Psyllid ID: psy6286

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------16
Protein Sequence
MSLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHcccccccccccccEEEEEEcccccHHHHHHccHHHHHHHHHHHHHHHcccccHHHHHHcccccHHHHHHHHHccccHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHccccEEEEccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHccccccccEEEEEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccHHHHHHHHHHHccccHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MSLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTINDKLELARHIARISIESkldldedsyvnqfkpslMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL
Flexible Loop (DISEMBL)
msllhmeeLKCRKRVLRRLGyateadviemkgrvacelskseeTVILTINDKLELARHIARISIeskldldedsYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRnigntlleekfneaiktvkrdIFLEILENL
Low Complexity Region (SEG)
MSLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL
Disordered region (IsUnstruct)
********LKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEIL***
Disordered Region (DISOPRED)
MSLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILEN*
Disordered Region (DISEMBL)
MSLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL
Disordered Region (DISPRO)
*SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL
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	159	2.2.26 [Sep-21-2011]
P42285	1042	Superkiller viralicidic a	yes	N/A	0.943	0.143	0.492	1e-45
Q9CZU3	1040	Superkiller viralicidic a	yes	N/A	0.943	0.144	0.492	1e-45
O14232	1117	ATP-dependent RNA helicas	yes	N/A	0.937	0.133	0.440	2e-38
Q23223	1026	mRNA transport homolog 4	yes	N/A	0.943	0.146	0.421	4e-35
O13799	1030	Uncharacterized helicase	no	N/A	0.955	0.147	0.355	1e-27
P47047	1073	ATP-dependent RNA helicas	yes	N/A	0.830	0.123	0.346	2e-24
Q15477	1246	Helicase SKI2W OS=Homo sa	no	N/A	0.905	0.115	0.266	7e-13
O59801	1213	Putative ATP-dependent RN	no	N/A	0.918	0.120	0.269	4e-12
P35207	1287	Antiviral helicase SKI2 O	no	N/A	0.534	0.066	0.329	1e-07

>sp|P42285|SK2L2_HUMAN Superkiller viralicidic activity 2-like 2 OS=Homo sapiens GN=SKIV2L2 PE=1 SV=3

 Score =  181 bits (460), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 94/191 (49%), Positives = 125/191 (65%), Gaps = 41/191 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTI------ND---- 51
            ++L M+ELKCRKRVLRRLG+AT +DVIEMKGRVACE+S ++E ++  +      ND    
Sbjct: 844  TVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAE 903

Query: 52   -------------------KL------------ELARHIARISIESKLDLDEDSYVNQFK 80
                               KL            E A+ IA++S E+KL++DE++Y++ FK
Sbjct: 904  QATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFK 963

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P LMDVV+ W  GA+F  +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF
Sbjct: 964  PHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKF 1023

Query: 141  NEAIKTVKRDI 151
             E I  +KRDI
Sbjct: 1024 AEGITKIKRDI 1034

May be involved in pre-mRNA splicing. Associated with the RNA exosome complex and involved in the 3'processing of the 7S pre-RNA to the mature 5.8S rRNA.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q9CZU3|SK2L2_MOUSE Superkiller viralicidic activity 2-like 2 OS=Mus musculus GN=Skiv2l2 PE=2 SV=1

 Score =  181 bits (460), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 94/191 (49%), Positives = 125/191 (65%), Gaps = 41/191 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILTI------ND---- 51
            ++L M+ELKCRKRVLRRLG+AT +DVIEMKGRVACE+S ++E ++  +      ND    
Sbjct: 842  TVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSSE 901

Query: 52   -------------------KL------------ELARHIARISIESKLDLDEDSYVNQFK 80
                               KL            E A+ IA++S E+KL++DE++Y++ FK
Sbjct: 902  QATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFK 961

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P LMDVV+ W  GA+F  +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF
Sbjct: 962  PHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKF 1021

Query: 141  NEAIKTVKRDI 151
             E I  +KRDI
Sbjct: 1022 AEGITKIKRDI 1032

May be involved in pre-mRNA splicing. Associated with the RNA exosome complex and involved in the 3'processing of the 7S pre-RNA to the mature 5.8S rRNA.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O14232|MTR4_SCHPO ATP-dependent RNA helicase mtr4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mtr4 PE=1 SV=1

 Score =  158 bits (399), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 85/193 (44%), Positives = 118/193 (61%), Gaps = 44/193 (22%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT-------INDKL- 53
            S++ ++EL  RKRVLRRLG+ T  DVIE+KGRVACE+S S + ++LT        ND   
Sbjct: 918  SIMQLDELNSRKRVLRRLGFTTSDDVIEVKGRVACEIS-SGDGLLLTELIFNGMFNDLTP 976

Query: 54   -----------------------------------ELARHIARISIESKLDLDEDSYVNQ 78
                                               E+AR IA++S ESK +L+E+ YVN 
Sbjct: 977  EQCAALLSCLVFQEKSEVENQRMKEELAGPLKILQEMARRIAKVSKESKQELNEEEYVNS 1036

Query: 79   FKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEE 138
            FKPSLM+VV+AW  GASF ++C +TD++EGS+IR  RRLEE++RQ+V A++ IGNT L++
Sbjct: 1037 FKPSLMEVVYAWAHGASFAQICKMTDVYEGSLIRMFRRLEELIRQMVDAAKVIGNTSLQQ 1096

Query: 139  KFNEAIKTVKRDI 151
            K  + I  + RDI
Sbjct: 1097 KMEDTIACIHRDI 1109

Component of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates (By similarity). Required for heterochromatic gene silencing at centromeric repeats by either exosome- or RNAi-mediated degradation of heterochromatic transcripts.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q23223|MTR4_CAEEL mRNA transport homolog 4 OS=Caenorhabditis elegans GN=mtr-4 PE=3 SV=1

 Score =  147 bits (370), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 80/190 (42%), Positives = 109/190 (57%), Gaps = 40/190 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVI--------------- 46
            S LH+EEL  RKRVLRRLGY    D + +KG VACELS S+E ++               
Sbjct: 829  STLHLEELNNRKRVLRRLGYLGNDDALVLKGSVACELSASDELILTEMLLKGIFNTLDVA 888

Query: 47   --------LTINDKL-----------------ELARHIARISIESKLDLDEDSYVNQFKP 81
                        DK                  E AR++A++S E K+++ ED YV+ F P
Sbjct: 889  QTAALLSCFVFQDKCAAPKLATELQTCLSELHEQARNVAKVSNECKMEVMEDKYVSSFNP 948

Query: 82   SLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFN 141
             LMDVV+ W  GA+F ++   TD+FEGSIIR +RRLEEVLR+++ A++ + N  LE+KF 
Sbjct: 949  GLMDVVYQWVNGATFSEIVKTTDVFEGSIIRTLRRLEEVLREMINAAKALANKELEQKFE 1008

Query: 142  EAIKTVKRDI 151
            +A K +KRDI
Sbjct: 1009 DARKNLKRDI 1018

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|O13799|YE02_SCHPO Uncharacterized helicase C17H9.02 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC17H9.02 PE=1 SV=1

 Score =  122 bits (305), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 69/194 (35%), Positives = 109/194 (56%), Gaps = 42/194 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVIL-------------- 47
            +++ + ELK R+RVLRRLG+ T  +VI++KGRVACE++  +E +++              
Sbjct: 831  AIIQLRELKIRQRVLRRLGFCTLENVIDIKGRVACEITSGDELLLVELIFQGFFNQMPPE 890

Query: 48   ------------------TINDK----------LELARHIARISIESKLDLDEDSYVNQF 79
                              T+N K          +E A+ IA +S+ESKL  +E  Y++QF
Sbjct: 891  EIAAALSCFVYEDKSEVSTLNLKEPFKKMYLTIIEAAKRIATVSLESKLQFNESDYLHQF 950

Query: 80   KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEK 139
            KP +M+ V  W  GASF ++C ++ ++EGSI+R  RRL+E+L+QL  A+  +GN  L+EK
Sbjct: 951  KPDIMEPVSLWINGASFQEICIVSKLYEGSIVRTFRRLDELLKQLEHAAIVLGNNELKEK 1010

Query: 140  FNEAIKTVKRDIFL 153
                 + + RDI  
Sbjct: 1011 SVLTEQKLHRDIIF 1024

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|P47047|MTR4_YEAST ATP-dependent RNA helicase DOB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MTR4 PE=1 SV=1

 Score =  111 bits (277), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 60/173 (34%), Positives = 93/173 (53%), Gaps = 41/173 (23%)

Query: 20   GYATEADVIEMKGRVACELSKSEETVI--LTINDKL------------------------ 53
            G+ T  D+IE+KGRVACE+S  +E ++  L  N                           
Sbjct: 893  GFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEA 952

Query: 54   ---------------ELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLK 98
                           E+A  IA+I  +SK+++ E  YV  F+  LM+VV+ WC GA+F +
Sbjct: 953  PRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQ 1012

Query: 99   VCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
            +C +TD++EGS+IR  +RLEE++++LV  +  IGN+ L+EK    +K + RDI
Sbjct: 1013 ICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDI 1065

ATP-dependent RNA helicase required for the 3'-end formation of 5.8S RNA. Cofactor for the exosome complex that unwinds secondary structure in pre-rRNA. Required for nucleocytoplasmic transport of mRNA. May serve as a chaperone which translocates or normalizes the structure of mRNAs in preparation for export. Component of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q15477|SKIV2_HUMAN Helicase SKI2W OS=Homo sapiens GN=SKIV2L PE=1 SV=3

 Score = 73.2 bits (178), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 81/184 (44%), Gaps = 40/184 (21%)

Query: 8    ELKCRKRVLRRLGYATEADVIEMKGRVACELS------------------KSEETVIL-- 47
            E   R  VLR LGY  EA  +++ GRVAC +S                  + EE   L  
Sbjct: 1054 EYHQRVEVLRTLGYVDEAGTVKLAGRVACAMSSHELLLTELMFDNALSTLRPEEIAALLS 1113

Query: 48   ----------------TINDKLE----LARHIARISIESKLDLDEDSYVNQFKPSLMDVV 87
                            T+   +E    +A+ I  + +   L+   + +V +    L++VV
Sbjct: 1114 GLVCQSPGDAGDQLPNTLKQGIERVRAVAKRIGEVQVACGLNQTVEEFVGELNFGLVEVV 1173

Query: 88   HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTV 147
            + W  G  F ++  ++   EG ++RC++RL E+ R L  A+R +G  +L  K   A   +
Sbjct: 1174 YEWARGMPFSELAGLSGTPEGLVVRCIQRLAEMCRSLRGAARLVGEPVLGAKMETAATLL 1233

Query: 148  KRDI 151
            +RDI
Sbjct: 1234 RRDI 1237

Helicase; has ATPase activity. Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C).

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|O59801|SKI2_SCHPO Putative ATP-dependent RNA helicase C550.03c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC550.03c PE=3 SV=1

 Score = 70.5 bits (171), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 93/189 (49%), Gaps = 43/189 (22%)

Query: 6    MEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVI------------------- 46
            + + + R +VL+ LGY      + +KGRVACE++ + E V+                   
Sbjct: 1017 LPDYEQRIKVLQELGYIDAERTVLLKGRVACEINSTSELVLTELILENSLADFSCEETIA 1076

Query: 47   ----LTINDKLE----LARHIAR-----ISIESKLDLDEDSYV-------NQF--KP--S 82
                   ++K E    ++ H+ +     +S+  K++  ++ Y        N F  +P   
Sbjct: 1077 LLSAFVFDEKTEVEPTISPHLQKGKEMILSVAEKVNQIQEHYQVLYFNEGNDFESQPRFG 1136

Query: 83   LMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNE 142
            LM+V + W  G SF ++  +TD+ EGSI+R + RL+EVLR+   A+R +G++ +  K  E
Sbjct: 1137 LMEVCYEWARGMSFNRITDLTDVLEGSIVRTIIRLDEVLRECRGAARVVGDSSMYTKMEE 1196

Query: 143  AIKTVKRDI 151
                ++R+I
Sbjct: 1197 CQNLIRRNI 1205

RNA helicase component of the SKI complex involved in 3'-mRNA degradation pathway.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|P35207|SKI2_YEAST Antiviral helicase SKI2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SKI2 PE=1 SV=2

 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 53/85 (62%)

Query: 67   KLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126
             L  DE  ++++ + ++M+VV+ W  G SF ++  ++   EG+++R +  L+E+ R++  
Sbjct: 1195 PLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKT 1254

Query: 127  ASRNIGNTLLEEKFNEAIKTVKRDI 151
            AS  IGN+ L  K + A + +KRDI
Sbjct: 1255 ASIIIGNSTLHMKMSRAQELIKRDI 1279

RNA helicase component of the SKI complex involved in 3'-mRNA degradation pathway. Represses dsRNA virus propagation by specifically blocking translation of viral mRNAs, perhaps recognizing the absence of CAP or poly(A). Essential for cell growth only in the presence of M1 replicon.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 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	159
156553729	1001	PREDICTED: superkiller viralicidic activ	0.943	0.149	0.554	4e-50
380026691	1022	PREDICTED: superkiller viralicidic activ	0.943	0.146	0.534	5e-49
328792378	1035	PREDICTED: superkiller viralicidic activ	0.943	0.144	0.534	5e-49
332030475	945	Superkiller viralicidic activity 2-like	0.943	0.158	0.528	1e-48
340708607	1079	PREDICTED: superkiller viralicidic activ	0.943	0.139	0.528	2e-48
350413173	1034	PREDICTED: superkiller viralicidic activ	0.943	0.145	0.528	3e-48
307188640	961	Superkiller viralicidic activity 2-like	0.943	0.156	0.523	4e-48
321468914	1034	hypothetical protein DAPPUDRAFT_304340 [	0.955	0.147	0.512	2e-47
157120596	1035	helicase [Aedes aegypti] gi|108874885|gb	0.943	0.144	0.554	5e-47
91092470	1052	PREDICTED: similar to helicase [Triboliu	0.955	0.144	0.497	7e-47

>gi|156553729|ref|XP_001600961.1| PREDICTED: superkiller viralicidic activity 2-like 2-like isoform 1 [Nasonia vitripennis] gi|345497584|ref|XP_003428027.1| PREDICTED: superkiller viralicidic activity 2-like 2-like isoform 2 [Nasonia vitripennis]

 Score =  202 bits (514), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 106/191 (55%), Positives = 134/191 (70%), Gaps = 41/191 (21%)

Query: 2   SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVI-----------LTI- 49
           S+L M+ELKCRKRVLRRL Y T ADVIE+KGRVACEL+ ++E ++           LT+ 
Sbjct: 803 SVLQMDELKCRKRVLRRLAYCTAADVIELKGRVACELNGADELLMTEMIFNGLFNALTVP 862

Query: 50  -----------NDK------------------LELARHIARISIESKLDLDEDSYVNQFK 80
                      +DK                   ++AR IA++S E+ L+LDEDSYV +FK
Sbjct: 863 QMTALISCFVCDDKSSETPKSIDELSGPLRQMQDIARRIAKVSTEANLELDEDSYVEKFK 922

Query: 81  PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
           P LMDVV+AWC+GA+FL++C +TDIFEGSIIRCMRRLEEVLRQL+QA++NIGNT LE KF
Sbjct: 923 PFLMDVVYAWCKGATFLQICKMTDIFEGSIIRCMRRLEEVLRQLLQAAKNIGNTDLENKF 982

Query: 141 NEAIKTVKRDI 151
           +EAIK +KRDI
Sbjct: 983 SEAIKLIKRDI 993

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380026691|ref|XP_003697078.1| PREDICTED: superkiller viralicidic activity 2-like 2 isoform 1 [Apis florea]

 Score =  199 bits (505), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 102/191 (53%), Positives = 130/191 (68%), Gaps = 41/191 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVI--------------- 46
            S+L M+ELKCRKRVLRR+ Y T +DVIE+KGRVACEL+ ++E ++               
Sbjct: 824  SILQMDELKCRKRVLRRMAYCTASDVIELKGRVACELNGADELLMTEMIFNGLFNSLSVP 883

Query: 47   --------LTINDK------------------LELARHIARISIESKLDLDEDSYVNQFK 80
                       +DK                   +LAR IA++S E+ L+LDED+YV +FK
Sbjct: 884  QMVALISCFVCDDKSNEMPKSTEELSGPLRQMQDLARRIAKVSTEANLELDEDTYVERFK 943

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P LMDVV+AWC+GA+FL++C +TDIFEGSIIRCMRRLEEVLRQL QA++NIGNT LE KF
Sbjct: 944  PYLMDVVYAWCKGATFLQICKMTDIFEGSIIRCMRRLEEVLRQLCQAAKNIGNTDLENKF 1003

Query: 141  NEAIKTVKRDI 151
            +EAIK +KRDI
Sbjct: 1004 SEAIKLIKRDI 1014

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328792378|ref|XP_003251718.1| PREDICTED: superkiller viralicidic activity 2-like 2-like isoform 1 [Apis mellifera]

 Score =  198 bits (504), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 102/191 (53%), Positives = 130/191 (68%), Gaps = 41/191 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVI--------------- 46
            S+L M+ELKCRKRVLRR+ Y T +DVIE+KGRVACEL+ ++E ++               
Sbjct: 837  SILQMDELKCRKRVLRRMAYCTASDVIELKGRVACELNGADELLMTEMIFNGLFNSLSVP 896

Query: 47   --------LTINDK------------------LELARHIARISIESKLDLDEDSYVNQFK 80
                       +DK                   +LAR IA++S E+ L+LDED+YV +FK
Sbjct: 897  QMVALISCFVCDDKSNEMPKSTEELSGPLRQMQDLARRIAKVSTEANLELDEDTYVERFK 956

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P LMDVV+AWC+GA+FL++C +TDIFEGSIIRCMRRLEEVLRQL QA++NIGNT LE KF
Sbjct: 957  PYLMDVVYAWCKGATFLQICKMTDIFEGSIIRCMRRLEEVLRQLCQAAKNIGNTDLENKF 1016

Query: 141  NEAIKTVKRDI 151
            +EAIK +KRDI
Sbjct: 1017 SEAIKLIKRDI 1027

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332030475|gb|EGI70163.1| Superkiller viralicidic activity 2-like 2 [Acromyrmex echinatior]

 Score =  197 bits (501), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 101/191 (52%), Positives = 127/191 (66%), Gaps = 41/191 (21%)

Query: 2   SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS---------------------- 39
           S+L M+ELKCRKRVLRR+ Y T ADVIE+KGRVACEL+                      
Sbjct: 747 SILQMDELKCRKRVLRRMAYCTSADVIELKGRVACELNGADELLMTEMIFNGLFNALSVP 806

Query: 40  -------------------KSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFK 80
                              KS E +   +    +LAR IA++S E+ L+LDED+YV++FK
Sbjct: 807 QMVALISCFVCDEKSNEMPKSTEELSGPLRQMQDLARRIAKVSTEANLELDEDAYVDRFK 866

Query: 81  PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
           P LMDV++AWC+GA+FL++C +TDIFEGSIIRCMRRLEEVLRQL QA++ IGNT LE KF
Sbjct: 867 PYLMDVIYAWCKGATFLQICKMTDIFEGSIIRCMRRLEEVLRQLCQAAKGIGNTDLENKF 926

Query: 141 NEAIKTVKRDI 151
           +EAIK +KRDI
Sbjct: 927 SEAIKLIKRDI 937

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340708607|ref|XP_003392914.1| PREDICTED: superkiller viralicidic activity 2-like 2-like [Bombus terrestris]

 Score =  196 bits (499), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 101/191 (52%), Positives = 129/191 (67%), Gaps = 41/191 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVI--------------- 46
            S+L M+ELKCRKRVLRR+ Y T +DVIE+KGRVACEL+ ++E ++               
Sbjct: 881  SILQMDELKCRKRVLRRMAYCTASDVIELKGRVACELNGADELLMTEMIFNGLFNSLSVP 940

Query: 47   --------LTINDK------------------LELARHIARISIESKLDLDEDSYVNQFK 80
                       +DK                   +LAR IA++S E+ L+LDE++YV QFK
Sbjct: 941  QMVALISCFVCDDKSNEMLKCTEELSGPLRQMQDLARRIAKVSTEANLELDENAYVEQFK 1000

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P LMDVV+AWC+GA+FL++C +TDIFEGSIIRCMRR EEVLRQL QA++NIGNT LE KF
Sbjct: 1001 PYLMDVVYAWCKGATFLQICKMTDIFEGSIIRCMRRSEEVLRQLCQAAKNIGNTDLENKF 1060

Query: 141  NEAIKTVKRDI 151
            +EAIK +KRDI
Sbjct: 1061 SEAIKLIKRDI 1071

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350413173|ref|XP_003489905.1| PREDICTED: superkiller viralicidic activity 2-like 2-like [Bombus impatiens]

 Score =  196 bits (498), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 101/191 (52%), Positives = 129/191 (67%), Gaps = 41/191 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVI--------------- 46
            S+L M+ELKCRKRVLRR+ Y T +DVIE+KGRVACEL+ ++E ++               
Sbjct: 836  SILQMDELKCRKRVLRRMAYCTASDVIELKGRVACELNGADELLMTEMIFNGLFNSLSVP 895

Query: 47   --------LTINDK------------------LELARHIARISIESKLDLDEDSYVNQFK 80
                       +DK                   +LAR IA++S E+ L+LDED+YV +FK
Sbjct: 896  QMVALISCFVCDDKSNEMPKCTEELGGPLRQMQDLARRIAKVSTEANLELDEDAYVERFK 955

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P LMDVV+AWC+GA+FL++C +TDIFEGSIIRCMRR EEVLRQL QA++NIGNT LE KF
Sbjct: 956  PYLMDVVYAWCKGATFLQICKMTDIFEGSIIRCMRRSEEVLRQLCQAAKNIGNTDLENKF 1015

Query: 141  NEAIKTVKRDI 151
            +EAIK +KRDI
Sbjct: 1016 SEAIKLIKRDI 1026

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307188640|gb|EFN73345.1| Superkiller viralicidic activity 2-like 2 [Camponotus floridanus]

 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 100/191 (52%), Positives = 126/191 (65%), Gaps = 41/191 (21%)

Query: 2   SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS---------------------- 39
           S+L M ELKCRKRVLRR+ Y T AD+IE+KGRVACEL+                      
Sbjct: 763 SILQMNELKCRKRVLRRMAYCTSADIIELKGRVACELNGADELLMTEMIFNGLFNALSVP 822

Query: 40  -------------------KSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFK 80
                              KS E +   +    +LAR IA++S E+ L+LDED+YV++FK
Sbjct: 823 QMVALISCFVCDEKSNEMPKSTEELSGPLRQMQDLARRIAKVSTEANLELDEDAYVDRFK 882

Query: 81  PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
           P LMDV++AWC+GA+FL++C +TDIFEGSIIRCMRRLEEVLRQL QA++ IGNT LE KF
Sbjct: 883 PYLMDVIYAWCKGATFLQICKMTDIFEGSIIRCMRRLEEVLRQLCQAAKGIGNTDLENKF 942

Query: 141 NEAIKTVKRDI 151
           +EAIK +KRDI
Sbjct: 943 SEAIKLIKRDI 953

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321468914|gb|EFX79897.1| hypothetical protein DAPPUDRAFT_304340 [Daphnia pulex]

 Score =  193 bits (490), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 99/193 (51%), Positives = 124/193 (64%), Gaps = 41/193 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVIL-------------- 47
            SLL M ELKCRKRVLRRLGY T ADVIE+KGRVACELS  +E ++               
Sbjct: 836  SLLQMTELKCRKRVLRRLGYCTAADVIELKGRVACELSSGDELLLTEMIFNGLFNALDVT 895

Query: 48   ---------------------------TINDKLELARHIARISIESKLDLDEDSYVNQFK 80
                                        +    +LAR IA++S+E+KL+L+ED YV +FK
Sbjct: 896  QTAALLSCFVCDEKSNEMPKLSEALSGPLKQMQDLARRIAKVSVEAKLELEEDEYVEKFK 955

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P +MD+V AWC G+SF  +C +TD+FEGSIIRCMRRLEE+LRQ+VQAS++IGNT LE KF
Sbjct: 956  PYMMDLVAAWCRGSSFGDICKMTDLFEGSIIRCMRRLEELLRQMVQASKSIGNTELENKF 1015

Query: 141  NEAIKTVKRDIFL 153
            +E IK +KRDI  
Sbjct: 1016 SEGIKLIKRDIIF 1028

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157120596|ref|XP_001659679.1| helicase [Aedes aegypti] gi|108874885|gb|EAT39110.1| AAEL009067-PA [Aedes aegypti]

 Score =  192 bits (487), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 106/191 (55%), Positives = 124/191 (64%), Gaps = 41/191 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS---------------------- 39
            SLLHM+ELK RKRVLRRLGY T ADVIE KGRVACELS                      
Sbjct: 837  SLLHMDELKHRKRVLRRLGYCTTADVIEFKGRVACELSCADELLLTEMIFNGTFTNLTTS 896

Query: 40   -------------KSEETVILT------INDKLELARHIARISIESKLDLDEDSYVNQFK 80
                         KS E    T      +    +LAR IA++S E K+DLDE+ YV  FK
Sbjct: 897  QACALLSCFVCDEKSSEVPAATEELSGPLRQMQDLARRIAKVSNECKVDLDEERYVESFK 956

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P LMDVV AWC+G+SFL++C +TDIFEGSIIRCMRRLEE+LRQ+VQAS+ IGNT LE KF
Sbjct: 957  PFLMDVVLAWCKGSSFLQLCKMTDIFEGSIIRCMRRLEELLRQMVQASKTIGNTDLENKF 1016

Query: 141  NEAIKTVKRDI 151
            +EAI+ +KRDI
Sbjct: 1017 SEAIRLLKRDI 1027

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91092470|ref|XP_970408.1| PREDICTED: similar to helicase [Tribolium castaneum]

 Score =  191 bits (486), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 96/193 (49%), Positives = 124/193 (64%), Gaps = 41/193 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVIL-------------- 47
            S+L ++ELKCRKRVLRRLGY T  DVI++KGRVACELS ++E +I               
Sbjct: 854  SVLQLDELKCRKRVLRRLGYCTNTDVIQLKGRVACELSSADELLITEMIFNGVFGNLSPA 913

Query: 48   ---------------------------TINDKLELARHIARISIESKLDLDEDSYVNQFK 80
                                        +    +LAR IA++S E++L LDED+YV +FK
Sbjct: 914  QACALLSTFVCDEKSNEMPKLSEELSGPLRQMQDLARRIAKVSTEARLPLDEDAYVERFK 973

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
            P LMDVV +WC G+SF  +C +T+IFEGSI+RCMRRLEE+LRQ++QAS+ IGNT LE+KF
Sbjct: 974  PGLMDVVFSWCNGSSFSDLCKMTEIFEGSIVRCMRRLEELLRQMIQASKTIGNTDLEDKF 1033

Query: 141  NEAIKTVKRDIFL 153
            N AIK +KRDI  
Sbjct: 1034 NTAIKVIKRDIIF 1046

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

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	159
RGD|1305984	337	Skiv2l2 "superkiller viralicid	0.723	0.341	0.539	2.3e-46
FB|FBgn0001986	1055	l(2)35Df "lethal (2) 35Df" [Dr	0.616	0.092	0.704	9e-45
UNIPROTKB|E2RCI5	1042	SKIV2L2 "Uncharacterized prote	0.723	0.110	0.547	2e-44
ZFIN|ZDB-GENE-040426-2854	1034	skiv2l2 "superkiller viralicid	0.735	0.113	0.555	3.1e-44
UNIPROTKB|F5H7E2	941	SKIV2L2 "Superkiller viralicid	0.723	0.122	0.539	4.7e-44
MGI|MGI:1919448	1040	Skiv2l2 "superkiller viralicid	0.723	0.110	0.539	6.8e-44
UNIPROTKB|P42285	1042	SKIV2L2 "Superkiller viralicid	0.723	0.110	0.539	6.8e-44
UNIPROTKB|F1SLL6	1046	SKIV2L2 "Uncharacterized prote	0.723	0.109	0.539	1.8e-43
UNIPROTKB|F1N993	1031	F1N993 "Uncharacterized protei	0.698	0.107	0.544	1.3e-42
UNIPROTKB|D4AE49	764	D4AE49 "Uncharacterized protei	0.723	0.150	0.539	8.8e-35

RGD|1305984 Skiv2l2 "superkiller viralicidic activity 2-like 2 (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 332 (121.9 bits), Expect = 2.3e-46, Sum P(2) = 2.3e-46
 Identities = 62/115 (53%), Positives = 85/115 (73%)

Query:    37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASF 96
             E+ K  E +   +    E A+ IA++S E+KL++DE++Y++ FKP LMDVV+ W  GA+F
Sbjct:   215 EMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATF 274

Query:    97 LKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
               +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF E I  +KRDI
Sbjct:   275 AHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDI 329

GO:0000460 "maturation of 5.8S rRNA" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:0000178 "exosome (RNase complex)" evidence=ISO

FB|FBgn0001986 l(2)35Df "lethal (2) 35Df" [Drosophila melanogaster (taxid:7227)]

 Score = 361 (132.1 bits), Expect = 9.0e-45, Sum P(2) = 9.0e-45
 Identities = 69/98 (70%), Positives = 84/98 (85%)

Query:    54 ELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRC 113
             +LAR IA++S E KLDLD D+YV++FKP LMDVV AWC+G+SFL VC +TDIFEGSIIRC
Sbjct:   950 DLARRIAKVSTECKLDLDADTYVDKFKPFLMDVVLAWCKGSSFLAVCKMTDIFEGSIIRC 1009

Query:   114 MRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
             MRRLEE+LRQ+ QAS+ IGNT LE KF+E I+ +KRDI
Sbjct:  1010 MRRLEELLRQMCQASKTIGNTDLENKFSEGIRLLKRDI 1047

GO:0004004 "ATP-dependent RNA helicase activity" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|E2RCI5 SKIV2L2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 337 (123.7 bits), Expect = 2.0e-44, Sum P(2) = 2.0e-44
 Identities = 63/115 (54%), Positives = 85/115 (73%)

Query:    37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASF 96
             E+ K  E +   +    E A+ IA++S E+KL++DE++Y+N FKP LMDVV+ W  GA+F
Sbjct:   920 EMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLNSFKPHLMDVVYTWATGATF 979

Query:    97 LKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
               +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF E I  +KRDI
Sbjct:   980 AHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDI 1034

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-040426-2854 skiv2l2 "superkiller viralicidic activity 2-like 2" [Danio rerio (taxid:7955)]

 Score = 339 (124.4 bits), Expect = 3.1e-44, Sum P(2) = 3.1e-44
 Identities = 65/117 (55%), Positives = 87/117 (74%)

Query:    35 ACELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGA 94
             A E+ K  E +   +    E A+ IA++S E+KL++DEDSY+NQF+P LMDVV+ W  G+
Sbjct:   910 ANEMPKLTEQLGGPLRQMQECAKRIAKVSAEAKLEVDEDSYLNQFRPHLMDVVYTWANGS 969

Query:    95 SFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
             SF ++C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF   I  +KRDI
Sbjct:   970 SFSQICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFATGITKIKRDI 1026

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0031101 "fin regeneration" evidence=IMP

GO:0051781 "positive regulation of cell division" evidence=IMP

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|F5H7E2 SKIV2L2 "Superkiller viralicidic activity 2-like 2" [Homo sapiens (taxid:9606)]

 Score = 332 (121.9 bits), Expect = 4.7e-44, Sum P(2) = 4.7e-44
 Identities = 62/115 (53%), Positives = 85/115 (73%)

Query:    37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASF 96
             E+ K  E +   +    E A+ IA++S E+KL++DE++Y++ FKP LMDVV+ W  GA+F
Sbjct:   819 EMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATF 878

Query:    97 LKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
               +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF E I  +KRDI
Sbjct:   879 AHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDI 933

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

MGI|MGI:1919448 Skiv2l2 "superkiller viralicidic activity 2-like 2 (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 332 (121.9 bits), Expect = 6.8e-44, Sum P(2) = 6.8e-44
 Identities = 62/115 (53%), Positives = 85/115 (73%)

Query:    37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASF 96
             E+ K  E +   +    E A+ IA++S E+KL++DE++Y++ FKP LMDVV+ W  GA+F
Sbjct:   918 EMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATF 977

Query:    97 LKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
               +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF E I  +KRDI
Sbjct:   978 AHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDI 1032

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000460 "maturation of 5.8S rRNA" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

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

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

UNIPROTKB|P42285 SKIV2L2 "Superkiller viralicidic activity 2-like 2" [Homo sapiens (taxid:9606)]

 Score = 332 (121.9 bits), Expect = 6.8e-44, Sum P(2) = 6.8e-44
 Identities = 62/115 (53%), Positives = 85/115 (73%)

Query:    37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASF 96
             E+ K  E +   +    E A+ IA++S E+KL++DE++Y++ FKP LMDVV+ W  GA+F
Sbjct:   920 EMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATF 979

Query:    97 LKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
               +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF E I  +KRDI
Sbjct:   980 AHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDI 1034

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:0000178 "exosome (RNase complex)" evidence=IDA

GO:0000460 "maturation of 5.8S rRNA" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|F1SLL6 SKIV2L2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 332 (121.9 bits), Expect = 1.8e-43, Sum P(2) = 1.8e-43
 Identities = 62/115 (53%), Positives = 85/115 (73%)

Query:    37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASF 96
             E+ K  E +   +    E A+ IA++S E+KL++DE++Y++ FKP LMDVV+ W  GA+F
Sbjct:   924 EMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATF 983

Query:    97 LKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
               +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF E I  +KRDI
Sbjct:   984 AHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDI 1038

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0000460 "maturation of 5.8S rRNA" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1N993 F1N993 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 320 (117.7 bits), Expect = 1.3e-42, Sum P(2) = 1.3e-42
 Identities = 61/112 (54%), Positives = 83/112 (74%)

Query:    37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASF 96
             E+ K  E +   +    E A+ IAR+S E+KL++DE++Y+N F+P+LMDVV+ W  GASF
Sbjct:   909 EMPKLTEQLAGPLRQMQECAKRIARVSAEAKLEIDEENYLNSFRPNLMDVVYTWANGASF 968

Query:    97 LKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVK 148
               +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF E  +T K
Sbjct:   969 AHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEG-RTYK 1019

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

GO:0000460 "maturation of 5.8S rRNA" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

UNIPROTKB|D4AE49 D4AE49 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 332 (121.9 bits), Expect = 8.8e-35, Sum P(2) = 8.8e-35
 Identities = 62/115 (53%), Positives = 85/115 (73%)

Query:    37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASF 96
             E+ K  E +   +    E A+ IA++S E+KL++DE++Y++ FKP LMDVV+ W  GA+F
Sbjct:   642 EMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATF 701

Query:    97 LKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
               +C +TD+FEGSIIRCMRRLEE+LRQ+ QA++ IGNT LE KF E I  +KRDI
Sbjct:   702 AHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDI 756

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

---

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 EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	159
pfam08148	178	pfam08148, DSHCT, DSHCT (NUC185) domain	1e-35
COG4581	1041	COG4581, COG4581, Superfamily II RNA helicase [DNA	2e-27

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

 Score =  121 bits (305), Expect = 1e-35
 Identities = 63/171 (36%), Positives = 91/171 (53%), Gaps = 46/171 (26%)

Query: 24  EADVIEMKGRVACELSKSEETVILT----------------------------------- 48
           +  V+ +KGRVACE+S SE+ ++LT                                   
Sbjct: 3   DDGVVTLKGRVACEIS-SEDELLLTELLFSGFFNDLDPEELAALLSAFVFEERRDDEGYP 61

Query: 49  --------INDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVC 100
                   +N  LE+AR +A++  E  LD  E  YV +F   LM+VV+ W  GASF ++C
Sbjct: 62  PSLELAEALNRLLEIARKLAKVEREHGLDEPE--YVERFDFGLMEVVYEWARGASFSEIC 119

Query: 101 SITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
             TD+FEG I+R +RRL+E+LRQL  A++ IG+  L EK  EAI+ ++RDI
Sbjct: 120 EETDLFEGDIVRVIRRLDELLRQLANAAKIIGDPELAEKAEEAIELIRRDI 170

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 =  106 bits (266), Expect = 2e-27
 Identities = 61/196 (31%), Positives = 95/196 (48%), Gaps = 47/196 (23%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS-------------------KSE 42
            +L  +++ K  + VL++LG+  +  V+ +KGRVA E+S                   + E
Sbjct: 841  ALSFLDDYKTLQEVLKKLGFIEDNAVVLIKGRVAAEISSEDELLLTELIFSGEFNDLEPE 900

Query: 43   ETVIL----TINDK----------------------LELARHIARISIESKLDLDEDSYV 76
            E   L       +K                      LELAR + +    S++++  +  +
Sbjct: 901  ELAALLSAFVFEEKTDDGTAEAPEITPALRDALLRLLELARKLNKDQNSSQIEIYPE--L 958

Query: 77   NQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLL 136
            N F   LM+VV+ W  G SF  +C +T + EGS +R  RRL E+LRQL +A+  IGN  L
Sbjct: 959  NDFSVGLMEVVYEWARGLSFADICGLTSLLEGSFVRIFRRLRELLRQLRKAASVIGNPEL 1018

Query: 137  EEKFNEAIKTVKRDIF 152
            EEK   AI+ ++RDI 
Sbjct: 1019 EEKAYRAIQEIRRDIV 1034

Length = 1041

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	159
KOG0948|consensus	1041		100.0
PF08148	180	DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961	100.0
KOG0947|consensus	1248		100.0
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.97
PF04408	102	HA2: Helicase associated domain (HA2); InterPro: I	88.65
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	86.04
smart00847	92	HA2 Helicase associated domain (HA2) Add an annota	85.5
PRK00254	720	ski2-like helicase; Provisional	84.53
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	84.14
PRK01172	674	ski2-like helicase; Provisional	83.95
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	83.58
PRK00118	104	putative DNA-binding protein; Validated	83.14
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	82.36
TIGR03643	72	conserved hypothetical protein TIGR03643. This mod	82.23
PF13518	52	HTH_28: Helix-turn-helix domain	82.1
PF10985	73	DUF2805: Protein of unknown function (DUF2805); In	80.82
PRK04217	110	hypothetical protein; Provisional	80.29

>KOG0948|consensus

Probab=100.00  E-value=4.2e-50  Score=363.32  Aligned_cols=158  Identities=59%  Similarity=0.955  Sum_probs=153.0

Q ss_pred             cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec--cC---------------------------cH
Q psy6286           2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT--IN---------------------------DK   52 (159)
Q Consensus         2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE--f~---------------------------p~   52 (159)
                      ++++++|+++|.+||++|||++.++++.+|||+||||+|+|||++||  |+                           |+
T Consensus       843 ~i~~ldELk~RkRVLrrLG~~t~ddvie~KGrvACEIsSgDELlLTEliFnG~Fndl~~eq~aaLLSCfVf~eks~e~~~  922 (1041)
T KOG0948|consen  843 AILQLDELKNRKRVLRRLGYCTSDDVIELKGRVACEISSGDELLLTELIFNGIFNDLPVEQAAALLSCFVFQEKSSEAPK  922 (1041)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCCeEEEcceEEEEecccchHHHHHHHHhccccCCCHHHHHHHHhheeehhccccccc
Confidence            57899999999999999999999999999999999999999999999  44                           11


Q ss_pred             ------------HHHHHHHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286          53 ------------LELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV  120 (159)
Q Consensus        53 ------------~~i~~~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el  120 (159)
                                  ++.|++|++++.+|++++++++|+++|+|.+|+|||.|++|+||.+||++|+++||+|||++|||+|+
T Consensus       923 l~~el~~~l~~lqe~ArrIAkVs~ecKlEide~~Yv~sFkp~LMdvVy~W~~GatF~eIckmTdvfEGSiIR~~RRLeEl 1002 (1041)
T KOG0948|consen  923 LKEELAGPLRQLQESARRIAKVSKECKLEIDEEDYVESFKPELMDVVYAWAKGATFAEICKMTDVFEGSIIRTFRRLEEL 1002 (1041)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhhccccCHHHHHHhcChHHHHHHHHHHccccHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence                        79999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286         121 LRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL  159 (159)
Q Consensus       121 Lrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~  159 (159)
                      ||||.+||+.|||.+|.+||++++.+|+|||||++||||
T Consensus      1003 LrQl~~AAk~iGnteLe~Kf~~~~~~ikRDIVFAaSLYL 1041 (1041)
T KOG0948|consen 1003 LRQLIDAAKVIGNTELENKFEEAIKKIKRDIVFAASLYL 1041 (1041)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHHhhceeehhhccC
Confidence            999999999999999999999999999999999999997

>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=2.2e-45  Score=288.78  Aligned_cols=136  Identities=43%  Similarity=0.745  Sum_probs=114.8

Q ss_pred             ccCCCccchhhHHHhhhcCCCceeeec------cC---c---------------------------H--------HHHHH
Q psy6286          22 ATEADVIEMKGRVACELSKSEETVILT------IN---D---------------------------K--------LELAR   57 (159)
Q Consensus        22 id~~~~vt~kGrva~~I~s~~eLlltE------f~---p---------------------------~--------~~i~~   57 (159)
                      ||++++||+|||+||+|++++||++||      |+   |                           .        .++++
T Consensus         1 id~~~~vt~kGr~a~~I~~~~eLl~te~l~~g~f~~L~p~elAa~lS~~v~e~~~~~~~~~~~~~~~l~~~~~~l~~~~~   80 (180)
T PF08148_consen    1 IDEDNVVTLKGRVACEIYSEDELLLTELLFSGVFDDLDPAELAALLSCFVYEPRREDEEERYPPSPRLREALEQLQEIAE   80 (180)
T ss_dssp             B-TTS-BSHHHHHHCC--SSTHHHHHHHHHCTCCCCS-HHHHHHHHHHHC-----SS---------HHHHHHHHHHHHHH
T ss_pred             CCCCCccCHHHHHHHHHcCcccHHHHHHHHcCCCCCCCHHHHHHHHHHhhcccccCcccccccccHHHHHHHHHHHHHHH
Confidence            688999999999999999999999999      33   1                           0        68889


Q ss_pred             HHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHH
Q psy6286          58 HIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLE  137 (159)
Q Consensus        58 ~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~  137 (159)
                      +|.+++.+||+  +.++|.+.++|++|+++|+||+|+||++||+.|+++||||||++||++|+||||++|++++|||+|+
T Consensus        81 ~l~~~~~~~~l--~~~~~~~~~~~~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~aa~~~g~~~L~  158 (180)
T PF08148_consen   81 RLAKVEREHGL--DEEEYVERFDPGLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANAAKIIGDPELA  158 (180)
T ss_dssp             HHHHHHHHTT---HHHHHHHCSTTTTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHHHHCCT-HHHH
T ss_pred             HHHHHHHHhCC--CCcccccCCCccHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCCHHHH
Confidence            99999999999  5667888889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCcccccccCC
Q psy6286         138 EKFNEAIKTVKRDIFLEILENL  159 (159)
Q Consensus       138 ~k~~~a~~~I~RdIV~~~sl~~  159 (159)
                      +|+++|+++|||||||++|||+
T Consensus       159 ~~~~~a~~~i~R~iV~~~SLYl  180 (180)
T PF08148_consen  159 EKAREAIDLIRRDIVFASSLYL  180 (180)
T ss_dssp             HHHHHHHHHHSHCCCC---TT-
T ss_pred             HHHHHHHHhccCCccccccccC
Confidence            9999999999999999999997

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

>KOG0947|consensus

Probab=100.00  E-value=4.9e-43  Score=322.95  Aligned_cols=158  Identities=32%  Similarity=0.570  Sum_probs=150.1

Q ss_pred             cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec--cC-------cH--------------------
Q psy6286           2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT--IN-------DK--------------------   52 (159)
Q Consensus         2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE--f~-------p~--------------------   52 (159)
                      +|.++|+|.+|++||+.+||+|+..+|++|||+||+|++++||++||  |+       |.                    
T Consensus      1049 ~L~l~pey~~RlevLk~~g~vD~~~~V~lkGRvAceI~s~~ELllteli~dn~l~~l~peeiaallSslV~e~~~e~~~~ 1128 (1248)
T KOG0947|consen 1049 SLLLSPEYHNRLEVLKPLGFVDEMRTVLLKGRVACEINSGNELLLTELIFDNALVDLSPEEIAALLSSLVCEGKTERPPT 1128 (1248)
T ss_pred             hhhhCHHHHHHHHHHhhcCcccccceeeecceeeeeecCCcchhHHHHHHhhhhhhcCHHHHHHHHHHHHhcCccccCCC
Confidence            67889999999999999999999999999999999999999999999  55       21                    


Q ss_pred             ------------HHHHHHHHHHHHHcCCCCChh-hhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286          53 ------------LELARHIARISIESKLDLDED-SYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE  119 (159)
Q Consensus        53 ------------~~i~~~i~~~~~~~~l~~~~~-~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e  119 (159)
                                  .+++.++..++..|++..+++ +|...++|+||++||+||+|.||.+||++|++.||+|||+|+||+|
T Consensus      1129 ~~~~l~k~~e~v~~v~~rl~ev~~~~~~~~~~~e~f~~~lrF~l~evVYeWA~G~sf~eim~~t~~~EG~iVR~I~RLdE 1208 (1248)
T KOG0947|consen 1129 LTPYLKKGKERVRDVAKRLEEVQSSHQLLQTPEEEFPCELRFGLVEVVYEWARGLSFKEIMELTDVLEGLIVRLIQRLDE 1208 (1248)
T ss_pred             CChhhhhHHHHHHHHHHHHHHHHHhhccccCchhhccccccccHHHHHHHHHcCCCHHHHHhhhCCcchhHHHHHHHHHH
Confidence                        688999999999999988774 6888999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286         120 VLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL  159 (159)
Q Consensus       120 lLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~  159 (159)
                      +|||+++|++++|||.|.+||++|.++|||||||++|||+
T Consensus      1209 ~cre~~~aa~ivGd~~L~~Km~~as~~ikRdIVFaaSLY~ 1248 (1248)
T KOG0947|consen 1209 VCRELRNAARIVGDPVLHEKMEAASALIKRDIVFAASLYL 1248 (1248)
T ss_pred             HHHhhhccceecCcHHHHHHHHHHHHHhccCccchhhccC
Confidence            9999999999999999999999999999999999999996

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

Probab=99.97  E-value=7.7e-31  Score=246.63  Aligned_cols=156  Identities=39%  Similarity=0.665  Sum_probs=145.9

Q ss_pred             cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec------cC--------------------c----
Q psy6286           2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT------IN--------------------D----   51 (159)
Q Consensus         2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE------f~--------------------p----   51 (159)
                      .+.++++|+.+..+|+.+||++.+..++.|||+||+|++++|+++||      |+                    |    
T Consensus       841 ~~~~l~~~~~l~~~l~~~g~~~~~~~v~~kGr~a~eI~s~~ellL~e~i~~g~f~~l~p~e~aallSa~v~e~~~~d~~~  920 (1041)
T COG4581         841 ALSFLDDYKTLQEVLKKLGFIEDNAVVLIKGRVAAEISSEDELLLTELIFSGEFNDLEPEELAALLSAFVFEEKTDDGTA  920 (1041)
T ss_pred             HhhhhHHHHHHHHHHHhhcCCCcccccccccceeeeecCCCchHHHHHHHcCCccCCCHHHHHHHHHheeeccCCccccc
Confidence            35678999999999999999998889999999999999999999999      43                    1    


Q ss_pred             H---------------HHHHHHHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHH
Q psy6286          52 K---------------LELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRR  116 (159)
Q Consensus        52 ~---------------~~i~~~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rR  116 (159)
                      .               .+++++|.++++.|++++..+  ++.+.+++|++||.||+|.+|.+||..|++.|||+||+++|
T Consensus       921 ~~~~~~~~l~~~~~~l~e~~~kl~~~~~~~~i~~~~~--l~~~~~~lm~vv~~wa~g~s~~~i~~~~~~~eGs~vR~~~r  998 (1041)
T COG4581         921 EAPEITPALRDALLRLLELARKLNKDQNSSQIEIYPE--LNDFSVGLMEVVYEWARGLSFADICGLTSLLEGSFVRIFRR  998 (1041)
T ss_pred             ccccCCHHHHhHHHHHHHHHHHHHHHHHhcCCcCCcc--cccccccHHHHHHHHHhhcchhhhhcCCcccccchhhhhhH
Confidence            0               688999999999999998654  56889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286         117 LEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL  159 (159)
Q Consensus       117 l~elLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~  159 (159)
                      +.|+|+|+.+++.++||++|.+|+..|+..|||||||..|||+
T Consensus       999 ~~ell~ql~~aa~~ig~~~L~~k~~~~~~~irr~iv~~~sly~ 1041 (1041)
T COG4581         999 LRELLRQLRKAASVIGNPELEEKAYRAIQEIRRDIVFVDSLYL 1041 (1041)
T ss_pred             HHHHHHHhhhcccccCCHHHHHHHHHHHHhhhcCeEecccccC
Confidence            9999999999999999999999999999999999999999996

>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length

Probab=88.65  E-value=0.39  Score=33.97  Aligned_cols=28  Identities=25%  Similarity=0.313  Sum_probs=22.2

Q ss_pred             HHHHhhhCCccCCCccchhhHHHhhhcC
Q psy6286          13 KRVLRRLGYATEADVIEMKGRVACELSK   40 (159)
Q Consensus        13 ~~vL~~lgyid~~~~vt~kGrva~~I~s   40 (159)
                      ++.|..+|.+|+++.+|..|+.++.+--
T Consensus         3 ~~~L~~Lgald~~~~lT~lG~~~~~lPl   30 (102)
T PF04408_consen    3 LELLKSLGALDENGNLTPLGRKMSQLPL   30 (102)
T ss_dssp             HHHHHHTTSB-TTS-B-HHHHHHTTSSS
T ss_pred             HHHHHHCCCCCCCCCcCHHHHHHHHCCC
Confidence            4679999999999999999999998765

It is found as a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.; GO: 0004386 helicase activity; PDB: 3I4U_A 2XAU_B 3KX2_B.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=86.04  E-value=2.2  Score=25.50  Aligned_cols=41  Identities=15%  Similarity=0.196  Sum_probs=32.9

Q ss_pred             CchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286          80 KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV  120 (159)
Q Consensus        80 ~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el  120 (159)
                      .+.-..++..+..|.|..+|.+..++.++.+=+.+.|+..-
T Consensus         5 ~~~e~~i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~k   45 (58)
T smart00421        5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRK   45 (58)
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            33334566678899999999999999999999988877443

lux regulon (activates the bioluminescence operon

>smart00847 HA2 Helicase associated domain (HA2) Add an annotation

Probab=85.50  E-value=0.8  Score=31.18  Aligned_cols=28  Identities=25%  Similarity=0.286  Sum_probs=24.7

Q ss_pred             HHHHhhhCCccCCCccchhhHHHhhhcC
Q psy6286          13 KRVLRRLGYATEADVIEMKGRVACELSK   40 (159)
Q Consensus        13 ~~vL~~lgyid~~~~vt~kGrva~~I~s   40 (159)
                      .+.|..+|-+|.++.+|..|+..+++-.
T Consensus         3 ~~~L~~LgAld~~~~lT~lG~~m~~lPl   30 (92)
T smart00847        3 LELLYELGALDDDGRLTPLGRKMAELPL   30 (92)
T ss_pred             HHHHHHCCCcCCCCCcCHHHHHHHHCCC
Confidence            4689999999998899999999998754

This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.

>PRK00254 ski2-like helicase; Provisional

Probab=84.53  E-value=4.4  Score=38.03  Aligned_cols=73  Identities=11%  Similarity=0.120  Sum_probs=58.3

Q ss_pred             CchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCC-hHHHHHHHHHHHhhcCCcc
Q psy6286          80 KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGN-TLLEEKFNEAIKTVKRDIF  152 (159)
Q Consensus        80 ~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~-~~L~~k~~~a~~~I~RdIV  152 (159)
                      .+...-+.+.|.+|.+...+++..++..||+=+.+.+..-++.-+...+..+|. +++...+.+....|+-|+-
T Consensus       568 ~~k~~~ll~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~~  641 (720)
T PRK00254        568 AFKTAKVLLDWINEVPEGEIVETYNIDPGDLYRILELADWLMYSLIELYKLFEPKQEVLDYLETLHLRVKHGVR  641 (720)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCCC
Confidence            345568899999999999999999999999999999999999999988887883 5555666655555555543

>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=84.14  E-value=2.6  Score=24.58  Aligned_cols=43  Identities=19%  Similarity=0.252  Sum_probs=32.8

Q ss_pred             CCchHHHHHHHhh-CCCCHHHHHhhcCCCccHHHHHHHHHHHHH
Q psy6286          79 FKPSLMDVVHAWC-EGASFLKVCSITDIFEGSIIRCMRRLEEVL  121 (159)
Q Consensus        79 ~~~~l~~~v~~Wa-~G~~f~~i~~~t~l~EG~iVR~~rRl~elL  121 (159)
                      +.+.--.++.... .|.+..+|.+..++.++.+-+++.+...-|
T Consensus        11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l   54 (55)
T cd06171          11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL   54 (55)
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence            4444445555544 999999999999999999999988876543

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

>PRK01172 ski2-like helicase; Provisional

Probab=83.95  E-value=18  Score=33.69  Aligned_cols=134  Identities=14%  Similarity=0.141  Sum_probs=80.7

Q ss_pred             HHHHHHHHhhhCCccCCC--ccchhhHHHhhhcCCCceee--ec-cC-------------------cH----HHHHHHHH
Q psy6286           9 LKCRKRVLRRLGYATEAD--VIEMKGRVACELSKSEETVI--LT-IN-------------------DK----LELARHIA   60 (159)
Q Consensus         9 ~~~~~~vL~~lgyid~~~--~vt~kGrva~~I~s~~eLll--tE-f~-------------------p~----~~i~~~i~   60 (159)
                      ...-++-|.+.|+|+.++  .+|.-|+++++.+-+-+...  .+ ++                   |-    .+...   
T Consensus       446 v~~~l~~L~~~~~i~~~~~~~~t~lG~~~s~~~l~~~t~~~~~~~l~~~~~~~~~l~~~~~~~e~~~~~~~~~~~~~---  522 (674)
T PRK01172        446 IESSLKFLKENGFIKGDVTLRATRLGKLTSDLYIDPESALILKSAFDHDYDEDLALYYISLCREIIPANTRDDYYAM---  522 (674)
T ss_pred             HHHHHHHHHHCCCcccCCcEeECHHHHHHHHhCCCHHHHHHHHHHhhccCCHHHHHHHhhcCccccccccchHHHHH---
Confidence            467788999999998553  68999999998776322110  00 11                   11    11111   


Q ss_pred             HHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHH
Q psy6286          61 RISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF  140 (159)
Q Consensus        61 ~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~  140 (159)
                      .+....+..   +.+  .+...-.-+.++|-++.++.+|.+.-++..|++=+++....-+..-+...++.+ .+++.+.+
T Consensus       523 ~~~~~~~~~---~~~--~~~~k~~~ll~~~~~~~~~~~i~~~~~~~~g~l~~~~~~~~~~~~a~~~~~~~~-~~~~~~~l  596 (674)
T PRK01172        523 EFLEDIGVI---DGD--ISAAKTAMVLRGWISEASMQKITDTYGIAPGDVQARASSADWISYSLARLSSIY-KPEMRRKL  596 (674)
T ss_pred             HHHHHhccc---cch--hHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHh-hHHHHHHH
Confidence            112222221   111  123344678999999999999999999999998887544444433444444443 37777776


Q ss_pred             HHHHHhhcCCc
Q psy6286         141 NEAIKTVKRDI  151 (159)
Q Consensus       141 ~~a~~~I~RdI  151 (159)
                      ......|.=|+
T Consensus       597 ~~~~~rl~~gv  607 (674)
T PRK01172        597 EILNIRIKEGI  607 (674)
T ss_pred             HHHHHHHHcCC
Confidence            65555554443

>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=83.58  E-value=3.2  Score=25.19  Aligned_cols=38  Identities=18%  Similarity=0.323  Sum_probs=31.7

Q ss_pred             HHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286          86 VVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ  123 (159)
Q Consensus        86 ~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq  123 (159)
                      +...|..|.|+.+|-+..++++|.+=+..+|..+-||+
T Consensus        13 i~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen   13 IRLRYFEGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            45567899999999999999999999988888877764

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 ....

>PRK00118 putative DNA-binding protein; Validated

Probab=83.14  E-value=8  Score=27.97  Aligned_cols=55  Identities=7%  Similarity=0.128  Sum_probs=44.6

Q ss_pred             ccCCchHHHHHHHh-hCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhh
Q psy6286          77 NQFKPSLMDVVHAW-CEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNI  131 (159)
Q Consensus        77 ~~~~~~l~~~v~~W-a~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~i  131 (159)
                      +.+.+.--.++..+ ..|.|..+|.+..+++++.+=+.+.|...-|++....-+.+
T Consensus        16 ~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~   71 (104)
T PRK00118         16 SLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLY   71 (104)
T ss_pred             ccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChH
Confidence            45555555666555 58999999999999999999999999999999977765443

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

Probab=82.36  E-value=3.8  Score=24.58  Aligned_cols=33  Identities=21%  Similarity=0.371  Sum_probs=28.4

Q ss_pred             HHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHH
Q psy6286          85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMRRL  117 (159)
Q Consensus        85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl  117 (159)
                      .+++.++.|.|..+|.+..++.++.+-+.+.|+
T Consensus         7 ~i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~   39 (57)
T cd06170           7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRNI   39 (57)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            355667899999999999999999998888766

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

>TIGR03643 conserved hypothetical protein TIGR03643

Probab=82.23  E-value=2  Score=29.22  Aligned_cols=30  Identities=23%  Similarity=0.387  Sum_probs=27.4

Q ss_pred             HHHhhCCCCHHHHHhhcCCCccHHHHHHHH
Q psy6286          87 VHAWCEGASFLKVCSITDIFEGSIIRCMRR  116 (159)
Q Consensus        87 v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rR  116 (159)
                      --+|.+-.||..|-...++.|+++|..||+
T Consensus         7 eMAweDRtpFeaI~~~fGL~E~eVi~lMR~   36 (72)
T TIGR03643         7 EMAWEDRTPFEAIEQQFGLSEKEVIKLMRQ   36 (72)
T ss_pred             HHHHccCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            357999999999999999999999998886

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.

>PF13518 HTH_28: Helix-turn-helix domain

Probab=82.10  E-value=3.7  Score=24.67  Aligned_cols=35  Identities=23%  Similarity=0.409  Sum_probs=30.8

Q ss_pred             HHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHH
Q psy6286          85 DVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEE  119 (159)
Q Consensus        85 ~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~e  119 (159)
                      .++..+.+|.|..+++...++....+-+|+++-.+
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            46667779999999999999999999999988765

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

Probab=80.82  E-value=2.4  Score=28.94  Aligned_cols=29  Identities=24%  Similarity=0.431  Sum_probs=27.0

Q ss_pred             HHhhCCCCHHHHHhhcCCCccHHHHHHHH
Q psy6286          88 HAWCEGASFLKVCSITDIFEGSIIRCMRR  116 (159)
Q Consensus        88 ~~Wa~G~~f~~i~~~t~l~EG~iVR~~rR  116 (159)
                      -+|.+-.||..|-...++.|.+++..||+
T Consensus         7 MAweDRtpFeaI~~qfGl~E~eVi~lMR~   35 (73)
T PF10985_consen    7 MAWEDRTPFEAIERQFGLSEKEVIKLMRK   35 (73)
T ss_pred             HHHccCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            57999999999999999999999998886

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.

>PRK04217 hypothetical protein; Provisional

Probab=80.29  E-value=7.4  Score=28.42  Aligned_cols=52  Identities=12%  Similarity=0.151  Sum_probs=43.9

Q ss_pred             cCCchHHHHHHHhh-CCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhh
Q psy6286          78 QFKPSLMDVVHAWC-EGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASR  129 (159)
Q Consensus        78 ~~~~~l~~~v~~Wa-~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~  129 (159)
                      .+...--.++..+. .|.|+.+|.+..++.++++=+.+.|....|++......
T Consensus        42 ~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~   94 (110)
T PRK04217         42 FMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGR   94 (110)
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            44555568888887 99999999999999999999999999999988665543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	159
2xgj_A	1010	Structure Of Mtr4, A Dexh Helicase Involved In Nucl		2e-25
3l9o_A	1108	Crystal Structure Of Mtr4, A Co-Factor Of The Nucle		2e-25
4a4z_A	997	Crystal Structure Of The S. Cerevisiae Dexh Helicas		1e-08

>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna Processing And Surveillance Length = 1010

Iteration: 1
 Score =  111 bits (278), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/173 (34%), Positives = 93/173 (53%), Gaps = 41/173 (23%)
Query: 20   GYATEADVIEMKGRVACELSKSEETVI--LTINDKL------------------------ 53
            G+ T  D+IE+KGRVACE+S  +E ++  L  N                           
Sbjct: 830  GFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEA 889
Query: 54   ---------------ELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLK 98
                           E+A  IA+I  +SK+++ E  YV  F+  LM+VV+ WC GA+F +
Sbjct: 890  PRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQ 949
Query: 99   VCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
            +C +TD++EGS+IR  +RLEE++++LV  +  IGN+ L+EK    +K + RDI
Sbjct: 950  ICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDI 1002

>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear Exosome Length = 1108

Iteration: 1
 Score =  111 bits (277), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/173 (34%), Positives = 93/173 (53%), Gaps = 41/173 (23%)
Query: 20   GYATEADVIEMKGRVACELSKSEETVI--LTINDKL------------------------ 53
            G+ T  D+IE+KGRVACE+S  +E ++  L  N                           
Sbjct: 928  GFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEA 987
Query: 54   ---------------ELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLK 98
                           E+A  IA+I  +SK+++ E  YV  F+  LM+VV+ WC GA+F +
Sbjct: 988  PRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQ 1047
Query: 99   VCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
            +C +TD++EGS+IR  +RLEE++++LV  +  IGN+ L+EK    +K + RDI
Sbjct: 1048 ICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDI 1100

>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2 Bound To Amppnp Length = 997

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 53/85 (62%)
Query: 67  KLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126
            L  DE  ++++ + ++M+VV+ W  G SF ++  ++   EG+++R +  L+E+ R++  
Sbjct: 905 PLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKT 964
Query: 127 ASRNIGNTLLEEKFNEAIKTVKRDI 151
           AS  IGN+ L  K + A + +KRDI
Sbjct: 965 ASIIIGNSTLHMKMSRAQELIKRDI 989

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	159
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	1e-46
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	1e-46
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	3e-42
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04

>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 =  161 bits (407), Expect = 1e-46
 Identities = 68/191 (35%), Positives = 108/191 (56%), Gaps = 41/191 (21%)

Query: 2    SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS---------------------- 39
            +++ +++L+ RKRVLRRLG+ T  D+IE+KGRVACE+S                      
Sbjct: 812  AVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPE 871

Query: 40   -------------KSEETVILT------INDKLELARHIARISIESKLDLDEDSYVNQFK 80
                         + +E   L       +    E+A  IA+I  +SK+++ E  YV  F+
Sbjct: 872  QAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFR 931

Query: 81   PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
              LM+VV+ WC GA+F ++C +TD++EGS+IR  +RLEE++++LV  +  IGN+ L+EK 
Sbjct: 932  HELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKM 991

Query: 141  NEAIKTVKRDI 151
               +K + RDI
Sbjct: 992  EAVLKLIHRDI 1002

>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 =  160 bits (406), Expect = 1e-46
 Identities = 68/192 (35%), Positives = 108/192 (56%), Gaps = 41/192 (21%)

Query: 1    MSLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS--------------------- 39
             +++ +++L+ RKRVLRRLG+ T  D+IE+KGRVACE+S                     
Sbjct: 909  QAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKP 968

Query: 40   --------------KSEETVILT------INDKLELARHIARISIESKLDLDEDSYVNQF 79
                          + +E   L       +    E+A  IA+I  +SK+++ E  YV  F
Sbjct: 969  EQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESF 1028

Query: 80   KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEK 139
            +  LM+VV+ WC GA+F ++C +TD++EGS+IR  +RLEE++++LV  +  IGN+ L+EK
Sbjct: 1029 RHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEK 1088

Query: 140  FNEAIKTVKRDI 151
                +K + RDI
Sbjct: 1089 MEAVLKLIHRDI 1100

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

 Score =  148 bits (374), Expect = 3e-42
 Identities = 43/195 (22%), Positives = 88/195 (45%), Gaps = 45/195 (23%)

Query: 2   SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS---------------------- 39
           +L  + + + R  VL+   +  +   + +KGRVACE++                      
Sbjct: 795 NLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVACEINSGYELVLTELILDNFLGSFEPE 854

Query: 40  -------------KSEETVILTINDKL--------ELARHIARISIESKLDL--DEDSYV 76
                        K+ E     +  +L        E+ + +  +    ++ L  DE  ++
Sbjct: 855 EIVALLSVFVYEGKTREEEPPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFL 914

Query: 77  NQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLL 136
           ++ + ++M+VV+ W  G SF ++  ++   EG+++R +  L+E+ R++  AS  IGN+ L
Sbjct: 915 DRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTL 974

Query: 137 EEKFNEAIKTVKRDI 151
             K + A + +KRDI
Sbjct: 975 HMKMSRAQELIKRDI 989

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

 Score = 38.3 bits (88), Expect = 5e-04
 Identities = 19/113 (16%), Positives = 38/113 (33%), Gaps = 18/113 (15%)

Query: 55  LARHIARISIESKLDLDEDSYVN-QF-KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIR 112
           +  H+  I    ++ L    +++ +F +  +     AW    S L        ++  I  
Sbjct: 477 IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICD 536

Query: 113 CMRRLEEVLRQLVQASRNIGNTLLEEK----------------FNEAIKTVKR 149
              + E ++  ++     I   L+  K                F EA K V+R
Sbjct: 537 NDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	159
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
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	96.62
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	95.13
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	93.62
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	93.1
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	85.19
3idw_A	72	Actin cytoskeleton-regulatory complex protein SLA;	85.13
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	80.49

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

Probab=100.00  E-value=1.9e-49  Score=373.94  Aligned_cols=158  Identities=26%  Similarity=0.454  Sum_probs=149.4

Q ss_pred             cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec--cC-------cH--------------------
Q psy6286           2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT--IN-------DK--------------------   52 (159)
Q Consensus         2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE--f~-------p~--------------------   52 (159)
                      ++.++++|+++++||++|||||++++||+|||+||||+|++||++||  |+       |.                    
T Consensus       795 ~~~~~~~~~~~~~vL~~l~~~~~~~~v~~kgr~a~~i~~~~el~~te~~~~~~~~~l~~~~~~a~ls~~v~~~~~~~~~~  874 (997)
T 4a4z_A          795 NLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVACEINSGYELVLTELILDNFLGSFEPEEIVALLSVFVYEGKTREEEP  874 (997)
T ss_dssp             --CHHHHHHHHHHHHHHTTSBCTTCCBCHHHHHHTTCCSSCHHHHHHHHHSSGGGGCCHHHHHHHHGGGSCCCCCSSCCC
T ss_pred             hHHHHHHHHHHHHHHHHcCCcCCCCcccHHhHHHhhhcCccHHHHHHHHHhCcccCCCHHHHHHHHhhhhccccCCCCCC
Confidence            57889999999999999999999999999999999999999999999  33       10                    


Q ss_pred             --------------HHHHHHHHHHHHHcCCCCCh--hhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHH
Q psy6286          53 --------------LELARHIARISIESKLDLDE--DSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRR  116 (159)
Q Consensus        53 --------------~~i~~~i~~~~~~~~l~~~~--~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rR  116 (159)
                                    +++|++|++++.+|+++++.  ++|+++|+||||++||+||+|+||++||++|+++||||||||||
T Consensus       875 ~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~l~~~v~~Wa~g~~f~~i~~~t~~~eG~~vR~~~r  954 (997)
T 4a4z_A          875 PIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITW  954 (997)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHHHTTCCCCHHHHHGGGSCTTTTHHHHHHHHHTCCHHHHHHTCSSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCccchhhhccCCChHHHHHHHHHhCCCCHHHHHhcCCCCchHHHHHHHH
Confidence                          79999999999999999864  67999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286         117 LEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL  159 (159)
Q Consensus       117 l~elLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~  159 (159)
                      |+|+||||++||++|||++|.+||++|+++|||||||++||||
T Consensus       955 l~e~~~q~~~aa~~~g~~~l~~k~~~a~~~i~R~iv~~~slyl  997 (997)
T 4a4z_A          955 LDEICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAASLYL  997 (997)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCGGGGCCCTTC
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcCCeeecccccC
Confidence            9999999999999999999999999999999999999999997

>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=6.5e-49  Score=370.76  Aligned_cols=158  Identities=44%  Similarity=0.820  Sum_probs=150.9

Q ss_pred             cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec------cC---cH--------------------
Q psy6286           2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT------IN---DK--------------------   52 (159)
Q Consensus         2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE------f~---p~--------------------   52 (159)
                      ++.+++||+++++||++|||||++++||+|||+||+|++++||++||      |+   |.                    
T Consensus       812 ~~~~~~~~~~~~~vL~~l~~~~~~~~v~~kGr~a~~i~~~~el~~~e~~~~g~~~~l~p~~~aa~~s~~v~~~~~~~~~~  891 (1010)
T 2xgj_A          812 AVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPR  891 (1010)
T ss_dssp             SCTTHHHHHHHHHHHHHHTSBCTTCCBCHHHHHHHTCCSSCHHHHHHHHHHTTTTTCCHHHHHHHHHHHHCCCCCSCCCC
T ss_pred             hhhhHHHHHHHHHHHHhcCCcCCCCcccHHHHHHHHhcCccHHHHHHHHHcCccCCCCHHHHHHHHeeeEeecCCCCCCC
Confidence            67889999999999999999998889999999999999999999999      44   11                    


Q ss_pred             ------------HHHHHHHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286          53 ------------LELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV  120 (159)
Q Consensus        53 ------------~~i~~~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el  120 (159)
                                  +++|++|++++.+|++++++++|+++|+|+||++||+||+|+||++||++|+++|||||||||||+|+
T Consensus       892 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~v~~Wa~g~~~~~i~~~t~~~eG~~vR~~~rl~el  971 (1010)
T 2xgj_A          892 LKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEEL  971 (1010)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCHHHHHHTSCCTTHHHHHHHTTTCCHHHHTTSCSSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhCCCCChhHhcccCChHHHHHHHHHhCCCCHHHHHhcCCCCchHHHHHHHHHHHH
Confidence                        78999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286         121 LRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL  159 (159)
Q Consensus       121 Lrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~  159 (159)
                      ||||++|+++|||++|.+||++|+++|||||||++|||+
T Consensus       972 l~q~~~a~~~~g~~~l~~~~~~a~~~i~R~iv~~~sly~ 1010 (1010)
T 2xgj_A          972 VKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL 1010 (1010)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHHSCGGGGCCCC-C
T ss_pred             HHHHHHHhhhcCCHHHHHHHHHHHHhccCCeEecccccC
Confidence            999999999999999999999999999999999999997

>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=1.5e-49  Score=377.80  Aligned_cols=158  Identities=44%  Similarity=0.823  Sum_probs=140.1

Q ss_pred             cchhHHHHHHHHHHHhhhCCccCCCccchhhHHHhhhcCCCceeeec------cC---c--------------------H
Q psy6286           2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELSKSEETVILT------IN---D--------------------K   52 (159)
Q Consensus         2 ~~~~~~e~~~~~~vL~~lgyid~~~~vt~kGrva~~I~s~~eLlltE------f~---p--------------------~   52 (159)
                      ++++++||+++++||++|||||++++||+|||+||+|++++||++||      |+   |                    .
T Consensus       910 ~~~~~~~~~~~~~vL~~l~~~~~~~~v~~kgr~a~~i~~~~el~~~e~~~~~~~~~l~~~~~aa~~s~~v~~~~~~~~~~  989 (1108)
T 3l9o_A          910 AVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPR  989 (1108)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSCTTTCCCSHHHHHHHC-CCTTHHHHHHHHHHHCCCSSCCTHHHHHTCC------------
T ss_pred             hhHHHHHHHHHHHHHHHcCCcCCCCcCcHHhHHHHHhcCccHHHHHHHHHhCcccCCCHHHHHHHHhheeeecccCCCCC
Confidence            57889999999999999999998899999999999999999999999      44   2                    1


Q ss_pred             ------------HHHHHHHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHH
Q psy6286          53 ------------LELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEV  120 (159)
Q Consensus        53 ------------~~i~~~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~el  120 (159)
                                  +++|++|++++.+|++++++++|++.|+|+||++||+||+|+||++||++|+++|||||||||||+|+
T Consensus       990 ~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~~v~~Wa~g~~f~~i~~~t~~~eG~~vR~~~rl~e~ 1069 (1108)
T 3l9o_A          990 LKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEEL 1069 (1108)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHCCSCHHHHHHHHC----CCGGGTC--CHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhCCCCChHHhccCCChHHHHHHHHHhCCCCHHHHHhcCCCCchhhhhHHHHHHHH
Confidence                        79999999999999999988999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhhhCChHHHHHHHHHHHhhcCCcccccccCC
Q psy6286         121 LRQLVQASRNIGNTLLEEKFNEAIKTVKRDIFLEILENL  159 (159)
Q Consensus       121 Lrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV~~~sl~~  159 (159)
                      ||||++||++|||++|.+||++|+++|||||||++||||
T Consensus      1070 l~q~~~aa~~~g~~~l~~k~~~a~~~i~r~iv~~~slyl 1108 (1108)
T 3l9o_A         1070 VKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL 1108 (1108)
T ss_dssp             HSCCCC----CCCHHHHHHHHHHHHHHHHHTCCCCCCC-
T ss_pred             HHHHHHHHhhcCCHHHHHHHHHHHHHhcCCEEeeccccC
Confidence            999999999999999999999999999999999999997

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

Probab=96.62  E-value=0.025  Score=50.69  Aligned_cols=145  Identities=12%  Similarity=0.063  Sum_probs=98.5

Q ss_pred             HHHHHHHHHhhhCCccCCC---ccchhhHHHhhhcCCCcee---eec---------------------cC-cH--HHHHH
Q psy6286           8 ELKCRKRVLRRLGYATEAD---VIEMKGRVACELSKSEETV---ILT---------------------IN-DK--LELAR   57 (159)
Q Consensus         8 e~~~~~~vL~~lgyid~~~---~vt~kGrva~~I~s~~eLl---ltE---------------------f~-p~--~~i~~   57 (159)
                      .+..-++.|.++|+|+.++   .+|.-|+.+++.+-+-.+.   +.-                     |. +.  ..-..
T Consensus       472 ~~~~al~~L~~~g~i~~~~~~~~~t~lG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~i~~~~e~~~~~~r~~e~~  551 (715)
T 2va8_A          472 YFDRAIRWLLEHSFIKEEGNTFALTNFGKRVADLYINPFTADIIRKGLEGHKASCELAYLHLLAFTPDGPLVSVGRNEEE  551 (715)
T ss_dssp             HHHHHHHHHHHTTSEEECSSEEEECHHHHHHHHHTCCHHHHHHHHHHHHHSCCCCHHHHHHHHHHSTTSCCCCCCHHHHH
T ss_pred             HHHHHHHHHHHCcCEeecCCeEeeChHHHHHHHHcCCHhHHHHHHHHhhhccCCCHHHHHHHhhcCcccccCccChHHHH
Confidence            4778899999999998763   8999999999987632210   000                     11 00  11111


Q ss_pred             HHHHHHHH---cC---CCCChhhhhc-cCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhh
Q psy6286          58 HIARISIE---SK---LDLDEDSYVN-QFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRN  130 (159)
Q Consensus        58 ~i~~~~~~---~~---l~~~~~~~~~-~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~  130 (159)
                      .+.+...+   .+   .+.....|.. ...+...-+..+|.++.++.+|++..+++.||+........-+++.+...+..
T Consensus       552 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~ll~~~~~~~~~~~i~~~y~~~~gdl~~l~~~a~~l~~a~~~i~~~  631 (715)
T 2va8_A          552 ELIELLEDLDCELLIEEPYEEDEYSLYINALKVALIMKDWMDEVDEDTILSKYNIGSGDLRNMVETMDWLTYSAYHLSRE  631 (715)
T ss_dssp             HHHHHHTTCSSCCSSCCCSSHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcchhhcccccccccchhhhHHHHHHHHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHHHHHHHH
Confidence            22222211   11   1111111110 02234567889999999999999999999999999999999999999999999


Q ss_pred             hCChHHHHHHHHHHHhhcCCcc
Q psy6286         131 IGNTLLEEKFNEAIKTVKRDIF  152 (159)
Q Consensus       131 ig~~~L~~k~~~a~~~I~RdIV  152 (159)
                      .|...+...+......|..|+-
T Consensus       632 ~~~~~~~~~l~~l~~rl~~gv~  653 (715)
T 2va8_A          632 LKLNEHADKLRILNLRVRDGIK  653 (715)
T ss_dssp             TTCHHHHHHHHHHHHHHHHTCC
T ss_pred             hCcHHHHHHHHHHHHHHHcCCC
Confidence            9998888888777777766653

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=95.13  E-value=0.11  Score=46.75  Aligned_cols=145  Identities=14%  Similarity=0.028  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHhhhCCcc-CCC---ccchhhHHHhhhcCCCce---eee------------c----------cC--c-HHH
Q psy6286           7 EELKCRKRVLRRLGYAT-EAD---VIEMKGRVACELSKSEET---VIL------------T----------IN--D-KLE   54 (159)
Q Consensus         7 ~e~~~~~~vL~~lgyid-~~~---~vt~kGrva~~I~s~~eL---llt------------E----------f~--p-~~~   54 (159)
                      +.+..-++.|.++|+|+ .++   .+|.-|+.+++.+-+-..   ++.            +          |+  | +..
T Consensus       454 ~~~~~~l~~L~~~~~i~~~~~~~~~~t~lG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~~~e~~~i~~r~~  533 (720)
T 2zj8_A          454 EKIRNILYFLLENEFIEISLEDKIRPLSLGIRTAKLYIDPYTAKMFKDKMEEVVKDPNPIGIFHLISLTPDITPFNYSKR  533 (720)
T ss_dssp             HHHHHHHHHHHHTTSEEECTTSCEEECHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCCHHHHHHHHHTSTTCCCCCCCHH
T ss_pred             HHHHHHHHHHHHCCCeeECCCCcEeeChHHHHHHHHcCCHHHHHHHHHHHHhhccCCCHHHHHHHhccCccccccccCHH
Confidence            35677889999999998 544   799999999997763221   000            0          11  0 011


Q ss_pred             HHHHHHHHHHHc---C---CCCCh--hh--hhc-cCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHH
Q psy6286          55 LARHIARISIES---K---LDLDE--DS--YVN-QFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQ  123 (159)
Q Consensus        55 i~~~i~~~~~~~---~---l~~~~--~~--~~~-~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrq  123 (159)
                      -...+..+..++   .   ++...  ++  +.. ...+-..-+.+.|.++.++.+|.+..++..||+.....+..-+++.
T Consensus       534 e~~~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~k~~llL~~~i~~~~l~~i~~~~~~~~gdl~~~~~~a~~l~~a  613 (720)
T 2zj8_A          534 EFERLEEEYYEFKDRLYFDDPYISGYDPYLERKFFRAFKTALVLLAWINEVPEGEIVEKYSVEPGDIYRIVETAEWLVYS  613 (720)
T ss_dssp             HHHHHHHHHHHHGGGCSSCCTTSSCCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccccccccccccccccchhhhhHHHHHHHHHHHHHHHhCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence            111222221111   1   12111  00  100 0223456788999999999999999999999999999999999999


Q ss_pred             HHHhhhhhCChHHHHHHHHHHHhhcCCc
Q psy6286         124 LVQASRNIGNTLLEEKFNEAIKTVKRDI  151 (159)
Q Consensus       124 l~~a~~~ig~~~L~~k~~~a~~~I~RdI  151 (159)
                      +...+...|...+...+.+-...|.-|+
T Consensus       614 ~~~i~~~~g~~~~~~~l~~l~~rl~~gv  641 (720)
T 2zj8_A          614 LKEIAKVLGAYEIVDYLETLRVRVKYGI  641 (720)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCcHHHHHHHHHHHHHHHcCC
Confidence            9999998887666555555554444433

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=93.62  E-value=0.15  Score=45.63  Aligned_cols=123  Identities=18%  Similarity=0.212  Sum_probs=83.0

Q ss_pred             HHHHHHHHHHhhhCCccCC--CccchhhHHHhhhcCCCce---ee--------ec------------cC-----cHHHHH
Q psy6286           7 EELKCRKRVLRRLGYATEA--DVIEMKGRVACELSKSEET---VI--------LT------------IN-----DKLELA   56 (159)
Q Consensus         7 ~e~~~~~~vL~~lgyid~~--~~vt~kGrva~~I~s~~eL---ll--------tE------------f~-----p~~~i~   56 (159)
                      +.+..-++.|.++|+|+.+  ..+|.-|+.++..+-+-..   ++        ++            |+     | .+  
T Consensus       453 ~~~~~al~~L~~~g~i~~~~~~~~t~lG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~i~~~~e~~~i~~r~-~e--  529 (702)
T 2p6r_A          453 YELERVVRQLENWGMVVEAAHLAPTKLGSLVSRLYIDPLTGFIFHDVLSRMELSDIGALHLICRTPDMERLTVRK-TD--  529 (702)
T ss_dssp             HHHHHHHHHHHHTTSEEESSSEEECHHHHHHHHTTCCHHHHHHHHHHTTTCCCCHHHHHHHHHHSTTSCCCCCCT-TT--
T ss_pred             HHHHHHHHHHHHCcCeeECCeeccChHHHHHHHHhCCHHHHHHHHHHhhcccCCHHHHHHHhhCCcccccCCCCC-ch--
Confidence            3567788999999999876  6899999999987752211   00        00            11     1 11  


Q ss_pred             HHHHHHHHH--cCC-CCC---h---hhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286          57 RHIARISIE--SKL-DLD---E---DSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA  127 (159)
Q Consensus        57 ~~i~~~~~~--~~l-~~~---~---~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a  127 (159)
                      ..+.+...+  +++ +.+   .   +++.  ..+...-+..+|.+|.++.+|++..++..||+.....+..-+++-+...
T Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~k~~~lL~~~~~~~~l~~i~~~~~~~~gdl~~i~~~a~~l~~a~~~i  607 (702)
T 2p6r_A          530 SWVEEEAFRLRKELSYYPSDFSVEYDWFL--SEVKTALCLKDWIEEKDEDEICAKYGIAPGDLRRIVETAEWLSNAMNRI  607 (702)
T ss_dssp             HHHHHHHHHHGGGSSCCCCTTSTTHHHHH--HHHHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccccCCcchhhhhhhhhh--hhHHHHHHHHHHHcCCChHHHHHHhCCcHHhHHHHHHHHHHHHHHHHHH
Confidence            222222222  222 111   0   1111  2234667899999999999999999999999999999999999998888


Q ss_pred             hhhhCCh
Q psy6286         128 SRNIGNT  134 (159)
Q Consensus       128 ~~~ig~~  134 (159)
                      +...|..
T Consensus       608 ~~~~g~~  614 (702)
T 2p6r_A          608 AEEVGNT  614 (702)
T ss_dssp             HHHTTCC
T ss_pred             HHHcCHH
Confidence            8877754

>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=93.10  E-value=0.28  Score=35.68  Aligned_cols=65  Identities=20%  Similarity=0.373  Sum_probs=52.2

Q ss_pred             cCCchHHHHHHHh-hCCCCHHHHHhhcCC-CccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHH
Q psy6286          78 QFKPSLMDVVHAW-CEGASFLKVCSITDI-FEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEA  143 (159)
Q Consensus        78 ~~~~~l~~~v~~W-a~G~~f~~i~~~t~l-~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a  143 (159)
                      .+++.+++-+..+ +.|.|+.+||...++ ..-+|-||+.+=.|+..++..|-.. +...+.+.+.+.
T Consensus        12 k~t~e~~e~I~~~i~~G~sl~~i~~~~~~ps~~T~~~W~~~~~ef~e~~~~Ar~~-~~~~~~~~~~~i   78 (140)
T 4dyq_A           12 DYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKYAKATEA-RADSIFEEIFEI   78 (140)
T ss_dssp             SCCTTHHHHHHHHHHTTCCHHHHHTSTTCCCHHHHHHHHHHCHHHHHHHHHHHHH-HHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCcHHHHHhcCCCCCHHHHHHHHHcCHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence            6888999888888 699999999999999 7899999999999999888887432 334444444443

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

Probab=85.19  E-value=1.7  Score=26.55  Aligned_cols=50  Identities=12%  Similarity=0.129  Sum_probs=38.4

Q ss_pred             cCCchHHHHHHH-hhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHh
Q psy6286          78 QFKPSLMDVVHA-WCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQA  127 (159)
Q Consensus        78 ~~~~~l~~~v~~-Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a  127 (159)
                      .+.+.--.++.. +..|.|+.+|.+..+++++.+=+.+.|...-|++.-..
T Consensus        15 ~L~~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~~   65 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEP   65 (70)
T ss_dssp             SSCHHHHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC----
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence            455555566654 68999999999999999999999999988888765543

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

Probab=85.13  E-value=0.62  Score=30.74  Aligned_cols=49  Identities=16%  Similarity=0.235  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHcCCCCChhhhhccCCchHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHH
Q psy6286          54 ELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVL  121 (159)
Q Consensus        54 ~i~~~i~~~~~~~~l~~~~~~~~~~~~~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elL  121 (159)
                      ..+.+.+..-.+.+++.+   -+..+++                +++..-++.||||||.++.++...
T Consensus        17 ~~c~rYA~~F~~~ri~e~---mL~Dl~~----------------~~Lr~LGi~eGDIIrVmk~l~~k~   65 (72)
T 3idw_A           17 SNCQRYTINFDREQLTED---MMPDINN----------------SMLRTLGLREGDIVRVMKHLDKKF   65 (72)
T ss_dssp             HHHHHHHHHHHHTTCCGG---GGGGCCH----------------HHHHHTTCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHccCCHH---HHhhCCH----------------HHHHHcCCchhhHHHHHHHHHHHh
Confidence            455566665566665532   2234444                366667889999999999988654

>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=80.49  E-value=1.5  Score=24.44  Aligned_cols=34  Identities=6%  Similarity=-0.117  Sum_probs=29.2

Q ss_pred             HHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHH
Q psy6286          84 MDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRL  117 (159)
Q Consensus        84 ~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl  117 (159)
                      ..++..+.+|.|..+|.+..++....+-|++++.
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

---

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	159
d2p6ra2	198	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	95.4
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	80.41

>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=95.40  E-value=0.012  Score=44.24  Aligned_cols=72  Identities=17%  Similarity=0.254  Sum_probs=57.2

Q ss_pred             chHHHHHHHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHHHHhhhhhCChHHHHHHHHHHHhhcCCcc
Q psy6286          81 PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIF  152 (159)
Q Consensus        81 ~~l~~~v~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~I~RdIV  152 (159)
                      +....+++.|.++.|..+|++..++..||+=+......=++..+...++.+|...+.+--.+....++.+++
T Consensus        73 ~KtAl~L~dwi~E~~~~~I~~~y~v~~Gdl~~~~~~a~wl~~~~~~~~~~~~~~~l~~L~~Rl~~Gv~~ell  144 (198)
T d2p6ra2          73 VKTALCLKDWIEEKDEDEICAKYGIAPGDLRRIVETAEWLSNAMNRIAEEVGNTSVSGLTERIKHGVKEELL  144 (198)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSTTHHHHHHHTCCGGGH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHccCCHHHH
Confidence            345688999999999999999999999999988888888889998888888876655544444445555443

>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=80.41  E-value=1.8  Score=25.52  Aligned_cols=47  Identities=15%  Similarity=0.121  Sum_probs=37.6

Q ss_pred             cCCchHHHHH-HHhhCCCCHHHHHhhcCCCccHHHHHHHHHHHHHHHH
Q psy6286          78 QFKPSLMDVV-HAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQL  124 (159)
Q Consensus        78 ~~~~~l~~~v-~~Wa~G~~f~~i~~~t~l~EG~iVR~~rRl~elLrql  124 (159)
                      .+.+.--.++ ..+..|.|+.+|.+..+++++.+=+.+.|...-|++.
T Consensus        21 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~   68 (71)
T d1rp3a2          21 KLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALERLREM   68 (71)
T ss_dssp             TSCHHHHHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhHhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            4555555555 4467999999999999999999988888888887765