Citrus Sinensis ID: 047062

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---

ADIDSTKQEILFSLPTSREKLDGELCDASIAKQTTEYHNMPSLHESRGDVHRKDDLMVDAIDNLGSLKEKTSKYVAYGGKLDSSRFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVDKSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCISLGPGVSPEVVVSPTIVRCIILALCYFWGWHIPKGIDSVHDQ

ccccHHHHHHHHHccccccccccccccccccccHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccEEEEEEEccHHHHHHHHHHHHHccHHHHcccccccccHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHccHHHHHHHHHHHHHHHcccEEEEEHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccc

ccccHHHHHHHHccccccHcccccccccHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccccccccHHHHccccccHHHHHHHHHHHccHHHHHHHHHHHHHHcccEEEEHHHHHHHHHHHHHHccccEEEEccccccccEEEcHHHHHHHHHHHHHHHHccccccccccccc

ADIDSTKQEILFSlptsrekldgelcDASIAKQtteyhnmpslhesrgdvhrkddlMVDAIDNLGSLKEKTSKYVayggkldssrfvEYWIPVQISNVQLEQYCGTLLSKslslcsplkndpvgvLHDILISArkccdhpylvdKSLQSLLVKDLELAEYLDvgvkasgkLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCislgpgvspevvvspTIVRCIILALCYfwgwhipkgidsvhdq

adidstkqeilfslptsrekldgeLCDASIAKqtteyhnmpslhesrgdvhrkDDLMVDAIDnlgslkektskyVAYGGKLDSSRFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVDKSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCISLGPGVSPEVVVSPTIVRCIILALCYFWGWHIPKGIDSVHDQ

ADIDSTKQEILFSLPTSREKLDGELCDASIAKQTTEYHNMPSLHESRGDVHRKDDLMVDAIDNLGSLKEKTSKYVAYGGKLDSSRFVEYWIPVQISNVQLEQYCGTllskslslcsplkNDPVGVLHDILISARKCCDHPYLVDKSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCISLgpgvspevvvspTIVRCIILALCYFWGWHIPKGIDSVHDQ

*******************************************************LMVDAIDNLGSLKEKTSKYVAYGGKLDSSRFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVDKSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCISLGPGVSPEVVVSPTIVRCIILALCYFWGWHIPKGI******

****STKQEILFSLPTSREKLDGELCDASIAKQTTEYHNMPSLHESRGDVHRKDDL*****DNLGSLKEKTSKYVAYGGKLDSSRFVEYWIPVQISNVQLEQYCGTLLSKS****************DILISARKCCDHPYLVDKSL************YLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCISLGPGVSPEVVVSPTIVRCIILALCYFWGWHIPKGI******

*DIDSTKQEILFSLPTSREKLDGELCDASIAKQTTEYHNMPSLHESRGDVHRKDDLMVDAIDNLGSLKEKTSKYVAYGGKLDSSRFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVDKSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCISLGPGVSPEVVVSPTIVRCIILALCYFWGWHIPKGID*****

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		253	2.2.26 [Sep-21-2011]
Q9M658		2001	Helicase protein MOM1 OS=	yes	no	0.446	0.056	0.578	1e-25
Q91ZW3		1051	SWI/SNF-related matrix-as	yes	no	0.391	0.094	0.388	3e-08
O60264		1052	SWI/SNF-related matrix-as	yes	no	0.391	0.094	0.388	3e-08
Q9P2D1		2997	Chromodomain-helicase-DNA	no	no	0.422	0.035	0.330	6e-08
A2AJK6		2986	Chromodomain-helicase-DNA	no	no	0.422	0.035	0.330	6e-08
P28370		1054	Probable global transcrip	no	no	0.395	0.094	0.373	9e-08
Q7KU24		1883	Chromodomain-helicase-DNA	yes	no	0.418	0.056	0.339	1e-07
Q9JIX5		2581	Chromodomain-helicase-DNA	no	no	0.422	0.041	0.304	1e-07
Q09XV5		2582	Chromodomain-helicase-DNA	no	no	0.422	0.041	0.304	1e-07
B0R0I6		2511	Chromodomain-helicase-DNA	no	no	0.422	0.042	0.310	1e-07

>sp\|Q9M658\|MOM1_ARATH Helicase protein MOM1 OS=Arabidopsis thaliana GN=MOM1 PE=1 SV=1	Back alignment and function desciption

 Score =  117 bits (292), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 66/114 (57%), Positives = 83/114 (72%), Gaps = 1/114 (0%)

Query: 80  KLDSSRFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDH 139
           K  SS + EYW+PVQ+S+VQLEQYC TL SKSLSL S  K D +G L + L S RK CDH
Sbjct: 471 KFYSSVYPEYWVPVQLSDVQLEQYCQTLFSKSLSLSSLSKID-LGALEETLNSVRKTCDH 529

Query: 140 PYLVDKSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQ 193
           PY++D SL+ LL K+LEL E LDV +KASGKL LLD ML+ +K  G + ++ +Q
Sbjct: 530 PYVMDASLKQLLTKNLELHEILDVEIKASGKLHLLDKMLTHIKKNGLKAVVFYQ 583

Required for the heritable maintenance of transcriptional gene silencing (TGS) in heterochromatin, and particularly in the intermediate bivalent heterochromatin, characterized by an unsual methylation pattern consisting in hypermethylated DNA and histone H3 'Lys-4' methylation (H3K4me) together with depletion of histone H3 'Lys-9' methylation (H3K9me), in a chromatin methylation-independent manner, in a non-CG methylation context. May play a role in the RNA polymerase IV/V (Pol-IV/V)-mediated RNA-directed DNA methylation (RdDM) leading to TGS (also called siRNA-mediated TGS pathway), probably by modulating small interfering RNA (siRNA) accumulation. Especially involved in the gene silencing of the transcriptionally silent information region (TSI), 5S ribosomal RNA genes (localized in the pericentromeric heterochromatin of chromosomes 3, 4, and 5) and of 180-bp satellite repeats and 106B long terminal repeat (LTR)-like repeats of the chromocenters. Prevents the aberrant mRNA transcriptional read-through.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -

>sp\|Q91ZW3\|SMCA5_MOUSE SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 OS=Mus musculus GN=Smarca5 PE=1 SV=1	Back alignment and function description

>sp\|O60264\|SMCA5_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 OS=Homo sapiens GN=SMARCA5 PE=1 SV=1	Back alignment and function description

>sp\|Q9P2D1\|CHD7_HUMAN Chromodomain-helicase-DNA-binding protein 7 OS=Homo sapiens GN=CHD7 PE=1 SV=3	Back alignment and function description

>sp\|A2AJK6\|CHD7_MOUSE Chromodomain-helicase-DNA-binding protein 7 OS=Mus musculus GN=Chd7 PE=1 SV=1	Back alignment and function description

>sp\|P28370\|SMCA1_HUMAN Probable global transcription activator SNF2L1 OS=Homo sapiens GN=SMARCA1 PE=1 SV=2	Back alignment and function description

>sp\|Q7KU24\|CHD1_DROME Chromodomain-helicase-DNA-binding protein 1 OS=Drosophila melanogaster GN=Chd1 PE=1 SV=1	Back alignment and function description

>sp\|Q9JIX5\|CHD8_RAT Chromodomain-helicase-DNA-binding protein 8 OS=Rattus norvegicus GN=Chd8 PE=1 SV=2	Back alignment and function description

>sp\|Q09XV5\|CHD8_MOUSE Chromodomain-helicase-DNA-binding protein 8 OS=Mus musculus GN=Chd8 PE=1 SV=1	Back alignment and function description

>sp\|B0R0I6\|CHD8_DANRE Chromodomain-helicase-DNA-binding protein 8 OS=Danio rerio GN=chd8 PE=3 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		253
359478708		1534	PREDICTED: uncharacterized protein LOC10	0.667	0.110	0.603	9e-51
297746282		1452	unnamed protein product [Vitis vinifera]	0.648	0.112	0.609	1e-49
255577062		1982	mom(plant), putative [Ricinus communis]	0.691	0.088	0.508	4e-44
147834624		431	hypothetical protein VITISV_044023 [Viti	0.743	0.436	0.484	4e-41
449443580		2887	PREDICTED: uncharacterized protein LOC10	0.612	0.053	0.531	3e-40
449499771		1675	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.616	0.093	0.522	7e-40
224132518		1996	chromatin remodeling complex subunit [Po	0.569	0.072	0.590	1e-37
224122872		2283	chromatin remodeling complex subunit [Po	0.588	0.065	0.569	1e-35
356547167		1086	PREDICTED: uncharacterized protein LOC10	0.711	0.165	0.455	3e-35
413953630		1990	hypothetical protein ZEAMMB73_952056 [Ze	0.719	0.091	0.465	6e-34

>gi\|359478708\|ref\|XP_002282476.2\| PREDICTED: uncharacterized protein LOC100258707 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  206 bits (523), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 102/169 (60%), Positives = 126/169 (74%)

Query: 25  LCDASIAKQTTEYHNMPSLHESRGDVHRKDDLMVDAIDNLGSLKEKTSKYVAYGGKLDSS 84
           L    I + T E+ N+ S  +S  DV+  + L  D  D++  LKE+ S+++AY  K DSS
Sbjct: 155 LFSGQIKESTLEFVNLLSFLDSGNDVNSSNVLKTDYNDSVSILKERLSQFIAYDCKSDSS 214

Query: 85  RFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVD 144
           RFVEYW+P+ +SNVQLEQYCGTLLS ++SLCS  KNDPVG L D+LIS RKCCDHPY+VD
Sbjct: 215 RFVEYWVPIPLSNVQLEQYCGTLLSNTISLCSCSKNDPVGALRDVLISTRKCCDHPYIVD 274

Query: 145 KSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQ 193
            SLQS L K L   EYLDVG+ ASGKLQLLD M+SE+KN+G RV+ILFQ
Sbjct: 275 LSLQSFLTKGLPEIEYLDVGINASGKLQLLDRMISEIKNRGLRVLILFQ 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297746282\|emb\|CBI16338.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255577062\|ref\|XP_002529415.1\| mom(plant), putative [Ricinus communis] gi\|223531092\|gb\|EEF32941.1\| mom(plant), putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|147834624\|emb\|CAN76401.1\| hypothetical protein VITISV_044023 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449443580\|ref\|XP_004139555.1\| PREDICTED: uncharacterized protein LOC101222705 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449499771\|ref\|XP_004160912.1\| PREDICTED: LOW QUALITY PROTEIN: uncharacterized LOC101222705 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224132518\|ref\|XP_002328309.1\| chromatin remodeling complex subunit [Populus trichocarpa] gi\|222837824\|gb\|EEE76189.1\| chromatin remodeling complex subunit [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224122872\|ref\|XP_002318937.1\| chromatin remodeling complex subunit [Populus trichocarpa] gi\|222857313\|gb\|EEE94860.1\| chromatin remodeling complex subunit [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356547167\|ref\|XP_003541988.1\| PREDICTED: uncharacterized protein LOC100810773 [Glycine max]	Back alignment and taxonomy information

>gi\|413953630\|gb\|AFW86279.1\| hypothetical protein ZEAMMB73_952056 [Zea mays]	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		253
TAIR\|locus:2205205		2001	MOM "MORPHEUS MOLECULE" [Arabi	0.446	0.056	0.5	2.3e-24
ZFIN\|ZDB-GENE-021125-1		1035	smarca5 "SWI/SNF related, matr	0.454	0.111	0.346	7.2e-06
UNIPROTKB\|F1P5V4		839	HELLS "Uncharacterized protein	0.268	0.081	0.402	2.2e-05
RGD\|1311921		2985	Chd7 "chromodomain helicase DN	0.415	0.035	0.306	3.1e-05
UNIPROTKB\|E1BS47		1326	CHD7 "Chromodomain-helicase-DN	0.415	0.079	0.297	3.8e-05
UNIPROTKB\|H0YJG4		873	CHD8 "Chromodomain-helicase-DN	0.415	0.120	0.270	3.9e-05
MGI\|MGI:2444748		2986	Chd7 "chromodomain helicase DN	0.415	0.035	0.306	4.1e-05
UNIPROTKB\|Q9P2D1		2997	CHD7 "Chromodomain-helicase-DN	0.415	0.035	0.306	4.1e-05
RGD\|2323132		760	LOC100359912 "SWI/SNF-related	0.454	0.151	0.338	4.3e-05
ZFIN\|ZDB-GENE-030131-9923		853	hells "helicase, lymphoid-spec	0.268	0.079	0.402	5e-05

TAIR\|locus:2205205 MOM "MORPHEUS MOLECULE" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 287 (106.1 bits), Expect = 2.3e-24, Sum P(2) = 2.3e-24
 Identities = 57/114 (50%), Positives = 74/114 (64%)

Query:    80 KLDSSRFVEYWIPVQISNVQLEQYCGTXXXXXXXXXXXXXNDPVGVLHDILISARKCCDH 139
             K  SS + EYW+PVQ+S+VQLEQYC T              D +G L + L S RK CDH
Sbjct:   471 KFYSSVYPEYWVPVQLSDVQLEQYCQTLFSKSLSLSSLSKID-LGALEETLNSVRKTCDH 529

Query:   140 PYLVDKSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQ 193
             PY++D SL+ LL K+LEL E LDV +KASGKL LLD ML+ +K  G + ++ +Q
Sbjct:   530 PYVMDASLKQLLTKNLELHEILDVEIKASGKLHLLDKMLTHIKKNGLKAVVFYQ 583

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006342 "chromatin silencing" evidence=IMP

GO:0032259 "methylation" evidence=IMP

GO:0006344 "maintenance of chromatin silencing" evidence=IMP

GO:0042803 "protein homodimerization activity" evidence=IPI

ZFIN\|ZDB-GENE-021125-1 smarca5 "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1P5V4 HELLS "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

RGD\|1311921 Chd7 "chromodomain helicase DNA binding protein 7" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BS47 CHD7 "Chromodomain-helicase-DNA-binding protein 7" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|H0YJG4 CHD8 "Chromodomain-helicase-DNA-binding protein 8" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:2444748 Chd7 "chromodomain helicase DNA binding protein 7" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9P2D1 CHD7 "Chromodomain-helicase-DNA-binding protein 7" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

RGD\|2323132 LOC100359912 "SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a5-like" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-9923 hells "helicase, lymphoid-specific" [Danio rerio (taxid:7955)]	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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		253
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	1e-06

>gnl\|CDD\|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional	Back alignment and domain information

 Score = 49.0 bits (117), Expect = 1e-06
 Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 18/75 (24%)

Query: 126 LHDILISARKCCDHPYLVDKSLQSLLVKDLELAE----YL--DVGVKASGKLQLLDTMLS 179
           L +I +  RKCC+HPYL             + AE    Y   +  V+ SGK+ LLD +L 
Sbjct: 434 LLNIAMQLRKCCNHPYL------------FQGAEPGPPYTTGEHLVENSGKMVLLDKLLP 481

Query: 180 ELKNQGSRVIILFQI 194
           +LK + SRV+I  Q+
Sbjct: 482 KLKERDSRVLIFSQM 496

Length = 1033

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		253
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	100.0
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	100.0
KOG0387		923	consensus Transcription-coupled repair protein CSB	100.0
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	100.0
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	100.0
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	100.0
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	100.0
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	100.0
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	100.0
KOG0383		696	consensus Predicted helicase [General function pre	100.0
KOG1015		1567	consensus Transcription regulator XNP/ATRX, DEAD-b	100.0
KOG4439		901	consensus RNA polymerase II transcription terminat	100.0
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	99.98
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.97
KOG1002		791	consensus Nucleotide excision repair protein RAD16	99.96
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	99.95
KOG1001		674	consensus Helicase-like transcription factor HLTF/	99.91
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.88
PRK04914		956	ATP-dependent helicase HepA; Validated	99.53
PF11496		297	HDA2-3: Class II histone deacetylase complex subun	99.32
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	99.21
KOG0298		1394	consensus DEAD box-containing helicase-like transc	99.01
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	97.91
PRK13766		773	Hef nuclease; Provisional	97.73
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	96.4
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	94.73
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	90.14
PTZ00110		545	helicase; Provisional	87.84
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	84.61
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	83.57
PRK12904		830	preprotein translocase subunit SecA; Reviewed	83.12
PHA02558		501	uvsW UvsW helicase; Provisional	81.46
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	80.88

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]	Back alignment and domain information

Probab=100.00  E-value=2.9e-54  Score=407.87  Aligned_cols=223  Identities=23%  Similarity=0.205  Sum_probs=195.8

Q ss_pred             CCcchHHHHHhhcchhhhcCCcccchhhhhhCHHHHHHHhhhhcCCCCC--cchhH-----HhhhHHhHHHHHHHHhhhh
Q 047062            2 DIDSTKQEILFSLPTSREKLDGELCDASIAKQTTEYHNMPSLHESRGDV--HRKDD-----LMVDAIDNLGSLKEKTSKY   74 (253)
Q Consensus         2 ~i~~~k~~~~~~~~~~r~~~~~~LTGTPiQN~L~EL~sL~~Fl~P~~~~--~~~~~-----~~~~~~~~~~~L~~~l~pf   74 (253)
                      -|||.++....-|+.+.+-.|++||||||||||.|||||++|+.|.-|.  +.|..     ......+.+.+|+.+++||
T Consensus       300 RiKN~~s~L~~~lr~f~~~nrLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pF  379 (971)
T KOG0385|consen  300 RIKNEKSKLSKILREFKTDNRLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPF  379 (971)
T ss_pred             hhcchhhHHHHHHHHhcccceeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHH
Confidence            3899999999999999999999999999999999999999999995443  33332     1223345789999999999


Q ss_pred             hhhccCCCC----CCceEEEEeecCCHHHHHHHHHHHHhccccccCCCCCCCcchHHHHHHHHHHHcCCccCcchhhh-h
Q 047062           75 VAYGGKLDS----SRFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVDKSLQ-S  149 (253)
Q Consensus        75 ~LRRtK~dv----P~K~e~vV~~~Ls~~Qr~lY~~~l~~~~~~l~~~~~~~~~~~ll~~L~~LRqiCnHP~L~~~~~~-~  149 (253)
                      +|||+|.+|    |||+|.++||.||+.|+++|++++.+....+...++. ....++|++|+||+|||||||+++.+. +
T Consensus       380 lLRR~K~dVe~sLppKkE~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~-~k~kL~NI~mQLRKccnHPYLF~g~ePg~  458 (971)
T KOG0385|consen  380 LLRRIKSDVEKSLPPKKELIIYVGMSSMQKKWYKAILMKDLDALNGEGKG-EKTKLQNIMMQLRKCCNHPYLFDGAEPGP  458 (971)
T ss_pred             HHHHHHHhHhhcCCCcceeeEeccchHHHHHHHHHHHHhcchhhcccccc-hhhHHHHHHHHHHHhcCCccccCCCCCCC
Confidence            999999987    9999999999999999999999999888777665543 356899999999999999999999654 4


Q ss_pred             hhhhhhhHHHHhhhhhhcCcHHHHHHHHHHHHHcCCCeEEEEccccccccchHHHHHHHHHHhcCCCCCceeeecCCchH
Q 047062          150 LLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCISLGPGVSPEVVVSPTIVR  229 (253)
Q Consensus       150 ~~~~~~~~~~~~~~li~~SgKl~~L~~lL~~l~~~g~KvLIFSq~~~~~~~~~~Ldile~~l~~~~g~~~~rl~g~t~~r  229 (253)
                      .++.+.+       ++..||||.+|++||+.++++|||||||||||+      ||||+|+||.. +||.|.|+||||.-.
T Consensus       459 pyttdeh-------Lv~nSGKm~vLDkLL~~Lk~~GhRVLIFSQmt~------mLDILeDyc~~-R~y~ycRiDGSt~~e  524 (971)
T KOG0385|consen  459 PYTTDEH-------LVTNSGKMLVLDKLLPKLKEQGHRVLIFSQMTR------MLDILEDYCML-RGYEYCRLDGSTSHE  524 (971)
T ss_pred             CCCcchH-------HHhcCcceehHHHHHHHHHhCCCeEEEeHHHHH------HHHHHHHHHHh-cCceeEeecCCCCcH
Confidence            4555444       489999999999999999999999999999999      99999999999 999999999999999


Q ss_pred             HHHHHHhhhh
Q 047062          230 CIILALCYFW  239 (253)
Q Consensus       230 ~~~~~~~~~~  239 (253)
                      -+.-|...|-
T Consensus       525 eR~~aI~~fn  534 (971)
T KOG0385|consen  525 EREDAIEAFN  534 (971)
T ss_pred             HHHHHHHhcC
Confidence            8888887764

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]	Back alignment and domain information

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]	Back alignment and domain information

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]	Back alignment and domain information

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]	Back alignment and domain information

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]	Back alignment and domain information

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional	Back alignment and domain information

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]	Back alignment and domain information

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]	Back alignment and domain information

>KOG0383 consensus Predicted helicase [General function prediction only]	Back alignment and domain information

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]	Back alignment and domain information

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]	Back alignment and domain information

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]	Back alignment and domain information

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]	Back alignment and domain information

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]	Back alignment and domain information

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]	Back alignment and domain information

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e	Back alignment and domain information

>PRK04914 ATP-dependent helicase HepA; Validated	Back alignment and domain information

>PF11496 HDA2-3: Class II histone deacetylase complex subunits 2 and 3; InterPro: IPR021006 This entry contains the class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi	Back alignment and domain information

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]	Back alignment and domain information

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]	Back alignment and domain information

>TIGR00603 rad25 DNA repair helicase rad25	Back alignment and domain information

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Back alignment and domain information

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>PTZ00110 helicase; Provisional	Back alignment and domain information

>PRK12900 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK12904 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PHA02558 uvsW UvsW helicase; Provisional	Back alignment and domain information

>PRK12898 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		253
3mwy_W		800	Crystal Structure Of The Chromodomain-atpase Portio		3e-05

>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of The Yeast Chd1 Chromatin Remodeler Length = 800

Back alignment and structure

Iteration: 1

Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust. Identities = 31/107 (28%), Positives = 51/107 (47%), Gaps = 5/107 (4%) Query: 93 VQISNVQLEQYCGTXXXXXXXXXXXXXNDPVGVLHDILISARKCCDHPYLVDKSLQSLLV 152 V++S+VQ E Y +L +I+ +K +HPYL D + + +L Sbjct: 477 VELSDVQTEYYKNILTKNYSALTAGAKGGHFSLL-NIMNELKKASNHPYLFDNAEERVLQ 535 Query: 153 K----DLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQIL 195 K + L + +SGK+ LLD +L+ LK G RV+I Q++ Sbjct: 536 KFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMV 582 Database: pdbaa

PyMOL of 3mwy

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		253
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	2e-16
3hgt_A		328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	7e-16
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	5e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-06

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae} Length = 800	Back alignment and structure

 Score = 77.1 bits (190), Expect = 2e-16
 Identities = 34/111 (30%), Positives = 55/111 (49%), Gaps = 5/111 (4%)

Query: 87  VEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVD-- 144
            E  + V++S+VQ  +Y   +L+K+ S  +         L +I+   +K  +HPYL D  
Sbjct: 471 TERILRVELSDVQ-TEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNA 529

Query: 145 --KSLQSLLVKDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQ 193
             + LQ      +     L   + +SGK+ LLD +L+ LK  G RV+I  Q
Sbjct: 530 EERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQ 580

PyMOL of 3mwy

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A Length = 328	Back alignment and structure

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19 Length = 644	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		253
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	100.0
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	100.0
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.96
3hgt_A		328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	99.94
1z5z_A		271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.9
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.36
1wp9_A		494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.78
2fwr_A		472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	97.66
4a2w_A		936	RIG-I, retinoic acid inducible protein I; hydrolas	97.65
4a2q_A		797	RIG-I, retinoic acid inducible protein I; hydrolas	97.45
4a2p_A		556	RIG-I, retinoic acid inducible protein I; hydrolas	97.32
3tbk_A		555	RIG-I helicase domain; DECH helicase, ATP binding,	97.23
2ykg_A		696	Probable ATP-dependent RNA helicase DDX58; hydrola	96.51
2oca_A		510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	96.11
1t5i_A		172	C_terminal domain of A probable ATP-dependent RNA	95.92
2hjv_A		163	ATP-dependent RNA helicase DBPA; parallel alpha-be	95.9
2jgn_A		185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	95.84
1fuk_A		165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	95.43
2rb4_A		175	ATP-dependent RNA helicase DDX25; rossmann fold, s	95.16
2p6n_A		191	ATP-dependent RNA helicase DDX41; DEAD, structural	95.15
3eaq_A		212	Heat resistant RNA dependent ATPase; DEAD box RNA	93.44
2yjt_D		170	ATP-dependent RNA helicase SRMB, regulator of ribo	91.45
3i32_A		300	Heat resistant RNA dependent ATPase; RNA helicase,	90.85
4gl2_A		699	Interferon-induced helicase C domain-containing P;	89.48
1xti_A		391	Probable ATP-dependent RNA helicase P47; alpha-bet	88.78
1s2m_A		400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	85.24
2i4i_A		417	ATP-dependent RNA helicase DDX3X; DEAD, structural	85.17
1hv8_A		367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	84.92
2j0s_A		410	ATP-dependent RNA helicase DDX48; mRNA processing,	82.42

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}	Back alignment and structure

Probab=100.00  E-value=8.5e-37  Score=303.35  Aligned_cols=230  Identities=20%  Similarity=0.239  Sum_probs=185.6

Q ss_pred             CCcchHHHHHhhcchhhhcCCcccchhhhhhCHHHHHHHhhhhcCCCCCcc--h--hHHhhhHHhHHHHHHHHhhhhhhh
Q 047062            2 DIDSTKQEILFSLPTSREKLDGELCDASIAKQTTEYHNMPSLHESRGDVHR--K--DDLMVDAIDNLGSLKEKTSKYVAY   77 (253)
Q Consensus         2 ~i~~~k~~~~~~~~~~r~~~~~~LTGTPiQN~L~EL~sL~~Fl~P~~~~~~--~--~~~~~~~~~~~~~L~~~l~pf~LR   77 (253)
                      +|||..++..+++..+++..||+|||||+||++.|||+|++|+.|+.+...  +  ..........+..|+..++|||+|
T Consensus       378 ~lkn~~s~~~~~l~~l~~~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lR  457 (800)
T 3mwy_W          378 RLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILR  457 (800)
T ss_dssp             GGCCSSSHHHHHHTTSEEEEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEE
T ss_pred             hhcCchhHHHHHHHHhhhccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhh
Confidence            478899999999999999999999999999999999999999999855422  1  112233445688999999999999


Q ss_pred             ccCCCC----CCceEEEEeecCCHHHHHHHHHHHHhccccccCCCCCCCcchHHHHHHHHHHHcCCccCcchhhhhhhh-
Q 047062           78 GGKLDS----SRFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVDKSLQSLLV-  152 (253)
Q Consensus        78 RtK~dv----P~K~e~vV~~~Ls~~Qr~lY~~~l~~~~~~l~~~~~~~~~~~ll~~L~~LRqiCnHP~L~~~~~~~~~~-  152 (253)
                      |+|.+|    |+|.+.+++|+||+.|+++|+.++.+....+..+... ....+++.++.||++||||+|+......... 
T Consensus       458 R~k~dv~~~LP~k~~~~v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~-~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~  536 (800)
T 3mwy_W          458 RLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKG-GHFSLLNIMNELKKASNHPYLFDNAEERVLQK  536 (800)
T ss_dssp             CCGGGGTTTSCCEEEEEEEECCCHHHHHHHHHHHHHCCC-----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCC
T ss_pred             hhHHhhhhccCCcEEEEEEeCCCHHHHHHHHHHHHHHHHHHhhcccc-chhhHHHHHHHHHHHhcChhhhcchHHHHHHh
Confidence            999865    9999999999999999999999998777666544433 3457899999999999999999875433211 


Q ss_pred             ---hhhhHHHHhhhhhhcCcHHHHHHHHHHHHHcCCCeEEEEccccccccchHHHHHHHHHHhcCCCCCceeeecCCchH
Q 047062          153 ---KDLELAEYLDVGVKASGKLQLLDTMLSELKNQGSRVIILFQILIIRAKVCENEILGYCISLGPGVSPEVVVSPTIVR  229 (253)
Q Consensus       153 ---~~~~~~~~~~~li~~SgKl~~L~~lL~~l~~~g~KvLIFSq~~~~~~~~~~Ldile~~l~~~~g~~~~rl~g~t~~r  229 (253)
                         ......+....++.+|||+.+|.++|.++.+.|+||||||||+.      ++++|+.+|.. .|+.|.|++|+|...
T Consensus       537 ~~~~~~~~~~~~~~l~~~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~------~ld~L~~~L~~-~g~~~~~i~G~~~~~  609 (800)
T 3mwy_W          537 FGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVR------MLDILGDYLSI-KGINFQRLDGTVPSA  609 (800)
T ss_dssp             C----CCSHHHHHHHHHTCHHHHHHHHHHHHHTTTTCCEEEEESCHH------HHHHHHHHHHH-HTCCCEEESTTSCHH
T ss_pred             cccccccHHHHHHHhhhcChHHHHHHHHHHHHhhCCCeEEEEechHH------HHHHHHHHHHh-CCCCEEEEeCCCCHH
Confidence               11111233455688999999999999999999999999999999      99999999998 899999999999998


Q ss_pred             HHHHHHhhhh
Q 047062          230 CIILALCYFW  239 (253)
Q Consensus       230 ~~~~~~~~~~  239 (253)
                      .+.-++..|-
T Consensus       610 eR~~~i~~F~  619 (800)
T 3mwy_W          610 QRRISIDHFN  619 (800)
T ss_dssp             HHHHHHHTTS
T ss_pred             HHHHHHHHhh
Confidence            8888887775

PyMOL of 3mwy

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A	Back alignment and structure

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A	Back alignment and structure

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19	Back alignment and structure

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}	Back alignment and structure

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*	Back alignment and structure

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}	Back alignment and structure

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}	Back alignment and structure

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*	Back alignment and structure

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}	Back alignment and structure

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*	Back alignment and structure

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}	Back alignment and structure

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19	Back alignment and structure

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}	Back alignment and structure

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}	Back alignment and structure

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19	Back alignment and structure

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}	Back alignment and structure

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}	Back alignment and structure

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A	Back alignment and structure

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}	Back alignment and structure

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}	Back alignment and structure

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}	Back alignment and structure

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A	Back alignment and structure

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A	Back alignment and structure

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}	Back alignment and structure

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		253
d1z3ix1		346	c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fi	2e-06

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 346	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

 Score = 46.1 bits (108), Expect = 2e-06
 Identities = 21/113 (18%), Positives = 44/113 (38%), Gaps = 8/113 (7%)

Query: 87  VEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVDKS 146
           +E  +   ++ +Q E Y    L ++  + S             + S +K C+HP L+ + 
Sbjct: 13  IEQVVCCNLTPLQKELYK-LFLKQAKPVESLQTGKISVSSLSSITSLKKLCNHPALIYEK 71

Query: 147 LQSLLVKDLELAEYL-------DVGVKASGKLQLLDTMLSELKNQGSRVIILF 192
             +         +          V  + SGK+ +LD +L+  +   S  ++L 
Sbjct: 72  CLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLV 124

PyMOL of d1z3ix1

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		253
d1z3ix1		346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.91
d1z5za1		244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.88
d1z63a1		230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.58
d1z3ix2		298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.49
d2fwra1		200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.93
d1t5ia_		168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	96.37
d1wp9a2		286	putative ATP-dependent RNA helicase PF2015 {Pyroco	96.31
d1s2ma2		171	Putative ATP-dependent RNA helicase DHH1 {Baker's	96.07
d1hv8a2		155	Putative DEAD box RNA helicase {Archaeon Methanoco	95.13
d1fuka_		162	Initiation factor 4a {Baker's yeast (Saccharomyces	94.96
d2j0sa2		168	Probable ATP-dependent RNA helicase DDX48 {Human (	94.77
d2rb4a1		168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	94.33
d1c4oa2		174	Nucleotide excision repair enzyme UvrB {Thermus th	92.85
d1t5la2		181	Nucleotide excision repair enzyme UvrB {Bacillus c	90.43
d1oywa3		200	RecQ helicase domain {Escherichia coli [TaxId: 562	90.32

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.91  E-value=1e-24  Score=195.29  Aligned_cols=151  Identities=13%  Similarity=0.013  Sum_probs=116.4

Q ss_pred             CCCCCceEEEEeecCCHHHHHHHHHHHHhccccccCCCCCCCcchHHHHHHHHHHHcCCccCcchhhhhhhhhhhhHH--
Q 047062           81 LDSSRFVEYWIPVQISNVQLEQYCGTLLSKSLSLCSPLKNDPVGVLHDILISARKCCDHPYLVDKSLQSLLVKDLELA--  158 (253)
Q Consensus        81 ~dvP~K~e~vV~~~Ls~~Qr~lY~~~l~~~~~~l~~~~~~~~~~~ll~~L~~LRqiCnHP~L~~~~~~~~~~~~~~~~--  158 (253)
                      +.+|+|+|++|+|+||+.|+++|+.++.+...... ...+.....+++.+++|||+||||+|+...............  
T Consensus         7 k~LP~K~e~vv~v~LS~~Q~~lY~~~l~~~~~~~~-~~~~~~~~~~L~~l~~LRkiCnHP~L~~~~~~~~~~~~~~~~~~   85 (346)
T d1z3ix1           7 KYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVES-LQTGKISVSSLSSITSLKKLCNHPALIYEKCLTGEEGFDGALDL   85 (346)
T ss_dssp             GTSCCEEEEEEEECCCHHHHHHHHHHHHHHCGGGS-SCTTCCCHHHHHHHHHHHHHHHCTHHHHHHHHHTCTTCTTGGGT
T ss_pred             ccCCCCEEEEEEeCCCHHHHHHHHHHHHHHHHHHh-hhcCCchHHHHHHHHHHHHHhCCHHHhhhhhccccccccchhhh
Confidence            35899999999999999999999998865443322 222333457889999999999999998664222110000000  


Q ss_pred             -----HHhhhhhhcCcHHHHHHHHHHHHH-cCCCeEEEEccccccccchHHHHHHHHHHhcCCCCCceeeecCCchHHHH
Q 047062          159 -----EYLDVGVKASGKLQLLDTMLSELK-NQGSRVIILFQILIIRAKVCENEILGYCISLGPGVSPEVVVSPTIVRCII  232 (253)
Q Consensus       159 -----~~~~~li~~SgKl~~L~~lL~~l~-~~g~KvLIFSq~~~~~~~~~~Ldile~~l~~~~g~~~~rl~g~t~~r~~~  232 (253)
                           .........|||+.+|+.+|.++. ..|+||||||||+.      ++|+|+.+|.. .|+.|.|++|+|....+.
T Consensus        86 ~~~~~~~~~~~~~~S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~------~ld~l~~~l~~-~g~~~~~l~G~~~~~~R~  158 (346)
T d1z3ix1          86 FPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQ------TLDLFEKLCRN-RRYLYVRLDGTMSIKKRA  158 (346)
T ss_dssp             SCSSCCSSSCCGGGSHHHHHHHHHHHHHHHHCCCEEEEEESCHH------HHHHHHHHHHH-HTCCEEEECSSCCHHHHH
T ss_pred             ccccccccccccccCHHHHHHHHHHHHHHHhcCCceeEEeehhh------hhHHHHHHHhh-hhccccccccchhHHHHH
Confidence                 001112567999999999999886 77999999999999      99999999998 899999999999998888


Q ss_pred             HHHhhhh
Q 047062          233 LALCYFW  239 (253)
Q Consensus       233 ~~~~~~~  239 (253)
                      -++-.|-
T Consensus       159 ~~i~~F~  165 (346)
T d1z3ix1         159 KIVERFN  165 (346)
T ss_dssp             HHHHHHH
T ss_pred             HHHHhhh
Confidence            8888885

PyMOL of d1z3ix1

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}	Back information, alignment and structure

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}	Back information, alignment and structure

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure