Citrus Sinensis ID: 028267

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-
Protein Sequence
MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCEL
Secondary Structure (PSIPRED)
cccccccccccccccccccHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHccccccccHHHHHHHHHHHHHHHHHHccccEEEccccccccccHHHHHccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHcccccccHHHHccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccEEccccccEEcccccccccccHHHHHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
MEKGASFLFagvsfdkkkfvTDFARFkenkesenladdfsfvegektdpeKAMVSFVKKRKrksiagetvegfnvfksskqlvpavdkekekvedgpsKAKKELNKQIERDAVFRKKYNihvsganvpsplRTFVKLSSRFGCESYLLRNLaelgykeptpiqrqaipvllsdrecfacaptgsgktlaFLCPMLMKLRvlfipfdyfcel
Flexible Loop (DISEMBL)
mekgasflfagvsfdkkkfVTDFARfkenkesenladdfsfvegektdpekamvsfvkkrkrksiagetvegfnvfksskqlvpavdkekekvedgpskakkelnkQIERDAVFRKKYNihvsganvpsplRTFVKLSSRFGCESYLLRNLAelgykeptpIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCEL
Low Complexity Region (SEG)
MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCEL
Disordered region (IsUnstruct)
******FLFAGVSFDKKKFVTDFARF************************************************************************************DAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFC**
Disordered Region (DISOPRED)
*****SFLFAGVSFDKKK*********************************************************************************************AVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIP******L
Disordered Region (DISEMBL)
MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVKKRKRKSIAGETVEGFNVFKSSKQLVP*****************KELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCEL
Disordered Region (DISPRO)
**************D**KFVT**A**K*****************************************************************VEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCEL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	211	2.2.26 [Sep-21-2011]
Q84TG1	541	DEAD-box ATP-dependent RN	yes	no	0.933	0.364	0.577	6e-54
Q5K5B6	540	DEAD-box ATP-dependent RN	yes	no	0.876	0.342	0.488	2e-47
Q9Y2R4	599	Probable ATP-dependent RN	yes	no	0.872	0.307	0.343	3e-24
A5D7C1	596	Probable ATP-dependent RN	yes	no	0.563	0.199	0.437	4e-23
Q86IZ9	668	Probable ATP-dependent RN	yes	no	0.469	0.148	0.486	2e-22
Q8K301	598	Probable ATP-dependent RN	yes	no	0.407	0.143	0.534	3e-22
Q99PT0	598	Probable ATP-dependent RN	yes	no	0.530	0.187	0.438	7e-22
P45818	564	ATP-dependent RNA helicas	yes	no	0.710	0.265	0.354	3e-21
A6ZU15	564	ATP-dependent RNA helicas	N/A	no	0.710	0.265	0.354	4e-21
Q6CSW1	579	ATP-dependent RNA helicas	yes	no	0.421	0.153	0.522	1e-20

>sp|Q84TG1|RH57_ARATH DEAD-box ATP-dependent RNA helicase 57 OS=Arabidopsis thaliana GN=RH57 PE=2 SV=1

 Score =  210 bits (534), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 119/206 (57%), Positives = 153/206 (74%), Gaps = 9/206 (4%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSF-----VEGEKTDPEKAMVS 55
           MEK + FLF G +F+KKKF  DFA+FK + E ++     +F      + E+ + EK +VS
Sbjct: 1   MEKSSYFLFGGTNFNKKKFAPDFAKFKNSTEDDDSNKKVNFFVEEEEDTEQPEAEKVIVS 60

Query: 56  FVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGP--SKAKKELNKQIERDAV 113
             KKRKR+S     VEGF+VFKSSK+   A  K +E++         KKELN+Q+ERDA+
Sbjct: 61  -SKKRKRRSSNSVPVEGFDVFKSSKK-ARAKGKAEEQITKNEIVENPKKELNRQMERDAL 118

Query: 114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
            RK+Y+IHVSG N+P PL++F +LSSR+GCE Y+LRNLAELG+KEPTPIQRQAIP+LLS 
Sbjct: 119 SRKQYSIHVSGNNIPPPLKSFAELSSRYGCEGYILRNLAELGFKEPTPIQRQAIPILLSG 178

Query: 174 RECFACAPTGSGKTLAFLCPMLMKLR 199
           RECFACAPTGSGKT AF+CPML+KL+
Sbjct: 179 RECFACAPTGSGKTFAFICPMLIKLK 204

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q5K5B6|RH57_ORYSJ DEAD-box ATP-dependent RNA helicase 57 OS=Oryza sativa subsp. japonica GN=Os07g0647900 PE=2 SV=2

 Score =  189 bits (479), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 109/223 (48%), Positives = 142/223 (63%), Gaps = 38/223 (17%)

Query: 1   MEKG--ASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVK 58
           MEK   +S LFAG  FD+K+F  DFARF++   + ++A            PEK       
Sbjct: 1   MEKAKLSSALFAGTHFDRKRFAGDFARFRQGPPAPDVA------SAAAPSPEK------- 47

Query: 59  KRKRKSI----------------AGETVEGFNVFKSSKQLVPAVDKEKEKVEDGPS---- 98
           KRKR+S                 A + VEGF+VFK         D EK KVE G S    
Sbjct: 48  KRKRQSKAKAKKSKKRRAEGADSASDAVEGFSVFKGLAAKKDEDDSEK-KVETGKSEDSE 106

Query: 99  --KAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGY 156
             + +KE+ ++IER A+ RKK++IH+SG NVP+PL  F +L SR+GC+SYL+ NL++LG+
Sbjct: 107 VVRRRKEVEREIERAAILRKKFDIHISGQNVPAPLENFEELVSRYGCDSYLVGNLSKLGF 166

Query: 157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
           +EPTPIQRQAIP+LLS RECFACAPTGSGKTLAFL P+LMK++
Sbjct: 167 QEPTPIQRQAIPILLSGRECFACAPTGSGKTLAFLFPILMKIK 209

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9Y2R4|DDX52_HUMAN Probable ATP-dependent RNA helicase DDX52 OS=Homo sapiens GN=DDX52 PE=1 SV=3

 Score =  111 bits (278), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 114/227 (50%), Gaps = 43/227 (18%)

Query: 8   LFAGVSFDKKKFVTDFARFKENK-----ESENLADDFSFVEGEKTDP------------- 49
           L AG  FD ++F  D ARF+  K     +S  +     F   +K+ P             
Sbjct: 10  LGAGAKFDTRRFSADAARFQIGKRKYDFDSSEVLQGLDFFGNKKSVPGVCGASQTHQKPQ 69

Query: 50  --EKAMVSFVK------KRKRKSIAGETV---EGFNVFKSSKQLVPAVDKEKEKVEDGPS 98
             EK   S  +      K+KRK++  E     EG  +     Q + +V+    K+ED   
Sbjct: 70  NGEKKEESLTERKREQSKKKRKTMTSEIASQEEGATI-----QWMSSVE---AKIEDKKV 121

Query: 99  KAKKEL------NKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLA 152
           + + +L      N + E+    R K+ IHV G ++P P+ TF +L   +   S LL+N+ 
Sbjct: 122 QRESKLTSGKLENLRKEKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNIL 181

Query: 153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
           + G++ PTPIQ QAIPV+L  RE  A APTGSGKTLAF  P+LM+L+
Sbjct: 182 DAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLK 228

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5D7C1|DDX52_BOVIN Probable ATP-dependent RNA helicase DDX52 OS=Bos taurus GN=DDX52 PE=2 SV=1

 Score =  108 bits (269), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 56/128 (43%), Positives = 81/128 (63%), Gaps = 9/128 (7%)

Query: 78  SSKQLVPAVDKEKEKVEDGPSKAKKELN----KQIERDAV--FRKKYNIHVSGANVPSPL 131
           S+ Q + +V+    K+ED   K K +L     +Q+ ++ +  FR K+ IHV G ++P P+
Sbjct: 102 STIQWISSVEA---KIEDKNVKRKNKLTSGKLEQLRKEKLNFFRNKHKIHVQGTDLPDPI 158

Query: 132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFL 191
            TF +L   +   S LL+N+ + G++ PTPIQ QAIPV+L  RE  A APTGSGKTLAF 
Sbjct: 159 ATFQQLDQEYKINSRLLQNILDAGFQTPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFS 218

Query: 192 CPMLMKLR 199
            P+LM L+
Sbjct: 219 IPILMHLK 226

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q86IZ9|DDX52_DICDI Probable ATP-dependent RNA helicase ddx52 OS=Dictyostelium discoideum GN=ddx52 PE=3 SV=1

 Score =  105 bits (263), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 53/109 (48%), Positives = 68/109 (62%), Gaps = 10/109 (9%)

Query: 90  KEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLR 149
           KE  ED   K K+E+       A FR K+ I V G ++P P+  F +L +RF    YLL 
Sbjct: 163 KETQED---KHKREI-------ATFRNKHRIKVDGTDIPDPMTEFSQLENRFKVRKYLLN 212

Query: 150 NLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           N+ E+GYKEP+PIQ Q IP+LL +RE  A APTGSGKT +F  P+L  L
Sbjct: 213 NINEIGYKEPSPIQMQVIPILLKEREVVAIAPTGSGKTASFSIPILQAL 261

ATP-binding RNA helicase which may be involved in the ribosome biogenesis.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8K301|DDX52_MOUSE Probable ATP-dependent RNA helicase DDX52 OS=Mus musculus GN=Ddx52 PE=2 SV=2

 Score =  105 bits (261), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 46/86 (53%), Positives = 61/86 (70%)

Query: 114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
           FR K+ IHV G ++P P+ TF +L   +   S LL+N+ + G++ PTPIQ QAIPV+L  
Sbjct: 144 FRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQVPTPIQMQAIPVMLHG 203

Query: 174 RECFACAPTGSGKTLAFLCPMLMKLR 199
           RE  A APTGSGKTLAF  P+LM+L+
Sbjct: 204 RELLASAPTGSGKTLAFSIPILMQLK 229

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q99PT0|DDX52_RAT Probable ATP-dependent RNA helicase DDX52 OS=Rattus norvegicus GN=Ddx52 PE=2 SV=1

 Score =  103 bits (258), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 50/114 (43%), Positives = 73/114 (64%), Gaps = 2/114 (1%)

Query: 88  KEKEKVEDGPSKAKKELNKQIERDAV--FRKKYNIHVSGANVPSPLRTFVKLSSRFGCES 145
           K ++K  +G  K   E  + + ++ +  FR K+ IHV G ++P P+ TF +L   +    
Sbjct: 116 KLQDKKANGEKKLTSEKLEHLRKEKINFFRNKHKIHVQGTDLPDPIATFQQLDQEYKISP 175

Query: 146 YLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
            LL+N+ + G++ PTPIQ QAIPV+L  RE  A APTGSGKTLAF  P+LM+L+
Sbjct: 176 RLLQNILDAGFQVPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLK 229

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P45818|ROK1_YEAST ATP-dependent RNA helicase ROK1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ROK1 PE=1 SV=1

 Score =  101 bits (252), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 62/175 (35%), Positives = 95/175 (54%), Gaps = 25/175 (14%)

Query: 36  ADDFSFVEGEKTDPEKAMVSFVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKV-- 93
           A D+S + G   +            K  +   + V+  + F++ K+++  V+ ++EK   
Sbjct: 23  AADYSVINGNDEN-----------HKEDNNESQIVKELDFFRN-KRIISKVEDDREKTTE 70

Query: 94  EDGPSKAKKELN----------KQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGC 143
            D P+K +K  N            +E  A  RK Y  +VSG ++P P+ +F  L SRF  
Sbjct: 71  NDSPNKEEKSGNDDGLIKPVITNTVEASA-LRKSYKGNVSGIDIPLPIGSFEDLISRFSF 129

Query: 144 ESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +  LL NL E G+ EPTPIQ + IPV L++R+  AC PTGSGKTLAFL P++ ++
Sbjct: 130 DKRLLNNLIENGFTEPTPIQCECIPVALNNRDVLACGPTGSGKTLAFLIPLVQQI 184

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA. May also have a gene-specific regulatory function since it affects nuclear fusion by regulating KAR4 expression and contributes with KEM1 to ISP-1 sensitivity.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A6ZU15|ROK1_YEAS7 ATP-dependent RNA helicase ROK1 OS=Saccharomyces cerevisiae (strain YJM789) GN=ROK1 PE=3 SV=1

 Score =  101 bits (252), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 62/175 (35%), Positives = 96/175 (54%), Gaps = 25/175 (14%)

Query: 36  ADDFSFVEGEKTDPEKAMVSFVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKV-- 93
           A D+S + G+  +            K  +   + V+  + F++ K+++  V+ ++EK   
Sbjct: 23  AADYSVINGKDEN-----------HKEDNNESQIVKELDFFRN-KRIISKVEDDREKTTE 70

Query: 94  EDGPSKAKKELN----------KQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGC 143
            D P+K +K  N            +E  A  RK Y  +VSG ++P P+ +F  L SRF  
Sbjct: 71  NDSPNKEEKSGNDDGLIKPVITNTVEASA-LRKSYKGNVSGIDIPLPIGSFEDLISRFSF 129

Query: 144 ESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +  LL NL E G+ EPTPIQ + IPV L++R+  AC PTGSGKTLAFL P++ ++
Sbjct: 130 DRRLLNNLIENGFTEPTPIQCECIPVALNNRDVLACGPTGSGKTLAFLIPLVQQI 184

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Saccharomyces cerevisiae (strain YJM789) (taxid: 307796)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6CSW1|ROK1_KLULA ATP-dependent RNA helicase ROK1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=ROK1 PE=3 SV=1

 Score =  100 bits (248), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/90 (52%), Positives = 64/90 (71%), Gaps = 1/90 (1%)

Query: 110 RDAV-FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIP 168
           +DA+  RK Y  +VSG +VP P+ +F  L +RF  +  LL NL E  + EPTPIQ ++IP
Sbjct: 106 QDALKLRKSYQGNVSGNSVPLPIGSFEDLITRFQFDKRLLNNLIENNFTEPTPIQSESIP 165

Query: 169 VLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +LL +R+  ACAPTGSGKTLAFL P+L ++
Sbjct: 166 ILLHERDMIACAPTGSGKTLAFLIPLLQQI 195

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

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	211
255559765	535	dead box ATP-dependent RNA helicase, put	0.938	0.370	0.665	5e-70
225439904	524	PREDICTED: DEAD-box ATP-dependent RNA he	0.890	0.358	0.663	2e-67
297741568	523	unnamed protein product [Vitis vinifera]	0.886	0.357	0.658	2e-65
147784525	554	hypothetical protein VITISV_032421 [Viti	0.872	0.332	0.643	8e-64
449440077	616	PREDICTED: DEAD-box ATP-dependent RNA he	0.943	0.323	0.611	1e-63
224127806	531	predicted protein [Populus trichocarpa]	0.919	0.365	0.601	1e-58
297833736	539	hypothetical protein ARALYDRAFT_478294 [	0.919	0.359	0.584	1e-57
356505198	537	PREDICTED: DEAD-box ATP-dependent RNA he	0.943	0.370	0.560	4e-54
6682259	545	putative RNA helicase [Arabidopsis thali	0.943	0.365	0.581	4e-53
22330935	541	DEAD-box ATP-dependent RNA helicase 57 [	0.933	0.364	0.577	3e-52

>gi|255559765|ref|XP_002520902.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223540033|gb|EEF41611.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  269 bits (688), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 135/203 (66%), Positives = 164/203 (80%), Gaps = 5/203 (2%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLA--DDFSFVEGEKTDPEKAMVSFVK 58
           MEKG SFLFAG++F+KKKF TDF+RFKE KE  + A  DD   +E  K++P++  VS VK
Sbjct: 1   MEKGTSFLFAGITFNKKKFATDFSRFKEKKECNDNAQTDDLRLLEAGKSEPDQVHVS-VK 59

Query: 59  KRKRKSIAG-ETVEGFNVFKSSKQLVPAVDKEKEKVE-DGPSKAKKELNKQIERDAVFRK 116
           KRKRK++A  E VEGFNVFKSSK +    +++ ++ E D P +  KELNKQIERDA+ RK
Sbjct: 60  KRKRKNVASSEKVEGFNVFKSSKSVALPSNQQNDQDEIDQPFRKNKELNKQIERDALLRK 119

Query: 117 KYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDREC 176
            ++IHVSG N+PSPL+ F +LSSR+GCESYLL NL ELG+KEPTPIQRQAIPVLLS REC
Sbjct: 120 HFHIHVSGNNIPSPLQNFSELSSRYGCESYLLHNLVELGFKEPTPIQRQAIPVLLSGREC 179

Query: 177 FACAPTGSGKTLAFLCPMLMKLR 199
           FACAPTGSGKTLAF+CPMLMKL+
Sbjct: 180 FACAPTGSGKTLAFVCPMLMKLK 202

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225439904|ref|XP_002279705.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57 [Vitis vinifera]

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 134/202 (66%), Positives = 160/202 (79%), Gaps = 14/202 (6%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVKKR 60
           MEKG SFLF+G++FDKKKF  DF+RFKE KES++L      VE  K++ E+     VKKR
Sbjct: 1   MEKGTSFLFSGITFDKKKFAADFSRFKEKKESDDL------VESGKSEAEEGARP-VKKR 53

Query: 61  KRKSIAGETVEGFNVFKSSK---QLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKK 117
           KRK+   + VEGFNVFK+SK   Q +   D+EK ++    S+AKKELN+QIERDA+ RKK
Sbjct: 54  KRKATVADPVEGFNVFKTSKSSAQGIQQNDQEKSEL----SQAKKELNRQIERDALLRKK 109

Query: 118 YNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECF 177
           + IH+SG NVPSPL  F +LSSR+GCESYLL NLAELG+KEPTPIQRQAIPVLLS RECF
Sbjct: 110 HKIHISGNNVPSPLENFSELSSRYGCESYLLHNLAELGFKEPTPIQRQAIPVLLSGRECF 169

Query: 178 ACAPTGSGKTLAFLCPMLMKLR 199
           ACAPTGSGKTLAF+CPMLMKL+
Sbjct: 170 ACAPTGSGKTLAFVCPMLMKLK 191

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741568|emb|CBI32700.3| unnamed protein product [Vitis vinifera]

 Score =  254 bits (649), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 133/202 (65%), Positives = 160/202 (79%), Gaps = 15/202 (7%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVKKR 60
           MEKG SFLF+G++FDKKKF  DF+RFK+ KES++L      VE  K++ E+     VKKR
Sbjct: 1   MEKGTSFLFSGITFDKKKFAADFSRFKK-KESDDL------VESGKSEAEEGARP-VKKR 52

Query: 61  KRKSIAGETVEGFNVFKSSK---QLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKK 117
           KRK+   + VEGFNVFK+SK   Q +   D+EK ++    S+AKKELN+QIERDA+ RKK
Sbjct: 53  KRKATVADPVEGFNVFKTSKSSAQGIQQNDQEKSEL----SQAKKELNRQIERDALLRKK 108

Query: 118 YNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECF 177
           + IH+SG NVPSPL  F +LSSR+GCESYLL NLAELG+KEPTPIQRQAIPVLLS RECF
Sbjct: 109 HKIHISGNNVPSPLENFSELSSRYGCESYLLHNLAELGFKEPTPIQRQAIPVLLSGRECF 168

Query: 178 ACAPTGSGKTLAFLCPMLMKLR 199
           ACAPTGSGKTLAF+CPMLMKL+
Sbjct: 169 ACAPTGSGKTLAFVCPMLMKLK 190

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147784525|emb|CAN61726.1| hypothetical protein VITISV_032421 [Vitis vinifera]

 Score =  248 bits (634), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 130/202 (64%), Positives = 156/202 (77%), Gaps = 18/202 (8%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVKKR 60
           MEKG SFLF+G++FDKKKF  DF+RFKE KES++L      VE  K++ E+     VKKR
Sbjct: 1   MEKGTSFLFSGITFDKKKFAADFSRFKEKKESDDL------VESGKSEAEEG-ARPVKKR 53

Query: 61  KRKSIAGETVEGFNVFKSSK---QLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKK 117
           KRK+   + VEGFNVFK+SK   Q +   D+EK ++    S+AKKELN+QIERDA+ RKK
Sbjct: 54  KRKATVADPVEGFNVFKTSKSSAQGIQQNDQEKSEL----SQAKKELNRQIERDALLRKK 109

Query: 118 YNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECF 177
           + IH+SG NVPSPL  F +LSSR+GCESYLL NLAELG+KEPTPIQRQAIP     RECF
Sbjct: 110 HXIHISGNNVPSPLENFSELSSRYGCESYLLHNLAELGFKEPTPIQRQAIP----GRECF 165

Query: 178 ACAPTGSGKTLAFLCPMLMKLR 199
           ACAPTGSGKTLAF+CPMLMKL+
Sbjct: 166 ACAPTGSGKTLAFVCPMLMKLK 187

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440077|ref|XP_004137811.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like [Cucumis sativus]

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 123/201 (61%), Positives = 157/201 (78%), Gaps = 2/201 (0%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVE-GEKTDPEKAMVSFVKK 59
           MEKG SFLFAG+ FDKK+F  DFA+F+  KES+N+ +  S ++ G+    E +  S  +K
Sbjct: 1   MEKGTSFLFAGIHFDKKRFAADFAKFEGKKESDNVVEGPSSIDNGDLEVHEGSTPSDKRK 60

Query: 60  RKRKSIAGETVEGFNVFKSSKQLV-PAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKY 118
           RKRKS   ++VEGF+VFK SK     ++++E    E+ PS+ KKE  +++ERDA+FRKKY
Sbjct: 61  RKRKSATAKSVEGFSVFKDSKSTADTSLNEENHLSENDPSEEKKEFYRKLERDALFRKKY 120

Query: 119 NIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFA 178
           NIHVSG NVPSPL+ F +LS+R+ C+SYLL NL ELG+KEPTPIQRQAIPVLLS RECFA
Sbjct: 121 NIHVSGNNVPSPLQNFGELSTRYDCDSYLLHNLVELGFKEPTPIQRQAIPVLLSGRECFA 180

Query: 179 CAPTGSGKTLAFLCPMLMKLR 199
           CAPTGSGKTLAF+CPMLM+L+
Sbjct: 181 CAPTGSGKTLAFVCPMLMRLK 201

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127806|ref|XP_002329182.1| predicted protein [Populus trichocarpa] gi|222870963|gb|EEF08094.1| predicted protein [Populus trichocarpa]

 Score =  231 bits (590), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 121/201 (60%), Positives = 150/201 (74%), Gaps = 7/201 (3%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKE--SENLADDFSFVEGEKTDPEKAMVSFVK 58
           MEK  SFL  G+ F+KK+F  DF+RFK+ K+   ++  DD S+ + E T+ EK +VS  K
Sbjct: 1   MEKDTSFLLTGIKFNKKRFAGDFSRFKKRKQRNDDSPVDDLSYFKREDTEAEKVVVSVNK 60

Query: 59  KRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKY 118
           KRKRK+ A E VEGF+VFK S  +    D+  E+ E+     +KELN+Q ERD   RKKY
Sbjct: 61  KRKRKTKA-ERVEGFSVFKGSDSVPVVTDEGSEQEENN----QKELNRQNERDLRLRKKY 115

Query: 119 NIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFA 178
            IHVSG NVPSPL++F +LS+R+GCESYLL NL +LG+KEPTPIQRQAIPVLLS RECFA
Sbjct: 116 GIHVSGNNVPSPLQSFAELSTRYGCESYLLHNLVKLGFKEPTPIQRQAIPVLLSGRECFA 175

Query: 179 CAPTGSGKTLAFLCPMLMKLR 199
            APTGSGKTLAF+ PMLMKL+
Sbjct: 176 KAPTGSGKTLAFVYPMLMKLK 196

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297833736|ref|XP_002884750.1| hypothetical protein ARALYDRAFT_478294 [Arabidopsis lyrata subsp. lyrata] gi|297330590|gb|EFH61009.1| hypothetical protein ARALYDRAFT_478294 [Arabidopsis lyrata subsp. lyrata]

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 121/207 (58%), Positives = 153/207 (73%), Gaps = 13/207 (6%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESE--NLADDFSFVEGEKTDPEKAMVSFVK 58
           MEK + FLF G +F+KKKF  DFA+FK   E +  N   +F   E +  + ++ +V F K
Sbjct: 1   MEKSSYFLFGGTNFNKKKFAPDFAKFKNCTEDDDSNKKVNFFVEEEDTEEQKEKVVVFSK 60

Query: 59  KRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGPSK------AKKELNKQIERDA 112
           KRKR+S     VEGF+VFKSSK+ +      K K E+G +K       KKELN+QIERDA
Sbjct: 61  KRKRRSSNSVPVEGFDVFKSSKKAL-----AKGKAEEGNTKNDILEDPKKELNRQIERDA 115

Query: 113 VFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLS 172
           + RK+YNIHVSG N+P PL++F +LSSR+GCE Y+L NLAELG+KEPTPIQRQAIP+LLS
Sbjct: 116 LSRKQYNIHVSGNNIPPPLKSFAELSSRYGCEGYILGNLAELGFKEPTPIQRQAIPILLS 175

Query: 173 DRECFACAPTGSGKTLAFLCPMLMKLR 199
            RECFACAPTGSGKT+AF+CPML+KL+
Sbjct: 176 GRECFACAPTGSGKTVAFICPMLIKLK 202

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505198|ref|XP_003521379.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like [Glycine max]

 Score =  216 bits (551), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 116/207 (56%), Positives = 144/207 (69%), Gaps = 8/207 (3%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVE--GEKT----DPEKAMV 54
           M   +SFLFAG+ FD+KKF  D ARF++     + A   S  E  GEKT    + EK   
Sbjct: 1   MANDSSFLFAGIRFDRKKFGADIARFQKKDSDTDSAMILSAAEDEGEKTIEPLEEEKVAA 60

Query: 55  SFVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEK--EKVEDGPSKAKKELNKQIERDA 112
           S  KKRKRK  + ETVEGFNVF+SS  +  + D+ +  E+  +  +  KKE NKQ+ERDA
Sbjct: 61  STTKKRKRKGTSSETVEGFNVFRSSTSVAQSNDEVRVIEESVELYNNNKKEQNKQLERDA 120

Query: 113 VFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLS 172
           +FRK++NIHVSG NVPSPL++F +L SR+ C SYLLRNL ELG++EPTPIQRQAIPVLL 
Sbjct: 121 IFRKQHNIHVSGYNVPSPLQSFDELKSRYNCPSYLLRNLKELGFREPTPIQRQAIPVLLQ 180

Query: 173 DRECFACAPTGSGKTLAFLCPMLMKLR 199
            RECFACAPTG      F+ PMLMKL+
Sbjct: 181 GRECFACAPTGCVVGSYFVWPMLMKLK 207

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6682259|gb|AAF23311.1|AC016661_36 putative RNA helicase [Arabidopsis thaliana]

 Score =  213 bits (542), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 121/208 (58%), Positives = 155/208 (74%), Gaps = 9/208 (4%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSF-----VEGEKTDPEKAMVS 55
           MEK + FLF G +F+KKKF  DFA+FK + E ++     +F      + E+ + EK +VS
Sbjct: 1   MEKSSYFLFGGTNFNKKKFAPDFAKFKNSTEDDDSNKKVNFFVEEEEDTEQPEAEKVIVS 60

Query: 56  FVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGP--SKAKKELNKQIERDAV 113
             KKRKR+S     VEGF+VFKSSK+   A  K +E++         KKELN+Q+ERDA+
Sbjct: 61  -SKKRKRRSSNSVPVEGFDVFKSSKK-ARAKGKAEEQITKNEIVENPKKELNRQMERDAL 118

Query: 114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
            RK+Y+IHVSG N+P PL++F +LSSR+GCE Y+LRNLAELG+KEPTPIQRQAIP+LLS 
Sbjct: 119 SRKQYSIHVSGNNIPPPLKSFAELSSRYGCEGYILRNLAELGFKEPTPIQRQAIPILLSG 178

Query: 174 RECFACAPTGSGKTLAFLCPMLMKLRVL 201
           RECFACAPTGSGKT AF+CPML+KL+VL
Sbjct: 179 RECFACAPTGSGKTFAFICPMLIKLKVL 206

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330935|ref|NP_187583.2| DEAD-box ATP-dependent RNA helicase 57 [Arabidopsis thaliana] gi|75328099|sp|Q84TG1.1|RH57_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 57 gi|29028778|gb|AAO64768.1| At3g09720 [Arabidopsis thaliana] gi|110742885|dbj|BAE99340.1| RNA helicase like protein [Arabidopsis thaliana] gi|332641282|gb|AEE74803.1| DEAD-box ATP-dependent RNA helicase 57 [Arabidopsis thaliana]

 Score =  210 bits (534), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 119/206 (57%), Positives = 153/206 (74%), Gaps = 9/206 (4%)

Query: 1   MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSF-----VEGEKTDPEKAMVS 55
           MEK + FLF G +F+KKKF  DFA+FK + E ++     +F      + E+ + EK +VS
Sbjct: 1   MEKSSYFLFGGTNFNKKKFAPDFAKFKNSTEDDDSNKKVNFFVEEEEDTEQPEAEKVIVS 60

Query: 56  FVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGP--SKAKKELNKQIERDAV 113
             KKRKR+S     VEGF+VFKSSK+   A  K +E++         KKELN+Q+ERDA+
Sbjct: 61  -SKKRKRRSSNSVPVEGFDVFKSSKK-ARAKGKAEEQITKNEIVENPKKELNRQMERDAL 118

Query: 114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
            RK+Y+IHVSG N+P PL++F +LSSR+GCE Y+LRNLAELG+KEPTPIQRQAIP+LLS 
Sbjct: 119 SRKQYSIHVSGNNIPPPLKSFAELSSRYGCEGYILRNLAELGFKEPTPIQRQAIPILLSG 178

Query: 174 RECFACAPTGSGKTLAFLCPMLMKLR 199
           RECFACAPTGSGKT AF+CPML+KL+
Sbjct: 179 RECFACAPTGSGKTFAFICPMLIKLK 204

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	211
TAIR|locus:2075034	541	AT3G09720 [Arabidopsis thalian	0.933	0.364	0.597	1.7e-57
UNIPROTKB|A5D7C1	596	DDX52 "Probable ATP-dependent	0.706	0.25	0.409	9.6e-26
MGI|MGI:1925644	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.663	0.234	0.424	1e-25
UNIPROTKB|Q9Y2R4	599	DDX52 "Probable ATP-dependent	0.658	0.232	0.416	1e-24
UNIPROTKB|E2RB54	601	DDX52 "Uncharacterized protein	0.872	0.306	0.377	9.9e-23
DICTYBASE|DDB_G0274325	668	ddx52 "DEAD/DEAH box helicase"	0.791	0.25	0.36	1.6e-22
UNIPROTKB|J9P4L6	598	DDX52 "Uncharacterized protein	0.658	0.232	0.419	3.4e-22
RGD|621743	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.668	0.235	0.4	3.4e-22
UNIPROTKB|I3LJA0	507	DDX52 "Uncharacterized protein	0.540	0.224	0.433	2.6e-21
ZFIN|ZDB-GENE-060623-1	606	ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.900	0.313	0.341	4.3e-21

TAIR|locus:2075034 AT3G09720 [Arabidopsis thaliana (taxid:3702)]

 Score = 591 (213.1 bits), Expect = 1.7e-57, P = 1.7e-57
 Identities = 123/206 (59%), Positives = 154/206 (74%)

Query:     1 MEKGASFLFAGVSFDKKKFVTDFARFKENKESE--NLADDFSFVEGEKTD-PE--KAMVS 55
             MEK + FLF G +F+KKKF  DFA+FK + E +  N   +F   E E T+ PE  K +VS
Sbjct:     1 MEKSSYFLFGGTNFNKKKFAPDFAKFKNSTEDDDSNKKVNFFVEEEEDTEQPEAEKVIVS 60

Query:    56 FVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGP--SKAKKELNKQIERDAV 113
               KKRKR+S     VEGF+VFKSSK+   A  K +E++         KKELN+Q+ERDA+
Sbjct:    61 S-KKRKRRSSNSVPVEGFDVFKSSKK-ARAKGKAEEQITKNEIVENPKKELNRQMERDAL 118

Query:   114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
              RK+Y+IHVSG N+P PL++F +LSSR+GCE Y+LRNLAELG+KEPTPIQRQAIP+LLS 
Sbjct:   119 SRKQYSIHVSGNNIPPPLKSFAELSSRYGCEGYILRNLAELGFKEPTPIQRQAIPILLSG 178

Query:   174 RECFACAPTGSGKTLAFLCPMLMKLR 199
             RECFACAPTGSGKT AF+CPML+KL+
Sbjct:   179 RECFACAPTGSGKTFAFICPMLIKLK 204

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

UNIPROTKB|A5D7C1 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Bos taurus (taxid:9913)]

 Score = 273 (101.2 bits), Expect = 9.6e-26, Sum P(2) = 9.6e-26
 Identities = 66/161 (40%), Positives = 95/161 (59%)

Query:    45 EKTDPEKAMVSFVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKEL 104
             EKT+ E  +    + RK+K I  E      V  S+ Q + +V+    K+ED   K K +L
Sbjct:    72 EKTE-ESQIERKKQNRKKKKITSEITSEEEV--STIQWISSVEA---KIEDKNVKRKNKL 125

Query:   105 N----KQIERDAV--FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKE 158
                  +Q+ ++ +  FR K+ IHV G ++P P+ TF +L   +   S LL+N+ + G++ 
Sbjct:   126 TSGKLEQLRKEKLNFFRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQT 185

Query:   159 PTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
             PTPIQ QAIPV+L  RE  A APTGSGKTLAF  P+LM L+
Sbjct:   186 PTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMHLK 226

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

MGI|MGI:1925644 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Mus musculus (taxid:10090)]

 Score = 268 (99.4 bits), Expect = 1.0e-25, Sum P(2) = 1.0e-25
 Identities = 62/146 (42%), Positives = 86/146 (58%)

Query:    58 KKRKRKSIAGETVEGFNVFKSSKQLVPAVDK--EKEKVEDGPSKAKKELNKQIERDAV-- 113
             KK+KRK +  E V     F    Q   +V+   + EKV  G  K      + + ++ V  
Sbjct:    86 KKKKRKKMTSE-VPAQEDFDGGIQWTSSVEAKLQDEKVS-GEKKLTSGKLEHLRKEKVNF 143

Query:   114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
             FR K+ IHV G ++P P+ TF +L   +   S LL+N+ + G++ PTPIQ QAIPV+L  
Sbjct:   144 FRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQVPTPIQMQAIPVMLHG 203

Query:   174 RECFACAPTGSGKTLAFLCPMLMKLR 199
             RE  A APTGSGKTLAF  P+LM+L+
Sbjct:   204 RELLASAPTGSGKTLAFSIPILMQLK 229

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|Q9Y2R4 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Homo sapiens (taxid:9606)]

 Score = 259 (96.2 bits), Expect = 1.0e-24, Sum P(2) = 1.0e-24
 Identities = 60/144 (41%), Positives = 85/144 (59%)

Query:    59 KRKRKSIAGETV---EGFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFR 115
             K+KRK++  E     EG  +   S       DK+ ++ E   +  K E N + E+    R
Sbjct:    87 KKKRKTMTSEIASQEEGATIQWMSSVEAKIEDKKVQR-ESKLTSGKLE-NLRKEKINFLR 144

Query:   116 KKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRE 175
              K+ IHV G ++P P+ TF +L   +   S LL+N+ + G++ PTPIQ QAIPV+L  RE
Sbjct:   145 NKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRE 204

Query:   176 CFACAPTGSGKTLAFLCPMLMKLR 199
               A APTGSGKTLAF  P+LM+L+
Sbjct:   205 LLASAPTGSGKTLAFSIPILMQLK 228

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|E2RB54 DDX52 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 271 (100.5 bits), Expect = 9.9e-23, P = 9.9e-23
 Identities = 74/196 (37%), Positives = 106/196 (54%)

Query:    14 FDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVK------KRKRKSIAG 67
             FD  + V     F  NK+S       S    E  D EK   S  +      K+KRK I+G
Sbjct:    37 FDSSE-VLQGLDFFGNKKSVPGERGASRTHQELQDEEKKEESLTERKREQNKKKRKMISG 95

Query:    68 --ETV--EGFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVS 123
               E +  E  +  + +  +   ++ +K K E+  +  K E N + E+   FR K+ IHV 
Sbjct:    96 ILEIISQEEGSTIQWTSSVEAKIEDKKIKRENKLTSGKLE-NLRKEKINFFRNKHKIHVQ 154

Query:   124 GANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTG 183
             G ++P P+ TF +L   +   S LL+N+ + G++ PTPIQ QAIPV+L  RE  A APTG
Sbjct:   155 GTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQTPTPIQMQAIPVMLHGRELLASAPTG 214

Query:   184 SGKTLAFLCPMLMKLR 199
             SGKTLAF  P+LM+L+
Sbjct:   215 SGKTLAFSIPILMQLK 230

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

DICTYBASE|DDB_G0274325 ddx52 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 270 (100.1 bits), Expect = 1.6e-22, P = 1.6e-22
 Identities = 63/175 (36%), Positives = 93/175 (53%)

Query:    30 KESENLADDFSFVEGEKTDPEKAMVSFVKKRKRKSIAGETVEGFNVFKSSKQLVPAVDKE 89
             ++ +N  DD    E E+ +  K    F+K +       E +  FN    ++    + D +
Sbjct:    89 EDDDNDDDDDDDDEDEENEEPKEK-EFIKHQVNNDEEEEDITLFNKSNENENSDDSDDSD 147

Query:    90 KEKVEDGPSKAKKELNKQIERD------AVFRKKYNIHVSGANVPSPLRTFVKLSSRFGC 143
                     +K KK ++K+ + D      A FR K+ I V G ++P P+  F +L +RF  
Sbjct:   148 DSGKNKNKNKNKK-VSKETQEDKHKREIATFRNKHRIKVDGTDIPDPMTEFSQLENRFKV 206

Query:   144 ESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
               YLL N+ E+GYKEP+PIQ Q IP+LL +RE  A APTGSGKT +F  P+L  L
Sbjct:   207 RKYLLNNINEIGYKEPSPIQMQVIPILLKEREVVAIAPTGSGKTASFSIPILQAL 261

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

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0016887 "ATPase activity" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|J9P4L6 DDX52 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 266 (98.7 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 60/143 (41%), Positives = 89/143 (62%)

Query:    59 KRKRKSIAGETV--EGFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRK 116
             K+KRK I+ E +  E  +  + +  +   ++ +K K E+  +  K E N + E+   FR 
Sbjct:    87 KKKRKMIS-EIISQEEGSTIQWTSSVEAKIEDKKIKRENKLTSGKLE-NLRKEKINFFRN 144

Query:   117 KYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDREC 176
             K+ IHV G ++P P+ TF +L   +   S LL+N+ + G++ PTPIQ QAIPV+L  RE 
Sbjct:   145 KHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQTPTPIQMQAIPVMLHGREL 204

Query:   177 FACAPTGSGKTLAFLCPMLMKLR 199
              A APTGSGKTLAF  P+LM+L+
Sbjct:   205 LASAPTGSGKTLAFSIPILMQLK 227

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

RGD|621743 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Rattus norvegicus (taxid:10116)]

 Score = 266 (98.7 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 58/145 (40%), Positives = 87/145 (60%)

Query:    58 KKRKRKSIAGETVEGFNVFKSSKQLVPAVD-KEKEKVEDGPSKAKKELNKQIERDAV--F 114
             KK+KRK +  + V        + Q   +V+ K ++K  +G  K   E  + + ++ +  F
Sbjct:    86 KKKKRKKMTAD-VPAQEDLDGTIQWTSSVEAKLQDKKANGEKKLTSEKLEHLRKEKINFF 144

Query:   115 RKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDR 174
             R K+ IHV G ++P P+ TF +L   +     LL+N+ + G++ PTPIQ QAIPV+L  R
Sbjct:   145 RNKHKIHVQGTDLPDPIATFQQLDQEYKISPRLLQNILDAGFQVPTPIQMQAIPVMLHGR 204

Query:   175 ECFACAPTGSGKTLAFLCPMLMKLR 199
             E  A APTGSGKTLAF  P+LM+L+
Sbjct:   205 ELLASAPTGSGKTLAFSIPILMQLK 229

GO:0003723 "RNA binding" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=NAS

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=TAS

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

UNIPROTKB|I3LJA0 DDX52 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 256 (95.2 bits), Expect = 2.6e-21, P = 2.6e-21
 Identities = 52/120 (43%), Positives = 78/120 (65%)

Query:    86 VDKEKEKVEDGPSKAKKELN----KQIERDAV--FRKKYNIHVSGANVPSPLRTFVKLSS 139
             +   + K+ED   K +K+L     +++ ++ +  FR K+ IHV G ++P P+ TF +L  
Sbjct:    17 ISSVEAKIEDTKVKREKKLTSGKLEELRKEKINFFRNKHKIHVQGTDLPDPITTFQQLDQ 76

Query:   140 RFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
              +   S LL+N+ + G++ PTPIQ QAIPV+L  RE  A APTGSGKTLAF  P+LM+L+
Sbjct:    77 EYKISSRLLQNILDAGFQLPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLK 136

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-060623-1 ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Danio rerio (taxid:7955)]

 Score = 256 (95.2 bits), Expect = 4.3e-21, P = 4.3e-21
 Identities = 69/202 (34%), Positives = 114/202 (56%)

Query:     3 KGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFVEGEK-TDPEKAMVSFVKKRK 61
             K +S   +G+S+  ++   D +   +++ +E+ A++ S  E ++ T+  KA     K  K
Sbjct:    36 KDSSDQLSGISYFGRETQEDTSL--DSRPNEDDAEEASDEEQKQATESLKAARKKKKGAK 93

Query:    62 RKS--IAGETVEGFNVFKSSKQLVPAVDKEKEKVEDGPS-KAKKEL-NKQIERDAVFRKK 117
             RKS     ET EG  +   S Q      + K++ +D PS K  K+L N+++ R    R +
Sbjct:    94 RKSEDAEPETREGEGIQWMSLQ--NKTKEAKQESKDKPSLKRLKQLHNEKVNR---IRHQ 148

Query:   118 YNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECF 177
               I+V G ++P P+ TF +L   +  +  ++ N+   G++ PTPIQ QA+P+++  RE  
Sbjct:   149 NRINVHGTDIPDPVTTFEELQKEYDLDPRIIHNIKAAGFQTPTPIQMQAVPLMMHKREIL 208

Query:   178 ACAPTGSGKTLAFLCPMLMKLR 199
             ACAPTGSGKT+AF  P+L  LR
Sbjct:   209 ACAPTGSGKTMAFCLPLLAHLR 230

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0016787 "hydrolase activity" 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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	211
cd00268	203	cd00268, DEADc, DEAD-box helicases	2e-20
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	4e-19
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-16
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	8e-16
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-15
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	6e-14
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	3e-13
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-12
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	2e-11
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-10
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	7e-09
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	6e-07
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-06
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	3e-05
COG1205	851	COG1205, COG1205, Distinct helicase family with a	2e-04
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-04
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	4e-04
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	0.001
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	0.002
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	0.003

>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases

 Score = 84.5 bits (210), Expect = 2e-20
 Identities = 31/54 (57%), Positives = 38/54 (70%)

Query: 145 SYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
             LLR +  LG+++PTPIQ +AIP LLS R+    A TGSGKT AFL P+L KL
Sbjct: 8   PELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKL 61

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Length = 203

>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

 Score = 84.5 bits (209), Expect = 4e-19
 Identities = 33/95 (34%), Positives = 48/95 (50%), Gaps = 4/95 (4%)

Query: 104 LNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQ 163
           L ++     V  K  +              F    +  G    LL+ L +LG++EPTPIQ
Sbjct: 1   LAREDYDRFVKLKSAHNVALSRGEEKTPPEF----ASLGLSPELLQALKDLGFEEPTPIQ 56

Query: 164 RQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
             AIP++L+ R+    A TG+GKT AFL P+L K+
Sbjct: 57  LAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKI 91

Length = 513

>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional

 Score = 77.5 bits (191), Expect = 1e-16
 Identities = 40/90 (44%), Positives = 50/90 (55%), Gaps = 4/90 (4%)

Query: 108 IERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAI 167
             +  + R+K  IHV G  VP P+ +F    S  G    LL NL   GY+ PTPIQ QAI
Sbjct: 97  SSQAELLRRKLEIHVKGEAVPPPILSF----SSCGLPPKLLLNLETAGYEFPTPIQMQAI 152

Query: 168 PVLLSDRECFACAPTGSGKTLAFLCPMLMK 197
           P  LS R     A TGSGKT +FL P++ +
Sbjct: 153 PAALSGRSLLVSADTGSGKTASFLVPIISR 182

Length = 518

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 74.8 bits (184), Expect = 8e-16
 Identities = 29/52 (55%), Positives = 37/52 (71%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +LR +AE GY+EPTPIQ+QAIP +L  R+  A A TG+GKT  F  P+L  L
Sbjct: 12  ILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHL 63

Length = 456

>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score = 74.4 bits (183), Expect = 1e-15
 Identities = 38/80 (47%), Positives = 49/80 (61%), Gaps = 5/80 (6%)

Query: 115 RKKYNIH-VSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
           RK+  I  ++G NVP P+ +F   S  F    Y+L++L   G+ EPTPIQ Q  P+ LS 
Sbjct: 112 RKEKEITIIAGENVPKPVVSFEYTS--F--PDYILKSLKNAGFTEPTPIQVQGWPIALSG 167

Query: 174 RECFACAPTGSGKTLAFLCP 193
           R+    A TGSGKTLAFL P
Sbjct: 168 RDMIGIAETGSGKTLAFLLP 187

Length = 545

>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score = 66.5 bits (163), Expect = 6e-14
 Identities = 26/51 (50%), Positives = 32/51 (62%), Gaps = 7/51 (13%)

Query: 160 TPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL-------RVLFI 203
           TPIQ QAIP +LS ++    APTGSGKTLAFL P+L  L       + L +
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVL 51

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 169

>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional

 Score = 67.1 bits (165), Expect = 3e-13
 Identities = 30/54 (55%), Positives = 37/54 (68%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV 200
           LL NL ELGY E TPIQ Q++P +L+ ++  A A TGSGKT AF   +L KL V
Sbjct: 15  LLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDV 68

Length = 460

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 65.3 bits (160), Expect = 1e-12
 Identities = 27/52 (51%), Positives = 31/52 (59%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LL  L + GY  PT IQ +AIP  L  R+    APTG+GKT AFL P L  L
Sbjct: 12  LLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHL 63

Length = 434

>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score = 60.6 bits (147), Expect = 2e-11
 Identities = 26/60 (43%), Positives = 34/60 (56%), Gaps = 7/60 (11%)

Query: 151 LAELGYKEPTPIQRQAIPVLLS-DRECFACAPTGSGKTLAFLCPMLMKL------RVLFI 203
           + + G++   P Q++AI  LLS  R+    APTGSGKTLA L P L  L      RVL +
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVL 60

Length = 201

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 59.5 bits (144), Expect = 2e-10
 Identities = 26/54 (48%), Positives = 37/54 (68%)

Query: 142 GCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPML 195
           G ++ +L  L +LGY++P+PIQ + IP LL+ R+    A TGSGKT AF  P+L
Sbjct: 12  GLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLL 65

Length = 629

>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction only]

 Score = 54.6 bits (132), Expect = 7e-09
 Identities = 21/55 (38%), Positives = 28/55 (50%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL 201
            +R   +  +   TP QR AIP + S       APTGSGKT A   P++ +L  L
Sbjct: 11  RVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSL 65

Length = 814

>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional

 Score = 49.1 bits (118), Expect = 6e-07
 Identities = 18/37 (48%), Positives = 23/37 (62%), Gaps = 1/37 (2%)

Query: 156 YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTL-AFL 191
           +   TP QR AIP++   +     +PTGSGKTL AFL
Sbjct: 30  FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFL 66

Length = 876

>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional

 Score = 47.7 bits (114), Expect = 1e-06
 Identities = 21/53 (39%), Positives = 31/53 (58%)

Query: 139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFL 191
           S F     ++  L + G+   TPIQ  A+P+ L+ R+    A TG+GKT+AFL
Sbjct: 11  SDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFL 63

Length = 423

>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional

 Score = 43.4 bits (102), Expect = 3e-05
 Identities = 24/60 (40%), Positives = 31/60 (51%)

Query: 139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           S F     LL  L   G+   TPIQ   +PV L   +    A TG+GKTLAFL  ++ +L
Sbjct: 12  SSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRL 71

Length = 572

>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 16/52 (30%), Positives = 24/52 (46%)

Query: 144 ESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPML 195
           +  L   L + G +     Q  A+ ++   R       TGSGKT +FL P+L
Sbjct: 56  DESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPIL 107

Length = 851

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 17/36 (47%), Positives = 21/36 (58%), Gaps = 6/36 (16%)

Query: 174 RECFACAPTGSGKTLAFLCPMLMKL------RVLFI 203
           R+    APTGSGKTLA L P+L  L      +VL +
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVL 36

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 40.4 bits (95), Expect = 4e-04
 Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 10/80 (12%)

Query: 134 FVKLSSRFGCESYLLRNLAEL----GYKEPTPIQRQAI-PVLLSDRECFACAPTGSGKTL 188
           F+K       +  L   + E+    G  E    Q++A+   LLSD      APTGSGKTL
Sbjct: 3   FMKEEKLATSKVKLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTL 62

Query: 189 AFLCPMLMKL-----RVLFI 203
             L  +L  L     +V++I
Sbjct: 63  IALLAILSTLLEGGGKVVYI 82

Length = 766

>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 19/56 (33%), Positives = 22/56 (39%), Gaps = 4/56 (7%)

Query: 153 ELGYKEPTPIQRQAI----PVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIP 204
                EP P QR+        L         APTG+GKTLA+L P L   R     
Sbjct: 10  AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKK 65

Length = 654

>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional

 Score = 38.4 bits (89), Expect = 0.002
 Identities = 19/52 (36%), Positives = 30/52 (57%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           L+  + +LG+   TPIQ Q +   L+  +    A TG+GKT AFL  ++ +L
Sbjct: 98  LMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQL 149

Length = 475

>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family

 Score = 37.4 bits (87), Expect = 0.003
 Identities = 16/41 (39%), Positives = 22/41 (53%)

Query: 155 GYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPML 195
           G     P+Q + I  +L  R+CF   PTG GK+L +  P L
Sbjct: 8   GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL 48

All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 470

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	211
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.85
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.78
PTZ00110	545	helicase; Provisional	99.77
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	99.7
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	99.7
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.7
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.7
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.68
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.66
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.65
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.65
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.64
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.62
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.62
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.61
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.61
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.59
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.58
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.58
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.57
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.57
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.57
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.54
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.54
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.53
PTZ00424	401	helicase 45; Provisional	99.51
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.51
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.49
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.48
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	99.45
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.43
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.42
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.4
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.4
KOG0327	397	consensus Translation initiation factor 4F, helica	99.32
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.32
PRK02362	737	ski2-like helicase; Provisional	99.29
PRK00254	720	ski2-like helicase; Provisional	99.24
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.23
PRK13767	876	ATP-dependent helicase; Provisional	99.22
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.17
KOG4284	980	consensus DEAD box protein [Transcription]	99.09
PRK01172	674	ski2-like helicase; Provisional	99.08
COG1205	851	Distinct helicase family with a unique C-terminal	99.01
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.01
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.97
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.93
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.91
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.88
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	98.84
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	98.64
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.63
PRK14701	1638	reverse gyrase; Provisional	98.52
PRK09401	1176	reverse gyrase; Reviewed	98.48
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	98.45
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	98.45
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	98.36
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.34
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.3
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.28
PRK10689	1147	transcription-repair coupling factor; Provisional	98.27
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.26
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.26
PHA02653	675	RNA helicase NPH-II; Provisional	98.02
COG1204	766	Superfamily II helicase [General function predicti	97.98
COG1202	830	Superfamily II helicase, archaea-specific [General	97.94
PRK09200	790	preprotein translocase subunit SecA; Reviewed	97.88
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	97.86
PRK05580	679	primosome assembly protein PriA; Validated	97.76
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	97.76
PHA02558	501	uvsW UvsW helicase; Provisional	97.72
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	97.7
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	97.44
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.31
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.29
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	97.29
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.23
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.18
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.16
KOG0353	695	consensus ATP-dependent DNA helicase [General func	97.08
KOG0354	746	consensus DEAD-box like helicase [General function	96.99
PRK13766	773	Hef nuclease; Provisional	96.95
PRK09694	878	helicase Cas3; Provisional	96.79
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	96.79
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	96.56
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	96.54
PRK12904	830	preprotein translocase subunit SecA; Reviewed	96.43
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	96.41
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.29
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	95.99
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	95.9
PRK13107	908	preprotein translocase subunit SecA; Reviewed	95.85
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.5
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	95.07
PRK13833	323	conjugal transfer protein TrbB; Provisional	94.91
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.61
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	94.39
PF13245	76	AAA_19: Part of AAA domain	94.26
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	94.13
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	93.96
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	93.8
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	93.8
PRK10536	262	hypothetical protein; Provisional	93.57
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	92.69
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	92.54
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	92.36
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	92.3
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	92.17
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	92.17
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	92.07
PRK12326	764	preprotein translocase subunit SecA; Reviewed	91.86
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	91.68
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	91.62
TIGR00376	637	DNA helicase, putative. The gene product may repre	91.48
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	91.46
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	91.22
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	91.05
CHL00122	870	secA preprotein translocase subunit SecA; Validate	90.97
PRK13764	602	ATPase; Provisional	90.97
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	90.61
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	90.55
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	90.37
COG1198	730	PriA Primosomal protein N' (replication factor Y)	90.29
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	90.25
PRK05973	237	replicative DNA helicase; Provisional	90.22
PRK08181	269	transposase; Validated	90.21
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	90.15
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	90.15
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	89.94
PRK13850	670	type IV secretion system protein VirD4; Provisiona	89.71
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	89.2
PRK13851	344	type IV secretion system protein VirB11; Provision	88.97
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	88.93
PRK13897	606	type IV secretion system component VirD4; Provisio	88.87
PRK10436	462	hypothetical protein; Provisional	88.63
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	88.25
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	87.94
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	87.93
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	87.81
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	87.71
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	87.65
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	87.6
PRK13880	636	conjugal transfer coupling protein TraG; Provision	87.53
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	87.43
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	87.26
PRK13876	663	conjugal transfer coupling protein TraG; Provision	86.76
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	86.68
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	86.58
TIGR02533	486	type_II_gspE general secretory pathway protein E.	85.77
KOG1803	649	consensus DNA helicase [Replication, recombination	85.62
PRK13889	988	conjugal transfer relaxase TraA; Provisional	85.49
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	85.15
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	84.95
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	84.81
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	84.47
PRK06921	266	hypothetical protein; Provisional	84.38
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	84.32
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	84.32
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	84.12
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	84.05
PRK13700	732	conjugal transfer protein TraD; Provisional	83.86
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	83.77
PRK06526	254	transposase; Provisional	83.71
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	82.51
PRK13822	641	conjugal transfer coupling protein TraG; Provision	82.42
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	81.79
PRK08116	268	hypothetical protein; Validated	81.62
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	81.42
PRK11054	684	helD DNA helicase IV; Provisional	81.28
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	81.0
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	80.38
TIGR00665	434	DnaB replicative DNA helicase. This model describe	80.32
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	80.26
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	80.12

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.85  E-value=1.6e-21  Score=182.48  Aligned_cols=198  Identities=36%  Similarity=0.488  Sum_probs=137.1

Q ss_pred             CCCcccccccccccccccchhhHHhhhhchhccccccccccc-cCCCCC--c-hhhhhhhhhhhhccccccCcccCcccc
Q 028267            1 MEKGASFLFAGVSFDKKKFVTDFARFKENKESENLADDFSFV-EGEKTD--P-EKAMVSFVKKRKRKSIAGETVEGFNVF   76 (211)
Q Consensus         1 ~~~~~~~l~~g~~f~~~~~~~d~~~~~~~k~~~~~~~~~~~~-~~~~~~--~-~~~~~~~~kkkk~k~~~~~~~e~~~~~   76 (211)
                      |.+-+..||+|+.|.++.|......|.-..+........... ..+..+  . ........+.+.+.+......++....
T Consensus         1 ~~~~f~~it~g~~~~~~~~~k~~~~~~~~lk~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~   80 (593)
T KOG0344|consen    1 MCKRFRSITLGDSRKKESFPKKYAESSSILKTLTDNSKEPLPMHGEWFDPDNLAEPLKSEEKEKLQNSDSSSPLEDIDRR   80 (593)
T ss_pred             CCCcccceecccccccccCCCcchhhhhhccCCccccccccccccccccccccccchhhccchhhhcccchhhhhhhhhc
Confidence            667889999999999999998888887776555543322211 111111  1 111112223344444444444554444


Q ss_pred             cCcccCCcccccccccccCCCchhHHHhhhhHHHHHHHHhhcCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCC
Q 028267           77 KSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGY  156 (211)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~  156 (211)
                      ..++..+....++  ..+.... ..+... ..+.....|..+.+++.|.++|.|+.+|.++..+|.+++.|+++|...||
T Consensus        81 ~~~k~~~~~~e~~--~~~~~~~-~~k~~~-~~~~~~~~Rk~~k~~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F  156 (593)
T KOG0344|consen   81 GSSKKTKPKMEEK--LSEDVIA-AKKKLQ-TSEKLLGIRKSNKINVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGF  156 (593)
T ss_pred             ccccccCchhhhh--ccccHHH-HHHHHh-hhcccccchhcceeeccCCCCCCccccccccchhhhhcHHHHHhHhhCCC
Confidence            4443222211111  1111111 111111 13555678899999999999999999999999999999999999999999


Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ..|+|||.+|||.++.++|+++||||||||||||++|+|++|....
T Consensus       157 ~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~  202 (593)
T KOG0344|consen  157 DEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLS  202 (593)
T ss_pred             CCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999998776

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=99.78  E-value=7.7e-19  Score=165.74  Aligned_cols=90  Identities=43%  Similarity=0.683  Sum_probs=84.2

Q ss_pred             hHHHHHHHHhhcCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchh
Q 028267          107 QIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGK  186 (211)
Q Consensus       107 ~~~~~~~~~~~~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGK  186 (211)
                      .....+.++..++|.+.|.++|.|+.+|.++    +|++.++++|...||..|||||.+|||.++.|+|+|++|+|||||
T Consensus        96 ~~~~~~~~r~~~~i~~~g~~~p~pi~~f~~~----~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGK  171 (518)
T PLN00206         96 SSSQAELLRRKLEIHVKGEAVPPPILSFSSC----GLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGK  171 (518)
T ss_pred             CHHHHHHHHHHCCCEecCCCCCchhcCHHhC----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCc
Confidence            3455677888999999999999999999988    999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHhc
Q 028267          187 TLAFLCPMLMKLRV  200 (211)
Q Consensus       187 Tlaf~lPil~~l~~  200 (211)
                      |++|+||+|.++..
T Consensus       172 TlayllPil~~l~~  185 (518)
T PLN00206        172 TASFLVPIISRCCT  185 (518)
T ss_pred             cHHHHHHHHHHHHh
Confidence            99999999999864

>PTZ00110 helicase; Provisional

Probab=99.77  E-value=1.6e-18  Score=164.61  Aligned_cols=90  Identities=40%  Similarity=0.672  Sum_probs=82.2

Q ss_pred             HHHHHHHHhhcCcee-ccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchh
Q 028267          108 IERDAVFRKKYNIHV-SGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGK  186 (211)
Q Consensus       108 ~~~~~~~~~~~~i~v-~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGK  186 (211)
                      .+....++..+.|.+ .|.++|.|+.+|.++    +|++.++++|..+||..|||||.++||.++.|+|+|++|+|||||
T Consensus       105 ~~~~~~~~~~~~i~~~~g~~~p~p~~~f~~~----~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGK  180 (545)
T PTZ00110        105 SKEVDEIRKEKEITIIAGENVPKPVVSFEYT----SFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGK  180 (545)
T ss_pred             HHHHHHHHHhcCcEEecCCCCCcccCCHhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChH
Confidence            344456777888886 699999999999998    999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHhcc
Q 028267          187 TLAFLCPMLMKLRVL  201 (211)
Q Consensus       187 Tlaf~lPil~~l~~~  201 (211)
                      |++|+||+|.++...
T Consensus       181 TlaylLP~l~~i~~~  195 (545)
T PTZ00110        181 TLAFLLPAIVHINAQ  195 (545)
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999998754

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.70  E-value=1.3e-17  Score=156.42  Aligned_cols=64  Identities=42%  Similarity=0.676  Sum_probs=60.9

Q ss_pred             hcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          137 LSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       137 l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .|+.++|++.+..+|...||..|||||+++||+++.|+|+|++|.|||||||||+||+|++|..
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~  155 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNN  155 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHh
Confidence            3455699999999999999999999999999999999999999999999999999999999986

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.70  E-value=1.5e-17  Score=150.30  Aligned_cols=70  Identities=44%  Similarity=0.621  Sum_probs=65.8

Q ss_pred             chhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCC
Q 028267          131 LRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIP  204 (211)
Q Consensus       131 ~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~  204 (211)
                      ..+|.+|    ++.+.|++++...||..||+||.++||.+|.|+|||+.|.||||||+||+||||++|...+..
T Consensus        60 ~~sf~dL----gv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~  129 (476)
T KOG0330|consen   60 FKSFADL----GVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKL  129 (476)
T ss_pred             hcchhhc----CcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCC
Confidence            3467777    999999999999999999999999999999999999999999999999999999999997766

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=99.70  E-value=1e-17  Score=155.89  Aligned_cols=98  Identities=47%  Similarity=0.730  Sum_probs=88.9

Q ss_pred             HHHhhhhHHH-HHHHHhhcCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEE
Q 028267          101 KKELNKQIER-DAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFAC  179 (211)
Q Consensus       101 ~k~~~~~~~~-~~~~~~~~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~  179 (211)
                      .+.+..+.++ ..++++.++|.+.|..+|.|+++|++.    +||..++..|...||..|||||.+|||.+++.+|+|++
T Consensus       213 ~k~l~Em~~rdwri~redynis~kg~~lpnplrnwEE~----~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igv  288 (673)
T KOG0333|consen  213 EKVLAEMTERDWRIFREDYNISIKGGRLPNPLRNWEES----GFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGV  288 (673)
T ss_pred             hhhHHhcCCccceeeecceeeeecCCCCCccccChhhc----CCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeE
Confidence            3344444433 367889999999999999999999999    99999999999999999999999999999999999999


Q ss_pred             cCCCchhHHHhHHHHHHHHhccc
Q 028267          180 APTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       180 A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      |.||||||+||+||+|..+..+|
T Consensus       289 aETgsGktaaf~ipLl~~IsslP  311 (673)
T KOG0333|consen  289 AETGSGKTAAFLIPLLIWISSLP  311 (673)
T ss_pred             EeccCCccccchhhHHHHHHcCC
Confidence            99999999999999999999887

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.70  E-value=9.2e-18  Score=155.80  Aligned_cols=70  Identities=43%  Similarity=0.636  Sum_probs=65.3

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCC
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPF  205 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~  205 (211)
                      .+|.++    +|+..||+++..+||..|||||..+||..|.|+||++||.||||||.||+||+|++|.-.|..-
T Consensus       181 ~sF~~m----NLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~  250 (691)
T KOG0338|consen  181 ESFQSM----NLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKV  250 (691)
T ss_pred             hhHHhc----ccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccC
Confidence            367666    9999999999999999999999999999999999999999999999999999999998877653

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.68  E-value=4.1e-17  Score=146.08  Aligned_cols=69  Identities=45%  Similarity=0.762  Sum_probs=64.9

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCC
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIP  204 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~  204 (211)
                      ..|..|    ||++++.+.|+.+|+..|||||..+||.||.|+|||+||.||||||+||.||+|++|...|-.
T Consensus         7 ~~F~~L----Gl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~g   75 (442)
T KOG0340|consen    7 KPFSIL----GLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYG   75 (442)
T ss_pred             Cchhhc----CccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCc
Confidence            457777    999999999999999999999999999999999999999999999999999999999997744

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.66  E-value=3e-16  Score=144.05  Aligned_cols=67  Identities=31%  Similarity=0.476  Sum_probs=62.6

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      .+|.++    +|++.++++|..+||..|||||.+|||.++.|+|+|++||||||||++|++|+++.|...+
T Consensus         8 ~~f~~~----~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~   74 (423)
T PRK04837          8 QKFSDF----ALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHP   74 (423)
T ss_pred             CCHhhC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcc
Confidence            467666    9999999999999999999999999999999999999999999999999999999997643

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=99.65  E-value=5.1e-17  Score=147.18  Aligned_cols=91  Identities=40%  Similarity=0.634  Sum_probs=84.2

Q ss_pred             hHHHHHHHHhhcCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchh
Q 028267          107 QIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGK  186 (211)
Q Consensus       107 ~~~~~~~~~~~~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGK  186 (211)
                      +.++.+..|....|.+.|.++|+|+.+|.++    .+|..+|+.|.+.|+.+|||||.+.||.+|.|||+|++|-|||||
T Consensus       145 S~e~~e~vRk~~~I~veGd~ipPPIksF~eM----KFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGK  220 (610)
T KOG0341|consen  145 SEEQRELVRKQLHILVEGDDIPPPIKSFKEM----KFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGK  220 (610)
T ss_pred             hHHHHHHHHHhheEEeeCCCCCCchhhhhhc----cCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCc
Confidence            4455577888999999999999999999998    899999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHhcc
Q 028267          187 TLAFLCPMLMKLRVL  201 (211)
Q Consensus       187 Tlaf~lPil~~l~~~  201 (211)
                      |+.|+||+|+-..+.
T Consensus       221 TlvFvLP~imf~Leq  235 (610)
T KOG0341|consen  221 TLVFVLPVIMFALEQ  235 (610)
T ss_pred             eEEEeHHHHHHHHHH
Confidence            999999999876543

>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

Probab=99.65  E-value=4.5e-16  Score=147.05  Aligned_cols=65  Identities=48%  Similarity=0.789  Sum_probs=62.1

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..|.++    +|++.++++|.++||..|||||.++||.++.|+|++++|+||||||+||+||+|++|..
T Consensus        29 ~~F~~l----~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~   93 (513)
T COG0513          29 PEFASL----GLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILK   93 (513)
T ss_pred             CCHhhc----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhc
Confidence            567777    99999999999999999999999999999999999999999999999999999999884

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.64  E-value=2.3e-16  Score=155.47  Aligned_cols=89  Identities=42%  Similarity=0.718  Sum_probs=80.6

Q ss_pred             HHHHHHhhcC-ceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHH
Q 028267          110 RDAVFRKKYN-IHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTL  188 (211)
Q Consensus       110 ~~~~~~~~~~-i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTl  188 (211)
                      ....++.... |.+.|.++|.|+.+|.+.    |++..+|..|+.+||..|+|||.+|||+|+.|+|||++|.||||||+
T Consensus       342 eV~~yr~~l~~i~v~g~~~pkpv~sW~q~----gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~  417 (997)
T KOG0334|consen  342 EVDEYRCELDGIKVKGKECPKPVTSWTQC----GLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTL  417 (997)
T ss_pred             HHHHhhcCccceeeccCCCCcccchHhhC----CchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccch
Confidence            3344554444 999999999999999999    99999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHhccc
Q 028267          189 AFLCPMLMKLRVLF  202 (211)
Q Consensus       189 af~lPil~~l~~~~  202 (211)
                      +|+||+|-++...+
T Consensus       418 af~LPmirhi~dQr  431 (997)
T KOG0334|consen  418 AFLLPMIRHIKDQR  431 (997)
T ss_pred             hhhcchhhhhhcCC
Confidence            99999998876654

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.62  E-value=7.7e-17  Score=146.81  Aligned_cols=75  Identities=37%  Similarity=0.647  Sum_probs=69.1

Q ss_pred             CCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          125 ANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       125 ~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ..+|.|..+|++.|   ...+++++++...||.+|||||.+|||.+|+|.|++++|+||+||||+|++|-+.++...+
T Consensus       212 rpIPnP~ctFddAF---q~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp  286 (629)
T KOG0336|consen  212 RPIPNPVCTFDDAF---QCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQP  286 (629)
T ss_pred             ccCCCCcCcHHHHH---hhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccc
Confidence            36889999999986   7889999999999999999999999999999999999999999999999999888776543

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.62  E-value=3.7e-16  Score=143.15  Aligned_cols=65  Identities=46%  Similarity=0.719  Sum_probs=61.5

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +|+++    +|.+.|++++..+||+.||-||..|||.+|.|+|||+.|+||||||+||+||+|+.|...
T Consensus        20 tFe~~----gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~   84 (569)
T KOG0346|consen   20 TFEEF----GLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAE   84 (569)
T ss_pred             cHHHh----CCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHh
Confidence            56665    999999999999999999999999999999999999999999999999999999998754

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.61  E-value=2e-15  Score=140.08  Aligned_cols=67  Identities=48%  Similarity=0.623  Sum_probs=62.1

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      .+|.++    +|++.++++|..+||..|||||.+|||.++.|+|+|++|+||||||++|++|+++++....
T Consensus         4 ~~f~~l----~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~   70 (460)
T PRK11776          4 TAFSTL----PLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKR   70 (460)
T ss_pred             CChhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhcc
Confidence            356666    9999999999999999999999999999999999999999999999999999999996543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.61  E-value=2e-15  Score=144.39  Aligned_cols=65  Identities=37%  Similarity=0.533  Sum_probs=61.4

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +|.++    +|++.|+++|..+||..|||||+++||.++.|+|||++|+||||||++|++|++++|...
T Consensus        10 ~f~~l----~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~   74 (572)
T PRK04537         10 TFSSF----DLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSR   74 (572)
T ss_pred             Chhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhc
Confidence            56666    999999999999999999999999999999999999999999999999999999998754

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.59  E-value=2.4e-15  Score=139.76  Aligned_cols=65  Identities=49%  Similarity=0.777  Sum_probs=61.2

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +|+++    +|++.++++|.++||..|||||.++||.++.|+|+|++|+||||||++|+||+++.|...
T Consensus         2 ~f~~l----~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~   66 (456)
T PRK10590          2 SFDSL----GLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITR   66 (456)
T ss_pred             CHHHc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhc
Confidence            46666    999999999999999999999999999999999999999999999999999999998654

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.58  E-value=7.2e-16  Score=144.26  Aligned_cols=70  Identities=33%  Similarity=0.461  Sum_probs=62.9

Q ss_pred             CchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          130 PLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       130 p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      .+..|.+|    .||..+|++|..+||..|||||+.+||++..| .||+|.|.|||||||||.|||+++|.....
T Consensus       179 DvsAW~~l----~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~  249 (731)
T KOG0347|consen  179 DVSAWKNL----FLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSD  249 (731)
T ss_pred             ChHHHhcC----CCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccc
Confidence            34556666    89999999999999999999999999999999 899999999999999999999997765543

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.58  E-value=7.9e-16  Score=142.79  Aligned_cols=80  Identities=40%  Similarity=0.620  Sum_probs=75.0

Q ss_pred             CceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          119 NIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       119 ~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .+.+.|.++|.++.+|++.    .+.+.|+.++..+||..|||||..+||.+..|+|+++||+||||||.||+||+|+++
T Consensus        61 ~v~~~G~~~p~~i~~f~~~----~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~  136 (482)
T KOG0335|consen   61 PVKVSGRDVPPHIPTFDEA----ILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYL  136 (482)
T ss_pred             eeeccCCccCCCccccccc----chhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHH
Confidence            3567899999999999877    899999999999999999999999999999999999999999999999999999999


Q ss_pred             hccc
Q 028267          199 RVLF  202 (211)
Q Consensus       199 ~~~~  202 (211)
                      ....
T Consensus       137 ~~~~  140 (482)
T KOG0335|consen  137 LDEG  140 (482)
T ss_pred             HhcC
Confidence            8763

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.57  E-value=6.7e-15  Score=142.17  Aligned_cols=72  Identities=42%  Similarity=0.681  Sum_probs=64.3

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      +|.++    +|++.++++|.++||..|||||+++||.++.|+|+|++|+||||||++|+||+++.|.......+++
T Consensus         7 ~f~~l----~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~L   78 (629)
T PRK11634          7 TFADL----GLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQIL   78 (629)
T ss_pred             CHhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEE
Confidence            46666    9999999999999999999999999999999999999999999999999999999987654333443

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.57  E-value=8.6e-15  Score=136.52  Aligned_cols=68  Identities=29%  Similarity=0.419  Sum_probs=63.2

Q ss_pred             chhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          131 LRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       131 ~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ...|.++    +|++.|+++|.+.||..||+||+++||.++.|+|+|++|+||||||++|+||+|++|...+
T Consensus        86 ~~~f~~~----~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~  153 (475)
T PRK01297         86 KTRFHDF----NLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTP  153 (475)
T ss_pred             CCCHhHC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcC
Confidence            4456666    9999999999999999999999999999999999999999999999999999999997764

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.57  E-value=8.6e-15  Score=134.63  Aligned_cols=65  Identities=46%  Similarity=0.711  Sum_probs=61.0

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +|+++    +|++.++++|..+||..||+||.++||.++.|+|+|++||||||||++|++|++++|...
T Consensus         2 ~f~~l----~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~   66 (434)
T PRK11192          2 TFSEL----ELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDF   66 (434)
T ss_pred             CHhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhc
Confidence            45555    999999999999999999999999999999999999999999999999999999998753

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.54  E-value=8.2e-15  Score=136.92  Aligned_cols=77  Identities=36%  Similarity=0.568  Sum_probs=66.9

Q ss_pred             chhhhhhcccCCCCHHHHHHHH-HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc----CCC
Q 028267          131 LRTFVKLSSRFGCESYLLRNLA-ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF----IPF  205 (211)
Q Consensus       131 ~~~f~~l~~~~~l~~~ll~~l~-~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~----~~~  205 (211)
                      -..|..+    ||++.|...|. .+++..||.||.+|||.+|.|+|+++.|+|||||||||+|||++.|+...    +..
T Consensus       135 s~~f~~L----GL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~  210 (708)
T KOG0348|consen  135 SAAFASL----GLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSD  210 (708)
T ss_pred             cccchhc----CCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccC
Confidence            3457667    99999999995 57999999999999999999999999999999999999999999998763    345


Q ss_pred             ceEEeC
Q 028267          206 DYFCEL  211 (211)
Q Consensus       206 ~~~~~~  211 (211)
                      ++|++|
T Consensus       211 G~~ALV  216 (708)
T KOG0348|consen  211 GPYALV  216 (708)
T ss_pred             CceEEE
Confidence            666653

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.54  E-value=9.5e-15  Score=134.70  Aligned_cols=67  Identities=42%  Similarity=0.620  Sum_probs=60.8

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +|+++  .++|+++|+++|..+||...||+|+.|||.++.++||++.|+|||||||||++|+++.|.+.
T Consensus         5 ~~~~l--~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr   71 (567)
T KOG0345|consen    5 SFSSL--APPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRR   71 (567)
T ss_pred             chhhc--CCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhh
Confidence            45555  23577999999999999999999999999999999999999999999999999999999554

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.53  E-value=1.3e-14  Score=130.97  Aligned_cols=94  Identities=30%  Similarity=0.471  Sum_probs=80.1

Q ss_pred             HHhhcCceeccCCCCCCchh---hhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC--CcEEEEcCCCchhHH
Q 028267          114 FRKKYNIHVSGANVPSPLRT---FVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD--RECFACAPTGSGKTL  188 (211)
Q Consensus       114 ~~~~~~i~v~g~~~p~p~~~---f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G--~dvi~~A~TGsGKTl  188 (211)
                      ........+.-.+...|+++   |++|    +|.|+|+++|..++|..|+.||+.|+|.+|..  +++|+++.+|||||.
T Consensus        69 l~~~~~~~vk~~dpnsPlyS~ksFeeL----~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTa  144 (477)
T KOG0332|consen   69 LNKFIESNVKLADPNSPLYSAKSFEEL----RLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTA  144 (477)
T ss_pred             hcchhhhceeecCCCCCccccccHHhh----CCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhH
Confidence            33333344444456677775   5555    99999999999999999999999999999987  799999999999999


Q ss_pred             HhHHHHHHHHhcccCCCceEEeC
Q 028267          189 AFLCPMLMKLRVLFIPFDYFCEL  211 (211)
Q Consensus       189 af~lPil~~l~~~~~~~~~~~~~  211 (211)
                      ||+|.+|.++...-.-.++.|+.
T Consensus       145 aFvL~MLsrvd~~~~~PQ~iCLa  167 (477)
T KOG0332|consen  145 AFVLTMLSRVDPDVVVPQCICLA  167 (477)
T ss_pred             HHHHHHHHhcCccccCCCceeeC
Confidence            99999999999998899999984

>PTZ00424 helicase 45; Provisional

Probab=99.51  E-value=4.4e-14  Score=127.88  Aligned_cols=67  Identities=27%  Similarity=0.457  Sum_probs=62.2

Q ss_pred             chhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          131 LRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       131 ~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ..+|.++    +|++.++++|...||..|+|+|.++|+.++.|+|++++||||||||++|++|++..+...
T Consensus        27 ~~~~~~l----~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~   93 (401)
T PTZ00424         27 VDSFDAL----KLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD   93 (401)
T ss_pred             cCCHhhC----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC
Confidence            4566666    999999999999999999999999999999999999999999999999999999998643

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.51  E-value=6.5e-15  Score=138.03  Aligned_cols=66  Identities=41%  Similarity=0.595  Sum_probs=62.2

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .-|.++    +|+..++++|++.+|..||.||..+||..|.|+|||+.|.|||||||||++|+|++|.+.
T Consensus        69 ~kF~dl----pls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~  134 (758)
T KOG0343|consen   69 KKFADL----PLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRL  134 (758)
T ss_pred             hhHHhC----CCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHc
Confidence            345555    999999999999999999999999999999999999999999999999999999999876

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase

Probab=99.49  E-value=6.2e-14  Score=137.72  Aligned_cols=64  Identities=23%  Similarity=0.224  Sum_probs=59.7

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCC
Q 028267          142 GCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPF  205 (211)
Q Consensus       142 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~  205 (211)
                      .|++.|+++|.++||..||+||++|||.++.|+|+|++||||||||+||+||+|+.|...+...
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~   83 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPRAT   83 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCCCcE
Confidence            5899999999999999999999999999999999999999999999999999999998755433

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.48  E-value=2.5e-14  Score=133.13  Aligned_cols=86  Identities=38%  Similarity=0.658  Sum_probs=80.7

Q ss_pred             HHHHhhcCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhH
Q 028267          112 AVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFL  191 (211)
Q Consensus       112 ~~~~~~~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~  191 (211)
                      ...+...++.|.|..+|.|+.+|..+    ++...|+.+++..-|+.|||||.+++|..|.|+||+++|.||||||.||+
T Consensus       203 ~~~r~~Lnlrv~g~s~~rpvtsfeh~----gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi  278 (731)
T KOG0339|consen  203 IDLRLTLNLRVSGSSPPRPVTSFEHF----GFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFI  278 (731)
T ss_pred             hhhHhhhcceeccCCCCCCcchhhhc----CchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHH
Confidence            45667788999999999999999888    99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q 028267          192 CPMLMKLRVL  201 (211)
Q Consensus       192 lPil~~l~~~  201 (211)
                      +|++.++...
T Consensus       279 ~pm~~himdq  288 (731)
T KOG0339|consen  279 WPMIVHIMDQ  288 (731)
T ss_pred             HHHHHHhcch
Confidence            9999998655

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]

Probab=99.45  E-value=2.3e-14  Score=125.68  Aligned_cols=80  Identities=30%  Similarity=0.476  Sum_probs=72.4

Q ss_pred             CCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCc
Q 028267          127 VPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFD  206 (211)
Q Consensus       127 ~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~  206 (211)
                      --.++.+|+++    +|.+.||+++.+.||..|+.||+.|||+++.|+|||++|.+|+|||.+|.+.+|+.+.-.-+..+
T Consensus        22 ~~~v~~~F~~M----gl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ   97 (400)
T KOG0328|consen   22 KVKVIPTFDDM----GLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQ   97 (400)
T ss_pred             Ccccccchhhc----CchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceee
Confidence            33456678887    99999999999999999999999999999999999999999999999999999999988777777


Q ss_pred             eEEe
Q 028267          207 YFCE  210 (211)
Q Consensus       207 ~~~~  210 (211)
                      .+++
T Consensus        98 ~lil  101 (400)
T KOG0328|consen   98 ALIL  101 (400)
T ss_pred             EEEe
Confidence            7664

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.43  E-value=1.6e-14  Score=128.48  Aligned_cols=72  Identities=31%  Similarity=0.487  Sum_probs=65.0

Q ss_pred             ccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceEEe
Q 028267          139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCE  210 (211)
Q Consensus       139 ~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~~  210 (211)
                      +.|.|.+.||..+.+.||..|+|||..+||.+|.|+|+++.|..|+|||.||+||+|+++......-+.+++
T Consensus        88 Ed~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~il  159 (459)
T KOG0326|consen   88 EDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIIL  159 (459)
T ss_pred             HHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEE
Confidence            344999999999999999999999999999999999999999999999999999999999876655555544

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=99.42  E-value=8.7e-14  Score=128.80  Aligned_cols=63  Identities=40%  Similarity=0.658  Sum_probs=59.5

Q ss_pred             ccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       139 ~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ..+.|++.++++|.++||..+|+||+.+||++|.|+|+++.|.||||||+||+||.++.+...
T Consensus        85 ~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~  147 (543)
T KOG0342|consen   85 EEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKL  147 (543)
T ss_pred             hccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhc
Confidence            444999999999999999999999999999999999999999999999999999999998654

>cd00268 DEADc DEAD-box helicases

Probab=99.40  E-value=1.1e-12  Score=107.85  Aligned_cols=63  Identities=51%  Similarity=0.760  Sum_probs=60.3

Q ss_pred             ccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       139 ~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +++++++.+++.|.+.||..|+++|.++|+.++.|+|++++|+||+|||++|++|+++.+...
T Consensus         2 ~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~   64 (203)
T cd00268           2 EELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPS   64 (203)
T ss_pred             CcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhh
Confidence            456999999999999999999999999999999999999999999999999999999999876

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.40  E-value=1.7e-13  Score=125.28  Aligned_cols=66  Identities=44%  Similarity=0.741  Sum_probs=62.3

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      +|..+    ||+..++++|...||..|||||..+||.+|.|+|+++.|+||||||+||+||++++|...-
T Consensus        22 ~fqsm----gL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s   87 (529)
T KOG0337|consen   22 GFQSM----GLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS   87 (529)
T ss_pred             Ccccc----CCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc
Confidence            45555    9999999999999999999999999999999999999999999999999999999998765

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=99.32  E-value=5.2e-13  Score=120.52  Aligned_cols=70  Identities=29%  Similarity=0.510  Sum_probs=63.7

Q ss_pred             CCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          129 SPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       129 ~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      .-+.+|+++    +|++.||+.+...||..||.||+.||+++..|+|++++|++|||||+||++++++++.-..
T Consensus        23 evvdsfddm----~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~   92 (397)
T KOG0327|consen   23 EVVDSFDDM----NLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSV   92 (397)
T ss_pred             HHhhhhhhc----CCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcch
Confidence            344577777    9999999999999999999999999999999999999999999999999999999975433

>COG1201 Lhr Lhr-like helicases [General function prediction only]

Probab=99.32  E-value=3.5e-12  Score=125.56  Aligned_cols=69  Identities=29%  Similarity=0.323  Sum_probs=62.7

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc---CCCceEEeC
Q 028267          142 GCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF---IPFDYFCEL  211 (211)
Q Consensus       142 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~---~~~~~~~~~  211 (211)
                      -|++.+.+.+... |+.|||+|.+|||.+++|+|++++||||||||+|..||+|..|....   ....++|+|
T Consensus         7 ~l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lY   78 (814)
T COG1201           7 ILDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALY   78 (814)
T ss_pred             hcCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEE
Confidence            4789999999888 99999999999999999999999999999999999999999998883   335688875

>PRK02362 ski2-like helicase; Provisional

Probab=99.29  E-value=6.9e-12  Score=123.11  Aligned_cols=63  Identities=29%  Similarity=0.329  Sum_probs=58.7

Q ss_pred             hhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          134 FVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       134 f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      |+++    +|++.++++|...||..|+|+|.+||+. ++.|+|+|++||||||||++|.+|++..+..
T Consensus         3 ~~~l----~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~   66 (737)
T PRK02362          3 IAEL----PLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR   66 (737)
T ss_pred             hhhc----CCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc
Confidence            4555    9999999999999999999999999998 7899999999999999999999999999863

>PRK00254 ski2-like helicase; Provisional

Probab=99.24  E-value=2.1e-11  Score=119.35  Aligned_cols=65  Identities=31%  Similarity=0.318  Sum_probs=59.6

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .|.++    +|++.+++.|...||..|+|+|.++|+. ++.|+|++++||||||||++|.+|++..+...
T Consensus         2 ~~~~l----~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~   67 (720)
T PRK00254          2 KVDEL----RVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE   67 (720)
T ss_pred             cHHHc----CCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc
Confidence            35555    8999999999999999999999999986 89999999999999999999999999998753

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.23  E-value=3.4e-12  Score=110.98  Aligned_cols=84  Identities=21%  Similarity=0.347  Sum_probs=73.6

Q ss_pred             eccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          122 VSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       122 v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ..|+.+..+...|.++    .|.|+|++++.++||.+|+.+|..+||...-|.|++++|.+|.|||..|+|..|++|.+.
T Consensus        32 ~kgsyv~ihssgfrdf----llkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv  107 (387)
T KOG0329|consen   32 KKGSYVSIHSSGFRDF----LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPV  107 (387)
T ss_pred             ccCcEEEEeccchhhh----hcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCC
Confidence            3456666666677776    899999999999999999999999999999999999999999999999999999999887


Q ss_pred             cCCCceEE
Q 028267          202 FIPFDYFC  209 (211)
Q Consensus       202 ~~~~~~~~  209 (211)
                      ++.-.++|
T Consensus       108 ~g~vsvlv  115 (387)
T KOG0329|consen  108 DGQVSVLV  115 (387)
T ss_pred             CCeEEEEE
Confidence            76655444

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.22  E-value=2.2e-11  Score=121.76  Aligned_cols=59  Identities=34%  Similarity=0.464  Sum_probs=52.6

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          142 GCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       142 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .|++.+...+.. +|..|||+|.+|||.++.|+|+|++||||||||++|++|+++.|...
T Consensus        17 ~l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~   75 (876)
T PRK13767         17 LLRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRL   75 (876)
T ss_pred             hcCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhh
Confidence            366766666554 89999999999999999999999999999999999999999998754

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.17  E-value=1.7e-11  Score=114.19  Aligned_cols=66  Identities=30%  Similarity=0.415  Sum_probs=56.5

Q ss_pred             CHHHHHHHHHcCCCCCcHHHHHHHhhHh---------cCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceEEe
Q 028267          144 ESYLLRNLAELGYKEPTPIQRQAIPVLL---------SDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCE  210 (211)
Q Consensus       144 ~~~ll~~l~~~g~~~pt~iQ~~aip~il---------~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~~  210 (211)
                      ...+.++|..+++...||||.+.+|.+|         .++||+|.|+|||||||||+|||++.|...+.+. +-|+
T Consensus       145 ea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~-LRav  219 (620)
T KOG0350|consen  145 EATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKR-LRAV  219 (620)
T ss_pred             HHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccc-eEEE
Confidence            3446677999999999999999999874         3789999999999999999999999999887765 4443

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.09  E-value=2.4e-11  Score=116.10  Aligned_cols=78  Identities=26%  Similarity=0.259  Sum_probs=68.4

Q ss_pred             CCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCC
Q 028267          126 NVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPF  205 (211)
Q Consensus       126 ~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~  205 (211)
                      ..+.....|+++    .|...++..|+.+||..||+||+.|||+++.|.|+|++|.+||||||.|.+-+++.|.......
T Consensus        19 V~~~~~~~fe~l----~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~   94 (980)
T KOG4284|consen   19 VQSNCTPGFEQL----ALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHI   94 (980)
T ss_pred             cccCCCCCHHHH----HHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcc
Confidence            335556678888    8999999999999999999999999999999999999999999999999999999987664443


Q ss_pred             ce
Q 028267          206 DY  207 (211)
Q Consensus       206 ~~  207 (211)
                      +.
T Consensus        95 q~   96 (980)
T KOG4284|consen   95 QK   96 (980)
T ss_pred             ee
Confidence            33

>PRK01172 ski2-like helicase; Provisional

Probab=99.08  E-value=3e-10  Score=110.41  Aligned_cols=59  Identities=22%  Similarity=0.291  Sum_probs=56.2

Q ss_pred             CCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       141 ~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ++|++.+++.+...||. |+++|.++|+.++.|+|++++||||||||++|.++++..+..
T Consensus         6 ~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~   64 (674)
T PRK01172          6 LGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA   64 (674)
T ss_pred             cCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh
Confidence            49999999999999997 999999999999999999999999999999999999998875

>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

Probab=99.01  E-value=5.3e-10  Score=111.48  Aligned_cols=66  Identities=26%  Similarity=0.258  Sum_probs=60.0

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          143 CESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       143 l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      ....+..+|...|+..|+++|.+||-.+..|+|||++++||||||++|+|||++++.+.+...++|
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~  120 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALL  120 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEE
Confidence            455678889999999999999999999999999999999999999999999999999988775554

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.01  E-value=3.5e-10  Score=105.67  Aligned_cols=44  Identities=36%  Similarity=0.706  Sum_probs=41.9

Q ss_pred             HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHH
Q 028267          153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      ..||..|+|+|.++|+.++.|+|+++++|||||||++|++|++.
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~   49 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC   49 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHH
Confidence            46999999999999999999999999999999999999999875

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.97  E-value=1.1e-09  Score=105.53  Aligned_cols=55  Identities=38%  Similarity=0.661  Sum_probs=46.5

Q ss_pred             CCHHHHHHHHH-cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          143 CESYLLRNLAE-LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       143 l~~~ll~~l~~-~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      +.......|.. .||..|+|+|..+|+.++.|+|+++++|||+|||++|++|++..
T Consensus         9 ~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~   64 (607)
T PRK11057          9 LESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL   64 (607)
T ss_pred             chhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc
Confidence            33334444433 59999999999999999999999999999999999999998854

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.93  E-value=1.5e-09  Score=108.04  Aligned_cols=62  Identities=24%  Similarity=0.410  Sum_probs=57.2

Q ss_pred             ccCCCCHHHHHHHH-----HcCCCCC---cHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          139 SRFGCESYLLRNLA-----ELGYKEP---TPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       139 ~~~~l~~~ll~~l~-----~~g~~~p---t~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +.|.+.+.+.+.+.     .+||..|   +|+|.++||.++.|+|+|++++||||||+||+||++.++..
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~  134 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALT  134 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhh
Confidence            45689999988887     7899999   99999999999999999999999999999999999998864

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional

Probab=98.91  E-value=2.1e-09  Score=108.83  Aligned_cols=58  Identities=31%  Similarity=0.454  Sum_probs=50.2

Q ss_pred             cCCCCHHHHHHHHH-cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          140 RFGCESYLLRNLAE-LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       140 ~~~l~~~ll~~l~~-~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      .|.....|...+.. .||..++|+|.++|++++.|+|+|+++|||+|||++|+||+|..
T Consensus       441 ~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~  499 (1195)
T PLN03137        441 NFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC  499 (1195)
T ss_pred             CCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc
Confidence            45666666665543 69999999999999999999999999999999999999999853

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=98.88  E-value=2.1e-09  Score=103.09  Aligned_cols=44  Identities=34%  Similarity=0.669  Sum_probs=42.1

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      .||..++|+|.++|+.++.|+|+++++|||+|||++|++|++..
T Consensus         9 fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~   52 (591)
T TIGR01389         9 FGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL   52 (591)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc
Confidence            79999999999999999999999999999999999999999853

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=98.84  E-value=1e-09  Score=101.40  Aligned_cols=62  Identities=37%  Similarity=0.506  Sum_probs=57.7

Q ss_pred             ccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       139 ~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ++|++-|+|-.+..++.+.-||.||+.+||.||.|-|++..|.||||||-||+||||+-+-+
T Consensus         5 ~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv~e   66 (725)
T KOG0349|consen    5 EEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWE   66 (725)
T ss_pred             HhhCcchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHHHH
Confidence            44599999999999999999999999999999999999999999999999999999987643

>TIGR01054 rgy reverse gyrase

Probab=98.64  E-value=7e-08  Score=99.29  Aligned_cols=53  Identities=28%  Similarity=0.221  Sum_probs=44.8

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       147 ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +.+.+.......||+||+.+||.++.|+|++++||||||||+ |++|++..+..
T Consensus        67 f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~  119 (1171)
T TIGR01054        67 FEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK  119 (1171)
T ss_pred             HHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh
Confidence            344455555568999999999999999999999999999997 88898887754

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype

Probab=98.63  E-value=4.1e-08  Score=97.50  Aligned_cols=41  Identities=29%  Similarity=0.387  Sum_probs=36.6

Q ss_pred             cCCCCCcHHHHHHHhhHhcCC-cEEEEcCCCchhHHHhHHHHH
Q 028267          154 LGYKEPTPIQRQAIPVLLSDR-ECFACAPTGSGKTLAFLCPML  195 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~-dvi~~A~TGsGKTlaf~lPil  195 (211)
                      .||. |||||.++||.++.|+ +++++|+||||||++|+++++
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll   53 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLL   53 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhc
Confidence            5898 9999999999999998 688889999999997776665

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>PRK14701 reverse gyrase; Provisional

Probab=98.52  E-value=2.1e-07  Score=98.20  Aligned_cols=51  Identities=24%  Similarity=0.199  Sum_probs=42.0

Q ss_pred             HHHHHHHH-cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          146 YLLRNLAE-LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       146 ~ll~~l~~-~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      .+.+.+.. .|| .||++|..+||.++.|+|++++||||||||+.++++.+..
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~  118 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFL  118 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHH
Confidence            34455655 899 6999999999999999999999999999999655555443

>PRK09401 reverse gyrase; Reviewed

Probab=98.48  E-value=2.8e-07  Score=94.88  Aligned_cols=45  Identities=36%  Similarity=0.349  Sum_probs=40.0

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .|+ .||++|..+||.++.|+|++++||||||||+ |++|++..+..
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~  121 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK  121 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh
Confidence            467 8999999999999999999999999999995 77887777654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=98.45  E-value=3.9e-07  Score=91.91  Aligned_cols=57  Identities=21%  Similarity=0.279  Sum_probs=48.0

Q ss_pred             CCHHHHHHHHH-cCCCCCcHHHHHHHhhHhcC------CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          143 CESYLLRNLAE-LGYKEPTPIQRQAIPVLLSD------RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       143 l~~~ll~~l~~-~g~~~pt~iQ~~aip~il~G------~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+..++..+.+ .+| .|||+|..||+.++.+      +|+++||+||||||++|++|++..+..
T Consensus       436 ~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~  499 (926)
T TIGR00580       436 PDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD  499 (926)
T ss_pred             CCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh
Confidence            34455566655 588 5999999999999985      799999999999999999999998865

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=98.45  E-value=4.6e-07  Score=87.88  Aligned_cols=53  Identities=30%  Similarity=0.389  Sum_probs=46.3

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHhhHhcC------CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          147 LLRNLAELGYKEPTPIQRQAIPVLLSD------RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       147 ll~~l~~~g~~~pt~iQ~~aip~il~G------~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +...+...+| .||++|..||+.++.+      .+.+++|+||||||++|++|++..+..
T Consensus       225 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~  283 (630)
T TIGR00643       225 LTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA  283 (630)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            4455678899 7999999999999887      368999999999999999999998864

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=98.36  E-value=1.2e-06  Score=85.90  Aligned_cols=54  Identities=28%  Similarity=0.386  Sum_probs=45.4

Q ss_pred             HHHHHH-HHcCCCCCcHHHHHHHhhHhcC------CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          146 YLLRNL-AELGYKEPTPIQRQAIPVLLSD------RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       146 ~ll~~l-~~~g~~~pt~iQ~~aip~il~G------~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+++.+ ...+| .||++|..||+.++.+      .++|++|+||||||++|++|++..+..
T Consensus       249 ~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~  309 (681)
T PRK10917        249 ELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA  309 (681)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            344443 55677 6999999999999887      489999999999999999999998864

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.34  E-value=8.7e-07  Score=86.25  Aligned_cols=44  Identities=34%  Similarity=0.278  Sum_probs=40.0

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .|. .||+||..++|.++.|+  |+++.||+|||++|++|++.....
T Consensus       100 lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~  143 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA  143 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc
Confidence            344 79999999999999999  899999999999999999988654

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.30  E-value=1.4e-06  Score=68.99  Aligned_cols=50  Identities=46%  Similarity=0.646  Sum_probs=45.7

Q ss_pred             HcCCCCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          153 ELGYKEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ..++..|++.|.+++..++.+ +.++++++||||||.+++++++..+....
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~   53 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK   53 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC
Confidence            356888999999999999999 99999999999999999999999988754

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=98.28  E-value=1.8e-06  Score=86.44  Aligned_cols=56  Identities=32%  Similarity=0.444  Sum_probs=47.9

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHh----hHhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          143 CESYLLRNLAELGYKEPTPIQRQAIP----VLLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       143 l~~~ll~~l~~~g~~~pt~iQ~~aip----~il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      +++.+...+...||. +.|.|.+.+.    .+..|+++++.|+||+|||+||++|++..+.
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~  290 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI  290 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc
Confidence            445677888889997 7899998776    4567899999999999999999999998876

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=98.27  E-value=1.7e-06  Score=89.01  Aligned_cols=52  Identities=29%  Similarity=0.387  Sum_probs=45.0

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHhhHhcC------CcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          147 LLRNLAELGYKEPTPIQRQAIPVLLSD------RECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       147 ll~~l~~~g~~~pt~iQ~~aip~il~G------~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      ..+.....+| .||++|..||+.++.+      +|+++||+||+|||++|+++++..+.
T Consensus       590 ~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~  647 (1147)
T PRK10689        590 YQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE  647 (1147)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH
Confidence            3444577788 7999999999999987      89999999999999999988877664

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.26  E-value=1.7e-06  Score=76.43  Aligned_cols=45  Identities=40%  Similarity=0.532  Sum_probs=37.9

Q ss_pred             CcHHHHHHH----hhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          159 PTPIQRQAI----PVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       159 pt~iQ~~ai----p~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      |+|+|.+.+    ..+..|.++|+.||||+|||++|++|++..+.....
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~   57 (289)
T smart00489        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE   57 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc
Confidence            689999944    456678999999999999999999999988776544

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.26  E-value=1.7e-06  Score=76.43  Aligned_cols=45  Identities=40%  Similarity=0.532  Sum_probs=37.9

Q ss_pred             CcHHHHHHH----hhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          159 PTPIQRQAI----PVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       159 pt~iQ~~ai----p~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      |+|+|.+.+    ..+..|.++|+.||||+|||++|++|++..+.....
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~   57 (289)
T smart00488        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE   57 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc
Confidence            689999944    456678999999999999999999999988776544

>PHA02653 RNA helicase NPH-II; Provisional

Probab=98.02  E-value=5.7e-06  Score=81.09  Aligned_cols=38  Identities=24%  Similarity=0.293  Sum_probs=34.4

Q ss_pred             HHHHHHhhHhcCCcEEEEcCCCchhHHH---------hHHHHHHHHh
Q 028267          162 IQRQAIPVLLSDRECFACAPTGSGKTLA---------FLCPMLMKLR  199 (211)
Q Consensus       162 iQ~~aip~il~G~dvi~~A~TGsGKTla---------f~lPil~~l~  199 (211)
                      ||.+.++.++.|+|+|++|+||||||.+         |++|.+..+.
T Consensus       168 iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~  214 (675)
T PHA02653        168 VQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLD  214 (675)
T ss_pred             HHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhh
Confidence            9999999999999999999999999997         6677777664

>COG1204 Superfamily II helicase [General function prediction only]

Probab=97.98  E-value=9.2e-06  Score=80.64  Aligned_cols=60  Identities=37%  Similarity=0.377  Sum_probs=52.1

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          142 GCESYLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       142 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .+++.++..+...|+..+++-|+.++.. ++.|.|+|+|||||||||+...+.|++.+...
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~   75 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG   75 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc
Confidence            3777888888999998888877777765 55679999999999999999999999999976

>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]

Probab=97.94  E-value=1.4e-05  Score=76.62  Aligned_cols=62  Identities=26%  Similarity=0.237  Sum_probs=56.4

Q ss_pred             cCCCCHHHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          140 RFGCESYLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       140 ~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ++.||+.+.+.|...|++.+.|+|..|+.. +|.|.|+++++.|+|||||.--|.-|.+++..
T Consensus       198 eLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~  260 (830)
T COG1202         198 ELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSG  260 (830)
T ss_pred             ccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhC
Confidence            349999999999999999999999999987 78999999999999999999888888887763

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=97.88  E-value=2e-05  Score=78.38  Aligned_cols=46  Identities=30%  Similarity=0.352  Sum_probs=40.0

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +..|. .|+++|..++++++.|+  |+++.||+|||++|++|++.....
T Consensus        73 R~~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~  118 (790)
T PRK09200         73 RVLGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE  118 (790)
T ss_pred             HHhCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc
Confidence            33466 89999999999999998  899999999999999999865543

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=97.86  E-value=1.1e-05  Score=81.02  Aligned_cols=48  Identities=31%  Similarity=0.501  Sum_probs=43.8

Q ss_pred             cCCCCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          154 LGYKEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .+|+.+..||..++|.++.. -|+|+|||||||||..|+|.||..+...
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~  154 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEH  154 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhh
Confidence            46888999999999999865 7999999999999999999999999863

>PRK05580 primosome assembly protein PriA; Validated

Probab=97.76  E-value=9e-05  Score=72.77  Aligned_cols=43  Identities=26%  Similarity=0.262  Sum_probs=38.5

Q ss_pred             CCcHHHHHHHhhHhcC---CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          158 EPTPIQRQAIPVLLSD---RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G---~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .||+.|.+++..++.+   .+++++|+||||||.+|+.++...+..
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~  189 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ  189 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc
Confidence            4899999999999874   889999999999999999988877764

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=97.76  E-value=3.6e-05  Score=76.15  Aligned_cols=46  Identities=30%  Similarity=0.318  Sum_probs=37.8

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +..|. .|+++|..++..+..|  .|++++||+|||++|++|++.+...
T Consensus        65 R~lgl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~  110 (762)
T TIGR03714        65 RVLGM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALT  110 (762)
T ss_pred             hhcCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhc
Confidence            34465 7888888888877777  6999999999999999998877654

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=97.72  E-value=6.5e-05  Score=71.07  Aligned_cols=37  Identities=27%  Similarity=0.213  Sum_probs=33.7

Q ss_pred             CCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHH
Q 028267          156 YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLC  192 (211)
Q Consensus       156 ~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~l  192 (211)
                      ...|+++|..|++.++.+.++|++++||+|||+++++
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~  148 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYL  148 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHH
Confidence            4589999999999999999999999999999997654

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=97.70  E-value=4.5e-05  Score=75.27  Aligned_cols=43  Identities=33%  Similarity=0.342  Sum_probs=37.5

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHH-HHHh
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPML-MKLR  199 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil-~~l~  199 (211)
                      .|. .|+++|..+++.++.|+  |++++||+|||++|++|++ ..|.
T Consensus        53 lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~   96 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT   96 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh
Confidence            354 79999999999999887  9999999999999999995 5554

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]

Probab=97.44  E-value=0.00011  Score=70.92  Aligned_cols=44  Identities=36%  Similarity=0.662  Sum_probs=41.8

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      .||....|-|..+|..+++|+|+++.-|||.||+++|.||.+-.
T Consensus        13 fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~   56 (590)
T COG0514          13 FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL   56 (590)
T ss_pred             hCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc
Confidence            48999999999999999999999999999999999999998765

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=97.31  E-value=0.0003  Score=70.53  Aligned_cols=47  Identities=34%  Similarity=0.488  Sum_probs=36.7

Q ss_pred             HHHcCCCCCcHHHHHHHhhH----hcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          151 LAELGYKEPTPIQRQAIPVL----LSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~i----l~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      +.--|| .+.+.|......+    ..|..++++|+||||||+||++|++...
T Consensus       239 ~~~~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~  289 (820)
T PRK07246        239 IALLGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS  289 (820)
T ss_pred             hccCCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc
Confidence            334466 4688888855443    4578899999999999999999999865

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=97.29  E-value=0.00064  Score=65.99  Aligned_cols=50  Identities=36%  Similarity=0.410  Sum_probs=39.9

Q ss_pred             HcCCCCCcHHHHHHHhhH----hcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          153 ELGYKEPTPIQRQAIPVL----LSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~i----l~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ....-.|.+.|.+++-.+    ..|+.+++.||||+|||++|++|+|.......
T Consensus        10 ~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~   63 (654)
T COG1199          10 AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG   63 (654)
T ss_pred             hCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC
Confidence            344567899999888643    34566999999999999999999999876543

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=97.29  E-value=0.0002  Score=66.73  Aligned_cols=51  Identities=29%  Similarity=0.573  Sum_probs=40.4

Q ss_pred             HHHHHHH-cCCCC-CcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHH
Q 028267          147 LLRNLAE-LGYKE-PTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       147 ll~~l~~-~g~~~-pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      +..+|.. .||.. -|+.|.+|+..+..+ .||.|+.|||+||.|+|.||.|..
T Consensus         7 VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~   60 (641)
T KOG0352|consen    7 VREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH   60 (641)
T ss_pred             HHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh
Confidence            3444533 25544 378999999998877 799999999999999999998764

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.23  E-value=0.00055  Score=67.44  Aligned_cols=47  Identities=28%  Similarity=0.338  Sum_probs=39.2

Q ss_pred             CCCCcHHHHHHHhh----HhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          156 YKEPTPIQRQAIPV----LLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       156 ~~~pt~iQ~~aip~----il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      |..+.|.|.+.+-.    +..|.++++.||||+|||++.+.|.|..+...+
T Consensus         8 y~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~   58 (705)
T TIGR00604         8 YEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP   58 (705)
T ss_pred             CCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc
Confidence            56668889887765    457889999999999999999999999877544

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.18  E-value=0.00098  Score=65.76  Aligned_cols=45  Identities=36%  Similarity=0.410  Sum_probs=35.0

Q ss_pred             CCCCCcHHHHHHHhhHh---c------CCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          155 GYKEPTPIQRQAIPVLL---S------DRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       155 g~~~pt~iQ~~aip~il---~------G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      || .+.+-|.+.+-.|.   .      +..+++-|+||+|||+||++|.+-....
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~   76 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARA   76 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHH
Confidence            55 56788888665543   3      3679999999999999999999876553

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=97.16  E-value=0.0006  Score=69.22  Aligned_cols=45  Identities=27%  Similarity=0.360  Sum_probs=36.5

Q ss_pred             CCCCCcHHHHHHHhhH----hcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          155 GYKEPTPIQRQAIPVL----LSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       155 g~~~pt~iQ~~aip~i----l~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      || .+.|-|.+.+..+    -.+..+++-|+||+|||+||++|++.....
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~  303 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK  303 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhc
Confidence            45 5788888866544    467899999999999999999999876653

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=97.08  E-value=0.00062  Score=62.84  Aligned_cols=58  Identities=28%  Similarity=0.402  Sum_probs=47.9

Q ss_pred             ccCCCCHHHHHHHHHc-CCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHH
Q 028267          139 SRFGCESYLLRNLAEL-GYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       139 ~~~~l~~~ll~~l~~~-g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      +.|+.+......|... ......|.|..+|.+.+.|.|++++-|||-||.|+|.||.|.
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~  132 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALC  132 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHh
Confidence            3457777666655443 356778999999999999999999999999999999999874

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=96.99  E-value=0.00093  Score=65.87  Aligned_cols=60  Identities=18%  Similarity=0.092  Sum_probs=47.3

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          143 CESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       143 l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      +.+...+.+.--+.-.+...|..-...+| |+++|+++|||+|||+..+.-++.++...+.
T Consensus        47 ~~~s~~~~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~  106 (746)
T KOG0354|consen   47 LDESAAQRWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK  106 (746)
T ss_pred             CChhhhccccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc
Confidence            44444444443445566778888888888 9999999999999999999999999987765

>PRK13766 Hef nuclease; Provisional

Probab=96.95  E-value=0.0015  Score=64.71  Aligned_cols=44  Identities=25%  Similarity=0.249  Sum_probs=38.6

Q ss_pred             CCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          155 GYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       155 g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      +.-.|.+.|...+..++.+ |+|++++||+|||++++++++..+.
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~   55 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH   55 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH
Confidence            3447888999998888887 8999999999999999999998884

>PRK09694 helicase Cas3; Provisional

Probab=96.79  E-value=0.0023  Score=64.65  Aligned_cols=51  Identities=27%  Similarity=0.184  Sum_probs=35.7

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      ..|+|+|..+......+.-+|+.||||+|||.+.++.+. +|........+|
T Consensus       285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~-~l~~~~~~~gi~  335 (878)
T PRK09694        285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAW-RLIDQGLADSII  335 (878)
T ss_pred             CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHH-HHHHhCCCCeEE
Confidence            479999998865544556789999999999999765544 444433333333

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=96.79  E-value=0.0016  Score=65.59  Aligned_cols=42  Identities=26%  Similarity=0.169  Sum_probs=35.1

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..|+++|...--++..|+  |+.++||+|||++|+||++..+..
T Consensus        81 ~~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~  122 (896)
T PRK13104         81 LRHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAIS  122 (896)
T ss_pred             CCcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhc
Confidence            468999988766666665  789999999999999999988754

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=96.56  E-value=0.0044  Score=64.12  Aligned_cols=67  Identities=24%  Similarity=0.266  Sum_probs=54.1

Q ss_pred             hhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          135 VKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       135 ~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      +.+..-..+|.+...++.  |...+..||....+.++.+ -++++|||||+|||...++.||+.|..+-.
T Consensus       288 Ekl~~iselP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r  355 (1674)
T KOG0951|consen  288 EKLVKISELPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLR  355 (1674)
T ss_pred             ceeEeecCCcchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccc
Confidence            334444466667776664  5667999999999999988 689999999999999999999999977644

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=96.54  E-value=0.0012  Score=66.99  Aligned_cols=49  Identities=39%  Similarity=0.558  Sum_probs=43.1

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHH
Q 028267          147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPML  195 (211)
Q Consensus       147 ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil  195 (211)
                      +.......|+....|.|.++|..++.|+|+++..|||.||.|+|.||.+
T Consensus       253 ~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~  301 (941)
T KOG0351|consen  253 ELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPAL  301 (941)
T ss_pred             HHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccc
Confidence            3334456689999999999999999999999999999999999999865

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=96.43  E-value=0.0032  Score=63.12  Aligned_cols=43  Identities=33%  Similarity=0.299  Sum_probs=36.3

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHH-HHHh
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPML-MKLR  199 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil-~~l~  199 (211)
                      .|. .|+++|..+.-++..|+  |+.+.||+|||++|++|++ ..|.
T Consensus        78 lg~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~  121 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALT  121 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHc
Confidence            444 78999999887788885  8999999999999999995 6664

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

Probab=96.41  E-value=0.0056  Score=62.56  Aligned_cols=52  Identities=33%  Similarity=0.461  Sum_probs=43.4

Q ss_pred             HHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          150 NLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       150 ~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ..+..|| .|-++|+.|+-++.+|..|++||+||+|||+.--+.|-..+....
T Consensus       112 ~~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~q  163 (1041)
T COG4581         112 PAREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQ  163 (1041)
T ss_pred             HHHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCC
Confidence            3455677 578999999999999999999999999999997777776666543

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.29  E-value=0.015  Score=52.28  Aligned_cols=52  Identities=29%  Similarity=0.408  Sum_probs=37.2

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          145 SYLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       145 ~~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      ...+..|...|+  +++.|...+-. +..+.+++++++|||||| +|+-.++..+.
T Consensus       121 ~~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~~  173 (319)
T PRK13894        121 IFTLDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEMV  173 (319)
T ss_pred             CCCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhhh
Confidence            344566666676  45667766654 567789999999999999 56666776653

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

Probab=95.99  E-value=0.0097  Score=55.68  Aligned_cols=43  Identities=30%  Similarity=0.454  Sum_probs=35.2

Q ss_pred             CCCCcHHHHHHHhhHhc----CCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          156 YKEPTPIQRQAIPVLLS----DRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       156 ~~~pt~iQ~~aip~il~----G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      ...|.+.|.+|+..+..    ++..+++.|||+|||..++ -++..+.
T Consensus        34 ~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~-~~~~~~~   80 (442)
T COG1061          34 EFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAA-EAIAELK   80 (442)
T ss_pred             CCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHH-HHHHHhc
Confidence            34589999999999988    8999999999999999885 3444443

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional

Probab=95.90  E-value=0.015  Score=60.32  Aligned_cols=45  Identities=24%  Similarity=0.227  Sum_probs=35.0

Q ss_pred             CCCcHHHHHHHhhHh----cC-CcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          157 KEPTPIQRQAIPVLL----SD-RECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       157 ~~pt~iQ~~aip~il----~G-~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ..|.+.|..||..+.    .| +.+|++.+||||||++. +.++.+|....
T Consensus       412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~~  461 (1123)
T PRK11448        412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKAK  461 (1123)
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhcC
Confidence            358999999998765    34 67999999999999984 56667765543

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=95.85  E-value=0.0069  Score=61.11  Aligned_cols=44  Identities=30%  Similarity=0.248  Sum_probs=34.9

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .|. .|+++|-..--.+..|+  |+.++||+||||+|.+|++.....
T Consensus        79 lgm-~~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~  122 (908)
T PRK13107         79 FEM-RHFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALT  122 (908)
T ss_pred             hCC-CcCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhc
Confidence            344 67899987655555665  789999999999999999977654

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.50  E-value=0.019  Score=51.79  Aligned_cols=57  Identities=23%  Similarity=0.290  Sum_probs=42.1

Q ss_pred             eccCCCCCCchhhhhhcccCCCCHHHHHHHHH-cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          122 VSGANVPSPLRTFVKLSSRFGCESYLLRNLAE-LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       122 v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~-~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..-..+|..+.+|+++    ++|+.+.+.+.. +|.                   |+|.+||||||+.+.+ .||.++.+
T Consensus        96 ~vlR~Ip~~i~~~e~L----glP~i~~~~~~~~~GL-------------------ILVTGpTGSGKSTTlA-amId~iN~  151 (353)
T COG2805          96 LVLRLIPSKIPTLEEL----GLPPIVRELAESPRGL-------------------ILVTGPTGSGKSTTLA-AMIDYINK  151 (353)
T ss_pred             EEEeccCccCCCHHHc----CCCHHHHHHHhCCCce-------------------EEEeCCCCCcHHHHHH-HHHHHHhc
Confidence            3335678888899988    999988873321 222                   8899999999988764 78888776


Q ss_pred             cc
Q 028267          201 LF  202 (211)
Q Consensus       201 ~~  202 (211)
                      ..
T Consensus       152 ~~  153 (353)
T COG2805         152 HK  153 (353)
T ss_pred             cC
Confidence            53

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=95.07  E-value=0.024  Score=44.72  Aligned_cols=26  Identities=42%  Similarity=0.576  Sum_probs=20.7

Q ss_pred             hcCCcEEEEcCCCchhHHHhHHHHHH
Q 028267          171 LSDRECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       171 l~G~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      ...+.+++.++||||||...+..+..
T Consensus        23 ~~~~~~ll~~~tGsGKT~~~~~~~~~   48 (184)
T PF04851_consen   23 KEERRVLLNAPTGSGKTIIALALILE   48 (184)
T ss_dssp             SGCSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCcChhhhhhhhc
Confidence            34688999999999999998754433

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=94.91  E-value=0.099  Score=47.25  Aligned_cols=50  Identities=22%  Similarity=0.153  Sum_probs=34.0

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          147 LLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       147 ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .+..+...|.  .++.|...|-. +..+.++|++++||||||... -.++..+.
T Consensus       119 tl~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i~  169 (323)
T PRK13833        119 PLDDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEIV  169 (323)
T ss_pred             CHHHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHHh
Confidence            3445556665  45667666554 456689999999999999743 45666554

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.61  E-value=0.13  Score=45.86  Aligned_cols=52  Identities=27%  Similarity=0.394  Sum_probs=34.1

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          146 YLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       146 ~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+..|...|.  .++-|...|-. +..+.+++++++||||||-.. -.++..+..
T Consensus       106 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~  158 (299)
T TIGR02782       106 FTLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAK  158 (299)
T ss_pred             CCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhc
Confidence            34555666665  44555555544 456689999999999999743 456666544

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=94.39  E-value=0.078  Score=52.76  Aligned_cols=42  Identities=33%  Similarity=0.276  Sum_probs=35.7

Q ss_pred             CcHHHHHHHhhHhcC---C-cEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          159 PTPIQRQAIPVLLSD---R-ECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       159 pt~iQ~~aip~il~G---~-dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +.+.|..++-.++.+   . .++..||||+|||.+.+++.+..+..
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~  241 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDE  241 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhc
Confidence            477888888877644   4 78899999999999999999998877

>PF13245 AAA_19: Part of AAA domain

Probab=94.26  E-value=0.11  Score=37.02  Aligned_cols=27  Identities=22%  Similarity=0.335  Sum_probs=17.8

Q ss_pred             cCCc-EEEEcCCCchhHHHhHHHHHHHH
Q 028267          172 SDRE-CFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       172 ~G~d-vi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .+.. +++.+++|||||...+--+...+
T Consensus         8 ~~~~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen    8 AGSPLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             hhCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            3444 55699999999976654444444

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=94.13  E-value=0.14  Score=46.84  Aligned_cols=28  Identities=25%  Similarity=0.417  Sum_probs=21.1

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+.-++++++||||||-.. -.++..+..
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~~  160 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELAE  160 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHhh
Confidence            4566999999999999865 456666644

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=93.96  E-value=0.16  Score=52.08  Aligned_cols=38  Identities=29%  Similarity=0.255  Sum_probs=33.0

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHH
Q 028267          151 LAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTL  188 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTl  188 (211)
                      +.+.....|+..|....-.++.|..+-+.||||.|||.
T Consensus        75 F~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTT  112 (1187)
T COG1110          75 FKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTT  112 (1187)
T ss_pred             HHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhH
Confidence            44444449999999999999999999999999999997

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=93.80  E-value=0.2  Score=46.12  Aligned_cols=26  Identities=23%  Similarity=0.300  Sum_probs=20.1

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          174 RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .-++++++||||||-.. -.++..+..
T Consensus       150 GlilI~G~TGSGKTT~l-~al~~~i~~  175 (372)
T TIGR02525       150 GLGLICGETGSGKSTLA-ASIYQHCGE  175 (372)
T ss_pred             CEEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            35889999999999754 467777654

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=93.80  E-value=0.26  Score=43.39  Aligned_cols=43  Identities=28%  Similarity=0.235  Sum_probs=33.2

Q ss_pred             CCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          156 YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       156 ~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      -..|+++|..++=.+..|+  |+.-.||-|||++-.+|.+-.-..
T Consensus        75 g~~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~  117 (266)
T PF07517_consen   75 GLRPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ  117 (266)
T ss_dssp             S----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT
T ss_pred             CCcccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh
Confidence            3479999999998888887  789999999999998887766543

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>PRK10536 hypothetical protein; Provisional

Probab=93.57  E-value=0.19  Score=44.20  Aligned_cols=47  Identities=19%  Similarity=0.099  Sum_probs=37.6

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .++.-.+..|...+-.+....-+++.+++|||||+..+.-.++.|..
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~  101 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIH  101 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            45666777999999989888889999999999999776666655543

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=92.69  E-value=0.19  Score=50.53  Aligned_cols=42  Identities=29%  Similarity=0.268  Sum_probs=36.4

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..|+++|..+--++..|+  |+.-.||+|||++..+|++-....
T Consensus        79 ~~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~  120 (796)
T PRK12906         79 LRPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT  120 (796)
T ss_pred             CCCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc
Confidence            478999999877778887  889999999999999998877664

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=92.54  E-value=0.22  Score=45.53  Aligned_cols=36  Identities=19%  Similarity=0.161  Sum_probs=31.1

Q ss_pred             cCCCCCcHHHHHHHhhHhcCC-cEEEEcCCCchhHHH
Q 028267          154 LGYKEPTPIQRQAIPVLLSDR-ECFACAPTGSGKTLA  189 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~-dvi~~A~TGsGKTla  189 (211)
                      ..|...++-|+..+-.+..++ ++|+++.||||||-.
T Consensus       153 i~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl  189 (355)
T COG4962         153 IIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL  189 (355)
T ss_pred             HHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH
Confidence            348889999999998887776 999999999999973

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=92.36  E-value=0.17  Score=43.68  Aligned_cols=31  Identities=26%  Similarity=0.354  Sum_probs=23.2

Q ss_pred             HhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          170 LLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +..+..++++++||||||-.. -.++..+...
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~~  154 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPPE  154 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHTT
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhcccc
Confidence            455789999999999999754 5566665543

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=92.30  E-value=0.2  Score=49.55  Aligned_cols=44  Identities=32%  Similarity=0.521  Sum_probs=34.2

Q ss_pred             CCcHHHHHHHhhHh----cCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          158 EPTPIQRQAIPVLL----SDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       158 ~pt~iQ~~aip~il----~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .|+.||..-+..++    .|+=-|.-+||||||||+.+...|..|...
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~   62 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDF   62 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHh
Confidence            46678877665443    577566789999999999999999988654

>TIGR00603 rad25 DNA repair helicase rad25

Probab=92.17  E-value=0.21  Score=49.86  Aligned_cols=41  Identities=20%  Similarity=0.382  Sum_probs=31.7

Q ss_pred             CCCcHHHHHHHhhHh-cC--CcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          157 KEPTPIQRQAIPVLL-SD--RECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       157 ~~pt~iQ~~aip~il-~G--~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      ..|.|.|..|+..++ .|  +.-|++.|||+|||+.-+ .++.++
T Consensus       254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai-~aa~~l  297 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGV-TAACTV  297 (732)
T ss_pred             CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHH-HHHHHh
Confidence            468899999998877 34  367889999999999875 344444

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=92.17  E-value=0.25  Score=52.16  Aligned_cols=26  Identities=27%  Similarity=0.359  Sum_probs=19.4

Q ss_pred             HhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          170 LLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      +..+..+|++|.||||||.  .||.+..
T Consensus        86 i~~~~VviI~GeTGSGKTT--qlPq~ll  111 (1294)
T PRK11131         86 IRDHQVVIVAGETGSGKTT--QLPKICL  111 (1294)
T ss_pred             HHhCCeEEEECCCCCCHHH--HHHHHHH
Confidence            3445567888999999999  6895443

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=92.07  E-value=0.11  Score=52.22  Aligned_cols=42  Identities=33%  Similarity=0.575  Sum_probs=32.8

Q ss_pred             CCcHHHHHHHhhHhc----CCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          158 EPTPIQRQAIPVLLS----DRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       158 ~pt~iQ~~aip~il~----G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .|+|.|...+-.+++    +.+.++-+||||||||+.+...|-..+
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q   66 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQ   66 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHH
Confidence            578888887776654    467889999999999999976665543

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=91.86  E-value=0.33  Score=48.46  Aligned_cols=44  Identities=30%  Similarity=0.201  Sum_probs=37.1

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .|. .|+++|..+.-.++.|.  |+.-.||+|||++..+|++-....
T Consensus        75 lg~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~  118 (764)
T PRK12326         75 LGL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ  118 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc
Confidence            344 78999999998899885  679999999999999998876543

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=91.68  E-value=0.26  Score=48.68  Aligned_cols=58  Identities=17%  Similarity=0.218  Sum_probs=45.7

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceEE
Q 028267          151 LAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFC  209 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~  209 (211)
                      +..-|+-.+..-|..|..++|...=-|+++|+|||||.+-. .|+-+|.+.....-++|
T Consensus       403 ~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa-~IVyhl~~~~~~~VLvc  460 (935)
T KOG1802|consen  403 FSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQHAGPVLVC  460 (935)
T ss_pred             hcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhH-HHHHHHHHhcCCceEEE
Confidence            34456777788999999999999888899999999999864 56666666665555665

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=91.62  E-value=0.48  Score=45.25  Aligned_cols=42  Identities=31%  Similarity=0.415  Sum_probs=30.3

Q ss_pred             cHHHHHHHhhHhcCCc--EEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          160 TPIQRQAIPVLLSDRE--CFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       160 t~iQ~~aip~il~G~d--vi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ++.|...+-.++....  +++.+|||||||.+. ..+|+.+....
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~~~  286 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL-YAALSELNTPE  286 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH-HHHHHHhcCCC
Confidence            5666666666665432  788999999999875 57777776543

>TIGR00376 DNA helicase, putative

Probab=91.48  E-value=0.44  Score=46.82  Aligned_cols=43  Identities=23%  Similarity=0.350  Sum_probs=32.8

Q ss_pred             CCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          157 KEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+.+.|..|+..++.. ..+++++|+|||||-.- .-++.++..
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~-~~ii~~~~~  199 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTL-VELIRQLVK  199 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHH-HHHHHHHHH
Confidence            35688999999998876 56889999999999654 444545443

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=91.46  E-value=0.069  Score=49.74  Aligned_cols=23  Identities=43%  Similarity=0.762  Sum_probs=20.7

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHH
Q 028267          174 RECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      .+++++|+||||||.+|++|.|-
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll   67 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLL   67 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHH
Confidence            46999999999999999999774

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=91.22  E-value=0.29  Score=40.03  Aligned_cols=32  Identities=25%  Similarity=0.345  Sum_probs=23.1

Q ss_pred             CcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHh
Q 028267          159 PTPIQRQAIPV-LLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       159 pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf  190 (211)
                      .++-|...+-. +..|..++++++||||||..+
T Consensus        10 ~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130          10 FSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            34445554443 456889999999999999754

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=91.05  E-value=0.39  Score=43.47  Aligned_cols=30  Identities=20%  Similarity=0.269  Sum_probs=22.3

Q ss_pred             hHhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          169 VLLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       169 ~il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      ++..+.+++++++||||||-. +-.++..+.
T Consensus       156 ~v~~~~nili~G~tgSGKTTl-l~aL~~~ip  185 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKTTF-TNAALREIP  185 (332)
T ss_pred             HHHcCCcEEEECCCCCCHHHH-HHHHHhhCC
Confidence            455789999999999999974 344555543

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=90.97  E-value=0.38  Score=48.76  Aligned_cols=42  Identities=31%  Similarity=0.266  Sum_probs=32.7

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHH
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      +..|. .|+++|..+.-++..|  -|+...||.||||++.+|++-
T Consensus        71 R~lG~-r~ydvQlig~l~L~~G--~IaEm~TGEGKTL~a~l~ayl  112 (870)
T CHL00122         71 RTLGL-RHFDVQLIGGLVLNDG--KIAEMKTGEGKTLVATLPAYL  112 (870)
T ss_pred             HHhCC-CCCchHhhhhHhhcCC--ccccccCCCCchHHHHHHHHH
Confidence            34455 5899999876555544  678999999999999999853

>PRK13764 ATPase; Provisional

Probab=90.97  E-value=0.51  Score=46.18  Aligned_cols=27  Identities=15%  Similarity=0.220  Sum_probs=21.0

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .+.+++++++||||||. |+-.++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTT-ll~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKST-FAQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHH-HHHHHHHHHh
Confidence            46789999999999997 4456666665

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=90.61  E-value=0.43  Score=50.39  Aligned_cols=42  Identities=24%  Similarity=0.422  Sum_probs=27.8

Q ss_pred             cCCCCCcHHHH--HHHhhHh-cCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          154 LGYKEPTPIQR--QAIPVLL-SDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       154 ~g~~~pt~iQ~--~aip~il-~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      ..|....||.+  ..|...+ ...-+|++|+||||||.  .+|.+..
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~ll  104 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTT--QLPKICL  104 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHH--HHHHHHH
Confidence            44655566655  2333334 44567889999999999  5686654

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

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

Probab=90.55  E-value=0.51  Score=48.34  Aligned_cols=43  Identities=28%  Similarity=0.383  Sum_probs=35.2

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHH--hHHHHHHH
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLA--FLCPMLMK  197 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTla--f~lPil~~  197 (211)
                      .+| .|=..|.+||=++.+|-.|+|.|.|-+|||+.  |+|.+.+.
T Consensus       294 ~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~  338 (1248)
T KOG0947|consen  294 YPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQK  338 (1248)
T ss_pred             CCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHh
Confidence            444 46679999999999999999999999999998  55554443

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=90.37  E-value=0.35  Score=47.72  Aligned_cols=36  Identities=28%  Similarity=0.401  Sum_probs=26.2

Q ss_pred             CcHHHHHHHhhHh----c------CCcEEEEcCCCchhHHHhHHHH
Q 028267          159 PTPIQRQAIPVLL----S------DRECFACAPTGSGKTLAFLCPM  194 (211)
Q Consensus       159 pt~iQ~~aip~il----~------G~dvi~~A~TGsGKTlaf~lPi  194 (211)
                      |.+.|..|+..++    .      .+..++..+||||||++.+.-+
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la  284 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAA  284 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHH
Confidence            4557888887642    2      2468899999999999875444

Members of this family are assumed to differ from each other in DNA site specificity.

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=90.29  E-value=0.97  Score=45.20  Aligned_cols=42  Identities=29%  Similarity=0.335  Sum_probs=33.0

Q ss_pred             CCcHHHHHHHhhHhcC----CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          158 EPTPIQRQAIPVLLSD----RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G----~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+.+-|+.++..+...    .-.+..+.||||||-.|+ .+|.....
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl-~~i~~~L~  243 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYL-EAIAKVLA  243 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHH-HHHHHHHH
Confidence            5677899999888655    678999999999999995 55555444

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=90.25  E-value=0.64  Score=34.30  Aligned_cols=25  Identities=24%  Similarity=0.430  Sum_probs=19.1

Q ss_pred             CCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          173 DRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      ++.+++.+++|+|||. ++--++..+
T Consensus        19 ~~~v~i~G~~G~GKT~-l~~~i~~~~   43 (151)
T cd00009          19 PKNLLLYGPPGTGKTT-LARAIANEL   43 (151)
T ss_pred             CCeEEEECCCCCCHHH-HHHHHHHHh
Confidence            6789999999999995 444455544

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PRK05973 replicative DNA helicase; Provisional

Probab=90.22  E-value=0.8  Score=39.64  Aligned_cols=40  Identities=23%  Similarity=0.260  Sum_probs=25.3

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      ..+||... .+.-+..|.=+++.|++|+|||. |++-++...
T Consensus        49 ~~~~p~~~-l~GGl~~Gsl~LIaG~PG~GKT~-lalqfa~~~   88 (237)
T PRK05973         49 AATTPAEE-LFSQLKPGDLVLLGARPGHGKTL-LGLELAVEA   88 (237)
T ss_pred             cCCCCHHH-hcCCCCCCCEEEEEeCCCCCHHH-HHHHHHHHH
Confidence            34555332 33345566778999999999998 444444443

>PRK08181 transposase; Validated

Probab=90.21  E-value=0.4  Score=42.21  Aligned_cols=20  Identities=25%  Similarity=0.421  Sum_probs=16.9

Q ss_pred             HhcCCcEEEEcCCCchhHHH
Q 028267          170 LLSDRECFACAPTGSGKTLA  189 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTla  189 (211)
                      +-.+.++++++++|+|||..
T Consensus       103 ~~~~~nlll~Gp~GtGKTHL  122 (269)
T PRK08181        103 LAKGANLLLFGPPGGGKSHL  122 (269)
T ss_pred             HhcCceEEEEecCCCcHHHH
Confidence            34678999999999999953

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=90.15  E-value=0.091  Score=54.88  Aligned_cols=38  Identities=34%  Similarity=0.431  Sum_probs=32.9

Q ss_pred             CcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHH
Q 028267          159 PTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       159 pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      -.|||.+.++.++.. .+++++||+|||||.+..+.++.
T Consensus      1144 ~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~ 1182 (1674)
T KOG0951|consen 1144 FNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR 1182 (1674)
T ss_pred             cCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC
Confidence            367999999998876 56999999999999998887776

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=90.15  E-value=0.29  Score=44.75  Aligned_cols=27  Identities=44%  Similarity=0.550  Sum_probs=19.6

Q ss_pred             hcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          171 LSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       171 l~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      |.-.|++..+||||||||-.  -.|.++.
T Consensus        95 L~KSNILLiGPTGsGKTlLA--qTLAk~L  121 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLA--QTLAKIL  121 (408)
T ss_pred             eeeccEEEECCCCCcHHHHH--HHHHHHh
Confidence            44568999999999999843  3444443

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=89.94  E-value=0.52  Score=38.79  Aligned_cols=36  Identities=19%  Similarity=0.294  Sum_probs=21.9

Q ss_pred             CCcEEEEcCCCchhHHHhHHHHHHHHhc--ccCCCceEE
Q 028267          173 DRECFACAPTGSGKTLAFLCPMLMKLRV--LFIPFDYFC  209 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~lPil~~l~~--~~~~~~~~~  209 (211)
                      ..++++.+.||||||.+... ++..+..  .+....+|+
T Consensus        38 ~~h~li~G~tgsGKS~~l~~-ll~~l~~~~~p~~~~l~i   75 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRT-LLLSLALTYSPDDVQLYI   75 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHH-HHHHHHTT--TTTEEEEE
T ss_pred             CceEEEEcCCCCCccHHHHH-HHHHHHHHhcCCccEEEE
Confidence            34899999999999997654 5555544  344455554

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=89.71  E-value=0.12  Score=51.05  Aligned_cols=25  Identities=28%  Similarity=0.561  Sum_probs=22.1

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          174 RECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .+++++|+||||||.+|+||-|-..
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~  164 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF  164 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC
Confidence            4799999999999999999987653

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=89.20  E-value=0.23  Score=42.61  Aligned_cols=29  Identities=31%  Similarity=0.224  Sum_probs=20.5

Q ss_pred             hHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          169 VLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       169 ~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      -+..|.-+++.|++|+|||.. ++-++..+
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l-~~~~~~~~   54 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTF-LREYALDL   54 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHH-HHHHHHHH
Confidence            455677899999999999973 33444443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=88.97  E-value=0.4  Score=43.68  Aligned_cols=29  Identities=28%  Similarity=0.502  Sum_probs=21.6

Q ss_pred             hHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          169 VLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       169 ~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      ++..+.+++++++||||||... -.++..+
T Consensus       158 ~v~~~~nilI~G~tGSGKTTll-~aLl~~i  186 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTMS-KTLISAI  186 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHHH-HHHHccc
Confidence            4567899999999999999743 3444443

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=88.93  E-value=0.58  Score=47.73  Aligned_cols=59  Identities=22%  Similarity=0.220  Sum_probs=46.9

Q ss_pred             CCHHHHH-HHHHcCCCCCcHHHHHHH--hhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          143 CESYLLR-NLAELGYKEPTPIQRQAI--PVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       143 l~~~ll~-~l~~~g~~~pt~iQ~~ai--p~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +++.+.. ..+..|+..++..|+.++  |.++.+.++|-.+||+.||||+.-|=++..+...
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~  268 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCR  268 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHH
Confidence            4444433 356779999999999987  6789999999999999999999887777766543

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=88.87  E-value=0.13  Score=50.29  Aligned_cols=25  Identities=40%  Similarity=0.675  Sum_probs=22.3

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          174 RECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .+++++|+||||||..|++|-|-..
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~  183 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW  183 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC
Confidence            4799999999999999999988763

>PRK10436 hypothetical protein; Provisional

Probab=88.63  E-value=1.1  Score=42.57  Aligned_cols=46  Identities=35%  Similarity=0.476  Sum_probs=28.4

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhc--CCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          151 LAELGYKEPTPIQRQAIPVLLS--DRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~--G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      |..+||   .+-|...|-.++.  +--++++++||||||.+. ..+|..+..
T Consensus       197 L~~LG~---~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~~  244 (462)
T PRK10436        197 LETLGM---TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLNT  244 (462)
T ss_pred             HHHcCc---CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhCC
Confidence            344454   3444444444432  234889999999999875 456777643

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=88.25  E-value=1.4  Score=42.69  Aligned_cols=45  Identities=29%  Similarity=0.474  Sum_probs=30.0

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhcC--CcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          151 LAELGYKEPTPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~G--~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      |...||   .+-|...|-.++..  --++++++||||||-+. ..++..+.
T Consensus       295 l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       295 IDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            556665   45555555554432  34789999999999875 45777664

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=87.94  E-value=0.77  Score=45.57  Aligned_cols=51  Identities=22%  Similarity=0.246  Sum_probs=35.4

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc-ccCCCceEEe
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV-LFIPFDYFCE  210 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~-~~~~~~~~~~  210 (211)
                      .++|-|..++-..  ...++|.|..|||||.+...=+..-+.. .-.|..++|+
T Consensus         9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~l   60 (721)
T PRK11773          9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAV   60 (721)
T ss_pred             hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEee
Confidence            5899999987542  3568899999999999876555544432 2345666654

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=87.93  E-value=0.76  Score=46.87  Aligned_cols=43  Identities=30%  Similarity=0.277  Sum_probs=33.5

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .|. .|+++|-..--++..|+  |+...||-||||+..+|++-.-.
T Consensus        82 lG~-r~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL  124 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNAL  124 (939)
T ss_pred             hCC-CcchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhh
Confidence            344 68999988765666664  68999999999999999876543

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=87.81  E-value=1.6  Score=39.46  Aligned_cols=28  Identities=25%  Similarity=0.395  Sum_probs=20.6

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+.-++++++||||||... ..++..+..
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~~  148 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYINK  148 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhCc
Confidence            3556899999999999865 345665543

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=87.71  E-value=0.86  Score=37.38  Aligned_cols=30  Identities=17%  Similarity=0.205  Sum_probs=20.8

Q ss_pred             HhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          170 LLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +-.+.++++.+++|+|||... ..+...+..
T Consensus        44 ~~~~~~l~l~G~~G~GKThLa-~ai~~~~~~   73 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTHLA-VAIANEAIR   73 (178)
T ss_dssp             -SC--EEEEEESTTSSHHHHH-HHHHHHHHH
T ss_pred             cccCeEEEEEhhHhHHHHHHH-HHHHHHhcc
Confidence            446889999999999999864 455555544

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=87.65  E-value=1  Score=42.53  Aligned_cols=58  Identities=16%  Similarity=0.327  Sum_probs=38.5

Q ss_pred             hhhhcccCCCCHHHHHHHHHcCCCC--CcH-H---HHHHH-hhHhcCCcEEEEcCCCchhHHHhH
Q 028267          134 FVKLSSRFGCESYLLRNLAELGYKE--PTP-I---QRQAI-PVLLSDRECFACAPTGSGKTLAFL  191 (211)
Q Consensus       134 f~~l~~~~~l~~~ll~~l~~~g~~~--pt~-i---Q~~ai-p~il~G~dvi~~A~TGsGKTlaf~  191 (211)
                      |.+...+|-..+++--.|+..||.-  .+. .   +-..+ |.+-.+.|+|..+|+|||||-.|.
T Consensus       163 ~~~~R~~FT~dEWid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       163 YKEGRKEFTLEEWIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHHHhhcCHHHHHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHH
Confidence            3444466667777777778888843  222 1   11222 566788999999999999995554

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=87.60  E-value=1.3  Score=38.69  Aligned_cols=45  Identities=33%  Similarity=0.469  Sum_probs=28.4

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhc-C-CcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          151 LAELGYKEPTPIQRQAIPVLLS-D-RECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~-G-~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      |...||   ++-|...|-.++. . .-++++++||||||-.. ..++..+.
T Consensus        59 l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          59 LEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            445554   4445555544432 3 35899999999999854 45666664

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=87.53  E-value=0.13  Score=50.53  Aligned_cols=24  Identities=33%  Similarity=0.629  Sum_probs=21.7

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHHH
Q 028267          174 RECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      .+++++|+||||||..|++|-|-.
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~  199 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLS  199 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhh
Confidence            579999999999999999998754

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=87.43  E-value=0.87  Score=46.48  Aligned_cols=45  Identities=22%  Similarity=0.154  Sum_probs=34.6

Q ss_pred             HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..| ..|+++|-..--.+..|+  |+...||+|||++..+|++-....
T Consensus        78 ~lG-m~~ydVQliGg~~Lh~G~--iaEM~TGEGKTLvA~l~a~l~al~  122 (913)
T PRK13103         78 VMG-MRHFDVQLIGGMTLHEGK--IAEMRTGEGKTLVGTLAVYLNALS  122 (913)
T ss_pred             HhC-CCcchhHHHhhhHhccCc--cccccCCCCChHHHHHHHHHHHHc
Confidence            345 578999988755555554  679999999999999999865543

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=87.26  E-value=0.4  Score=42.10  Aligned_cols=22  Identities=32%  Similarity=0.567  Sum_probs=18.7

Q ss_pred             hHhcCCcEEEEcCCCchhHHHh
Q 028267          169 VLLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       169 ~il~G~dvi~~A~TGsGKTlaf  190 (211)
                      .+..++.+++++++|||||..-
T Consensus        29 l~~~~~pvLl~G~~GtGKT~li   50 (272)
T PF12775_consen   29 LLSNGRPVLLVGPSGTGKTSLI   50 (272)
T ss_dssp             HHHCTEEEEEESSTTSSHHHHH
T ss_pred             HHHcCCcEEEECCCCCchhHHH
Confidence            3557899999999999999843

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=86.76  E-value=0.23  Score=49.06  Aligned_cols=25  Identities=32%  Similarity=0.590  Sum_probs=22.4

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          174 RECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .++++.|+||||||..|+||-|-..
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~  169 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTW  169 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhC
Confidence            5799999999999999999987654

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=86.68  E-value=0.7  Score=42.74  Aligned_cols=35  Identities=23%  Similarity=0.359  Sum_probs=25.6

Q ss_pred             HHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          166 AIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       166 aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .||.-+..+++++.|+||||||.. +..++..+...
T Consensus        35 ~~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~~   69 (410)
T cd01127          35 PFPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRAR   69 (410)
T ss_pred             eCCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHhc
Confidence            355556678999999999999985 45566665543

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=86.58  E-value=0.97  Score=41.68  Aligned_cols=43  Identities=23%  Similarity=0.242  Sum_probs=33.4

Q ss_pred             CCCcHHHHHHHhhHh----cCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          157 KEPTPIQRQAIPVLL----SDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       157 ~~pt~iQ~~aip~il----~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+||.|..+-..++    .-.|+|+.|-||+|||-- +++.+++...
T Consensus        96 G~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~  142 (441)
T COG4098          96 GTLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALN  142 (441)
T ss_pred             cccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHh
Confidence            368999988776554    458999999999999984 3577777655

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=85.77  E-value=1.1  Score=42.55  Aligned_cols=45  Identities=31%  Similarity=0.470  Sum_probs=28.6

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhcC-Cc-EEEEcCCCchhHHHhHHHHHHHHh
Q 028267          151 LAELGYKEPTPIQRQAIPVLLSD-RE-CFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~G-~d-vi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      |...||   ++-|...|-.++.. .. ++++++||||||... ..+|..+.
T Consensus       221 l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       221 LETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            445555   44555555554443 33 789999999999865 34566664

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=85.62  E-value=1.2  Score=43.45  Aligned_cols=43  Identities=16%  Similarity=0.326  Sum_probs=32.5

Q ss_pred             CCcHHHHHHHhhHhcCCc-EEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          158 EPTPIQRQAIPVLLSDRE-CFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~d-vi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+-+-|..|+......++ +++++|+|||||.+...=|.+-+++
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~  228 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ  228 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc
Confidence            345688899988888865 5779999999999886555555554

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=85.49  E-value=3  Score=43.23  Aligned_cols=44  Identities=18%  Similarity=0.159  Sum_probs=33.6

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCc-EEEEcCCCchhHHHhHHHHHHHHh
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRE-CFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~d-vi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .|+ .+++-|..|+..++.+.+ +++++..|||||.. +-.++..+.
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e  387 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWE  387 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHH
Confidence            344 689999999999998765 68899999999975 334444443

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=85.15  E-value=0.33  Score=47.66  Aligned_cols=23  Identities=22%  Similarity=0.252  Sum_probs=20.7

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHH
Q 028267          174 RECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      .++++.|+||||||..++||-+-
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL  234 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTAL  234 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhh
Confidence            58999999999999999999643

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=84.95  E-value=0.83  Score=40.95  Aligned_cols=34  Identities=26%  Similarity=0.338  Sum_probs=25.6

Q ss_pred             CCCCcHHHHHH-HhhHhcCCcEEEEcCCCchhHHH
Q 028267          156 YKEPTPIQRQA-IPVLLSDRECFACAPTGSGKTLA  189 (211)
Q Consensus       156 ~~~pt~iQ~~a-ip~il~G~dvi~~A~TGsGKTla  189 (211)
                      +..+++.|..- |-++-.++++++|++||||||-.
T Consensus       125 ~gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~  159 (312)
T COG0630         125 YGTISPEQAAYLWLAIEARKSIIICGGTASGKTTL  159 (312)
T ss_pred             cCCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH
Confidence            34456666554 45567889999999999999974

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=84.81  E-value=4.1  Score=40.72  Aligned_cols=43  Identities=19%  Similarity=0.196  Sum_probs=34.5

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+++-|..|+-.++..+-+++.+..|||||... -.++..+..
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~  364 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEE  364 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHH
Confidence            4689999999999999899999999999999743 344444443

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=84.47  E-value=1.8  Score=39.24  Aligned_cols=43  Identities=23%  Similarity=0.284  Sum_probs=29.7

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHh
Q 028267          146 YLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       146 ~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf  190 (211)
                      ..+..|...|+  .++-+...+-. +..+.+++++++||||||..+
T Consensus       152 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll  195 (340)
T TIGR03819       152 FTLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTLL  195 (340)
T ss_pred             CCHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH
Confidence            34666667776  34455555544 445689999999999998744

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>PRK06921 hypothetical protein; Provisional

Probab=84.38  E-value=4.7  Score=35.23  Aligned_cols=29  Identities=21%  Similarity=0.119  Sum_probs=21.0

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .+..+++.+++|+|||... ..|...+...
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~  144 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRK  144 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhh
Confidence            4678999999999999633 4555555543

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=84.32  E-value=1.5  Score=36.65  Aligned_cols=26  Identities=31%  Similarity=0.340  Sum_probs=21.1

Q ss_pred             CCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          173 DRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      ++++.+.|.||||||.+- --+++.+.
T Consensus        23 ~~H~~I~G~TGsGKS~~~-~~ll~~l~   48 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTV-KVLLEELL   48 (229)
T ss_pred             cceEEEECCCCCCHHHHH-HHHHHHHH
Confidence            578999999999999865 46667766

It contains several conserved aspartates and histidines that could be metal ligands.

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]

Probab=84.32  E-value=1.9  Score=41.34  Aligned_cols=44  Identities=25%  Similarity=0.203  Sum_probs=32.9

Q ss_pred             CcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          159 PTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       159 pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      +...|..-..-++.+ +++++.|||-|||...++-+..+|...++
T Consensus        16 ~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~   59 (542)
T COG1111          16 PRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG   59 (542)
T ss_pred             HHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC
Confidence            334454444444444 89999999999999999989888887665

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

Probab=84.12  E-value=1.2  Score=44.86  Aligned_cols=44  Identities=27%  Similarity=0.309  Sum_probs=39.2

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .+-|.|..||-++-++..|+|+|-|.+|||...-+.|.+.|...
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~k  172 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREK  172 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhc
Confidence            45689999999999999999999999999999888888887653

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=84.05  E-value=1.1  Score=43.49  Aligned_cols=53  Identities=21%  Similarity=0.290  Sum_probs=32.1

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHhh---HhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          146 YLLRNLAELGYKEPTPIQRQAIPV---LLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       146 ~ll~~l~~~g~~~pt~iQ~~aip~---il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ++.+.|+..+=  .+++.---+|.   -...+++++.|+||||||. ++-.+|..+...
T Consensus       148 ~l~~~l~~~~~--~~~~~igg~pl~~~~~e~~h~li~G~tGsGKs~-~i~~ll~~~~~~  203 (566)
T TIGR02759       148 ELIKKLKKSRR--ASDIKIGGLPLIKFGSETQHILIHGTTGSGKSV-AIRKLLRWIRQR  203 (566)
T ss_pred             HHHHHHHhcCC--CCceeeCCccCCCCcccccceEEEcCCCCCHHH-HHHHHHHHHHhc
Confidence            45555655552  22333233344   3345799999999999996 445567666544

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=83.86  E-value=1.1  Score=44.66  Aligned_cols=57  Identities=16%  Similarity=0.004  Sum_probs=40.4

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          145 SYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       145 ~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ..|.+.|+..|-..+..|--.-||.-+..+++++++-||||||.++ .-+|..+....
T Consensus       157 ~~l~k~lk~~~~~s~i~I~gvPip~~~E~~H~li~GttGSGKS~~i-~~LL~~ir~RG  213 (732)
T PRK13700        157 KDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVI-RRLANYARQRG  213 (732)
T ss_pred             HHHHHHHHhcCCCCCeeEccccCCcchhhcceEEeCCCCCCHHHHH-HHHHHHHHHcC
Confidence            4566777777765555554444444567799999999999999966 57777776543

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=83.77  E-value=1.7  Score=44.34  Aligned_cols=41  Identities=29%  Similarity=0.377  Sum_probs=33.9

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      .|. .|+++|...--.+..|+  |+.-.||-||||+..+|++-.
T Consensus        75 lG~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLn  115 (925)
T PRK12903         75 LGK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLN  115 (925)
T ss_pred             hCC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHH
Confidence            355 78999999887777775  689999999999999998643

>PRK06526 transposase; Provisional

Probab=83.71  E-value=0.71  Score=40.16  Aligned_cols=22  Identities=23%  Similarity=0.380  Sum_probs=18.0

Q ss_pred             HhcCCcEEEEcCCCchhHHHhH
Q 028267          170 LLSDRECFACAPTGSGKTLAFL  191 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTlaf~  191 (211)
                      +-.+.++++++|+|+|||....
T Consensus        95 i~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHHH
Confidence            4467899999999999997543

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=82.51  E-value=1.1  Score=40.17  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=15.5

Q ss_pred             EEEEcCCCchhHHHhHHHHHHH
Q 028267          176 CFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       176 vi~~A~TGsGKTlaf~lPil~~  197 (211)
                      ||++++|||||..+.+ .++.+
T Consensus       130 viiVGaTGSGKSTtmA-aMi~y  150 (375)
T COG5008         130 VIIVGATGSGKSTTMA-AMIGY  150 (375)
T ss_pred             EEEECCCCCCchhhHH-HHhcc
Confidence            7889999999987653 44443

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=82.42  E-value=0.48  Score=46.65  Aligned_cols=23  Identities=22%  Similarity=0.286  Sum_probs=20.8

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHH
Q 028267          174 RECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      .++++.|+||||||..++||-|-
T Consensus       225 ~H~Lv~ApTgsGKt~g~VIPnLL  247 (641)
T PRK13822        225 THGLVFAGSGGFKTTSVVVPTAL  247 (641)
T ss_pred             ceEEEEeCCCCCccceEehhhhh
Confidence            57999999999999999999754

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]

Probab=81.79  E-value=2.3  Score=42.01  Aligned_cols=57  Identities=32%  Similarity=0.417  Sum_probs=44.4

Q ss_pred             CCHHHHHH-HHHcCCCCCcHHHHHHHhhHhcC------CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          143 CESYLLRN-LAELGYKEPTPIQRQAIPVLLSD------RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       143 l~~~ll~~-l~~~g~~~pt~iQ~~aip~il~G------~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ....++.. +....| .||.-|..+|.-|+..      .+=++++--|||||+..++.++.-+..
T Consensus       247 ~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~  310 (677)
T COG1200         247 ANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA  310 (677)
T ss_pred             ccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc
Confidence            33444554 466677 7999999999988765      345679999999999999999988765

>PRK08116 hypothetical protein; Validated

Probab=81.62  E-value=5.4  Score=34.82  Aligned_cols=28  Identities=18%  Similarity=0.131  Sum_probs=21.4

Q ss_pred             CCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          173 DRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +.-+++.+++|+|||... ..|...|...
T Consensus       114 ~~gl~l~G~~GtGKThLa-~aia~~l~~~  141 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLA-ACIANELIEK  141 (268)
T ss_pred             CceEEEECCCCCCHHHHH-HHHHHHHHHc
Confidence            345999999999999754 4677777654

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=81.42  E-value=5.8  Score=39.76  Aligned_cols=55  Identities=9%  Similarity=0.059  Sum_probs=36.9

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          143 CESYLLRNLAELGYKEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       143 l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      +++..+...-..+ ..+++-|..|+-.++.+ +=++++++.|||||... -.+++.+.
T Consensus       338 ~~~~~~~~~l~~~-~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~  393 (744)
T TIGR02768       338 VSPPIVDAAIDQH-YRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWE  393 (744)
T ss_pred             CCHHHHHHHHhcc-CCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHH
Confidence            4444444333333 35899999999998875 56789999999998653 23444443

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK11054 helD DNA helicase IV; Provisional

Probab=81.28  E-value=5.1  Score=39.85  Aligned_cols=51  Identities=22%  Similarity=0.157  Sum_probs=32.7

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc-cCCCceEE
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL-FIPFDYFC  209 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~-~~~~~~~~  209 (211)
                      ..+++-|..|+-.  ....+++.|..|||||.+.+-=+..-|... ..|..+++
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~  246 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILL  246 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEE
Confidence            4688999888643  334688999999999998754443333222 23445544

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=81.00  E-value=4.2  Score=35.69  Aligned_cols=64  Identities=22%  Similarity=0.152  Sum_probs=36.0

Q ss_pred             CCCchhhhhhcccCCCCHHHHHHHHHc--CCCCCcHHHHHHHhhH--------------hcCCcEEEEcCCCchhHHHhH
Q 028267          128 PSPLRTFVKLSSRFGCESYLLRNLAEL--GYKEPTPIQRQAIPVL--------------LSDRECFACAPTGSGKTLAFL  191 (211)
Q Consensus       128 p~p~~~f~~l~~~~~l~~~ll~~l~~~--g~~~pt~iQ~~aip~i--------------l~G~dvi~~A~TGsGKTlaf~  191 (211)
                      +..+..+.......++++.+.+.|...  .+..+..++......+              -.++-++++++||+|||....
T Consensus       133 ~~~l~~l~~~L~~~gv~~~la~~L~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       133 DPEGAKLLERLLRAGVSPELARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHhccCCccccccCCCeEEEEECCCCCCHHHHHH
Confidence            444445544445568888887776542  2222222222222111              134568899999999997643

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=80.38  E-value=2  Score=38.20  Aligned_cols=21  Identities=33%  Similarity=0.433  Sum_probs=18.1

Q ss_pred             HhcCCcEEEEcCCCchhHHHh
Q 028267          170 LLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTlaf  190 (211)
                      +..|..++++++||||||...
T Consensus       141 v~~~~~ili~G~tGsGKTTll  161 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFL  161 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHH
Confidence            457899999999999999854

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>TIGR00665 DnaB replicative DNA helicase

Probab=80.32  E-value=3  Score=38.55  Aligned_cols=27  Identities=19%  Similarity=0.164  Sum_probs=20.3

Q ss_pred             CCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          173 DRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      |.=+|+.|+||+|||. |++-++.++..
T Consensus       195 G~l~vi~g~pg~GKT~-~~l~~a~~~a~  221 (434)
T TIGR00665       195 SDLIILAARPSMGKTA-FALNIAENAAI  221 (434)
T ss_pred             CeEEEEEeCCCCChHH-HHHHHHHHHHH
Confidence            4457889999999995 66777766543

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=80.26  E-value=2  Score=42.40  Aligned_cols=17  Identities=41%  Similarity=0.765  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCchhHHHh
Q 028267          174 RECFACAPTGSGKTLAF  190 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf  190 (211)
                      ..|+.|+|+|+||||-.
T Consensus       546 sGvLL~GPPGCGKTLlA  562 (802)
T KOG0733|consen  546 SGVLLCGPPGCGKTLLA  562 (802)
T ss_pred             CceEEeCCCCccHHHHH
Confidence            45899999999999953

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=80.12  E-value=1.5  Score=35.99  Aligned_cols=25  Identities=36%  Similarity=0.468  Sum_probs=20.0

Q ss_pred             HHHhhHhcCCc--EEEEcCCCchhHHH
Q 028267          165 QAIPVLLSDRE--CFACAPTGSGKTLA  189 (211)
Q Consensus       165 ~aip~il~G~d--vi~~A~TGsGKTla  189 (211)
                      .++..++.|.|  |++.++||||||.+
T Consensus        14 ~~v~~~~~G~n~~i~~yG~tGsGKT~T   40 (186)
T cd01363          14 PLLQSALDGYNVCIFAYGQTGSGKTYT   40 (186)
T ss_pred             HHHHHHhCCcceeEEEECCCCCcceEe
Confidence            55667788865  78899999999954

These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	211
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		1e-22
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-15
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		6e-10
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-09
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-08
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		1e-07
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-07
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		1e-07
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		6e-07
3ly5_A	262	Ddx18 Dead-Domain Length = 262		7e-07
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		7e-07
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		1e-06
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		4e-05
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		8e-05
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		1e-04
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		2e-04
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-04
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		3e-04
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		3e-04
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		3e-04
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		4e-04
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		4e-04
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-04
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		6e-04
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		6e-04
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		6e-04
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-04
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		7e-04
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		7e-04
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		7e-04

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score =  102 bits (255), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 45/86 (52%), Positives = 60/86 (69%)
Query: 114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
            R K+ IHV G ++P P+ TF +L   +   S LL+N+ + G++ PTPIQ QAIPV+L  
Sbjct: 7   LRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHG 66
Query: 174 RECFACAPTGSGKTLAFLCPMLMKLR 199
           RE  A APTGSGKTLAF  P+LM+L+
Sbjct: 67  RELLASAPTGSGKTLAFSIPILMQLK 92

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 77.4 bits (189), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 43/105 (40%), Positives = 60/105 (57%), Gaps = 7/105 (6%)
Query: 97  PSKAKKELNKQIERDAVFRKKYN---IHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAE 153
           PS    E+        +   KYN   + V+G++VP P++ F     R      ++ N+ +
Sbjct: 18  PSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLR----DIIIDNVNK 73
Query: 154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
            GYK PTPIQ+ +IPV+ S R+  ACA TGSGKT AFL P+L KL
Sbjct: 74  SGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKL 118

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 60.8 bits (146), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 120 IHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFAC 179
           +  +G N P  + +F    S       ++ N+    Y  PTP+Q+ AIP++   R+  AC
Sbjct: 3   VEATGNNCPPHIESF----SDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMAC 58
Query: 180 APTGSGKTLAFLCPMLMKL 198
           A TGSGKT AFL P+L ++
Sbjct: 59  AQTGSGKTAAFLLPILSQI 77

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 33/49 (67%)
Query: 150 NLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           N+    Y+ PTPIQ+ AIP +L  R+  ACA TGSGKT AFL P++  L
Sbjct: 37  NILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHL 85

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 38/52 (73%)
Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LL  + E+G+++P+PIQ ++IP+ LS R+  A A  G+GK+ A+L P+L +L
Sbjct: 14  LLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERL 65

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 57/110 (51%), Gaps = 8/110 (7%)
Query: 89  EKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLL 148
           EK   ++ P  A++   +++E    +R+   I V G N P P+  F + +      + ++
Sbjct: 4   EKNFYQEHPDLARRT-AQEVE---TYRRSKEITVRGHNCPKPVLNFYEANF----PANVM 55
Query: 149 RNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
             +A   + EPT IQ Q  PV LS  +    A TGSGKTL++L P ++ +
Sbjct: 56  DVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHI 105

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 37/53 (69%)
Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
           LL  + E G+++P+PIQ +AIPV ++ R+  A A  G+GKT AF+ P L K++
Sbjct: 32  LLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVK 84

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
           +R+   I V G N P P+  F +  + F   + ++  +A   + EPT IQ Q  PV LS 
Sbjct: 11  YRRSKEITVRGHNCPKPVLNFYE--ANF--PANVMDVIARQNFTEPTAIQAQGWPVALSG 66
Query: 174 RECFACAPTGSGKTLAFLCPMLMKL 198
            +    A TGSGKTL++L P ++ +
Sbjct: 67  LDMVGVAQTGSGKTLSYLLPAIVHI 91

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 34/52 (65%)
Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LL+++  +G  +PTPIQ QA P++L   +    A TG+GKTL++L P  + L
Sbjct: 31  LLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHL 82

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 39/60 (65%), Gaps = 5/60 (8%)
Query: 148 LRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCP---MLMKLRVLFIP 204
           L+ + E+G+   T IQ ++I  LL  R+  A A TGSGKTLAFL P   +++KLR  F+P
Sbjct: 66  LKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR--FMP 123

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 32/92 (34%), Positives = 44/92 (47%), Gaps = 7/92 (7%)
Query: 107 QIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQA 166
           Q+ER+++ R   N      N  +         S F      L+ L E  Y+  T IQ+Q 
Sbjct: 3   QVERESISRLMQNYEKINVNEITRF-------SDFPLSKKTLKGLQEAQYRLVTEIQKQT 55
Query: 167 IPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           I + L  ++    A TGSGKTLAFL P+L  L
Sbjct: 56  IGLALQGKDVLGAAKTGSGKTLAFLVPVLEAL 87

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 32/58 (55%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
            G    L     +LG+ +PT IQ +AIP+ L  R+    A TGSGKT AF  P+L  L
Sbjct: 48  LGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNAL 105

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 32/58 (55%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           F  +  +L  L   G   PTPIQ  A+P+ L  ++    A TG+GKTLAF  P+  +L
Sbjct: 6   FPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERL 63

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 151 LAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPML 195
           + E+G+K  T +Q + IP++L  +     A TGSGKT A+  P+L
Sbjct: 9   IREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPIL 53

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 32/58 (55%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           F  +  +L  L   G   PTPI+  A+P+ L  ++    A TG+GKTLAF  P+  +L
Sbjct: 6   FPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERL 63

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 41/84 (48%)
Query: 119 NIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFA 178
           N++  G  + S     V        +  LLR +   G+++P+ IQ++AI   +   +  A
Sbjct: 13  NLYFQGGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIA 72
Query: 179 CAPTGSGKTLAFLCPMLMKLRVLF 202
            A +G+GKT  F   +L +L + F
Sbjct: 73  QAQSGTGKTATFAISILQQLEIEF 96

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDR-ECFACAPTGSGKTLAFLCPML 195
           +L  +   G+++PT IQ + IP+ L+D     A A TGSGKT +F  P++
Sbjct: 17  ILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 155 GYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM--KLRVLFIPF 205
           GY++  P Q + I  +LS R+C    PTG GK+L +  P L+   L V+  P 
Sbjct: 22  GYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVSPL 74

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 53/101 (52%), Gaps = 4/101 (3%)
Query: 100 AKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEP 159
           A+  LNK I R  +      + V   +  SPL + VK       +  LL+ +  +G+  P
Sbjct: 58  AQSLLNKLI-RSNLVDNTNQVEVLQRDPNSPLYS-VKSFEELRLKPQLLQGVYAMGFNRP 115
Query: 160 TPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLCPMLMKL 198
           + IQ  A+P++L++  +   A + +G+GKT AF+  ML ++
Sbjct: 116 SKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 53/101 (52%), Gaps = 4/101 (3%)
Query: 100 AKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEP 159
           A+  LNK I R  +      + V   +  SPL + VK       +  LL+ +  +G+  P
Sbjct: 28  AQSLLNKLI-RSNLVDNTNQVEVLQRDPNSPLYS-VKSFEELRLKPQLLQGVYAMGFNRP 85
Query: 160 TPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLCPMLMKL 198
           + IQ  A+P++L++  +   A + +G+GKT AF+  ML ++
Sbjct: 86  SKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 126

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 53/101 (52%), Gaps = 4/101 (3%)
Query: 100 AKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEP 159
           A+  LNK I R  +      + V   +  SPL + VK       +  LL+ +  +G+  P
Sbjct: 7   AQSLLNKLI-RSNLVDNTNQVEVLQRDPNSPLYS-VKSFEELRLKPQLLQGVYAMGFNRP 64
Query: 160 TPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLCPMLMKL 198
           + IQ  A+P++L++  +   A + +G+GKT AF+  ML ++
Sbjct: 65  SKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 105

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 155 GYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM 196
           GY++  P Q + I  +LS R+C    PTG GK+L +  P L+
Sbjct: 22  GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL 63

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 53/101 (52%), Gaps = 4/101 (3%)
Query: 100 AKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEP 159
           A+  LNK I R  +      + V   +  SPL + VK       +  LL+ +  +G+  P
Sbjct: 58  AQSLLNKLI-RSNLVDNTNQVEVLQRDPNSPLYS-VKSFEELRLKPQLLQGVYAMGFNRP 115
Query: 160 TPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLCPMLMKL 198
           + IQ  A+P++L++  +   A + +G+GKT AF+  ML ++
Sbjct: 116 SKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV 200
            G    LLR +   G+++P+ IQ++AI  ++  R+  A + +G+GKT  F   +L  L +
Sbjct: 6   MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDI 65

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV 200
            G    LLR +   G+++P+ IQ++AI  ++  R+  A + +G+GKT  F   +L  L +
Sbjct: 43  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 102

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV 200
            G    LLR +   G+++P+ IQ++AI  ++  R+  A + +G+GKT  F   +L  L +
Sbjct: 42  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 101

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV 200
            G    LLR +   G+++P+ IQ++AI  ++  R+  A + +G+GKT  F   +L  L +
Sbjct: 43  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 102

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 160 TPIQRQAIPVLLS--DRECFACAPTGSGKTLAFLCPMLMKL 198
           TP+Q++ I  +LS  D +  A A TG+GKT AFL P+   L
Sbjct: 45  TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL 85

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV 200
            G    LLR +   G+++P+ IQ++AI  ++  R+  A + +G+GKT  F   +L  L +
Sbjct: 21  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 80

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV 200
            G    LLR +   G+++P+ IQ++AI  ++  R+  A + +G+GKT  F   +L  L +
Sbjct: 6   MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDI 65

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	211
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	7e-45
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	4e-31
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-28
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	3e-27
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	7e-27
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-25
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	8e-21
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	4e-20
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	5e-20
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	6e-20
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	8e-19
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	8e-19
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-17
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-17
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	2e-16
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	9e-16
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-15
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-15
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	3e-15
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	2e-14
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	4e-14
3bor_A	237	Human initiation factor 4A-II; translation initiat	6e-14
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	6e-14
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	9e-14
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-13
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-13
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-12
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	3e-12
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	5e-12
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	6e-11
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	6e-08
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	7e-07
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	3e-06
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	1e-04
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	2e-04
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	6e-04

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  148 bits (376), Expect = 7e-45
 Identities = 46/95 (48%), Positives = 63/95 (66%), Gaps = 3/95 (3%)

Query: 105 NKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQR 164
           + +I      R K+ IHV G ++P P+ TF +L   +   S LL+N+ + G++ PTPIQ 
Sbjct: 1   SMKINF---LRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQM 57

Query: 165 QAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
           QAIPV+L  RE  A APTGSGKTLAF  P+LM+L+
Sbjct: 58  QAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLK 92

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score =  113 bits (284), Expect = 4e-31
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 114 FRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
           +R+   I V G N P P+  F          + ++  +A   + EPT IQ Q  PV LS 
Sbjct: 11  YRRSKEITVRGHNCPKPVLNF----YEANFPANVMDVIARQNFTEPTAIQAQGWPVALSG 66

Query: 174 RECFACAPTGSGKTLAFLCPMLM 196
            +    A TGSGKTL++L P ++
Sbjct: 67  LDMVGVAQTGSGKTLSYLLPAIV 89

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score =  109 bits (275), Expect = 2e-28
 Identities = 44/121 (36%), Positives = 63/121 (52%), Gaps = 10/121 (8%)

Query: 84  PAVDKEKEK---VEDGPSKAKKELNKQIERDAVFRKKYN---IHVSGANVPSPLRTFVKL 137
           P    E      +   PS    E+        +   KYN   + V+G++VP P++ F   
Sbjct: 2   PLGSPEFPGEFYIPPEPSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHF--- 58

Query: 138 SSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK 197
            +       ++ N+ + GYK PTPIQ+ +IPV+ S R+  ACA TGSGKT AFL P+L K
Sbjct: 59  -TSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSK 117

Query: 198 L 198
           L
Sbjct: 118 L 118

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  106 bits (266), Expect = 3e-27
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 4/79 (5%)

Query: 120 IHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFAC 179
           +  +G N P  + +F    S       ++ N+    Y  PTP+Q+ AIP++   R+  AC
Sbjct: 3   VEATGNNCPPHIESF----SDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMAC 58

Query: 180 APTGSGKTLAFLCPMLMKL 198
           A TGSGKT AFL P+L ++
Sbjct: 59  AQTGSGKTAAFLLPILSQI 77

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score =  101 bits (254), Expect = 7e-27
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 122 VSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAP 181
                +P P   F      F     LL+++  +G  +PTPIQ QA P++L   +    A 
Sbjct: 9   GEKRLIPKPTCRF---KDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQ 65

Query: 182 TGSGKTLAFLCPMLMKL 198
           TG+GKTL++L P  + L
Sbjct: 66  TGTGKTLSYLMPGFIHL 82

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score = 99.2 bits (248), Expect = 1e-25
 Identities = 31/87 (35%), Positives = 46/87 (52%), Gaps = 9/87 (10%)

Query: 117 KYN---IHVSGAN--VPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLL 171
           KY+   + V+G +    + +  F         +  +  N+    Y+ PTPIQ+ AIP +L
Sbjct: 3   KYDSIPVSVTGPDYSATNVIENF----DELKLDPTIRNNILLASYQRPTPIQKNAIPAIL 58

Query: 172 SDRECFACAPTGSGKTLAFLCPMLMKL 198
             R+  ACA TGSGKT AFL P++  L
Sbjct: 59  EHRDIMACAQTGSGKTAAFLIPIINHL 85

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 88.2 bits (219), Expect = 8e-21
 Identities = 13/53 (24%), Positives = 19/53 (35%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
                 +   K+ T  QR     ++  +     APTG GKT   +   L   R
Sbjct: 10  FRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR 62

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score = 83.8 bits (208), Expect = 4e-20
 Identities = 32/92 (34%), Positives = 45/92 (48%), Gaps = 7/92 (7%)

Query: 107 QIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQA 166
           Q+ER+++ R   N         + +  F    S F      L+ L E  Y+  T IQ+Q 
Sbjct: 3   QVERESISRLMQNYEKIN---VNEITRF----SDFPLSKKTLKGLQEAQYRLVTEIQKQT 55

Query: 167 IPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           I + L  ++    A TGSGKTLAFL P+L  L
Sbjct: 56  IGLALQGKDVLGAAKTGSGKTLAFLVPVLEAL 87

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score = 83.9 bits (208), Expect = 5e-20
 Identities = 24/52 (46%), Positives = 31/52 (59%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           L     +LG+ +PT IQ +AIP+ L  R+    A TGSGKT AF  P+L  L
Sbjct: 54  LCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNAL 105

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score = 83.9 bits (208), Expect = 6e-20
 Identities = 31/114 (27%), Positives = 48/114 (42%), Gaps = 7/114 (6%)

Query: 85  AVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCE 144
            VD   E +        ++ +   +   V          G        +F  L +    E
Sbjct: 10  GVDLGTENLYFQSMNNVEKPDNDEDESEVPSLP-----LGLTGAFEDTSFASLCNLV-NE 63

Query: 145 SYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +  L+ + E+G+   T IQ ++I  LL  R+  A A TGSGKTLAFL P +  +
Sbjct: 64  N-TLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELI 116

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 79.9 bits (198), Expect = 8e-19
 Identities = 19/60 (31%), Positives = 34/60 (56%)

Query: 139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +RF  + +++  +  L + +PT IQ + IP  L        + TG+GKT A+L P++ K+
Sbjct: 7   TRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKI 66

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 79.9 bits (198), Expect = 8e-19
 Identities = 22/52 (42%), Positives = 30/52 (57%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +L  L   G   PTPIQ  A+P+ L  ++    A TG+GKTLAF  P+  +L
Sbjct: 12  ILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERL 63

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score = 78.3 bits (194), Expect = 1e-17
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK 197
           + + + E+G+K  T +Q + IP++L  +     A TGSGKT A+  P+L  
Sbjct: 5   IEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL 55

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score = 78.7 bits (194), Expect = 2e-17
 Identities = 27/127 (21%), Positives = 49/127 (38%), Gaps = 4/127 (3%)

Query: 74  NVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPLRT 133
             F  +++   +      +    P    +E + ++  D     K        N      T
Sbjct: 12  RNFGRNQRNNNSNRYRNSRFNSRPRTRSREDDDEVHFDKTTFSKLIHVPKEDNSKEV--T 69

Query: 134 FVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLS--DRECFACAPTGSGKTLAFL 191
              L      +  + + +  + +   TP+Q++ I  +LS  D +  A A TG+GKT AFL
Sbjct: 70  LDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFL 129

Query: 192 CPMLMKL 198
            P+   L
Sbjct: 130 IPIFQHL 136

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 73.3 bits (181), Expect = 2e-16
 Identities = 23/58 (39%), Positives = 40/58 (68%)

Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +  +  LL  + E+G+++P+PIQ ++IP+ LS R+  A A  G+GK+ A+L P+L +L
Sbjct: 8   YCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERL 65

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 74.1 bits (182), Expect = 9e-16
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLS--DRECFACAPTGSGKTLAF 190
           T   L      +  + + +  + +   TP+Q++ I  +LS  D +  A A TG+GKT AF
Sbjct: 18  TLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAF 77

Query: 191 LCPMLMKL 198
           L P+   L
Sbjct: 78  LIPIFQHL 85

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score = 72.7 bits (179), Expect = 2e-15
 Identities = 30/126 (23%), Positives = 62/126 (49%), Gaps = 9/126 (7%)

Query: 78  SSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPL---RTF 134
           +   +    + EK   E+   +A + L  ++ R  +      + V   +  SPL   ++F
Sbjct: 35  NGAVVKTNANAEKTDEEEKEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSF 94

Query: 135 VKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLC 192
            +L      +  LL+ +  +G+  P+ IQ  A+P++L++  +   A + +G+GKT AF+ 
Sbjct: 95  EEL----RLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150

Query: 193 PMLMKL 198
            ML ++
Sbjct: 151 AMLSQV 156

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 72.1 bits (177), Expect = 2e-15
 Identities = 30/120 (25%), Positives = 60/120 (50%), Gaps = 9/120 (7%)

Query: 84  PAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPSPL---RTFVKLSSR 140
              + EK   E+   +A + L  ++ R  +      + V   +  SPL   ++F +L   
Sbjct: 41  TNANAEKTDEEEKEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEEL--- 97

Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLCPMLMKL 198
              +  LL+ +  +G+  P+ IQ  A+P++L++  +   A + +G+GKT AF+  ML ++
Sbjct: 98  -RLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score = 72.2 bits (178), Expect = 3e-15
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRE-CFACAPTGSGKTLAFLCPMLMKL 198
                 +L  +   G+++PT IQ + IP+ L+D     A A TGSGKT +F  P++  +
Sbjct: 11  LNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELV 69

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score = 69.9 bits (172), Expect = 2e-14
 Identities = 24/52 (46%), Positives = 36/52 (69%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LL  + E G+++P+PIQ +AIPV ++ R+  A A  G+GKT AF+ P L K+
Sbjct: 32  LLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKV 83

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 67.6 bits (166), Expect = 4e-14
 Identities = 17/52 (32%), Positives = 27/52 (51%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +L  L   G++ P+P+Q +AIP+     +    A +G+GKT  F    L  L
Sbjct: 35  VLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSL 86

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 67.2 bits (165), Expect = 6e-14
 Identities = 18/52 (34%), Positives = 31/52 (59%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LLR +   G+++P+ IQ++AI   +   +  A A +G+GKT  F   +L +L
Sbjct: 41  LLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQL 92

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 66.8 bits (164), Expect = 6e-14
 Identities = 18/52 (34%), Positives = 31/52 (59%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LLR +   G++EP+ IQ++AI  ++   +  A A +G+GKT  F    L ++
Sbjct: 25  LLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI 76

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score = 67.9 bits (167), Expect = 9e-14
 Identities = 18/52 (34%), Positives = 31/52 (59%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LLR +   G++EP+ IQ++AI  ++   +  A A +G+GKT  F    L ++
Sbjct: 32  LLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI 83

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score = 67.6 bits (166), Expect = 1e-13
 Identities = 18/52 (34%), Positives = 32/52 (61%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LLR +   G+++P+ IQ++AI  ++  R+  A + +G+GKT  F   +L  L
Sbjct: 48  LLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCL 99

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 67.2 bits (165), Expect = 2e-13
 Identities = 17/52 (32%), Positives = 31/52 (59%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           LLR +   G+++P+ IQ++AI   +   +  A A +G+GKT  F   +L ++
Sbjct: 51  LLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQI 102

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           F  +  LLR + + G++ P+ +Q + IP  +   +    A +G GKT  F+   L +L
Sbjct: 19  FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQL 76

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score = 63.7 bits (156), Expect = 3e-12
 Identities = 19/54 (35%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 147 LLRNLAELGYKEPTPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLCPMLMKL 198
           LL+ +  + +++P+ IQ +A+P+LL +  R   A + +G+GKT AF   ML ++
Sbjct: 16  LLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score = 63.0 bits (154), Expect = 5e-12
 Identities = 24/87 (27%), Positives = 47/87 (54%), Gaps = 9/87 (10%)

Query: 117 KYNIHVSGANVPSPL---RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD 173
              + V   +  SPL   ++F +L      +  LL+ +  +G+  P+ IQ  A+P++L++
Sbjct: 7   TNQVEVLQRDPNSPLYSVKSFEEL----RLKPQLLQGVYAMGFNRPSKIQENALPLMLAE 62

Query: 174 --RECFACAPTGSGKTLAFLCPMLMKL 198
             +   A + +G+GKT AF+  ML ++
Sbjct: 63  PPQNLIAQSQSGTGKTAAFVLAMLSQV 89

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score = 59.9 bits (146), Expect = 6e-11
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           F  +  LLR + + G++ P+ +Q + IP  +   +    A +G GKT  F+   L +L
Sbjct: 13  FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQL 70

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 51.3 bits (123), Expect = 6e-08
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 7/74 (9%)

Query: 139 SRFGCESYLLRNLAELGYKEPTPIQRQAIP-VLLSDRECFACAPTGSGKTLAFLCPML-- 195
                 S ++  + + G K+  P Q +A+   LL        +PTGSGKTL     ++  
Sbjct: 11  EDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISF 70

Query: 196 ---MKLRVLFI-PF 205
                 + +++ P 
Sbjct: 71  LLKNGGKAIYVTPL 84

>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 Length = 702

 Score = 46.3 bits (110), Expect = 3e-06
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 4/57 (7%)

Query: 151 LAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL----RVLFI 203
           L E G +E  P Q +A+  + S +      PT +GKTL     M+ +     + L++
Sbjct: 18  LKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYV 74

>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 = 41.4 bits (96), Expect = 1e-04
 Identities = 26/198 (13%), Positives = 57/198 (28%), Gaps = 20/198 (10%)

Query: 11  GVSFDKKKFVTDFARFKENKESENLADDFSFVEGEKTDPEKAMVSFVKKRKRKSIAGETV 70
           G+   +  +      F E  +S +L D F     E         +            +  
Sbjct: 17  GLDSTENLYFQGIDPFTEFMDSTDLFDVFEETPVELPTDSNGEKNADTNVGDTPDHTQDK 76

Query: 71  E-GFNVFKSSKQLVPAVDKEKEKVEDGPSKAKKELNKQIERDAVFRKKYNIHVSGANVPS 129
           + G    K   +   + +K+ +  +       K++   +  D+  ++      +   + +
Sbjct: 77  KHGLEEEKEEHEENNSENKKIKSNKSKTEDKNKKVVVPVLADSFEQEASREVDASKGLTN 136

Query: 130 PLRTFVKLSSRFGCESYLLRNLAELGYKEPTPI-------------------QRQAIPVL 170
                V+   +      +   +A     + TPI                   Q  AI  +
Sbjct: 137 SETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCI 196

Query: 171 LSDRECFACAPTGSGKTL 188
                    A T +GKT+
Sbjct: 197 DRGESVLVSAHTSAGKTV 214

>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* Length = 720

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 151 LAELGYKEPTPIQRQAIP-VLLSDRECFACAPTGSGKTLAFLCPMLMKL-----RVLFI 203
           L E G +   P Q +A+   +L  +      PT SGKTL     M+ ++     + ++I
Sbjct: 16  LKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYI 74

>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 = 39.4 bits (91), Expect = 6e-04
 Identities = 9/31 (29%), Positives = 12/31 (38%)

Query: 158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTL 188
              P Q  AI  +         A T +GKT+
Sbjct: 86  TLDPFQDTAISCIDRGESVLVSAHTSAGKTV 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	211
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.8
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.8
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.77
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.74
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.69
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.66
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.66
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.66
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.65
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.64
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.64
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.62
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.61
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.61
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.6
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.59
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.58
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.56
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.55
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.53
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.5
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.5
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.49
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.48
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.47
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.47
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.46
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.41
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.28
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.2
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.17
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.16
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.15
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.14
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.12
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.11
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.01
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	98.98
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	98.88
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	98.88
3b6e_A	216	Interferon-induced helicase C domain-containing P;	98.83
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	98.8
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.79
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.74
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	98.71
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.7
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.68
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	98.62
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.61
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.61
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	98.6
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.57
4gl2_A	699	Interferon-induced helicase C domain-containing P;	98.56
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	98.56
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	98.54
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	98.42
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.38
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.36
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	98.31
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.3
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.28
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	98.25
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.24
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	98.17
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.17
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	97.91
3h1t_A	590	Type I site-specific restriction-modification syst	97.78
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	97.74
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	97.67
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	97.45
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.37
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	96.99
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	96.9
3jux_A	822	Protein translocase subunit SECA; protein transloc	96.25
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	96.17
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	95.2
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.01
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	94.73
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	94.22
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	94.01
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	93.94
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	93.6
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	93.51
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	93.26
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	92.78
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	91.27
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	90.19
3co5_A	143	Putative two-component system transcriptional RES	88.9
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	88.4
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	88.24
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	88.01
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	87.54
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	86.53
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	85.74
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	85.26
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	84.31
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	84.2
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	83.78
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	83.46
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	83.07
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	82.64
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	82.5
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	82.13
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	81.41
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	81.41
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	81.17
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	81.15
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	81.07

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.80  E-value=5e-20  Score=160.63  Aligned_cols=110  Identities=24%  Similarity=0.417  Sum_probs=81.7

Q ss_pred             hHHHhhhhHHHHHHHHhhcCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC--CcEE
Q 028267          100 AKKELNKQIERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD--RECF  177 (211)
Q Consensus       100 ~~k~~~~~~~~~~~~~~~~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G--~dvi  177 (211)
                      ...+......+....+..+.+.+.+.+.+.|+.++..+ +.++|++.++++|..+||..||+||.++||.++.|  +|+|
T Consensus        57 ~~~~~~~~~~~~~~~~~~~~v~v~~~~~~~p~~~~~~f-~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l  135 (300)
T 3fmo_B           57 AAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSF-EELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI  135 (300)
T ss_dssp             ------------CCCCCCSCEEEECSSTTCCCCCCCCS-GGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEE
T ss_pred             hHHHHHHhhhhcccccccccceeccCCCCCCcCCcCCH-hhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEE
Confidence            33444444555555666788899999888876543322 34499999999999999999999999999999998  9999


Q ss_pred             EEcCCCchhHHHhHHHHHHHHhcccCCCceEEe
Q 028267          178 ACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCE  210 (211)
Q Consensus       178 ~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~~  210 (211)
                      ++|+||||||++|++|+++++........++++
T Consensus       136 ~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil  168 (300)
T 3fmo_B          136 AQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCL  168 (300)
T ss_dssp             EECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEE
T ss_pred             EECCCCCCccHHHHHHHHHhhhccCCCceEEEE
Confidence            999999999999999999999776544444443

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.80  E-value=2.3e-19  Score=150.04  Aligned_cols=91  Identities=49%  Similarity=0.812  Sum_probs=86.3

Q ss_pred             HHHHHhhcCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHh
Q 028267          111 DAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       111 ~~~~~~~~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf  190 (211)
                      ...++..++|.+.|.++|.|+.+|.++.+.|+|++.++++|..+||..|+|+|.++|+.++.|+|++++|+||||||++|
T Consensus         4 ~~~~~~~~~i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~   83 (245)
T 3dkp_A            4 INFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAF   83 (245)
T ss_dssp             HHHHHHHTTEEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHH
T ss_pred             HHHHHHhCceEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHH
Confidence            45788889999999999999999999988889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcc
Q 028267          191 LCPMLMKLRVL  201 (211)
Q Consensus       191 ~lPil~~l~~~  201 (211)
                      ++|+++++...
T Consensus        84 ~l~~l~~l~~~   94 (245)
T 3dkp_A           84 SIPILMQLKQP   94 (245)
T ss_dssp             HHHHHHHHCSC
T ss_pred             HHHHHHHHhhc
Confidence            99999999753

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.77  E-value=1.3e-18  Score=145.75  Aligned_cols=89  Identities=33%  Similarity=0.550  Sum_probs=83.8

Q ss_pred             HHHHHHHhhcCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHH
Q 028267          109 ERDAVFRKKYNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTL  188 (211)
Q Consensus       109 ~~~~~~~~~~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTl  188 (211)
                      ++...++..+.|.+.|.+.|.|+.+|.++    +|++.++++|...||..|+|+|.++||.++.|+|++++|+||||||+
T Consensus         6 ~~~~~~~~~~~i~~~~~~~p~~~~~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~   81 (242)
T 3fe2_A            6 QEVETYRRSKEITVRGHNCPKPVLNFYEA----NFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTL   81 (242)
T ss_dssp             CHHHHHHHHHTEEEESSCCCCCCSSTTTT----TCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHH
T ss_pred             HHHHHHHhcCceEEeCCCCCCccCCHhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHH
Confidence            34567888899999999999999999888    99999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHhcc
Q 028267          189 AFLCPMLMKLRVL  201 (211)
Q Consensus       189 af~lPil~~l~~~  201 (211)
                      +|++|++.++...
T Consensus        82 ~~~l~~l~~l~~~   94 (242)
T 3fe2_A           82 SYLLPAIVHINHQ   94 (242)
T ss_dssp             HHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999998754

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.74  E-value=6.8e-18  Score=153.25  Aligned_cols=81  Identities=44%  Similarity=0.735  Sum_probs=76.9

Q ss_pred             cCceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          118 YNIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       118 ~~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      ..|.+.|.++|.|+.+|.++    +|++.++++|..+||..|||||.++||.++.|+|+|++|+||||||++|++|++++
T Consensus        42 ~~~~~~~~~~p~~~~~f~~~----~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~  117 (434)
T 2db3_A           42 IPVKVTGSDVPQPIQHFTSA----DLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSK  117 (434)
T ss_dssp             SCEEEESSSCCCCCCCGGGS----CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceeEecCCCCCCCcCChhhc----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHH
Confidence            46889999999999999988    99999999999999999999999999999999999999999999999999999999


Q ss_pred             Hhccc
Q 028267          198 LRVLF  202 (211)
Q Consensus       198 l~~~~  202 (211)
                      +...+
T Consensus       118 l~~~~  122 (434)
T 2db3_A          118 LLEDP  122 (434)
T ss_dssp             HHHSC
T ss_pred             HHhcc
Confidence            97654

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

Probab=99.69  E-value=1e-16  Score=141.99  Aligned_cols=79  Identities=35%  Similarity=0.668  Sum_probs=74.8

Q ss_pred             CceeccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          119 NIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       119 ~i~v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .|.+.|.++|.|+.+|.++    +|++.++++|..+||..|||+|.++||.++.|+|+|++|+||||||++|++|+++.+
T Consensus         2 ~~~~~~~~~p~~~~~f~~~----~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~   77 (417)
T 2i4i_A            2 MVEATGNNCPPHIESFSDV----EMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQI   77 (417)
T ss_dssp             CEEEESTTCCCCCSSGGGS----CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CcccCCCcCCcccCCHhhC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHH
Confidence            4678899999999999988    999999999999999999999999999999999999999999999999999999998


Q ss_pred             hcc
Q 028267          199 RVL  201 (211)
Q Consensus       199 ~~~  201 (211)
                      ...
T Consensus        78 ~~~   80 (417)
T 2i4i_A           78 YSD   80 (417)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            654

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.66  E-value=2.1e-16  Score=130.57  Aligned_cols=74  Identities=35%  Similarity=0.583  Sum_probs=68.6

Q ss_pred             cCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          124 GANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       124 g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +..+|.|+.+|.++   |++++.++++|...||..|+|+|.++|+.++.|+|++++|+||||||++|++|++..+..
T Consensus        11 ~~~~p~p~~~f~~~---~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~   84 (228)
T 3iuy_A           11 KRLIPKPTCRFKDA---FQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDS   84 (228)
T ss_dssp             CCCCCCCCCSHHHH---HTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-
T ss_pred             cCcCCCChhhHhhh---hccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            45789999999984   289999999999999999999999999999999999999999999999999999998864

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.66  E-value=6.7e-17  Score=147.39  Aligned_cols=97  Identities=27%  Similarity=0.473  Sum_probs=78.8

Q ss_pred             HHHHHHhhcCceeccCCCCCCch---hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC--CcEEEEcCCCc
Q 028267          110 RDAVFRKKYNIHVSGANVPSPLR---TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD--RECFACAPTGS  184 (211)
Q Consensus       110 ~~~~~~~~~~i~v~g~~~p~p~~---~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G--~dvi~~A~TGs  184 (211)
                      ........+.+.+.+.+.+.|+.   +|.++    +|++.++++|..+||..|+|||.++||.++.|  +|+|++|+|||
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~----~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGs  142 (479)
T 3fmp_B           67 RSNLVDNTNQVEVLQRDPNSPLYSVKSFEEL----RLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGT  142 (479)
T ss_dssp             ---CCCCCSCEEEECSSTTSCCCCCCCSGGG----TCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSS
T ss_pred             hhhhccCCccceecCCCCCCCccCcCCHHHc----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCC
Confidence            33344455667788888777754   55555    99999999999999999999999999999997  99999999999


Q ss_pred             hhHHHhHHHHHHHHhcccCCCceEEe
Q 028267          185 GKTLAFLCPMLMKLRVLFIPFDYFCE  210 (211)
Q Consensus       185 GKTlaf~lPil~~l~~~~~~~~~~~~  210 (211)
                      |||++|++|+++.+........++++
T Consensus       143 GKT~~~~l~il~~l~~~~~~~~~lil  168 (479)
T 3fmp_B          143 GKTAAFVLAMLSQVEPANKYPQCLCL  168 (479)
T ss_dssp             SHHHHHHHHHHTTCCTTSCSCCEEEE
T ss_pred             chhHHHHHHHHHHHhhcCCCCcEEEE
Confidence            99999999999998766544455544

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.66  E-value=2e-16  Score=132.20  Aligned_cols=83  Identities=27%  Similarity=0.415  Sum_probs=68.5

Q ss_pred             eccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          122 VSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       122 v~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +...++|.+..+|+++    +|++.++++|...||..|+++|.++|+.++.|+|++++|+||||||++|++|+++.+...
T Consensus        20 ~~~~~~~~~~~~f~~l----~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~   95 (237)
T 3bor_A           20 VIESNWNEIVDNFDDM----NLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE   95 (237)
T ss_dssp             -------CCCCSGGGS----CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTT
T ss_pred             cccCCCCCccCChhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc
Confidence            3455677888888888    999999999999999999999999999999999999999999999999999999998755


Q ss_pred             cCCCceE
Q 028267          202 FIPFDYF  208 (211)
Q Consensus       202 ~~~~~~~  208 (211)
                      .....++
T Consensus        96 ~~~~~~l  102 (237)
T 3bor_A           96 FKETQAL  102 (237)
T ss_dssp             SCSCCEE
T ss_pred             CCCceEE
Confidence            4333333

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.65  E-value=4.1e-16  Score=129.59  Aligned_cols=80  Identities=25%  Similarity=0.318  Sum_probs=65.3

Q ss_pred             cCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          124 GANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       124 g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      +...|.+..+|.++    +|++.++++|..+||..|+++|.++|+.++.|+|++++|+||||||++|++|++..+.....
T Consensus        16 ~~~~~~~~~~f~~l----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~   91 (230)
T 2oxc_A           16 GDVLLAEPADFESL----LLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENL   91 (230)
T ss_dssp             --------CCGGGG----TCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSC
T ss_pred             CCCCCCCCCCHhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCC
Confidence            45566777788888    99999999999999999999999999999999999999999999999999999999865443


Q ss_pred             CCce
Q 028267          204 PFDY  207 (211)
Q Consensus       204 ~~~~  207 (211)
                      ...+
T Consensus        92 ~~~~   95 (230)
T 2oxc_A           92 STQI   95 (230)
T ss_dssp             SCCE
T ss_pred             CceE
Confidence            3333

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.64  E-value=6.1e-16  Score=127.05  Aligned_cols=82  Identities=24%  Similarity=0.373  Sum_probs=71.9

Q ss_pred             cCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          124 GANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       124 g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      ..+.+.++.+|.++    +|++.++++|...||..|+|+|.++|+.++.|+|++++++||||||++|++|+++.+.....
T Consensus         6 ~~~~~~~~~~f~~l----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~   81 (224)
T 1qde_A            6 QTNYDKVVYKFDDM----ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK   81 (224)
T ss_dssp             CBSCCCCCCCGGGG----TCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCC
T ss_pred             ccccCcccCChhhc----CCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCC
Confidence            34567778889888    99999999999999999999999999999999999999999999999999999999876544


Q ss_pred             CCceEE
Q 028267          204 PFDYFC  209 (211)
Q Consensus       204 ~~~~~~  209 (211)
                      ...++.
T Consensus        82 ~~~~li   87 (224)
T 1qde_A           82 APQALM   87 (224)
T ss_dssp             SCCEEE
T ss_pred             CceEEE
Confidence            434433

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.64  E-value=1.4e-16  Score=133.86  Aligned_cols=80  Identities=38%  Similarity=0.657  Sum_probs=73.9

Q ss_pred             cCceeccCCCCC--CchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHH
Q 028267          118 YNIHVSGANVPS--PLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPML  195 (211)
Q Consensus       118 ~~i~v~g~~~p~--p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil  195 (211)
                      ..+.+.|...|.  ++.+|.++    +|++.++++|..+||..|+|+|.++|+.++.|+|++++|+||||||++|++|++
T Consensus         7 ~~~~~~~~~~~~~~~~~~f~~l----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l   82 (253)
T 1wrb_A            7 IPVSVTGPDYSATNVIENFDEL----KLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPII   82 (253)
T ss_dssp             CCCCEECCSSSCCSCCCSSGGG----SCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CceeeeCCCCCCCCccCCHhhC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHH
Confidence            356678888887  88899888    999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcc
Q 028267          196 MKLRVL  201 (211)
Q Consensus       196 ~~l~~~  201 (211)
                      ..+...
T Consensus        83 ~~l~~~   88 (253)
T 1wrb_A           83 NHLVCQ   88 (253)
T ss_dssp             HHHHTT
T ss_pred             HHHHhh
Confidence            998754

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.62  E-value=9.6e-16  Score=126.07  Aligned_cols=70  Identities=26%  Similarity=0.465  Sum_probs=63.3

Q ss_pred             chhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCC
Q 028267          131 LRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIP  204 (211)
Q Consensus       131 ~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~  204 (211)
                      ..+|+++    +|++.++++|..+||..|+++|.++|+.++.|+|++++|+||||||++|++|+++.+......
T Consensus         3 ~~~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~   72 (219)
T 1q0u_A            3 ETQFTRF----PFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAE   72 (219)
T ss_dssp             -CCGGGS----CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCS
T ss_pred             CCCHhhC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCC
Confidence            3457666    999999999999999999999999999999999999999999999999999999998765433

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.61  E-value=1.7e-15  Score=122.74  Aligned_cols=67  Identities=36%  Similarity=0.602  Sum_probs=61.6

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      +|+++    +|++.++++|..+||..|+|+|.++|+.++.|+|++++|+||||||++|++|++..+.....
T Consensus         4 ~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~   70 (206)
T 1vec_A            4 EFEDY----CLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKD   70 (206)
T ss_dssp             SGGGS----CCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSC
T ss_pred             Chhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCC
Confidence            45555    99999999999999999999999999999999999999999999999999999999865443

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.61  E-value=1.6e-15  Score=124.39  Aligned_cols=71  Identities=24%  Similarity=0.381  Sum_probs=62.1

Q ss_pred             CCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          129 SPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       129 ~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      .+..+|.++    +|++.++++|...||..|+|+|.++|+.++.|+|++++++||||||++|++|++..+.....
T Consensus        11 ~~~~~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~   81 (220)
T 1t6n_A           11 IHSSGFRDF----LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG   81 (220)
T ss_dssp             ---CCSTTS----CCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTT
T ss_pred             ccCCCHhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCC
Confidence            333445555    99999999999999999999999999999999999999999999999999999999876443

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.60  E-value=1.8e-15  Score=127.89  Aligned_cols=76  Identities=37%  Similarity=0.460  Sum_probs=67.0

Q ss_pred             chhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceEEe
Q 028267          131 LRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCE  210 (211)
Q Consensus       131 ~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~~  210 (211)
                      ..+|.++    +|++.++++|..+||..|+++|.++|+.++.|+|++++|+||||||++|++|+++.+........++++
T Consensus        42 ~~~f~~l----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil  117 (249)
T 3ber_A           42 TKTFKDL----GVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVL  117 (249)
T ss_dssp             HCCTGGG----TCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEE
T ss_pred             cCCHHHc----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEE
Confidence            3456666    999999999999999999999999999999999999999999999999999999998876554444443

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.59  E-value=2.7e-15  Score=124.53  Aligned_cols=69  Identities=36%  Similarity=0.511  Sum_probs=63.8

Q ss_pred             CCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          128 PSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       128 p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +.++.+|.++    +|++.++++|..+||..|+|+|.++|+.++.|+|++++|+||||||++|++|+++.+..
T Consensus        21 ~~~~~~f~~~----~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~   89 (236)
T 2pl3_A           21 VNEITRFSDF----PLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYR   89 (236)
T ss_dssp             GGGCSBGGGS----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             CcccCCHhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHh
Confidence            3455677776    99999999999999999999999999999999999999999999999999999999865

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.58  E-value=2.7e-15  Score=132.13  Aligned_cols=89  Identities=27%  Similarity=0.507  Sum_probs=72.1

Q ss_pred             hcCceeccCCCCCC---chhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC--CcEEEEcCCCchhHHHhH
Q 028267          117 KYNIHVSGANVPSP---LRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD--RECFACAPTGSGKTLAFL  191 (211)
Q Consensus       117 ~~~i~v~g~~~p~p---~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G--~dvi~~A~TGsGKTlaf~  191 (211)
                      .+.+.+.....+.|   +.+|.++    +|++.++++|...||..|+|+|.++|+.++.|  +++|++|+||||||++|+
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~   82 (412)
T 3fht_A            7 TNQVEVLQRDPNSPLYSVKSFEEL----RLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFV   82 (412)
T ss_dssp             -CHHHHHTTCTTSTTCCSSCTGGG----TCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHH
T ss_pred             cccceeecccCCCCccccCCHhhC----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHH
Confidence            34444555555555   4456655    99999999999999999999999999999998  999999999999999999


Q ss_pred             HHHHHHHhcccCCCceEE
Q 028267          192 CPMLMKLRVLFIPFDYFC  209 (211)
Q Consensus       192 lPil~~l~~~~~~~~~~~  209 (211)
                      +|+++.+........++.
T Consensus        83 ~~~~~~~~~~~~~~~~li  100 (412)
T 3fht_A           83 LAMLSQVEPANKYPQCLC  100 (412)
T ss_dssp             HHHHHHCCTTSCSCCEEE
T ss_pred             HHHHHHhhhcCCCCCEEE
Confidence            999999876554434443

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

Probab=99.56  E-value=9.3e-15  Score=129.50  Aligned_cols=81  Identities=26%  Similarity=0.415  Sum_probs=69.2

Q ss_pred             cCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          124 GANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       124 g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      ....+.+..+|.++    +|++.++++|...||..|+|+|.++|+.++.|+|++++|+||||||++|++|+++.+.....
T Consensus        29 ~~~~~~~~~~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~  104 (410)
T 2j0s_A           29 TSEEVDVTPTFDTM----GLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVR  104 (410)
T ss_dssp             CCTTCCCCCSGGGG----CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSC
T ss_pred             CCCCccCCCCHhhc----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccC
Confidence            33444566678887    99999999999999999999999999999999999999999999999999999999865433


Q ss_pred             CCceE
Q 028267          204 PFDYF  208 (211)
Q Consensus       204 ~~~~~  208 (211)
                      ...++
T Consensus       105 ~~~~l  109 (410)
T 2j0s_A          105 ETQAL  109 (410)
T ss_dssp             SCCEE
T ss_pred             CceEE
Confidence            33333

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.55  E-value=1.1e-14  Score=117.73  Aligned_cols=64  Identities=36%  Similarity=0.562  Sum_probs=60.2

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +|.++    +|++.++++|..+||..|+|+|.++|+.++.|+|++++++||||||++|++|+++.+..
T Consensus         2 ~f~~~----~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~   65 (207)
T 2gxq_A            2 EFKDF----PLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAP   65 (207)
T ss_dssp             CGGGS----CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCC
T ss_pred             Chhhc----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhh
Confidence            35555    99999999999999999999999999999999999999999999999999999999865

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.53  E-value=1.1e-14  Score=123.88  Aligned_cols=59  Identities=41%  Similarity=0.597  Sum_probs=57.2

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          143 CESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       143 l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      |++.++++|..+||..|+|+|.++|+.++.|+|+|++|+||||||++|++|+++.+...
T Consensus        61 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~  119 (262)
T 3ly5_A           61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKL  119 (262)
T ss_dssp             CCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999998763

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.50  E-value=4.5e-14  Score=123.22  Aligned_cols=75  Identities=31%  Similarity=0.541  Sum_probs=65.4

Q ss_pred             chhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC--CcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          131 LRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD--RECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       131 ~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G--~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      ..+|+++    +|++.++++|...||..|+|+|.++|+.++.|  +++|++|+||||||++|++|++..+........++
T Consensus         4 ~~~f~~~----~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~l   79 (395)
T 3pey_A            4 AKSFDEL----GLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAI   79 (395)
T ss_dssp             CCSSTTS----CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEE
T ss_pred             ccCHhhC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEE
Confidence            3466666    99999999999999999999999999999998  99999999999999999999999987654443443


Q ss_pred             E
Q 028267          209 C  209 (211)
Q Consensus       209 ~  209 (211)
                      .
T Consensus        80 i   80 (395)
T 3pey_A           80 C   80 (395)
T ss_dssp             E
T ss_pred             E
Confidence            3

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.50  E-value=5.5e-14  Score=124.04  Aligned_cols=83  Identities=23%  Similarity=0.371  Sum_probs=72.2

Q ss_pred             ccCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          123 SGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       123 ~g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ...+.+..+.+|.++    +|++.++++|...||..|+++|.++|+.++.|+|+|++|+||||||++|++|+++.+....
T Consensus        31 ~~~~~~~~~~~f~~~----~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~  106 (414)
T 3eiq_A           31 IESNWNEIVDSFDDM----NLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL  106 (414)
T ss_dssp             CCCCCCCCCCCGGGG----CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTS
T ss_pred             cCCCccchhcCHhhC----CCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcC
Confidence            345566777788887    9999999999999999999999999999999999999999999999999999999987654


Q ss_pred             CCCceEE
Q 028267          203 IPFDYFC  209 (211)
Q Consensus       203 ~~~~~~~  209 (211)
                      ....++.
T Consensus       107 ~~~~~li  113 (414)
T 3eiq_A          107 KATQALV  113 (414)
T ss_dssp             CSCCEEE
T ss_pred             CceeEEE
Confidence            4444443

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.49  E-value=5.8e-14  Score=122.92  Aligned_cols=79  Identities=25%  Similarity=0.393  Sum_probs=69.1

Q ss_pred             CCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCC
Q 028267          126 NVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPF  205 (211)
Q Consensus       126 ~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~  205 (211)
                      ....+..+|+++    +|++.++++|...||..|+|+|.++|+.++.|+|++++|+||+|||++|++|++..+.......
T Consensus        15 ~~~~~~~~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~   90 (394)
T 1fuu_A           15 NYDKVVYKFDDM----ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAP   90 (394)
T ss_dssp             SSCCCCCSSGGG----CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSC
T ss_pred             hcccccCChhhc----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCC
Confidence            345566778887    9999999999999999999999999999999999999999999999999999999987654443


Q ss_pred             ceE
Q 028267          206 DYF  208 (211)
Q Consensus       206 ~~~  208 (211)
                      .++
T Consensus        91 ~~l   93 (394)
T 1fuu_A           91 QAL   93 (394)
T ss_dssp             CEE
T ss_pred             CEE
Confidence            333

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

Probab=99.48  E-value=7e-14  Score=123.27  Aligned_cols=71  Identities=37%  Similarity=0.562  Sum_probs=63.3

Q ss_pred             CchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCC
Q 028267          130 PLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIP  204 (211)
Q Consensus       130 p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~  204 (211)
                      +..+|.++    +|++.++++|..+||..|+|+|.++|+.++.|+|++++|+||||||++|++|++..+......
T Consensus        19 ~~~~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~   89 (400)
T 1s2m_A           19 KGNTFEDF----YLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNK   89 (400)
T ss_dssp             --CCGGGG----CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCS
T ss_pred             ccCChhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCC
Confidence            34467777    999999999999999999999999999999999999999999999999999999998654333

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.47  E-value=9.2e-14  Score=130.15  Aligned_cols=75  Identities=28%  Similarity=0.372  Sum_probs=66.8

Q ss_pred             CCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHh--cCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          128 PSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLL--SDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       128 p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il--~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      +.+..+|.++.+...|++.++++|..+||..|+|+|.++|+.++  .|+|+|++|+||||||++|++|+++.+....
T Consensus        13 ~~~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~   89 (579)
T 3sqw_A           13 NSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK   89 (579)
T ss_dssp             SCCCCCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT
T ss_pred             CCCCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcc
Confidence            34445677776666799999999999999999999999999999  7899999999999999999999999987653

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

Probab=99.47  E-value=1.2e-13  Score=121.09  Aligned_cols=72  Identities=24%  Similarity=0.406  Sum_probs=63.8

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      +|+++    +|++.++++|..+||..|+|+|.++|+.++.|+|++++|+||+|||++|++|++..+........++
T Consensus         9 ~f~~~----~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~l   80 (391)
T 1xti_A            9 GFRDF----LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVL   80 (391)
T ss_dssp             CGGGG----CCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEE
T ss_pred             Chhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEE
Confidence            46665    9999999999999999999999999999999999999999999999999999999987654443333

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.46  E-value=1.4e-13  Score=127.66  Aligned_cols=74  Identities=28%  Similarity=0.381  Sum_probs=65.7

Q ss_pred             CCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHh--cCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          129 SPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLL--SDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       129 ~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il--~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      .+..+|.++.+...|++.++++|...||..|+|+|.++|+.++  .|+|+|++|+||||||++|++|+++.+....
T Consensus        65 ~~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~  140 (563)
T 3i5x_A           65 SKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK  140 (563)
T ss_dssp             CCCCCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT
T ss_pred             CCCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcc
Confidence            3344677776666699999999999999999999999999999  6799999999999999999999999997754

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

Probab=99.41  E-value=4.1e-13  Score=115.98  Aligned_cols=70  Identities=31%  Similarity=0.429  Sum_probs=62.6

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHHHhcccCCC
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMKLRVLFIPF  205 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~  205 (211)
                      .+|.++    +|++.++++|..+||..|+|+|.++|+.++.| ++++++|+||||||++|++|++..+.......
T Consensus         6 ~~f~~~----~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~   76 (367)
T 1hv8_A            6 MNFNEL----NLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIE   76 (367)
T ss_dssp             CCGGGS----SCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCC
T ss_pred             Cchhhc----CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccCCCc
Confidence            356666    99999999999999999999999999999998 79999999999999999999999887654333

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.28  E-value=9.3e-12  Score=106.40  Aligned_cols=55  Identities=33%  Similarity=0.553  Sum_probs=52.7

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          143 CESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       143 l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      |++.++++|..+||..|+|+|.++|+.++.|++++++++||+|||++|++|+++.
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~   55 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL   55 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh
Confidence            5789999999999999999999999999999999999999999999999999874

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.20  E-value=1e-11  Score=115.75  Aligned_cols=61  Identities=36%  Similarity=0.566  Sum_probs=56.3

Q ss_pred             hhhhhcccCCCCHHHHHHHHH-cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          133 TFVKLSSRFGCESYLLRNLAE-LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~-~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      +|+++    +|++.+++.|.. .||..|+|+|.++|+.++.|+|+++++|||+|||++|++|++..
T Consensus         3 ~fe~l----~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~   64 (523)
T 1oyw_A            3 QAEVL----NLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL   64 (523)
T ss_dssp             CCCCS----SHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS
T ss_pred             ChhhC----CCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh
Confidence            45555    999999999998 89999999999999999999999999999999999999999853

>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=99.17  E-value=3.7e-11  Score=115.32  Aligned_cols=64  Identities=25%  Similarity=0.337  Sum_probs=59.5

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +|+++    +|++.+++.|...||..|+|+|.++|+. ++.|+++|++||||||||++|.+|+++.+..
T Consensus         2 ~f~~l----~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~   66 (720)
T 2zj8_A            2 RVDEL----RVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILT   66 (720)
T ss_dssp             BGGGC----CSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHH
T ss_pred             cHhhc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHh
Confidence            35555    9999999999999999999999999998 8999999999999999999999999998874

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

Probab=99.16  E-value=5.4e-11  Score=113.85  Aligned_cols=65  Identities=28%  Similarity=0.312  Sum_probs=60.4

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhh-HhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPV-LLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+|+++    +|++.+++.|...||..|+|+|.++|+. ++.|+++|++||||||||++|.+|+++.+..
T Consensus         8 ~~~~~l----~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~   73 (715)
T 2va8_A            8 MPIEDL----KLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK   73 (715)
T ss_dssp             CBGGGS----SSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             CcHHHc----CCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence            456666    9999999999999999999999999999 7899999999999999999999999998874

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.15  E-value=3.3e-11  Score=114.23  Aligned_cols=66  Identities=27%  Similarity=0.440  Sum_probs=58.3

Q ss_pred             CCchhhhhhcccCCCCHHHHHHHHH-cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHH
Q 028267          129 SPLRTFVKLSSRFGCESYLLRNLAE-LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       129 ~p~~~f~~l~~~~~l~~~ll~~l~~-~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      .....|..  .+|++++.++..|.. .||..|+|+|.++|+.++.|+|+|+++|||+|||++|++|++.
T Consensus        16 ~~~~~w~~--~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~   82 (591)
T 2v1x_A           16 SSPAAWNK--EDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALC   82 (591)
T ss_dssp             CCGGGGCC--SCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHT
T ss_pred             cchhcccc--ccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHH
Confidence            33445543  356999999999998 5999999999999999999999999999999999999999985

>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=99.12  E-value=2.6e-11  Score=116.02  Aligned_cols=64  Identities=28%  Similarity=0.328  Sum_probs=56.7

Q ss_pred             hhhhhcccCC--CCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          133 TFVKLSSRFG--CESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       133 ~f~~l~~~~~--l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +|+++    +  |++.+++.|...||..|+|+|.++|+.++.|+++|++||||||||++|.+|++..+..
T Consensus         2 ~f~~l----~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~   67 (702)
T 2p6r_A            2 KVEEL----AESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK   67 (702)
T ss_dssp             CSHHH----HHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT
T ss_pred             chhhh----hhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh
Confidence            45666    6  9999999999999999999999999999999999999999999999999999998864

>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=99.11  E-value=2.4e-11  Score=122.65  Aligned_cols=59  Identities=20%  Similarity=0.099  Sum_probs=54.1

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          142 GCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       142 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ++++.+...+...++..|+|+|.++|+.++.|+|+|++|+||||||++|++|++..+..
T Consensus       168 ~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~  226 (1108)
T 3l9o_A          168 PIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN  226 (1108)
T ss_dssp             TTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT
T ss_pred             CCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc
Confidence            77777777777888889999999999999999999999999999999999999999854

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.01  E-value=3.6e-10  Score=100.66  Aligned_cols=51  Identities=24%  Similarity=0.210  Sum_probs=44.7

Q ss_pred             HHHHHHH-cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          147 LLRNLAE-LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       147 ll~~l~~-~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      +.+.|.. .|| .|||+|.++|+.++.|+|++++||||||||++|++|++..+
T Consensus        10 ~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~   61 (414)
T 3oiy_A           10 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA   61 (414)
T ss_dssp             HHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh
Confidence            4445555 356 89999999999999999999999999999999999998877

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

Probab=98.98  E-value=5e-10  Score=106.07  Aligned_cols=55  Identities=22%  Similarity=0.260  Sum_probs=46.5

Q ss_pred             HHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          148 LRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       148 l~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ..+|..+||..|+|+|..+|+.++.|+|+|++++||+|||++|++|+++.+...+
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~   57 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFP   57 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSC
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCc
Confidence            3467788999999999999999999999999999999999999999999987654

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

Probab=98.88  E-value=1.6e-09  Score=98.82  Aligned_cols=49  Identities=22%  Similarity=0.336  Sum_probs=42.4

Q ss_pred             cCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          154 LGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ++...|+|+|.++|+.++.|+|+|++++||||||++|++|+++.+...+
T Consensus         3 ~~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~   51 (556)
T 4a2p_A            3 METKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP   51 (556)
T ss_dssp             -----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCc
Confidence            4566899999999999999999999999999999999999999998765

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=98.88  E-value=2e-09  Score=105.54  Aligned_cols=44  Identities=27%  Similarity=0.264  Sum_probs=40.6

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      +.+|| .|||||..+||.++.|+  |++|+||+|||++|+||++...
T Consensus        78 r~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~a  121 (844)
T 1tf5_A           78 RVTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNA  121 (844)
T ss_dssp             HHHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHH
T ss_pred             HHcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHH
Confidence            35899 99999999999999999  8999999999999999998553

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=98.83  E-value=3.9e-09  Score=84.90  Aligned_cols=50  Identities=24%  Similarity=0.227  Sum_probs=44.7

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ...+...|+++|.++++.++.|++++++++||+|||++|++|++..+...
T Consensus        27 ~~~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~   76 (216)
T 3b6e_A           27 SPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKK   76 (216)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhc
Confidence            34456689999999999999999999999999999999999999887654

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

Probab=98.80  E-value=5.2e-09  Score=101.61  Aligned_cols=50  Identities=22%  Similarity=0.298  Sum_probs=43.4

Q ss_pred             HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      -.|+..|+|+|..+|+.++.|+|+|++++||||||++|++|++..+...+
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~  292 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP  292 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhcc
Confidence            46899999999999999999999999999999999999999999998764

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=98.79  E-value=3.6e-09  Score=110.85  Aligned_cols=67  Identities=24%  Similarity=0.228  Sum_probs=57.9

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          142 GCESYLLRNLAELGYKEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       142 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      .|.+..+++|...+|..++|||.++|+.++.+ .|++++||||||||++|.+||+..|...++...+|
T Consensus       910 ~L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~kavy  977 (1724)
T 4f92_B          910 ALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVY  977 (1724)
T ss_dssp             GSCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEE
T ss_pred             cccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEE
Confidence            35567888899999999999999999999865 67999999999999999999999998766554444

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=98.74  E-value=1.4e-08  Score=102.40  Aligned_cols=45  Identities=27%  Similarity=0.252  Sum_probs=41.8

Q ss_pred             HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      ..|| .|||+|.++||.++.|+|+|++|+||||||++|++|++..+
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~  118 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA  118 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH
Confidence            4688 69999999999999999999999999999999988888877

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=98.71  E-value=1.2e-08  Score=102.53  Aligned_cols=46  Identities=33%  Similarity=0.332  Sum_probs=43.2

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+||. | |+|.++||.++.|+|+|++|+||||||+ |++|++.++..
T Consensus        52 ~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~   97 (1054)
T 1gku_B           52 KCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL   97 (1054)
T ss_dssp             TTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT
T ss_pred             HhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh
Confidence            458999 9 9999999999999999999999999999 99999999875

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=98.70  E-value=7.3e-10  Score=105.61  Aligned_cols=58  Identities=12%  Similarity=0.060  Sum_probs=46.8

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          142 GCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       142 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ++++.++++|... +..|+|||++++|.++.|+|+|++|+||||||++|++|+|+.+..
T Consensus       156 ~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~  213 (618)
T 2whx_A          156 TKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK  213 (618)
T ss_dssp             ------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH
T ss_pred             cchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh
Confidence            5666666666543 589999999999999999999999999999999999999999875

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=98.68  E-value=2.2e-08  Score=83.23  Aligned_cols=59  Identities=15%  Similarity=0.059  Sum_probs=48.3

Q ss_pred             CHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          144 ESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       144 ~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ++.+...+...+...++++|..+++.+..|++++++|+||||||.+|.++++..+....
T Consensus        47 ~~~~~~~~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~  105 (235)
T 3llm_A           47 DHDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQND  105 (235)
T ss_dssp             CHHHHHHHHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcC
Confidence            34444444444555679999999999999999999999999999999999999876544

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

Probab=98.62  E-value=2.4e-08  Score=98.99  Aligned_cols=51  Identities=22%  Similarity=0.294  Sum_probs=43.0

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      .-.|+..|+|+|.++|+.++.|+|+|++++||||||++|++|++..+...+
T Consensus       242 ~l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~  292 (936)
T 4a2w_A          242 PVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP  292 (936)
T ss_dssp             ------CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCC
T ss_pred             cccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhcc
Confidence            345788999999999999999999999999999999999999999987754

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=98.61  E-value=1.4e-08  Score=106.32  Aligned_cols=48  Identities=35%  Similarity=0.497  Sum_probs=44.3

Q ss_pred             CCCCCcHHHHHHHhhHhc-CCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          155 GYKEPTPIQRQAIPVLLS-DRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       155 g~~~pt~iQ~~aip~il~-G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      ||.++++||.+++|.++. +.|+|+|||||||||++|.|||+..|.+..
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~  124 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHI  124 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGC
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhc
Confidence            899999999999999874 789999999999999999999999997643

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=98.61  E-value=2.9e-08  Score=97.42  Aligned_cols=44  Identities=27%  Similarity=0.211  Sum_probs=39.6

Q ss_pred             HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      ..|. .||+||..++|.++.|+  |++++||||||++|+||++....
T Consensus        70 ~lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l  113 (853)
T 2fsf_A           70 VFGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNAL  113 (853)
T ss_dssp             HHSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHT
T ss_pred             HcCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHH
Confidence            3564 89999999999999999  89999999999999999997654

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=98.60  E-value=4.4e-08  Score=96.63  Aligned_cols=45  Identities=27%  Similarity=0.293  Sum_probs=40.8

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      +..|+ .||+||..++|.++.|+  |++++||+|||++|+||++....
T Consensus       106 R~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL  150 (922)
T 1nkt_A          106 RVLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNAL  150 (922)
T ss_dssp             HHHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHT
T ss_pred             HHcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHH
Confidence            45798 99999999999999999  99999999999999999976544

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.57  E-value=6.8e-08  Score=95.47  Aligned_cols=45  Identities=27%  Similarity=0.228  Sum_probs=40.6

Q ss_pred             HHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          152 AELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       152 ~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      +.+|+ .||+||..+||+++.|+  |++++||||||++|+||++....
T Consensus        74 R~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL  118 (997)
T 2ipc_A           74 RYLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNAL  118 (997)
T ss_dssp             HHTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHT
T ss_pred             HHhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHH
Confidence            45799 99999999999999999  89999999999999999965443

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

Probab=98.56  E-value=4.2e-08  Score=92.83  Aligned_cols=45  Identities=24%  Similarity=0.276  Sum_probs=42.4

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      .|+|+|..+|+.++.|+|+|++++||+|||++|++|+++.+....
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~   51 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKK   51 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhcc
Confidence            699999999999999999999999999999999999999987653

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=98.56  E-value=8.4e-08  Score=93.77  Aligned_cols=53  Identities=21%  Similarity=0.204  Sum_probs=47.0

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHhhHhcC------CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          147 LLRNLAELGYKEPTPIQRQAIPVLLSD------RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       147 ll~~l~~~g~~~pt~iQ~~aip~il~G------~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +...+...|| .||++|.++|+.++.+      +|++++|+||||||++|++|++..+..
T Consensus       358 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~  416 (780)
T 1gm5_A          358 AEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA  416 (780)
T ss_dssp             HHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            4444678899 9999999999999876      699999999999999999999998864

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=98.54  E-value=5.1e-09  Score=100.77  Aligned_cols=51  Identities=18%  Similarity=0.148  Sum_probs=43.6

Q ss_pred             HHHHcCCC-----CCcHHHH-----HHHhhHh------cCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          150 NLAELGYK-----EPTPIQR-----QAIPVLL------SDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       150 ~l~~~g~~-----~pt~iQ~-----~aip~il------~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +|..+||.     .||+||+     .+||.++      .|+|+|++|+||||||++|++|+++.+..
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~  268 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ  268 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            45667887     9999999     9999988      89999999999999999999999998765

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

Probab=98.42  E-value=2.3e-07  Score=92.98  Aligned_cols=49  Identities=20%  Similarity=0.259  Sum_probs=44.1

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          151 LAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ....+|. |+|+|.++|+.++.|+++|++|+||||||++|.+|++..+..
T Consensus        80 ~~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~  128 (1010)
T 2xgj_A           80 ARTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN  128 (1010)
T ss_dssp             SCCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             HHhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc
Confidence            3445775 999999999999999999999999999999999999998854

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=98.38  E-value=3.2e-07  Score=89.44  Aligned_cols=61  Identities=21%  Similarity=0.212  Sum_probs=52.2

Q ss_pred             CchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcC-CcEEEEcCCCchhHHHhHHHHHHH
Q 028267          130 PLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSD-RECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       130 p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G-~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      ++.+|.++    ++++.+++.|..+| ..|+++|..+|+.++.+ .+++++|+||||||+  ++|++..
T Consensus        70 ~~~~f~~~----~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~  131 (773)
T 2xau_A           70 KINPFTGR----EFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVL  131 (773)
T ss_dssp             SBCTTTCS----BCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHH
T ss_pred             CCCCcccc----CCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHH
Confidence            45567766    99999999999998 79999999999988755 679999999999999  6777733

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

Probab=98.36  E-value=3.6e-07  Score=91.37  Aligned_cols=47  Identities=23%  Similarity=0.282  Sum_probs=42.1

Q ss_pred             HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+|. |+|+|.++|+.++.|+|++++|+||||||++|++|++..+..
T Consensus        35 ~~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~   81 (997)
T 4a4z_A           35 SWPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN   81 (997)
T ss_dssp             CCSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc
Confidence            34664 899999999999999999999999999999999999887653

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

Probab=98.31  E-value=2.9e-07  Score=84.01  Aligned_cols=45  Identities=24%  Similarity=0.172  Sum_probs=41.7

Q ss_pred             CCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          156 YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       156 ~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ...|+|+|..+++.++.++|++++++||+|||++|++|++..+..
T Consensus       111 ~~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~  155 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN  155 (510)
T ss_dssp             EECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC
Confidence            448999999999999999999999999999999999999988764

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

Probab=98.30  E-value=1.3e-06  Score=78.89  Aligned_cols=40  Identities=28%  Similarity=0.293  Sum_probs=37.7

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      .|+|+|..+++.++.+.++|++++||+|||++|++++...
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~  132 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL  132 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc
Confidence            6999999999999999999999999999999999998764

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.28  E-value=4.7e-07  Score=84.52  Aligned_cols=43  Identities=19%  Similarity=0.127  Sum_probs=33.9

Q ss_pred             cCCCCCcHHHHHHHh----hHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          154 LGYKEPTPIQRQAIP----VLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip----~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      .|| .|+|+|..++.    .+..|++++++|+||||||++|++|++..
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~   50 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL   50 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC
Confidence            467 89999999865    45689999999999999999999998764

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=98.25  E-value=5.4e-07  Score=76.53  Aligned_cols=44  Identities=25%  Similarity=0.189  Sum_probs=39.9

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      -.|+++|.++++.++.+.+.|++++||+|||+++++++...+..
T Consensus       112 ~~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~  155 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN  155 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             cCccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc
Confidence            37999999999999998889999999999999999998887753

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

Probab=98.24  E-value=1.4e-06  Score=76.71  Aligned_cols=41  Identities=27%  Similarity=0.354  Sum_probs=39.3

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .|+|+|..+++.++.| ++|++++||+|||++|+++++..+.
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~   49 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT   49 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            6999999999999999 9999999999999999999999887

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=98.17  E-value=3.6e-06  Score=85.29  Aligned_cols=58  Identities=22%  Similarity=0.310  Sum_probs=47.6

Q ss_pred             CCCHHHHHHH-HHcCCCCCcHHHHHHHhhHhc----CC--cEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          142 GCESYLLRNL-AELGYKEPTPIQRQAIPVLLS----DR--ECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       142 ~l~~~ll~~l-~~~g~~~pt~iQ~~aip~il~----G~--dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .++..+.+.+ ...||. |||+|..||+.++.    |+  |+|+|++||+|||++|+++++..+..
T Consensus       587 ~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~  651 (1151)
T 2eyq_A          587 KHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN  651 (1151)
T ss_dssp             CCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            4555666665 445775 79999999999986    66  99999999999999999999887654

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=98.17  E-value=3.3e-06  Score=70.56  Aligned_cols=40  Identities=28%  Similarity=0.293  Sum_probs=36.9

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHH
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      ..|+++|..++..++.+.++|++++||+|||++++.++..
T Consensus        92 ~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~  131 (237)
T 2fz4_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINE  131 (237)
T ss_dssp             CCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHH
Confidence            4799999999999999999999999999999999887765

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=97.91  E-value=7.5e-06  Score=77.88  Aligned_cols=33  Identities=30%  Similarity=0.234  Sum_probs=29.9

Q ss_pred             hhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          168 PVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       168 p~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+..|+|+|++||||||||++|++|++..+..
T Consensus        17 ~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~   49 (620)
T 4a15_A           17 SSLQKSYGVALESPTGSGKTIMALKSALQYSSE   49 (620)
T ss_dssp             HHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh
Confidence            566789999999999999999999999998754

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=97.78  E-value=2.2e-05  Score=73.12  Aligned_cols=44  Identities=25%  Similarity=0.276  Sum_probs=35.0

Q ss_pred             CCCcHHHHHHHhhHhc----C-CcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          157 KEPTPIQRQAIPVLLS----D-RECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~----G-~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ..|+|+|..+|+.++.    | ++++++++||||||+++ ++++.+|...
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~-~~~~~~l~~~  225 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVA-FQISWKLWSA  225 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHHHHT
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHH-HHHHHHHHhc
Confidence            3699999999999876    5 66999999999999995 5666666543

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=97.74  E-value=1.8e-05  Score=73.77  Aligned_cols=32  Identities=41%  Similarity=0.272  Sum_probs=28.1

Q ss_pred             HHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          166 AIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       166 aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      ....+..|+|++++|+||||||++|++|++..
T Consensus        15 v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~   46 (551)
T 3crv_A           15 VIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV   46 (551)
T ss_dssp             HHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHcCCcEEEECCCCccHHHHHHHHHHhC
Confidence            34567789999999999999999999999864

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=97.67  E-value=4e-05  Score=77.08  Aligned_cols=57  Identities=26%  Similarity=0.174  Sum_probs=42.9

Q ss_pred             HHHHHHHHHcC-------CCCCcHHHHHHHhhHhc--------------CCcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          145 SYLLRNLAELG-------YKEPTPIQRQAIPVLLS--------------DRECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       145 ~~ll~~l~~~g-------~~~pt~iQ~~aip~il~--------------G~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      +.++..|...-       ...|+|+|..|++.++.              +++++++++||||||+++ ++++..+...+
T Consensus       251 ~~ll~~l~~f~~~~~~~~~~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~  328 (1038)
T 2w00_A          251 HTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELD  328 (1038)
T ss_dssp             HHHHHHHHHSEEECTTCCEEECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCT
T ss_pred             HHHHHHHHhheeeccccccccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcC
Confidence            44555554432       23599999999999875              478999999999999997 78886665433

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=97.45  E-value=1.5e-05  Score=76.65  Aligned_cols=37  Identities=24%  Similarity=0.136  Sum_probs=29.5

Q ss_pred             cHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHH
Q 028267          160 TPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       160 t~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      ++.|...++.+..++|+|++|+||||||++|.+|+++
T Consensus       219 ~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~  255 (666)
T 3o8b_A          219 FTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA  255 (666)
T ss_dssp             CCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH
Confidence            3444444445557889999999999999999999987

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=97.37  E-value=0.00039  Score=65.83  Aligned_cols=40  Identities=30%  Similarity=0.368  Sum_probs=37.4

Q ss_pred             cHHHHHHHhhHhcCCcEEEEcCCCchhH--HHhHHHHHHHHh
Q 028267          160 TPIQRQAIPVLLSDRECFACAPTGSGKT--LAFLCPMLMKLR  199 (211)
Q Consensus       160 t~iQ~~aip~il~G~dvi~~A~TGsGKT--laf~lPil~~l~  199 (211)
                      +++|..|++.++.++++++++++|||||  ++++++++..+.
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~  192 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMA  192 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhh
Confidence            7899999999999999999999999999  889999998764

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

Probab=96.99  E-value=0.0011  Score=59.98  Aligned_cols=44  Identities=16%  Similarity=0.107  Sum_probs=35.5

Q ss_pred             CCCcHHHHHHHhhH----hcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          157 KEPTPIQRQAIPVL----LSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       157 ~~pt~iQ~~aip~i----l~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ..|+|+|.+++..+    ..|+++|++.+||+|||+.. +.++..+...
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~a-i~~i~~~~~~   83 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQT-IAVFSDAKKE   83 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHH-HHHHHHHHHT
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHH-HHHHHHHHhc
Confidence            46999999999876    35789999999999999996 4566665543

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=96.90  E-value=0.00053  Score=66.03  Aligned_cols=35  Identities=23%  Similarity=0.213  Sum_probs=25.9

Q ss_pred             HHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          163 QRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       163 Q~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      |.+.....+.|++++++|+||||||+    +++..+...
T Consensus       145 ~~~p~ar~l~rk~vlv~apTGSGKT~----~al~~l~~~  179 (677)
T 3rc3_A          145 NWYPDARAMQRKIIFHSGPTNSGKTY----HAIQKYFSA  179 (677)
T ss_dssp             GGCHHHHTSCCEEEEEECCTTSSHHH----HHHHHHHHS
T ss_pred             hhCHHHHhcCCCEEEEEcCCCCCHHH----HHHHHHHhc
Confidence            33333456799999999999999998    555555543

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=96.25  E-value=0.0055  Score=59.86  Aligned_cols=43  Identities=33%  Similarity=0.396  Sum_probs=37.3

Q ss_pred             HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      ..|. .|+++|......+..|+  |+...||+||||+|.+|++-..
T Consensus        71 ~lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnA  113 (822)
T 3jux_A           71 TLGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNA  113 (822)
T ss_dssp             HTSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHH
T ss_pred             HhCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHH
Confidence            3455 68999999999999998  8899999999999999987543

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

Probab=96.17  E-value=0.0054  Score=61.02  Aligned_cols=45  Identities=16%  Similarity=0.021  Sum_probs=37.4

Q ss_pred             CCCcHHHHHHHhhHhc--CCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          157 KEPTPIQRQAIPVLLS--DRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~--G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      ..|+|+|..++..++.  +..+|++.+||+|||+.++..+...+...
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g  198 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG  198 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC
Confidence            4689999999998876  45899999999999999987776666543

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

Probab=95.20  E-value=0.023  Score=55.10  Aligned_cols=42  Identities=17%  Similarity=0.128  Sum_probs=33.9

Q ss_pred             CCCcHHHHHHHhhHh----cCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          157 KEPTPIQRQAIPVLL----SDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       157 ~~pt~iQ~~aip~il----~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      ..|.|.|..++..++    .|++.|++.++|+|||+..+..+...+
T Consensus       235 ~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~  280 (800)
T 3mwy_W          235 GELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLI  280 (800)
T ss_dssp             SCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHH
Confidence            368899999998765    789999999999999998755444433

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=95.01  E-value=0.044  Score=51.72  Aligned_cols=53  Identities=19%  Similarity=0.195  Sum_probs=39.8

Q ss_pred             CCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceEE
Q 028267          156 YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFC  209 (211)
Q Consensus       156 ~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~  209 (211)
                      +..+.+-|..|+-.++.+.-+++++|+|||||.+. .-++..|.......-++|
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~-~~~i~~l~~~~~~~ilv~  230 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQGNGPVLVC  230 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHH-HHHHHHHHTSSSCCEEEE
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHH-HHHHHHHHHcCCCeEEEE
Confidence            45688999999999888888899999999999875 355666654333444444

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=94.73  E-value=0.041  Score=49.80  Aligned_cols=51  Identities=16%  Similarity=0.176  Sum_probs=37.3

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhcC-----CcEEEEcCCCchhHHHhHHHHHHHHhccc
Q 028267          151 LAELGYKEPTPIQRQAIPVLLSD-----RECFACAPTGSGKTLAFLCPMLMKLRVLF  202 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~G-----~dvi~~A~TGsGKTlaf~lPil~~l~~~~  202 (211)
                      .+-+.|..+++-|..++-.++..     ..+++.|+.|||||.. +.-++..|....
T Consensus        18 ~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~l-l~~~~~~l~~~~   73 (459)
T 3upu_A           18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTL-TKFIIEALISTG   73 (459)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHH-HHHHHHHHHHTT
T ss_pred             cCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHH-HHHHHHHHHhcC
Confidence            45567999999999999876532     3899999999999954 356666665543

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=94.22  E-value=0.075  Score=50.20  Aligned_cols=41  Identities=24%  Similarity=0.393  Sum_probs=31.8

Q ss_pred             CCcHHHHHHHhhHhcCCc-EEEEcCCCchhHHHhHHHHHHHHh
Q 028267          158 EPTPIQRQAIPVLLSDRE-CFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~d-vi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .+.+-|..|+-.++..++ .|+++|+|||||.+-+- +|.++.
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~-~I~~l~  230 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVE-IILQAV  230 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHH-HHHHHH
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHH-HHHHHH
Confidence            467899999999988776 58899999999987543 444443

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=94.01  E-value=0.078  Score=51.80  Aligned_cols=44  Identities=20%  Similarity=0.343  Sum_probs=35.0

Q ss_pred             CCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          156 YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       156 ~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +..+.+-|..|+-.++.+.-++++|++|||||.+.+ -++.+|..
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~-~~i~~l~~  401 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSA-TIVYHLSK  401 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHH-HHHHHHHH
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH-HHHHHHHh
Confidence            456889999999999887778999999999998643 44555543

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=93.94  E-value=0.1  Score=51.01  Aligned_cols=53  Identities=19%  Similarity=0.195  Sum_probs=39.4

Q ss_pred             CCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceEE
Q 028267          156 YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFC  209 (211)
Q Consensus       156 ~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~  209 (211)
                      ...+.+-|..|+-.++.+.-+++++++|||||.+. .-++..|.......-++|
T Consensus       354 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti-~~~i~~l~~~~~~~ilv~  406 (800)
T 2wjy_A          354 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQGNGPVLVC  406 (800)
T ss_dssp             SCCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHH-HHHHHHHHTTCSSCEEEE
T ss_pred             ccCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHH-HHHHHHHHHcCCCcEEEE
Confidence            45678999999999988888899999999999874 456666654333333333

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=93.60  E-value=0.083  Score=49.15  Aligned_cols=51  Identities=22%  Similarity=0.290  Sum_probs=36.0

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc-CCCceEE
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF-IPFDYFC  209 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~-~~~~~~~  209 (211)
                      ..+++-|..++-.  .+..+++.|+.|||||.+.+-=+...+.... .+..+++
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~   59 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMA   59 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEE
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEE
Confidence            4689999999863  3566899999999999987665655555422 3344444

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

Probab=93.51  E-value=0.083  Score=49.97  Aligned_cols=44  Identities=25%  Similarity=0.366  Sum_probs=35.4

Q ss_pred             CCcHHHHHHHhhHh---------cCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          158 EPTPIQRQAIPVLL---------SDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       158 ~pt~iQ~~aip~il---------~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      .|.|+|..++..++         .+..+|++..||+|||+..+..+...+...
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~  107 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQS  107 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCC
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhC
Confidence            68899999998774         457899999999999999876666655543

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=93.26  E-value=0.09  Score=53.52  Aligned_cols=51  Identities=24%  Similarity=0.135  Sum_probs=40.8

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhccc---CCCceEEe
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLF---IPFDYFCE  210 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~---~~~~~~~~  210 (211)
                      .+|+-|..+|-..  +.+++|.|.-|||||.+.+-=++..|....   .+..++|+
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~   63 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVV   63 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEE
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEE
Confidence            5799999998654  889999999999999998877888877643   44566664

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=92.78  E-value=0.16  Score=47.76  Aligned_cols=42  Identities=14%  Similarity=0.071  Sum_probs=34.1

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+++-|..++..++.+..+++.++.|||||... .-++..+..
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~  230 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAES  230 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHh
Confidence            578999999999999999999999999999753 345554443

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=91.27  E-value=0.3  Score=46.74  Aligned_cols=52  Identities=17%  Similarity=0.225  Sum_probs=37.7

Q ss_pred             CCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc-cCCCceEEe
Q 028267          157 KEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL-FIPFDYFCE  210 (211)
Q Consensus       157 ~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~-~~~~~~~~~  210 (211)
                      ..+++-|.+++-.  .+..+++.|..|||||.+.+-=+...+... ..+..++|+
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~v   62 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAI   62 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEE
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEE
Confidence            4689999998865  346789999999999998776666666542 245556554

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=90.19  E-value=0.33  Score=37.47  Aligned_cols=26  Identities=19%  Similarity=0.209  Sum_probs=19.3

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .|..+++.+++|+|||.... -+...+
T Consensus        37 ~g~~~~l~G~~G~GKTtL~~-~i~~~~   62 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLAV-ATLKAI   62 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHHH-HHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH-HHHHHH
Confidence            48899999999999997543 334444

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=88.90  E-value=0.28  Score=36.88  Aligned_cols=20  Identities=15%  Similarity=0.074  Sum_probs=17.0

Q ss_pred             HhcCCcEEEEcCCCchhHHH
Q 028267          170 LLSDRECFACAPTGSGKTLA  189 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTla  189 (211)
                      +..+..|++.+++|||||..
T Consensus        24 ~~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHH
T ss_pred             hCCCCcEEEECCCCccHHHH
Confidence            45678899999999999975

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=88.40  E-value=0.11  Score=44.24  Aligned_cols=56  Identities=13%  Similarity=0.121  Sum_probs=31.3

Q ss_pred             hhhhcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          134 FVKLSSRFGCESYLLRNLAEL---GYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       134 f~~l~~~~~l~~~ll~~l~~~---g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      |+.++.+|-+++.++..+...   .|-.        ++.+-..+.+++.+|+|+|||... -.+...+
T Consensus         2 ~~~~~~~~y~~~~~~~~~~~~~~k~~l~--------~~~~~~p~~lLl~GppGtGKT~la-~aiA~~l   60 (293)
T 3t15_A            2 LDNKLDGFYIAPAFMDKLVVHITKNFLK--------LPNIKVPLILGIWGGKGQGKSFQC-ELVFRKM   60 (293)
T ss_dssp             CCCEETTEECCHHHHHHHHHHHHHTTSC--------CTTCCCCSEEEEEECTTSCHHHHH-HHHHHHH
T ss_pred             cccccCcccCCHHHHHHHHHHHHHHHHh--------cCCCCCCeEEEEECCCCCCHHHHH-HHHHHHh
Confidence            455556667777766654321   1111        111222356889999999999843 3344433

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=88.24  E-value=0.39  Score=36.06  Aligned_cols=21  Identities=14%  Similarity=0.246  Sum_probs=17.6

Q ss_pred             HhcCCcEEEEcCCCchhHHHh
Q 028267          170 LLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTlaf  190 (211)
                      ...+..|++.+++|||||...
T Consensus        21 a~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           21 SETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TTCCSCEEEESSTTSSHHHHH
T ss_pred             hCCCCCEEEECCCCCCHHHHH
Confidence            346788999999999999854

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=88.01  E-value=0.3  Score=43.34  Aligned_cols=31  Identities=16%  Similarity=0.169  Sum_probs=23.1

Q ss_pred             hHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          169 VLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       169 ~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .-....++++.|+||||||..+ -+++.++..
T Consensus        49 ~~~~~~h~~i~G~tGsGKs~~~-~~li~~~~~   79 (437)
T 1e9r_A           49 RDAEPRHLLVNGATGTGKSVLL-RELAYTGLL   79 (437)
T ss_dssp             GGGGGGCEEEEECTTSSHHHHH-HHHHHHHHH
T ss_pred             cccCcceEEEECCCCCCHHHHH-HHHHHHHHH
Confidence            3344678999999999999974 556666654

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=87.54  E-value=0.29  Score=40.40  Aligned_cols=20  Identities=30%  Similarity=0.453  Sum_probs=16.5

Q ss_pred             hcCCcEEEEcCCCchhHHHh
Q 028267          171 LSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       171 l~G~dvi~~A~TGsGKTlaf  190 (211)
                      ..++.+++.+++|+|||...
T Consensus        49 ~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           49 EPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCeEEEECCCCCcHHHHH
Confidence            34678999999999999743

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=86.53  E-value=0.56  Score=37.42  Aligned_cols=24  Identities=29%  Similarity=0.475  Sum_probs=18.3

Q ss_pred             CCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          173 DRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      |.=+++.|++|+|||. |++-++..
T Consensus        30 G~l~~i~G~pG~GKT~-l~l~~~~~   53 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTT-FAAQFIYK   53 (251)
T ss_dssp             TCEEEEECCTTSSHHH-HHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHH-HHHHHHHH
Confidence            5679999999999996 55555444

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=85.74  E-value=1  Score=38.54  Aligned_cols=17  Identities=29%  Similarity=0.528  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCchhHHHh
Q 028267          174 RECFACAPTGSGKTLAF  190 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf  190 (211)
                      +.+++.+|+|||||+..
T Consensus        46 ~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             SEEEEESSSSSCHHHHH
T ss_pred             ceEEEECCCCccHHHHH
Confidence            67999999999999853

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=85.26  E-value=0.45  Score=45.30  Aligned_cols=43  Identities=30%  Similarity=0.346  Sum_probs=32.3

Q ss_pred             cCCCCCcHHHHHHHhhHhc----C-CcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          154 LGYKEPTPIQRQAIPVLLS----D-RECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       154 ~g~~~pt~iQ~~aip~il~----G-~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .|| .|++.|..+|..+..    | +..++.+.||||||++++ -++.++
T Consensus         5 ~~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a-~~~~~~   52 (664)
T 1c4o_A            5 RGP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEAL   52 (664)
T ss_dssp             CSC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHH
T ss_pred             CCC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHH-HHHHHh
Confidence            367 899999999986653    3 356788999999999775 345554

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=84.31  E-value=1.7  Score=36.98  Aligned_cols=47  Identities=17%  Similarity=0.227  Sum_probs=33.6

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHH-hhHhcCC-----cEEEEcCCCchhHHHhHHHHHH
Q 028267          146 YLLRNLAELGYKEPTPIQRQAI-PVLLSDR-----ECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       146 ~ll~~l~~~g~~~pt~iQ~~ai-p~il~G~-----dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      .+.+.|+-+||.   |++...+ -..+.|+     .|++.+|+|||||+.+. .+..
T Consensus        74 ~i~~~l~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~-ala~  126 (267)
T 1u0j_A           74 RIYKILELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE-AIAH  126 (267)
T ss_dssp             HHHHHHHHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH-HHHH
T ss_pred             HHHHHHHHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH-HHHh
Confidence            678888888886   6665543 3445553     59999999999999764 4444

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.20  E-value=0.45  Score=43.33  Aligned_cols=55  Identities=24%  Similarity=0.363  Sum_probs=31.9

Q ss_pred             CCchhhhhhcccCCCCHHHHHHHHHcC---CCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHh
Q 028267          129 SPLRTFVKLSSRFGCESYLLRNLAELG---YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       129 ~p~~~f~~l~~~~~l~~~ll~~l~~~g---~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf  190 (211)
                      .|-.+|+++    +--+...+.|...=   +.+|--.+..-+   ---+.++..+|+|||||+..
T Consensus       175 ~p~~t~~di----gGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          175 KPTETYSDV----GGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             SCSCCGGGS----CSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChHhc----CcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHH
Confidence            355678887    55556666665421   112222222211   12378999999999999853

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=83.78  E-value=1.2  Score=41.22  Aligned_cols=41  Identities=20%  Similarity=0.089  Sum_probs=26.3

Q ss_pred             HHHHHHcCCCCCcHHHHHHHh-hHhcCCcEEEEcCCCchhHHHh
Q 028267          148 LRNLAELGYKEPTPIQRQAIP-VLLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       148 l~~l~~~g~~~pt~iQ~~aip-~il~G~dvi~~A~TGsGKTlaf  190 (211)
                      +..|...|.-  ++.+..-+. .+..|..++++++||||||...
T Consensus       236 ~~~l~~~G~~--~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL  277 (511)
T 2oap_1          236 PIDLIEKGTV--PSGVLAYLWLAIEHKFSAIVVGETASGKTTTL  277 (511)
T ss_dssp             HHHHHHTTSS--CHHHHHHHHHHHHTTCCEEEEESTTSSHHHHH
T ss_pred             hhhHHhcCCC--CHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            4445566632  233333232 3567889999999999999754

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=83.46  E-value=0.43  Score=40.38  Aligned_cols=19  Identities=32%  Similarity=0.522  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCchhHHHh
Q 028267          172 SDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf  190 (211)
                      .++.+++.+++|||||+..
T Consensus        48 ~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           48 PSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCSEEEEECSSSSSHHHHH
T ss_pred             CCceEEEECCCCcCHHHHH
Confidence            4678999999999999853

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=83.07  E-value=0.95  Score=38.64  Aligned_cols=26  Identities=27%  Similarity=0.324  Sum_probs=19.0

Q ss_pred             CCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          173 DRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      |+.+++.+++|+|||... --+...+.
T Consensus        70 ~~~vLl~GppGtGKT~la-~~la~~l~   95 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIA-MGMAQALG   95 (368)
T ss_dssp             TCEEEEEESTTSSHHHHH-HHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHhc
Confidence            568999999999999853 34444443

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=82.64  E-value=1.6  Score=37.57  Aligned_cols=19  Identities=42%  Similarity=0.569  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCchhHHHh
Q 028267          172 SDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf  190 (211)
                      .+..+++.+|+|||||...
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4578999999999999853

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=82.50  E-value=2.3  Score=33.07  Aligned_cols=25  Identities=20%  Similarity=0.333  Sum_probs=18.9

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          174 RECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      ..+++.+++|+|||... .-+...+.
T Consensus        55 ~~~~l~G~~GtGKT~la-~~i~~~~~   79 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL-AAIANELA   79 (202)
T ss_dssp             CEEEEECSTTSSHHHHH-HHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            78999999999999853 34555554

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=82.13  E-value=1.6  Score=37.01  Aligned_cols=17  Identities=24%  Similarity=0.438  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCchhHHHh
Q 028267          174 RECFACAPTGSGKTLAF  190 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf  190 (211)
                      +.+++.+++|||||+..
T Consensus        52 ~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CEEEEECSSSSCHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            57999999999999753

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=81.41  E-value=1.7  Score=35.71  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCchhHHHh
Q 028267          172 SDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf  190 (211)
                      .+..+++.+++|+|||...
T Consensus        49 ~~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4678999999999999743

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=81.41  E-value=1.1  Score=38.37  Aligned_cols=28  Identities=18%  Similarity=0.120  Sum_probs=20.7

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .|.=++++|++|+|||. |++-++..+..
T Consensus        67 ~G~l~li~G~pG~GKTt-l~l~ia~~~a~   94 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTA-FALKQAKNMSD   94 (315)
T ss_dssp             TTCEEEEECCTTSSHHH-HHHHHHHHHHT
T ss_pred             CCcEEEEEeCCCCCHHH-HHHHHHHHHHH
Confidence            45669999999999995 56666655543

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=81.17  E-value=0.74  Score=34.51  Aligned_cols=25  Identities=16%  Similarity=0.189  Sum_probs=18.3

Q ss_pred             CCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          173 DRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      +..+++.+++|+|||... --+...+
T Consensus        43 ~~~~ll~G~~G~GKT~l~-~~~~~~~   67 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV-EGLAQRI   67 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             CCceEEECCCCCCHHHHH-HHHHHHH
Confidence            467999999999999753 3444444

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=81.15  E-value=0.7  Score=40.24  Aligned_cols=28  Identities=11%  Similarity=0.080  Sum_probs=21.0

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+..+++.+++|||||+.. --++..|..
T Consensus        44 ~~~~lli~GpPGTGKT~~v-~~v~~~L~~   71 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLV-NDVMDELIT   71 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHH-HHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH-HHHHHHHHH
Confidence            3578999999999999864 345566643

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=81.07  E-value=1.8  Score=35.20  Aligned_cols=18  Identities=33%  Similarity=0.586  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCchhHHHh
Q 028267          173 DRECFACAPTGSGKTLAF  190 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf  190 (211)
                      .+.+++.+++|||||...
T Consensus        45 ~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            356999999999999743

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	211
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	1e-17
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	1e-16
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	2e-15
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	2e-15
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	2e-14
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	2e-14
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	7e-14
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	7e-14
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	8e-14
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	4e-13
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	1e-12
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	6e-10
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	1e-07
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-04

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 76.5 bits (187), Expect = 1e-17
 Identities = 31/87 (35%), Positives = 46/87 (52%), Gaps = 9/87 (10%)

Query: 117 KYN---IHVSG--ANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLL 171
           KY+   + V+G   +  + +  F         +  +  N+    Y+ PTPIQ+ AIP +L
Sbjct: 1   KYDSIPVSVTGPDYSATNVIENF----DELKLDPTIRNNILLASYQRPTPIQKNAIPAIL 56

Query: 172 SDRECFACAPTGSGKTLAFLCPMLMKL 198
             R+  ACA TGSGKT AFL P++  L
Sbjct: 57  EHRDIMACAQTGSGKTAAFLIPIINHL 83

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.0 bits (178), Expect = 1e-16
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 125 ANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGS 184
           +N    + +F            LLR +   G+++P+ IQ++AI   +   +  A A +G+
Sbjct: 5   SNWNEIVDSF----DDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGT 60

Query: 185 GKTLAFLCPMLMKLR 199
           GKT  F   +L ++ 
Sbjct: 61  GKTATFAISILQQIE 75

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.3 bits (171), Expect = 2e-15
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 4/79 (5%)

Query: 119 NIHVSGANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFA 178
            +    +       TF       G    LLR +   G+++P+ IQ++AI  ++  R+  A
Sbjct: 4   KVEFETSEEVDVTPTF----DTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIA 59

Query: 179 CAPTGSGKTLAFLCPMLMK 197
            + +G+GKT  F   +L  
Sbjct: 60  QSQSGTGKTATFSISVLQC 78

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 69.2 bits (168), Expect = 2e-15
 Identities = 17/54 (31%), Positives = 26/54 (48%)

Query: 145 SYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           SY +  L E G +E  P Q +A+  + S +      PT +GKTL     M+ + 
Sbjct: 12  SYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREA 65

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.3 bits (163), Expect = 2e-14
 Identities = 22/57 (38%), Positives = 39/57 (68%)

Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK 197
           +  +  LL  + E+G+++P+PIQ ++IP+ LS R+  A A  G+GK+ A+L P+L +
Sbjct: 8   YCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 67.1 bits (163), Expect = 2e-14
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 125 ANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGS 184
            N    +  F         +  LLR +   G++EP+ IQ++AI  ++   +  A A +G+
Sbjct: 3   TNYDKVVYKF----DDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGT 58

Query: 185 GKTLAFLCPMLMKLR 199
           GKT  F    L ++ 
Sbjct: 59  GKTGTFSIAALQRID 73

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 65.5 bits (158), Expect = 7e-14
 Identities = 19/73 (26%), Positives = 35/73 (47%)

Query: 139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL 198
           +RF  + +++  +  L + +PT IQ + IP  L        + TG+GKT A+L P++ K+
Sbjct: 4   TRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKI 63

Query: 199 RVLFIPFDYFCEL 211
           +            
Sbjct: 64  KPERAEVQAVITA 76

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 65.4 bits (158), Expect = 7e-14
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM 196
           F  +  LL  + E G+++P+PIQ +AIPV ++ R+  A A  G+GKT AF+ P L 
Sbjct: 6   FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 61

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.3 bits (158), Expect = 8e-14
 Identities = 16/56 (28%), Positives = 28/56 (50%)

Query: 141 FGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLM 196
           F  +  LLR + + G++ P+ +Q + IP  +   +    A +G GKT  F+   L 
Sbjct: 6   FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 63.8 bits (154), Expect = 4e-13
 Identities = 15/52 (28%), Positives = 17/52 (32%)

Query: 148 LRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
                     EP  IQ+     +L      A APTG GKT   L   L    
Sbjct: 33  FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLAL 84

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 62.3 bits (150), Expect = 1e-12
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 141 FGCESYLLRNLAEL-GYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
              ES   + L E  GY++  P Q + I  +LS R+C    PTG GK+L +  P L+   
Sbjct: 7   LNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNG 66

Query: 200 V 200
           +
Sbjct: 67  L 67

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 54.7 bits (131), Expect = 6e-10
 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRE-CFACAPTGSGKTLAFLCPM 194
           +       +L  +   G+++PT IQ + IP+ L+D     A A TGSGKT +F  P+
Sbjct: 7   NELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPL 63

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 48.2 bits (113), Expect = 1e-07
 Identities = 11/49 (22%), Positives = 16/49 (32%), Gaps = 1/49 (2%)

Query: 151 LAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLR 199
           +      +P   Q         +  C    PTG GKTL  +     +L 
Sbjct: 2   VLRRDLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLT 49

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 38.7 bits (89), Expect = 3e-04
 Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 5/40 (12%)

Query: 169 VLLSDRECFACAPTGSGKTLAFLCPMLMKL-----RVLFI 203
           +    R        G+GKT  +L  ++ +      R L +
Sbjct: 5   IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLIL 44

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	211
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.84
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.83
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.83
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.82
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.81
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.81
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.79
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.78
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.7
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.41
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.36
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.27
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.38
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.45
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.96
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	96.84
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.1
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	94.63
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	94.25
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	93.41
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	92.09
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	91.79
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	91.22
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.99
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	90.65
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	90.28
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	90.21
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	88.7
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	88.07
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	86.19
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	85.12
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	85.0
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	84.78
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	84.73
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	82.76
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	82.15
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	81.58
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	80.7
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	80.52
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	80.45
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	80.38
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	80.33
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	80.18

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=1.7e-21  Score=160.88  Aligned_cols=82  Identities=24%  Similarity=0.373  Sum_probs=75.1

Q ss_pred             cCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          124 GANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       124 g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      |.+.|.++.+|+++    +|++.++++|.++||.+|||||++|||.++.|+|++++|+||||||+||++|+++++.....
T Consensus         2 ~~~~~~~~~sF~~l----~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~   77 (212)
T d1qdea_           2 QTNYDKVVYKFDDM----ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK   77 (212)
T ss_dssp             CBSCCCCCCCGGGG----TCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCC
T ss_pred             CCCCcccccChhhC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCC
Confidence            67889999999999    99999999999999999999999999999999999999999999999999999999976655


Q ss_pred             CCceEE
Q 028267          204 PFDYFC  209 (211)
Q Consensus       204 ~~~~~~  209 (211)
                      ...++.
T Consensus        78 ~~~~li   83 (212)
T d1qdea_          78 APQALM   83 (212)
T ss_dssp             SCCEEE
T ss_pred             CcceEE
Confidence            444433

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=4.2e-21  Score=159.91  Aligned_cols=81  Identities=26%  Similarity=0.415  Sum_probs=70.7

Q ss_pred             cCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          124 GANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       124 g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      +........+|+++    +|++.|+++|.++||..|||||++|||.++.|+|++++|+||||||+||++|++++|.....
T Consensus         9 ~~~~~~~~~sF~~l----~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~   84 (222)
T d2j0sa1           9 TSEEVDVTPTFDTM----GLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVR   84 (222)
T ss_dssp             CCTTCCCCCSGGGG----CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSC
T ss_pred             cCCCCCCCCCHHHC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccccccccccccc
Confidence            33334555688888    99999999999999999999999999999999999999999999999999999999977655


Q ss_pred             CCceE
Q 028267          204 PFDYF  208 (211)
Q Consensus       204 ~~~~~  208 (211)
                      ....+
T Consensus        85 ~~~~l   89 (222)
T d2j0sa1          85 ETQAL   89 (222)
T ss_dssp             SCCEE
T ss_pred             CceeE
Confidence            44433

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=4.5e-21  Score=159.01  Aligned_cols=81  Identities=23%  Similarity=0.388  Sum_probs=73.4

Q ss_pred             cCCCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccC
Q 028267          124 GANVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFI  203 (211)
Q Consensus       124 g~~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~  203 (211)
                      ..++|.++.+|+++    +|++.++++|.++||.+|||||++|||+++.|+|++++|+||||||+||++|+++++.....
T Consensus         4 ~~~~~e~i~sF~~l----~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~   79 (218)
T d2g9na1           4 ESNWNEIVDSFDDM----NLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLK   79 (218)
T ss_dssp             CCCCCCCCCCGGGS----CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCC
T ss_pred             CCCCCCccCCHHHC----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccccc
Confidence            45678899999998    99999999999999999999999999999999999999999999999999999999976654


Q ss_pred             CCceE
Q 028267          204 PFDYF  208 (211)
Q Consensus       204 ~~~~~  208 (211)
                      ....+
T Consensus        80 ~~~al   84 (218)
T d2g9na1          80 ATQAL   84 (218)
T ss_dssp             SCCEE
T ss_pred             CccEE
Confidence            44433

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=7.5e-21  Score=156.00  Aligned_cols=74  Identities=32%  Similarity=0.535  Sum_probs=66.9

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceEEe
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFCE  210 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~~  210 (211)
                      +|+++    +|++.|+++|.++||..|||||++|||.++.|+|+|++|+||||||+||++|+|+++.........+++
T Consensus         4 ~F~~l----~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil   77 (206)
T d1veca_           4 EFEDY----CLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVI   77 (206)
T ss_dssp             SGGGS----CCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEE
T ss_pred             Chhcc----CcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEE
Confidence            56666    999999999999999999999999999999999999999999999999999999999877655555443

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.4e-20  Score=154.45  Aligned_cols=70  Identities=24%  Similarity=0.418  Sum_probs=63.1

Q ss_pred             ccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          139 SRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       139 ~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      ++|+|++.++++|.++||++|||||++|||.++.|+|++++|+||||||+||++|+++++.........+
T Consensus         4 ~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~l   73 (207)
T d1t6na_           4 RDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVL   73 (207)
T ss_dssp             TTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEE
T ss_pred             cccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEE
Confidence            3449999999999999999999999999999999999999999999999999999999987765444433

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.81  E-value=2.7e-20  Score=151.29  Aligned_cols=73  Identities=25%  Similarity=0.449  Sum_probs=65.5

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceEE
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYFC  209 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~~  209 (211)
                      .|+++    +|++.++++|.++||.+|||||.+|||.++.|+|++++|+||||||+||++|+++.+..........+
T Consensus         2 ~F~~l----~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~   74 (209)
T d1q0ua_           2 QFTRF----PFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVI   74 (209)
T ss_dssp             CGGGS----CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEE
T ss_pred             ccccC----CcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccc
Confidence            35555    99999999999999999999999999999999999999999999999999999999987665554443

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.79  E-value=1.1e-19  Score=148.48  Aligned_cols=72  Identities=36%  Similarity=0.583  Sum_probs=65.4

Q ss_pred             hhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          133 TFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       133 ~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      +|+++    +|++.++++|.++||.+|||||.+|||+++.|+|+|++|+||||||+||++|+++++..........
T Consensus         2 sF~~l----~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~   73 (206)
T d1s2ma1           2 TFEDF----YLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQAL   73 (206)
T ss_dssp             CGGGG----CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEE
T ss_pred             ChHHc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccce
Confidence            57666    9999999999999999999999999999999999999999999999999999999987765554433

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.78  E-value=3.3e-20  Score=155.44  Aligned_cols=78  Identities=38%  Similarity=0.678  Sum_probs=70.0

Q ss_pred             ceeccC--CCCCCchhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHH
Q 028267          120 IHVSGA--NVPSPLRTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMK  197 (211)
Q Consensus       120 i~v~g~--~~p~p~~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~  197 (211)
                      +.++|.  +.|.++.+|+++    +|++.++++|..+||..|||||++|||+++.|+|++++|+||||||+||+||+|++
T Consensus         7 ~~~~~~~~~~~~~~~~F~~l----~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~   82 (238)
T d1wrba1           7 VSVTGPDYSATNVIENFDEL----KLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINH   82 (238)
T ss_dssp             CCEECCSSSCCSCCCSSGGG----SCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eeeeCCCCCCCCccCCHHHC----CCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHH
Confidence            344554  445678899988    99999999999999999999999999999999999999999999999999999999


Q ss_pred             Hhcc
Q 028267          198 LRVL  201 (211)
Q Consensus       198 l~~~  201 (211)
                      +...
T Consensus        83 l~~~   86 (238)
T d1wrba1          83 LVCQ   86 (238)
T ss_dssp             HHTT
T ss_pred             HHhc
Confidence            8643

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.70  E-value=9.8e-18  Score=137.08  Aligned_cols=73  Identities=30%  Similarity=0.422  Sum_probs=65.5

Q ss_pred             hhhhhhcccCCCCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCC-cEEEEcCCCchhHHHhHHHHHHHHhcccCCCceE
Q 028267          132 RTFVKLSSRFGCESYLLRNLAELGYKEPTPIQRQAIPVLLSDR-ECFACAPTGSGKTLAFLCPMLMKLRVLFIPFDYF  208 (211)
Q Consensus       132 ~~f~~l~~~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~-dvi~~A~TGsGKTlaf~lPil~~l~~~~~~~~~~  208 (211)
                      .+|+++    +|++.++++|.++||..|||||.++||.++.|+ |+|++|+||||||++|++|+++.......+..++
T Consensus         4 msf~~l----~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~li   77 (208)
T d1hv8a1           4 MNFNEL----NLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAII   77 (208)
T ss_dssp             CCGGGS----SCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEE
T ss_pred             cCHHHc----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccccCcceEE
Confidence            477777    999999999999999999999999999999985 9999999999999999999999987766554443

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.41  E-value=9.2e-14  Score=111.65  Aligned_cols=59  Identities=36%  Similarity=0.560  Sum_probs=54.6

Q ss_pred             cCCCCHHHHHHHHHc-CCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          140 RFGCESYLLRNLAEL-GYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       140 ~~~l~~~ll~~l~~~-g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      ..+|++.+.+.|++. ||..++|+|.+||++++.|+|+++++|||||||++|.+|++...
T Consensus         6 ~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~~   65 (206)
T d1oywa2           6 VLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLN   65 (206)
T ss_dssp             CSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSS
T ss_pred             hCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhcc
Confidence            348899999999988 99999999999999999999999999999999999999998653

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.36  E-value=1.5e-13  Score=110.32  Aligned_cols=59  Identities=29%  Similarity=0.309  Sum_probs=52.8

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          143 CESYLLRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       143 l~~~ll~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +++.++..|.+.||..|+|+|.+||+.+++|+|+|++||||||||++++++++..+...
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~   68 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG   68 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhcc
Confidence            67889999999999999999999999999999999999999999999999999988653

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.27  E-value=2.3e-12  Score=105.76  Aligned_cols=53  Identities=28%  Similarity=0.214  Sum_probs=48.6

Q ss_pred             HHHHHHcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          148 LRNLAELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       148 l~~l~~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +.++..++|..|++||..+|+.++.|+|++++||||+|||++|++|++..+..
T Consensus        33 ~~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~   85 (237)
T d1gkub1          33 FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK   85 (237)
T ss_dssp             HHHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh
Confidence            45567789999999999999999999999999999999999999999987765

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=98.38  E-value=1.7e-07  Score=73.25  Aligned_cols=45  Identities=24%  Similarity=0.312  Sum_probs=38.3

Q ss_pred             CCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          156 YKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       156 ~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      +-.|.++|..++..++ ++|+|+++|||||||+++++++...+...
T Consensus         7 ~~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~   51 (200)
T d1wp9a1           7 LIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY   51 (200)
T ss_dssp             HHCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc
Confidence            3469999999998876 56899999999999999999988877654

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.45  E-value=6.1e-05  Score=59.50  Aligned_cols=40  Identities=30%  Similarity=0.370  Sum_probs=33.6

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHH
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKL  198 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l  198 (211)
                      .|.+.|.+++..++.+...+++++||+|||+..+ .++.++
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~-~~~~~~  109 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAM-AAINEL  109 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHH-HHHHHS
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHH-hHHHHh
Confidence            5899999999999999888999999999999764 444443

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.96  E-value=0.0012  Score=53.66  Aligned_cols=59  Identities=24%  Similarity=0.232  Sum_probs=45.9

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHhhHhc----C--CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          142 GCESYLLRNLAELGYKEPTPIQRQAIPVLLS----D--RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       142 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~il~----G--~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+....+.+...=--.+|+=|..+|..+..    +  .+.++|+.||||||..|+..++..+..
T Consensus        39 ~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~  103 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN  103 (233)
T ss_dssp             CCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc
Confidence            3455666666655455789999999987643    3  478999999999999999999888754

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.84  E-value=0.0004  Score=57.62  Aligned_cols=35  Identities=29%  Similarity=0.307  Sum_probs=31.4

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHH
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLC  192 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~l  192 (211)
                      .|.+.|..|+..++..+..+++++||+|||+..++
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~  147 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQAL  147 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHH
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHH
Confidence            58899999999999888899999999999997654

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.10  E-value=0.0058  Score=50.30  Aligned_cols=49  Identities=20%  Similarity=0.253  Sum_probs=40.6

Q ss_pred             HHHcCCCCCcHHHHHHHhhHhc----C--CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          151 LAELGYKEPTPIQRQAIPVLLS----D--RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       151 l~~~g~~~pt~iQ~~aip~il~----G--~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      +....| .+|+-|..|+..+..    +  .+.++++-||||||..|++.++..+..
T Consensus        77 ~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~  131 (264)
T d1gm5a3          77 IKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA  131 (264)
T ss_dssp             HHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH
T ss_pred             Hhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc
Confidence            455566 699999999998753    2  478999999999999999999888765

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=94.63  E-value=0.023  Score=45.86  Aligned_cols=50  Identities=18%  Similarity=0.236  Sum_probs=34.3

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc-cCCCceEE
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL-FIPFDYFC  209 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~-~~~~~~~~  209 (211)
                      .+++=|..++-..  +..++|.|+.|||||.+.+--+...|... ..|..+++
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~   61 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILA   61 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEE
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEe
Confidence            4788899988642  34599999999999998876565555433 23344443

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=94.25  E-value=0.0059  Score=43.86  Aligned_cols=19  Identities=37%  Similarity=0.382  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCchhHHHhH
Q 028267          173 DRECFACAPTGSGKTLAFL  191 (211)
Q Consensus       173 G~dvi~~A~TGsGKTlaf~  191 (211)
                      -+..|++||||||||+.+.
T Consensus         8 ~~~~ll~apTGsGKT~~~~   26 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVP   26 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHH
T ss_pred             CCEEEEEeCCCCCHHHHHH
Confidence            3557899999999997653

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=92.09  E-value=0.098  Score=44.18  Aligned_cols=33  Identities=27%  Similarity=0.329  Sum_probs=29.1

Q ss_pred             CCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHh
Q 028267          158 EPTPIQRQAIPVLLSDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       158 ~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf  190 (211)
                      ..+..|..|+-.++.++=++++++.|||||..-
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i  180 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTV  180 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehH
Confidence            356689999999999999999999999999864

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=91.79  E-value=0.064  Score=44.80  Aligned_cols=42  Identities=26%  Similarity=0.306  Sum_probs=27.4

Q ss_pred             HHHHHHcCCCCCc---HHHHHHH-hhHhcCCcEEEEcCCCchhHHH
Q 028267          148 LRNLAELGYKEPT---PIQRQAI-PVLLSDRECFACAPTGSGKTLA  189 (211)
Q Consensus       148 l~~l~~~g~~~pt---~iQ~~ai-p~il~G~dvi~~A~TGsGKTla  189 (211)
                      +..|...|+-..-   +-+...+ -++..+++++++++||||||..
T Consensus       137 l~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~  182 (323)
T d1g6oa_         137 HSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY  182 (323)
T ss_dssp             HHHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH
T ss_pred             hHHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH
Confidence            4456666654322   2222222 3456789999999999999985

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=91.22  E-value=0.096  Score=42.98  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCchhHHHh
Q 028267          172 SDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf  190 (211)
                      .++.++.++|||+|||+..
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999965

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=90.99  E-value=0.058  Score=45.42  Aligned_cols=33  Identities=18%  Similarity=0.213  Sum_probs=23.7

Q ss_pred             hhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhcc
Q 028267          168 PVLLSDRECFACAPTGSGKTLAFLCPMLMKLRVL  201 (211)
Q Consensus       168 p~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~~  201 (211)
                      |.=...+++++.+.||||||.++ ..++.++...
T Consensus        45 ~~~~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~   77 (433)
T d1e9ra_          45 PRDAEPRHLLVNGATGTGKSVLL-RELAYTGLLR   77 (433)
T ss_dssp             CGGGGGGCEEEEECTTSSHHHHH-HHHHHHHHHT
T ss_pred             CCCcccceEEEEeCCCCcHHHHH-HHHHHHHHhC
Confidence            33355678999999999999764 5566665543

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=90.65  E-value=0.29  Score=37.71  Aligned_cols=42  Identities=17%  Similarity=0.136  Sum_probs=31.2

Q ss_pred             CCcHHHHHHHhhHh----cCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          158 EPTPIQRQAIPVLL----SDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       158 ~pt~iQ~~aip~il----~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      .+.|+|..++..++    .+..+|++-..|.|||+.. |.++..+..
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~-i~~~~~~~~   57 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQT-IAVFSDAKK   57 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHH-HHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHH-HHhhhhhhh
Confidence            57899999987543    4567888999999999986 455555543

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=90.28  E-value=0.053  Score=47.32  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCchhHHHh
Q 028267          172 SDRECFACAPTGSGKTLAF  190 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf  190 (211)
                      ...|||.++|||||||+-.
T Consensus        48 ~ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             ccccEEEECCCCCCHHHHH
Confidence            4579999999999999954

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=90.21  E-value=0.2  Score=41.08  Aligned_cols=45  Identities=27%  Similarity=0.247  Sum_probs=36.7

Q ss_pred             HcCCCCCcHHHHHHHhhHhcCCcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          153 ELGYKEPTPIQRQAIPVLLSDRECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       153 ~~g~~~pt~iQ~~aip~il~G~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..|. +|+++|-..--.+..|+  |+.-.||-||||+-.+|++-.-..
T Consensus        76 tlG~-RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~  120 (273)
T d1tf5a3          76 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT  120 (273)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             hhce-EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhc
Confidence            3454 78999999888888885  789999999999999997765443

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=88.70  E-value=0.26  Score=37.61  Aligned_cols=26  Identities=15%  Similarity=0.189  Sum_probs=19.5

Q ss_pred             CcEEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          174 RECFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ..+++.+++|+|||...- -+...|..
T Consensus        44 ~~lll~GppGtGKT~l~~-~l~~~l~~   69 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLR-KLWELYKD   69 (276)
T ss_dssp             CEEEEECCTTSSHHHHHH-HHHHHHTT
T ss_pred             CceEEECCCCCCHHHHHH-HHHHHHhc
Confidence            679999999999997643 35555543

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=88.07  E-value=0.31  Score=41.37  Aligned_cols=24  Identities=33%  Similarity=0.512  Sum_probs=19.6

Q ss_pred             EEEEcCCCchhHHHhHHHHHHHHhc
Q 028267          176 CFACAPTGSGKTLAFLCPMLMKLRV  200 (211)
Q Consensus       176 vi~~A~TGsGKTlaf~lPil~~l~~  200 (211)
                      ||+++|||||||-+.. .+|..+..
T Consensus       161 iLvtGpTGSGKSTTl~-~~l~~~~~  184 (401)
T d1p9ra_         161 ILVTGPTGSGKSTTLY-AGLQELNS  184 (401)
T ss_dssp             EEEECSTTSCHHHHHH-HHHHHHCC
T ss_pred             EEEEcCCCCCccHHHH-HHhhhhcC
Confidence            8899999999998764 57777754

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=86.19  E-value=0.35  Score=37.85  Aligned_cols=27  Identities=15%  Similarity=0.275  Sum_probs=20.1

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .|.=+++.|+||+|||. |++-++.++.
T Consensus        34 ~G~l~vi~G~~G~GKT~-~~~~la~~~a   60 (277)
T d1cr2a_          34 GGEVIMVTSGSGMGKST-FVRQQALQWG   60 (277)
T ss_dssp             TTCEEEEECSTTSSHHH-HHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHH-HHHHHHHhhh
Confidence            46678899999999995 5556665543

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=85.12  E-value=0.19  Score=38.63  Aligned_cols=18  Identities=28%  Similarity=0.366  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCchhHHHhH
Q 028267          174 RECFACAPTGSGKTLAFL  191 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf~  191 (211)
                      ..+|..+|+|+|||.+.-
T Consensus        36 ~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            479999999999999653

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=85.00  E-value=0.5  Score=39.67  Aligned_cols=17  Identities=47%  Similarity=0.628  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCchhHHHh
Q 028267          174 RECFACAPTGSGKTLAF  190 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf  190 (211)
                      .+++.++|||+|||...
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999754

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=84.78  E-value=0.34  Score=36.92  Aligned_cols=32  Identities=25%  Similarity=0.256  Sum_probs=23.4

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHhcccCC
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLRVLFIP  204 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~~~~~~  204 (211)
                      .|.=+++.+++|+|||. |++-++..+......
T Consensus        25 ~gsl~li~G~pGsGKT~-l~~qia~~~~~~~~~   56 (242)
T d1tf7a2          25 KDSIILATGATGTGKTL-LVSRFVENACANKER   56 (242)
T ss_dssp             SSCEEEEEECTTSSHHH-HHHHHHHHHHTTTCC
T ss_pred             CCeEEEEEeCCCCCHHH-HHHHHHHHHHHhccc
Confidence            46779999999999998 556666666554433

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=84.73  E-value=0.49  Score=35.97  Aligned_cols=17  Identities=35%  Similarity=0.454  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCchhHHHh
Q 028267          174 RECFACAPTGSGKTLAF  190 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf  190 (211)
                      .++|..+|+|+|||...
T Consensus        46 ~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            46999999999998754

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.15  E-value=1  Score=33.91  Aligned_cols=16  Identities=31%  Similarity=0.546  Sum_probs=13.7

Q ss_pred             cEEEEcCCCchhHHHh
Q 028267          175 ECFACAPTGSGKTLAF  190 (211)
Q Consensus       175 dvi~~A~TGsGKTlaf  190 (211)
                      .++..+|+|+|||...
T Consensus        37 ~lLl~Gp~G~GKttl~   52 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTI   52 (227)
T ss_dssp             CEEEECSSSSSHHHHH
T ss_pred             eEEEECCCCCChhHHH
Confidence            5899999999999643

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=81.58  E-value=0.37  Score=36.93  Aligned_cols=17  Identities=29%  Similarity=0.383  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCchhHHHh
Q 028267          174 RECFACAPTGSGKTLAF  190 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf  190 (211)
                      .++|..+|+|+|||...
T Consensus        36 ~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            47999999999999754

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=80.70  E-value=0.64  Score=34.47  Aligned_cols=24  Identities=33%  Similarity=0.562  Sum_probs=18.1

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHH
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLM  196 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~  196 (211)
                      .|.=+++.+++|+|||. |++-++.
T Consensus        25 ~G~~~~I~G~~G~GKT~-la~~~~~   48 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTL-FSIQFLY   48 (242)
T ss_dssp             TTSEEEEEESTTSSHHH-HHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHH-HHHHHHH
Confidence            47789999999999996 3444433

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.52  E-value=0.43  Score=36.04  Aligned_cols=28  Identities=18%  Similarity=-0.020  Sum_probs=20.4

Q ss_pred             hcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          171 LSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       171 l~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      ..|+=+++.+++|+|||.- ++-++....
T Consensus        35 p~G~~~~i~G~~GsGKT~l-alq~~~~~~   62 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQL-SHTLCVTAQ   62 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHH-HHHHHHHTT
T ss_pred             cCCEEEEEECCCCCCHHHH-HHHHHHHHH
Confidence            3467799999999999984 455554443

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.45  E-value=0.47  Score=34.14  Aligned_cols=29  Identities=10%  Similarity=0.041  Sum_probs=21.4

Q ss_pred             HhcCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          170 LLSDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       170 il~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      +..|.=+++.+++|||||. |++-++.+..
T Consensus        20 i~~G~v~~i~G~~GsGKT~-l~l~la~~~~   48 (242)
T d1n0wa_          20 IETGSITEMFGEFRTGKTQ-ICHTLAVTCQ   48 (242)
T ss_dssp             EETTSEEEEECCTTSSHHH-HHHHHHHHTT
T ss_pred             CcCCEEEEEEeCCCCCHHH-HHHHHHHHHH
Confidence            3458889999999999996 4555555543

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.38  E-value=0.59  Score=38.21  Aligned_cols=24  Identities=33%  Similarity=0.426  Sum_probs=20.0

Q ss_pred             HhhHhcCCc--EEEEcCCCchhHHHh
Q 028267          167 IPVLLSDRE--CFACAPTGSGKTLAF  190 (211)
Q Consensus       167 ip~il~G~d--vi~~A~TGsGKTlaf  190 (211)
                      +..++.|.+  |++.++||||||.+.
T Consensus        68 v~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          68 VKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHcCCCcceeeecccCCCCceec
Confidence            455688975  889999999999986

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.33  E-value=0.34  Score=37.21  Aligned_cols=17  Identities=41%  Similarity=0.573  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCchhHHHh
Q 028267          174 RECFACAPTGSGKTLAF  190 (211)
Q Consensus       174 ~dvi~~A~TGsGKTlaf  190 (211)
                      +.++..+|+|+|||.+.
T Consensus        53 ~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            56999999999999754

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=80.18  E-value=0.39  Score=36.47  Aligned_cols=27  Identities=19%  Similarity=0.199  Sum_probs=20.6

Q ss_pred             cCCcEEEEcCCCchhHHHhHHHHHHHHh
Q 028267          172 SDRECFACAPTGSGKTLAFLCPMLMKLR  199 (211)
Q Consensus       172 ~G~dvi~~A~TGsGKTlaf~lPil~~l~  199 (211)
                      .|+=+++.+++|||||. |++-++.+..
T Consensus        35 ~G~~~li~G~pGsGKT~-~~lq~~~~~~   61 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQ-LAHTLAVMVQ   61 (254)
T ss_dssp             SSEEEEEEESTTSSHHH-HHHHHHHHTT
T ss_pred             CCEEEEEEcCCCCCHHH-HHHHHHHHhh
Confidence            46779999999999998 5556655544