Citrus Sinensis ID: 043012

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-
Protein Sequence
MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDRPPISELAG
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHccccccccHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccHHHHcc
Coil and Loop (DISEMBL)
mvlrnkilldlkpAQLAAVCASLVSEGIKVRlwknnsyiyepstTVINVINVLDEHRSSFLELQekhgveipccldsqfSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAqipklpdvdqrlqknavdasnvmdrppiselag
Flexible Loop (DISEMBL)
MVLRNKIlldlkpaqLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLaqipklpdvdqrlqknavdasnvmdrppiselag
Low Complexity Region (SEG)
MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMdcalddgdlarllrrTIDLLAQIPKLPDVDQRLQKNAVDASNVMDRPPISELAG
Disordered region (IsUnstruct)
****NKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKL****************************
Disordered Region (DISOPRED)
MVLRNKILLDLKPAQLAAVCASLVSEGI*****************VINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDRPPISEL*G
Disordered Region (DISEMBL)
MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDRPPISELAG
Disordered Region (DISPRO)
MVL*NKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDRPPIS****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDVDQRLQKNAVDASNVMDRPPISELAG
Positional Conservation
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	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	151	2.2.26 [Sep-21-2011]
B9DFG3	1171	DEAD-box ATP-dependent RN	yes	no	1.0	0.128	0.748	1e-65

>sp|B9DFG3|ISE2_ARATH DEAD-box ATP-dependent RNA helicase ISE2, chloroplastic OS=Arabidopsis thaliana GN=ISE2 PE=1 SV=2

 Score =  248 bits (632), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 113/151 (74%), Positives = 136/151 (90%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLRNK L+DLKP QLA VCASLVSEGIKVR W++N+YIYEPS TV++++N L++ RSS 
Sbjct: 1021 MVLRNKALVDLKPPQLAGVCASLVSEGIKVRPWRDNNYIYEPSDTVVDMVNFLEDQRSSL 1080

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
            ++LQEKH V IPCCLD QFSGMVEAWASGL+W+EMMM+CA+D+GDLARLLRRTIDLLAQI
Sbjct: 1081 IKLQEKHEVMIPCCLDVQFSGMVEAWASGLSWKEMMMECAMDEGDLARLLRRTIDLLAQI 1140

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            PKLPD+D  LQ++A  A+++MDRPPISELAG
Sbjct: 1141 PKLPDIDPVLQRSAAAAADIMDRPPISELAG 1171

Essential protein required during embryogenesis. Involved in post-transcriptional gene silencing. Modulates the determination of cell fate. Necessary for normal plasmodesmata (PD) development and aperture regulation.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	151
291464071	1159	increased size exclusion limit 2 [Nicoti	1.0	0.130	0.827	3e-70
296086480	1064	unnamed protein product [Vitis vinifera]	1.0	0.141	0.841	3e-70
225424807	1174	PREDICTED: DEAD-box ATP-dependent RNA he	1.0	0.128	0.841	4e-70
147769115	239	hypothetical protein VITISV_039406 [Viti	1.0	0.631	0.841	7e-70
224110980	736	predicted protein [Populus trichocarpa]	1.0	0.205	0.801	7e-68
255558340	1161	helicase, putative [Ricinus communis] gi	1.0	0.130	0.794	1e-66
357486299	1201	ATP-dependent RNA helicase DOB1 [Medicag	1.0	0.125	0.801	2e-66
449486574	1168	PREDICTED: DEAD-box ATP-dependent RNA he	1.0	0.129	0.794	2e-65
449452156	1193	PREDICTED: LOW QUALITY PROTEIN: DEAD-box	1.0	0.126	0.794	2e-65
357138189	1168	PREDICTED: DEAD-box ATP-dependent RNA he	1.0	0.129	0.781	1e-64

>gi|291464071|gb|ADE05573.1| increased size exclusion limit 2 [Nicotiana benthamiana]

 Score =  269 bits (688), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 125/151 (82%), Positives = 142/151 (94%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLRNK+LLDLKPAQLAAVC SLVSEGI++R WKNNS++YEPSTTV+NVI++L+E +SS 
Sbjct: 1009 MVLRNKLLLDLKPAQLAAVCGSLVSEGIRLRPWKNNSFVYEPSTTVLNVIDLLEETKSSI 1068

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
            LELQEKHGV+IPCCLDSQFSGMVEAWASGLTW+E+MMDCA+D+GDLARLLRRTIDLLAQI
Sbjct: 1069 LELQEKHGVQIPCCLDSQFSGMVEAWASGLTWKEIMMDCAMDEGDLARLLRRTIDLLAQI 1128

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            PKLPD+D  LQ NA  AS+VMDRPPISELAG
Sbjct: 1129 PKLPDIDPLLQSNAKGASSVMDRPPISELAG 1159

Source: Nicotiana benthamiana

Species: Nicotiana benthamiana

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086480|emb|CBI32069.3| unnamed protein product [Vitis vinifera]

 Score =  269 bits (687), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 127/151 (84%), Positives = 140/151 (92%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLR+K+LL LKPAQLAAVC SLVSEGIKVR WKNNSYIYE STTVINVI++LDE R+S 
Sbjct: 914  MVLRSKVLLGLKPAQLAAVCGSLVSEGIKVRPWKNNSYIYEASTTVINVISLLDEQRNSL 973

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
            L+LQEKH V+IPCCLDSQFSGMVEAWASGLTWRE+MMDCA+D+GDLARLLRRTID+LAQI
Sbjct: 974  LQLQEKHDVQIPCCLDSQFSGMVEAWASGLTWREIMMDCAMDEGDLARLLRRTIDILAQI 1033

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            PKLPD+D  LQ NA+ ASNVMDRPPISELAG
Sbjct: 1034 PKLPDIDPLLQSNAMTASNVMDRPPISELAG 1064

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424807|ref|XP_002267766.1| PREDICTED: DEAD-box ATP-dependent RNA helicase ISE2, chloroplastic-like [Vitis vinifera]

 Score =  268 bits (686), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 127/151 (84%), Positives = 140/151 (92%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLR+K+LL LKPAQLAAVC SLVSEGIKVR WKNNSYIYE STTVINVI++LDE R+S 
Sbjct: 1024 MVLRSKVLLGLKPAQLAAVCGSLVSEGIKVRPWKNNSYIYEASTTVINVISLLDEQRNSL 1083

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
            L+LQEKH V+IPCCLDSQFSGMVEAWASGLTWRE+MMDCA+D+GDLARLLRRTID+LAQI
Sbjct: 1084 LQLQEKHDVQIPCCLDSQFSGMVEAWASGLTWREIMMDCAMDEGDLARLLRRTIDILAQI 1143

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            PKLPD+D  LQ NA+ ASNVMDRPPISELAG
Sbjct: 1144 PKLPDIDPLLQSNAMTASNVMDRPPISELAG 1174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147769115|emb|CAN76232.1| hypothetical protein VITISV_039406 [Vitis vinifera]

 Score =  268 bits (684), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 127/151 (84%), Positives = 140/151 (92%)

Query: 1   MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
           MVLR+K+LL LKPAQLAAVC SLVSEGIKVR WKNNSYIYE STTVINVI++LDE R+S 
Sbjct: 89  MVLRSKVLLGLKPAQLAAVCGSLVSEGIKVRPWKNNSYIYEASTTVINVISLLDEQRNSL 148

Query: 61  LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
           L+LQEKH V+IPCCLDSQFSGMVEAWASGLTWRE+MMDCA+D+GDLARLLRRTID+LAQI
Sbjct: 149 LQLQEKHDVQIPCCLDSQFSGMVEAWASGLTWREIMMDCAMDEGDLARLLRRTIDILAQI 208

Query: 121 PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
           PKLPD+D  LQ NA+ ASNVMDRPPISELAG
Sbjct: 209 PKLPDIDPLLQSNAMTASNVMDRPPISELAG 239

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224110980|ref|XP_002315703.1| predicted protein [Populus trichocarpa] gi|222864743|gb|EEF01874.1| predicted protein [Populus trichocarpa]

 Score =  261 bits (667), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 121/151 (80%), Positives = 138/151 (91%)

Query: 1   MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
           MVLR++ILLDLKP QLAAVCAS+VSEGIKVR W+NN+YIYEPS+ VINVIN+L+E RS+ 
Sbjct: 586 MVLRSRILLDLKPGQLAAVCASVVSEGIKVRAWENNNYIYEPSSAVINVINILNEQRSNL 645

Query: 61  LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
            +LQEKHGVEI CCLDSQFSGMVEAWA+GLTW+EMMMDCA+DDGDLARLLRRTID+LAQI
Sbjct: 646 SKLQEKHGVEITCCLDSQFSGMVEAWAAGLTWKEMMMDCAMDDGDLARLLRRTIDILAQI 705

Query: 121 PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
           PKLPD+D  LQ NA  AS++MDRPPISEL G
Sbjct: 706 PKLPDIDPVLQSNAKTASSIMDRPPISELTG 736

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255558340|ref|XP_002520197.1| helicase, putative [Ricinus communis] gi|223540689|gb|EEF42252.1| helicase, putative [Ricinus communis]

 Score =  256 bits (655), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 120/151 (79%), Positives = 136/151 (90%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLR+KILLDLKPAQLAAVCAS+VSEGIKVR W+NNSYIYEPS+ V N+I  L+E RSS 
Sbjct: 1011 MVLRSKILLDLKPAQLAAVCASVVSEGIKVRAWENNSYIYEPSSAVFNIIGKLEEQRSSL 1070

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
            L+LQEKHGVEI C LDSQFSGMVEAWASGL+W+EMMMDCA+DDGDLARL+R+TIDLLAQI
Sbjct: 1071 LQLQEKHGVEISCYLDSQFSGMVEAWASGLSWKEMMMDCAMDDGDLARLIRQTIDLLAQI 1130

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            PKLPD+D  LQ NA  A ++MDRPPISEL+G
Sbjct: 1131 PKLPDIDPALQSNAKTAYDIMDRPPISELSG 1161

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357486299|ref|XP_003613437.1| ATP-dependent RNA helicase DOB1 [Medicago truncatula] gi|355514772|gb|AES96395.1| ATP-dependent RNA helicase DOB1 [Medicago truncatula]

 Score =  256 bits (653), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 121/151 (80%), Positives = 134/151 (88%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLR+KIL +LKPAQLAAVCA LVSEGIKVR WKNN+YIYEPS TV+N+I +LDE R++ 
Sbjct: 1039 MVLRSKILAELKPAQLAAVCAGLVSEGIKVRPWKNNNYIYEPSATVVNIIGLLDEQRNAL 1098

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
            L +QEKHGV I CCLDSQF GMVEAWASGLTWRE+MMDCA+DDGDLARLLRRTIDLLAQI
Sbjct: 1099 LTIQEKHGVTISCCLDSQFCGMVEAWASGLTWREIMMDCAMDDGDLARLLRRTIDLLAQI 1158

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            P LPD+D  LQKNA  A +VMDRPPISELAG
Sbjct: 1159 PNLPDIDPLLQKNARAACDVMDRPPISELAG 1189

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449486574|ref|XP_004157336.1| PREDICTED: DEAD-box ATP-dependent RNA helicase ISE2, chloroplastic-like [Cucumis sativus]

 Score =  253 bits (646), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 120/151 (79%), Positives = 135/151 (89%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLRNK L+ LKP +LAAVCASLVSEGIKVR  +NNSYI+EPS TVIN+IN L+E R+S 
Sbjct: 1018 MVLRNKFLVQLKPTELAAVCASLVSEGIKVRPGRNNSYIFEPSRTVINMINFLEEQRNSL 1077

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
             +LQEKHGV I CCLDSQFSGMVEAWASGLTWRE+MMDCA+D+GDLARLLRRTIDLLAQI
Sbjct: 1078 EDLQEKHGVNISCCLDSQFSGMVEAWASGLTWREIMMDCAMDEGDLARLLRRTIDLLAQI 1137

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            PKLPD+D  LQ+NA  AS+VM+RPPISELAG
Sbjct: 1138 PKLPDIDPSLQRNASTASDVMNRPPISELAG 1168

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452156|ref|XP_004143826.1| PREDICTED: LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase ISE2, chloroplastic-like [Cucumis sativus]

 Score =  253 bits (646), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 120/151 (79%), Positives = 135/151 (89%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLRNK L+ LKP +LAAVCASLVSEGIKVR  +NNSYI+EPS TVIN+IN L+E R+S 
Sbjct: 1043 MVLRNKFLVQLKPTELAAVCASLVSEGIKVRPGRNNSYIFEPSRTVINMINFLEEQRNSL 1102

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
             +LQEKHGV I CCLDSQFSGMVEAWASGLTWRE+MMDCA+D+GDLARLLRRTIDLLAQI
Sbjct: 1103 EDLQEKHGVNISCCLDSQFSGMVEAWASGLTWREIMMDCAMDEGDLARLLRRTIDLLAQI 1162

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            PKLPD+D  LQ+NA  AS+VM+RPPISELAG
Sbjct: 1163 PKLPDIDPSLQRNASTASDVMNRPPISELAG 1193

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357138189|ref|XP_003570680.1| PREDICTED: DEAD-box ATP-dependent RNA helicase ISE2, chloroplastic-like [Brachypodium distachyon]

 Score =  250 bits (639), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 118/151 (78%), Positives = 135/151 (89%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            MVLRNK+LLDLKP+QLAAVC SLVSEGIK+R WKN+SY+YEPS+ V  VIN LDE R+S 
Sbjct: 1018 MVLRNKVLLDLKPSQLAAVCGSLVSEGIKLRPWKNSSYVYEPSSVVTGVINYLDEQRNSL 1077

Query: 61   LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI 120
            +ELQEKHGV+IPC +D+QF+GMVEAWASGLTWRE+MMD A+DDGDLARLLRRT+DLLAQI
Sbjct: 1078 IELQEKHGVKIPCEIDTQFAGMVEAWASGLTWREIMMDSAMDDGDLARLLRRTMDLLAQI 1137

Query: 121  PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
            PKLPD+D  LQKNA  A NVMDR P+SELAG
Sbjct: 1138 PKLPDIDPVLQKNAQIACNVMDRVPLSELAG 1168

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	151
TAIR|locus:2020573	1171	EMB25 "EMBRYO DEFECTIVE 25" [A	1.0	0.128	0.668	1.1e-49

TAIR|locus:2020573 EMB25 "EMBRYO DEFECTIVE 25" [Arabidopsis thaliana (taxid:3702)]

 Score = 528 (190.9 bits), Expect = 1.1e-49, P = 1.1e-49
 Identities = 101/151 (66%), Positives = 121/151 (80%)

Query:     1 MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
             MVLRNK L+DLKP QLA VCASLVSEGIKVR W++N+YIYEPS TV++++N L++ RSS 
Sbjct:  1021 MVLRNKALVDLKPPQLAGVCASLVSEGIKVRPWRDNNYIYEPSDTVVDMVNFLEDQRSSL 1080

Query:    61 LELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMXXXXXXXXXXXXXXXTIDLLAQI 120
             ++LQEKH V IPCCLD QFSGMVEAWASGL+W+EMMM               TIDLLAQI
Sbjct:  1081 IKLQEKHEVMIPCCLDVQFSGMVEAWASGLSWKEMMMECAMDEGDLARLLRRTIDLLAQI 1140

Query:   121 PKLPDVDQRLQKNAVDASNVMDRPPISELAG 151
             PKLPD+D  LQ++A  A+++MDRPPISELAG
Sbjct:  1141 PKLPDIDPVLQRSAAAAADIMDRPPISELAG 1171


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.133   0.394    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      151       136   0.00091  102 3  11 22  0.41    31
                                                     30  0.45    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  593 (63 KB)
  Total size of DFA:  140 KB (2086 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  12.40u 0.11s 12.51t   Elapsed:  00:00:01
  Total cpu time:  12.40u 0.11s 12.51t   Elapsed:  00:00:01
  Start:  Sat May 11 14:17:01 2013   End:  Sat May 11 14:17:02 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP

GO:0010497 "plasmodesmata-mediated intercellular transport" evidence=NAS;IMP

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0016441 "posttranscriptional gene silencing" evidence=IMP

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0016556 "mRNA modification" evidence=RCA

---

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)
B9DFG3	ISE2_ARATH	3, ., 6, ., 4, ., 1, 3	0.7483	1.0	0.1289	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00028926001 SubName- Full=Chromosome chr1 scaffold_46, whole genome shotgun sequence; (1064 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	151
pfam08148	178	pfam08148, DSHCT, DSHCT (NUC185) domain	1e-26
COG4581	1041	COG4581, COG4581, Superfamily II RNA helicase [DNA	1e-10

>gnl|CDD|219729 pfam08148, DSHCT, DSHCT (NUC185) domain

 Score = 98.1 bits (245), Expect = 1e-26
 Identities = 37/153 (24%), Positives = 71/153 (46%), Gaps = 11/153 (7%)

Query: 1   MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            +L +    DL P +LAA+ ++ V E       + +   Y PS  +   +N L E     
Sbjct: 27  ELLFSGFFNDLDPEELAALLSAFVFEE------RRDDEGYPPSLELAEALNRLLEIARKL 80

Query: 61  LELQEKHGVEIPCCLDS---QFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLL 117
            +++ +HG++ P  ++        +V  WA G ++ E+  +  L +GD+ R++RR  +LL
Sbjct: 81  AKVEREHGLDEPEYVERFDFGLMEVVYEWARGASFSEICEETDLFEGDIVRVIRRLDELL 140

Query: 118 AQIPK--LPDVDQRLQKNAVDASNVMDRPPISE 148
            Q+        D  L + A +A  ++ R  +  
Sbjct: 141 RQLANAAKIIGDPELAEKAEEAIELIRRDIVFA 173

This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases. Length = 178

>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication, recombination, and repair]

 Score = 57.8 bits (140), Expect = 1e-10
 Identities = 35/157 (22%), Positives = 62/157 (39%), Gaps = 30/157 (19%)

Query: 3    LRNKILLDLKPAQLAAVCASLVSEG-----------IKVRLWKNNSYIYEPSTTVINVIN 51
            + +    DL+P +LAA+ ++ V E            I   L      + E +  +     
Sbjct: 889  IFSGEFNDLEPEELAALLSAFVFEEKTDDGTAEAPEITPALRDALLRLLELARKLN---- 944

Query: 52   VLDEHRSSFLELQEKHGVEIPCCLDSQFSGM---VEAWASGLTWREMMMDCALDDGDLAR 108
                      + Q    +EI   L+    G+   V  WA GL++ ++    +L +G   R
Sbjct: 945  ----------KDQNSSQIEIYPELNDFSVGLMEVVYEWARGLSFADICGLTSLLEGSFVR 994

Query: 109  LLRRTIDLLAQIPKLPDV--DQRLQKNAVDASNVMDR 143
            + RR  +LL Q+ K   V  +  L++ A  A   + R
Sbjct: 995  IFRRLRELLRQLRKAASVIGNPELEEKAYRAIQEIRR 1031

Length = 1041

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	151
PF08148	180	DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961	100.0
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	100.0
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	100.0
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.95
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	90.25
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	88.85
TIGR03643	72	conserved hypothetical protein TIGR03643. This mod	88.02
PF10985	73	DUF2805: Protein of unknown function (DUF2805); In	87.82
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	86.53
PRK04217	110	hypothetical protein; Provisional	86.47
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	82.7
PF13518	52	HTH_28: Helix-turn-helix domain	82.68

>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases []

Probab=100.00  E-value=1.7e-44  Score=275.68  Aligned_cols=142  Identities=29%  Similarity=0.449  Sum_probs=113.3

Q ss_pred             ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCC----CCCCCCCc
Q 043012            2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGV----EIPCCLDS   77 (151)
Q Consensus         2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l----~~~~~~~~   77 (151)
                      |||+|+|++|+|+||||++||||||+++++.  .  ..+.|+..+.++++++.+++++|.++|.+||+    ..+ .++|
T Consensus        28 ~l~~g~f~~L~p~elAa~lS~~v~e~~~~~~--~--~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~~~~~-~~~~  102 (180)
T PF08148_consen   28 LLFSGVFDDLDPAELAALLSCFVYEPRREDE--E--ERYPPSPRLREALEQLQEIAERLAKVEREHGLDEEEYVE-RFDP  102 (180)
T ss_dssp             HHHCTCCCCS-HHHHHHHHHHHC-----SS-------------HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH-CSTT
T ss_pred             HHHcCCCCCCCHHHHHHHHHHhhcccccCcc--c--ccccccHHHHHHHHHHHHHHHHHHHHHHHhCCCCccccc-CCCc
Confidence            7999999999999999999999999997532  1  11223348999999999999999999999999    333 3499


Q ss_pred             hHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC--CCHHHHHHHHHHHhhcCCCcccc
Q 043012           78 QFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD--VDQRLQKNAVDASNVMDRPPISE  148 (151)
Q Consensus        78 ~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~--~~~~L~~k~~~a~~~i~R~iV~~  148 (151)
                      ++|++||+||+|+||.+||+.|+++||||||++||++|+||||+++++  +||+|++|+++|+++|||||||+
T Consensus       103 ~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~aa~~~g~~~L~~~~~~a~~~i~R~iV~~  175 (180)
T PF08148_consen  103 GLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANAAKIIGDPELAEKAREAIDLIRRDIVFA  175 (180)
T ss_dssp             TTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHHHHCCT-HHHHHHHHHHHHHHSHCCCC-
T ss_pred             cHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccCCcccc
Confidence            999999999999999999999999999999999999999999999944  59999999999999999999996

; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=100.00  E-value=3.1e-39  Score=283.00  Aligned_cols=141  Identities=21%  Similarity=0.268  Sum_probs=132.4

Q ss_pred             ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCC-----CCCC
Q 043012            2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIP-----CCLD   76 (151)
Q Consensus         2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~-----~~~~   76 (151)
                      .+|+|.|++|+|+|+||+||||||+++..+.       ..+.+.|...+..+++.+++|++++.+|++++.     .+|+
T Consensus       890 liFnG~Fndl~~eq~aaLLSCfVf~eks~e~-------~~l~~el~~~l~~lqe~ArrIAkVs~ecKlEide~~Yv~sFk  962 (1041)
T KOG0948|consen  890 LIFNGIFNDLPVEQAAALLSCFVFQEKSSEA-------PKLKEELAGPLRQLQESARRIAKVSKECKLEIDEEDYVESFK  962 (1041)
T ss_pred             HHHhccccCCCHHHHHHHHhheeehhccccc-------ccchHHHHHHHHHHHHHHHHHHHHHHhhccccCHHHHHHhcC
Confidence            4799999999999999999999999997531       346789999999999999999999999999986     5799


Q ss_pred             chHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC--CCHHHHHHHHHHHhhcCCCccccc
Q 043012           77 SQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD--VDQRLQKNAVDASNVMDRPPISEL  149 (151)
Q Consensus        77 ~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~--~~~~L~~k~~~a~~~i~R~iV~~~  149 (151)
                      |.+|++||+|++|+||.+||++|+++||+|||++|||+|||||+.+||+  +|.+|.+|++.++.+|+||||||.
T Consensus       963 p~LMdvVy~W~~GatF~eIckmTdvfEGSiIR~~RRLeElLrQl~~AAk~iGnteLe~Kf~~~~~~ikRDIVFAa 1037 (1041)
T KOG0948|consen  963 PELMDVVYAWAKGATFAEICKMTDVFEGSIIRTFRRLEELLRQLIDAAKVIGNTELENKFEEAIKKIKRDIVFAA 1037 (1041)
T ss_pred             hHHHHHHHHHHccccHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHhhceeehh
Confidence            9999999999999999999999999999999999999999999999997  399999999999999999999984

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=100.00  E-value=5.9e-35  Score=260.70  Aligned_cols=143  Identities=22%  Similarity=0.327  Sum_probs=132.9

Q ss_pred             CccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCC------CC
Q 043012            1 MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIP------CC   74 (151)
Q Consensus         1 ~~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~------~~   74 (151)
                      ++||++.|.+|+|+|+||+||+||||+++.       .++..++.+.++-+.+.+++.++.+++..|++.++      ..
T Consensus      1095 eli~dn~l~~l~peeiaallSslV~e~~~e-------~~~~~~~~l~k~~e~v~~v~~rl~ev~~~~~~~~~~~e~f~~~ 1167 (1248)
T KOG0947|consen 1095 ELIFDNALVDLSPEEIAALLSSLVCEGKTE-------RPPTLTPYLKKGKERVRDVAKRLEEVQSSHQLLQTPEEEFPCE 1167 (1248)
T ss_pred             HHHHhhhhhhcCHHHHHHHHHHHHhcCccc-------cCCCCChhhhhHHHHHHHHHHHHHHHHHhhccccCchhhcccc
Confidence            379999999999999999999999999863       23456889999999999999999999999998764      56


Q ss_pred             CCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCC--CHHHHHHHHHHHhhcCCCcccccC
Q 043012           75 LDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDV--DQRLQKNAVDASNVMDRPPISELA  150 (151)
Q Consensus        75 ~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~--~~~L~~k~~~a~~~i~R~iV~~~~  150 (151)
                      ++|+||++||+||+|.||.+||++|++.||+|||+|+||+|+|||+++|+.+  ||.|.+||++|.++|||||||++.
T Consensus      1168 lrF~l~evVYeWA~G~sf~eim~~t~~~EG~iVR~I~RLdE~cre~~~aa~ivGd~~L~~Km~~as~~ikRdIVFaaS 1245 (1248)
T KOG0947|consen 1168 LRFGLVEVVYEWARGLSFKEIMELTDVLEGLIVRLIQRLDEVCRELRNAARIVGDPVLHEKMEAASALIKRDIVFAAS 1245 (1248)
T ss_pred             ccccHHHHHHHHHcCCCHHHHHhhhCCcchhHHHHHHHHHHHHHhhhccceecCcHHHHHHHHHHHHHhccCccchhh
Confidence            8999999999999999999999999999999999999999999999999874  999999999999999999999874

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=99.95  E-value=1.5e-27  Score=217.27  Aligned_cols=144  Identities=23%  Similarity=0.257  Sum_probs=131.1

Q ss_pred             ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCCC---CCCch
Q 043012            2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIPC---CLDSQ   78 (151)
Q Consensus         2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~~---~~~~~   78 (151)
                      |+++|.|++|+|+++||++||||||+++++..   ...+.+++.++++...+.+++.+|.+++..|+++++.   .+.++
T Consensus       888 ~i~~g~f~~l~p~e~aallSa~v~e~~~~d~~---~~~~~~~~~l~~~~~~l~e~~~kl~~~~~~~~i~~~~~l~~~~~~  964 (1041)
T COG4581         888 LIFSGEFNDLEPEELAALLSAFVFEEKTDDGT---AEAPEITPALRDALLRLLELARKLNKDQNSSQIEIYPELNDFSVG  964 (1041)
T ss_pred             HHHcCCccCCCHHHHHHHHHheeeccCCcccc---cccccCCHHHHhHHHHHHHHHHHHHHHHHhcCCcCCccccccccc
Confidence            68999999999999999999999999875320   1234568999999999999999999999999999864   46689


Q ss_pred             HHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCC--CHHHHHHHHHHHhhcCCCcccc
Q 043012           79 FSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDV--DQRLQKNAVDASNVMDRPPISE  148 (151)
Q Consensus        79 l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~--~~~L~~k~~~a~~~i~R~iV~~  148 (151)
                      +|++||.||+|.+|.+|+.+|++.|||+||+++|+.|+|+|+.+++..  |++|.+|++.++..|||||||.
T Consensus       965 lm~vv~~wa~g~s~~~i~~~~~~~eGs~vR~~~r~~ell~ql~~aa~~ig~~~L~~k~~~~~~~irr~iv~~ 1036 (1041)
T COG4581         965 LMEVVYEWARGLSFADICGLTSLLEGSFVRIFRRLRELLRQLRKAASVIGNPELEEKAYRAIQEIRRDIVFV 1036 (1041)
T ss_pred             HHHHHHHHHhhcchhhhhcCCcccccchhhhhhHHHHHHHHhhhcccccCCHHHHHHHHHHHHhhhcCeEec
Confidence            999999999999999999999999999999999999999999999874  8999999999999999999985

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=90.25  E-value=1.6  Score=25.36  Aligned_cols=44  Identities=18%  Similarity=0.245  Sum_probs=35.8

Q ss_pred             CCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHh
Q 043012           75 LDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLA  118 (151)
Q Consensus        75 ~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLr  118 (151)
                      +++.-..++..+..|.|..+|.+..+++.+.+=+.++|+..-|+
T Consensus         4 l~~~e~~i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421        4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            34444556777899999999999999999999999998855543

lux regulon (activates the bioluminescence operon

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=88.85  E-value=1.6  Score=25.70  Aligned_cols=37  Identities=22%  Similarity=0.377  Sum_probs=32.4

Q ss_pred             HHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012           83 VEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ  119 (151)
Q Consensus        83 v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ  119 (151)
                      ...|-.|.|+.||-+..++++|.+=+..+|..+-||+
T Consensus        14 ~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen   14 RLRYFEGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HHHHTST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            3677899999999999999999999999999888874

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>TIGR03643 conserved hypothetical protein TIGR03643

Probab=88.02  E-value=0.83  Score=29.86  Aligned_cols=30  Identities=17%  Similarity=0.479  Sum_probs=27.8

Q ss_pred             HHhhCCCCHHHHHhhcCCChhHHHHHHHHH
Q 043012           84 EAWASGLTWREMMMDCALDDGDLARLLRRT  113 (151)
Q Consensus        84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl  113 (151)
                      -+|.+-.||..|-...++.|++++..+|+-
T Consensus         8 MAweDRtpFeaI~~~fGL~E~eVi~lMR~~   37 (72)
T TIGR03643         8 MAWEDRTPFEAIEQQFGLSEKEVIKLMRQN   37 (72)
T ss_pred             HHHccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            689999999999999999999999998863

This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.

>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family

Probab=87.82  E-value=0.85  Score=29.90  Aligned_cols=30  Identities=17%  Similarity=0.478  Sum_probs=27.8

Q ss_pred             HHhhCCCCHHHHHhhcCCChhHHHHHHHHH
Q 043012           84 EAWASGLTWREMMMDCALDDGDLARLLRRT  113 (151)
Q Consensus        84 ~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl  113 (151)
                      -+|.+-.||..|-...++.|.+++..+|+-
T Consensus         7 MAweDRtpFeaI~~qfGl~E~eVi~lMR~~   36 (73)
T PF10985_consen    7 MAWEDRTPFEAIERQFGLSEKEVIKLMRKE   36 (73)
T ss_pred             HHHccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            689999999999999999999999998863

Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=86.53  E-value=3.4  Score=24.09  Aligned_cols=35  Identities=17%  Similarity=0.213  Sum_probs=30.2

Q ss_pred             HHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012           81 GMVEAWASGLTWREMMMDCALDDGDLARLLRRTID  115 (151)
Q Consensus        81 ~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e  115 (151)
                      .+++.+..|.|..+|.+..+++++.+-+.++|+..
T Consensus         7 ~i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~~   41 (57)
T cd06170           7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMR   41 (57)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45666889999999999999999999999888744

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PRK04217 hypothetical protein; Provisional

Probab=86.47  E-value=3.2  Score=29.34  Aligned_cols=50  Identities=18%  Similarity=0.101  Sum_probs=42.2

Q ss_pred             CCCCchHHHHHHHhh-CCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCC
Q 043012           73 CCLDSQFSGMVEAWA-SGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPK  122 (151)
Q Consensus        73 ~~~~~~l~~~v~~Wa-~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~  122 (151)
                      ..++..--+++..+. .|.|+.+|.+..+++.+++-+.++|....|++.-.
T Consensus        41 ~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~   91 (110)
T PRK04217         41 IFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLV   91 (110)
T ss_pred             ccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            345555567788886 99999999999999999999999999999988543

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=82.70  E-value=5.1  Score=22.58  Aligned_cols=31  Identities=19%  Similarity=0.377  Sum_probs=27.8

Q ss_pred             hCCCCHHHHHhhcCCChhHHHHHHHHHHHHH
Q 043012           87 ASGLTWREMMMDCALDDGDLARLLRRTIDLL  117 (151)
Q Consensus        87 a~G~~f~eil~~t~l~EGdiVR~~rRl~elL  117 (151)
                      ..|.+..+|.+..++.++.+-+++.|...-|
T Consensus        24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l   54 (55)
T cd06171          24 GEGLSYEEIAEILGISRSTVRQRLHRALKKL   54 (55)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence            4999999999999999999999999876654

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>PF13518 HTH_28: Helix-turn-helix domain

Probab=82.68  E-value=4.8  Score=23.39  Aligned_cols=35  Identities=20%  Similarity=0.378  Sum_probs=31.1

Q ss_pred             HHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH
Q 043012           81 GMVEAWASGLTWREMMMDCALDDGDLARLLRRTID  115 (151)
Q Consensus        81 ~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e  115 (151)
                      .+|..+.+|.|..++....+++...+-+|+++-.+
T Consensus         4 ~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~   38 (52)
T PF13518_consen    4 QIVELYLEGESVREIAREFGISRSTVYRWIKRYRE   38 (52)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence            46677779999999999999999999999998765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	151
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	6e-27
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	2e-26
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	3e-25

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score =  104 bits (260), Expect = 6e-27
 Identities = 21/150 (14%), Positives = 57/150 (38%), Gaps = 14/150 (9%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
             ++ N    +LKP Q AA+ +    +       +    + EP   +  +        +  
Sbjct: 858  ELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREI-------AAKI 910

Query: 61   LELQEKHGVEIP-----CCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115
             ++ +   +E+           +   +V  W  G T+ ++     + +G L R+ +R  +
Sbjct: 911  AKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEE 970

Query: 116  LLAQIPKLPDV--DQRLQKNAVDASNVMDR 143
            L+ ++  + +   +  L++       ++ R
Sbjct: 971  LVKELVDVANTIGNSSLKEKMEAVLKLIHR 1000

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae} Length = 1108

 Score =  102 bits (256), Expect = 2e-26
 Identities = 20/150 (13%), Positives = 55/150 (36%), Gaps = 14/150 (9%)

Query: 1    MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
             ++ N    +LKP Q AA+ +    +                   +   +  + E  +  
Sbjct: 956  ELIFNGNFNELKPEQAAALLSCFAFQE-------RCKEAPRLKPELAEPLKAMREIAAKI 1008

Query: 61   LELQEKHGVEIPC-----CLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTID 115
             ++ +   +E+           +   +V  W  G T+ ++     + +G L R+ +R  +
Sbjct: 1009 AKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEE 1068

Query: 116  LLAQIPKLPDV--DQRLQKNAVDASNVMDR 143
            L+ ++  + +   +  L++       ++ R
Sbjct: 1069 LVKELVDVANTIGNSSLKEKMEAVLKLIHR 1098

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A Length = 997

 Score = 99.5 bits (247), Expect = 3e-25
 Identities = 21/152 (13%), Positives = 53/152 (34%), Gaps = 14/152 (9%)

Query: 1   MVLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSF 60
            ++ +  L   +P ++ A+ +  V EG               +  +      ++E     
Sbjct: 841 ELILDNFLGSFEPEEIVALLSVFVYEG-----KTREEEPPIVTPRLAKGKQRIEEIYKKM 895

Query: 61  LELQEKHGVEIPCC-------LDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRT 113
           L +   H + +                 +V  WA GL+++E+M      +G + R++   
Sbjct: 896 LCVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWL 955

Query: 114 IDLLAQIPKLPDV--DQRLQKNAVDASNVMDR 143
            ++  ++     +  +  L      A  ++ R
Sbjct: 956 DEICREVKTASIIIGNSTLHMKMSRAQELIKR 987

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	151
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	92.37
3idw_A	72	Actin cytoskeleton-regulatory complex protein SLA;	88.73
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	86.21
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	84.65
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	80.76
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	80.56
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	80.5

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=100.00  E-value=1.5e-41  Score=311.18  Aligned_cols=143  Identities=15%  Similarity=0.220  Sum_probs=132.8

Q ss_pred             ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCC-------CC
Q 043012            2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIP-------CC   74 (151)
Q Consensus         2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~-------~~   74 (151)
                      |||+|+|++|+|+||||+|||||||+|+.+.    . .+.+++.|.+++.++++++.+|++++.+|+++++       ..
T Consensus       842 ~~~~~~~~~l~~~~~~a~ls~~v~~~~~~~~----~-~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~  916 (997)
T 4a4z_A          842 LILDNFLGSFEPEEIVALLSVFVYEGKTREE----E-PPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDR  916 (997)
T ss_dssp             HHHSSGGGGCCHHHHHHHHGGGSCCCCCSSC----C-CCCSSHHHHHHHHHHHHHHHHHHHHHHHTTCCCCHHHHHGGGS
T ss_pred             HHHhCcccCCCHHHHHHHHhhhhccccCCCC----C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCccchhhhccC
Confidence            7999999999999999999999999987321    1 2357899999999999999999999999999885       46


Q ss_pred             CCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC--CCHHHHHHHHHHHhhcCCCccccc
Q 043012           75 LDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD--VDQRLQKNAVDASNVMDRPPISEL  149 (151)
Q Consensus        75 ~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~--~~~~L~~k~~~a~~~i~R~iV~~~  149 (151)
                      ++|+||++||+||+|+||++||++|+++|||||||||||+|+||||++|++  +|++|++||++|+++|||||||+-
T Consensus       917 ~~~~l~~~v~~Wa~g~~f~~i~~~t~~~eG~~vR~~~rl~e~~~q~~~aa~~~g~~~l~~k~~~a~~~i~R~iv~~~  993 (997)
T 4a4z_A          917 KRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAA  993 (997)
T ss_dssp             CTTTTHHHHHHHHHTCCHHHHHHTCSSCHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCGGGGCC
T ss_pred             CChHHHHHHHHHhCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcCCeeecc
Confidence            899999999999999999999999999999999999999999999999996  499999999999999999999973

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.7e-41  Score=309.94  Aligned_cols=141  Identities=15%  Similarity=0.264  Sum_probs=132.5

Q ss_pred             ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCC-----CCCC
Q 043012            2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIP-----CCLD   76 (151)
Q Consensus         2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~-----~~~~   76 (151)
                      |||+|+|++|+|+||||++||||||+++++      . +.+++.|.++++++++++.+|.++|.+|+++++     ..++
T Consensus       859 ~~~~g~~~~l~p~~~aa~~s~~v~~~~~~~------~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  931 (1010)
T 2xgj_A          859 LIFNGNFNELKPEQAAALLSCFAFQERCKE------A-PRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFR  931 (1010)
T ss_dssp             HHHHTTTTTCCHHHHHHHHHHHHCCCCCSC------C-CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCHHHHHHTSC
T ss_pred             HHHcCccCCCCHHHHHHHHeeeEeecCCCC------C-CCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCChhHhcccCC
Confidence            799999999999999999999999998632      1 345699999999999999999999999999988     5899


Q ss_pred             chHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCC--CHHHHHHHHHHHhhcCCCccccc
Q 043012           77 SQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDV--DQRLQKNAVDASNVMDRPPISEL  149 (151)
Q Consensus        77 ~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~--~~~L~~k~~~a~~~i~R~iV~~~  149 (151)
                      |+||++||+||+|+||++||++|+++|||||||||||+||||||++|+++  |++|++||++|+++|||||||+-
T Consensus       932 ~~l~~~v~~Wa~g~~~~~i~~~t~~~eG~~vR~~~rl~ell~q~~~a~~~~g~~~l~~~~~~a~~~i~R~iv~~~ 1006 (1010)
T 2xgj_A          932 HELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAG 1006 (1010)
T ss_dssp             CTTHHHHHHHTTTCCHHHHTTSCSSCHHHHHHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSCGGGGCC
T ss_pred             hHHHHHHHHHhCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHhccCCeEecc
Confidence            99999999999999999999999999999999999999999999999874  99999999999999999999973

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.8e-41  Score=311.17  Aligned_cols=141  Identities=15%  Similarity=0.267  Sum_probs=109.5

Q ss_pred             ccccCCCCCCCHHHHHHHHHHhhccccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcCCCCC-----CCCC
Q 043012            2 VLRNKILLDLKPAQLAAVCASLVSEGIKVRLWKNNSYIYEPSTTVINVINVLDEHRSSFLELQEKHGVEIP-----CCLD   76 (151)
Q Consensus         2 ~L~~g~f~~L~p~elAAllS~~v~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~l~~~-----~~~~   76 (151)
                      |||+|+|++|+|+||||+|||||||+++++.       +.+++.|.+++..+++++.+|+++|.+|+++++     ..|+
T Consensus       957 ~~~~~~~~~l~~~~~aa~~s~~v~~~~~~~~-------~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 1029 (1108)
T 3l9o_A          957 LIFNGNFNELKPEQAAALLSCFAFQERCKEA-------PRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFR 1029 (1108)
T ss_dssp             HHHHHCCCSSCCTHHHHHTCC-------------------------CHHHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHC
T ss_pred             HHHhCcccCCCHHHHHHHHhheeeecccCCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCChHHhccCCC
Confidence            7999999999999999999999999987431       235788999999999999999999999999986     3589


Q ss_pred             chHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCCC--CHHHHHHHHHHHhhcCCCccccc
Q 043012           77 SQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPDV--DQRLQKNAVDASNVMDRPPISEL  149 (151)
Q Consensus        77 ~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~~--~~~L~~k~~~a~~~i~R~iV~~~  149 (151)
                      |+||++||+||+|+||++||++|+++|||||||||||+|+||||++|+++  |++|.+||++|+++|||||||+-
T Consensus      1030 ~~l~~~v~~Wa~g~~f~~i~~~t~~~eG~~vR~~~rl~e~l~q~~~aa~~~g~~~l~~k~~~a~~~i~r~iv~~~ 1104 (1108)
T 3l9o_A         1030 HELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAG 1104 (1108)
T ss_dssp             CSCHHHHHHHHC----CCGGGTC--CHHHHHHHHHHHHHHHSCCCC----CCCHHHHHHHHHHHHHHHHHTCCCC
T ss_pred             hHHHHHHHHHhCCCCHHHHHhcCCCCchhhhhHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHhcCCEEeec
Confidence            99999999999999999999999999999999999999999999999974  99999999999999999999974

>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A

Probab=92.37  E-value=0.15  Score=36.11  Aligned_cols=53  Identities=15%  Similarity=0.179  Sum_probs=46.6

Q ss_pred             CCCCCchHHHHHHHh-hCCCCHHHHHhhcCC-ChhHHHHHHHHHHHHHhhcCCCC
Q 043012           72 PCCLDSQFSGMVEAW-ASGLTWREMMMDCAL-DDGDLARLLRRTIDLLAQIPKLP  124 (151)
Q Consensus        72 ~~~~~~~l~~~v~~W-a~G~~f~eil~~t~l-~EGdiVR~~rRl~elLrQl~~a~  124 (151)
                      |..+++.+++-+..+ +.|.|+.+||...+| +.-+|=||+.+=.|+..++..|-
T Consensus        10 Ptk~t~e~~e~I~~~i~~G~sl~~i~~~~~~ps~~T~~~W~~~~~ef~e~~~~Ar   64 (140)
T 4dyq_A           10 PSDYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKYAKAT   64 (140)
T ss_dssp             CCSCCTTHHHHHHHHHHTTCCHHHHHTSTTCCCHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHCCCcHHHHHhcCCCCCHHHHHHHHHcCHHHHHHHHHHH
Confidence            568889999888777 899999999999999 79999999999888888777663

>3idw_A Actin cytoskeleton-regulatory complex protein SLA; clathrin adaptor, endocytosis, SAM domain, yeast, actin-BIND membrane, endosome; 1.85A {Saccharomyces cerevisiae}

Probab=88.73  E-value=0.4  Score=30.47  Aligned_cols=26  Identities=19%  Similarity=0.451  Sum_probs=21.1

Q ss_pred             HHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012           94 EMMMDCALDDGDLARLLRRTIDLLAQ  119 (151)
Q Consensus        94 eil~~t~l~EGdiVR~~rRl~elLrQ  119 (151)
                      ++|..-++.||||+|.++.++...++
T Consensus        42 ~~Lr~LGi~eGDIIrVmk~l~~k~~r   67 (72)
T 3idw_A           42 SMLRTLGLREGDIVRVMKHLDKKFGR   67 (72)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHcCCchhhHHHHHHHHHHHhCc
Confidence            46667788999999999999876544

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=86.21  E-value=1.5  Score=23.78  Aligned_cols=34  Identities=9%  Similarity=-0.001  Sum_probs=29.4

Q ss_pred             HHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHH
Q 043012           80 SGMVEAWASGLTWREMMMDCALDDGDLARLLRRT  113 (151)
Q Consensus        80 ~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl  113 (151)
                      ..++..+..|.|..+|.+..+++...+-|++++.
T Consensus        12 ~~i~~~~~~g~s~~~IA~~lgis~~Tv~~~~~~~   45 (51)
T 1tc3_C           12 AQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDP   45 (51)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCS
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhhH
Confidence            3666778899999999999999999999988753

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=84.65  E-value=3.7  Score=26.02  Aligned_cols=51  Identities=10%  Similarity=0.028  Sum_probs=40.2

Q ss_pred             CCCchH-HHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCC
Q 043012           74 CLDSQF-SGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLP  124 (151)
Q Consensus        74 ~~~~~l-~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~  124 (151)
                      .+++.+ ..++..+..|.|..+|.+..++....|-||+++....-.+.....
T Consensus        22 ~ys~e~k~~~v~~~~~g~s~~~iA~~~gIs~sTl~rW~k~~~~~~~~~~~~~   73 (87)
T 2elh_A           22 SLTPRDKIHAIQRIHDGESKASVARDIGVPESTLRGWCKNEDKLRFMSRQSA   73 (87)
T ss_dssp             SCCHHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHhccccccCCC
Confidence            455555 455566678999999999999999999999998887766665554

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=80.76  E-value=6.6  Score=23.30  Aligned_cols=47  Identities=11%  Similarity=0.106  Sum_probs=40.5

Q ss_pred             CCCCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhh
Q 043012           73 CCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQ  119 (151)
Q Consensus        73 ~~~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQ  119 (151)
                      ..+++.-..++..+..|.|..+|.+..+++++.+=+.++|+.+-|+.
T Consensus        10 ~~L~~~e~~il~~~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   56 (74)
T 1fse_A           10 PLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGV   56 (74)
T ss_dssp             CCCCHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            45667777888778999999999999999999999999988877764

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=80.56  E-value=1.4  Score=38.41  Aligned_cols=71  Identities=10%  Similarity=0.064  Sum_probs=53.4

Q ss_pred             hHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcCCCCC--CCHHHHHHHHHHHhhcCCCcccc
Q 043012           78 QFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIPKLPD--VDQRLQKNAVDASNVMDRPPISE  148 (151)
Q Consensus        78 ~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~~a~~--~~~~L~~k~~~a~~~i~R~iV~~  148 (151)
                      ...-+.++|.++.++.+|++..+++.||+........-+++.+...+.  ....+...+.+-...|..|+-.+
T Consensus       583 k~~~ll~~~~~~~~~~~i~~~y~~~~gdl~~l~~~a~~l~~a~~~i~~~~~~~~~~~~l~~l~~rl~~gv~~e  655 (715)
T 2va8_A          583 KVALIMKDWMDEVDEDTILSKYNIGSGDLRNMVETMDWLTYSAYHLSRELKLNEHADKLRILNLRVRDGIKEE  655 (715)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCCGG
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHcCCChh
Confidence            356677999999999999999999999999988877777777655543  25566666666666666555443

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=80.50  E-value=6.3  Score=23.14  Aligned_cols=48  Identities=17%  Similarity=0.181  Sum_probs=38.8

Q ss_pred             CCCchHHHHHH-HhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012           74 CLDSQFSGMVE-AWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP  121 (151)
Q Consensus        74 ~~~~~l~~~v~-~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~  121 (151)
                      .+++.--.++. .+..|.|+.+|.+..+++++.+=+.+.|...-|++.-
T Consensus        15 ~L~~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l   63 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLADA   63 (70)
T ss_dssp             SSCHHHHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC--
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            34455556664 4699999999999999999999999999999888754

---

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	Length	Definition	Probability
Query	151
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	84.05
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	83.04
d2p6ra2	198	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	81.93

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=84.05  E-value=1.3  Score=25.47  Aligned_cols=46  Identities=11%  Similarity=0.118  Sum_probs=37.5

Q ss_pred             CCchHHHHH-HHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhc
Q 043012           75 LDSQFSGMV-EAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQI  120 (151)
Q Consensus        75 ~~~~l~~~v-~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl  120 (151)
                      +++.--.++ ..+-.|.|+.||.+..+++++.+=+.+.|...-||+.
T Consensus        22 L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~   68 (71)
T d1rp3a2          22 LPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALERLREM   68 (71)
T ss_dssp             SCHHHHHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhHhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            334455555 5578999999999999999999999999988888764

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=83.04  E-value=1.2  Score=29.10  Aligned_cols=64  Identities=16%  Similarity=0.226  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCchHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHH--HHhhcCC
Q 043012           56 HRSSFLELQEKHGVEIPCCLDSQFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTID--LLAQIPK  122 (151)
Q Consensus        56 ~~~~l~~~~~~~~l~~~~~~~~~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~e--lLrQl~~  122 (151)
                      +...+..+.+.+|++.+   ...+....+..-.+.|+.+|.+.++++-|.+=+.+++|.+  ++....+
T Consensus        11 ~~~~~~~~~~~~Gl~~~---~~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~   76 (151)
T d1ku9a_          11 IIELFSELAKIHGLNKS---VGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWI   76 (151)
T ss_dssp             HHHHHHHHHHHTTCCHH---HHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHHHHHcCCCHH---HHHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEEc
Confidence            44556666788998732   1234444444444578999999999999999999999998  6654443

>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: Sec63 N-terminal domain-like
superfamily: Sec63 N-terminal domain-like
family: Achaeal helicase C-terminal domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=81.93  E-value=1.4  Score=31.32  Aligned_cols=44  Identities=16%  Similarity=0.234  Sum_probs=35.1

Q ss_pred             hHHHHHHHhhCCCCHHHHHhhcCCChhHHHHHHHHHHHHHhhcC
Q 043012           78 QFSGMVEAWASGLTWREMMMDCALDDGDLARLLRRTIDLLAQIP  121 (151)
Q Consensus        78 ~l~~~v~~Wa~G~~f~eil~~t~l~EGdiVR~~rRl~elLrQl~  121 (151)
                      ..+-+++.|.++.|..+|.+..++..||+=+......=++..+.
T Consensus        74 KtAl~L~dwi~E~~~~~I~~~y~v~~Gdl~~~~~~a~wl~~~~~  117 (198)
T d2p6ra2          74 KTALCLKDWIEEKDEDEICAKYGIAPGDLRRIVETAEWLSNAMN  117 (198)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCcHHHHHHHHHHHHHHHHHH
Confidence            55677899999999999999999999999766655555554443