure

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}	Back information, alignment and structure