Citrus Sinensis ID: 031654

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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-----
Protein Sequence
MSASWAADSVFASENAAPASSSTNTLSSPAARFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQKK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccHHHHHcHHccccccccccHHHHHHHHHHcccEEEEEccccccccccHHHHHHHHHHHccccHHHHHHHHccccEEEEcccHHHHHHHccccccccccEEEEEEccccHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEcccccccccEEEcccccccccHcHHcHHHHHHHHHHHccccccccHHHccHHHHHccccHHHEccccccHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccEEEEcccHHHHHHHcccccHHHHHHEEEHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
msaswaadsvfasenaapassstntlsspaarfayvpqhlrnkprtykyvkptpvqrhATSILVAGRDLMacaqtgsrkttpfcfpIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQKK
Flexible Loop (DISEMBL)
MSASWAADSVFasenaapassstntlsspAARFAyvpqhlrnkprtykyvkptpvqrHATSILVAGRDLMACaqtgsrkttpfcfPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQKK
Low Complexity Region (SEG)
MSASWAADSVFASENAAPASSSTNTLSSPAARFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQKK
Disordered region (IsUnstruct)
********************************FAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEA*************
Disordered Region (DISOPRED)
******A**VFASENAAPASSSTNTLSSPAARFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI*************LARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQ**
Disordered Region (DISEMBL)
**************************SSPAARFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQKK
Disordered Region (DISPRO)
****WAADSVFASENAAPASSSTNTLSSPAARFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSASWAADSVFASENAAPASSSTNTLSSPAARFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQKK
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	155	2.2.26 [Sep-21-2011]
Q6Z4K6	638	DEAD-box ATP-dependent RN	yes	no	0.941	0.228	0.413	7e-27
Q84W89	633	DEAD-box ATP-dependent RN	yes	no	0.896	0.219	0.406	1e-26
Q9M2F9	646	DEAD-box ATP-dependent RN	no	no	0.896	0.215	0.401	2e-26
Q2R1M8	623	DEAD-box ATP-dependent RN	no	no	0.916	0.227	0.411	5e-26
Q75HJ0	637	DEAD-box ATP-dependent RN	no	no	0.896	0.218	0.416	3e-25
Q8LA13	612	DEAD-box ATP-dependent RN	no	no	0.896	0.227	0.395	6e-25
Q1DJF0	665	ATP-dependent RNA helicas	N/A	no	0.896	0.209	0.333	9e-18
A1CXK7	676	ATP-dependent RNA helicas	N/A	no	0.896	0.205	0.333	1e-17
Q4WP13	674	ATP-dependent RNA helicas	yes	no	0.896	0.206	0.333	1e-17
Q0CLJ6	674	ATP-dependent RNA helicas	N/A	no	0.896	0.206	0.333	4e-17

>sp|Q6Z4K6|RH52B_ORYSJ DEAD-box ATP-dependent RNA helicase 52B OS=Oryza sativa subsp. japonica GN=PL10B PE=2 SV=1

 Score =  119 bits (298), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 86/208 (41%), Positives = 102/208 (49%), Gaps = 62/208 (29%)

Query: 4   SWAADSVFASENAA---------PASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKP 52
           S AA+  F  EN           P  +S + +  PA  FA +     L    R  KYVKP
Sbjct: 133 SEAAEVDFEGENTGINFEAYEDIPVETSGHDVPPPANTFAEIDLGDALNENIRRCKYVKP 192

Query: 53  TPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE------------------ 94
           TPVQR+A  I +AGRDLMACAQTGS KT  FCFPII+GIMR                   
Sbjct: 193 TPVQRYAIPISIAGRDLMACAQTGSGKTAAFCFPIISGIMRSRPPPRSRGSRTAYPLALI 252

Query: 95  -----------YYSARK--------------------ELRELARWVDNLMATLRRLVNLL 123
                      +  ARK                    +LREL R V+ L+AT  RL++LL
Sbjct: 253 LSPTRELSVQIHEEARKFAYQTGVKVVVAYGGAPITQQLRELERGVEILVATPGRLMDLL 312

Query: 124 ERGRVSLQMIIRYLALKEAADQTLDMAL 151
           ER RVSLQM I+YLAL E AD+ LDM  
Sbjct: 313 ERARVSLQM-IKYLALDE-ADRMLDMGF 338

Oryza sativa subsp. japonica (taxid: 39947)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q84W89|RH37_ARATH DEAD-box ATP-dependent RNA helicase 37 OS=Arabidopsis thaliana GN=RH37 PE=2 SV=2

 Score =  119 bits (297), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 78/192 (40%), Positives = 96/192 (50%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S + +  P   FA +   + L    R  KYVKPTPVQRHA  IL+ GRD
Sbjct: 139 FDAYEDIPIETSGDNVPPPVNTFAEIDLGEALNLNIRRCKYVKPTPVQRHAIPILLEGRD 198

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII+GIM++ +  R                             
Sbjct: 199 LMACAQTGSGKTAAFCFPIISGIMKDQHVQRPRGSRTVYPLAVILSPTRELASQIHDEAK 258

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               ++LREL R VD L+AT  RL +LLER RVS+QM IR+LAL
Sbjct: 259 KFSYQTGVKVVVAYGGTPINQQLRELERGVDILVATPGRLNDLLERARVSMQM-IRFLAL 317

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 318 DE-ADRMLDMGF 328

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9M2F9|RH52_ARATH DEAD-box ATP-dependent RNA helicase 52 OS=Arabidopsis thaliana GN=RH52 PE=2 SV=1

 Score =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 77/192 (40%), Positives = 97/192 (50%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S + +  P   FA +   + L    +  KYVKPTPVQR+A  IL AGRD
Sbjct: 126 FEAYEDIPIETSGDNVPPPVNTFAEIDLGEALNLNIQRCKYVKPTPVQRNAIPILAAGRD 185

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII+GIM++ +  R                             
Sbjct: 186 LMACAQTGSGKTAAFCFPIISGIMKDQHIERPRGVRGVYPLAVILSPTRELACQIHDEAR 245

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               +++REL R VD L+AT  RL +LLERGRVSLQM +R+LAL
Sbjct: 246 KFSYQTGVKVVVAYGGTPVNQQIRELERGVDILVATPGRLNDLLERGRVSLQM-VRFLAL 304

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 305 DE-ADRMLDMGF 315

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2R1M8|RH52C_ORYSJ DEAD-box ATP-dependent RNA helicase 52C OS=Oryza sativa subsp. japonica GN=Os11g0599500 PE=3 SV=1

 Score =  116 bits (291), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 81/197 (41%), Positives = 97/197 (49%), Gaps = 55/197 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S   +  P   FA +   Q L +  R  KYV+PTPVQR+A  I +AGRD
Sbjct: 135 FDAYEDIPVETSGREVPPPVGTFAEIDLGQALNDNIRRCKYVRPTPVQRYAIPISLAGRD 194

Query: 69  LMACAQTGSRKTTPFCFPIINGIMRE-------------------------------YYS 97
           LMACAQTGS KT  FCFPII+GIMR                                +  
Sbjct: 195 LMACAQTGSGKTAAFCFPIISGIMRGPPAQRPQRGGMRTACPLALILSPTRELSMQIHEE 254

Query: 98  ARK--------------------ELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYL 137
           ARK                    +LR+L R VD L+AT  RLV+LLER RVSLQ  IRYL
Sbjct: 255 ARKFSYQTGVRVVVAYGGAPINQQLRDLERGVDILVATPGRLVDLLERARVSLQS-IRYL 313

Query: 138 ALKEAADQTLDMALNQK 154
           AL E AD+ LDM    +
Sbjct: 314 ALDE-ADRMLDMGFEPQ 329

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q75HJ0|RH37_ORYSJ DEAD-box ATP-dependent RNA helicase 37 OS=Oryza sativa subsp. japonica GN=PL10A PE=2 SV=1

 Score =  114 bits (284), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 80/192 (41%), Positives = 97/192 (50%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S + +  P   FA +     L    R  KYVKPTPVQR+A  I +AGRD
Sbjct: 154 FDAYEDIPVETSGHDVPPPVNTFAEIDLGDALNENIRRCKYVKPTPVQRYAIPISIAGRD 213

Query: 69  LMACAQTGSRKTTPFCFPIINGIM------------------------RE-----YYSAR 99
           LMACAQTGS KT  FCFPII+GIM                        RE     +  AR
Sbjct: 214 LMACAQTGSGKTAAFCFPIISGIMSSRPPQRPRGSRTAYPLALILSPTRELSVQIHEEAR 273

Query: 100 K--------------------ELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
           K                    +LREL R V+ L+AT  RL++LLER RVSLQM ++YLAL
Sbjct: 274 KFAYQTGVRVVVAYGGAPIHQQLRELERGVEILVATPGRLMDLLERARVSLQM-VKYLAL 332

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 333 DE-ADRMLDMGF 343

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8LA13|RH11_ARATH DEAD-box ATP-dependent RNA helicase 11 OS=Arabidopsis thaliana GN=RH11 PE=2 SV=1

 Score =  113 bits (282), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 76/192 (39%), Positives = 93/192 (48%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S   +  P   FA +     L    R  KYV+PTPVQRHA  IL+A RD
Sbjct: 131 FDAYEDIPVETSGGDVPPPVNTFADIDLGDALNLNIRRCKYVRPTPVQRHAIPILLAERD 190

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII+GIM++ +  R                             
Sbjct: 191 LMACAQTGSGKTAAFCFPIISGIMKDQHVERPRGSRAVYPFAVILSPTRELACQIHDEAK 250

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               ++LREL R  D L+AT  RL +LLER RVS+QM IR+LAL
Sbjct: 251 KFSYQTGVKVVVAYGGTPIHQQLRELERGCDILVATPGRLNDLLERARVSMQM-IRFLAL 309

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 310 DE-ADRMLDMGF 320

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q1DJF0|DED1_COCIM ATP-dependent RNA helicase DED1 OS=Coccidioides immitis (strain RS) GN=DED1 PE=3 SV=2

 Score = 89.4 bits (220), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 67/201 (33%), Positives = 91/201 (45%), Gaps = 62/201 (30%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           FA+ +  P  +S + +  P   F   P   HL +  +   Y  PTPVQ+++  I++ GRD
Sbjct: 161 FANYDDIPVEASGHDVPEPVTTFTNPPLDDHLISNIKLATYKTPTPVQKYSIPIVMGGRD 220

Query: 69  LMACAQTGSRKTTPFCFPII-----NG--------------------------------- 90
           LMACAQTGS KT  F FPI+     NG                                 
Sbjct: 221 LMACAQTGSGKTGGFLFPILSQAFKNGPSAVPTQNANQFSYGRQRKAYPTSLILAPTREL 280

Query: 91  IMREYYSARK--------------------ELRELARWVDNLMATLRRLVNLLERGRVSL 130
           + + Y  ARK                    +LR++ R  D L+AT  RLV+L+ERGR+SL
Sbjct: 281 VSQIYDEARKFAYRSWVRPCVVYGGADIGSQLRQIERGCDLLVATPGRLVDLIERGRISL 340

Query: 131 QMIIRYLALKEAADQTLDMAL 151
              I+YL L E AD+ LDM  
Sbjct: 341 -CNIKYLVLDE-ADRMLDMGF 359

ATP-binding RNA helicase involved in translation initiation. Remodels RNA in response to ADP and ATP concentrations by facilitating disruption, but also formation of RNA duplexes.

Coccidioides immitis (strain RS) (taxid: 246410)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1CXK7|DED1_NEOFI ATP-dependent RNA helicase ded1 OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=ded1 PE=3 SV=1

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 67/201 (33%), Positives = 93/201 (46%), Gaps = 62/201 (30%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           FA+ +  P  +S + +  P   F   P   HL +  +  +Y  PTPVQ+++  I++ GRD
Sbjct: 170 FANYDDIPVEASGHDVPEPVNAFTNPPLDDHLISNIKLARYQTPTPVQKYSIPIVMNGRD 229

Query: 69  LMACAQTGSRKTTPFCFPIIN--------------------GIMREYY------------ 96
           LMACAQTGS KT  F FPI++                    G  R+ Y            
Sbjct: 230 LMACAQTGSGKTGGFLFPILSQAFQTGPSAVPAQASGQFGYGRQRKAYPTSLILAPTREL 289

Query: 97  ------SARK--------------------ELRELARWVDNLMATLRRLVNLLERGRVSL 130
                  ARK                    +LR++ R  D L+AT  RLV+L+ERGR+SL
Sbjct: 290 VSQIFDEARKFAYRSWVRPCVVYGGADIGSQLRQIERGCDLLVATPGRLVDLIERGRISL 349

Query: 131 QMIIRYLALKEAADQTLDMAL 151
            + I+YL L E AD+ LDM  
Sbjct: 350 -VNIKYLVLDE-ADRMLDMGF 368

ATP-binding RNA helicase involved in translation initiation. Remodels RNA in response to ADP and ATP concentrations by facilitating disruption, but also formation of RNA duplexes.

Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) (taxid: 331117)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4WP13|DED1_ASPFU ATP-dependent RNA helicase ded1 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=ded1 PE=3 SV=1

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 67/201 (33%), Positives = 93/201 (46%), Gaps = 62/201 (30%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           FA+ +  P  +S + +  P   F   P   HL +  +  +Y  PTPVQ+++  I++ GRD
Sbjct: 168 FANYDDIPVEASGHDVPEPVNAFTNPPLDDHLISNIKLARYQTPTPVQKYSIPIVMNGRD 227

Query: 69  LMACAQTGSRKTTPFCFPIIN--------------------GIMREYY------------ 96
           LMACAQTGS KT  F FPI++                    G  R+ Y            
Sbjct: 228 LMACAQTGSGKTGGFLFPILSQAFQTGPSPVPAQASGQFGYGRQRKAYPTSLILAPTREL 287

Query: 97  ------SARK--------------------ELRELARWVDNLMATLRRLVNLLERGRVSL 130
                  ARK                    +LR++ R  D L+AT  RLV+L+ERGR+SL
Sbjct: 288 VSQIFDEARKFAYRSWVRPCVVYGGADIGSQLRQIERGCDLLVATPGRLVDLIERGRISL 347

Query: 131 QMIIRYLALKEAADQTLDMAL 151
            + I+YL L E AD+ LDM  
Sbjct: 348 -VNIKYLVLDE-ADRMLDMGF 366

ATP-binding RNA helicase involved in translation initiation. Remodels RNA in response to ADP and ATP concentrations by facilitating disruption, but also formation of RNA duplexes.

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0CLJ6|DED1_ASPTN ATP-dependent RNA helicase ded1 OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) GN=ded1 PE=3 SV=1

 Score = 87.0 bits (214), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 67/201 (33%), Positives = 92/201 (45%), Gaps = 62/201 (30%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           FA+ +  P  +S   +  P   F   P   HL +     +Y+ PTPVQ+++  I++ GRD
Sbjct: 166 FANYDDIPVEASGQDVPEPVNAFTNPPLDDHLISNIALARYLTPTPVQKYSIPIVMNGRD 225

Query: 69  LMACAQTGSRKTTPFCFPIIN--------------------GIMREYY------------ 96
           LMACAQTGS KT  F FPI++                    G  R+ Y            
Sbjct: 226 LMACAQTGSGKTGGFLFPILSQAFQNGPSPTPAPAGGQLGYGRQRKAYPTSLILAPTREL 285

Query: 97  ------SARK--------------------ELRELARWVDNLMATLRRLVNLLERGRVSL 130
                  ARK                    +LR++ R  D L+AT  RLV+L+ERGR+SL
Sbjct: 286 VSQIFDEARKFAYRSWVRPCVVYGGADIGSQLRQIERGCDLLVATPGRLVDLIERGRISL 345

Query: 131 QMIIRYLALKEAADQTLDMAL 151
            + I+YL L E AD+ LDM  
Sbjct: 346 -VNIKYLILDE-ADRMLDMGF 364

ATP-binding RNA helicase involved in translation initiation. Remodels RNA in response to ADP and ATP concentrations by facilitating disruption, but also formation of RNA duplexes.

Aspergillus terreus (strain NIH 2624 / FGSC A1156) (taxid: 341663)

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	155
255580688	585	dead box ATP-dependent RNA helicase, put	0.896	0.237	0.427	1e-27
356530675	611	PREDICTED: DEAD-box ATP-dependent RNA he	0.896	0.227	0.427	3e-27
224139932	611	predicted protein [Populus trichocarpa]	0.896	0.227	0.432	4e-27
224088162	509	predicted protein [Populus trichocarpa]	0.896	0.273	0.427	6e-27
356500387	611	PREDICTED: DEAD-box ATP-dependent RNA he	0.896	0.227	0.421	2e-26
356525235	619	PREDICTED: DEAD-box ATP-dependent RNA he	0.896	0.224	0.430	4e-26
225435708	612	PREDICTED: DEAD-box ATP-dependent RNA he	0.896	0.227	0.414	8e-26
225441549	622	PREDICTED: DEAD-box ATP-dependent RNA he	0.896	0.223	0.411	8e-26
356512483	614	PREDICTED: DEAD-box ATP-dependent RNA he	0.896	0.226	0.424	8e-26
356540089	604	PREDICTED: DEAD-box ATP-dependent RNA he	0.677	0.173	0.490	2e-25

>gi|255580688|ref|XP_002531166.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223529236|gb|EEF31209.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 82/192 (42%), Positives = 98/192 (51%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S + +  P   FA +   + L    R  KYVKPTPVQR+A  I++AGRD
Sbjct: 108 FDAYEDIPVETSGDNVPPPVNTFAEIDLGEALNQNIRRCKYVKPTPVQRNAIPIILAGRD 167

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII+GIMRE Y  R                             
Sbjct: 168 LMACAQTGSGKTAAFCFPIISGIMREQYVQRPRGPRTVYPLALILSPTRELSCQIHDEAK 227

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               ++LREL R VD L+AT  RLV+LLER R+SLQM IRYLAL
Sbjct: 228 KFSYQTGVKVVVAYGGAPINQQLRELERGVDILVATPGRLVDLLERARISLQM-IRYLAL 286

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 287 DE-ADRMLDMGF 297

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530675|ref|XP_003533906.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 37-like [Glycine max]

 Score =  126 bits (317), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 82/192 (42%), Positives = 98/192 (51%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F + +  P  +S   +  P   FA +   + L    +  KYVKPTPVQR+A  I +AGRD
Sbjct: 136 FDAYDDIPVETSGENVPPPVNTFAEIDLGEALNQNIQRCKYVKPTPVQRYAIPISLAGRD 195

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII+GIMRE Y+ R                             
Sbjct: 196 LMACAQTGSGKTAAFCFPIISGIMREQYAQRPRVARTAYPLALILSPTRELSCQIHDEAK 255

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               ++LREL R VD L+AT  RLV+LLER RVSLQM IRYLAL
Sbjct: 256 KFSYQTGVKVVVAYGGAPINQQLRELERGVDILVATPGRLVDLLERARVSLQM-IRYLAL 314

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 315 DE-ADRMLDMGF 325

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224139932|ref|XP_002323346.1| predicted protein [Populus trichocarpa] gi|222867976|gb|EEF05107.1| predicted protein [Populus trichocarpa]

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 83/192 (43%), Positives = 98/192 (51%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P ++S + +  P   FA +   + +    R  KYVKPTPVQR+A  IL+AGRD
Sbjct: 135 FDAYEDIPVATSGHNVPPPVNTFADIDLGEAVNQNIRRCKYVKPTPVQRNAIPILLAGRD 194

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII GIMRE Y  R                             
Sbjct: 195 LMACAQTGSGKTAAFCFPIIAGIMREQYVQRPHGGRTMYPLALILSPTRELSSQIHDEAK 254

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               ++LREL R VD L+AT  RLV+LLER RVSLQM IRYLAL
Sbjct: 255 KFSYQTGVKVVVVYGGAPINQQLRELERGVDILVATPGRLVDLLERARVSLQM-IRYLAL 313

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 314 DE-ADRMLDMGF 324

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088162|ref|XP_002308349.1| predicted protein [Populus trichocarpa] gi|222854325|gb|EEE91872.1| predicted protein [Populus trichocarpa]

 Score =  125 bits (314), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 82/192 (42%), Positives = 96/192 (50%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S   +  P   FA +   + +    R  KYVKPTPVQR+A  IL+AGRD
Sbjct: 32  FDAYEDIPVETSGQNVPPPVNTFAEIDLGEAVNQNIRRCKYVKPTPVQRNAIPILLAGRD 91

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII GIMRE Y  R                             
Sbjct: 92  LMACAQTGSGKTAAFCFPIIAGIMREQYVQRPHGGRTVYPLALILSPTRELSCQIHDEAK 151

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               ++LREL R VD L+AT  RLV+L+ER RVSLQM IRYLAL
Sbjct: 152 KFAYQTGVKVVVVYGGAPVNQQLRELERGVDVLVATPGRLVDLVERARVSLQM-IRYLAL 210

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 211 DE-ADRMLDMGF 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500387|ref|XP_003519013.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 37-like [Glycine max]

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/192 (42%), Positives = 97/192 (50%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVPQH--LRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F + +  P  +S   +  P   FA +     L    +  KYVKPTPVQR+A  I +AGRD
Sbjct: 136 FEAYDDIPVETSGENVPLPVNSFAEIDLGVALNQNIQRCKYVKPTPVQRYAIPISLAGRD 195

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII+GIMRE Y+ R                             
Sbjct: 196 LMACAQTGSGKTAAFCFPIISGIMREQYAQRPRVARTAYPLALILSPTRELSCQIHDEAK 255

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               ++LREL R VD L+AT  RLV+LLER R+SLQM IRYLAL
Sbjct: 256 KFSYQTGVKVVVAYGGAPITQQLRELERGVDILVATPGRLVDLLERARLSLQM-IRYLAL 314

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 315 DE-ADRMLDMGF 325

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356525235|ref|XP_003531232.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 37-like [Glycine max]

 Score =  122 bits (307), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 83/193 (43%), Positives = 97/193 (50%), Gaps = 54/193 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S + +  P   FA +   + L    R  KYVKPTPVQRHA  I +AGRD
Sbjct: 139 FDAYEDIPVETSGDNVPPPVNTFAEIDLGEALNQNIRRCKYVKPTPVQRHAIPISLAGRD 198

Query: 69  LMACAQTGSRKTTPFCFPIINGIMRE------------------------------YYSA 98
           LMACAQTGS KT  FCFPII+GIMR                               +  A
Sbjct: 199 LMACAQTGSGKTAAFCFPIISGIMRGQPVQRPPRGVRTVYPLALVLSPTRELSMQIHEEA 258

Query: 99  RK--------------------ELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLA 138
           RK                    +LR+L R VD L+AT  RLV+LLER RVSLQM IRYLA
Sbjct: 259 RKFSYQTGVRVVVAYGGAPINQQLRDLERGVDILVATPGRLVDLLERARVSLQM-IRYLA 317

Query: 139 LKEAADQTLDMAL 151
           L E AD+ LDM  
Sbjct: 318 LDE-ADRMLDMGF 329

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225435708|ref|XP_002283489.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 37 [Vitis vinifera] gi|147854540|emb|CAN78578.1| hypothetical protein VITISV_013679 [Vitis vinifera]

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 80/193 (41%), Positives = 96/193 (49%), Gaps = 54/193 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S + +  P   FA +   + L    +  KYVKPTPVQRHA  I +AGRD
Sbjct: 133 FDAYEDIPVETSGDNVPPPVNTFAEIDLGEALNQNIKRCKYVKPTPVQRHAIPISLAGRD 192

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII+GIM+   S R                             
Sbjct: 193 LMACAQTGSGKTAAFCFPIISGIMKGQASQRPPRGARTVYPLALILSPTRELSCQIHDEA 252

Query: 100 ---------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLA 138
                                ++LR+L R VD L+AT  RLV+LLER RVSLQM IRYLA
Sbjct: 253 KKFSYQTGVKVVVAYGGAPISQQLRDLERGVDILVATPGRLVDLLERARVSLQM-IRYLA 311

Query: 139 LKEAADQTLDMAL 151
           L E AD+ LDM  
Sbjct: 312 LDE-ADRMLDMGF 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225441549|ref|XP_002281113.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 37-like [Vitis vinifera]

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 79/192 (41%), Positives = 96/192 (50%), Gaps = 53/192 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S + +  P   FA +   + L    R  KYVKPTPVQRHA  I ++G+D
Sbjct: 143 FDAYEDIPVETSGDNVPPPVNTFAEIDLGEALNQNIRRCKYVKPTPVQRHAIPISLSGKD 202

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSAR----------------------------- 99
           LMACAQTGS KT  FCFPII+GIM   ++ R                             
Sbjct: 203 LMACAQTGSGKTAAFCFPIISGIMTGQFAQRPRGARTVYPLALILSPTRELSCQIHDEAR 262

Query: 100 --------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL 139
                               ++LREL R VD L+AT  RLV+LLER RVSLQM IRYLAL
Sbjct: 263 KFSYQTGVKVVVAYGGAPINQQLRELERGVDILVATPGRLVDLLERARVSLQM-IRYLAL 321

Query: 140 KEAADQTLDMAL 151
            E AD+ LDM  
Sbjct: 322 DE-ADRMLDMGF 332

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512483|ref|XP_003524948.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 37-like [Glycine max]

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 82/193 (42%), Positives = 97/193 (50%), Gaps = 54/193 (27%)

Query: 11  FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
           F +    P  +S + +  P   FA +   + L    R  KYV+PTPVQRHA  I +AGRD
Sbjct: 134 FDAYEDIPVETSGDNVPPPVNTFAEIDLGEALNQNIRRCKYVRPTPVQRHAIPISLAGRD 193

Query: 69  LMACAQTGSRKTTPFCFPIINGIMRE------------------------------YYSA 98
           LMACAQTGS KT  FCFPII+GIMR                               +  A
Sbjct: 194 LMACAQTGSGKTAAFCFPIISGIMRGQSVQRPPRGVRTVYPLALVLSPTRELSMQIHEEA 253

Query: 99  RK--------------------ELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLA 138
           RK                    +LR+L R VD L+AT  RLV+LLER RVSLQM IRYLA
Sbjct: 254 RKFSYQTGVRVVVAYGGAPINQQLRDLERGVDILVATPGRLVDLLERARVSLQM-IRYLA 312

Query: 139 LKEAADQTLDMAL 151
           L E AD+ LDM  
Sbjct: 313 LDE-ADRMLDMGF 324

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356540089|ref|XP_003538523.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 37-like [Glycine max]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 78/159 (49%), Positives = 84/159 (52%), Gaps = 54/159 (33%)

Query: 45  RTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE---------- 94
           R  KYVKPTPVQRHA  I +AGRDLMACAQTGS KT  FCFPIINGIMR           
Sbjct: 159 RRCKYVKPTPVQRHAIPISLAGRDLMACAQTGSGKTAAFCFPIINGIMRGQAQPLQRPPR 218

Query: 95  ----------------------YYSARK--------------------ELRELARWVDNL 112
                                 +  ARK                    +LREL R VD L
Sbjct: 219 GVRIVYPLALVLSPTRELSMQIHEEARKFSYQTGVRVVVAYGGAPINQQLRELERGVDIL 278

Query: 113 MATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL 151
           +AT  RLV+LLER RVSLQM IRYLAL E AD+ LDM  
Sbjct: 279 VATPGRLVDLLERARVSLQM-IRYLALDE-ADRMLDMGF 315

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	155
DICTYBASE|DDB_G0283661	712	ddx3 "DEAD/DEAH box helicase"	0.290	0.063	0.666	2.4e-21
RGD|1564771	662	Ddx3x "DEAD (Asp-Glu-Ala-Asp)	0.393	0.092	0.467	1.2e-19
FB|FBgn0263231	798	bel "belle" [Drosophila melano	0.322	0.062	0.6	2.1e-19
UNIPROTKB|G5E631	661	DDX3X "Uncharacterized protein	0.393	0.092	0.467	3e-19
UNIPROTKB|F1RX16	661	DDX3X "Uncharacterized protein	0.393	0.092	0.467	3e-19
UNIPROTKB|J9P0V9	662	DDX3X "Uncharacterized protein	0.393	0.092	0.467	3e-19
UNIPROTKB|O00571	662	DDX3X "ATP-dependent RNA helic	0.393	0.092	0.467	3e-19
MGI|MGI:103064	662	Ddx3x "DEAD/H (Asp-Glu-Ala-Asp	0.393	0.092	0.467	3e-19
UNIPROTKB|E2RRQ7	706	DDX3X "Uncharacterized protein	0.393	0.086	0.467	3.9e-19
ASPGD|ASPL0000077157	668	AN10557 [Emericella nidulans (	0.509	0.118	0.419	4.4e-19

DICTYBASE|DDB_G0283661 ddx3 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 157 (60.3 bits), Expect = 2.4e-21, Sum P(3) = 2.4e-21
 Identities = 30/45 (66%), Positives = 35/45 (77%)

Query:    48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM 92
             KY KPTPVQ+ A  I++  RDLMACAQTGS KT  F FPII+GI+
Sbjct:   266 KYTKPTPVQKSALPIILKNRDLMACAQTGSGKTAAFLFPIISGIL 310

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:0006397 "mRNA processing" evidence=ISS

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

RGD|1564771 Ddx3x "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked" [Rattus norvegicus (taxid:10116)]

 Score = 138 (53.6 bits), Expect = 1.2e-19, Sum P(3) = 1.2e-19
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query:    48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-ARKELRELA 106
             +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I  +    A + ++E  
Sbjct:   199 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYADGPGEALRAMKENG 258

Query:   107 RW 108
             R+
Sbjct:   259 RY 260

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

FB|FBgn0263231 bel "belle" [Drosophila melanogaster (taxid:7227)]

 Score = 158 (60.7 bits), Expect = 2.1e-19, Sum P(3) = 2.1e-19
 Identities = 30/50 (60%), Positives = 36/50 (72%)

Query:    40 LRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIIN 89
             +RN     +Y KPTPVQ+HA  I++ GRDLMACAQTGS KT  F  PI+N
Sbjct:   306 IRNNVALARYDKPTPVQKHAIPIIINGRDLMACAQTGSGKTAAFLVPILN 355

GO:0007286 "spermatid development" evidence=IMP

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

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0043186 "P granule" evidence=IDA

GO:0007283 "spermatogenesis" evidence=IMP

GO:0002168 "instar larval development" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP

GO:0016442 "RNA-induced silencing complex" evidence=IDA

GO:0016246 "RNA interference" evidence=IMP

GO:0005811 "lipid particle" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0043025 "neuronal cell body" evidence=IDA

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0000070 "mitotic sister chromatid segregation" evidence=IMP

UNIPROTKB|G5E631 DDX3X "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 138 (53.6 bits), Expect = 3.0e-19, Sum P(3) = 3.0e-19
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query:    48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-ARKELRELA 106
             +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I  +    A + ++E  
Sbjct:   198 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENG 257

Query:   107 RW 108
             R+
Sbjct:   258 RY 259

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IEA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IEA

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IEA

GO:0071470 "cellular response to osmotic stress" evidence=IEA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IEA

GO:0048027 "mRNA 5'-UTR binding" evidence=IEA

GO:0045948 "positive regulation of translational initiation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043024 "ribosomal small subunit binding" evidence=IEA

GO:0042256 "mature ribosome assembly" evidence=IEA

GO:0035613 "RNA stem-loop binding" evidence=IEA

GO:0034063 "stress granule assembly" evidence=IEA

GO:0031333 "negative regulation of protein complex assembly" evidence=IEA

GO:0030308 "negative regulation of cell growth" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1RX16 DDX3X "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 138 (53.6 bits), Expect = 3.0e-19, Sum P(3) = 3.0e-19
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query:    48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-ARKELRELA 106
             +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I  +    A + ++E  
Sbjct:   199 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENG 258

Query:   107 RW 108
             R+
Sbjct:   259 RY 260

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IEA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IEA

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IEA

GO:0071470 "cellular response to osmotic stress" evidence=IEA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IEA

GO:0048027 "mRNA 5'-UTR binding" evidence=IEA

GO:0045948 "positive regulation of translational initiation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043024 "ribosomal small subunit binding" evidence=IEA

GO:0042256 "mature ribosome assembly" evidence=IEA

GO:0035613 "RNA stem-loop binding" evidence=IEA

GO:0034063 "stress granule assembly" evidence=IEA

GO:0031333 "negative regulation of protein complex assembly" evidence=IEA

GO:0030308 "negative regulation of cell growth" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|J9P0V9 DDX3X "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 138 (53.6 bits), Expect = 3.0e-19, Sum P(3) = 3.0e-19
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query:    48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-ARKELRELA 106
             +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I  +    A + ++E  
Sbjct:   199 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENG 258

Query:   107 RW 108
             R+
Sbjct:   259 RY 260

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|O00571 DDX3X "ATP-dependent RNA helicase DDX3X" [Homo sapiens (taxid:9606)]

 Score = 138 (53.6 bits), Expect = 3.0e-19, Sum P(3) = 3.0e-19
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query:    48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-ARKELRELA 106
             +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I  +    A + ++E  
Sbjct:   199 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENG 258

Query:   107 RW 108
             R+
Sbjct:   259 RY 260

GO:0005524 "ATP binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0005741 "mitochondrial outer membrane" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0030307 "positive regulation of cell growth" evidence=IMP

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IDA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IMP

GO:0045948 "positive regulation of translational initiation" evidence=IMP

GO:0031333 "negative regulation of protein complex assembly" evidence=IDA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IDA

GO:0017148 "negative regulation of translation" evidence=IMP

GO:0034063 "stress granule assembly" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0071470 "cellular response to osmotic stress" evidence=IDA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IDA

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IMP

GO:0007059 "chromosome segregation" evidence=IMP

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0045727 "positive regulation of translation" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0031369 "translation initiation factor binding" evidence=IDA

GO:0042256 "mature ribosome assembly" evidence=IMP

GO:0043024 "ribosomal small subunit binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0016887 "ATPase activity" evidence=IDA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IDA

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

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IMP;IDA

GO:0009615 "response to virus" evidence=IDA

GO:0007243 "intracellular protein kinase cascade" evidence=IDA

GO:0032728 "positive regulation of interferon-beta production" evidence=TAS

GO:0045087 "innate immune response" evidence=IMP

GO:0071651 "positive regulation of chemokine (C-C motif) ligand 5 production" evidence=TAS

GO:0035613 "RNA stem-loop binding" evidence=IDA

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

GO:0048027 "mRNA 5'-UTR binding" evidence=IDA

GO:0008134 "transcription factor binding" evidence=IDA

GO:0030308 "negative regulation of cell growth" evidence=IDA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IMP

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IMP

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IMP

GO:0043065 "positive regulation of apoptotic process" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0006200 "ATP catabolic process" evidence=IDA

MGI|MGI:103064 Ddx3x "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked" [Mus musculus (taxid:10090)]

 Score = 138 (53.6 bits), Expect = 3.0e-19, Sum P(3) = 3.0e-19
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query:    48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-ARKELRELA 106
             +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I  +    A + ++E  
Sbjct:   199 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYADGPGEALRAMKENG 258

Query:   107 RW 108
             R+
Sbjct:   259 RY 260

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=ISO

GO:0003723 "RNA binding" evidence=ISO

GO:0004003 "ATP-dependent DNA helicase activity" evidence=ISO

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005739 "mitochondrion" evidence=IEA

GO:0005741 "mitochondrial outer membrane" evidence=IEA

GO:0006200 "ATP catabolic process" evidence=IEA;ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0007059 "chromosome segregation" evidence=ISO

GO:0007243 "intracellular protein kinase cascade" evidence=ISO

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

GO:0008134 "transcription factor binding" evidence=ISO

GO:0008143 "poly(A) RNA binding" evidence=ISO

GO:0008152 "metabolic process" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=ISO

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=ISO

GO:0009615 "response to virus" evidence=ISO

GO:0010494 "cytoplasmic stress granule" evidence=ISO

GO:0010501 "RNA secondary structure unwinding" evidence=ISO

GO:0016020 "membrane" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISO

GO:0017148 "negative regulation of translation" evidence=ISO

GO:0030307 "positive regulation of cell growth" evidence=ISO

GO:0030308 "negative regulation of cell growth" evidence=ISO

GO:0031333 "negative regulation of protein complex assembly" evidence=ISO

GO:0031369 "translation initiation factor binding" evidence=ISO

GO:0034063 "stress granule assembly" evidence=ISO

GO:0035613 "RNA stem-loop binding" evidence=ISO

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0042256 "mature ribosome assembly" evidence=ISO

GO:0043024 "ribosomal small subunit binding" evidence=ISO

GO:0043065 "positive regulation of apoptotic process" evidence=ISO

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=ISO

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=ISO

GO:0045087 "innate immune response" evidence=ISO

GO:0045727 "positive regulation of translation" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0045948 "positive regulation of translational initiation" evidence=ISO

GO:0048027 "mRNA 5'-UTR binding" evidence=ISO

GO:0071243 "cellular response to arsenic-containing substance" evidence=ISO

GO:0071470 "cellular response to osmotic stress" evidence=ISO

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=ISO

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=ISO

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=ISO

UNIPROTKB|E2RRQ7 DDX3X "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 138 (53.6 bits), Expect = 3.9e-19, Sum P(3) = 3.9e-19
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query:    48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-ARKELRELA 106
             +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I  +    A + ++E  
Sbjct:   241 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENG 300

Query:   107 RW 108
             R+
Sbjct:   301 RY 302

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

ASPGD|ASPL0000077157 AN10557 [Emericella nidulans (taxid:162425)]

 Score = 155 (59.6 bits), Expect = 4.4e-19, Sum P(2) = 4.4e-19
 Identities = 34/81 (41%), Positives = 48/81 (59%)

Query:    11 FASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRD 68
             FA+ +  P  +S + +  P   F   P   HL +     +Y  PTPVQ+++  I++ GRD
Sbjct:   166 FANYDDIPVEASGHDVPEPVNTFTNPPLDDHLISNIALARYQTPTPVQKYSIPIVMNGRD 225

Query:    69 LMACAQTGSRKTTPFCFPIIN 89
             LMACAQTGS KT  F FPI++
Sbjct:   226 LMACAQTGSGKTGGFLFPILS 246

GO:0071470 "cellular response to osmotic stress" evidence=IEA

GO:0007346 "regulation of mitotic cell cycle" evidence=IEA

GO:0031137 "regulation of conjugation with cellular fusion" evidence=IEA

GO:0002183 "cytoplasmic translational initiation" evidence=IEA

GO:0031047 "gene silencing by RNA" evidence=IEA

GO:0010628 "positive regulation of gene expression" evidence=IEA

GO:0097308 "cellular response to farnesol" evidence=IEP

GO:0005524 "ATP binding" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

GO:0033592 "RNA strand annealing 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

Your Input: eugene3.00160548 hypothetical protein (611 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	155
cd00268	203	cd00268, DEADc, DEAD-box helicases	2e-14
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	2e-12
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	5e-10
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	7e-08
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-07
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	4e-07
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	4e-07
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	7e-07
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-05
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	1e-05

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

 Score = 66.7 bits (164), Expect = 2e-14
 Identities = 44/144 (30%), Positives = 64/144 (44%), Gaps = 43/144 (29%)

Query: 47  YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY---------- 96
             + KPTP+Q  A   L++GRD++  AQTGS KT  F  PI+  +               
Sbjct: 17  LGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILA 76

Query: 97  -------------------------------SARKELRELARWVDNLMATLRRLVNLLER 125
                                          S  K++R+L R    ++AT  RL++LLER
Sbjct: 77  PTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLER 136

Query: 126 GRVSLQMIIRYLALKEAADQTLDM 149
           G++ L   ++YL L E AD+ LDM
Sbjct: 137 GKLDLSK-VKYLVLDE-ADRMLDM 158

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 = 63.3 bits (154), Expect = 2e-12
 Identities = 44/143 (30%), Positives = 69/143 (48%), Gaps = 44/143 (30%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM----REYYSA------ 98
           + +PTP+Q  A  +++AGRD++  AQTG+ KT  F  P++  I+    R+Y SA      
Sbjct: 49  FEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT 108

Query: 99  --------------------------------RKELRELARWVDNLMATLRRLVNLLERG 126
                                           RK++  L R VD ++AT  RL++L++RG
Sbjct: 109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRG 168

Query: 127 RVSLQMIIRYLALKEAADQTLDM 149
           ++ L   +  L L E AD+ LDM
Sbjct: 169 KLDLSG-VETLVLDE-ADRMLDM 189

Length = 513

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

 Score = 56.4 bits (136), Expect = 5e-10
 Identities = 44/146 (30%), Positives = 62/146 (42%), Gaps = 47/146 (32%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM---------------- 92
           Y +PTP+Q+ A   ++ GRDLMA AQTG+ KT  F  P++  ++                
Sbjct: 21  YREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALI 80

Query: 93  ----REY----------YSARKELRELARW---------------VDNLMATLRRLVNLL 123
               RE           YS    +R L  +               VD L+AT  RL++L 
Sbjct: 81  LTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLE 140

Query: 124 ERGRVSLQMIIRYLALKEAADQTLDM 149
            +  V L   +  L L E AD+ LDM
Sbjct: 141 HQNAVKLDQ-VEILVLDE-ADRMLDM 164

Length = 456

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

 Score = 50.2 bits (121), Expect = 7e-08
 Identities = 35/141 (24%), Positives = 62/141 (43%), Gaps = 42/141 (29%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSAR--------- 99
           Y + TP+Q  +   ++AG+D++A A+TGS KT  F   ++  +  + +  +         
Sbjct: 24  YTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRE 83

Query: 100 ------KELRELARWVDNL-------------------------MATLRRLVNLLERGRV 128
                 KE+R LAR++ N+                         + T  R+++ L +G +
Sbjct: 84  LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTL 143

Query: 129 SLQMIIRYLALKEAADQTLDM 149
            L   +  L L E AD+ LDM
Sbjct: 144 DLDA-LNTLVLDE-ADRMLDM 162

Length = 460

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 36/137 (26%), Positives = 59/137 (43%), Gaps = 41/137 (29%)

Query: 53  TPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSAR-------KEL--- 102
           TP+Q  A   +++G+D++  A TGS KT  F  PI+  ++ +    +       +EL   
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 103 -------------------------RELARWVDN-----LMATLRRLVNLLERGRVSLQM 132
                                    +E AR +       L+ T  RL++LL RG++ L  
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120

Query: 133 IIRYLALKEAADQTLDM 149
            ++ L L E A + LDM
Sbjct: 121 NLKLLVLDE-AHRLLDM 136

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|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 45/167 (26%), Positives = 66/167 (39%), Gaps = 48/167 (28%)

Query: 29  PAARFAYV--PQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFP 86
           P   F Y   P ++    +   + +PTP+Q     I ++GRD++  A+TGS KT  F  P
Sbjct: 128 PVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLP 187

Query: 87  IINGIM-------------------REY----------YSARKELR-------------- 103
            I  I                    RE           + A  ++R              
Sbjct: 188 AIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQI 247

Query: 104 -ELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM 149
             L R V+ L+A   RL++ LE    +L   + YL L E AD+ LDM
Sbjct: 248 YALRRGVEILIACPGRLIDFLESNVTNL-RRVTYLVLDE-ADRMLDM 292

Length = 545

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

 Score = 47.9 bits (114), Expect = 4e-07
 Identities = 18/43 (41%), Positives = 27/43 (62%)

Query: 49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI 91
          Y KP+P+Q      L+ GRD++  AQTGS KT  F  P+++ +
Sbjct: 26 YEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNL 68

Length = 629

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

 Score = 47.1 bits (112), Expect = 7e-07
 Identities = 22/52 (42%), Positives = 26/52 (50%)

Query: 37  PQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPII 88
           P  L     T  Y  PTP+Q  A    ++GR L+  A TGS KT  F  PII
Sbjct: 129 PPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPII 180

Length = 518

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

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 25/104 (24%), Positives = 40/104 (38%), Gaps = 17/104 (16%)

Query: 47  YKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYY------SAR 99
           + +    P Q+ A   L++G RD++  A TGS KT     P +  + R            
Sbjct: 4   FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPT 63

Query: 100 KEL-----RELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLA 138
           +EL      EL +   +L      L  +   G  S +  +R L 
Sbjct: 64  RELAEQWAEELKKLGPSL-----GLKVVGLYGGDSKREQLRKLE 102

Length = 201

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

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 41/144 (28%), Positives = 59/144 (40%), Gaps = 49/144 (34%)

Query: 53  TPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM-----REYYSAR-------- 99
           TP+Q       +AG D +  AQTG+ KT  F   IIN ++     +E Y           
Sbjct: 111 TPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAP 170

Query: 100 ---------------------------------KELREL-ARWVDNLMATLRRLVNLLER 125
                                            K+L++L AR+ D L+AT  RL++  +R
Sbjct: 171 TRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQR 230

Query: 126 GRVSLQMIIRYLALKEAADQTLDM 149
           G V L M +  + L E AD+ LDM
Sbjct: 231 GEVHLDM-VEVMVLDE-ADRMLDM 252

Length = 475

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	155
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00110	545	helicase; Provisional	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.98
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.98
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.97
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.97
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.97
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.96
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.96
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.96
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.96
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.96
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.96
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.96
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.95
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.95
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.95
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	99.94
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.94
PTZ00424	401	helicase 45; Provisional	99.93
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.92
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.92
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.92
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.91
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.91
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.9
KOG0327	397	consensus Translation initiation factor 4F, helica	99.89
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.87
KOG4284	980	consensus DEAD box protein [Transcription]	99.87
PRK02362	737	ski2-like helicase; Provisional	99.86
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.86
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.86
PRK00254	720	ski2-like helicase; Provisional	99.85
PRK13767	876	ATP-dependent helicase; Provisional	99.85
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.84
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.84
PRK01172	674	ski2-like helicase; Provisional	99.81
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.79
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.79
PRK09401	1176	reverse gyrase; Reviewed	99.78
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.77
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.77
COG1205	851	Distinct helicase family with a unique C-terminal	99.77
PRK14701	1638	reverse gyrase; Provisional	99.77
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.76
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.75
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.72
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.63
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.62
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.61
PRK10689	1147	transcription-repair coupling factor; Provisional	99.56
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.55
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.53
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.52
COG1204	766	Superfamily II helicase [General function predicti	99.5
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.5
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.49
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.44
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.42
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.42
COG1202	830	Superfamily II helicase, archaea-specific [General	99.42
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.41
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.4
PHA02558	501	uvsW UvsW helicase; Provisional	99.34
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.32
PRK13766	773	Hef nuclease; Provisional	99.32
PHA02653	675	RNA helicase NPH-II; Provisional	99.28
PRK05580	679	primosome assembly protein PriA; Validated	99.27
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.26
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.25
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.24
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.23
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.2
KOG0354	746	consensus DEAD-box like helicase [General function	99.2
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.16
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.12
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.11
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.09
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.07
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.02
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	98.99
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.95
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.91
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.88
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.88
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.87
KOG0353	695	consensus ATP-dependent DNA helicase [General func	98.82
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.81
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.77
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.66
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.66
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	98.61
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.52
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.52
PRK09694	878	helicase Cas3; Provisional	98.5
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.49
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.43
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.42
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.41
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.34
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.34
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.3
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.27
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.26
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.24
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.16
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.13
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.13
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.1
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	98.07
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	98.06
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.06
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.01
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.01
KOG1803	649	consensus DNA helicase [Replication, recombination	97.88
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	97.86
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.85
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	97.82
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	97.81
PRK10536	262	hypothetical protein; Provisional	97.76
COG4889	1518	Predicted helicase [General function prediction on	97.65
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.65
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.63
COG4096	875	HsdR Type I site-specific restriction-modification	97.63
PRK08181	269	transposase; Validated	97.63
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.63
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.56
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	97.55
PRK06526	254	transposase; Provisional	97.53
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.48
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.48
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.42
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	97.36
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	97.36
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	97.32
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	97.31
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.29
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.23
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.2
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	97.12
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.1
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.08
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.08
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.03
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	96.98
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	96.97
PRK10875	615	recD exonuclease V subunit alpha; Provisional	96.94
PRK06835	329	DNA replication protein DnaC; Validated	96.9
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	96.89
PRK08727	233	hypothetical protein; Validated	96.88
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.85
KOG1805	1100	consensus DNA replication helicase [Replication, r	96.85
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.83
PRK04914	956	ATP-dependent helicase HepA; Validated	96.8
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	96.8
PHA00729	226	NTP-binding motif containing protein	96.79
PRK06893	229	DNA replication initiation factor; Validated	96.78
PRK07952	244	DNA replication protein DnaC; Validated	96.77
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.77
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.76
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	96.74
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.73
PRK12377	248	putative replication protein; Provisional	96.7
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	96.67
PRK08116	268	hypothetical protein; Validated	96.57
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	96.53
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.51
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.49
PRK08084	235	DNA replication initiation factor; Provisional	96.49
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.46
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.44
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	96.4
PRK05642	234	DNA replication initiation factor; Validated	96.38
PF13245	76	AAA_19: Part of AAA domain	96.34
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.28
PRK10436	462	hypothetical protein; Provisional	96.27
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	96.22
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	96.2
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	96.17
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.15
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.14
PRK06921	266	hypothetical protein; Provisional	96.11
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.09
PRK00411	394	cdc6 cell division control protein 6; Reviewed	96.08
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	96.05
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.04
PRK09183	259	transposase/IS protein; Provisional	96.03
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	95.99
PRK08769	319	DNA polymerase III subunit delta'; Validated	95.98
PRK08939	306	primosomal protein DnaI; Reviewed	95.93
TIGR02533	486	type_II_gspE general secretory pathway protein E.	95.88
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	95.84
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.83
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.82
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.75
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	95.74
PRK14087	450	dnaA chromosomal replication initiation protein; P	95.74
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.73
CHL00181	287	cbbX CbbX; Provisional	95.73
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.73
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.69
KOG1131	755	consensus RNA polymerase II transcription initiati	95.68
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	95.64
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.63
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.61
PRK14088	440	dnaA chromosomal replication initiation protein; P	95.56
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	95.55
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	95.54
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	95.48
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	95.44
PRK04296	190	thymidine kinase; Provisional	95.44
COG0610	962	Type I site-specific restriction-modification syst	95.43
PRK00149	450	dnaA chromosomal replication initiation protein; R	95.41
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	95.41
PHA02244	383	ATPase-like protein	95.38
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.37
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.34
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	95.34
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.32
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.3
PRK12422	445	chromosomal replication initiation protein; Provis	95.26
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	95.22
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.21
PRK12402	337	replication factor C small subunit 2; Reviewed	95.2
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.18
PLN03025	319	replication factor C subunit; Provisional	95.15
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	95.09
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	95.07
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.07
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	95.02
KOG2340	698	consensus Uncharacterized conserved protein [Funct	95.0
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	94.98
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	94.98
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	94.97
KOG3089	271	consensus Predicted DEAD-box-containing helicase [	94.9
PRK04195	482	replication factor C large subunit; Provisional	94.79
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	94.78
PRK13851	344	type IV secretion system protein VirB11; Provision	94.78
PF13479	213	AAA_24: AAA domain	94.73
PRK11054	684	helD DNA helicase IV; Provisional	94.66
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.6
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.59
PRK06964	342	DNA polymerase III subunit delta'; Validated	94.48
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	94.46
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	94.46
PRK14086	617	dnaA chromosomal replication initiation protein; P	94.42
PRK07940	394	DNA polymerase III subunit delta'; Validated	94.4
smart00382	148	AAA ATPases associated with a variety of cellular	94.35
PRK06090	319	DNA polymerase III subunit delta'; Validated	94.27
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.25
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	94.23
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	94.2
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	94.19
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	94.17
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	94.16
KOG1123	776	consensus RNA polymerase II transcription initiati	94.13
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.1
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	94.08
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	94.06
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	94.06
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.04
PRK07993	334	DNA polymerase III subunit delta'; Validated	94.02
PRK08699	325	DNA polymerase III subunit delta'; Validated	94.01
PRK06871	325	DNA polymerase III subunit delta'; Validated	93.99
PRK13850	670	type IV secretion system protein VirD4; Provisiona	93.98
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	93.96
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	93.86
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	93.82
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	93.81
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	93.8
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	93.76
PHA02544	316	44 clamp loader, small subunit; Provisional	93.73
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	93.73
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	93.71
PRK13897	606	type IV secretion system component VirD4; Provisio	93.67
PRK03992	389	proteasome-activating nucleotidase; Provisional	93.66
PRK00440	319	rfc replication factor C small subunit; Reviewed	93.6
PRK14873	665	primosome assembly protein PriA; Provisional	93.49
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	93.42
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	93.4
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	93.32
PRK13880	636	conjugal transfer coupling protein TraG; Provision	93.26
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	93.22
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	93.17
PF14516	331	AAA_35: AAA-like domain	93.15
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	93.14
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	93.11
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	93.06
PRK13876	663	conjugal transfer coupling protein TraG; Provision	92.99
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	92.98
PRK13342	413	recombination factor protein RarA; Reviewed	92.91
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	92.87
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	92.87
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	92.85
PF12846	304	AAA_10: AAA-like domain	92.7
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	92.69
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	92.67
PRK15483	986	type III restriction-modification system StyLTI en	92.65
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	92.63
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	92.63
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	92.56
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	92.56
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	92.55
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	92.55
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	92.55
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	92.52
COG1674	858	FtsK DNA segregation ATPase FtsK/SpoIIIE and relat	92.49
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	92.41
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	92.41
PRK10865	857	protein disaggregation chaperone; Provisional	92.36
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	92.35
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	92.32
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	92.18
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	92.16
PRK09112	351	DNA polymerase III subunit delta'; Validated	92.1
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	92.07
TIGR02237	209	recomb_radB DNA repair and recombination protein R	92.01
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	91.98
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	91.97
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	91.96
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	91.77
COG0606	490	Predicted ATPase with chaperone activity [Posttran	91.74
CHL00195	489	ycf46 Ycf46; Provisional	91.72
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	91.7
CHL00095	821	clpC Clp protease ATP binding subunit	91.68
PF13555	62	AAA_29: P-loop containing region of AAA domain	91.68
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	91.64
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	91.62
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	91.61
TIGR00767	415	rho transcription termination factor Rho. Members	91.56
TIGR00064	272	ftsY signal recognition particle-docking protein F	91.53
PRK13341	725	recombination factor protein RarA/unknown domain f	91.5
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	91.49
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	91.46
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	91.4
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	91.4
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	91.31
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	91.29
TIGR00959	428	ffh signal recognition particle protein. This mode	91.29
PRK00771	437	signal recognition particle protein Srp54; Provisi	91.29
CHL00176	638	ftsH cell division protein; Validated	91.28
PRK13764	602	ATPase; Provisional	91.26
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	91.24
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	91.23
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	91.19
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	91.12
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	91.1
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	91.1
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	91.1
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	91.06
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	90.96
PF13337	457	Lon_2: Putative ATP-dependent Lon protease	90.95
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	90.91
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	90.9
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	90.88
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	90.88
PRK13531	498	regulatory ATPase RavA; Provisional	90.88
PRK13822	641	conjugal transfer coupling protein TraG; Provision	90.87
PHA01747	425	putative ATP-dependent protease	90.81
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	90.79
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	90.78
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	90.75
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	90.72
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	90.71
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	90.56
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	90.5
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	90.41
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	90.39
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	90.38
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	90.36
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	90.27
KOG2373	514	consensus Predicted mitochondrial DNA helicase twi	90.17
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	90.16
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	90.16
PF00004	132	AAA: ATPase family associated with various cellula	90.11
cd01394	218	radB RadB. The archaeal protein radB shares simila	90.07
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	90.03
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	90.02
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	89.97
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	89.92
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	89.92
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	89.9
PRK07399	314	DNA polymerase III subunit delta'; Validated	89.85
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	89.8
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	89.75
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	89.75
CHL00095	821	clpC Clp protease ATP binding subunit	89.74
PHA00012	361	I assembly protein	89.73
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	89.67
cd01368	345	KISc_KIF23_like Kinesin motor domain, KIF23-like s	89.61
PRK07471	365	DNA polymerase III subunit delta'; Validated	89.56
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	89.49
cd01370	338	KISc_KIP3_like Kinesin motor domain, KIP3-like sub	89.38
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	89.35
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	89.25
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	89.24
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	89.23
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	89.22
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	89.19
cd01367	322	KISc_KIF2_like Kinesin motor domain, KIF2-like gro	89.18
cd01365	356	KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like p	89.1
cd01373	337	KISc_KLP2_like Kinesin motor domain, KLP2-like sub	89.07
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	89.05
PF09439	181	SRPRB: Signal recognition particle receptor beta s	88.9
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	88.84
cd01369	325	KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy	88.68
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	88.65
PRK14530	215	adenylate kinase; Provisional	88.61
cd01376	319	KISc_KID_like Kinesin motor domain, KIF22/Kid-like	88.58
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	88.55
KOG0060	659	consensus Long-chain acyl-CoA transporter, ABC sup	88.45
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	88.43
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	88.32
PHA00350	399	putative assembly protein	88.21
PRK04328	249	hypothetical protein; Provisional	88.18
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	88.17
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	88.13
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	88.1
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	88.06
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	88.06
PF00225	335	Kinesin: Kinesin motor domain; InterPro: IPR001752	87.97
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	87.91
cd01375	334	KISc_KIF9_like Kinesin motor domain, KIF9-like sub	87.9
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	87.83
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	87.56
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	87.47
COG2256	436	MGS1 ATPase related to the helicase subunit of the	87.47
PRK09354	349	recA recombinase A; Provisional	87.46
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	87.4
cd01374	321	KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like	87.38
PRK05298	652	excinuclease ABC subunit B; Provisional	87.13
PRK08058	329	DNA polymerase III subunit delta'; Validated	87.09
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	86.96
KOG1533	290	consensus Predicted GTPase [General function predi	86.95
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	86.83
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	86.8
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	86.79
cd01372	341	KISc_KIF4 Kinesin motor domain, KIF4-like subfamil	86.78
COG0714	329	MoxR-like ATPases [General function prediction onl	86.71
PLN02165	334	adenylate isopentenyltransferase	86.61
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	86.59
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	86.55
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	86.51
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	86.48
PRK00131	175	aroK shikimate kinase; Reviewed	86.42
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	86.38
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	86.36
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	86.33
COG0593	408	DnaA ATPase involved in DNA replication initiation	86.33
PRK00300	205	gmk guanylate kinase; Provisional	86.27
PRK11823	446	DNA repair protein RadA; Provisional	86.26
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	86.25
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	86.21
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	86.18
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	86.16
PRK14974	336	cell division protein FtsY; Provisional	86.05
KOG1969	877	consensus DNA replication checkpoint protein CHL12	86.01
PRK05973	237	replicative DNA helicase; Provisional	85.97
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	85.96
cd01364	352	KISc_BimC_Eg5 Kinesin motor domain, BimC/Eg5 spind	85.95
PRK07261	171	topology modulation protein; Provisional	85.9
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	85.9
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	85.77
cd00106	328	KISc Kinesin motor domain. This catalytic (head) d	85.77
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	85.66
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	85.66
cd01371	333	KISc_KIF3 Kinesin motor domain, kinesins II or KIF	85.49
PRK08118	167	topology modulation protein; Reviewed	85.47
PF05729	166	NACHT: NACHT domain	85.46
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	85.38
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	85.37
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	85.31
smart00129	335	KISc Kinesin motor, catalytic domain. ATPase. Micr	85.28
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	85.27
PLN03130	1622	ABC transporter C family member; Provisional	85.15
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	85.14
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	85.12
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	85.05
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	85.02
PF00005	137	ABC_tran: ABC transporter This structure is on hol	84.99
TIGR00957	1522	MRP_assoc_pro multi drug resistance-associated pro	84.94
TIGR02653	675	Lon_rel_chp conserved hypothetical protein. This m	84.65
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	84.6
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	84.56
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	84.5
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	84.43
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	84.43
cd01366	329	KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/	84.4
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	84.28
TIGR00958	711	3a01208 Conjugate Transporter-2 (CT2) Family prote	84.19
PRK06620	214	hypothetical protein; Validated	84.1
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	84.06

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

Probab=100.00  E-value=8.2e-36  Score=245.52  Aligned_cols=148  Identities=38%  Similarity=0.547  Sum_probs=138.1

Q ss_pred             cccCccccccCCcCcccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654            5 WAADSVFASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..+||.+++++.+.+.|.+.|.++.+|.+..  +.+..+++..||..|||+|+.+||.+..|+|+++||+||||||.|
T Consensus        48 ~~~~~nfd~~~~i~v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~a  127 (482)
T KOG0335|consen   48 ISTGINFDKYNDIPVKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAA  127 (482)
T ss_pred             cchhhccCCccceeeeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHH
Confidence            567889999999999999999999999999765  888899999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHHHHhhhch-------------------------------------------------HHHHHHHhcCCcEEE
Q 031654           83 FCFPIINGIMREYYSA-------------------------------------------------RKELRELARWVDNLM  113 (155)
Q Consensus        83 yllp~l~~l~~~~~~~-------------------------------------------------~~~~~~l~~~~~IlI  113 (155)
                      ||+|+++++.......                                                 ..|.+.+.++|||+|
T Consensus       128 FLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlv  207 (482)
T KOG0335|consen  128 FLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILV  207 (482)
T ss_pred             HHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEE
Confidence            9999999998764422                                                 578888889999999


Q ss_pred             EChHHHHHHHHcCCCCcccccceEEEEcccccccc-cccccC
Q 031654          114 ATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD-MALNQK  154 (155)
Q Consensus       114 ~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~-~gf~~~  154 (155)
                      +|||||.++++++.+.++++ +||||||| |+|+| |||++|
T Consensus       208 aTpGrL~d~~e~g~i~l~~~-k~~vLDEA-DrMlD~mgF~p~  247 (482)
T KOG0335|consen  208 ATPGRLKDLIERGKISLDNC-KFLVLDEA-DRMLDEMGFEPQ  247 (482)
T ss_pred             ecCchhhhhhhcceeehhhC-cEEEecch-HHhhhhcccccc
Confidence            99999999999999999999 99999999 99999 999986

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

Probab=100.00  E-value=1.8e-34  Score=240.41  Aligned_cols=120  Identities=38%  Similarity=0.569  Sum_probs=108.9

Q ss_pred             cccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHh-hhch-----------
Q 031654           33 FAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE-YYSA-----------   98 (155)
Q Consensus        33 f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~-~~~~-----------   98 (155)
                      |++++  +++..+|+..||+.|||||+++||.++.|+|+++.|.||||||++|++|++.++... ....           
T Consensus        93 f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~  172 (519)
T KOG0331|consen   93 FQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLA  172 (519)
T ss_pred             hhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEc
Confidence            44444  567778889999999999999999999999999999999999999999999999863 1111           


Q ss_pred             ---------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654           99 ---------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 ---------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                                                       ..|.+.+.++++|+|+|||||.++++.+.+++++| +|+||||| |+
T Consensus       173 PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v-~ylVLDEA-Dr  250 (519)
T KOG0331|consen  173 PTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRV-TYLVLDEA-DR  250 (519)
T ss_pred             CcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccce-eEEEeccH-Hh
Confidence                                             78999999999999999999999999999999999 99999999 99


Q ss_pred             ccccccccC
Q 031654          146 TLDMALNQK  154 (155)
Q Consensus       146 ll~~gf~~~  154 (155)
                      ||||||++|
T Consensus       251 MldmGFe~q  259 (519)
T KOG0331|consen  251 MLDMGFEPQ  259 (519)
T ss_pred             hhccccHHH
Confidence            999999986

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

Probab=100.00  E-value=1.8e-34  Score=231.02  Aligned_cols=124  Identities=31%  Similarity=0.450  Sum_probs=114.6

Q ss_pred             CCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------
Q 031654           28 SPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------   98 (155)
Q Consensus        28 ~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------   98 (155)
                      +...+|.+|+  |++++++++.||..||+||+++||.++.|+||++.|+||||||.+|++|+++++..+....       
T Consensus        58 e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtP  137 (476)
T KOG0330|consen   58 ESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTP  137 (476)
T ss_pred             hhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecC
Confidence            4456899998  9999999999999999999999999999999999999999999999999999998765443       


Q ss_pred             --------------------------------HHHHHHHhcCCcEEEEChHHHHHHHH-cCCCCcccccceEEEEccccc
Q 031654           99 --------------------------------RKELRELARWVDNLMATLRRLVNLLE-RGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 --------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~-~~~~~l~~l~~~lVlDEa~D~  145 (155)
                                                      ..|...+.+.|||+|+|||||.+++. .+.+++..+ +|||+||| |+
T Consensus       138 tRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~l-k~LVlDEA-Dr  215 (476)
T KOG0330|consen  138 TRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQL-KFLVLDEA-DR  215 (476)
T ss_pred             cHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHh-HHHhhchH-Hh
Confidence                                            67778888899999999999999999 578999999 99999999 99


Q ss_pred             cccccccc
Q 031654          146 TLDMALNQ  153 (155)
Q Consensus       146 ll~~gf~~  153 (155)
                      +||+.|++
T Consensus       216 lLd~dF~~  223 (476)
T KOG0330|consen  216 LLDMDFEE  223 (476)
T ss_pred             hhhhhhHH
Confidence            99999975

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=4.5e-33  Score=237.15  Aligned_cols=132  Identities=31%  Similarity=0.508  Sum_probs=118.3

Q ss_pred             cCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc-
Q 031654           21 SSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-   97 (155)
Q Consensus        21 ~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~-   97 (155)
                      +.|.++|.|+.+|++++  +.++++|+++||++|||+|.++||.+++|+|++++||||||||++|++|++.++...... 
T Consensus       120 ~~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~  199 (545)
T PTZ00110        120 IAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLR  199 (545)
T ss_pred             ecCCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhccccc
Confidence            46888999999999876  999999999999999999999999999999999999999999999999999887653210 


Q ss_pred             ------h-------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCccccc
Q 031654           98 ------A-------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMII  134 (155)
Q Consensus        98 ------~-------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~  134 (155)
                            .                                     ..+...+.++++|+|+||++|.+++.++..+++++ 
T Consensus       200 ~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v-  278 (545)
T PTZ00110        200 YGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRV-  278 (545)
T ss_pred             CCCCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhC-
Confidence                  0                                     45566677889999999999999999999999999 


Q ss_pred             ceEEEEcccccccccccccC
Q 031654          135 RYLALKEAADQTLDMALNQK  154 (155)
Q Consensus       135 ~~lVlDEa~D~ll~~gf~~~  154 (155)
                      ++|||||| |+|+++||+++
T Consensus       279 ~~lViDEA-d~mld~gf~~~  297 (545)
T PTZ00110        279 TYLVLDEA-DRMLDMGFEPQ  297 (545)
T ss_pred             cEEEeehH-HhhhhcchHHH
Confidence            99999999 99999999753

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

Probab=100.00  E-value=6.4e-33  Score=234.67  Aligned_cols=122  Identities=37%  Similarity=0.596  Sum_probs=111.9

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH--hhhc--h------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR--EYYS--A------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~--~~~~--~------   98 (155)
                      .+|++++  ++++++|.++||..|||||.++||.++.|+|++++|+||||||+||++|+++++..  ....  .      
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PT  108 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCC
Confidence            6799987  99999999999999999999999999999999999999999999999999999873  2211  1      


Q ss_pred             --------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 --------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 --------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                      ..|...+..++||||||||||++++.++.++++.+ +++|+||| |+|
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v-~~lVlDEA-Drm  186 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGV-ETLVLDEA-DRM  186 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhc-CEEEeccH-hhh
Confidence                                            56678888889999999999999999999999999 99999999 999


Q ss_pred             cccccccC
Q 031654          147 LDMALNQK  154 (155)
Q Consensus       147 l~~gf~~~  154 (155)
                      |||||.++
T Consensus       187 Ld~Gf~~~  194 (513)
T COG0513         187 LDMGFIDD  194 (513)
T ss_pred             hcCCCHHH
Confidence            99999875

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

Probab=99.98  E-value=1.8e-32  Score=232.31  Aligned_cols=136  Identities=26%  Similarity=0.378  Sum_probs=120.6

Q ss_pred             CcCcccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           16 AAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        16 ~~~~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      ...+.+.|...|.|+.+|++++  +.++++|+++||+.|||+|.++||.++.|+|++++||||||||++|++|++.++..
T Consensus       106 ~~~i~~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~  185 (518)
T PLN00206        106 KLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCT  185 (518)
T ss_pred             HCCCEecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHh
Confidence            4456778999999999999976  99999999999999999999999999999999999999999999999999988754


Q ss_pred             hh-------hch---------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCC
Q 031654           94 EY-------YSA---------------------------------------RKELRELARWVDNLMATLRRLVNLLERGR  127 (155)
Q Consensus        94 ~~-------~~~---------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~  127 (155)
                      ..       ...                                       ..+...+..+++|+|+||++|.+++.++.
T Consensus       186 ~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~  265 (518)
T PLN00206        186 IRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHD  265 (518)
T ss_pred             hccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCC
Confidence            21       000                                       34555666789999999999999999999


Q ss_pred             CCcccccceEEEEccccccccccccc
Q 031654          128 VSLQMIIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       128 ~~l~~l~~~lVlDEa~D~ll~~gf~~  153 (155)
                      +.++++ ++||+||| |+|+++||++
T Consensus       266 ~~l~~v-~~lViDEa-d~ml~~gf~~  289 (518)
T PLN00206        266 IELDNV-SVLVLDEV-DCMLERGFRD  289 (518)
T ss_pred             ccchhe-eEEEeecH-HHHhhcchHH
Confidence            999999 99999999 9999999975

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

Probab=99.98  E-value=2.1e-33  Score=226.67  Aligned_cols=129  Identities=32%  Similarity=0.460  Sum_probs=118.9

Q ss_pred             CCCCCCCcccccCC---HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--
Q 031654           24 NTLSSPAARFAYVP---QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--   98 (155)
Q Consensus        24 ~~~p~~~~~f~~l~---~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--   98 (155)
                      ..+|+|..+|++..   +++++.+++.||.+|||||++|||.+++|.|++++|+||+|||++||+|-+-++..+....  
T Consensus       212 rpIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~q  291 (629)
T KOG0336|consen  212 RPIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQ  291 (629)
T ss_pred             ccCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhc
Confidence            34789999999965   9999999999999999999999999999999999999999999999999887776543322  


Q ss_pred             ------------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccce
Q 031654           99 ------------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRY  136 (155)
Q Consensus        99 ------------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~  136 (155)
                                                                ..|+..++++.+|+|+||+||.++...+.+++..+ .|
T Consensus       292 r~~p~~lvl~ptreLalqie~e~~kysyng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~si-TY  370 (629)
T KOG0336|consen  292 RNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASI-TY  370 (629)
T ss_pred             cCCCceEEEeccHHHHHHHHhHHhHhhhcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeee-EE
Confidence                                                      78999999999999999999999999999999999 99


Q ss_pred             EEEEcccccccccccccC
Q 031654          137 LALKEAADQTLDMALNQK  154 (155)
Q Consensus       137 lVlDEa~D~ll~~gf~~~  154 (155)
                      |||||| |+||||||++|
T Consensus       371 lVlDEA-DrMLDMgFEpq  387 (629)
T KOG0336|consen  371 LVLDEA-DRMLDMGFEPQ  387 (629)
T ss_pred             EEecch-hhhhcccccHH
Confidence            999999 99999999986

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

Probab=99.97  E-value=3.2e-32  Score=224.58  Aligned_cols=139  Identities=27%  Similarity=0.347  Sum_probs=128.7

Q ss_pred             cCCcCcccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           14 ENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        14 ~~~~~~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      .+++++...|..+|.|+.+|++.+  .++++.+.+.||..|||||..+||..++.+|++.+|.||||||+||++|++..+
T Consensus       228 redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~I  307 (673)
T KOG0333|consen  228 REDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWI  307 (673)
T ss_pred             ecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHH
Confidence            567788899999999999999976  999999999999999999999999999999999999999999999999999988


Q ss_pred             HHhhhch------------------------------------------------HHHHHHHhcCCcEEEEChHHHHHHH
Q 031654           92 MREYYSA------------------------------------------------RKELRELARWVDNLMATLRRLVNLL  123 (155)
Q Consensus        92 ~~~~~~~------------------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l  123 (155)
                      .+..+..                                                .+|--.++.+|+|+|+||+||.+.+
T Consensus       308 sslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~L  387 (673)
T KOG0333|consen  308 SSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSL  387 (673)
T ss_pred             HcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHH
Confidence            7665322                                                5666688899999999999999999


Q ss_pred             HcCCCCcccccceEEEEcccccccccccccC
Q 031654          124 ERGRVSLQMIIRYLALKEAADQTLDMALNQK  154 (155)
Q Consensus       124 ~~~~~~l~~l~~~lVlDEa~D~ll~~gf~~~  154 (155)
                      .+..+-+++| .|||+||| |+|+||||++|
T Consensus       388 enr~lvl~qc-tyvvldea-drmiDmgfE~d  416 (673)
T KOG0333|consen  388 ENRYLVLNQC-TYVVLDEA-DRMIDMGFEPD  416 (673)
T ss_pred             HHHHHHhccC-ceEeccch-hhhhcccccHH
Confidence            9999999999 99999999 99999999986

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

Probab=99.97  E-value=6.1e-32  Score=223.42  Aligned_cols=124  Identities=31%  Similarity=0.489  Sum_probs=112.6

Q ss_pred             CCcccccCC--HHHHHhHH-hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------
Q 031654           29 PAARFAYVP--QHLRNKPR-TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------   98 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~-~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------   98 (155)
                      .-..|..|+  +.+...|+ .|++..||.+|+++||.+++|+|++|.|+||||||+||++|+++.|.......       
T Consensus       134 ts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~  213 (708)
T KOG0348|consen  134 TSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPY  213 (708)
T ss_pred             ccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCce
Confidence            345789988  99999986 56999999999999999999999999999999999999999999998765544       


Q ss_pred             ---------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC-CCCcccccceEE
Q 031654           99 ---------------------------------------RKELRELARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLA  138 (155)
Q Consensus        99 ---------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lV  138 (155)
                                                             +.+...++.|++|||+|||||+|++.+. .+.++++ +|||
T Consensus       214 ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~L-RwlV  292 (708)
T KOG0348|consen  214 ALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRL-RWLV  292 (708)
T ss_pred             EEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeee-eEEE
Confidence                                                   6777889999999999999999999985 6899999 9999


Q ss_pred             EEcccccccccccccC
Q 031654          139 LKEAADQTLDMALNQK  154 (155)
Q Consensus       139 lDEa~D~ll~~gf~~~  154 (155)
                      +||| |+|+|+||+++
T Consensus       293 lDEa-DrlleLGfekd  307 (708)
T KOG0348|consen  293 LDEA-DRLLELGFEKD  307 (708)
T ss_pred             ecch-hHHHhccchhh
Confidence            9999 99999999975

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

Probab=99.97  E-value=2.5e-32  Score=224.76  Aligned_cols=123  Identities=30%  Similarity=0.464  Sum_probs=114.3

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      ..+|.+++  ..+++++..+||..|||||..+||..+-|+|+++||-||||||.||++|+|+++...+...         
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~  259 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLV  259 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEe
Confidence            45899988  8899999999999999999999999999999999999999999999999999998665544         


Q ss_pred             ---------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEEcccc
Q 031654           99 ---------------------------------RKELRELARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        99 ---------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlDEa~D  144 (155)
                                                       +.|...|+.+|||||+|||||.+++++. .++++++ ..||+||| |
T Consensus       260 PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsi-EVLvlDEA-D  337 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSI-EVLVLDEA-D  337 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccce-eEEEechH-H
Confidence                                             7888899999999999999999999885 7999999 99999999 9


Q ss_pred             cccccccccC
Q 031654          145 QTLDMALNQK  154 (155)
Q Consensus       145 ~ll~~gf~~~  154 (155)
                      +||+.||.+|
T Consensus       338 RMLeegFade  347 (691)
T KOG0338|consen  338 RMLEEGFADE  347 (691)
T ss_pred             HHHHHHHHHH
Confidence            9999999875

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

Probab=99.97  E-value=2.7e-31  Score=216.77  Aligned_cols=121  Identities=28%  Similarity=0.420  Sum_probs=104.0

Q ss_pred             ccccCC----HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           32 RFAYVP----QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        32 ~f~~l~----~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      +|++++    +++++++.++||+..||+|..+||.+++++||++.|+||||||+||++|+++.+.......         
T Consensus         5 ~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalI   84 (567)
T KOG0345|consen    5 SFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALI   84 (567)
T ss_pred             chhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEE
Confidence            566665    9999999999999999999999999999999999999999999999999999995443222         


Q ss_pred             ------------------------------------HHHHH-HHhcCCcEEEEChHHHHHHHHcC--CCCcccccceEEE
Q 031654           99 ------------------------------------RKELR-ELARWVDNLMATLRRLVNLLERG--RVSLQMIIRYLAL  139 (155)
Q Consensus        99 ------------------------------------~~~~~-~l~~~~~IlI~TP~~l~~~l~~~--~~~l~~l~~~lVl  139 (155)
                                                          .+.+. -..++|+|+|||||||.+++.+.  .+++..+ ++||+
T Consensus        85 IsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsL-e~LVL  163 (567)
T KOG0345|consen   85 ISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSL-EILVL  163 (567)
T ss_pred             ecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhcccccc-ceEEe
Confidence                                                23333 33458999999999999999985  4667799 99999


Q ss_pred             EcccccccccccccC
Q 031654          140 KEAADQTLDMALNQK  154 (155)
Q Consensus       140 DEa~D~ll~~gf~~~  154 (155)
                      ||| |+|+||||+.+
T Consensus       164 DEA-DrLldmgFe~~  177 (567)
T KOG0345|consen  164 DEA-DRLLDMGFEAS  177 (567)
T ss_pred             cch-HhHhcccHHHH
Confidence            999 99999999853

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

Probab=99.97  E-value=5.2e-32  Score=217.53  Aligned_cols=139  Identities=29%  Similarity=0.442  Sum_probs=127.3

Q ss_pred             cCCcCcccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           14 ENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        14 ~~~~~~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      ++...+.+.|+.+|.|+.+|.++.  ..+++.|++.|+.+|||||.+.+|.+++|+|.+..|-||||||+.|.+|++-..
T Consensus       153 Rk~~~I~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~  232 (610)
T KOG0341|consen  153 RKQLHILVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFA  232 (610)
T ss_pred             HHhheEEeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHH
Confidence            455677899999999999999965  999999999999999999999999999999999999999999999999988776


Q ss_pred             HHhhhch-----------------------------------------------------HHHHHHHhcCCcEEEEChHH
Q 031654           92 MREYYSA-----------------------------------------------------RKELRELARWVDNLMATLRR  118 (155)
Q Consensus        92 ~~~~~~~-----------------------------------------------------~~~~~~l~~~~~IlI~TP~~  118 (155)
                      ......-                                                     .+|...++.+.||+|+||||
T Consensus       233 LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGR  312 (610)
T KOG0341|consen  233 LEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGR  312 (610)
T ss_pred             HHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcch
Confidence            6543221                                                     78888889999999999999


Q ss_pred             HHHHHHcCCCCcccccceEEEEcccccccccccccC
Q 031654          119 LVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQK  154 (155)
Q Consensus       119 l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~~~  154 (155)
                      |.+++..+.+++.-| +||++||| |+|+||||++|
T Consensus       313 L~DmL~KK~~sLd~C-RyL~lDEA-DRmiDmGFEdd  346 (610)
T KOG0341|consen  313 LMDMLAKKIMSLDAC-RYLTLDEA-DRMIDMGFEDD  346 (610)
T ss_pred             HHHHHHHhhccHHHH-HHhhhhhH-HHHhhccchhh
Confidence            999999999999999 99999999 99999999986

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=1.6e-30  Score=215.35  Aligned_cols=121  Identities=27%  Similarity=0.396  Sum_probs=107.6

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc---------h-
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS---------A-   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~---------~-   98 (155)
                      .+|++++  ++++++|.++||..|||+|++|||.+++|+|++++||||||||++|++|+++.+......         . 
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~l   87 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRAL   87 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            5798887  999999999999999999999999999999999999999999999999999988653220         1 


Q ss_pred             ------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcc
Q 031654           99 ------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus        99 ------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa  142 (155)
                                                          ..+...+..++||+|+||++|.+++.++.++++++ ++||+|||
T Consensus        88 il~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v-~~lViDEa  166 (423)
T PRK04837         88 IMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAI-QVVVLDEA  166 (423)
T ss_pred             EECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccc-cEEEEecH
Confidence                                                33444556679999999999999999999999999 99999999


Q ss_pred             ccccccccccc
Q 031654          143 ADQTLDMALNQ  153 (155)
Q Consensus       143 ~D~ll~~gf~~  153 (155)
                       |+|+++||..
T Consensus       167 -d~l~~~~f~~  176 (423)
T PRK04837        167 -DRMFDLGFIK  176 (423)
T ss_pred             -HHHhhcccHH
Confidence             9999999864

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.96  E-value=4.1e-30  Score=208.71  Aligned_cols=122  Identities=25%  Similarity=0.373  Sum_probs=110.1

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      .+|++++  +++++++.++||++||.||+.|||.++.|+|+++.|.||||||+||++|+++.+.......          
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~i   98 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVI   98 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEE
Confidence            5899988  9999999999999999999999999999999999999999999999999999998766542          


Q ss_pred             -------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCC-CCcccccceEEEE
Q 031654           99 -------------------------------------RKELRELARWVDNLMATLRRLVNLLERGR-VSLQMIIRYLALK  140 (155)
Q Consensus        99 -------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~-~~l~~l~~~lVlD  140 (155)
                                                           ......|...|||+|+||++++.++..+. ..+..+ ++||+|
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l-~~LVvD  177 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSL-SFLVVD  177 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhhe-eeEEec
Confidence                                                 22224455679999999999999999987 788999 999999


Q ss_pred             cccccccccccccC
Q 031654          141 EAADQTLDMALNQK  154 (155)
Q Consensus       141 Ea~D~ll~~gf~~~  154 (155)
                      || |-||..||+++
T Consensus       178 EA-DLllsfGYeed  190 (569)
T KOG0346|consen  178 EA-DLLLSFGYEED  190 (569)
T ss_pred             hh-hhhhhcccHHH
Confidence            99 99999999975

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.96  E-value=6.5e-30  Score=223.40  Aligned_cols=134  Identities=27%  Similarity=0.471  Sum_probs=123.0

Q ss_pred             cccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh
Q 031654           19 ASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY   96 (155)
Q Consensus        19 ~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~   96 (155)
                      +.+.|..+|.|+.+|.+.+  +.++..++++||.+|||||.+|||+++.|+|||++|.||||||++|++|++.++..+..
T Consensus       353 i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~  432 (997)
T KOG0334|consen  353 IKVKGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRP  432 (997)
T ss_pred             eeeccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCC
Confidence            7889999999999999998  99999999999999999999999999999999999999999999999999988775544


Q ss_pred             ch--------------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCC---CC
Q 031654           97 SA--------------------------------------------RKELRELARWVDNLMATLRRLVNLLERGR---VS  129 (155)
Q Consensus        97 ~~--------------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~---~~  129 (155)
                      ..                                            .+|+..+++++.|+||||||+++++..+.   .+
T Consensus       433 ~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtn  512 (997)
T KOG0334|consen  433 LEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTN  512 (997)
T ss_pred             hhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCcccc
Confidence            33                                            78999999999999999999999987654   45


Q ss_pred             cccccceEEEEcccccccccccccC
Q 031654          130 LQMIIRYLALKEAADQTLDMALNQK  154 (155)
Q Consensus       130 l~~l~~~lVlDEa~D~ll~~gf~~~  154 (155)
                      +.++ .|||+||| |+|+|+||++|
T Consensus       513 lrR~-t~lv~dea-DrmfdmgfePq  535 (997)
T KOG0334|consen  513 LRRV-TYLVLDEA-DRMFDMGFEPQ  535 (997)
T ss_pred             cccc-ceeeechh-hhhheeccCcc
Confidence            6777 79999999 99999999987

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

Probab=99.96  E-value=3.2e-30  Score=212.42  Aligned_cols=141  Identities=29%  Similarity=0.435  Sum_probs=130.7

Q ss_pred             cccCCcCcccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHH
Q 031654           12 ASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        12 ~~~~~~~~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      +.+..+++.+.|.++|.|+.+|+.++  +.|+.++++..|+.|||+|.+++|..+.|+||+..|.||||||.||+.|++.
T Consensus       204 ~~r~~Lnlrv~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~  283 (731)
T KOG0339|consen  204 DLRLTLNLRVSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIV  283 (731)
T ss_pred             hhHhhhcceeccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHH
Confidence            33556678899999999999999997  9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhch--------------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHc
Q 031654           90 GIMREYYSA--------------------------------------------RKELRELARWVDNLMATLRRLVNLLER  125 (155)
Q Consensus        90 ~l~~~~~~~--------------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~  125 (155)
                      +++.+....                                            .+|...|..+|+||||||+||+++++.
T Consensus       284 himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~Vkm  363 (731)
T KOG0339|consen  284 HIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKM  363 (731)
T ss_pred             HhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHh
Confidence            998654432                                            788999999999999999999999999


Q ss_pred             CCCCcccccceEEEEcccccccccccccC
Q 031654          126 GRVSLQMIIRYLALKEAADQTLDMALNQK  154 (155)
Q Consensus       126 ~~~~l~~l~~~lVlDEa~D~ll~~gf~~~  154 (155)
                      +..++.++ .||||||| |+|+++||++|
T Consensus       364 Katn~~rv-S~LV~DEa-drmfdmGfe~q  390 (731)
T KOG0339|consen  364 KATNLSRV-SYLVLDEA-DRMFDMGFEPQ  390 (731)
T ss_pred             hcccceee-eEEEEech-hhhhccccHHH
Confidence            99999999 99999999 99999999976

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.96  E-value=3e-29  Score=209.66  Aligned_cols=121  Identities=26%  Similarity=0.465  Sum_probs=107.6

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      .+|++++  +.++++|.++||+.|||+|++|||.+++|+|++++||||||||++|++|+++++.......          
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~Ptre   83 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRE   83 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHH
Confidence            4788877  9999999999999999999999999999999999999999999999999999886433111          


Q ss_pred             ------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 ------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 ------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                                    ..+...+..+++|+|+||+++.+++.++.+.++++ ++||+||| |+|++
T Consensus        84 La~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l-~~lViDEa-d~~l~  161 (460)
T PRK11776         84 LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDAL-NTLVLDEA-DRMLD  161 (460)
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHC-CEEEEECH-HHHhC
Confidence                                          34445566789999999999999999999999999 99999999 99999


Q ss_pred             ccccc
Q 031654          149 MALNQ  153 (155)
Q Consensus       149 ~gf~~  153 (155)
                      +||..
T Consensus       162 ~g~~~  166 (460)
T PRK11776        162 MGFQD  166 (460)
T ss_pred             cCcHH
Confidence            99864

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.96  E-value=6.6e-30  Score=212.08  Aligned_cols=123  Identities=30%  Similarity=0.443  Sum_probs=108.2

Q ss_pred             CCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------
Q 031654           29 PAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------   98 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------   98 (155)
                      .+..|++||  ...+++|++.+|..||.||+.+||..+.|+||+..|.||||||+||++|++++|....-..        
T Consensus        67 ~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalI  146 (758)
T KOG0343|consen   67 TIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALI  146 (758)
T ss_pred             hhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEE
Confidence            356899999  8999999999999999999999999999999999999999999999999999998765443        


Q ss_pred             ----------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEEccc
Q 031654           99 ----------------------------------RKELRELARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALKEAA  143 (155)
Q Consensus        99 ----------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlDEa~  143 (155)
                                                        .......-++++|||||||||++++.++ .++.+++ .+||+||| 
T Consensus       147 ISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~l-QmLvLDEA-  224 (758)
T KOG0343|consen  147 ISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERISQMNILVCTPGRLLQHMDENPNFSTSNL-QMLVLDEA-  224 (758)
T ss_pred             ecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhhcCCeEEechHHHHHHhhhcCCCCCCcc-eEEEeccH-
Confidence                                              1111222246999999999999999986 6899999 99999999 


Q ss_pred             cccccccccc
Q 031654          144 DQTLDMALNQ  153 (155)
Q Consensus       144 D~ll~~gf~~  153 (155)
                      |+||||||..
T Consensus       225 DR~LDMGFk~  234 (758)
T KOG0343|consen  225 DRMLDMGFKK  234 (758)
T ss_pred             HHHHHHhHHH
Confidence            9999999975

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.96  E-value=4.6e-29  Score=208.58  Aligned_cols=119  Identities=34%  Similarity=0.512  Sum_probs=105.4

Q ss_pred             ccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc--------h---
Q 031654           32 RFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS--------A---   98 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~--------~---   98 (155)
                      +|++|+  ++++++|.++||..|||+|.++||.+++|+|++++||||||||++|++|+++.+......        .   
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            688876  999999999999999999999999999999999999999999999999999998653211        1   


Q ss_pred             ----------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccc
Q 031654           99 ----------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        99 ----------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D  144 (155)
                                                        ..+...+..+++|+|+||++|++++..+.+.++++ ++||+||| |
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v-~~lViDEa-h  159 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQV-EILVLDEA-D  159 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccc-eEEEeecH-H
Confidence                                              23444556689999999999999999998999999 99999999 9


Q ss_pred             cccccccc
Q 031654          145 QTLDMALN  152 (155)
Q Consensus       145 ~ll~~gf~  152 (155)
                      +|+++||.
T Consensus       160 ~ll~~~~~  167 (456)
T PRK10590        160 RMLDMGFI  167 (456)
T ss_pred             HHhccccH
Confidence            99999985

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

Probab=99.96  E-value=2e-29  Score=206.59  Aligned_cols=122  Identities=27%  Similarity=0.400  Sum_probs=108.0

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      ..|++++  +..+++++++||+.+|++|+.+||.++.|+|+++.|.||||||+||++|+++.+.......          
T Consensus        82 ~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~  161 (543)
T KOG0342|consen   82 FRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIIC  161 (543)
T ss_pred             hHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEec
Confidence            4566666  9999999999999999999999999999999999999999999999999999998765433          


Q ss_pred             ----------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEEccc
Q 031654           99 ----------------------------------RKELRELARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALKEAA  143 (155)
Q Consensus        99 ----------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlDEa~  143 (155)
                                                        ......+..+|+|+|+|||||++++.+. .+...++ +++|+||| 
T Consensus       162 PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~-k~lvlDEA-  239 (543)
T KOG0342|consen  162 PTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNL-KCLVLDEA-  239 (543)
T ss_pred             ccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhcc-ceeEeecc-
Confidence                                              4445566669999999999999999985 4677888 99999999 


Q ss_pred             ccccccccccC
Q 031654          144 DQTLDMALNQK  154 (155)
Q Consensus       144 D~ll~~gf~~~  154 (155)
                      |++||+||+++
T Consensus       240 DrlLd~GF~~d  250 (543)
T KOG0342|consen  240 DRLLDIGFEED  250 (543)
T ss_pred             hhhhhcccHHH
Confidence            99999999875

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.96  E-value=1.1e-28  Score=204.78  Aligned_cols=120  Identities=26%  Similarity=0.390  Sum_probs=105.6

Q ss_pred             ccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc------h-----
Q 031654           32 RFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS------A-----   98 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~------~-----   98 (155)
                      +|++|+  +.++++|.++||..||++|.++||.+++|+|++++||||||||++|++|+++++......      .     
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~P   81 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTP   81 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECC
Confidence            688877  999999999999999999999999999999999999999999999999999988642111      1     


Q ss_pred             --------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 --------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 --------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                      ..+...+..+++|+|+||++|.+++..+.+++.++ ++||+||| |+|
T Consensus        82 t~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v-~~lViDEa-h~~  159 (434)
T PRK11192         82 TRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAV-ETLILDEA-DRM  159 (434)
T ss_pred             cHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccC-CEEEEECH-HHH
Confidence                                            23334455678999999999999999999999999 99999999 999


Q ss_pred             ccccccc
Q 031654          147 LDMALNQ  153 (155)
Q Consensus       147 l~~gf~~  153 (155)
                      +++||.+
T Consensus       160 l~~~~~~  166 (434)
T PRK11192        160 LDMGFAQ  166 (434)
T ss_pred             hCCCcHH
Confidence            9999864

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

Probab=99.96  E-value=1.6e-29  Score=200.76  Aligned_cols=123  Identities=29%  Similarity=0.454  Sum_probs=111.4

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      ...|+.|+  +|+.+.|+.+|++.|||+|..|||.++.|+|++.+|.||||||.+|.+|+++++.......         
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTr   85 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTR   85 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchH
Confidence            46799999  9999999999999999999999999999999999999999999999999999998766544         


Q ss_pred             ------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC----CCCcccccceEEEEcccc
Q 031654           99 ------------------------------RKELRELARWVDNLMATLRRLVNLLERG----RVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        99 ------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~----~~~l~~l~~~lVlDEa~D  144 (155)
                                                    -.|...|..+||+||+||||+.+++..+    ...+.++ +|+|+||| |
T Consensus        86 ELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rl-kflVlDEA-D  163 (442)
T KOG0340|consen   86 ELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRL-KFLVLDEA-D  163 (442)
T ss_pred             HHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhce-eeEEecch-h
Confidence                                          4566777789999999999999999876    3568999 99999999 9


Q ss_pred             cccccccccC
Q 031654          145 QTLDMALNQK  154 (155)
Q Consensus       145 ~ll~~gf~~~  154 (155)
                      +|++.+|.++
T Consensus       164 rvL~~~f~d~  173 (442)
T KOG0340|consen  164 RVLAGCFPDI  173 (442)
T ss_pred             hhhccchhhH
Confidence            9999998753

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=1.9e-28  Score=209.80  Aligned_cols=121  Identities=26%  Similarity=0.362  Sum_probs=105.3

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh---------ch-
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY---------SA-   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~---------~~-   98 (155)
                      .+|++|+  +.++++|.++||+.|||+|+++||.++.|+|++++||||||||++|++|+++++.....         .. 
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raL   88 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            4688877  99999999999999999999999999999999999999999999999999998864321         11 


Q ss_pred             ------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEEc
Q 031654           99 ------------------------------------RKELRELARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALKE  141 (155)
Q Consensus        99 ------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlDE  141 (155)
                                                          ..+...+..+++|||+||++|++++.++ .+.+..+ ++|||||
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v-~~lViDE  167 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHAC-EICVLDE  167 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhhe-eeeEecC
Confidence                                                3344456667999999999999999875 5789999 9999999


Q ss_pred             cccccccccccc
Q 031654          142 AADQTLDMALNQ  153 (155)
Q Consensus       142 a~D~ll~~gf~~  153 (155)
                      | |+|+++||.+
T Consensus       168 A-h~lld~gf~~  178 (572)
T PRK04537        168 A-DRMFDLGFIK  178 (572)
T ss_pred             H-HHHhhcchHH
Confidence            9 9999999864

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.95  E-value=3.3e-28  Score=210.00  Aligned_cols=121  Identities=31%  Similarity=0.486  Sum_probs=107.2

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      .+|.+|+  +.++++|.++||+.|||+|+++||.++.|+|++++||||||||++|++|+++.+.......          
T Consensus         6 ~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTre   85 (629)
T PRK11634          6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRE   85 (629)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHH
Confidence            4688876  9999999999999999999999999999999999999999999999999999886542211          


Q ss_pred             ------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 ------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 ------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                                    ..+.+.+..+++|||+||+++.+++.++.++++++ ++|||||| |.|++
T Consensus        86 La~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l-~~lVlDEA-d~ml~  163 (629)
T PRK11634         86 LAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKL-SGLVLDEA-DEMLR  163 (629)
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhc-eEEEeccH-HHHhh
Confidence                                          33445556689999999999999999999999999 99999999 99999


Q ss_pred             ccccc
Q 031654          149 MALNQ  153 (155)
Q Consensus       149 ~gf~~  153 (155)
                      +||.+
T Consensus       164 ~gf~~  168 (629)
T PRK11634        164 MGFIE  168 (629)
T ss_pred             cccHH
Confidence            99864

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.95  E-value=3.1e-28  Score=202.03  Aligned_cols=123  Identities=24%  Similarity=0.375  Sum_probs=107.6

Q ss_pred             CCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----
Q 031654           27 SSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----   98 (155)
Q Consensus        27 p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----   98 (155)
                      +..+..|.+|+  .+++++|..+||.+||+||+.++|.+..| .||+..|.||||||+||-+|+++++.......     
T Consensus       177 ~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~  256 (731)
T KOG0347|consen  177 KVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSN  256 (731)
T ss_pred             ccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhh
Confidence            34455677766  99999999999999999999999999999 89999999999999999999999665433222     


Q ss_pred             -----------------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCC---
Q 031654           99 -----------------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRV---  128 (155)
Q Consensus        99 -----------------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~---  128 (155)
                                                                     ..|.+.++..|||||+|||||+.++..+..   
T Consensus       257 ~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~  336 (731)
T KOG0347|consen  257 TSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLG  336 (731)
T ss_pred             HHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhh
Confidence                                                           678888888999999999999999998754   


Q ss_pred             CcccccceEEEEccccccccccc
Q 031654          129 SLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       129 ~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      +++++ ++||+||| |+|++.|+
T Consensus       337 ~~k~v-kcLVlDEa-DRmvekgh  357 (731)
T KOG0347|consen  337 NFKKV-KCLVLDEA-DRMVEKGH  357 (731)
T ss_pred             hhhhc-eEEEEccH-HHHhhhcc
Confidence            68889 99999999 99999985

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

Probab=99.94  E-value=5.1e-28  Score=187.90  Aligned_cols=129  Identities=21%  Similarity=0.384  Sum_probs=115.7

Q ss_pred             CCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---
Q 031654           24 NTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---   98 (155)
Q Consensus        24 ~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---   98 (155)
                      ...-.++.+|++++  +++++.+.+.||++|+.||+.|||++++|+||+++|++|+|||.+|.+.+++.+.-.....   
T Consensus        20 s~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~l   99 (400)
T KOG0328|consen   20 SEKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQAL   99 (400)
T ss_pred             ccCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEE
Confidence            33445677999999  9999999999999999999999999999999999999999999999999988775443321   


Q ss_pred             ------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcc
Q 031654           99 ------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus        99 ------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa  142 (155)
                                                          .+.++.+..|+|++.|||||+.++++++.+....+ +++|+|||
T Consensus       100 ilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~v-kmlVLDEa  178 (400)
T KOG0328|consen  100 ILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAV-KMLVLDEA  178 (400)
T ss_pred             EecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccce-eEEEeccH
Confidence                                                56677777899999999999999999999999999 99999999


Q ss_pred             cccccccccccC
Q 031654          143 ADQTLDMALNQK  154 (155)
Q Consensus       143 ~D~ll~~gf~~~  154 (155)
                       |.||+.||.+|
T Consensus       179 -DemL~kgfk~Q  189 (400)
T KOG0328|consen  179 -DEMLNKGFKEQ  189 (400)
T ss_pred             -HHHHHhhHHHH
Confidence             99999999876

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=6.9e-27  Score=196.26  Aligned_cols=122  Identities=34%  Similarity=0.502  Sum_probs=105.3

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc---------h
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS---------A   98 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~---------~   98 (155)
                      ..+|.+++  +.++++|.++||..||++|+++|+.+++|+|++++||||||||++|++|+++.+......         .
T Consensus        86 ~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~a  165 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRA  165 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceE
Confidence            45677766  999999999999999999999999999999999999999999999999999998764310         1


Q ss_pred             -------------------------------------HHHHHHHh-cCCcEEEEChHHHHHHHHcCCCCcccccceEEEE
Q 031654           99 -------------------------------------RKELRELA-RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALK  140 (155)
Q Consensus        99 -------------------------------------~~~~~~l~-~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlD  140 (155)
                                                           ..+.+.+. ..++|+|+||++|++++.++...++++ ++||||
T Consensus       166 Lil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l-~~lViD  244 (475)
T PRK01297        166 LIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMV-EVMVLD  244 (475)
T ss_pred             EEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccC-ceEEec
Confidence                                                 23333443 468999999999999999888999999 999999


Q ss_pred             ccccccccccccc
Q 031654          141 EAADQTLDMALNQ  153 (155)
Q Consensus       141 Ea~D~ll~~gf~~  153 (155)
                      || |+++++||..
T Consensus       245 Ea-h~l~~~~~~~  256 (475)
T PRK01297        245 EA-DRMLDMGFIP  256 (475)
T ss_pred             hH-HHHHhcccHH
Confidence            99 9999998853

>PTZ00424 helicase 45; Provisional

Probab=99.93  E-value=6.8e-26  Score=185.76  Aligned_cols=122  Identities=20%  Similarity=0.376  Sum_probs=105.8

Q ss_pred             CCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------
Q 031654           29 PAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------   98 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------   98 (155)
                      ...+|++++  +.+.++|.++||..|+|+|.++|+.+++|+|++++||||||||++|++|++..+.......        
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt  105 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPT  105 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCC
Confidence            457899987  9999999999999999999999999999999999999999999999999998875322111        


Q ss_pred             -------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccc
Q 031654           99 -------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 -------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                                                     ..+...+..+++|+|+||+++.+++.++.+.++++ +++|+||| |+++
T Consensus       106 ~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i-~lvViDEa-h~~~  183 (401)
T PTZ00424        106 RELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDL-KLFILDEA-DEML  183 (401)
T ss_pred             HHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccc-cEEEEecH-HHHH
Confidence                                           23334455678999999999999999988899999 99999999 9999


Q ss_pred             ccccc
Q 031654          148 DMALN  152 (155)
Q Consensus       148 ~~gf~  152 (155)
                      +.||.
T Consensus       184 ~~~~~  188 (401)
T PTZ00424        184 SRGFK  188 (401)
T ss_pred             hcchH
Confidence            98875

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

Probab=99.92  E-value=1.9e-26  Score=186.57  Aligned_cols=123  Identities=25%  Similarity=0.436  Sum_probs=111.6

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      ..+|+.++  ..+++++.+.||..|||||+.+||.++.|+|++..|.||||||.||++|+++++.......         
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilspt   99 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPT   99 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCc
Confidence            46899988  9999999999999999999999999999999999999999999999999999998766211         


Q ss_pred             -------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccc
Q 031654           99 -------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 -------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                                                     .+|...+..++|||++||+++..+..+-.+.++.+ +|+|+||| |+|+
T Consensus       100 reLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sv-eyVVfdEa-drlf  177 (529)
T KOG0337|consen  100 RELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSV-EYVVFDEA-DRLF  177 (529)
T ss_pred             HHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccce-eeeeehhh-hHHH
Confidence                                           57777788899999999999988877777899999 99999999 9999


Q ss_pred             ccccccC
Q 031654          148 DMALNQK  154 (155)
Q Consensus       148 ~~gf~~~  154 (155)
                      +|||.+|
T Consensus       178 emgfqeq  184 (529)
T KOG0337|consen  178 EMGFQEQ  184 (529)
T ss_pred             hhhhHHH
Confidence            9999875

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

Probab=99.92  E-value=4.2e-27  Score=185.33  Aligned_cols=121  Identities=26%  Similarity=0.432  Sum_probs=108.8

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      ..|+++.  .+++..+.+.||++|+|+|.++||..+.|+|+++.|..|+|||.||++|+++++.......          
T Consensus        85 ~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtre  164 (459)
T KOG0326|consen   85 NEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRE  164 (459)
T ss_pred             ccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecch
Confidence            4588876  9999999999999999999999999999999999999999999999999999987554333          


Q ss_pred             -----------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 -----------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 -----------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                                   .+.+-.+.+.+|++|+||||++++..++--.++++ ..+|+||| |+||+.
T Consensus       165 lALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c-~~lV~DEA-DKlLs~  242 (459)
T KOG0326|consen  165 LALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDC-VILVMDEA-DKLLSV  242 (459)
T ss_pred             hhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhc-eEEEechh-hhhhch
Confidence                                         55556666789999999999999999999999999 99999999 999999


Q ss_pred             cccc
Q 031654          150 ALNQ  153 (155)
Q Consensus       150 gf~~  153 (155)
                      .|.+
T Consensus       243 ~F~~  246 (459)
T KOG0326|consen  243 DFQP  246 (459)
T ss_pred             hhhh
Confidence            8854

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

Probab=99.92  E-value=1.3e-25  Score=187.19  Aligned_cols=141  Identities=26%  Similarity=0.404  Sum_probs=120.6

Q ss_pred             cccCCcCcccCCCCCCCCCcccccCC------HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhh
Q 031654           12 ASENAAPASSSTNTLSSPAARFAYVP------QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        12 ~~~~~~~~~~~~~~~p~~~~~f~~l~------~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yll   85 (155)
                      ..+++..+.+.|.+.|.++.+|.+|-      +.+++++...+|..|+|+|.+|||.++.++|+++|||||||||++|++
T Consensus       113 ~~Rk~~k~~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~  192 (593)
T KOG0344|consen  113 GIRKSNKINVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNL  192 (593)
T ss_pred             cchhcceeeccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhh
Confidence            34556677899999999999999965      899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhch-----------------------------------------------HHHHHHHhcCCcEEEEChHH
Q 031654           86 PIINGIMREYYSA-----------------------------------------------RKELRELARWVDNLMATLRR  118 (155)
Q Consensus        86 p~l~~l~~~~~~~-----------------------------------------------~~~~~~l~~~~~IlI~TP~~  118 (155)
                      |+++++.......                                               ..+.......++|+|+||.|
T Consensus       193 Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~r  272 (593)
T KOG0344|consen  193 PILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMR  272 (593)
T ss_pred             HHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHH
Confidence            9999998766311                                               11111122347999999999


Q ss_pred             HHHHHHcCC--CCcccccceEEEEccccccccc-ccccC
Q 031654          119 LVNLLERGR--VSLQMIIRYLALKEAADQTLDM-ALNQK  154 (155)
Q Consensus       119 l~~~l~~~~--~~l~~l~~~lVlDEa~D~ll~~-gf~~~  154 (155)
                      +..++..+.  ++++.| .++|+||| |++++. +|.+|
T Consensus       273 i~~~~~~~~~~idl~~V-~~lV~dEa-D~lfe~~~f~~Q  309 (593)
T KOG0344|consen  273 IVGLLGLGKLNIDLSKV-EWLVVDEA-DLLFEPEFFVEQ  309 (593)
T ss_pred             HHHHhcCCCccchhhee-eeEeechH-HhhhChhhHHHH
Confidence            999999876  899999 99999999 999998 77654

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

Probab=99.91  E-value=3.5e-25  Score=182.25  Aligned_cols=113  Identities=30%  Similarity=0.396  Sum_probs=95.7

Q ss_pred             HHHHhHHhCCCCCCCHHHHHHHHHHh---------cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------
Q 031654           39 HLRNKPRTYKYVKPTPVQRHATSILV---------AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------   98 (155)
Q Consensus        39 ~l~~~l~~~g~~~pt~iQ~~~i~~~l---------~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------   98 (155)
                      .+.+++..+++++..|+|..++|.++         .++||.|.||||||||+||.+||++.+.......           
T Consensus       147 ~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~  226 (620)
T KOG0350|consen  147 TIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRE  226 (620)
T ss_pred             HHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHH
Confidence            34567999999999999999999884         3689999999999999999999999887664333           


Q ss_pred             -----------------------------HHHHHHHhc-C----CcEEEEChHHHHHHHHc-CCCCcccccceEEEEccc
Q 031654           99 -----------------------------RKELRELAR-W----VDNLMATLRRLVNLLER-GRVSLQMIIRYLALKEAA  143 (155)
Q Consensus        99 -----------------------------~~~~~~l~~-~----~~IlI~TP~~l~~~l~~-~~~~l~~l~~~lVlDEa~  143 (155)
                                                   .+..+.|.+ .    .||+|+|||||++++++ ..++|+++ +|+|+||| 
T Consensus       227 L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~L-rfLVIDEA-  304 (620)
T KOG0350|consen  227 LALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHL-RFLVIDEA-  304 (620)
T ss_pred             HHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhc-eEEEechH-
Confidence                                         444455544 3    39999999999999995 67999999 99999999 


Q ss_pred             cccccccccc
Q 031654          144 DQTLDMALNQ  153 (155)
Q Consensus       144 D~ll~~gf~~  153 (155)
                      |+|++..|.+
T Consensus       305 DRll~qsfQ~  314 (620)
T KOG0350|consen  305 DRLLDQSFQE  314 (620)
T ss_pred             HHHHHHHHHH
Confidence            9999998853

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

Probab=99.91  E-value=5.7e-24  Score=186.70  Aligned_cols=112  Identities=15%  Similarity=0.200  Sum_probs=92.9

Q ss_pred             CCHHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------------
Q 031654           36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------------   98 (155)
Q Consensus        36 l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------------   98 (155)
                      +++++.++|+++||++||++|+++||.+++|+|++++||||||||+||++|+++.+.......                 
T Consensus        21 l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraLa~q~~~~  100 (742)
T TIGR03817        21 AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRA  100 (742)
T ss_pred             CCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHHHHHHHHH
Confidence            459999999999999999999999999999999999999999999999999999987543211                 


Q ss_pred             -------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC----CCCcccccceEEEEccccccccc
Q 031654           99 -------------------RKELRELARWVDNLMATLRRLVNLLERG----RVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 -------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~----~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                         ..+...+..+++|+|+||++|...+...    ...++++ ++|||||| |.|.+.
T Consensus       101 l~~l~~~~i~v~~~~Gdt~~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l-~~vViDEa-h~~~g~  172 (742)
T TIGR03817       101 VRELTLRGVRPATYDGDTPTEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRL-RYVVIDEC-HSYRGV  172 (742)
T ss_pred             HHHhccCCeEEEEEeCCCCHHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcC-CEEEEeCh-hhccCc
Confidence                               3344455667999999999987543221    1348899 99999999 999763

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.

>cd00268 DEADc DEAD-box helicases

Probab=99.90  E-value=3.8e-23  Score=155.00  Aligned_cols=118  Identities=38%  Similarity=0.580  Sum_probs=101.4

Q ss_pred             cccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHh--hhch----------
Q 031654           33 FAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE--YYSA----------   98 (155)
Q Consensus        33 f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~--~~~~----------   98 (155)
                      |++++  +.+.+.+.++|++.|++.|+++++.+++|+|+++++|||+|||++|++|+++.+...  ....          
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~   80 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRE   80 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHH
Confidence            56666  899999999999999999999999999999999999999999999999999998876  1111          


Q ss_pred             -----------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 -----------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 -----------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                                   ......+.++++|+|+||+++.+++.++...+.++ +++|+||+ |.+.+.
T Consensus        81 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l-~~lIvDE~-h~~~~~  158 (203)
T cd00268          81 LALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKV-KYLVLDEA-DRMLDM  158 (203)
T ss_pred             HHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhC-CEEEEeCh-HHhhcc
Confidence                                         12223334478999999999999999888899999 99999999 999887


Q ss_pred             ccc
Q 031654          150 ALN  152 (155)
Q Consensus       150 gf~  152 (155)
                      +|.
T Consensus       159 ~~~  161 (203)
T cd00268         159 GFE  161 (203)
T ss_pred             ChH
Confidence            764

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.

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

Probab=99.89  E-value=4.2e-24  Score=171.08  Aligned_cols=128  Identities=25%  Similarity=0.369  Sum_probs=109.1

Q ss_pred             CCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----
Q 031654           25 TLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----   98 (155)
Q Consensus        25 ~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----   98 (155)
                      +.-+-+.+|++++  ++|+..+...||++|+.||++||+.+..|.|+.+++++|||||.+|++++++.+.......    
T Consensus        20 n~~evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qali   99 (397)
T KOG0327|consen   20 NWNEVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALI   99 (397)
T ss_pred             cHHHHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHH
Confidence            3344567999988  9999999999999999999999999999999999999999999999999999853222111    


Q ss_pred             -----------------------------------H-HHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcc
Q 031654           99 -----------------------------------R-KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus        99 -----------------------------------~-~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa  142 (155)
                                                         . +..+.....+||+|+||||+.++++.+.+....+ +++|+|||
T Consensus       100 laPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~i-KmfvlDEa  178 (397)
T KOG0327|consen  100 LAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGI-KMFVLDEA  178 (397)
T ss_pred             hcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccce-eEEeecch
Confidence                                               1 2222333468999999999999999998889999 99999999


Q ss_pred             cccccccccccC
Q 031654          143 ADQTLDMALNQK  154 (155)
Q Consensus       143 ~D~ll~~gf~~~  154 (155)
                       |.|+..||.+|
T Consensus       179 -DEmLs~gfkdq  189 (397)
T KOG0327|consen  179 -DEMLSRGFKDQ  189 (397)
T ss_pred             -HhhhccchHHH
Confidence             99999999875

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

Probab=99.87  E-value=3.2e-23  Score=159.52  Aligned_cols=123  Identities=20%  Similarity=0.266  Sum_probs=106.9

Q ss_pred             CCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----
Q 031654           25 TLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----   98 (155)
Q Consensus        25 ~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----   98 (155)
                      ...-+...|.++-  |+++.++-..||++|+.+|..+||...-|-|++++|.+|.|||..|.+..++++.......    
T Consensus        36 yv~ihssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlv  115 (387)
T KOG0329|consen   36 YVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLV  115 (387)
T ss_pred             EEEEeccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEE
Confidence            3333445677765  9999999999999999999999999999999999999999999999999998886543322    


Q ss_pred             ------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcc
Q 031654           99 ------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus        99 ------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa  142 (155)
                                                          +.....+.+.|||+|+||||++.+.+++.++++++ +++|+||+
T Consensus       116 mchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~v-khFvlDEc  194 (387)
T KOG0329|consen  116 MCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNV-KHFVLDEC  194 (387)
T ss_pred             EeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhc-ceeehhhH
Confidence                                                45556677789999999999999999999999999 99999999


Q ss_pred             ccccccc
Q 031654          143 ADQTLDM  149 (155)
Q Consensus       143 ~D~ll~~  149 (155)
                       |+||+.
T Consensus       195 -dkmle~  200 (387)
T KOG0329|consen  195 -DKMLEQ  200 (387)
T ss_pred             -HHHHHH
Confidence             999864

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.87  E-value=4.7e-23  Score=174.06  Aligned_cols=125  Identities=22%  Similarity=0.331  Sum_probs=106.9

Q ss_pred             CCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----
Q 031654           26 LSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----   98 (155)
Q Consensus        26 ~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----   98 (155)
                      .+.-...|++|-  ..++..|++.+|..||+||..|||.++.+-|++|+|..|+|||+.|.+.+++.+..+....     
T Consensus        20 ~~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv   99 (980)
T KOG4284|consen   20 QSNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIV   99 (980)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEE
Confidence            455566899987  9999999999999999999999999999999999999999999999998888776544322     


Q ss_pred             -----------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccc
Q 031654           99 -----------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAA  143 (155)
Q Consensus        99 -----------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~  143 (155)
                                                         ......+ +.++|+||||||+..++..+.++.+.+ +++||||| 
T Consensus       100 ~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rl-k~~rIvIGtPGRi~qL~el~~~n~s~v-rlfVLDEA-  176 (980)
T KOG4284|consen  100 TPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRL-KQTRIVIGTPGRIAQLVELGAMNMSHV-RLFVLDEA-  176 (980)
T ss_pred             ecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhh-hhceEEecCchHHHHHHHhcCCCccce-eEEEeccH-
Confidence                                               2233333 358999999999999999999999999 99999999 


Q ss_pred             cccccc-cccc
Q 031654          144 DQTLDM-ALNQ  153 (155)
Q Consensus       144 D~ll~~-gf~~  153 (155)
                      |+|++. .|.+
T Consensus       177 DkL~~t~sfq~  187 (980)
T KOG4284|consen  177 DKLMDTESFQD  187 (980)
T ss_pred             HhhhchhhHHH
Confidence            999995 4654

>PRK02362 ski2-like helicase; Provisional

Probab=99.86  E-value=7.9e-22  Score=173.37  Aligned_cols=118  Identities=20%  Similarity=0.196  Sum_probs=96.4

Q ss_pred             ccccCC--HHHHHhHHhCCCCCCCHHHHHHHHH-HhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------H
Q 031654           32 RFAYVP--QHLRNKPRTYKYVKPTPVQRHATSI-LVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------R   99 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~-~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~   99 (155)
                      .|++++  +.+++++++.||.+|+|+|.+|++. ++.|+|++++||||||||++|.+|++..+.......         .
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~~~kal~i~P~raLa~   81 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPLRALAS   81 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcCCcEEEEeChHHHHH
Confidence            466654  9999999999999999999999998 789999999999999999999999999886433222         1


Q ss_pred             HH---HHHH--------------------hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654          100 KE---LREL--------------------ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       100 ~~---~~~l--------------------~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      +.   ...+                    ...++|+|+||+++..+++++...++++ +++|+||+ |.|.+.++
T Consensus        82 q~~~~~~~~~~~g~~v~~~tGd~~~~~~~l~~~~IiV~Tpek~~~llr~~~~~l~~v-~lvViDE~-H~l~d~~r  154 (737)
T PRK02362         82 EKFEEFERFEELGVRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRNGAPWLDDI-TCVVVDEV-HLIDSANR  154 (737)
T ss_pred             HHHHHHHHhhcCCCEEEEEeCCcCccccccCCCCEEEECHHHHHHHHhcChhhhhhc-CEEEEECc-cccCCCcc
Confidence            11   1111                    1247999999999999988766668899 99999999 99887655

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

Probab=99.86  E-value=8.9e-22  Score=172.09  Aligned_cols=115  Identities=23%  Similarity=0.285  Sum_probs=99.2

Q ss_pred             ccccCCHHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhh--hc---h--------
Q 031654           32 RFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY--YS---A--------   98 (155)
Q Consensus        32 ~f~~l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~--~~---~--------   98 (155)
                      .|+-|++.+++.+++. |..|||.|.+|||.+.+|+|++++||||||||+|..+|+++.+....  ..   .        
T Consensus         4 ~~~~l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPL   82 (814)
T COG1201           4 IFNILDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPL   82 (814)
T ss_pred             hhhhcCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcH
Confidence            4677889999999987 99999999999999999999999999999999999999999998873  11   1        


Q ss_pred             -------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCC--CCcccccceEEEEccccc
Q 031654           99 -------------------------------RKELRELARWVDNLMATLRRLVNLLERGR--VSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 -------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~--~~l~~l~~~lVlDEa~D~  145 (155)
                                                     .+..+.+.+.|||||+||+.|.-++....  -.+.++ +++|+||+ |.
T Consensus        83 kALn~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~v-r~VIVDEi-He  160 (814)
T COG1201          83 KALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDV-RYVIVDEI-HA  160 (814)
T ss_pred             HHHHHHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCC-cEEEeehh-hh
Confidence                                           34445556789999999999988887754  368999 99999999 99


Q ss_pred             cccc
Q 031654          146 TLDM  149 (155)
Q Consensus       146 ll~~  149 (155)
                      |.+.
T Consensus       161 l~~s  164 (814)
T COG1201         161 LAES  164 (814)
T ss_pred             hhcc
Confidence            8754

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

Probab=99.86  E-value=1.1e-22  Score=162.94  Aligned_cols=125  Identities=22%  Similarity=0.337  Sum_probs=106.1

Q ss_pred             CCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----
Q 031654           28 SPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----   98 (155)
Q Consensus        28 ~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----   98 (155)
                      ..+.+|++|.  |++++.|..|+|.+|+.||..|+|.++..  +|+++++++|||||.||.|.+|+++.......     
T Consensus        87 yS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCL  166 (477)
T KOG0332|consen   87 YSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICL  166 (477)
T ss_pred             cccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceee
Confidence            5678999998  99999999999999999999999999987  89999999999999999999999886543322     


Q ss_pred             ------HHH-------------------------HHHHhcCCcEEEEChHHHHHHHHc-CCCCcccccceEEEEcccccc
Q 031654           99 ------RKE-------------------------LRELARWVDNLMATLRRLVNLLER-GRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ------~~~-------------------------~~~l~~~~~IlI~TP~~l~~~l~~-~~~~l~~l~~~lVlDEa~D~l  146 (155)
                            ..|                         .+.-.-..+|+|+|||.+.+++.. +.++++.+ +.+|+||| |.|
T Consensus       167 aPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG~~i~eqIviGTPGtv~Dlm~klk~id~~ki-kvfVlDEA-D~M  244 (477)
T KOG0332|consen  167 APTRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRGNKLTEQIVIGTPGTVLDLMLKLKCIDLEKI-KVFVLDEA-DVM  244 (477)
T ss_pred             CchHHHHHHHHHHHHHhcCceeeeEEEEecCcccccCCcchhheeeCCCccHHHHHHHHHhhChhhc-eEEEecch-hhh
Confidence                  000                         000001359999999999999988 89999999 99999999 999


Q ss_pred             ccc-ccccC
Q 031654          147 LDM-ALNQK  154 (155)
Q Consensus       147 l~~-gf~~~  154 (155)
                      ++. ||.++
T Consensus       245 i~tqG~~D~  253 (477)
T KOG0332|consen  245 IDTQGFQDQ  253 (477)
T ss_pred             hhccccccc
Confidence            977 89876

>PRK00254 ski2-like helicase; Provisional

Probab=99.85  E-value=1.4e-21  Score=171.42  Aligned_cols=118  Identities=19%  Similarity=0.212  Sum_probs=97.3

Q ss_pred             ccccCC--HHHHHhHHhCCCCCCCHHHHHHHHH-HhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           32 RFAYVP--QHLRNKPRTYKYVKPTPVQRHATSI-LVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~-~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      +|++++  +.+.+.+++.||+.|+|+|.++++. +++|+|++++||||||||++|.+|+++.+.......          
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aLa   81 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALA   81 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHHH
Confidence            466665  9999999999999999999999986 789999999999999999999999999886533222          


Q ss_pred             HHHHHH-----------------------HhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654           99 RKELRE-----------------------LARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 ~~~~~~-----------------------l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      .++...                       ....++|+|+||+++..+++.+...++++ +++|+||+ |.+.+.++
T Consensus        82 ~q~~~~~~~~~~~g~~v~~~~Gd~~~~~~~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l-~lvViDE~-H~l~~~~r  155 (720)
T PRK00254         82 EEKYREFKDWEKLGLRVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLRHGSSWIKDV-KLVVADEI-HLIGSYDR  155 (720)
T ss_pred             HHHHHHHHHHhhcCCEEEEEeCCCCCchhhhccCCEEEEcHHHHHHHHhCCchhhhcC-CEEEEcCc-CccCCccc
Confidence            111111                       11357999999999999988777778999 99999999 99987654

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.85  E-value=2.9e-21  Score=172.32  Aligned_cols=116  Identities=21%  Similarity=0.286  Sum_probs=92.4

Q ss_pred             ccccCCHHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc--------h-----
Q 031654           32 RFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS--------A-----   98 (155)
Q Consensus        32 ~f~~l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~--------~-----   98 (155)
                      .|+-+++.+.+.+++ +|..|||+|+++||.+++|+|++++||||||||++|++|+++.+......        .     
T Consensus        14 ~~~~l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsP   92 (876)
T PRK13767         14 ILDLLRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSP   92 (876)
T ss_pred             HHhhcCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcC
Confidence            355566888887766 79999999999999999999999999999999999999999988642110        0     


Q ss_pred             -----H---------------------------------------HHHHHHhcCCcEEEEChHHHHHHHHcCCC--Cccc
Q 031654           99 -----R---------------------------------------KELRELARWVDNLMATLRRLVNLLERGRV--SLQM  132 (155)
Q Consensus        99 -----~---------------------------------------~~~~~l~~~~~IlI~TP~~l~~~l~~~~~--~l~~  132 (155)
                           .                                       ...+.+.+.++|+|+||++|..++....+  .+++
T Consensus        93 traLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~  172 (876)
T PRK13767         93 LRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRT  172 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhc
Confidence                 1                                       11122334789999999999888876543  5789


Q ss_pred             ccceEEEEcccccccccc
Q 031654          133 IIRYLALKEAADQTLDMA  150 (155)
Q Consensus       133 l~~~lVlDEa~D~ll~~g  150 (155)
                      + ++||+||+ |.|++..
T Consensus       173 l-~~VVIDE~-H~l~~~~  188 (876)
T PRK13767        173 V-KWVIVDEI-HSLAENK  188 (876)
T ss_pred             C-CEEEEech-hhhccCc
Confidence            9 99999999 9998753

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=99.84  E-value=8.8e-21  Score=137.67  Aligned_cols=98  Identities=23%  Similarity=0.452  Sum_probs=82.4

Q ss_pred             CHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh-ch---------------------------------
Q 031654           53 TPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY-SA---------------------------------   98 (155)
Q Consensus        53 t~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~-~~---------------------------------   98 (155)
                      ||+|.++|+.+.+|+|+++.||||+|||++|++|++..+..... ..                                 
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~   80 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHG   80 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEEST
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecccccccccccccccccccccccccccc
Confidence            79999999999999999999999999999999999998877621 11                                 


Q ss_pred             -----HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654           99 -----RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus        99 -----~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                           ......+..+++|+|+||+++.+++..+..++.++ +++|+||+ |.+.+.+|.
T Consensus        81 ~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~-~~iViDE~-h~l~~~~~~  137 (169)
T PF00270_consen   81 GQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRL-SLIVIDEA-HHLSDETFR  137 (169)
T ss_dssp             TSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTE-SEEEEETH-HHHHHTTHH
T ss_pred             cccccccccccccccccccccCcchhhccccccccccccc-eeeccCcc-cccccccHH
Confidence                 13344455679999999999999999876688889 99999999 999886543

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. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

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

Probab=99.84  E-value=1.9e-21  Score=158.68  Aligned_cols=64  Identities=30%  Similarity=0.514  Sum_probs=59.9

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      ..|++++  |++-.+..++.|.-||.+|+++||.++.|.||+..|.||||||-||.+|+++-....
T Consensus         2 ~af~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv~et   67 (725)
T KOG0349|consen    2 TAFEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWET   67 (725)
T ss_pred             cchHhhCcchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHHHHH
Confidence            4689998  999999999999999999999999999999999999999999999999999876644

>PRK01172 ski2-like helicase; Provisional

Probab=99.81  E-value=5e-20  Score=160.58  Aligned_cols=117  Identities=14%  Similarity=0.111  Sum_probs=95.4

Q ss_pred             ccccC--CHHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HH
Q 031654           32 RFAYV--PQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RK  100 (155)
Q Consensus        32 ~f~~l--~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~  100 (155)
                      .|+++  ++++.+.+++.+|+ ++++|.++++.+.+|+|++++||||||||++|.++++..+.......         .+
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~~k~v~i~P~raLa~q   80 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAME   80 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhCCcEEEEechHHHHHH
Confidence            35554  49999999999997 99999999999999999999999999999999999998876543222         11


Q ss_pred             HHH-----------------------HHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654          101 ELR-----------------------ELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       101 ~~~-----------------------~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      ...                       .....+||+|+||+++..++++....++++ +++|+||| |.+.+.++
T Consensus        81 ~~~~~~~l~~~g~~v~~~~G~~~~~~~~~~~~dIiv~Tpek~~~l~~~~~~~l~~v-~lvViDEa-H~l~d~~r  152 (674)
T PRK01172         81 KYEELSRLRSLGMRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHDPYIINDV-GLIVADEI-HIIGDEDR  152 (674)
T ss_pred             HHHHHHHHhhcCCeEEEEeCCCCCChhhhccCCEEEECHHHHHHHHhCChhHHhhc-CEEEEecc-hhccCCCc
Confidence            111                       111357999999999998888877778999 99999999 99887654

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=4e-19  Score=156.54  Aligned_cols=108  Identities=14%  Similarity=0.171  Sum_probs=87.5

Q ss_pred             HHHHHhHH-----hCCCCCC---CHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------
Q 031654           38 QHLRNKPR-----TYKYVKP---TPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------   98 (155)
Q Consensus        38 ~~l~~~l~-----~~g~~~p---t~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------   98 (155)
                      +++...+.     .+||+.|   +|+|.++||.++.++|++++++||||||++|++|++..+.......           
T Consensus        71 re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~~v~IVTpTrELA~Q  150 (970)
T PRK12899         71 KNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGKPVHLVTVNDYLAQR  150 (970)
T ss_pred             HHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcCCeEEEeCCHHHHHH
Confidence            55555544     6799999   9999999999999999999999999999999999998876543211           


Q ss_pred             -------------------------HHHHHHHhcCCcEEEEChHHH-HHHHHcCCCCcc-------cccceEEEEccccc
Q 031654           99 -------------------------RKELRELARWVDNLMATLRRL-VNLLERGRVSLQ-------MIIRYLALKEAADQ  145 (155)
Q Consensus        99 -------------------------~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~~~l~-------~l~~~lVlDEa~D~  145 (155)
                                               ..+...+  +|||+||||++| .++++.+.+.++       .+ +++||||| |.
T Consensus       151 dae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~-~~~IIDEA-Ds  226 (970)
T PRK12899        151 DCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGF-YFAIIDEV-DS  226 (970)
T ss_pred             HHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcccc-cEEEEech-hh
Confidence                                     2332222  599999999999 999998866554       66 89999999 99


Q ss_pred             cccc
Q 031654          146 TLDM  149 (155)
Q Consensus       146 ll~~  149 (155)
                      ||-+
T Consensus       227 mLiD  230 (970)
T PRK12899        227 ILID  230 (970)
T ss_pred             hhhh
Confidence            9853

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.79  E-value=3.6e-19  Score=149.54  Aligned_cols=105  Identities=18%  Similarity=0.219  Sum_probs=76.4

Q ss_pred             HhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHH------------HHHhhhch--------------
Q 031654           45 RTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIING------------IMREYYSA--------------   98 (155)
Q Consensus        45 ~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~------------l~~~~~~~--------------   98 (155)
                      +.+||+.|+|+|.++|+.+++|+|+++++|||||||++|++|++..            |.......              
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~   84 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCSDGITLVISPLISLMEDQVLQLKASGIPATFLNSS   84 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHcCCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCC
Confidence            3569999999999999999999999999999999999999998641            00000000              


Q ss_pred             --HH----HHHHH-hcCCcEEEEChHHHHHHHH-cCCC-CcccccceEEEEccccccccccc
Q 031654           99 --RK----ELREL-ARWVDNLMATLRRLVNLLE-RGRV-SLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 --~~----~~~~l-~~~~~IlI~TP~~l~~~l~-~~~~-~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                        ..    ....+ ...++|+++||+++..... ...+ ...++ +++|+||| |++.++|+
T Consensus        85 ~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i-~~iViDEa-H~i~~~g~  144 (470)
T TIGR00614        85 QSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGI-TLIAVDEA-HCISQWGH  144 (470)
T ss_pred             CCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCc-CEEEEeCC-cccCcccc
Confidence              11    11222 2358999999999753221 1112 56789 99999999 99999884

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

>PRK09401 reverse gyrase; Reviewed

Probab=99.78  E-value=1.2e-18  Score=158.71  Aligned_cols=105  Identities=21%  Similarity=0.232  Sum_probs=78.6

Q ss_pred             HHHHHhHHhC-CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------------
Q 031654           38 QHLRNKPRTY-KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------------   98 (155)
Q Consensus        38 ~~l~~~l~~~-g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------------   98 (155)
                      .++.+.+++. |+ .||++|+.++|.++.|+|++++||||||||. |.+|++..+.......                  
T Consensus        67 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~  144 (1176)
T PRK09401         67 KEFEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLE  144 (1176)
T ss_pred             HHHHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHHH
Confidence            3444455444 77 8999999999999999999999999999996 6666655554322111                  


Q ss_pred             --------------------HH----HHHHHh-cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 --------------------RK----ELRELA-RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 --------------------~~----~~~~l~-~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                          ..    +...+. ..+||+|+||++|.+++.  .+...++ +++|+||| |+|++
T Consensus       145 ~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~-~~lVvDEa-D~~L~  215 (1176)
T PRK09401        145 KFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKF-DFVFVDDV-DAVLK  215 (1176)
T ss_pred             HHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hcccccc-CEEEEECh-HHhhh
Confidence                                01    122233 359999999999999886  4566779 99999999 99997

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

Probab=99.77  E-value=5.8e-19  Score=158.14  Aligned_cols=112  Identities=18%  Similarity=0.242  Sum_probs=80.2

Q ss_pred             HHHHHhHH-hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHH------------HHhhhch------
Q 031654           38 QHLRNKPR-TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI------------MREYYSA------   98 (155)
Q Consensus        38 ~~l~~~l~-~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l------------~~~~~~~------   98 (155)
                      ..+...++ .+||..++|+|.++|+.++.|+|+++++|||+|||+||++|++..-            .......      
T Consensus       446 ~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~~GiTLVISPLiSLmqDQV~~L~~~GI  525 (1195)
T PLN03137        446 KKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSLIQDQIMNLLQANI  525 (1195)
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHcCCcEEEEeCHHHHHHHHHHHHHhCCC
Confidence            55555555 4599999999999999999999999999999999999999986421            1000000      


Q ss_pred             -----------HHHH---HHHh---cCCcEEEEChHHHHH--HHHcC--CC-CcccccceEEEEccccccccccc
Q 031654           99 -----------RKEL---RELA---RWVDNLMATLRRLVN--LLERG--RV-SLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 -----------~~~~---~~l~---~~~~IlI~TP~~l~~--~l~~~--~~-~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                                 .++.   +.+.   ..++||++||++|..  .+.+.  .+ ....+ .+|||||| |+|+++|+
T Consensus       526 ~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~L-slIVIDEA-HcVSqWGh  598 (1195)
T PLN03137        526 PAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLL-ARFVIDEA-HCVSQWGH  598 (1195)
T ss_pred             eEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhcccc-ceeccCcc-hhhhhccc
Confidence                       1222   2222   468999999999862  22221  11 23457 99999999 99999983

>TIGR01054 rgy reverse gyrase

Probab=99.77  E-value=1.8e-18  Score=157.58  Aligned_cols=111  Identities=14%  Similarity=0.175  Sum_probs=83.2

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------------   98 (155)
                      .++.+.+.+.....|+++|+.++|.++.|+|++++||||||||+ |.+|++..+.......                   
T Consensus        65 ~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~l~~  143 (1171)
T TIGR01054        65 KEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISS  143 (1171)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHhcCCeEEEEeCHHHHHHHHHHHHHH
Confidence            44556666554558999999999999999999999999999997 7777766554322111                   


Q ss_pred             ---------------------H---HHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc-----
Q 031654           99 ---------------------R---KELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD-----  148 (155)
Q Consensus        99 ---------------------~---~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~-----  148 (155)
                                           .   .+...+.+ +++|||+||++|.+.+..-  .. ++ +++|+||| |+|++     
T Consensus       144 l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l--~~-~~-~~iVvDEa-D~~L~~~k~v  218 (1171)
T TIGR01054       144 LAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDEL--GP-KF-DFIFVDDV-DALLKASKNV  218 (1171)
T ss_pred             HHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHh--cC-CC-CEEEEeCh-HhhhhccccH
Confidence                                 0   11222333 5999999999999887652  12 88 99999999 99999     


Q ss_pred             ------cccccC
Q 031654          149 ------MALNQK  154 (155)
Q Consensus       149 ------~gf~~~  154 (155)
                            +||.+|
T Consensus       219 d~il~llGF~~e  230 (1171)
T TIGR01054       219 DKLLKLLGFSEE  230 (1171)
T ss_pred             HHHHHHcCCCHH
Confidence                  789763

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.

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

Probab=99.77  E-value=2.1e-18  Score=153.10  Aligned_cols=110  Identities=23%  Similarity=0.306  Sum_probs=92.3

Q ss_pred             ccccCC-HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------
Q 031654           32 RFAYVP-QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------   98 (155)
Q Consensus        32 ~f~~l~-~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------   98 (155)
                      .|..+. ..+..++.+.|+..++++|.+|+..+.+|+||||+++||||||.||++|+++++.......            
T Consensus        50 ~~~~~~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~  129 (851)
T COG1205          50 EFPELRDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALAN  129 (851)
T ss_pred             cchhhhhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHh
Confidence            345555 6678899999999999999999999999999999999999999999999999999877663            


Q ss_pred             ----------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCC----CCcccccceEEEEcc
Q 031654           99 ----------------------------RKELRELARWVDNLMATLRRLVNLLERGR----VSLQMIIRYLALKEA  142 (155)
Q Consensus        99 ----------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~----~~l~~l~~~lVlDEa  142 (155)
                                                  .+......+.||||++||..|..++-+..    ..++++ +|||+||+
T Consensus       130 DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~L-k~lVvDEl  204 (851)
T COG1205         130 DQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNL-KYLVVDEL  204 (851)
T ss_pred             hHHHHHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcC-cEEEEecc
Confidence                                        12224456789999999999988665542    457889 99999999

>PRK14701 reverse gyrase; Provisional

Probab=99.77  E-value=1.3e-18  Score=161.79  Aligned_cols=106  Identities=14%  Similarity=0.142  Sum_probs=80.2

Q ss_pred             HHHHHhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------------
Q 031654           38 QHLRNKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------------   98 (155)
Q Consensus        38 ~~l~~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------------   98 (155)
                      .++.+.+++ .|| .|+++|+.+||.+++|+|++++||||||||++++++.+..........                  
T Consensus        66 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~~g~~aLVl~PTreLa~Qi~~~l~~  144 (1638)
T PRK14701         66 EEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLALKGKKCYIILPTTLLVKQTVEKIES  144 (1638)
T ss_pred             HHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHhcCCeEEEEECHHHHHHHHHHHHHH
Confidence            677777876 799 699999999999999999999999999999977666554322211000                  


Q ss_pred             --------------------HHH---HHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 --------------------RKE---LRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 --------------------~~~---~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                          .++   ...+.+ .++|||+||++|.+.+...  ...++ +++|+||| |+|++
T Consensus       145 l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l--~~~~i-~~iVVDEA-D~ml~  214 (1638)
T PRK14701        145 FCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM--KHLKF-DFIFVDDV-DAFLK  214 (1638)
T ss_pred             HHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH--hhCCC-CEEEEECc-eeccc
Confidence                                111   223444 4999999999998877642  22778 99999999 99997

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.76  E-value=1.4e-18  Score=149.57  Aligned_cols=105  Identities=19%  Similarity=0.157  Sum_probs=80.3

Q ss_pred             HhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------------
Q 031654           42 NKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------------   98 (155)
Q Consensus        42 ~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------------   98 (155)
                      +.|++ +||+.++|+|.++|+.+++|+|+++++|||+|||+||++|++..   .....                      
T Consensus         3 ~~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~---~g~~lVisPl~sL~~dq~~~l~~~gi~   79 (591)
T TIGR01389         3 QVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL---KGLTVVISPLISLMKDQVDQLRAAGVA   79 (591)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc---CCcEEEEcCCHHHHHHHHHHHHHcCCc
Confidence            44544 69999999999999999999999999999999999999998742   11111                      


Q ss_pred             ---------HH----HHHHH-hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654           99 ---------RK----ELREL-ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 ---------~~----~~~~l-~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                               ..    ....+ ...++|+++||+++......+.+...++ +++|+||| |++.++|+
T Consensus        80 ~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l-~~iViDEa-H~i~~~g~  144 (591)
T TIGR01389        80 AAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPI-ALVAVDEA-HCVSQWGH  144 (591)
T ss_pred             EEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCC-CEEEEeCC-cccccccC
Confidence                     11    11112 2468999999999865433344566789 99999999 99999874

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.75  E-value=5.4e-18  Score=146.42  Aligned_cols=109  Identities=16%  Similarity=0.131  Sum_probs=78.4

Q ss_pred             HHhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHH------------Hhhhch---------
Q 031654           41 RNKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM------------REYYSA---------   98 (155)
Q Consensus        41 ~~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~------------~~~~~~---------   98 (155)
                      .+.|++ +||+.|+|+|.++|+.+++|+|+++++|||+|||++|++|++..-.            ......         
T Consensus        14 ~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~~g~tlVisPl~sL~~dqv~~l~~~gi~~~   93 (607)
T PRK11057         14 KQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQLLANGVAAA   93 (607)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHcCCCEEEEecHHHHHHHHHHHHHHcCCcEE
Confidence            344443 6999999999999999999999999999999999999999774310            000000         


Q ss_pred             --------HH---HHHHHh-cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654           99 --------RK---ELRELA-RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 --------~~---~~~~l~-~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                              ..   ....+. ...+++++||+++........+...++ .++|+||| |++.++|+
T Consensus        94 ~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l-~~iVIDEa-H~i~~~G~  156 (607)
T PRK11057         94 CLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNP-ALLAVDEA-HCISQWGH  156 (607)
T ss_pred             EEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCC-CEEEEeCc-cccccccC
Confidence                    11   111222 357999999999864222223445678 99999999 99999874

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

Probab=99.72  E-value=1.1e-17  Score=147.21  Aligned_cols=99  Identities=18%  Similarity=0.148  Sum_probs=74.5

Q ss_pred             CCCCCCCHHHHHHHHHHhcCC-cEEEEccCCCCcchhhhhHHHHHHH-----------------------------Hhhh
Q 031654           47 YKYVKPTPVQRHATSILVAGR-DLMACAQTGSRKTTPFCFPIINGIM-----------------------------REYY   96 (155)
Q Consensus        47 ~g~~~pt~iQ~~~i~~~l~g~-dvl~~a~TGsGKT~~yllp~l~~l~-----------------------------~~~~   96 (155)
                      .||+ |||+|.++||.++.|+ ++++++|||||||.+|+++++....                             +...
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l~   90 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERLP   90 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccccccccccceEEEeCchHHHHHHHHHHHHHHHHHhc
Confidence            4898 9999999999999998 6888899999999955433332100                             0000


Q ss_pred             ----------------------ch-----------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCC--------------
Q 031654           97 ----------------------SA-----------RKELRELARWVDNLMATLRRLVNLLERGRVS--------------  129 (155)
Q Consensus        97 ----------------------~~-----------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~--------------  129 (155)
                                            ..           ..|...+..+|+|||||+    +++.++.++              
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~----D~i~sr~L~~gYg~~~~~~pi~a  166 (844)
T TIGR02621        91 DVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTV----DMIGSRLLFSGYGCGFKSRPLHA  166 (844)
T ss_pred             ccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECH----HHHcCCccccccccccccccchh
Confidence                                  00           577777778899999994    667666652              


Q ss_pred             --cccccceEEEEcccccccccccccC
Q 031654          130 --LQMIIRYLALKEAADQTLDMALNQK  154 (155)
Q Consensus       130 --l~~l~~~lVlDEa~D~ll~~gf~~~  154 (155)
                        ++++ +++||||| |  +++||.++
T Consensus       167 g~L~~v-~~LVLDEA-D--Ld~gF~~~  189 (844)
T TIGR02621       167 GFLGQD-ALIVHDEA-H--LEPAFQEL  189 (844)
T ss_pred             hhhccc-eEEEEehh-h--hccccHHH
Confidence              7889 99999999 9  89999763

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.63  E-value=1.3e-15  Score=133.18  Aligned_cols=97  Identities=18%  Similarity=0.220  Sum_probs=75.3

Q ss_pred             HhHHhCCCCCCCHHHHHHHHHHhcC------CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------------
Q 031654           42 NKPRTYKYVKPTPVQRHATSILVAG------RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------------   98 (155)
Q Consensus        42 ~~l~~~g~~~pt~iQ~~~i~~~l~g------~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------------   98 (155)
                      +....++| .||++|.+|++.+.++      .|++++|+||||||++|++|++..+.......                 
T Consensus       253 ~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l~  331 (681)
T PRK10917        253 KFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLK  331 (681)
T ss_pred             HHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHHH
Confidence            34466788 5999999999999887      48999999999999999999988775422111                 


Q ss_pred             ----------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 ----------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ----------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                            ..+...+.. .++|+||||+++.     ..+.+.++ +++|+||+ |++
T Consensus       332 ~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~-----~~v~~~~l-~lvVIDE~-Hrf  395 (681)
T PRK10917        332 KLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQ-----DDVEFHNL-GLVIIDEQ-HRF  395 (681)
T ss_pred             HHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhc-----ccchhccc-ceEEEech-hhh
Confidence                                  222334444 4999999998864     34568899 99999999 985

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.62  E-value=2.1e-15  Score=135.05  Aligned_cols=101  Identities=22%  Similarity=0.277  Sum_probs=77.2

Q ss_pred             HHHHHhH-HhCCCCCCCHHHHHHHHHHhcC------CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------
Q 031654           38 QHLRNKP-RTYKYVKPTPVQRHATSILVAG------RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------   98 (155)
Q Consensus        38 ~~l~~~l-~~~g~~~pt~iQ~~~i~~~l~g------~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------   98 (155)
                      ..+.+.+ ..++|+ ||++|..||+.++++      .|++++|+||||||.+|++|++..+.......            
T Consensus       438 ~~~~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~  516 (926)
T TIGR00580       438 LEWQQEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQH  516 (926)
T ss_pred             HHHHHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHH
Confidence            4555555 456885 999999999999885      79999999999999999999988776543221            


Q ss_pred             ---------------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 ---------------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ---------------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                 ......+.. .++||||||..    + .+.+.+.++ +++||||+ |++
T Consensus       517 ~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~l----l-~~~v~f~~L-~llVIDEa-hrf  585 (926)
T TIGR00580       517 FETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKL----L-QKDVKFKDL-GLLIIDEE-QRF  585 (926)
T ss_pred             HHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHH----h-hCCCCcccC-CEEEeecc-ccc
Confidence                                       122233433 58999999942    2 356789999 99999999 985

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=99.61  E-value=2.6e-15  Score=130.34  Aligned_cols=101  Identities=16%  Similarity=0.226  Sum_probs=77.4

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcC------CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAG------RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g------~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------   98 (155)
                      ..+.+.++.++| .||+.|.+||+.++++      .+.+++|+||||||++|++|++..+.......             
T Consensus       223 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g~qvlilaPT~~LA~Q~~  301 (630)
T TIGR00643       223 ELLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHY  301 (630)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEECCHHHHHHHHH
Confidence            445566788899 7999999999999876      26899999999999999999988765432211             


Q ss_pred             --------------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 --------------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 --------------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                ..+...+.. .++|+|+||+++.+     .+.+.++ .++|+||+ |++
T Consensus       302 ~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l-~lvVIDEa-H~f  369 (630)
T TIGR00643       302 NSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRL-ALVIIDEQ-HRF  369 (630)
T ss_pred             HHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----ccccccc-ceEEEech-hhc
Confidence                                      112233332 58999999998643     4568899 99999999 983

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.56  E-value=1.9e-14  Score=131.24  Aligned_cols=101  Identities=19%  Similarity=0.243  Sum_probs=75.9

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcC------CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAG------RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g------~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------   98 (155)
                      ++..+...+++| .||++|.+||+.++.+      +|++++|+||||||.+|+.+++..+.......             
T Consensus       588 ~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~g~qvlvLvPT~eLA~Q~~  666 (1147)
T PRK10689        588 EQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHY  666 (1147)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHH
Confidence            455566678889 7999999999999987      89999999999999999888765543221111             


Q ss_pred             -----------------------HHHH---HHHh-cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 -----------------------RKEL---RELA-RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 -----------------------~~~~---~~l~-~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                             .++.   ..+. ..+||+||||+.+     ...+.+.++ ++|||||+ |++
T Consensus       667 ~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL-----~~~v~~~~L-~lLVIDEa-hrf  734 (1147)
T PRK10689        667 DNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL-----QSDVKWKDL-GLLIVDEE-HRF  734 (1147)
T ss_pred             HHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH-----hCCCCHhhC-CEEEEech-hhc
Confidence                                   1222   2222 3689999999643     245678899 99999999 996

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.55  E-value=3.8e-14  Score=103.47  Aligned_cols=101  Identities=33%  Similarity=0.471  Sum_probs=82.0

Q ss_pred             hCCCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------
Q 031654           46 TYKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------   98 (155)
Q Consensus        46 ~~g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------   98 (155)
                      ..++..|++.|.+++..+..+ ++++++++||||||.+++.+++..+.......                          
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~   82 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLGPSLG   82 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHhccCC
Confidence            457889999999999999999 99999999999999999999888776541111                          


Q ss_pred             ------------HHHHHHHhcCC-cEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 ------------RKELRELARWV-DNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 ------------~~~~~~l~~~~-~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                  ......+..+. +++++|++.+.+.+.........+ +++|+||+ |.+..
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~-~~iIiDE~-h~~~~  143 (201)
T smart00487       83 LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNV-DLVILDEA-HRLLD  143 (201)
T ss_pred             eEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHC-CEEEEECH-HHHhc
Confidence                        11122233344 999999999999999887788889 99999999 88775

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.53  E-value=2.9e-14  Score=125.46  Aligned_cols=103  Identities=20%  Similarity=0.227  Sum_probs=78.7

Q ss_pred             HHHhHH-hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------
Q 031654           40 LRNKPR-TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------   98 (155)
Q Consensus        40 l~~~l~-~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------   98 (155)
                      +.++.. .+|. +|+++|..+++.+..|+  ++.+.||+|||++|++|++..........                    
T Consensus        67 vrea~~R~~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~G~~v~VvTpt~~LA~qd~e~~~~l~  143 (790)
T PRK09200         67 VREAAKRVLGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEGKGVHLITVNDYLAKRDAEEMGQVY  143 (790)
T ss_pred             HHHHHHHHhCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHHHHH
Confidence            334443 3466 89999999999999987  99999999999999999986555433222                    


Q ss_pred             --------------H-HHHHHHhcCCcEEEEChHHH-HHHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 --------------R-KELRELARWVDNLMATLRRL-VNLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --------------~-~~~~~l~~~~~IlI~TP~~l-~~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                                    . ...+....+|||++|||+++ .++++.+.      ..++.+ +++||||| |.||
T Consensus       144 ~~lGl~v~~i~g~~~~~~~r~~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~-~~~IvDEa-DsiL  212 (790)
T PRK09200        144 EFLGLTVGLNFSDIDDASEKKAIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPL-NYAIIDEI-DSIL  212 (790)
T ss_pred             hhcCCeEEEEeCCCCcHHHHHHhcCCCEEEECCccccchhHHhccccchhhhccccc-ceEEEecc-ccce
Confidence                          2 34444456799999999999 56665432      356888 99999999 9998

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.52  E-value=2.1e-14  Score=125.13  Aligned_cols=104  Identities=21%  Similarity=0.192  Sum_probs=78.6

Q ss_pred             HHHhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------
Q 031654           40 LRNKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------   98 (155)
Q Consensus        40 l~~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------   98 (155)
                      +.++..+ +|. +|+++|..+.+.+..|+  ++.++||+|||++|++|++-.........                    
T Consensus        45 vrEa~~R~lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~~V~VvTpt~~LA~qdae~~~~l~  121 (745)
T TIGR00963        45 VREASKRVLGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAEWMGQVY  121 (745)
T ss_pred             HHHHHHHHhCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhCCCEEEEcCCHHHHHHHHHHHHHHh
Confidence            3344433 354 88999999999998887  99999999999999999964444332211                    


Q ss_pred             --------------HHHHHHHhcCCcEEEEChHHH-HHHHHcC------CCCcccccceEEEEcccccccc
Q 031654           99 --------------RKELRELARWVDNLMATLRRL-VNLLERG------RVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 --------------~~~~~~l~~~~~IlI~TP~~l-~~~l~~~------~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                    ..+.+.....+||++|||++| .++++.+      .+.++.+ .++|+||+ |.|+=
T Consensus       122 ~~LGLsv~~i~g~~~~~~r~~~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l-~~aIIDEa-Ds~LI  190 (745)
T TIGR00963       122 RFLGLSVGLILSGMSPEERREAYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPF-HFAIIDEV-DSILI  190 (745)
T ss_pred             ccCCCeEEEEeCCCCHHHHHHhcCCCEEEECCCchhhHHHhcccccchhhhhcccc-ceeEeecH-HHHhH
Confidence                          222233334589999999999 8998876      3578899 99999999 99984

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.

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.50  E-value=3.3e-14  Score=125.28  Aligned_cols=112  Identities=14%  Similarity=0.128  Sum_probs=86.7

Q ss_pred             CCHHHHHhHHhCCCCCCCHHHHHHHHHH-hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHH
Q 031654           36 VPQHLRNKPRTYKYVKPTPVQRHATSIL-VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRE  104 (155)
Q Consensus        36 l~~~l~~~l~~~g~~~pt~iQ~~~i~~~-l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~  104 (155)
                      +++.+.+.++..|+....+-|+.++... ..|+|+++++|||||||+..++.+++.+.......          .+..+.
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~   95 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEE   95 (766)
T ss_pred             ccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHH
Confidence            4478888888889987777777777655 45699999999999999999999999998752222          222222


Q ss_pred             Hh-----------------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          105 LA-----------------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       105 l~-----------------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      +.                       .+++|+|+||+++-.++++...-...+ ++||+||+ |.+-|.
T Consensus        96 ~~~~~~~GirV~~~TgD~~~~~~~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V-~lvViDEi-H~l~d~  161 (766)
T COG1204          96 FSRLEELGIRVGISTGDYDLDDERLARYDVIVTTPEKLDSLTRKRPSWIEEV-DLVVIDEI-HLLGDR  161 (766)
T ss_pred             hhhHHhcCCEEEEecCCcccchhhhccCCEEEEchHHhhHhhhcCcchhhcc-cEEEEeee-eecCCc
Confidence            21                       358999999999888887777778899 99999999 666543

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.50  E-value=4.5e-14  Score=123.55  Aligned_cols=98  Identities=20%  Similarity=0.153  Sum_probs=73.0

Q ss_pred             CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------------------
Q 031654           47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------------------   98 (155)
Q Consensus        47 ~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------------------   98 (155)
                      +|. +|+++|..+...+..|  .+++++||+|||++|++|++..........                            
T Consensus        67 lgl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~  143 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALTGKGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVS  143 (762)
T ss_pred             cCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhcCCceEEeCCCHHHHHHHHHHHHHHHhhcCCcEE
Confidence            365 7888888888777776  699999999999999999876665433211                            


Q ss_pred             -----------HHHHHHHhcCCcEEEEChHHH-HHHHHcC------CCCcccccceEEEEccccccccc
Q 031654           99 -----------RKELRELARWVDNLMATLRRL-VNLLERG------RVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 -----------~~~~~~l~~~~~IlI~TP~~l-~~~l~~~------~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                 ..+.+....+|||++|||++| .+++..+      ...++.+ .++|+||| |.||-+
T Consensus       144 ~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l-~~~IVDEa-DsILiD  210 (762)
T TIGR03714       144 LGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPF-NYVIVDEV-DSVLLD  210 (762)
T ss_pred             EEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccC-cEEEEecH-hhHhhc
Confidence                       112233345899999999999 5655432      3457889 99999999 999754

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.

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

Probab=99.49  E-value=2.2e-14  Score=126.74  Aligned_cols=111  Identities=16%  Similarity=0.208  Sum_probs=81.0

Q ss_pred             ccccCCHHHHHhHHhCCCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------
Q 031654           32 RFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------   98 (155)
Q Consensus        32 ~f~~l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------   98 (155)
                      +.++|+..-.  ..-++|+.++.+|+.++|.+.+. .|.+||||||||||..|+|.+++.+.+.....            
T Consensus        93 ~isdld~~~r--k~~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYI  170 (1230)
T KOG0952|consen   93 SISDLDDVGR--KGFFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYI  170 (1230)
T ss_pred             eEEecchhhh--hhcccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEE
Confidence            3444443322  34457899999999999999876 79999999999999999999999998622111            


Q ss_pred             --------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCC----CcccccceEEEEcc
Q 031654           99 --------------------------------RKELRELARWVDNLMATLRRLVNLLERGRV----SLQMIIRYLALKEA  142 (155)
Q Consensus        99 --------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~----~l~~l~~~lVlDEa  142 (155)
                                                      .--..+ ...++|||+||++ .|.+.++..    .++.+ ++||+||+
T Consensus       171 aPmKALa~Em~~~~~kkl~~~gi~v~ELTGD~ql~~te-i~~tqiiVTTPEK-wDvvTRk~~~d~~l~~~V-~LviIDEV  247 (1230)
T KOG0952|consen  171 APMKALAAEMVDKFSKKLAPLGISVRELTGDTQLTKTE-IADTQIIVTTPEK-WDVVTRKSVGDSALFSLV-RLVIIDEV  247 (1230)
T ss_pred             echHHHHHHHHHHHhhhcccccceEEEecCcchhhHHH-HHhcCEEEecccc-eeeeeeeeccchhhhhhe-eeEEeeee
Confidence                                            011111 2358999999999 677776543    35677 99999999


Q ss_pred             cccccc
Q 031654          143 ADQTLD  148 (155)
Q Consensus       143 ~D~ll~  148 (155)
                       |.|-|
T Consensus       248 -HlLhd  252 (1230)
T KOG0952|consen  248 -HLLHD  252 (1230)
T ss_pred             -hhhcC
Confidence             65544

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

Probab=99.44  E-value=1.8e-13  Score=116.70  Aligned_cols=112  Identities=18%  Similarity=0.243  Sum_probs=81.4

Q ss_pred             HHhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHH------------HHHhhhch---------
Q 031654           41 RNKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIING------------IMREYYSA---------   98 (155)
Q Consensus        41 ~~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~------------l~~~~~~~---------   98 (155)
                      .+.|+. +||..+.+-|.++|..+++|+|+++.-|||.||++||.+|.+-.            |++.....         
T Consensus         6 ~~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~~G~TLVVSPLiSLM~DQV~~l~~~Gi~A~   85 (590)
T COG0514           6 QQVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLLEGLTLVVSPLISLMKDQVDQLEAAGIRAA   85 (590)
T ss_pred             HHHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhcCCCEEEECchHHHHHHHHHHHHHcCceee
Confidence            344544 49999999999999999999999999999999999999998754            11110000         


Q ss_pred             -----------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccc--cccC
Q 031654           99 -----------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMA--LNQK  154 (155)
Q Consensus        99 -----------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~g--f~~~  154 (155)
                                 ......+.. ..++|.-+|++|..--..+.+.-..+ .++||||| |++.++|  |.++
T Consensus        86 ~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i-~l~vIDEA-HCiSqWGhdFRP~  153 (590)
T COG0514          86 YLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPI-SLVAIDEA-HCISQWGHDFRPD  153 (590)
T ss_pred             hhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCC-ceEEechH-HHHhhcCCccCHh
Confidence                       112222222 47999999999855433333335567 89999999 9999998  6653

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.42  E-value=4.2e-13  Score=116.12  Aligned_cols=93  Identities=25%  Similarity=0.242  Sum_probs=73.0

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      +|+++|..++|.++.|+  ++.+.||+|||++|++|++..........                                
T Consensus       103 ~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~G~~v~VvTptreLA~qdae~~~~l~~~lGlsv~~i~g  180 (656)
T PRK12898        103 RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALAGLPVHVITVNDYLAERDAELMRPLYEALGLTVGCVVE  180 (656)
T ss_pred             CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcCCeEEEEcCcHHHHHHHHHHHHHHHhhcCCEEEEEeC
Confidence            78999999999999999  99999999999999999998776433221                                


Q ss_pred             --HHHHHHHhcCCcEEEEChHHH-HHHHHcCC-------------------------CCcccccceEEEEccccccc
Q 031654           99 --RKELRELARWVDNLMATLRRL-VNLLERGR-------------------------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~-------------------------~~l~~l~~~lVlDEa~D~ll  147 (155)
                        ..+.+....+|||++||...+ .|+|+.+.                         .-...+ .+.||||| |.+|
T Consensus       181 g~~~~~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~-~~aIvDEv-DSiL  255 (656)
T PRK12898        181 DQSPDERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGL-HFAIVDEA-DSVL  255 (656)
T ss_pred             CCCHHHHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhccccc-ceeEeecc-ccee
Confidence              344555567899999999887 44554331                         113557 89999999 9887

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.42  E-value=1.9e-13  Score=126.52  Aligned_cols=77  Identities=21%  Similarity=0.191  Sum_probs=59.7

Q ss_pred             EEccCCCCcchhhhhHHHHHHHHhh----------hch------------H-----------------------------
Q 031654           71 ACAQTGSRKTTPFCFPIINGIMREY----------YSA------------R-----------------------------   99 (155)
Q Consensus        71 ~~a~TGsGKT~~yllp~l~~l~~~~----------~~~------------~-----------------------------   99 (155)
                      ++||||||||+||.+|+++++....          ...            .                             
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            5799999999999999999997542          011            1                             


Q ss_pred             ----------HHHHHHhcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEEccccccccc
Q 031654          100 ----------KELRELARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       100 ----------~~~~~l~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                ++.+.+++.+||||+||++|..++.++ ...++++ ++|||||+ |.|++.
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~V-r~VIVDE~-H~L~g~  139 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGV-ETVIIDEV-HAVAGS  139 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccC-CEEEEecH-HHhccc
Confidence                      111223357899999999999988764 3578999 99999999 999975

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

Probab=99.42  E-value=9.5e-13  Score=111.12  Aligned_cols=111  Identities=20%  Similarity=0.199  Sum_probs=83.2

Q ss_pred             cCCHHHHHhHHhCCCCCCCHHHHHHHHH-HhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh-----------------
Q 031654           35 YVPQHLRNKPRTYKYVKPTPVQRHATSI-LVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY-----------------   96 (155)
Q Consensus        35 ~l~~~l~~~l~~~g~~~pt~iQ~~~i~~-~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~-----------------   96 (155)
                      ++|+.+.+.|+..|++.+.|+|..|+.. ++.|.|.+++++|+||||+.--++-+.++.....                 
T Consensus       200 dipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVALANQKy~  279 (830)
T COG1202         200 DIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYE  279 (830)
T ss_pred             CCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCCeEEEEehhHHhhcchHH
Confidence            3459999999999999999999999975 5799999999999999998854444444443221                 


Q ss_pred             chHHHHH------------------------HHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           97 SARKELR------------------------ELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        97 ~~~~~~~------------------------~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      ...+...                        .....+||+|||-+.+-.+++.+ .++.++ ..+|+||+ |.|=|
T Consensus       280 dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdi-GtVVIDEi-HtL~d  352 (830)
T COG1202         280 DFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDI-GTVVIDEI-HTLED  352 (830)
T ss_pred             HHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-Cccccc-ceEEeeee-eeccc
Confidence            1111111                        11125799999999988888777 789999 99999999 55443

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.41  E-value=3.8e-13  Score=118.99  Aligned_cols=93  Identities=20%  Similarity=0.196  Sum_probs=70.7

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      +|+++|-..--.+..|+  ++.++||+|||++|++|++..+.......                                
T Consensus        82 ~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~i~g  159 (896)
T PRK13104         82 RHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISGRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGVIYP  159 (896)
T ss_pred             CcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhcCCCEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeC
Confidence            67888877655555555  88999999999999999998776543221                                


Q ss_pred             --HHHHHHHhcCCcEEEEChHHH-HHHHHcC-CCCc-----ccccceEEEEccccccc
Q 031654           99 --RKELRELARWVDNLMATLRRL-VNLLERG-RVSL-----QMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --~~~~~~l~~~~~IlI~TP~~l-~~~l~~~-~~~l-----~~l~~~lVlDEa~D~ll  147 (155)
                        ....+.....|||++|||++| .++++.+ .+++     ..+ .++||||| |.||
T Consensus       160 g~~~~~r~~~y~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l-~~~IvDEa-DsiL  215 (896)
T PRK13104        160 DMSHKEKQEAYKADIVYGTNNEYGFDYLRDNMAFSLTDKVQREL-NFAIVDEV-DSIL  215 (896)
T ss_pred             CCCHHHHHHHhCCCEEEECChhhhHHHHhcCCccchHhhhcccc-ceEEeccH-hhhh
Confidence              112222233699999999999 9999877 3455     588 99999999 9998

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

Probab=99.40  E-value=2.8e-12  Score=114.72  Aligned_cols=59  Identities=15%  Similarity=0.168  Sum_probs=48.1

Q ss_pred             cccCCHHHHHhHHhCCCCCCCHHHHHHHH----HHhcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           33 FAYVPQHLRNKPRTYKYVKPTPVQRHATS----ILVAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        33 f~~l~~~l~~~l~~~g~~~pt~iQ~~~i~----~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      |..+.+.+.+.+...||+ ++|.|.+.+.    .+.+|+++++.||||+|||++|++|++..+.
T Consensus       228 ~~~~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~  290 (850)
T TIGR01407       228 YNTLSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI  290 (850)
T ss_pred             cccccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc
Confidence            333335778888888997 7899998665    5567899999999999999999999987654

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.34  E-value=4e-12  Score=107.86  Aligned_cols=97  Identities=10%  Similarity=0.019  Sum_probs=68.5

Q ss_pred             CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh-ch-------------HHHHHHHh--------
Q 031654           49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY-SA-------------RKELRELA--------  106 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~-~~-------------~~~~~~l~--------  106 (155)
                      ...|++.|.++++.++.+++.++++|||+|||+++..-+ ..+..... ..             ........        
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~-~~~~~~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~  190 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLS-RYYLENYEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMH  190 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHH-HHHHhcCCCeEEEEECcHHHHHHHHHHHHHhcccccccee
Confidence            458999999999999999999999999999999765422 22222221 11             11111110        


Q ss_pred             ---------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654          107 ---------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       107 ---------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                               .+++|+|+||+++.+...   ..++++ .++|+||| |++....|
T Consensus       191 ~i~~g~~~~~~~~I~VaT~qsl~~~~~---~~~~~~-~~iIvDEa-H~~~~~~~  239 (501)
T PHA02558        191 KIYSGTAKDTDAPIVVSTWQSAVKQPK---EWFDQF-GMVIVDEC-HLFTGKSL  239 (501)
T ss_pred             EEecCcccCCCCCEEEeeHHHHhhchh---hhcccc-CEEEEEch-hcccchhH
Confidence                     236899999999875432   246789 99999999 99986554

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.32  E-value=2.3e-12  Score=114.50  Aligned_cols=91  Identities=18%  Similarity=0.168  Sum_probs=67.0

Q ss_pred             HHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------HHHH-H------------------HHh
Q 031654           58 HATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------RKEL-R------------------ELA  106 (155)
Q Consensus        58 ~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------~~~~-~------------------~l~  106 (155)
                      ..+..+.++.+++++|+||||||.+|.+|+++.........            .... .                  ...
T Consensus         9 ~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~~~~~s   88 (819)
T TIGR01970         9 ALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRGENKVS   88 (819)
T ss_pred             HHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhccCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEccccccC
Confidence            44556667899999999999999999999998753211111            1111 1                  112


Q ss_pred             cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccc-ccccccc
Q 031654          107 RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAAD-QTLDMAL  151 (155)
Q Consensus       107 ~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D-~ll~~gf  151 (155)
                      ...+|+|+|||+|++++..+ ..++++ ++|||||+ | ++++.+|
T Consensus        89 ~~t~I~v~T~G~Llr~l~~d-~~L~~v-~~VIiDEa-HER~L~~Dl  131 (819)
T TIGR01970        89 RRTRLEVVTEGILTRMIQDD-PELDGV-GALIFDEF-HERSLDADL  131 (819)
T ss_pred             CCCcEEEECCcHHHHHHhhC-cccccC-CEEEEecc-chhhhccch
Confidence            35799999999999999864 579999 99999999 9 5777543

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>PRK13766 Hef nuclease; Provisional

Probab=99.32  E-value=9.5e-12  Score=110.22  Aligned_cols=96  Identities=20%  Similarity=0.195  Sum_probs=76.8

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------------------------
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------------------------   98 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------------------------   98 (155)
                      -.|++.|......++.+ |+++++|||+|||++|++++...+.......                               
T Consensus        14 ~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~   92 (773)
T PRK13766         14 IEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVF   92 (773)
T ss_pred             CCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEE
Confidence            46789999999888887 9999999999999999999887764221111                               


Q ss_pred             -----HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 -----RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 -----~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                           ..+...+..+++|+|+||+.+...+..+.+.+.++ .++|+||| |++..
T Consensus        93 ~g~~~~~~r~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~-~liVvDEa-H~~~~  145 (773)
T PRK13766         93 TGEVSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDV-SLLIFDEA-HRAVG  145 (773)
T ss_pred             eCCCCHHHHHHHHhCCCEEEECHHHHHHHHHcCCCChhhC-cEEEEECC-ccccc
Confidence                 12223344568999999999998888888899999 99999999 98864

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.28  E-value=4.8e-12  Score=110.38  Aligned_cols=88  Identities=13%  Similarity=0.127  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHhcCCcEEEEccCCCCcchh---------hhhHHHHHHHH---hhh--ch-------------HHHH----
Q 031654           54 PVQRHATSILVAGRDLMACAQTGSRKTTP---------FCFPIINGIMR---EYY--SA-------------RKEL----  102 (155)
Q Consensus        54 ~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~---------yllp~l~~l~~---~~~--~~-------------~~~~----  102 (155)
                      .+|.++++.+++|+|++++|+||||||.+         |++|.+..+..   ...  ..             ....    
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~v  246 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSL  246 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHh
Confidence            48999999999999999999999999997         66666665532   110  01             0000    


Q ss_pred             ----------------------HHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccc
Q 031654          103 ----------------------RELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       103 ----------------------~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                            ....++.+|+|+|++.       ....++++ ++|||||| |++..++
T Consensus       247 g~~~~~g~~v~v~~Gg~~~~~~~t~~k~~~Ilv~T~~L-------~l~~L~~v-~~VVIDEa-HEr~~~~  307 (675)
T PHA02653        247 GFDEIDGSPISLKYGSIPDELINTNPKPYGLVFSTHKL-------TLNKLFDY-GTVIIDEV-HEHDQIG  307 (675)
T ss_pred             CccccCCceEEEEECCcchHHhhcccCCCCEEEEeCcc-------cccccccC-CEEEcccc-ccCccch
Confidence                                  1111245789999752       12357889 99999999 9998876

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.27  E-value=1.8e-11  Score=107.33  Aligned_cols=87  Identities=16%  Similarity=0.183  Sum_probs=65.8

Q ss_pred             CCCHHHHHHHHHHhcC---CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------------------------
Q 031654           51 KPTPVQRHATSILVAG---RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g---~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------------------------   98 (155)
                      .+|+.|++++..+.++   +++++.++||||||.+|+.++...+..+....                             
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s  223 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHS  223 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEEC
Confidence            5899999999999874   88999999999999999988776665432211                             


Q ss_pred             ----HH---HHHHH-hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 ----RK---ELREL-ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ----~~---~~~~l-~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                          .+   ....+ ...++|+||||+.+.       ..++++ .++|+||+ |..
T Consensus       224 ~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l-~liVvDEe-h~~  270 (679)
T PRK05580        224 GLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNL-GLIIVDEE-HDS  270 (679)
T ss_pred             CCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCC-CEEEEECC-Ccc
Confidence                11   11222 235899999998763       457899 99999999 853

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.26  E-value=4.6e-12  Score=112.63  Aligned_cols=89  Identities=16%  Similarity=0.125  Sum_probs=64.1

Q ss_pred             HHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------HHHH-HH------------------Hh
Q 031654           58 HATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------RKEL-RE------------------LA  106 (155)
Q Consensus        58 ~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------~~~~-~~------------------l~  106 (155)
                      +.+..+.++++++++|+||||||++|.+|+++.........            .... ..                  ..
T Consensus        12 ~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~~~~   91 (812)
T PRK11664         12 ELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAESKVG   91 (812)
T ss_pred             HHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCcCCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCccccC
Confidence            34455667899999999999999999999987542211111            1111 11                  11


Q ss_pred             cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc-cccc
Q 031654          107 RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ-TLDM  149 (155)
Q Consensus       107 ~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~-ll~~  149 (155)
                      ...+|+|+|||+|++++..+ ..++++ +++||||+ |. +++.
T Consensus        92 ~~t~I~v~T~G~Llr~l~~d-~~L~~v-~~IIlDEa-HER~l~~  132 (812)
T PRK11664         92 PNTRLEVVTEGILTRMIQRD-PELSGV-GLVILDEF-HERSLQA  132 (812)
T ss_pred             CCCcEEEEChhHHHHHHhhC-CCcCcC-cEEEEcCC-Ccccccc
Confidence            23589999999999998864 579999 99999999 96 5553

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.25  E-value=2e-11  Score=99.62  Aligned_cols=35  Identities=23%  Similarity=0.302  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhcCCc--EEEEccCCCCcchhhhhHHHH
Q 031654           55 VQRHATSILVAGRD--LMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        55 iQ~~~i~~~l~g~d--vl~~a~TGsGKT~~yllp~l~   89 (155)
                      +|.++++.+.++.+  ++++||||||||.+|++|++.
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~   37 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLH   37 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            59999999999974  789999999999999998764

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.24  E-value=1.3e-11  Score=108.91  Aligned_cols=95  Identities=21%  Similarity=0.160  Sum_probs=70.6

Q ss_pred             CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------------------------
Q 031654           48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------------------------   98 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------------------------   98 (155)
                      |. +|+++|-..--.+..|+  ++.++||+|||+++.+|++-.........                             
T Consensus        79 g~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~~V~IvTpn~yLA~rd~e~~~~l~~~LGlsv~~  155 (830)
T PRK12904         79 GM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTGKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGV  155 (830)
T ss_pred             CC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcCCCEEEEecCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            44 78999998887777775  88999999999999999963333322211                             


Q ss_pred             -----HHHHHHHhcCCcEEEEChHHH-HHHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 -----RKELRELARWVDNLMATLRRL-VNLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 -----~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                           ....+.-.-.+||++|||++| .++++.+.      ..++.+ .++||||| |.||
T Consensus       156 i~~~~~~~er~~~y~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~-~~aIvDEa-DsiL  214 (830)
T PRK12904        156 ILSGMSPEERREAYAADITYGTNNEFGFDYLRDNMVFSLEERVQRGL-NYAIVDEV-DSIL  214 (830)
T ss_pred             EcCCCCHHHHHHhcCCCeEEECCcchhhhhhhcccccchhhhccccc-ceEEEech-hhhe
Confidence                 111111113589999999999 89998764      346788 99999999 9998

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

Probab=99.23  E-value=3e-11  Score=99.24  Aligned_cols=112  Identities=18%  Similarity=0.223  Sum_probs=77.9

Q ss_pred             HHHHHhHHhC-CCCCC-CHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------
Q 031654           38 QHLRNKPRTY-KYVKP-TPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------   98 (155)
Q Consensus        38 ~~l~~~l~~~-g~~~p-t~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------   98 (155)
                      ..+.++|++. |+.++ ++.|..|+..+..+ +||.|+.|||+||++||.||.|-.   .....                
T Consensus         5 r~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~---~gITIV~SPLiALIkDQiDHL   81 (641)
T KOG0352|consen    5 RKVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH---GGITIVISPLIALIKDQIDHL   81 (641)
T ss_pred             HHHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh---CCeEEEehHHHHHHHHHHHHH
Confidence            4567788765 77755 89999999999877 799999999999999999987532   11110                


Q ss_pred             -------------------HHHHHHHh---cCCcEEEEChHHHHHH----HHcCCCCcccccceEEEEcccccccccc--
Q 031654           99 -------------------RKELRELA---RWVDNLMATLRRLVNL----LERGRVSLQMIIRYLALKEAADQTLDMA--  150 (155)
Q Consensus        99 -------------------~~~~~~l~---~~~~IlI~TP~~l~~~----l~~~~~~l~~l~~~lVlDEa~D~ll~~g--  150 (155)
                                         .+.+..|.   ....+|..||+....-    +-++..+-.-+ +|+|+||| |+.-++|  
T Consensus        82 ~~LKVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L-~Y~vVDEA-HCVSQWGHD  159 (641)
T KOG0352|consen   82 KRLKVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVL-RYIVVDEA-HCVSQWGHD  159 (641)
T ss_pred             HhcCCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhcee-eeEEechh-hhHhhhccc
Confidence                               22222332   2568999999874211    11222344567 99999999 9999987  


Q ss_pred             cccC
Q 031654          151 LNQK  154 (155)
Q Consensus       151 f~~~  154 (155)
                      |.+|
T Consensus       160 FRPD  163 (641)
T KOG0352|consen  160 FRPD  163 (641)
T ss_pred             cCcc
Confidence            4443

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.20  E-value=1.4e-11  Score=99.81  Aligned_cols=82  Identities=17%  Similarity=0.079  Sum_probs=56.0

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------HHHHHHH----------------------------
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------RKELREL----------------------------  105 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------~~~~~~l----------------------------  105 (155)
                      |++++||||||||++|++|++..+.......              .+....+                            
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLLHSSSSFKRIKEMGDSEEFEH   80 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHHhCcccEEeeccHHHHHHhccCCchhHHH
Confidence            6899999999999999999998765432111              0000000                            


Q ss_pred             ------h-----cCCcEEEEChHHHHHHHHcCC----CCc--ccccceEEEEccccccccccc
Q 031654          106 ------A-----RWVDNLMATLRRLVNLLERGR----VSL--QMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       106 ------~-----~~~~IlI~TP~~l~~~l~~~~----~~l--~~l~~~lVlDEa~D~ll~~gf  151 (155)
                            .     -.++|+|+||+++...+..+.    ..+  -.. +++|+||| |.+.+.++
T Consensus        81 ~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~-~~iViDE~-h~~~~~~~  141 (358)
T TIGR01587        81 LFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIAN-SLLIFDEV-HFYDEYTL  141 (358)
T ss_pred             HHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcC-CEEEEeCC-CCCCHHHH
Confidence                  0     125799999999988876521    111  234 68999999 99998654

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

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

Probab=99.20  E-value=2.9e-11  Score=105.06  Aligned_cols=107  Identities=16%  Similarity=0.100  Sum_probs=81.9

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------HHHH----
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------RKEL----  102 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------~~~~----  102 (155)
                      +...+...--..-.+..-|.......+ |+|+++++|||+|||...+.-+++++.......           .+|.    
T Consensus        49 ~s~~~~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~  127 (746)
T KOG0354|consen   49 ESAAQRWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFS  127 (746)
T ss_pred             hhhhccccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHh
Confidence            444443333344467888999888888 999999999999999999999999987665533           2222    


Q ss_pred             ---------------------HHHhcCCcEEEEChHHHHHHHHcCCCC-cccccceEEEEccccccc
Q 031654          103 ---------------------RELARWVDNLMATLRRLVNLLERGRVS-LQMIIRYLALKEAADQTL  147 (155)
Q Consensus       103 ---------------------~~l~~~~~IlI~TP~~l~~~l~~~~~~-l~~l~~~lVlDEa~D~ll  147 (155)
                                           ..+....+|+++||.-|.+.|.++..+ ++.+ .++|+||| |+-.
T Consensus       128 ~~~~~~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~f-s~iv~DE~-Hra~  192 (746)
T KOG0354|consen  128 IYLIPYSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDF-SLIVFDEC-HRTS  192 (746)
T ss_pred             hccCcccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceE-EEEEEccc-cccc
Confidence                                 233346899999999999999887544 5999 99999999 8743

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.16  E-value=4.3e-11  Score=109.69  Aligned_cols=89  Identities=19%  Similarity=0.185  Sum_probs=60.8

Q ss_pred             HHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc-h------------------HHHHH---------------H
Q 031654           59 ATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-A------------------RKELR---------------E  104 (155)
Q Consensus        59 ~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~-~------------------~~~~~---------------~  104 (155)
                      .+..+..+..++++|+||||||.  .+|.+..-...... .                  .+...               .
T Consensus        82 Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~vrf~~~  159 (1294)
T PRK11131         82 ILEAIRDHQVVIVAGETGSGKTT--QLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKVRFNDQ  159 (1294)
T ss_pred             HHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceeceeecCccc
Confidence            44455555677888999999999  57843322111100 0                  01110               1


Q ss_pred             HhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccc-cccccccc
Q 031654          105 LARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAAD-QTLDMALN  152 (155)
Q Consensus       105 l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D-~ll~~gf~  152 (155)
                      ...+++|+++|||+|++.+..+. .++++ ++|||||| | ++++.+|.
T Consensus       160 ~s~~t~I~v~TpG~LL~~l~~d~-~Ls~~-~~IIIDEA-HERsLn~DfL  205 (1294)
T PRK11131        160 VSDNTMVKLMTDGILLAEIQQDR-LLMQY-DTIIIDEA-HERSLNIDFI  205 (1294)
T ss_pred             cCCCCCEEEEChHHHHHHHhcCC-ccccC-cEEEecCc-cccccccchH
Confidence            12358999999999999998664 49999 99999999 9 68998874

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

Probab=99.12  E-value=3.2e-10  Score=102.41  Aligned_cols=45  Identities=18%  Similarity=0.202  Sum_probs=36.5

Q ss_pred             CCCCCCHHHHHHHHHH----hcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           48 KYVKPTPVQRHATSIL----VAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~----l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      || .+.|-|.+....+    ..++.+++.||||+|||++|++|++.....
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 6799999955544    467899999999999999999999866543

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.11  E-value=6e-11  Score=105.11  Aligned_cols=95  Identities=20%  Similarity=0.161  Sum_probs=70.7

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      +|+++|-..--.+..|+  ++.++||+|||++|.+|++..........                                
T Consensus        82 ~~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~g~~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv~~i~~  159 (908)
T PRK13107         82 RHFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALTGKGVHVITVNDYLARRDAENNRPLFEFLGLTVGINVA  159 (908)
T ss_pred             CcCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEEecC
Confidence            67888876554554554  88999999999999999988776554322                                


Q ss_pred             --HHHHHHHhcCCcEEEEChHHH-HHHHHcC-CCCc-----ccccceEEEEccccccccc
Q 031654           99 --RKELRELARWVDNLMATLRRL-VNLLERG-RVSL-----QMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 --~~~~~~l~~~~~IlI~TP~~l-~~~l~~~-~~~l-----~~l~~~lVlDEa~D~ll~~  149 (155)
                        ....+.-.-.|||++|||+++ .++|+.+ .++.     ..+ .++|+||| |.||-.
T Consensus       160 ~~~~~~r~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~-~~aIvDEv-DsiLiD  217 (908)
T PRK13107        160 GLGQQEKKAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPL-HYALIDEV-DSILID  217 (908)
T ss_pred             CCCHHHHHhcCCCCeEEeCCCcccchhhhccCccchhhhhcccc-ceeeecch-hhhccc
Confidence              112222223799999999999 8988877 4444     778 99999999 999854

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

Probab=99.09  E-value=3.4e-10  Score=94.44  Aligned_cols=93  Identities=23%  Similarity=0.171  Sum_probs=74.5

Q ss_pred             CCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------------------------------
Q 031654           52 PTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------------------------------   98 (155)
Q Consensus        52 pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------------------------------   98 (155)
                      +..-|.......+.+ |++++.|||-|||...++-+.+++.......                                 
T Consensus        16 ~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltG   94 (542)
T COG1111          16 PRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTG   94 (542)
T ss_pred             HHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCCeEEEecCCchHHHHHHHHHHHHhCCChhheeeecC
Confidence            344444444444444 9999999999999999999988887766522                                 


Q ss_pred             ---HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccc
Q 031654           99 ---RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 ---~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                         .+.....+...+|+|+||..+.+-+..+.+++.++ .++|+||| |+=.
T Consensus        95 ev~p~~R~~~w~~~kVfvaTPQvveNDl~~Grid~~dv-~~lifDEA-HRAv  144 (542)
T COG1111          95 EVRPEEREELWAKKKVFVATPQVVENDLKAGRIDLDDV-SLLIFDEA-HRAV  144 (542)
T ss_pred             CCChHHHHHHHhhCCEEEeccHHHHhHHhcCccChHHc-eEEEechh-hhcc
Confidence               44456666778999999999999999999999999 99999999 8743

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.07  E-value=5.6e-10  Score=76.83  Aligned_cols=82  Identities=30%  Similarity=0.368  Sum_probs=60.2

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------------------------------HHHHHHHhcCC
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------------------------------RKELRELARWV  109 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------------------------------~~~~~~l~~~~  109 (155)
                      +++++.++||+|||..++..+...........                                     ..........+
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQEKLLSGKT   80 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcchhHHHHHhcCCC
Confidence            47899999999999999888877665311111                                     11111224578


Q ss_pred             cEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccc
Q 031654          110 DNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       110 ~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                      +|+++|++.+...+.......... .++|+||+ |.+....
T Consensus        81 ~i~i~t~~~~~~~~~~~~~~~~~~-~~iiiDE~-h~~~~~~  119 (144)
T cd00046          81 DIVVGTPGRLLDELERLKLSLKKL-DLLILDEA-HRLLNQG  119 (144)
T ss_pred             CEEEECcHHHHHHHHcCCcchhcC-CEEEEeCH-HHHhhcc
Confidence            999999999988887766666778 99999999 8887654

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

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

Probab=99.02  E-value=2.1e-09  Score=96.73  Aligned_cols=103  Identities=27%  Similarity=0.363  Sum_probs=80.8

Q ss_pred             HHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHH----------
Q 031654           44 PRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRE----------  104 (155)
Q Consensus        44 l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~----------  104 (155)
                      ....+| .+.++|++++-++-+|..|+++||||||||+..-.++...+..+....         ++..++          
T Consensus       113 ~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~qrviYTsPIKALsNQKyrdl~~~fgdv~~  191 (1041)
T COG4581         113 AREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQRVIYTSPIKALSNQKYRDLLAKFGDVAD  191 (1041)
T ss_pred             HHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCCceEeccchhhhhhhHHHHHHHHhhhhhh
Confidence            345677 678999999999999999999999999999997777665555444322         111111          


Q ss_pred             ----------HhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          105 ----------LARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       105 ----------l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                +..++.++|.|-+-|-+++.++...+..+ .+||+||+ |.|=|.
T Consensus       192 ~vGL~TGDv~IN~~A~clvMTTEILRnMlyrg~~~~~~i-~~ViFDEv-Hyi~D~  244 (1041)
T COG4581         192 MVGLMTGDVSINPDAPCLVMTTEILRNMLYRGSESLRDI-EWVVFDEV-HYIGDR  244 (1041)
T ss_pred             hccceecceeeCCCCceEEeeHHHHHHHhccCccccccc-ceEEEEee-eecccc
Confidence                      11257899999999999999999999999 99999999 887664

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

Probab=98.99  E-value=6.1e-10  Score=99.92  Aligned_cols=111  Identities=18%  Similarity=0.192  Sum_probs=78.5

Q ss_pred             HHHHh-HHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHH------------HHHhhhch-------
Q 031654           39 HLRNK-PRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIING------------IMREYYSA-------   98 (155)
Q Consensus        39 ~l~~~-l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~------------l~~~~~~~-------   98 (155)
                      ++... ...+|.+.+.+-|.++|-..+.|+|+++..|||.||++||.+|++-.            |+......       
T Consensus       251 ~~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~~gitvVISPL~SLm~DQv~~L~~~~I~  330 (941)
T KOG0351|consen  251 ELELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLLGGVTVVISPLISLMQDQVTHLSKKGIP  330 (941)
T ss_pred             HHHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeeccccccCCceEEeccHHHHHHHHHHhhhhcCcc
Confidence            34444 45669999999999999999999999999999999999999986421            11000000       


Q ss_pred             -------------HHHHHHHhc---CCcEEEEChHHHHHHHH--cCCCCccc---ccceEEEEccccccccccc
Q 031654           99 -------------RKELRELAR---WVDNLMATLRRLVNLLE--RGRVSLQM---IIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 -------------~~~~~~l~~---~~~IlI~TP~~l~~~l~--~~~~~l~~---l~~~lVlDEa~D~ll~~gf  151 (155)
                                   ....+.+..   .++|+.-||+++...-.  ....++..   + .++|+||| |+...+|+
T Consensus       331 a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~l-al~vIDEA-HCVSqWgH  402 (941)
T KOG0351|consen  331 ACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLL-ALFVIDEA-HCVSQWGH  402 (941)
T ss_pred             eeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCee-EEEEecHH-HHhhhhcc
Confidence                         122233333   48999999999754321  12233444   7 89999999 99999973

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

Probab=98.95  E-value=3e-09  Score=95.09  Aligned_cols=44  Identities=23%  Similarity=0.301  Sum_probs=35.1

Q ss_pred             CCCCCCCHHHHHHHHH----HhcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           47 YKYVKPTPVQRHATSI----LVAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        47 ~g~~~pt~iQ~~~i~~----~l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      -|| .+++.|.+....    +..++.+++.|+||||||++|++|++...
T Consensus       242 ~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~  289 (820)
T PRK07246        242 LGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS  289 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc
Confidence            356 579999984443    34668999999999999999999988753

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.91  E-value=7.6e-09  Score=91.09  Aligned_cols=47  Identities=30%  Similarity=0.266  Sum_probs=36.4

Q ss_pred             CCCCCCHHHHHHHHHHh---cC------CcEEEEccCCCCcchhhhhHHHHHHHHhh
Q 031654           48 KYVKPTPVQRHATSILV---AG------RDLMACAQTGSRKTTPFCFPIINGIMREY   95 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l---~g------~dvl~~a~TGsGKT~~yllp~l~~l~~~~   95 (155)
                      || .+.+-|.+....+.   .+      +.+++.||||+|||+|||+|++-......
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~   78 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEK   78 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcC
Confidence            55 56999999665553   33      67899999999999999999987655443

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.88  E-value=1.9e-09  Score=99.30  Aligned_cols=102  Identities=20%  Similarity=0.202  Sum_probs=67.5

Q ss_pred             hCCCCCCCHHHHH---HHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc-h---------------HHHHHHH-
Q 031654           46 TYKYVKPTPVQRH---ATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-A---------------RKELREL-  105 (155)
Q Consensus        46 ~~g~~~pt~iQ~~---~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~-~---------------~~~~~~l-  105 (155)
                      ...|....|+.+.   .+..+.++..++++|+||||||.  .+|.+..-...... .               ......+ 
T Consensus        59 ~~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~elg  136 (1283)
T TIGR01967        59 EIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTT--QLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELG  136 (1283)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHH--HHHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHhC
Confidence            3467666777663   34444455678889999999999  46754322111100 0               1111111 


Q ss_pred             -----------------hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccc-cccccccc
Q 031654          106 -----------------ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAAD-QTLDMALN  152 (155)
Q Consensus       106 -----------------~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D-~ll~~gf~  152 (155)
                                       ....+|.++|||.|++.+..+. .++++ ++|||||| | ++++.+|.
T Consensus       137 ~~lG~~VGY~vR~~~~~s~~T~I~~~TdGiLLr~l~~d~-~L~~~-~~IIIDEa-HERsL~~D~L  198 (1283)
T TIGR01967       137 TPLGEKVGYKVRFHDQVSSNTLVKLMTDGILLAETQQDR-FLSRY-DTIIIDEA-HERSLNIDFL  198 (1283)
T ss_pred             CCcceEEeeEEcCCcccCCCceeeeccccHHHHHhhhCc-ccccC-cEEEEcCc-chhhccchhH
Confidence                             1246799999999999987654 48999 99999999 9 59888763

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.

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

Probab=98.88  E-value=1.6e-09  Score=97.95  Aligned_cols=110  Identities=15%  Similarity=0.228  Sum_probs=81.0

Q ss_pred             ccCCHHHHHhHHhCCCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------
Q 031654           34 AYVPQHLRNKPRTYKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------   98 (155)
Q Consensus        34 ~~l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------   98 (155)
                      .++|.+-..++.  |+..++++|.......+.+ .|+++|||||+|||...++.+++.+..+....              
T Consensus       294 selP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIA  371 (1674)
T KOG0951|consen  294 SELPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIA  371 (1674)
T ss_pred             cCCcchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEe
Confidence            344445455443  6777999999999999988 79999999999999999999999998766522              


Q ss_pred             ------HHHHHHHh------------------------cCCcEEEEChHHHHHHHHcCCCC---cccccceEEEEccccc
Q 031654           99 ------RKELRELA------------------------RWVDNLMATLRRLVNLLERGRVS---LQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 ------~~~~~~l~------------------------~~~~IlI~TP~~l~~~l~~~~~~---l~~l~~~lVlDEa~D~  145 (155)
                            .+....+.                        .+.+|+||||++ .|.+.++.-+   .+-+ +.+|+||. |.
T Consensus       372 PmKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~qieeTqVIV~TPEK-~DiITRk~gdraY~qlv-rLlIIDEI-HL  448 (1674)
T KOG0951|consen  372 PMKALVQEMVGSFSKRLAPLGITVLELTGDSQLGKEQIEETQVIVTTPEK-WDIITRKSGDRAYEQLV-RLLIIDEI-HL  448 (1674)
T ss_pred             eHHHHHHHHHHHHHhhccccCcEEEEecccccchhhhhhcceeEEeccch-hhhhhcccCchhHHHHH-HHHhhhhh-hh
Confidence                  11111111                        247899999999 6777776433   3456 89999999 65


Q ss_pred             ccc
Q 031654          146 TLD  148 (155)
Q Consensus       146 ll~  148 (155)
                      +-|
T Consensus       449 LhD  451 (1674)
T KOG0951|consen  449 LHD  451 (1674)
T ss_pred             ccc
Confidence            544

>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=98.87  E-value=4.8e-09  Score=76.37  Aligned_cols=95  Identities=18%  Similarity=0.107  Sum_probs=63.5

Q ss_pred             CCCHHHHHHHHHHhc-------CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------HHH--------------
Q 031654           51 KPTPVQRHATSILVA-------GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------RKE--------------  101 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~-------g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------~~~--------------  101 (155)
                      ++++.|.+++..+..       .+.+++.+|||||||.+++..+.....  ....        .+.              
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~--~~l~~~p~~~l~~Q~~~~~~~~~~~~~~~   80 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR--KVLIVAPNISLLEQWYDEFDDFGSEKYNF   80 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC--EEEEEESSHHHHHHHHHHHHHHSTTSEEE
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc--ceeEecCHHHHHHHHHHHHHHhhhhhhhh
Confidence            478999999998874       689999999999999998754333222  1000        111              


Q ss_pred             ------------------------HHHHhcCCcEEEEChHHHHHHHHcCC-----------CCcccccceEEEEcccccc
Q 031654          102 ------------------------LRELARWVDNLMATLRRLVNLLERGR-----------VSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       102 ------------------------~~~l~~~~~IlI~TP~~l~~~l~~~~-----------~~l~~l~~~lVlDEa~D~l  146 (155)
                                              ...-....+++++|..++........           ...... .++|+||| |++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~vI~DEa-H~~  158 (184)
T PF04851_consen   81 FEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKF-DLVIIDEA-HHY  158 (184)
T ss_dssp             EE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSE-SEEEEETG-GCT
T ss_pred             cccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccC-CEEEEehh-hhc
Confidence                                    11122357999999999988776421           234456 79999999 987


Q ss_pred             ccc
Q 031654          147 LDM  149 (155)
Q Consensus       147 l~~  149 (155)
                      -..
T Consensus       159 ~~~  161 (184)
T PF04851_consen  159 PSD  161 (184)
T ss_dssp             HHH
T ss_pred             CCH
Confidence            654

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 ....

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

Probab=98.82  E-value=6.2e-09  Score=84.93  Aligned_cols=116  Identities=15%  Similarity=0.270  Sum_probs=80.3

Q ss_pred             ccCC--HHHHHhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHH------------HHHhhhch
Q 031654           34 AYVP--QHLRNKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIING------------IMREYYSA   98 (155)
Q Consensus        34 ~~l~--~~l~~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~------------l~~~~~~~   98 (155)
                      +++|  .+....|++ +..+++.|.|..+|...+.|+|+++.-|||.||++||.+|++-.            +.......
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~adg~alvi~plislmedqil~  153 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCADGFALVICPLISLMEDQILQ  153 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhcCCceEeechhHHHHHHHHHH
Confidence            4566  555555543 35778899999999999999999999999999999999997631            00000000


Q ss_pred             ----------------HHHHH----HHh---cCCcEEEEChHHHHH---HHHc--CCCCcccccceEEEEcccccccccc
Q 031654           99 ----------------RKELR----ELA---RWVDNLMATLRRLVN---LLER--GRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus        99 ----------------~~~~~----~l~---~~~~IlI~TP~~l~~---~l~~--~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                      ++...    .+.   ....++..||+++..   ++++  +.+....+ +.+.+||+ ++--++|
T Consensus       154 lkqlgi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~-~~iaidev-hccsqwg  231 (695)
T KOG0353|consen  154 LKQLGIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFF-KLIAIDEV-HCCSQWG  231 (695)
T ss_pred             HHHhCcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhccee-EEEeecce-eehhhhC
Confidence                            11111    111   246899999999743   2322  34567778 89999999 9988887


Q ss_pred             c
Q 031654          151 L  151 (155)
Q Consensus       151 f  151 (155)
                      +
T Consensus       232 h  232 (695)
T KOG0353|consen  232 H  232 (695)
T ss_pred             c
Confidence            3

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

Probab=98.81  E-value=3.2e-08  Score=86.37  Aligned_cols=51  Identities=25%  Similarity=0.369  Sum_probs=41.1

Q ss_pred             HhCCCCCCCHHHHHHHHHH----hcCCcEEEEccCCCCcchhhhhHHHHHHHHhh
Q 031654           45 RTYKYVKPTPVQRHATSIL----VAGRDLMACAQTGSRKTTPFCFPIINGIMREY   95 (155)
Q Consensus        45 ~~~g~~~pt~iQ~~~i~~~----l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~   95 (155)
                      .......|++.|.+.+..+    .+|+.+++.||||+|||++|++|++.......
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~   63 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG   63 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC
Confidence            4445668999999988544    35566999999999999999999998875543

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=98.77  E-value=3.9e-08  Score=85.50  Aligned_cols=32  Identities=25%  Similarity=0.150  Sum_probs=27.7

Q ss_pred             HHHhcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           61 SILVAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        61 ~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      ..+.+++.+++.|+||||||++|++|++..+.
T Consensus        11 ~al~~~~~lliEA~TGtGKTlAYLlpal~~~~   42 (636)
T TIGR03117        11 TSLRQKRIGMLEASTGVGKTLAMIMAALTMLK   42 (636)
T ss_pred             HHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHH
Confidence            44567789999999999999999999988665

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.66  E-value=5.1e-08  Score=77.58  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=37.0

Q ss_pred             CCHHHHH----HHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           52 PTPVQRH----ATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        52 pt~iQ~~----~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      |+|.|.+    +...+.+|.++++.||||+|||++|++|++..+...
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~   55 (289)
T smart00489        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSF   55 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhC
Confidence            5999999    555667889999999999999999999999876643

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.66  E-value=5.1e-08  Score=77.58  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=37.0

Q ss_pred             CCHHHHH----HHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           52 PTPVQRH----ATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        52 pt~iQ~~----~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      |+|.|.+    +...+.+|.++++.||||+|||++|++|++..+...
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~   55 (289)
T smart00488        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSF   55 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhC
Confidence            5999999    555667889999999999999999999999876643

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

Probab=98.61  E-value=2.1e-07  Score=82.87  Aligned_cols=101  Identities=19%  Similarity=0.246  Sum_probs=75.0

Q ss_pred             hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHh----------
Q 031654           46 TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELA----------  106 (155)
Q Consensus        46 ~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~----------  106 (155)
                      ...| +|-+.|++||-++.+|..|+|.|.|.+|||+..-.++...-.......         ++..++.+          
T Consensus       293 ~~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h~TR~iYTSPIKALSNQKfRDFk~tF~DvgLlT  371 (1248)
T KOG0947|consen  293 IYPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFKETFGDVGLLT  371 (1248)
T ss_pred             hCCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhhccceEecchhhhhccchHHHHHHhccccceee
Confidence            3345 678999999999999999999999999999986554322111111111         23333333          


Q ss_pred             ------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          107 ------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       107 ------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                            ..+.+||.|-+-|..++-++.--++++ .++|+||+ |.+=|.
T Consensus       372 GDvqinPeAsCLIMTTEILRsMLYrgadliRDv-E~VIFDEV-HYiND~  418 (1248)
T KOG0947|consen  372 GDVQINPEASCLIMTTEILRSMLYRGADLIRDV-EFVIFDEV-HYINDV  418 (1248)
T ss_pred             cceeeCCCcceEeehHHHHHHHHhcccchhhcc-ceEEEeee-eecccc
Confidence                  236889999999999999988888999 99999999 887654

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

Probab=98.52  E-value=7e-07  Score=82.21  Aligned_cols=94  Identities=15%  Similarity=0.215  Sum_probs=62.9

Q ss_pred             CCCHHHHHHHHHHh----cC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------HHH-------------
Q 031654           51 KPTPVQRHATSILV----AG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------RKE-------------  101 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l----~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------~~~-------------  101 (155)
                      .+.+.|..||..+.    +| +..+++.+||||||.+. +.++.++.......           ..|             
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            58999999998775    34 68999999999999874 33444444322111           000             


Q ss_pred             --------HHHH-----hcCCcEEEEChHHHHHHHHcC-----CCCcccccceEEEEccccccc
Q 031654          102 --------LREL-----ARWVDNLMATLRRLVNLLERG-----RVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus       102 --------~~~l-----~~~~~IlI~TP~~l~~~l~~~-----~~~l~~l~~~lVlDEa~D~ll  147 (155)
                              ...+     .....|+|+|...+...+...     .+.+... .++|+||| |+-.
T Consensus       492 ~~~~~i~~i~~L~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~f-dlIIiDEa-HRs~  553 (1123)
T PRK11448        492 QTFASIYDIKGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQY-DCIIVDEA-HRGY  553 (1123)
T ss_pred             cchhhhhchhhhhhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcc-cEEEEECC-CCCC
Confidence                    0111     124689999999987765321     2456788 89999999 9853

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.52  E-value=3.8e-07  Score=80.53  Aligned_cols=47  Identities=23%  Similarity=0.190  Sum_probs=39.1

Q ss_pred             CCCCCCHHHHHHHHHH----hcCCcEEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           48 KYVKPTPVQRHATSIL----VAGRDLMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~----l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      -|..++|.|.+.+..+    ..|.+.++.||||+|||++-|.|++......
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~   57 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEK   57 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhc
Confidence            4677799999876544    5779999999999999999999999876543

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).

>PRK09694 helicase Cas3; Provisional

Probab=98.50  E-value=3.1e-07  Score=82.52  Aligned_cols=41  Identities=20%  Similarity=0.059  Sum_probs=32.3

Q ss_pred             CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHH
Q 031654           49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      ...|+|+|+.+......+.-+++.||||+|||.+.+..+..
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~  324 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWR  324 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHH
Confidence            44899999988654445677999999999999998765543

>TIGR00595 priA primosomal protein N'

Probab=98.49  E-value=1.9e-07  Score=79.55  Aligned_cols=69  Identities=14%  Similarity=0.131  Sum_probs=45.0

Q ss_pred             EEEccCCCCcchhhhhHHHHHHHHhhhch------------------------------------HHHHHHHh-cCCcEE
Q 031654           70 MACAQTGSRKTTPFCFPIINGIMREYYSA------------------------------------RKELRELA-RWVDNL  112 (155)
Q Consensus        70 l~~a~TGsGKT~~yllp~l~~l~~~~~~~------------------------------------~~~~~~l~-~~~~Il  112 (155)
                      ++.|+||||||.+|+..+...+.......                                    .+....+. ..++|+
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IV   80 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV   80 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEE
Confidence            46899999999999765544433221111                                    11122222 357999


Q ss_pred             EEChHHHHHHHHcCCCCcccccceEEEEccccccc
Q 031654          113 MATLRRLVNLLERGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus       113 I~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                      |||+..+.       ..+.++ .++||||+ |...
T Consensus        81 VGTrsalf-------~p~~~l-~lIIVDEe-h~~s  106 (505)
T TIGR00595        81 IGTRSALF-------LPFKNL-GLIIVDEE-HDSS  106 (505)
T ss_pred             ECChHHHc-------CcccCC-CEEEEECC-Cccc
Confidence            99998753       357899 99999999 7543

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=98.43  E-value=2e-07  Score=78.18  Aligned_cols=98  Identities=17%  Similarity=0.099  Sum_probs=64.7

Q ss_pred             CCCCHHHHHHHHHHhc----CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------HHHHH-HH------------
Q 031654           50 VKPTPVQRHATSILVA----GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------RKELR-EL------------  105 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~----g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------~~~~~-~l------------  105 (155)
                      ..+++.|.+++..+.+    ++..+++.|||+|||..++-.+.. +... ...       ..|.. .+            
T Consensus        35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~-~~~~-~Lvlv~~~~L~~Qw~~~~~~~~~~~~~~g~  112 (442)
T COG1061          35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAE-LKRS-TLVLVPTKELLDQWAEALKKFLLLNDEIGI  112 (442)
T ss_pred             CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHH-hcCC-EEEEECcHHHHHHHHHHHHHhcCCccccce
Confidence            3689999999999988    899999999999999987544322 2111 000       12221 00            


Q ss_pred             -h----c-C-CcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654          106 -A----R-W-VDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       106 -~----~-~-~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                       .    + . ..|.|+|-..+........+..+.. .++|+||+ |++....|
T Consensus       113 ~~~~~~~~~~~~i~vat~qtl~~~~~l~~~~~~~~-~liI~DE~-Hh~~a~~~  163 (442)
T COG1061         113 YGGGEKELEPAKVTVATVQTLARRQLLDEFLGNEF-GLIIFDEV-HHLPAPSY  163 (442)
T ss_pred             ecCceeccCCCcEEEEEhHHHhhhhhhhhhccccc-CEEEEEcc-ccCCcHHH
Confidence             0    0 1 2599999877655321123344467 89999999 99987654

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

Probab=98.42  E-value=7.1e-07  Score=77.99  Aligned_cols=97  Identities=21%  Similarity=0.247  Sum_probs=80.2

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHhc--------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELAR--------------  107 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~~--------------  107 (155)
                      .+-|.|+.||..+-++..|+|.|-|.+|||.+.-.++...+..+....         ++..+.+..              
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQRVIYTSPIKALSNQKYREl~~EF~DVGLMTGDVTI  208 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQRVIYTSPIKALSNQKYRELLEEFKDVGLMTGDVTI  208 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcCeEEeeChhhhhcchhHHHHHHHhcccceeecceee
Confidence            467899999999999999999999999999998888877776554433         333343331              


Q ss_pred             --CCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          108 --WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       108 --~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                        .+.-+|.|-+-|..++-++.--+..+ .|+|+||+ |.|-|.
T Consensus       209 nP~ASCLVMTTEILRsMLYRGSEvmrEV-aWVIFDEI-HYMRDk  250 (1041)
T KOG0948|consen  209 NPDASCLVMTTEILRSMLYRGSEVMREV-AWVIFDEI-HYMRDK  250 (1041)
T ss_pred             CCCCceeeeHHHHHHHHHhccchHhhee-eeEEeeee-hhcccc
Confidence              35679999999999999999889999 99999999 999775

>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=98.41  E-value=4.8e-07  Score=71.19  Aligned_cols=101  Identities=22%  Similarity=0.173  Sum_probs=66.6

Q ss_pred             HhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------------------
Q 031654           42 NKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------------------   98 (155)
Q Consensus        42 ~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------------------   98 (155)
                      ++.++.--.+|+++|..++-.+..|+  ++.-.||-|||++..+|++-.........                       
T Consensus        68 ea~~r~~g~~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G~~V~vvT~NdyLA~RD~~~~~~~y~~L  145 (266)
T PF07517_consen   68 EAARRTLGLRPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQGKGVHVVTSNDYLAKRDAEEMRPFYEFL  145 (266)
T ss_dssp             HHHHHHTS----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTSS-EEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCcccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhcCCcEEEeccHHHhhccHHHHHHHHHHh
Confidence            34433323489999999998887777  88999999999999988776665543322                       


Q ss_pred             ------------HHHHHHHhcCCcEEEEChHHHH-HHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 ------------RKELRELARWVDNLMATLRRLV-NLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 ------------~~~~~~l~~~~~IlI~TP~~l~-~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                                  ..+.+ -...++|+.+|...+. ++|+.+.      ...... .++||||| |.||
T Consensus       146 Glsv~~~~~~~~~~~r~-~~Y~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~-~~~ivDEv-Ds~L  210 (266)
T PF07517_consen  146 GLSVGIITSDMSSEERR-EAYAADIVYGTNSEFGFDYLRDNLALSKNEQVQRGF-DFAIVDEV-DSIL  210 (266)
T ss_dssp             T--EEEEETTTEHHHHH-HHHHSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSS-SEEEECTH-HHHT
T ss_pred             hhccccCccccCHHHHH-HHHhCcccccccchhhHHHHHHHHhhccchhccCCC-CEEEEecc-ceEE
Confidence                        12212 2234899999998874 3454431      124677 89999999 9887

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 ....

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

Probab=98.34  E-value=1.6e-06  Score=75.12  Aligned_cols=99  Identities=19%  Similarity=0.263  Sum_probs=76.4

Q ss_pred             HHHhHHhCCCCCCCHHHHHHHHHHhcC------CcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------------
Q 031654           40 LRNKPRTYKYVKPTPVQRHATSILVAG------RDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------------   98 (155)
Q Consensus        40 l~~~l~~~g~~~pt~iQ~~~i~~~l~g------~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------------   98 (155)
                      +.+.++.+.| ++|.-|++++..|...      -+=++++--|||||+..++.++..+..+....               
T Consensus       252 ~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~  330 (677)
T COG1200         252 LAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMAPTEILAEQHYES  330 (677)
T ss_pred             HHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHH
Confidence            3445577788 7899999999999755      25688999999999999999998777644333               


Q ss_pred             ------------------------HHHHHHHhcC-CcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 ------------------------RKELRELARW-VDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ------------------------~~~~~~l~~~-~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                              ......+.+| .||+|||..-+     ...+.+.++ .++|+||= |+.
T Consensus       331 ~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALi-----Qd~V~F~~L-gLVIiDEQ-HRF  396 (677)
T COG1200         331 LRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALI-----QDKVEFHNL-GLVIIDEQ-HRF  396 (677)
T ss_pred             HHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhh-----hcceeecce-eEEEEecc-ccc
Confidence                                    3444555555 99999997543     456789999 99999998 763

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

Probab=98.34  E-value=1.5e-07  Score=85.54  Aligned_cols=114  Identities=17%  Similarity=0.162  Sum_probs=74.5

Q ss_pred             CCCCcccccCC-HHHHHhHHhCCCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------
Q 031654           27 SSPAARFAYVP-QHLRNKPRTYKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------   98 (155)
Q Consensus        27 p~~~~~f~~l~-~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------   98 (155)
                      |.++..|..+| ..+.+-...--|...+|+|.++++.+.+. .++++.+|+|||||.|.-+.++..-......-      
T Consensus      1118 pt~lld~~~~~~~~l~N~~~~~lf~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~~~~~~~~vyi~p~~~ 1197 (1674)
T KOG0951|consen 1118 PTELLDLQPLPVSALRNPSFETLFQDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLRPDTIGRAVYIAPLEE 1197 (1674)
T ss_pred             CchhhhccccchhccCCcchhhhccccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcCCccceEEEEecchHH
Confidence            44555566666 33333322223555699999999999876 67999999999999998887765110000000      


Q ss_pred             ---------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 ---------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 ---------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                                 ...-..+....+|+|+||++ .+.++    +.+.+ ++.|.||+  +|+.
T Consensus      1198 i~~~~~~~w~~~f~~~~G~~~~~l~ge~s~~lkl~~~~~vii~tpe~-~d~lq----~iQ~v-~l~i~d~l--h~ig 1266 (1674)
T KOG0951|consen 1198 IADEQYRDWEKKFSKLLGLRIVKLTGETSLDLKLLQKGQVIISTPEQ-WDLLQ----SIQQV-DLFIVDEL--HLIG 1266 (1674)
T ss_pred             HHHHHHHHHHHhhccccCceEEecCCccccchHHhhhcceEEechhH-HHHHh----hhhhc-ceEeeehh--hhhc
Confidence                                       11112233457999999999 45553    77888 99999999  5554

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.30  E-value=9.3e-07  Score=79.02  Aligned_cols=93  Identities=18%  Similarity=0.120  Sum_probs=64.5

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------------------------
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------------------------   98 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------------------------   98 (155)
                      -+|+++|-..--.+..|  -++.-.||+|||++..+|++-.........                               
T Consensus        81 m~~ydVQliGg~~Lh~G--~iaEM~TGEGKTLvA~l~a~l~al~G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~i~  158 (913)
T PRK13103         81 MRHFDVQLIGGMTLHEG--KIAEMRTGEGKTLVGTLAVYLNALSGKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIVT  158 (913)
T ss_pred             CCcchhHHHhhhHhccC--ccccccCCCCChHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEEEC
Confidence            47888988765455444  377899999999999999887666554332                               


Q ss_pred             ----HHHHHHHhcCCcEEEEChHHH-HHHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 ----RKELRELARWVDNLMATLRRL-VNLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 ----~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                          ..+.+.. -.+||++||..-+ .|+|+.+.      .....+ .+.|+||+ |.+|
T Consensus       159 ~~~~~~err~~-Y~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l-~~aIVDEv-DsiL  215 (913)
T PRK13103        159 PFQPPEEKRAA-YAADITYGTNNEFGFDYLRDNMAFSLDDKFQREL-NFAVIDEV-DSIL  215 (913)
T ss_pred             CCCCHHHHHHH-hcCCEEEEcccccccchhhccceechhhhccccc-ceeEechh-hhee
Confidence                1222222 2499999999886 34444331      124778 89999999 9987

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.27  E-value=1.5e-06  Score=77.19  Aligned_cols=104  Identities=20%  Similarity=0.200  Sum_probs=72.3

Q ss_pred             HHHHhHHhC-CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------------
Q 031654           39 HLRNKPRTY-KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------------   98 (155)
Q Consensus        39 ~l~~~l~~~-g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------------   98 (155)
                      -+.++.++. |. +|+++|-.+--.+..|+  ++.-.||+|||++..+|++-.........                   
T Consensus        68 ~vrEa~~R~~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~~v~vvT~neyLA~Rd~e~~~~~  144 (796)
T PRK12906         68 VAREGAKRVLGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGKGVHVVTVNEYLSSRDATEMGEL  144 (796)
T ss_pred             HHHHHHHHHhCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCCCeEEEeccHHHHHhhHHHHHHH
Confidence            334444333 43 78999999877777777  88999999999999999888777655433                   


Q ss_pred             ---------------HHHHHHHhcCCcEEEEChHHHH-HHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 ---------------RKELRELARWVDNLMATLRRLV-NLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 ---------------~~~~~~l~~~~~IlI~TP~~l~-~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                                     ....+.-.-.|||+.+|...+- ++|+.+.      .....+ .+.||||+ |.||
T Consensus       145 ~~~LGl~vg~i~~~~~~~~r~~~y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~-~~aIvDEv-DSiL  213 (796)
T PRK12906        145 YRWLGLTVGLNLNSMSPDEKRAAYNCDITYSTNSELGFDYLRDNMVVYKEQMVQRPL-NYAIVDEV-DSIL  213 (796)
T ss_pred             HHhcCCeEEEeCCCCCHHHHHHHhcCCCeecCCccccccchhhccccchhhhhccCc-ceeeeccc-hhee
Confidence                           1222222336899999997763 3444321      123567 89999999 9987

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.26  E-value=1.3e-06  Score=65.68  Aligned_cols=32  Identities=25%  Similarity=0.257  Sum_probs=25.9

Q ss_pred             CCCHHHHHHHHHHhcCCc-EEEEccCCCCcchh
Q 031654           51 KPTPVQRHATSILVAGRD-LMACAQTGSRKTTP   82 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~d-vl~~a~TGsGKT~~   82 (155)
                      ++++-|..|+..+++..+ .++.||+|||||..
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~   33 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTT   33 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHH
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHH
Confidence            357899999999999999 99999999999943

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.24  E-value=3.1e-06  Score=75.61  Aligned_cols=93  Identities=23%  Similarity=0.174  Sum_probs=66.4

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      +|+++|-..--.+..|+  ++...||.|||+++.+|++-.........                                
T Consensus        85 r~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL~GkgVhVVTvNdYLA~RDae~m~~vy~~LGLtvg~i~~  162 (939)
T PRK12902         85 RHFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNALTGKGVHVVTVNDYLARRDAEWMGQVHRFLGLSVGLIQQ  162 (939)
T ss_pred             CcchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhhcCCCeEEEeCCHHHHHhHHHHHHHHHHHhCCeEEEECC
Confidence            78889887665555554  78999999999999999887666544332                                


Q ss_pred             --HHHHHHHhcCCcEEEEChHHH-----HHHHHc--CCCCcccccceEEEEccccccc
Q 031654           99 --RKELRELARWVDNLMATLRRL-----VNLLER--GRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --~~~~~~l~~~~~IlI~TP~~l-----~~~l~~--~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                        ....+...-.|||+.+|+..+     .+.+..  .......+ .|.||||| |.||
T Consensus       163 ~~~~~err~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~-~faIVDEv-DSIL  218 (939)
T PRK12902        163 DMSPEERKKNYACDITYATNSELGFDYLRDNMATDISEVVQRPF-NYCVIDEV-DSIL  218 (939)
T ss_pred             CCChHHHHHhcCCCeEEecCCcccccchhhhhcccccccccCcc-ceEEEecc-ccee
Confidence              233333445799999999887     343332  12345777 89999999 9987

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.16  E-value=3.1e-06  Score=74.31  Aligned_cols=96  Identities=21%  Similarity=0.146  Sum_probs=68.2

Q ss_pred             CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------------------------
Q 031654           48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------------------------   98 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------------------------   98 (155)
                      |. +|+.+|-.+.-.++.|+  ++.-.||+|||++..+|++-.........                             
T Consensus        76 g~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~G~~VhvvT~NdyLA~RDae~m~~ly~~LGLsvg~  152 (764)
T PRK12326         76 GL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQGRRVHVITVNDYLARRDAEWMGPLYEALGLTVGW  152 (764)
T ss_pred             CC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcCCCeEEEcCCHHHHHHHHHHHHHHHHhcCCEEEE
Confidence            44 78999999998888885  67899999999999999887776544332                             


Q ss_pred             -----HHHHHHHhcCCcEEEEChHHH-HHHHHcC------CCCcccccceEEEEcccccccc
Q 031654           99 -----RKELRELARWVDNLMATLRRL-VNLLERG------RVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 -----~~~~~~l~~~~~IlI~TP~~l-~~~l~~~------~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                           ....+.-.-.|||+.+|...+ .++|+.+      ......+ .+.|+||+ |.||=
T Consensus       153 i~~~~~~~err~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~-~faIVDEv-DSiLI  212 (764)
T PRK12326        153 ITEESTPEERRAAYACDVTYASVNEIGFDVLRDQLVTDVADLVSPNP-DVAIIDEA-DSVLV  212 (764)
T ss_pred             ECCCCCHHHHHHHHcCCCEEcCCcccccccchhhhccChHhhcCCcc-ceeeecch-hhhee
Confidence                 111122223689999999765 2333332      1234567 89999999 99883

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.13  E-value=1.9e-06  Score=64.78  Aligned_cols=32  Identities=22%  Similarity=0.175  Sum_probs=25.2

Q ss_pred             CCCHHHHHHHHHHhcCC--cEEEEccCCCCcchh
Q 031654           51 KPTPVQRHATSILVAGR--DLMACAQTGSRKTTP   82 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~--dvl~~a~TGsGKT~~   82 (155)
                      ++++-|..++..++.+.  =++++++.|||||.+
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~   34 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL   34 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH
Confidence            36889999999997654  477789999999974

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=98.13  E-value=5.6e-06  Score=62.84  Aligned_cols=45  Identities=13%  Similarity=0.067  Sum_probs=34.5

Q ss_pred             CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      ++..|+-|..++..++...-+++.+|.|||||+..+...++.+..
T Consensus         2 I~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~   46 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKE   46 (205)
T ss_dssp             ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT
T ss_pred             ccCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            445689999999999988889999999999999988888887765

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.10  E-value=2.2e-06  Score=75.65  Aligned_cols=97  Identities=11%  Similarity=0.103  Sum_probs=59.4

Q ss_pred             CCCHHHHHHHHHHh-cC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------HHHHHHHh----------
Q 031654           51 KPTPVQRHATSILV-AG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------RKELRELA----------  106 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l-~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------~~~~~~l~----------  106 (155)
                      .+.|.|.+++..++ +|  +.-+++.|||+|||+..+..+. ++.. ....           ..+.....          
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~-~l~k-~tLILvps~~Lv~QW~~ef~~~~~l~~~~I~~~  332 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAAC-TVKK-SCLVLCTSAVSVEQWKQQFKMWSTIDDSQICRF  332 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHH-HhCC-CEEEEeCcHHHHHHHHHHHHHhcCCCCceEEEE
Confidence            47889999999887 44  4789999999999999765443 2210 0000           11222110          


Q ss_pred             ---------cCCcEEEEChHHHHHHHHcC--------CCCcccccceEEEEccccccccccc
Q 031654          107 ---------RWVDNLMATLRRLVNLLERG--------RVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       107 ---------~~~~IlI~TP~~l~~~l~~~--------~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                               ....|+|+|...+.....+.        .+.-... .++|+||| |++-...|
T Consensus       333 tg~~k~~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~-gLII~DEv-H~lpA~~f  392 (732)
T TIGR00603       333 TSDAKERFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREW-GLILLDEV-HVVPAAMF  392 (732)
T ss_pred             ecCcccccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccC-CEEEEEcc-ccccHHHH
Confidence                     12579999997654322221        1222356 78999999 98854433

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).

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

Probab=98.07  E-value=8.6e-06  Score=72.21  Aligned_cols=44  Identities=14%  Similarity=0.136  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHh----cCCcEEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           51 KPTPVQRHATSILV----AGRDLMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l----~g~dvl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      .|++.|...+..++    ++.+.+..+|||||||++-+...|......
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~   68 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHL   68 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHh
Confidence            57999988766554    557899999999999999988777765543

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=98.06  E-value=9.4e-06  Score=72.87  Aligned_cols=94  Identities=18%  Similarity=0.117  Sum_probs=67.2

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      .|..+|.+.+-.+-.+..++++|||.+|||.+--..+=..+.......                                
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~s  590 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLRGVS  590 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccccchh
Confidence            688999999999999999999999999999863222222222211111                                


Q ss_pred             --HHHHHHHh---cCCcEEEEChHHHHHHHHc---CCCCcccccceEEEEcccccc
Q 031654           99 --RKELRELA---RWVDNLMATLRRLVNLLER---GRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 --~~~~~~l~---~~~~IlI~TP~~l~~~l~~---~~~~l~~l~~~lVlDEa~D~l  146 (155)
                        ...-++.+   -.|+|+|+-|+.+..++..   ......++ +|+|+||+ +.+
T Consensus       591 l~g~ltqEYsinp~nCQVLITvPecleslLlspp~~q~~cerI-RyiIfDEV-H~i  644 (1330)
T KOG0949|consen  591 LLGDLTQEYSINPWNCQVLITVPECLESLLLSPPHHQKFCERI-RYIIFDEV-HLI  644 (1330)
T ss_pred             hHhhhhHHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcc-eEEEechh-hhc
Confidence              11111111   2699999999999999887   34567899 99999999 765

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

Probab=98.06  E-value=2e-05  Score=69.46  Aligned_cols=94  Identities=18%  Similarity=0.175  Sum_probs=56.2

Q ss_pred             CCHHHHHHHHHHh----c------CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------H------------
Q 031654           52 PTPVQRHATSILV----A------GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------R------------   99 (155)
Q Consensus        52 pt~iQ~~~i~~~l----~------g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~------------   99 (155)
                      |.+.|..|+..+.    +      .+..+++.+||||||+..+.-+...+.......          .            
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~  318 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQK  318 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhCC
Confidence            6778988887663    2      257899999999999886544433221111111          0            


Q ss_pred             ---------HHH-HHHhc-CCcEEEEChHHHHHHHHcC--CCC--cccccceEEEEcccccccc
Q 031654          100 ---------KEL-RELAR-WVDNLMATLRRLVNLLERG--RVS--LQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       100 ---------~~~-~~l~~-~~~IlI~TP~~l~~~l~~~--~~~--l~~l~~~lVlDEa~D~ll~  148 (155)
                               ... ..+.. ...|+|+|...+...+...  .+.  ..++  ++|+||| |+.--
T Consensus       319 ~~~~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~--lvIvDEa-Hrs~~  379 (667)
T TIGR00348       319 DCAERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEV--VVIFDEA-HRSQY  379 (667)
T ss_pred             CCCcccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCE--EEEEEcC-ccccc
Confidence                     111 11111 3689999999987644331  111  1223  7999999 98653

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

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.01  E-value=7.2e-06  Score=73.16  Aligned_cols=103  Identities=21%  Similarity=0.132  Sum_probs=66.8

Q ss_pred             HHHhHH-hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------
Q 031654           40 LRNKPR-TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------   98 (155)
Q Consensus        40 l~~~l~-~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------   98 (155)
                      +.++.. .+|. +|+++|-.+--.+.  +.-++...||.|||+++.+|++-.........                    
T Consensus        65 vrEa~~R~lG~-r~ydvQlig~l~L~--~G~IaEm~TGEGKTL~a~l~ayl~aL~G~~VhVvT~NdyLA~RD~e~m~pvy  141 (870)
T CHL00122         65 TREASFRTLGL-RHFDVQLIGGLVLN--DGKIAEMKTGEGKTLVATLPAYLNALTGKGVHIVTVNDYLAKRDQEWMGQIY  141 (870)
T ss_pred             HHHHHHHHhCC-CCCchHhhhhHhhc--CCccccccCCCCchHHHHHHHHHHHhcCCceEEEeCCHHHHHHHHHHHHHHH
Confidence            334443 3355 58999988654443  45688999999999999999865444333221                    


Q ss_pred             --------------HHHHHHHhcCCcEEEEChHHHH-HHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 --------------RKELRELARWVDNLMATLRRLV-NLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --------------~~~~~~l~~~~~IlI~TP~~l~-~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                                    ....+.-.-.|||+.+|...+- ++|+.+.      .....+ .+.|+||| |.||
T Consensus       142 ~~LGLsvg~i~~~~~~~err~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~-~faIVDEv-DSiL  209 (870)
T CHL00122        142 RFLGLTVGLIQEGMSSEERKKNYLKDITYVTNSELGFDYLRDNMALSLSDVVQRPF-NYCIIDEV-DSIL  209 (870)
T ss_pred             HHcCCceeeeCCCCChHHHHHhcCCCCEecCCccccccchhhccCcChHHhhcccc-ceeeeecc-hhhe
Confidence                          1222233346899999997542 3443321      234667 89999999 9987

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

Probab=98.01  E-value=4.6e-05  Score=68.80  Aligned_cols=109  Identities=19%  Similarity=0.159  Sum_probs=70.1

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------------   98 (155)
                      +++-+.+++....+|+..|+.--..++.|++.-+.||||.|||..-++-.+-...+++...                   
T Consensus        69 e~~~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~  148 (1187)
T COG1110          69 EEFEEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKF  148 (1187)
T ss_pred             HHHHHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHH
Confidence            4444555555333999999998899999999999999999999753332222111111100                   


Q ss_pred             ----------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccc
Q 031654           99 ----------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus        99 ----------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                            ......+.+ +.||+|+|..-|..-+..  +.--+. +++.+|++ |.+|..+
T Consensus       149 ~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~--L~~~kF-dfifVDDV-DA~Lkas  219 (1187)
T COG1110         149 AEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE--LSKLKF-DFIFVDDV-DAILKAS  219 (1187)
T ss_pred             HhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH--hcccCC-CEEEEccH-HHHHhcc
Confidence                                  122233333 699999998776544432  111356 78999999 9988654

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

Probab=97.88  E-value=5.3e-05  Score=65.09  Aligned_cols=42  Identities=21%  Similarity=0.249  Sum_probs=31.8

Q ss_pred             CCCHHHHHHHHHHhcCCc-EEEEccCCCCcchhhhhHHHHHHH
Q 031654           51 KPTPVQRHATSILVAGRD-LMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~d-vl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .+.+-|..|+....+.++ .++++|+|||||..-..-+.+.+.
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk  227 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVK  227 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHH
Confidence            567889999999988865 677899999999876544444333

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=97.86  E-value=4.2e-05  Score=68.41  Aligned_cols=103  Identities=20%  Similarity=0.179  Sum_probs=70.1

Q ss_pred             HHHhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------
Q 031654           40 LRNKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------   98 (155)
Q Consensus        40 l~~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------   98 (155)
                      +.++.++ +|. +|+++|-..--.+..|+  ++.-.||-|||++..+|++-.........                    
T Consensus        67 vREA~~R~lG~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~GkgVhVVTvNdYLA~RDae~mg~vy  143 (925)
T PRK12903         67 AREATKRVLGK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTGKGVIVSTVNEYLAERDAEEMGKVF  143 (925)
T ss_pred             HHHHHHHHhCC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcCCceEEEecchhhhhhhHHHHHHHH
Confidence            3344433 354 88999998876666664  68999999999999999876555443322                    


Q ss_pred             --------------HHHHHHHhcCCcEEEEChHHH-HHHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 --------------RKELRELARWVDNLMATLRRL-VNLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --------------~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                                    ....+.-.-.|||..+|...+ .++|+.+.      .....+ .|.|+||+ |.+|
T Consensus       144 ~fLGLsvG~i~~~~~~~~rr~aY~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~-~faIVDEV-DSIL  211 (925)
T PRK12903        144 NFLGLSVGINKANMDPNLKREAYACDITYSVHSELGFDYLRDNMVSSKEEKVQRGL-NFCLIDEV-DSIL  211 (925)
T ss_pred             HHhCCceeeeCCCCChHHHHHhccCCCeeecCcccchhhhhhcccccHHHhcCccc-ceeeeccc-hhee
Confidence                          112222234699999999776 34454332      224667 89999999 9987

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.85  E-value=0.00014  Score=66.45  Aligned_cols=95  Identities=18%  Similarity=0.075  Sum_probs=56.7

Q ss_pred             CCCHHHHHHHHHHhcCCc-EEEEccCCCCcchhhhhHHHHHHHHhhhch------HHHHHHHhcCCcEEEEChHHHHHHH
Q 031654           51 KPTPVQRHATSILVAGRD-LMACAQTGSRKTTPFCFPIINGIMREYYSA------RKELRELARWVDNLMATLRRLVNLL  123 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~d-vl~~a~TGsGKT~~yllp~l~~l~~~~~~~------~~~~~~l~~~~~IlI~TP~~l~~~l  123 (155)
                      .+++-|..|+..++.+++ +++.++.|||||.. +-.+...+.......      ......+.....+--.|-.++..-.
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~~G~~V~~~ApTGkAA~~L~e~tGi~a~TI~sll~~~  424 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEAAGYEVRGAALSGIAAENLEGGSGIASRTIASLEHGW  424 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHcCCeEEEecCcHHHHHHHhhccCcchhhHHHHHhhh
Confidence            689999999999998765 68899999999975 233333332211111      3333444433333333433332222


Q ss_pred             HcCCCCcccccceEEEEccccccccc
Q 031654          124 ERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       124 ~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      ..+...+... .+||||||  -|++.
T Consensus       425 ~~~~~~l~~~-~vlIVDEA--SMv~~  447 (988)
T PRK13889        425 GQGRDLLTSR-DVLVIDEA--GMVGT  447 (988)
T ss_pred             cccccccccC-cEEEEECc--ccCCH
Confidence            2233346666 79999999  56653

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

Probab=97.82  E-value=1.5e-05  Score=71.24  Aligned_cols=112  Identities=13%  Similarity=0.155  Sum_probs=79.2

Q ss_pred             CHHHHHh-HHhCCCCCCCHHHHHHH--HHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHH
Q 031654           37 PQHLRNK-PRTYKYVKPTPVQRHAT--SILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELR  103 (155)
Q Consensus        37 ~~~l~~~-l~~~g~~~pt~iQ~~~i--~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~  103 (155)
                      ++.+... .+..|....+.+|..++  |.++.++|++..+||+.|||++.-+-++..+.......          .+...
T Consensus       208 ~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsiv~Ek~~  287 (1008)
T KOG0950|consen  208 PTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKIS  287 (1008)
T ss_pred             chHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhhceeEecceeehhHHHHh
Confidence            3444443 45668999999999987  67889999999999999999999888887776555444          11111


Q ss_pred             H-----------------------HhcCCcEEEEChHHHHHHHHc--CCCCcccccceEEEEcccccccccc
Q 031654          104 E-----------------------LARWVDNLMATLRRLVNLLER--GRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       104 ~-----------------------l~~~~~IlI~TP~~l~~~l~~--~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                      .                       ..+.-++.|||-++-.-++++  ..=.+..+ .++|+||. |.+.|.|
T Consensus       288 ~l~~~~~~~G~~ve~y~g~~~p~~~~k~~sv~i~tiEkanslin~lie~g~~~~~-g~vvVdEl-hmi~d~~  357 (1008)
T KOG0950|consen  288 ALSPFSIDLGFPVEEYAGRFPPEKRRKRESVAIATIEKANSLINSLIEQGRLDFL-GMVVVDEL-HMIGDKG  357 (1008)
T ss_pred             hhhhhccccCCcchhhcccCCCCCcccceeeeeeehHhhHhHHHHHHhcCCcccc-CcEEEeee-eeeeccc
Confidence            1                       112358999999986555543  12246677 89999999 7666654

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

Probab=97.81  E-value=4.9e-05  Score=61.64  Aligned_cols=86  Identities=22%  Similarity=0.216  Sum_probs=58.1

Q ss_pred             CCCHHHHHHHHHH----hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHH----h------
Q 031654           51 KPTPVQRHATSIL----VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELREL----A------  106 (155)
Q Consensus        51 ~pt~iQ~~~i~~~----l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l----~------  106 (155)
                      .+|+.|+.+-..+    .+.+|.++.|-||+|||-- +.+.++....++...          .+....+    .      
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~  175 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSNCDIDL  175 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhhccCCeee
Confidence            6899999876655    4568999999999999975 345555555544332          1111111    1      


Q ss_pred             --------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654          107 --------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       107 --------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                              -..+++|+|--+|+.+-.       .. +++++||+ |..
T Consensus       176 Lyg~S~~~fr~plvVaTtHQLlrFk~-------aF-D~liIDEV-DAF  214 (441)
T COG4098         176 LYGDSDSYFRAPLVVATTHQLLRFKQ-------AF-DLLIIDEV-DAF  214 (441)
T ss_pred             EecCCchhccccEEEEehHHHHHHHh-------hc-cEEEEecc-ccc
Confidence                    125788888877776644       56 88999999 864

>PRK10536 hypothetical protein; Provisional

Probab=97.76  E-value=0.00021  Score=56.07  Aligned_cols=47  Identities=13%  Similarity=0.106  Sum_probs=38.4

Q ss_pred             CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        47 ~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .++..-+..|...+..+.++..+++.+++|||||+..+.-.++.+..
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            35666788999999999988899999999999999877666655533

>COG4889 Predicted helicase [General function prediction only]

Probab=97.65  E-value=9.9e-05  Score=66.14  Aligned_cols=112  Identities=24%  Similarity=0.293  Sum_probs=78.0

Q ss_pred             cccccCCH-HHHHhHHhCCCCCCCHHHHHHHHHHhcC-------CcEEEEccCCCCcchh--------------hhhHHH
Q 031654           31 ARFAYVPQ-HLRNKPRTYKYVKPTPVQRHATSILVAG-------RDLMACAQTGSRKTTP--------------FCFPII   88 (155)
Q Consensus        31 ~~f~~l~~-~l~~~l~~~g~~~pt~iQ~~~i~~~l~g-------~dvl~~a~TGsGKT~~--------------yllp~l   88 (155)
                      -.|+.+.| ++..+|.-..=++|.|+|+.||...++|       +=+++|   |+|||..              ||+|.+
T Consensus       140 IDW~~f~p~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAc---GTGKTfTsLkisEala~~~iL~LvPSI  216 (1518)
T COG4889         140 IDWDIFDPTELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMAC---GTGKTFTSLKISEALAAARILFLVPSI  216 (1518)
T ss_pred             CChhhcCccccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEec---CCCccchHHHHHHHHhhhheEeecchH
Confidence            45776663 7777776666779999999999998765       334433   6899976              777888


Q ss_pred             HHHHHhhhch--------------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHH
Q 031654           89 NGIMREYYSA--------------------------------------------RKELRELARWVDNLMATLRRLVNLLE  124 (155)
Q Consensus        89 ~~l~~~~~~~--------------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~  124 (155)
                      +.|.+....-                                            ....+.-.++--|+.+|-..+...-.
T Consensus       217 sLLsQTlrew~~~~~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~e  296 (1518)
T COG4889         217 SLLSQTLREWTAQKELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKE  296 (1518)
T ss_pred             HHHHHHHHHHhhccCccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHH
Confidence            7776544322                                            11112223466788999888776655


Q ss_pred             cCCCCcccccceEEEEccccccc
Q 031654          125 RGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus       125 ~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                      ....-+..+ .++|-||| |+-.
T Consensus       297 AQe~G~~~f-DliicDEA-HRTt  317 (1518)
T COG4889         297 AQEAGLDEF-DLIICDEA-HRTT  317 (1518)
T ss_pred             HHHcCCCCc-cEEEecch-hccc
Confidence            555567788 89999999 9864

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

Probab=97.65  E-value=0.00015  Score=64.30  Aligned_cols=85  Identities=14%  Similarity=0.123  Sum_probs=59.0

Q ss_pred             CCCCHHHHHHHHHHhcC----CcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------------------------
Q 031654           50 VKPTPVQRHATSILVAG----RDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------------------------   98 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g----~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------------------------   98 (155)
                      ..+++-|+.+...+...    +-.++.+.||||||-+|+=.+-..+...+..-                           
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vl  276 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVL  276 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhh
Confidence            46788999999988655    67899999999999999655555444432211                           


Q ss_pred             ---------HHHHHHH-hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcc
Q 031654           99 ---------RKELREL-ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus        99 ---------~~~~~~l-~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa  142 (155)
                               .+..+.. .....|+|||=--+       ...++++ .++|+||=
T Consensus       277 HS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl-------F~Pf~~L-GLIIvDEE  322 (730)
T COG1198         277 HSGLSPGERYRVWRRARRGEARVVIGTRSAL-------FLPFKNL-GLIIVDEE  322 (730)
T ss_pred             cccCChHHHHHHHHHHhcCCceEEEEechhh-------cCchhhc-cEEEEecc
Confidence                     2222222 24688999983221       1358899 99999997

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

Probab=97.63  E-value=0.00022  Score=52.85  Aligned_cols=64  Identities=23%  Similarity=0.315  Sum_probs=42.1

Q ss_pred             hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCC---------CCccccc
Q 031654           64 VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGR---------VSLQMII  134 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~---------~~l~~l~  134 (155)
                      -+++++++.|++|+|||... ..+...+.             ..+..++..+-..|++.++...         -.+.++ 
T Consensus        45 ~~~~~l~l~G~~G~GKThLa-~ai~~~~~-------------~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~-  109 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLA-VAIANEAI-------------RKGYSVLFITASDLLDELKQSRSDGSYEELLKRLKRV-  109 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHH-HHHHHHHH-------------HTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTS-
T ss_pred             ccCeEEEEEhhHhHHHHHHH-HHHHHHhc-------------cCCcceeEeecCceeccccccccccchhhhcCccccc-
Confidence            46789999999999999853 23333222             2456677777777777776542         126778 


Q ss_pred             ceEEEEcc
Q 031654          135 RYLALKEA  142 (155)
Q Consensus       135 ~~lVlDEa  142 (155)
                      ++|||||.
T Consensus       110 dlLilDDl  117 (178)
T PF01695_consen  110 DLLILDDL  117 (178)
T ss_dssp             SCEEEETC
T ss_pred             cEeccccc
Confidence            99999998

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.

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=97.63  E-value=0.00012  Score=64.95  Aligned_cols=92  Identities=16%  Similarity=0.244  Sum_probs=65.9

Q ss_pred             CCCHHHHHHHHHH----hcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------HHHHH----HH-----
Q 031654           51 KPTPVQRHATSIL----VAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------RKELR----EL-----  105 (155)
Q Consensus        51 ~pt~iQ~~~i~~~----l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------~~~~~----~l-----  105 (155)
                      .|..-|..||..+    -.| +-++++.-||||||-.. +.++.+|.+.....           .+|..    ..     
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~~  243 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFGT  243 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCcc
Confidence            5778899988654    566 34999999999999875 66777776654433           11211    10     


Q ss_pred             ----------hcCCcEEEEChHHHHHHHHcC-----CCCcccccceEEEEccccc
Q 031654          106 ----------ARWVDNLMATLRRLVNLLERG-----RVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus       106 ----------~~~~~IlI~TP~~l~~~l~~~-----~~~l~~l~~~lVlDEa~D~  145 (155)
                                ...++|.|+|-..+..-+...     .+..... .++|+||| |+
T Consensus       244 ~~n~i~~~~~~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~F-DlIvIDEa-HR  296 (875)
T COG4096         244 KMNKIEDKKGDTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFF-DLIVIDEA-HR  296 (875)
T ss_pred             ceeeeecccCCcceeEEEeehHHHHhhhhccccccccCCCCce-eEEEechh-hh
Confidence                      124799999999988877654     4667778 89999999 87

>PRK08181 transposase; Validated

Probab=97.63  E-value=0.00031  Score=55.47  Aligned_cols=78  Identities=19%  Similarity=0.201  Sum_probs=47.8

Q ss_pred             CHHHHHHHH----HHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcC--
Q 031654           53 TPVQRHATS----ILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERG--  126 (155)
Q Consensus        53 t~iQ~~~i~----~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~--  126 (155)
                      .+.|..++.    .+-.+++++++||+|+|||.-.. .+...+             ...+..++..|...|.+.+...  
T Consensus        89 ~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~-Aia~~a-------------~~~g~~v~f~~~~~L~~~l~~a~~  154 (269)
T PRK08181         89 SKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAA-AIGLAL-------------IENGWRVLFTRTTDLVQKLQVARR  154 (269)
T ss_pred             CHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHH-HHHHHH-------------HHcCCceeeeeHHHHHHHHHHHHh
Confidence            344554442    23477899999999999996432 222222             2245667766666666655321  


Q ss_pred             --C-----CCcccccceEEEEcccccc
Q 031654          127 --R-----VSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       127 --~-----~~l~~l~~~lVlDEa~D~l  146 (155)
                        .     -.+.++ .+|||||. +.+
T Consensus       155 ~~~~~~~l~~l~~~-dLLIIDDl-g~~  179 (269)
T PRK08181        155 ELQLESAIAKLDKF-DLLILDDL-AYV  179 (269)
T ss_pred             CCcHHHHHHHHhcC-CEEEEecc-ccc
Confidence              1     125677 89999999 764

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.63  E-value=0.00032  Score=62.64  Aligned_cols=95  Identities=18%  Similarity=0.083  Sum_probs=54.1

Q ss_pred             CCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------HHHHHHHhcCCcEEEEChHHHHHHH
Q 031654           51 KPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------RKELRELARWVDNLMATLRRLVNLL  123 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------~~~~~~l~~~~~IlI~TP~~l~~~l  123 (155)
                      .+++-|..|+..++.+ +-+++.++.|+|||... -.++..+.......      ......+.....+--.|-.++..-+
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~~g~~V~~~ApTg~Aa~~L~~~~g~~a~Ti~~~~~~~  430 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEAAGYRVIGAALSGKAAEGLQAESGIESRTLASLEYAW  430 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHhCCCeEEEEeCcHHHHHHHHhccCCceeeHHHHHhhh
Confidence            5799999999999875 56789999999998652 12222222211111      2233333332223233333332222


Q ss_pred             HcCCCCcccccceEEEEccccccccc
Q 031654          124 ERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       124 ~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      ..+.-.+... .+||||||  -|++.
T Consensus       431 ~~~~~~~~~~-~llIvDEa--sMv~~  453 (744)
T TIGR02768       431 ANGRDLLSDK-DVLVIDEA--GMVGS  453 (744)
T ss_pred             ccCcccCCCC-cEEEEECc--ccCCH
Confidence            2233345677 89999999  66654

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.

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.56  E-value=0.00026  Score=55.38  Aligned_cols=42  Identities=29%  Similarity=0.398  Sum_probs=38.2

Q ss_pred             HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEc
Q 031654           99 RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKE  141 (155)
Q Consensus        99 ~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDE  141 (155)
                      .+|...+.. ..+|.||||+||..++..+.+.++++ +++|||-
T Consensus       167 ~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l-~~ivlD~  209 (252)
T PF14617_consen  167 EEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNL-KRIVLDW  209 (252)
T ss_pred             HHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccC-eEEEEcC
Confidence            677777774 79999999999999999999999999 9999995

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=97.55  E-value=0.00031  Score=63.17  Aligned_cols=85  Identities=15%  Similarity=0.082  Sum_probs=54.5

Q ss_pred             HHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------HHHHHHHh-----------------
Q 031654           58 HATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------RKELRELA-----------------  106 (155)
Q Consensus        58 ~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------~~~~~~l~-----------------  106 (155)
                      +.+..+.+..-++++|+||||||...-.-+++.-.......              ......+.                 
T Consensus        57 ~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~iRfe~~~  136 (845)
T COG1643          57 EILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYSIRFESKV  136 (845)
T ss_pred             HHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEEEEeeccC
Confidence            33445555667899999999999873333333222111011              11222222                 


Q ss_pred             -cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654          107 -RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus       107 -~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                       ..-.|-+.|.|-|+..+..+. .++.+ .++|+||| |.
T Consensus       137 s~~Trik~mTdGiLlrei~~D~-~Ls~y-s~vIiDEa-HE  173 (845)
T COG1643         137 SPRTRIKVMTDGILLREIQNDP-LLSGY-SVVIIDEA-HE  173 (845)
T ss_pred             CCCceeEEeccHHHHHHHhhCc-ccccC-CEEEEcch-hh
Confidence             135788999999999988665 48999 99999999 63

>PRK06526 transposase; Provisional

Probab=97.53  E-value=0.0002  Score=56.12  Aligned_cols=69  Identities=19%  Similarity=0.094  Sum_probs=41.5

Q ss_pred             HHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcC----C-----CCccc
Q 031654           62 ILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERG----R-----VSLQM  132 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~----~-----~~l~~  132 (155)
                      .+-.+++++++||+|+|||....- +...+.             ..+..++..|...+.+.+...    .     ..+..
T Consensus        94 fi~~~~nlll~Gp~GtGKThLa~a-l~~~a~-------------~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~  159 (254)
T PRK06526         94 FVTGKENVVFLGPPGTGKTHLAIG-LGIRAC-------------QAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGR  159 (254)
T ss_pred             hhhcCceEEEEeCCCCchHHHHHH-HHHHHH-------------HCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhcc
Confidence            334668999999999999975432 212121             234455555555554444211    1     12456


Q ss_pred             ccceEEEEcccccc
Q 031654          133 IIRYLALKEAADQT  146 (155)
Q Consensus       133 l~~~lVlDEa~D~l  146 (155)
                      . .+|||||+ +.+
T Consensus       160 ~-dlLIIDD~-g~~  171 (254)
T PRK06526        160 Y-PLLIVDEV-GYI  171 (254)
T ss_pred             C-CEEEEccc-ccC
Confidence            7 89999999 765

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.48  E-value=0.00069  Score=60.31  Aligned_cols=35  Identities=17%  Similarity=0.182  Sum_probs=31.1

Q ss_pred             CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        47 ~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .++ .+++-|+.|+..+..++-+++.++.|||||..
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~  354 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTI  354 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHH
Confidence            343 68999999999999999999999999999974

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.

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=97.48  E-value=0.00053  Score=52.86  Aligned_cols=110  Identities=20%  Similarity=0.221  Sum_probs=72.3

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhc---CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVA---GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~---g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------   98 (155)
                      .+++=.+.. ++ -..+.|......+.+   |.|.+.+.-.|.|||.+ ++|++..+..++..-                
T Consensus        12 ~wLl~E~e~-~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~~LvrviVpk~Ll~q~~~~   88 (229)
T PF12340_consen   12 DWLLFEIES-NI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSV-IVPMLALALADGSRLVRVIVPKALLEQMRQM   88 (229)
T ss_pred             HHHHHHHHc-Cc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccch-HHHHHHHHHcCCCcEEEEEcCHHHHHHHHHH
Confidence            444443433 33 458999998888875   58999999999999987 478887777655432                


Q ss_pred             --------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHc-------CCC-----------
Q 031654           99 --------------------------------RKELRELARWVDNLMATLRRLVNLLER-------GRV-----------  128 (155)
Q Consensus        99 --------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~-------~~~-----------  128 (155)
                                                      ....+.....-.|+++||+.++.+.-.       +..           
T Consensus        89 L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~~~~~~~~~~l~~~q~  168 (229)
T PF12340_consen   89 LRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQDGKPEEARELLKIQK  168 (229)
T ss_pred             HHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence                                            112223333457999999998665321       111           


Q ss_pred             CcccccceEEEEcccccccccccc
Q 031654          129 SLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       129 ~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                      -+.+. ..=|+||+ |..|..-|+
T Consensus       169 ~l~~~-~rdilDEs-De~L~~k~q  190 (229)
T PF12340_consen  169 WLDEH-SRDILDES-DEILSVKYQ  190 (229)
T ss_pred             HHHhc-CCeEeECc-hhccCcceE
Confidence            02233 45689999 999986553

There are two conserved sequence motifs: LLE and NMG.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.42  E-value=0.00013  Score=66.17  Aligned_cols=93  Identities=20%  Similarity=0.194  Sum_probs=65.0

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      .|+++|-..=-.+..|+  ++.-.||-|||++..+|++-.........                                
T Consensus       138 ~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~i~~  215 (1025)
T PRK12900        138 VPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALTGRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGVILN  215 (1025)
T ss_pred             cccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHcCCCcEEEeechHhhhhhHHHHHHHHHHhCCeeeeeCC
Confidence            68888887655555554  67889999999999999877666554332                                


Q ss_pred             --HHHHHHHhcCCcEEEEChHHH-HHHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 --RKELRELARWVDNLMATLRRL-VNLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                        ....+.-.-.|||..||..-+ .|+|+.+.      .-.... .|.||||+ |.+|
T Consensus       216 ~~~~~~Rr~aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~-~faIVDEv-DSvL  271 (1025)
T PRK12900        216 TMRPEERREQYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDF-YFAIVDEV-DSVL  271 (1025)
T ss_pred             CCCHHHHHHhCCCcceecCCCccccccchhccccchhhhhccCC-ceEEEech-hhhh
Confidence              233344445799999999665 33443321      234667 89999999 9877

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=97.36  E-value=0.001  Score=61.19  Aligned_cols=99  Identities=24%  Similarity=0.310  Sum_probs=68.8

Q ss_pred             HHHHhH-HhCCCCCCCHHHHHHHHHHhc----C--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------
Q 031654           39 HLRNKP-RTYKYVKPTPVQRHATSILVA----G--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------   98 (155)
Q Consensus        39 ~l~~~l-~~~g~~~pt~iQ~~~i~~~l~----g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------   98 (155)
                      +..+.+ ..++|+. |+=|..||..+.+    +  -|=++|+--|-|||-+.+=++...+..++...             
T Consensus       582 ~~q~~F~~~FPyeE-T~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy  660 (1139)
T COG1197         582 EWQEEFEASFPYEE-TPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHY  660 (1139)
T ss_pred             HHHHHHHhcCCCcC-CHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCCCeEEEEcccHHhHHHHH
Confidence            333333 4456654 9999999999863    3  48899999999999887766555444432221             


Q ss_pred             --------------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654           99 --------------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 --------------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                                                ......+.+ ..||||||..-    | .+.+.+.++ .++||||= ++
T Consensus       661 ~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrL----L-~kdv~FkdL-GLlIIDEE-qR  727 (1139)
T COG1197         661 ETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRL----L-SKDVKFKDL-GLLIIDEE-QR  727 (1139)
T ss_pred             HHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHh----h-CCCcEEecC-CeEEEech-hh
Confidence                                      223334433 68999999643    2 566889999 99999997 55

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

Probab=97.36  E-value=0.00077  Score=58.94  Aligned_cols=47  Identities=13%  Similarity=-0.019  Sum_probs=38.0

Q ss_pred             HHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHH
Q 031654           44 PRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIING   90 (155)
Q Consensus        44 l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~   90 (155)
                      +...|..+++.-|..|..++++..=.++++|+|+|||..-.--+++.
T Consensus       403 ~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl  449 (935)
T KOG1802|consen  403 FSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHL  449 (935)
T ss_pred             hcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHH
Confidence            34456778899999999999999999999999999998764444433

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=97.32  E-value=0.00047  Score=62.26  Aligned_cols=90  Identities=16%  Similarity=0.158  Sum_probs=62.9

Q ss_pred             CHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------HHHHHH------------
Q 031654           53 TPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------RKELRE------------  104 (155)
Q Consensus        53 t~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------~~~~~~------------  104 (155)
                      +..+...+..+.+..-+++++.||+|||.-----+++........+                ..-..+            
T Consensus       175 ~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VGYq  254 (924)
T KOG0920|consen  175 YKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVGYQ  254 (924)
T ss_pred             HHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeeeEE
Confidence            5667777888888899999999999999864333555443333221                111111            


Q ss_pred             ------HhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654          105 ------LARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus       105 ------l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                            ......++.||-|-|++.+.. .-.+..+ .++|+||+ |.
T Consensus       255 vrl~~~~s~~t~L~fcTtGvLLr~L~~-~~~l~~v-thiivDEV-HE  298 (924)
T KOG0920|consen  255 VRLESKRSRETRLLFCTTGVLLRRLQS-DPTLSGV-THIIVDEV-HE  298 (924)
T ss_pred             EeeecccCCceeEEEecHHHHHHHhcc-CcccccC-ceeeeeeE-EE
Confidence                  112357999999999999877 5578889 99999999 53

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

Probab=97.31  E-value=0.00059  Score=54.68  Aligned_cols=55  Identities=15%  Similarity=0.128  Sum_probs=35.9

Q ss_pred             CCCCCcccccCC-HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch
Q 031654           26 LSSPAARFAYVP-QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA   98 (155)
Q Consensus        26 ~p~~~~~f~~l~-~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~   98 (155)
                      +|..+.+|++|+ |.++..+.+..                 .-=|+|.+|||||||... ..+++.+.++....
T Consensus       101 Ip~~i~~~e~LglP~i~~~~~~~~-----------------~GLILVTGpTGSGKSTTl-AamId~iN~~~~~H  156 (353)
T COG2805         101 IPSKIPTLEELGLPPIVRELAESP-----------------RGLILVTGPTGSGKSTTL-AAMIDYINKHKAKH  156 (353)
T ss_pred             cCccCCCHHHcCCCHHHHHHHhCC-----------------CceEEEeCCCCCcHHHHH-HHHHHHHhccCCcc
Confidence            567777888777 55554443321                 124899999999998763 56777776655443

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.29  E-value=0.00031  Score=57.25  Aligned_cols=79  Identities=13%  Similarity=0.074  Sum_probs=42.4

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHH--HHhhhch----------HHHHHHHhcC-----CcEEEEChHHHHHHHHcCCCCc
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGI--MREYYSA----------RKELRELARW-----VDNLMATLRRLVNLLERGRVSL  130 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l--~~~~~~~----------~~~~~~l~~~-----~~IlI~TP~~l~~~l~~~~~~l  130 (155)
                      -++|.+.+|||||+..+ -++..+  .......          ......+...     ....+..|..+...+.......
T Consensus         3 v~~I~G~aGTGKTvla~-~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   81 (352)
T PF09848_consen    3 VILITGGAGTGKTVLAL-NLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNPKLKKSDFRKPTSFINNYSESDKEK   81 (352)
T ss_pred             EEEEEecCCcCHHHHHH-HHHHHhhccccCCceEEEEecchHHHHHHHHHhhhcccchhhhhhhhhHHHHhhcccccccC
Confidence            36889999999999753 233333  1111111          1111222221     1334444544443333222345


Q ss_pred             ccccceEEEEccccccccc
Q 031654          131 QMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       131 ~~l~~~lVlDEa~D~ll~~  149 (155)
                      ... .++|+||| ++|.+.
T Consensus        82 ~~~-DviivDEA-qrl~~~   98 (352)
T PF09848_consen   82 NKY-DVIIVDEA-QRLRTK   98 (352)
T ss_pred             CcC-CEEEEehh-Hhhhhc
Confidence            677 89999999 999883

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.23  E-value=0.00032  Score=63.91  Aligned_cols=93  Identities=22%  Similarity=0.188  Sum_probs=63.8

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      +|+.+|-..=-.+..|+  ++.-.||-|||++..+|++-..+......                                
T Consensus       169 ~~yDVQliGgivLh~G~--IAEM~TGEGKTLvAtlp~yLnAL~GkgVHvVTVNDYLA~RDaewmgply~fLGLsvg~i~~  246 (1112)
T PRK12901        169 VHYDVQLIGGVVLHQGK--IAEMATGEGKTLVATLPVYLNALTGNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDCIDK  246 (1112)
T ss_pred             cccchHHhhhhhhcCCc--eeeecCCCCchhHHHHHHHHHHHcCCCcEEEEechhhhhccHHHHHHHHHHhCCceeecCC
Confidence            57888877554454554  77899999999999999877766654433                                


Q ss_pred             ---HHHHHHHhcCCcEEEEChHHH-HHHHHcC------CCCcccccceEEEEccccccc
Q 031654           99 ---RKELRELARWVDNLMATLRRL-VNLLERG------RVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 ---~~~~~~l~~~~~IlI~TP~~l-~~~l~~~------~~~l~~l~~~lVlDEa~D~ll  147 (155)
                         ....+.-.-.|||..+|...+ .|+|+.+      ......+ .|.|+||+ |.+|
T Consensus       247 ~~~~~~~rr~aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~-~fAIVDEv-DSIL  303 (1112)
T PRK12901        247 HQPNSEARRKAYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKH-NYAIVDEV-DSVL  303 (1112)
T ss_pred             CCCCHHHHHHhCCCcceecCCCccccccchhccccchHhhhCcCC-ceeEeech-hhhh
Confidence               222333334799999998665 3344332      1234567 89999999 9887

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=97.20  E-value=0.00061  Score=53.05  Aligned_cols=73  Identities=22%  Similarity=0.335  Sum_probs=40.7

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHh----cCCcEEEEChHHHHHHHHcCCCCc--ccccceEEEE
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELA----RWVDNLMATLRRLVNLLERGRVSL--QMIIRYLALK  140 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~----~~~~IlI~TP~~l~~~l~~~~~~l--~~l~~~lVlD  140 (155)
                      -++++.+|+|+|||.+.+.-+-..+-...   ++-.-++.    +|.|++=   .+ ..++-.+.+.+  .+- +.+|+|
T Consensus        49 P~liisGpPG~GKTTsi~~LAr~LLG~~~---ke~vLELNASdeRGIDvVR---n~-IK~FAQ~kv~lp~grh-KIiILD  120 (333)
T KOG0991|consen   49 PNLIISGPPGTGKTTSILCLARELLGDSY---KEAVLELNASDERGIDVVR---NK-IKMFAQKKVTLPPGRH-KIIILD  120 (333)
T ss_pred             CceEeeCCCCCchhhHHHHHHHHHhChhh---hhHhhhccCccccccHHHH---HH-HHHHHHhhccCCCCce-eEEEee
Confidence            58999999999999986543322221111   11122221    2333321   11 22333344444  667 889999


Q ss_pred             cccccccc
Q 031654          141 EAADQTLD  148 (155)
Q Consensus       141 Ea~D~ll~  148 (155)
                      || |.|-+
T Consensus       121 EA-DSMT~  127 (333)
T KOG0991|consen  121 EA-DSMTA  127 (333)
T ss_pred             cc-chhhh
Confidence            99 99865

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

Probab=97.12  E-value=0.0014  Score=55.59  Aligned_cols=49  Identities=18%  Similarity=0.169  Sum_probs=34.9

Q ss_pred             HHhCCCCCCCHHHHHHHHHHhcCC--cEEEEccCCCCcchhhhhHHHHHHHHhhh
Q 031654           44 PRTYKYVKPTPVQRHATSILVAGR--DLMACAQTGSRKTTPFCFPIINGIMREYY   96 (155)
Q Consensus        44 l~~~g~~~pt~iQ~~~i~~~l~g~--dvl~~a~TGsGKT~~yllp~l~~l~~~~~   96 (155)
                      +.++|+   ++-|...+..+++..  =+++.+|||||||.. +..+++.+.....
T Consensus       237 l~~Lg~---~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~~~  287 (500)
T COG2804         237 LEKLGM---SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTPER  287 (500)
T ss_pred             HHHhCC---CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCCCc
Confidence            445554   778888888887664  388899999999986 3556666655443

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.10  E-value=0.0014  Score=51.39  Aligned_cols=80  Identities=21%  Similarity=0.306  Sum_probs=48.2

Q ss_pred             CCCCCCHHHHHHHHHHh-------cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHH
Q 031654           48 KYVKPTPVQRHATSILV-------AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLV  120 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l-------~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~  120 (155)
                      .|.....++..++..+.       ++.++++.|++|+|||.-. .++.+.+.             ..+..+++.|-..+.
T Consensus        80 d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa-~Ai~~~l~-------------~~g~sv~f~~~~el~  145 (254)
T COG1484          80 DFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLA-IAIGNELL-------------KAGISVLFITAPDLL  145 (254)
T ss_pred             cccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHH-HHHHHHHH-------------HcCCeEEEEEHHHHH
Confidence            44445555555444332       6679999999999999743 22322222             235556555554444


Q ss_pred             HHHHc----CC-----CC-cccccceEEEEcc
Q 031654          121 NLLER----GR-----VS-LQMIIRYLALKEA  142 (155)
Q Consensus       121 ~~l~~----~~-----~~-l~~l~~~lVlDEa  142 (155)
                      .-+..    +.     .. +.++ ++|||||.
T Consensus       146 ~~Lk~~~~~~~~~~~l~~~l~~~-dlLIiDDl  176 (254)
T COG1484         146 SKLKAAFDEGRLEEKLLRELKKV-DLLIIDDI  176 (254)
T ss_pred             HHHHHHHhcCchHHHHHHHhhcC-CEEEEecc
Confidence            44432    11     23 7788 99999998

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.08  E-value=0.0021  Score=56.06  Aligned_cols=30  Identities=20%  Similarity=0.192  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           54 PVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        54 ~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..|+.|+-.++.++-.++.+++|||||...
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v  177 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTV  177 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHH
Confidence            689999999999999999999999999863

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>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=97.08  E-value=0.003  Score=43.25  Aligned_cols=17  Identities=29%  Similarity=0.429  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      ++.+++.||+|+|||..
T Consensus        19 ~~~v~i~G~~G~GKT~l   35 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            67899999999999963

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.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.03  E-value=0.0053  Score=56.90  Aligned_cols=95  Identities=19%  Similarity=0.113  Sum_probs=56.4

Q ss_pred             CCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------HHHHHHHhcCCcEEEEChHHHHHHH
Q 031654           51 KPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------RKELRELARWVDNLMATLRRLVNLL  123 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------~~~~~~l~~~~~IlI~TP~~l~~~l  123 (155)
                      .+++-|..++..+..+ +=++++++.|||||...- ++...+.......      ......|.....|--.|-.+++.-.
T Consensus       381 ~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~-~~~~~~e~~G~~V~g~ApTgkAA~~L~e~~Gi~a~TIas~ll~~  459 (1102)
T PRK13826        381 RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMK-AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRW  459 (1102)
T ss_pred             CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHH-HHHHHHHHcCCeEEEEcCcHHHHHHHHHhhCCCeeeHHHHHhhh
Confidence            6899999999988654 568889999999997532 2333332222111      4444444443344444544432112


Q ss_pred             HcCCCCcccccceEEEEccccccccc
Q 031654          124 ERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       124 ~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      ..+...+..- .+||||||  -|++.
T Consensus       460 ~~~~~~l~~~-~vlVIDEA--sMv~~  482 (1102)
T PRK13826        460 NQGRDQLDNK-TVFVLDEA--GMVAS  482 (1102)
T ss_pred             ccCccCCCCC-cEEEEECc--ccCCH
Confidence            2233445666 78999999  67653

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=96.98  E-value=0.0026  Score=58.55  Aligned_cols=93  Identities=16%  Similarity=0.128  Sum_probs=57.9

Q ss_pred             CCCHHHHHHHHHHh----cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc--h--------------------------
Q 031654           51 KPTPVQRHATSILV----AGRDLMACAQTGSRKTTPFCFPIINGIMREYYS--A--------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l----~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~--~--------------------------   98 (155)
                      .+.+.|..++..++    +|.+.+++-..|.|||+.. +.++..+......  .                          
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQa-IalL~~L~~~~~~~gp~LIVvP~SlL~nW~~Ei~kw~p~l~v  247 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQT-ISLLGYLHEYRGITGPHMVVAPKSTLGNWMNEIRRFCPVLRA  247 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHH-HHHHHHHHHhcCCCCCEEEEeChHHHHHHHHHHHHHCCCCce
Confidence            56889999987664    6788999999999999864 3333333321110  0                          


Q ss_pred             ------HHHHH----H--HhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 ------RKELR----E--LARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 ------~~~~~----~--l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                            .....    .  ....++|+|+|.+.+.....  .+.--.. .++|+||| |++=+
T Consensus       248 ~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~--~L~k~~W-~~VIvDEA-HrIKN  305 (1033)
T PLN03142        248 VKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT--ALKRFSW-RYIIIDEA-HRIKN  305 (1033)
T ss_pred             EEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH--HhccCCC-CEEEEcCc-cccCC
Confidence                  11111    1  12357899999887654322  1222245 68999999 88754

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

Probab=96.97  E-value=8.5e-05  Score=67.24  Aligned_cols=96  Identities=20%  Similarity=0.179  Sum_probs=67.7

Q ss_pred             CCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------------H----------
Q 031654           48 KYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------------R----------   99 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------------~----------   99 (155)
                      -+....|+|.+.+-.+..- .+.++-+|||+|||++|-+.+...+.......                 .          
T Consensus       924 ~~~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~~kvvyIap~kalvker~~Dw~~r~~~~g~k 1003 (1230)
T KOG0952|consen  924 LYKYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPGSKVVYIAPDKALVKERSDDWSKRDELPGIK 1003 (1230)
T ss_pred             hhcccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCCccEEEEcCCchhhcccccchhhhcccCCce
Confidence            3446677888776555443 68899999999999999998877666544433                 0          


Q ss_pred             ---------HHHHHHhcCCcEEEEChHHHHHHHHc--CCCCcccccceEEEEcccccc
Q 031654          100 ---------KELRELARWVDNLMATLRRLVNLLER--GRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       100 ---------~~~~~l~~~~~IlI~TP~~l~~~l~~--~~~~l~~l~~~lVlDEa~D~l  146 (155)
                               .....+ ..++++|+||++.-.+.++  +.-.+.++ ..+|+||. +.+
T Consensus      1004 ~ie~tgd~~pd~~~v-~~~~~~ittpek~dgi~Rsw~~r~~v~~v-~~iv~de~-hll 1058 (1230)
T KOG0952|consen 1004 VIELTGDVTPDVKAV-READIVITTPEKWDGISRSWQTRKYVQSV-SLIVLDEI-HLL 1058 (1230)
T ss_pred             eEeccCccCCChhhe-ecCceEEcccccccCccccccchhhhccc-cceeeccc-ccc
Confidence                     001111 2479999999997766663  34568889 99999999 443

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=96.94  E-value=0.0013  Score=57.49  Aligned_cols=31  Identities=23%  Similarity=0.242  Sum_probs=28.3

Q ss_pred             CHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           53 TPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        53 t~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ...|+.|+-..+..+-.++.+++|||||..-
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v  184 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTV  184 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHH
Confidence            5799999999999999999999999999763

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.90  E-value=0.0034  Score=51.01  Aligned_cols=67  Identities=19%  Similarity=0.153  Sum_probs=45.0

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcC----C-------CCcccc
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERG----R-------VSLQMI  133 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~----~-------~~l~~l  133 (155)
                      .+.++++.|+||+|||.-. ..+...+             +..+..|+..|...+.+.+...    .       -.+.++
T Consensus       182 ~~~~Lll~G~~GtGKThLa-~aIa~~l-------------~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~  247 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLS-NCIAKEL-------------LDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINC  247 (329)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHH-------------HHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccC
Confidence            4589999999999999732 2333322             2346778888877777766331    1       124678


Q ss_pred             cceEEEEccccccc
Q 031654          134 IRYLALKEAADQTL  147 (155)
Q Consensus       134 ~~~lVlDEa~D~ll  147 (155)
                       .+||||+. ....
T Consensus       248 -DLLIIDDl-G~e~  259 (329)
T PRK06835        248 -DLLIIDDL-GTEK  259 (329)
T ss_pred             -CEEEEecc-CCCC
Confidence             99999999 6543

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=96.89  E-value=0.00066  Score=46.79  Aligned_cols=19  Identities=37%  Similarity=0.370  Sum_probs=12.6

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      +++-+++.|++|+|||...
T Consensus         3 ~~~~~~i~G~~G~GKT~~~   21 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLI   21 (131)
T ss_dssp             ----EEEEE-TTSSHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHH
Confidence            3567899999999999863

>PRK08727 hypothetical protein; Validated

Probab=96.88  E-value=0.0019  Score=49.70  Aligned_cols=65  Identities=14%  Similarity=0.038  Sum_probs=38.4

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                      ..+++.|++|+|||.... .+...+.             ..+..++..+...+...+..-.-.+.++ ..|||||+ |.+
T Consensus        42 ~~l~l~G~~G~GKThL~~-a~~~~~~-------------~~~~~~~y~~~~~~~~~~~~~~~~l~~~-dlLiIDDi-~~l  105 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLAL-ALCAAAE-------------QAGRSSAYLPLQAAAGRLRDALEALEGR-SLVALDGL-ESI  105 (233)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHH-------------HcCCcEEEEeHHHhhhhHHHHHHHHhcC-CEEEEeCc-ccc
Confidence            359999999999996422 2222221             1244555555544433322211245677 89999999 876


Q ss_pred             c
Q 031654          147 L  147 (155)
Q Consensus       147 l  147 (155)
                      .
T Consensus       106 ~  106 (233)
T PRK08727        106 A  106 (233)
T ss_pred             c
Confidence            5

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=96.85  E-value=0.0035  Score=51.67  Aligned_cols=17  Identities=24%  Similarity=0.440  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .|+++.|+||||||..-
T Consensus        43 ~n~~iyG~~GTGKT~~~   59 (366)
T COG1474          43 SNIIIYGPTGTGKTATV   59 (366)
T ss_pred             ccEEEECCCCCCHhHHH
Confidence            47999999999999873

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=96.85  E-value=0.0022  Score=58.05  Aligned_cols=35  Identities=26%  Similarity=0.271  Sum_probs=29.9

Q ss_pred             CCCCCHHHHHHHHHHhcCCc-EEEEccCCCCcchhh
Q 031654           49 YVKPTPVQRHATSILVAGRD-LMACAQTGSRKTTPF   83 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l~g~d-vl~~a~TGsGKT~~y   83 (155)
                      +..++.-|++|+-.++..+| .++.+=+|||||..-
T Consensus       667 ~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI  702 (1100)
T KOG1805|consen  667 LLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTI  702 (1100)
T ss_pred             HhhcCHHHHHHHHHHHhccchheeecCCCCCchhhH
Confidence            34678899999999999987 678899999999864

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.83  E-value=0.0062  Score=49.29  Aligned_cols=47  Identities=32%  Similarity=0.323  Sum_probs=31.8

Q ss_pred             HhHHhCCCCCCCHHHHHHHHH-HhcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           42 NKPRTYKYVKPTPVQRHATSI-LVAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        42 ~~l~~~g~~~pt~iQ~~~i~~-~l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      +.+.+.|+  +++.|...+.. +..+++++++++||||||. ++-.++..+
T Consensus       125 ~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTT-ll~aL~~~~  172 (319)
T PRK13894        125 DQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTT-LVNAIINEM  172 (319)
T ss_pred             HHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHH-HHHHHHHhh
Confidence            33444554  46777777764 4566899999999999994 444555443

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=96.80  E-value=0.0021  Score=58.86  Aligned_cols=95  Identities=14%  Similarity=0.055  Sum_probs=58.1

Q ss_pred             CCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------HHHH-HHH---------
Q 031654           51 KPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------RKEL-REL---------  105 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------~~~~-~~l---------  105 (155)
                      .|.|+|..+.-.++..  ..+++.-..|.|||.-..+-+-..+..+....             ..+. +..         
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~~~rvLIVvP~sL~~QW~~El~~kF~l~~~i~~~  231 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPETLQHQWLVEMLRRFNLRFSLFDE  231 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCCCCcEEEEcCHHHHHHHHHHHHHHhCCCeEEEcC
Confidence            4899999988766543  47899999999999987655544444332211             1111 110         


Q ss_pred             -------------hcCCcEEEEChHHHHHHHH-cCCCCcccccceEEEEccccccc
Q 031654          106 -------------ARWVDNLMATLRRLVNLLE-RGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus       106 -------------~~~~~IlI~TP~~l~~~l~-~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                                   ....+++|++-+.+...-. ...+.-... +++|+||| |++-
T Consensus       232 ~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~w-dlvIvDEA-H~lk  285 (956)
T PRK04914        232 ERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEW-DLLVVDEA-HHLV  285 (956)
T ss_pred             cchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCC-CEEEEech-hhhc
Confidence                         0135688888766543110 011222356 88999999 9985

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

Probab=96.80  E-value=0.0022  Score=50.06  Aligned_cols=23  Identities=22%  Similarity=0.099  Sum_probs=14.5

Q ss_pred             cCCcEEEEccCCCCcchhhhhHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPI   87 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~   87 (155)
                      ..+..+++-..|+|||+..+.-+
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~~~   46 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIALI   46 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCchhhhhhhh
Confidence            34689999999999998865443

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>PHA00729 NTP-binding motif containing protein

Probab=96.79  E-value=0.0066  Score=46.81  Aligned_cols=74  Identities=11%  Similarity=0.078  Sum_probs=40.8

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa  142 (155)
                      .++++.|++|+|||... ..+...+................+-..++.+...+.+.+....-...++ .++|+||+
T Consensus        18 ~nIlItG~pGvGKT~LA-~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L~~a~~~~~~~-dlLIIDd~   91 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYA-LKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDALEKIQDAIDNDYRI-PLIIFDDA   91 (226)
T ss_pred             EEEEEECCCCCCHHHHH-HHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHHHHHHHHHhcCCCC-CEEEEeCC
Confidence            38999999999999643 2233332211000000111223344566677777777765422223456 78999995

>PRK06893 DNA replication initiation factor; Validated

Probab=96.78  E-value=0.0021  Score=49.34  Aligned_cols=65  Identities=9%  Similarity=0.032  Sum_probs=35.3

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                      ..++++||+|+|||.-. ..+.+.+..             ++..++..+..........-.-.+.+. ++|||||+ |.+
T Consensus        40 ~~l~l~G~~G~GKThL~-~ai~~~~~~-------------~~~~~~y~~~~~~~~~~~~~~~~~~~~-dlLilDDi-~~~  103 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLL-KAVSNHYLL-------------NQRTAIYIPLSKSQYFSPAVLENLEQQ-DLVCLDDL-QAV  103 (229)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHH-------------cCCCeEEeeHHHhhhhhHHHHhhcccC-CEEEEeCh-hhh
Confidence            34799999999999632 222222221             223444444332211111101135677 89999999 877


Q ss_pred             c
Q 031654          147 L  147 (155)
Q Consensus       147 l  147 (155)
                      .
T Consensus       104 ~  104 (229)
T PRK06893        104 I  104 (229)
T ss_pred             c
Confidence            5

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.77  E-value=0.0053  Score=47.87  Aligned_cols=65  Identities=15%  Similarity=0.229  Sum_probs=40.6

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcC----C-------CCcccccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERG----R-------VSLQMIIR  135 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~----~-------~~l~~l~~  135 (155)
                      ..+++.+++|+|||.... .+...+..             .+..+++.|-..+...+...    .       -.+.++ .
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~-------------~g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l~~~-d  164 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLL-------------RGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDLSNV-D  164 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHh-------------cCCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHhccC-C
Confidence            479999999999997432 33333322             24556666665555443321    0       125678 9


Q ss_pred             eEEEEccccccc
Q 031654          136 YLALKEAADQTL  147 (155)
Q Consensus       136 ~lVlDEa~D~ll  147 (155)
                      +|||||+ +..-
T Consensus       165 lLvIDDi-g~~~  175 (244)
T PRK07952        165 LLVIDEI-GVQT  175 (244)
T ss_pred             EEEEeCC-CCCC
Confidence            9999999 7754

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.77  E-value=0.0038  Score=47.17  Aligned_cols=67  Identities=15%  Similarity=0.100  Sum_probs=36.0

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccc
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D  144 (155)
                      .+..+++.|++|+|||..... +.....             ..+..++..+-..+......-.-.+... .+|||||+ |
T Consensus        37 ~~~~lll~G~~G~GKT~la~~-~~~~~~-------------~~~~~~~~i~~~~~~~~~~~~~~~~~~~-~lLvIDdi-~  100 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQA-ACAAAE-------------ERGKSAIYLPLAELAQADPEVLEGLEQA-DLVCLDDV-E  100 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHH-HHHHHH-------------hcCCcEEEEeHHHHHHhHHHHHhhcccC-CEEEEeCh-h
Confidence            457899999999999975321 111111             1223444444333322111000123456 78999999 8


Q ss_pred             ccc
Q 031654          145 QTL  147 (155)
Q Consensus       145 ~ll  147 (155)
                      .+-
T Consensus       101 ~l~  103 (226)
T TIGR03420       101 AIA  103 (226)
T ss_pred             hhc
Confidence            764

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.76  E-value=0.012  Score=48.57  Aligned_cols=51  Identities=14%  Similarity=0.087  Sum_probs=39.7

Q ss_pred             hCCCCCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhh
Q 031654           46 TYKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYY   96 (155)
Q Consensus        46 ~~g~~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~   96 (155)
                      ..|+..-+.-|..|+..++.-  .=|-..++.|||||+-.+.+.+.+....+.
T Consensus       223 vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~  275 (436)
T COG1875         223 VWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKR  275 (436)
T ss_pred             hhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhh
Confidence            447877788899999998876  346677999999999988887777765443

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=96.74  E-value=0.0031  Score=54.96  Aligned_cols=34  Identities=18%  Similarity=0.083  Sum_probs=26.8

Q ss_pred             CcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654          109 VDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus       109 ~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                      ..|...|-|.|++.+-.+. .++.. .++||||| |.
T Consensus       141 TrikymTDG~LLRE~l~Dp-~LskY-svIIlDEA-HE  174 (674)
T KOG0922|consen  141 TRIKYMTDGMLLREILKDP-LLSKY-SVIILDEA-HE  174 (674)
T ss_pred             eeEEEecchHHHHHHhcCC-ccccc-cEEEEech-hh
Confidence            5788999999887765443 57888 89999999 64

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.73  E-value=0.0044  Score=52.31  Aligned_cols=31  Identities=13%  Similarity=0.076  Sum_probs=24.6

Q ss_pred             CHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           53 TPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        53 t~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      -......+..+..++++++.+++|+|||...
T Consensus       181 e~~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        181 ETTIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             HHHHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            3344556677778999999999999999754

>PRK12377 putative replication protein; Provisional

Probab=96.70  E-value=0.008  Score=46.98  Aligned_cols=64  Identities=19%  Similarity=0.236  Sum_probs=39.0

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHc----C------CCCcccccce
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLER----G------RVSLQMIIRY  136 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~----~------~~~l~~l~~~  136 (155)
                      .++++.|++|+|||... ..+.+.+.             ..+..+++.|-..+...+..    +      .-.+.++ .+
T Consensus       102 ~~l~l~G~~GtGKThLa-~AIa~~l~-------------~~g~~v~~i~~~~l~~~l~~~~~~~~~~~~~l~~l~~~-dL  166 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLA-AAIGNRLL-------------AKGRSVIVVTVPDVMSRLHESYDNGQSGEKFLQELCKV-DL  166 (248)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHH-------------HcCCCeEEEEHHHHHHHHHHHHhccchHHHHHHHhcCC-CE
Confidence            68999999999999642 23333222             23444555544455554432    1      0135788 99


Q ss_pred             EEEEcccccc
Q 031654          137 LALKEAADQT  146 (155)
Q Consensus       137 lVlDEa~D~l  146 (155)
                      |||||+ ...
T Consensus       167 LiIDDl-g~~  175 (248)
T PRK12377        167 LVLDEI-GIQ  175 (248)
T ss_pred             EEEcCC-CCC
Confidence            999999 654

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=96.67  E-value=0.0043  Score=52.02  Aligned_cols=89  Identities=12%  Similarity=0.093  Sum_probs=55.8

Q ss_pred             HHHHHh-HHhCCCCCC--CHHHHH-----HHHHHhcCCcEEEEccCCCCcchhhhh-HHHHHHHHhhhchHHHHHHHhcC
Q 031654           38 QHLRNK-PRTYKYVKP--TPVQRH-----ATSILVAGRDLMACAQTGSRKTTPFCF-PIINGIMREYYSARKELRELARW  108 (155)
Q Consensus        38 ~~l~~~-l~~~g~~~p--t~iQ~~-----~i~~~l~g~dvl~~a~TGsGKT~~yll-p~l~~l~~~~~~~~~~~~~l~~~  108 (155)
                      ++.+.. |.+.||+..  +.-|+.     .+|.+-++.|++..+|+|+|||..|.- ....              .+..|
T Consensus       173 dEWid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~~l~~~~--------------a~~sG  238 (449)
T TIGR02688       173 EEWIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYNNLSPYV--------------ILISG  238 (449)
T ss_pred             HHHHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHHHHhHHH--------------HHHcC
Confidence            445554 567888642  332221     226667889999999999999976641 1111              12233


Q ss_pred             CcEEEEChHHHHHHHHcCCC-CcccccceEEEEccccc
Q 031654          109 VDNLMATLRRLVNLLERGRV-SLQMIIRYLALKEAADQ  145 (155)
Q Consensus       109 ~~IlI~TP~~l~~~l~~~~~-~l~~l~~~lVlDEa~D~  145 (155)
                         -..|+..|...+..+.+ .+... ++||+||+ -.
T Consensus       239 ---~f~T~a~Lf~~L~~~~lg~v~~~-DlLI~DEv-gy  271 (449)
T TIGR02688       239 ---GTITVAKLFYNISTRQIGLVGRW-DVVAFDEV-AT  271 (449)
T ss_pred             ---CcCcHHHHHHHHHHHHHhhhccC-CEEEEEcC-CC
Confidence               55677777776666433 36677 89999999 44

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.

>PRK08116 hypothetical protein; Validated

Probab=96.57  E-value=0.017  Score=45.56  Aligned_cols=63  Identities=21%  Similarity=0.251  Sum_probs=39.2

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcC-----------CC-Cccccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERG-----------RV-SLQMII  134 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~-----------~~-~l~~l~  134 (155)
                      ..+++.|++|+|||.... .+.+.+..             .+..+++.+...+++.+...           .+ .+.++ 
T Consensus       115 ~gl~l~G~~GtGKThLa~-aia~~l~~-------------~~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~~~-  179 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAA-CIANELIE-------------KGVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLVNA-  179 (268)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHH-------------cCCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhcCC-
Confidence            349999999999987532 34443322             24456666655555554321           01 25678 


Q ss_pred             ceEEEEccccc
Q 031654          135 RYLALKEAADQ  145 (155)
Q Consensus       135 ~~lVlDEa~D~  145 (155)
                      .+|||||+ ..
T Consensus       180 dlLviDDl-g~  189 (268)
T PRK08116        180 DLLILDDL-GA  189 (268)
T ss_pred             CEEEEecc-cC
Confidence            89999998 53

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=96.53  E-value=0.023  Score=48.52  Aligned_cols=52  Identities=23%  Similarity=0.230  Sum_probs=35.5

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHH-HHHhcCCcEEEEccCCCCcchh
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHAT-SILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i-~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      +.-|...|  ++-.+.|++. -+-|-=-|++.+ ..+.+.+-+++++.||||||.-
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R-~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQ   78 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKR-RELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQ   78 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHH-hcCchHHhHHHHHHHHhcCceEEEEecCCCCcccc
Confidence            56688888  6666666654 233433455544 4555667899999999999975

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=96.51  E-value=0.002  Score=51.77  Aligned_cols=22  Identities=14%  Similarity=-0.010  Sum_probs=18.1

Q ss_pred             CCcEEEEccCCCCcchhhhhHH
Q 031654           66 GRDLMACAQTGSRKTTPFCFPI   87 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~   87 (155)
                      +-+.+..+|+|||||.+.++-.
T Consensus        57 lp~~LFyGPpGTGKTStalafa   78 (346)
T KOG0989|consen   57 LPHYLFYGPPGTGKTSTALAFA   78 (346)
T ss_pred             CceEEeeCCCCCcHhHHHHHHH
Confidence            3578999999999999876544

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.49  E-value=0.011  Score=44.92  Aligned_cols=62  Identities=8%  Similarity=0.035  Sum_probs=37.9

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccc
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D  144 (155)
                      .++.++++|++|+|||.... .+...             ....+..+++.+...+...+.    ..... +.|||||+ |
T Consensus        41 ~~~~~~l~G~~G~GKT~La~-ai~~~-------------~~~~~~~~~~i~~~~~~~~~~----~~~~~-~~liiDdi-~  100 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQ-ALVAD-------------ASYGGRNARYLDAASPLLAFD----FDPEA-ELYAVDDV-E  100 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHH-HHHHH-------------HHhCCCcEEEEehHHhHHHHh----hcccC-CEEEEeCh-h
Confidence            34689999999999996421 11111             112345566666655443321    23456 78999999 8


Q ss_pred             cc
Q 031654          145 QT  146 (155)
Q Consensus       145 ~l  146 (155)
                      .+
T Consensus       101 ~l  102 (227)
T PRK08903        101 RL  102 (227)
T ss_pred             hc
Confidence            76

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.49  E-value=0.006  Score=47.04  Aligned_cols=66  Identities=5%  Similarity=0.044  Sum_probs=35.9

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                      +..++++||+|+|||.-.. .+.+.+..             .+..++..+..........-.-.+.++ .+|+|||+ |.
T Consensus        45 ~~~l~l~Gp~G~GKThLl~-a~~~~~~~-------------~~~~v~y~~~~~~~~~~~~~~~~~~~~-dlliiDdi-~~  108 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLH-AACAELSQ-------------RGRAVGYVPLDKRAWFVPEVLEGMEQL-SLVCIDNI-EC  108 (235)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHh-------------CCCeEEEEEHHHHhhhhHHHHHHhhhC-CEEEEeCh-hh
Confidence            4689999999999996432 22222221             234454444433221111000123456 78999999 87


Q ss_pred             cc
Q 031654          146 TL  147 (155)
Q Consensus       146 ll  147 (155)
                      +-
T Consensus       109 ~~  110 (235)
T PRK08084        109 IA  110 (235)
T ss_pred             hc
Confidence            64

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.46  E-value=0.012  Score=48.27  Aligned_cols=32  Identities=16%  Similarity=0.215  Sum_probs=27.6

Q ss_pred             CCHHHHHHHHHH------hcCCcEEEEccCCCCcchhh
Q 031654           52 PTPVQRHATSIL------VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        52 pt~iQ~~~i~~~------l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +++-|+.++..+      ..|..+++.++-|+|||..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~   39 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI   39 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH
Confidence            577899998888      77899999999999998754

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR00376 DNA helicase, putative

Probab=96.44  E-value=0.0073  Score=53.18  Aligned_cols=41  Identities=17%  Similarity=0.282  Sum_probs=31.5

Q ss_pred             CCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           51 KPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .+++.|..|+..++.. ..+++.||+|||||..-. .++..+.
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~-~ii~~~~  198 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLV-ELIRQLV  198 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHH-HHHHHHH
Confidence            4589999999999877 678899999999996543 3333333

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.

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

Probab=96.40  E-value=0.0056  Score=49.63  Aligned_cols=18  Identities=28%  Similarity=0.335  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      ...|++..+|||||||+-
T Consensus        96 ~KSNILLiGPTGsGKTlL  113 (408)
T COG1219          96 SKSNILLIGPTGSGKTLL  113 (408)
T ss_pred             eeccEEEECCCCCcHHHH
Confidence            335899999999999984

>PRK05642 DNA replication initiation factor; Validated

Probab=96.38  E-value=0.0065  Score=46.83  Aligned_cols=65  Identities=11%  Similarity=0.015  Sum_probs=39.9

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                      ..++++|++|+|||.- +-.+.+.+.             ..+..++..+.+.+......-.-.+.++ .+||+|++ +.+
T Consensus        46 ~~l~l~G~~G~GKTHL-l~a~~~~~~-------------~~~~~v~y~~~~~~~~~~~~~~~~~~~~-d~LiiDDi-~~~  109 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL-LQAACLRFE-------------QRGEPAVYLPLAELLDRGPELLDNLEQY-ELVCLDDL-DVI  109 (234)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHH-------------hCCCcEEEeeHHHHHhhhHHHHHhhhhC-CEEEEech-hhh
Confidence            5689999999999964 223332221             2245667777666654321111135577 88999999 765


Q ss_pred             c
Q 031654          147 L  147 (155)
Q Consensus       147 l  147 (155)
                      -
T Consensus       110 ~  110 (234)
T PRK05642        110 A  110 (234)
T ss_pred             c
Confidence            3

>PF13245 AAA_19: Part of AAA domain

Probab=96.34  E-value=0.0065  Score=38.80  Aligned_cols=49  Identities=20%  Similarity=0.163  Sum_probs=26.8

Q ss_pred             HHHHhcCCc-EEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHH
Q 031654           60 TSILVAGRD-LMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRR  118 (155)
Q Consensus        60 i~~~l~g~d-vl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~  118 (155)
                      +...+.+.. +++.+|+|||||...+--+...+..         .... +-.|+|.||.+
T Consensus         3 v~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~---------~~~~-~~~vlv~a~t~   52 (76)
T PF13245_consen    3 VRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAA---------RADP-GKRVLVLAPTR   52 (76)
T ss_pred             HHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHH---------hcCC-CCeEEEECCCH
Confidence            443333545 5559999999997653333222210         0111 45688888855

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.28  E-value=0.0096  Score=51.71  Aligned_cols=46  Identities=17%  Similarity=0.210  Sum_probs=32.3

Q ss_pred             hHHhCCCCCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           43 KPRTYKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        43 ~l~~~g~~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .|.++||   .+-|...+..++..  .-+++++|||||||... ..++..+.
T Consensus       294 ~l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       294 DIDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             CHHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            4677786   56677777666543  46889999999999874 34555553

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.

>PRK10436 hypothetical protein; Provisional

Probab=96.27  E-value=0.01  Score=50.33  Aligned_cols=46  Identities=20%  Similarity=0.226  Sum_probs=31.5

Q ss_pred             hHHhCCCCCCCHHHHHHHHHHhc--CCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           43 KPRTYKYVKPTPVQRHATSILVA--GRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        43 ~l~~~g~~~pt~iQ~~~i~~~l~--g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .|..+|+   .+-|...+..+..  +.-+++++|||||||... ..++..+.
T Consensus       196 ~L~~LG~---~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        196 DLETLGM---TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             CHHHcCc---CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            4567775   5667777766543  356999999999999864 34455553

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

Probab=96.22  E-value=0.0051  Score=50.09  Aligned_cols=35  Identities=23%  Similarity=0.128  Sum_probs=30.9

Q ss_pred             CCCCCCHHHHHHHHHHhcCC-cEEEEccCCCCcchh
Q 031654           48 KYVKPTPVQRHATSILVAGR-DLMACAQTGSRKTTP   82 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l~g~-dvl~~a~TGsGKT~~   82 (155)
                      .|...++-|...+-.+..++ |+++++.||||||..
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl  189 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL  189 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH
Confidence            57789999999998888775 999999999999974

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=96.20  E-value=0.005  Score=48.25  Aligned_cols=41  Identities=27%  Similarity=0.155  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           52 PTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        52 pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      +|+-|.+++..  ...+++|.|+.|||||.+.+--++..+...
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~   41 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEG   41 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTS
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccc
Confidence            47889998877  778999999999999998766655555443

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=96.17  E-value=0.0047  Score=55.26  Aligned_cols=35  Identities=20%  Similarity=0.098  Sum_probs=27.9

Q ss_pred             CCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654          108 WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus       108 ~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                      ...|...|-|-|+.-+.+. +.|+.- ..+|+||| |.
T Consensus       349 ~T~IkFMTDGVLLrEi~~D-flL~kY-SvIIlDEA-HE  383 (1172)
T KOG0926|consen  349 DTSIKFMTDGVLLREIEND-FLLTKY-SVIILDEA-HE  383 (1172)
T ss_pred             CceeEEecchHHHHHHHHh-Hhhhhc-eeEEechh-hh
Confidence            3579999999988877643 567778 89999999 64

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.15  E-value=0.016  Score=47.06  Aligned_cols=17  Identities=24%  Similarity=0.354  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        41 ~~i~I~G~~GtGKT~l~   57 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT   57 (365)
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            68999999999999753

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.14  E-value=0.023  Score=51.85  Aligned_cols=17  Identities=18%  Similarity=0.305  Sum_probs=14.1

Q ss_pred             cE-EEEccCCCCcchhhh
Q 031654           68 DL-MACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dv-l~~a~TGsGKT~~yl   84 (155)
                      ++ ++.|+||+|||++--
T Consensus       782 nvLYIyG~PGTGKTATVK  799 (1164)
T PTZ00112        782 QILYISGMPGTGKTATVY  799 (1164)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            45 599999999999853

>PRK06921 hypothetical protein; Provisional

Probab=96.11  E-value=0.011  Score=46.51  Aligned_cols=66  Identities=18%  Similarity=0.152  Sum_probs=38.6

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcC-------CCCcccccceE
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERG-------RVSLQMIIRYL  137 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~-------~~~l~~l~~~l  137 (155)
                      .+.++++.|++|+|||... ..++..+...            .+..++..|...+...+...       .-.+.++ .+|
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~------------~g~~v~y~~~~~l~~~l~~~~~~~~~~~~~~~~~-dlL  181 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRK------------KGVPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKV-EVL  181 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhh------------cCceEEEEEHHHHHHHHHHHHHHHHHHHHHhcCC-CEE
Confidence            4678999999999999643 2333333221            04455555544443333211       1135678 899


Q ss_pred             EEEccccc
Q 031654          138 ALKEAADQ  145 (155)
Q Consensus       138 VlDEa~D~  145 (155)
                      ||||+ +.
T Consensus       182 iIDDl-~~  188 (266)
T PRK06921        182 FIDDL-FK  188 (266)
T ss_pred             EEecc-cc
Confidence            99998 54

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.09  E-value=0.02  Score=54.97  Aligned_cols=33  Identities=36%  Similarity=0.355  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhh
Q 031654           51 KPTPVQRHATSILVAG--RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~y   83 (155)
                      .+++-|+.|+..++.+  +-+++++..|+|||...
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l  869 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQF  869 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHH
Confidence            6899999999999966  67999999999999763

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=96.08  E-value=0.01  Score=48.73  Aligned_cols=17  Identities=24%  Similarity=0.378  Sum_probs=15.2

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        56 ~~~lI~G~~GtGKT~l~   72 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTV   72 (394)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            68999999999999863

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

Probab=96.05  E-value=0.018  Score=50.80  Aligned_cols=48  Identities=15%  Similarity=0.084  Sum_probs=39.1

Q ss_pred             CCCHHHHHHHHHH----hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch
Q 031654           51 KPTPVQRHATSIL----VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~----l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~   98 (155)
                      .|+.||...+..+    -.|+=-+..+|||||||++.+...+..|.......
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~eek~   66 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDFEEKK   66 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHhHHhh
Confidence            6889998877654    47887788999999999999999999987765444

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.04  E-value=0.018  Score=46.72  Aligned_cols=94  Identities=13%  Similarity=0.057  Sum_probs=54.3

Q ss_pred             CCHHHHHHHHHHhcC----CcEEEEccCCCCcchhhhhHHHHHHHHhhhc----h----HHHHHHHhcCCcEEEEChH--
Q 031654           52 PTPVQRHATSILVAG----RDLMACAQTGSRKTTPFCFPIINGIMREYYS----A----RKELRELARWVDNLMATLR--  117 (155)
Q Consensus        52 pt~iQ~~~i~~~l~g----~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~----~----~~~~~~l~~~~~IlI~TP~--  117 (155)
                      .+|+|...|..+...    +-+++++|.|+|||..... +...+......    +    ....-.-...||+.+-.|+  
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~-~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~   82 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAER-LAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEA   82 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHH-HHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCC
Confidence            479999999888754    2588999999999865432 22233221110    0    1222222345788877763  


Q ss_pred             -------HHHHHHHcC--CCCcccccceEEEEcccccccc
Q 031654          118 -------RLVNLLERG--RVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       118 -------~l~~~l~~~--~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                             .+.++...-  .-....- +.+||||| |+|=.
T Consensus        83 ~~~i~id~iR~l~~~~~~~~~~~~~-kv~iI~~a-~~m~~  120 (328)
T PRK05707         83 DKTIKVDQVRELVSFVVQTAQLGGR-KVVLIEPA-EAMNR  120 (328)
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCC-eEEEECCh-hhCCH
Confidence                   222222211  1123456 78999999 99854

>PRK09183 transposase/IS protein; Provisional

Probab=96.03  E-value=0.013  Score=45.92  Aligned_cols=68  Identities=16%  Similarity=0.134  Sum_probs=39.0

Q ss_pred             HhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHc----CCC------Cccc
Q 031654           63 LVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLER----GRV------SLQM  132 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~----~~~------~l~~  132 (155)
                      +-.|.++++.||+|+|||..... +...+             ...+..+...+...+...+..    +.+      .+..
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~a-l~~~a-------------~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~~  164 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIA-LGYEA-------------VRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMA  164 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHH-HHHHH-------------HHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhcC
Confidence            45688999999999999964321 11111             123455655554444322211    110      1345


Q ss_pred             ccceEEEEcccccc
Q 031654          133 IIRYLALKEAADQT  146 (155)
Q Consensus       133 l~~~lVlDEa~D~l  146 (155)
                      . .++|+||+ +.+
T Consensus       165 ~-dlLiiDdl-g~~  176 (259)
T PRK09183        165 P-RLLIIDEI-GYL  176 (259)
T ss_pred             C-CEEEEccc-ccC
Confidence            5 78999999 653

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=95.99  E-value=0.013  Score=42.14  Aligned_cols=78  Identities=12%  Similarity=0.036  Sum_probs=45.3

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHh----------------cCCcEEEEChHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELA----------------RWVDNLMATLRR  118 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~----------------~~~~IlI~TP~~  118 (155)
                      .|+=.++-..+|+|||--.+.-++..........          .+..+.+.                .+.-|=|.|.+.
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~rvLvL~PTRvva~em~~aL~~~~~~~~t~~~~~~~~g~~~i~vMc~at   82 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKRRLRVLVLAPTRVVAEEMYEALKGLPVRFHTNARMRTHFGSSIIDVMCHAT   82 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTSSEEEESTTSS----SSSSEEEEEHHH
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHccCeEEEecccHHHHHHHHHHHhcCCcccCceeeeccccCCCcccccccHH
Confidence            3445677788999999987666665554433332          22222222                233456667777


Q ss_pred             HHHHHHcCCCCcccccceEEEEccccc
Q 031654          119 LVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus       119 l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                      +.+.+.+ .....+. +++|+||+ |.
T Consensus        83 ~~~~~~~-p~~~~~y-d~II~DEc-H~  106 (148)
T PF07652_consen   83 YGHFLLN-PCRLKNY-DVIIMDEC-HF  106 (148)
T ss_dssp             HHHHHHT-SSCTTS--SEEEECTT-T-
T ss_pred             HHHHhcC-cccccCc-cEEEEecc-cc
Confidence            7666655 4456788 99999999 64

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=95.98  E-value=0.032  Score=45.21  Aligned_cols=97  Identities=16%  Similarity=0.188  Sum_probs=55.8

Q ss_pred             CCCCCHHHHHHHHHHh----cCC---cEEEEccCCCCcchhhhhHHHHHHHHhhhch-----HHHHHHHhcCCcEEEE--
Q 031654           49 YVKPTPVQRHATSILV----AGR---DLMACAQTGSRKTTPFCFPIINGIMREYYSA-----RKELRELARWVDNLMA--  114 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l----~g~---dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----~~~~~~l~~~~~IlI~--  114 (155)
                      +..++|+|..+|..+.    +|+   -+++.+|.|+||+.... .+...+.......     ..+.-.-.+.||+.+-  
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~-~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~   80 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVAL-ALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSF   80 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHH-HHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEec
Confidence            4578999999998775    443   48999999999986542 2333333221110     1111122235788876  


Q ss_pred             ChHH---------HHHHHHc------CCCCcccccceEEEEcccccccc
Q 031654          115 TLRR---------LVNLLER------GRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       115 TP~~---------l~~~l~~------~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      .|+.         -.+-++.      ..-..... +.+|||+| |.|-.
T Consensus        81 ~p~~~~~k~~~~I~idqIR~l~~~~~~~p~~g~~-kV~iI~~a-e~m~~  127 (319)
T PRK08769         81 IPNRTGDKLRTEIVIEQVREISQKLALTPQYGIA-QVVIVDPA-DAINR  127 (319)
T ss_pred             CCCcccccccccccHHHHHHHHHHHhhCcccCCc-EEEEeccH-hhhCH
Confidence            5631         1222211      01123466 89999999 99854

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.93  E-value=0.022  Score=45.82  Aligned_cols=62  Identities=16%  Similarity=0.230  Sum_probs=36.3

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHc----CC-----CCcccccce
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLER----GR-----VSLQMIIRY  136 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~----~~-----~~l~~l~~~  136 (155)
                      ++.+++.|++|+|||.... .+.+.+.             ..+..+.+.+-..+..-+..    +.     -.+.++ .+
T Consensus       156 ~~gl~L~G~~G~GKThLa~-Aia~~l~-------------~~g~~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l~~~-dl  220 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLA-AIANELA-------------KKGVSSTLLHFPEFIRELKNSISDGSVKEKIDAVKEA-PV  220 (306)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHH-------------HcCCCEEEEEHHHHHHHHHHHHhcCcHHHHHHHhcCC-CE
Confidence            4689999999999986432 3333222             23444444433333333322    11     126788 99


Q ss_pred             EEEEcc
Q 031654          137 LALKEA  142 (155)
Q Consensus       137 lVlDEa  142 (155)
                      |||||.
T Consensus       221 LiIDDi  226 (306)
T PRK08939        221 LMLDDI  226 (306)
T ss_pred             EEEecC
Confidence            999998

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=95.88  E-value=0.02  Score=48.87  Aligned_cols=46  Identities=20%  Similarity=0.250  Sum_probs=31.5

Q ss_pred             hHHhCCCCCCCHHHHHHHHHHhcC-C-cEEEEccCCCCcchhhhhHHHHHHH
Q 031654           43 KPRTYKYVKPTPVQRHATSILVAG-R-DLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        43 ~l~~~g~~~pt~iQ~~~i~~~l~g-~-dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .|..+|+   ++-|...+..+... + -+++++|||||||... ..++..+.
T Consensus       220 ~l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       220 DLETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            4667776   66777777766654 3 3789999999999864 23445443

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=95.84  E-value=0.0068  Score=48.08  Aligned_cols=17  Identities=29%  Similarity=0.251  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.+|+|+|||...
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            56999999999999753

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.83  E-value=0.027  Score=46.55  Aligned_cols=20  Identities=30%  Similarity=0.257  Sum_probs=17.1

Q ss_pred             cCCcEEEEccCCCCcchhhh
Q 031654           65 AGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yl   84 (155)
                      .|..+++++|||+|||....
T Consensus       136 ~g~ii~lvGptGvGKTTtia  155 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTA  155 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            36789999999999998754

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.82  E-value=0.035  Score=44.01  Aligned_cols=71  Identities=21%  Similarity=0.217  Sum_probs=38.9

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHh-h-hch------------HHHHHHHhc--CCc-EEEEChHHHHHHHHcCCC
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMRE-Y-YSA------------RKELRELAR--WVD-NLMATLRRLVNLLERGRV  128 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~-~-~~~------------~~~~~~l~~--~~~-IlI~TP~~l~~~l~~~~~  128 (155)
                      ++.+++++|||+|||....-- ...+... . ...            ..+.....+  ++. ..+.+|..+...+..   
T Consensus       194 ~~vi~~vGptGvGKTTt~~kL-a~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~---  269 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKL-AARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDR---  269 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHH-HHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHH---
Confidence            457889999999999865322 2222221 1 111            222222221  222 344567766666652   


Q ss_pred             CcccccceEEEEcc
Q 031654          129 SLQMIIRYLALKEA  142 (155)
Q Consensus       129 ~l~~l~~~lVlDEa  142 (155)
                       +.+. +++++|.+
T Consensus       270 -~~~~-d~vliDt~  281 (282)
T TIGR03499       270 -LRDK-DLILIDTA  281 (282)
T ss_pred             -ccCC-CEEEEeCC
Confidence             3457 88999975

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.75  E-value=0.011  Score=46.07  Aligned_cols=17  Identities=24%  Similarity=0.216  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.+|+|||||...
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            58999999999999864

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=95.74  E-value=0.024  Score=43.25  Aligned_cols=67  Identities=13%  Similarity=0.162  Sum_probs=42.8

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHH----HcCCC-----CcccccceEE
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLL----ERGRV-----SLQMIIRYLA  138 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l----~~~~~-----~l~~l~~~lV  138 (155)
                      -+++.|++|+|||. -+-.+.+.+           .....+..|+..+...+.+.+    ..+..     .+... ++|+
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~-----------~~~~~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~~~~-DlL~  102 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEA-----------QKQHPGKRVVYLSAEEFIREFADALRDGEIEEFKDRLRSA-DLLI  102 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHH-----------HHHCTTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHHCTS-SEEE
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHH-----------HhccccccceeecHHHHHHHHHHHHHcccchhhhhhhhcC-CEEE
Confidence            48999999999998 233333322           223345678888877665433    22221     36778 9999


Q ss_pred             EEcccccccc
Q 031654          139 LKEAADQTLD  148 (155)
Q Consensus       139 lDEa~D~ll~  148 (155)
                      ||++ |.+-.
T Consensus       103 iDDi-~~l~~  111 (219)
T PF00308_consen  103 IDDI-QFLAG  111 (219)
T ss_dssp             EETG-GGGTT
T ss_pred             Eecc-hhhcC
Confidence            9999 87754

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=95.74  E-value=0.022  Score=48.18  Aligned_cols=67  Identities=10%  Similarity=-0.020  Sum_probs=40.6

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHc------CCC-----Ccccccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLER------GRV-----SLQMIIR  135 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~------~~~-----~l~~l~~  135 (155)
                      ..+++.|++|+|||.-. -.+.+.+.           ....+..++..|++.+...+..      +.+     .+.++ .
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~-----------~~~~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~-d  208 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIE-----------SNFSDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEICQN-D  208 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHH-----------HhCCCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHhccC-C
Confidence            45899999999999421 23332222           1223566777777665544321      111     14567 8


Q ss_pred             eEEEEccccccc
Q 031654          136 YLALKEAADQTL  147 (155)
Q Consensus       136 ~lVlDEa~D~ll  147 (155)
                      +|||||+ +.+-
T Consensus       209 vLiIDDi-q~l~  219 (450)
T PRK14087        209 VLIIDDV-QFLS  219 (450)
T ss_pred             EEEEecc-cccc
Confidence            9999999 7664

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

Probab=95.73  E-value=0.033  Score=43.78  Aligned_cols=46  Identities=17%  Similarity=0.220  Sum_probs=31.0

Q ss_pred             HhHHhCCCCCCCHHHHHHHHHHhc--CCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           42 NKPRTYKYVKPTPVQRHATSILVA--GRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        42 ~~l~~~g~~~pt~iQ~~~i~~~l~--g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      ..|.++|+   .+-|.+.+..++.  +.-++++++||||||... -.++..+
T Consensus        57 ~~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i  104 (264)
T cd01129          57 LDLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSEL  104 (264)
T ss_pred             CCHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhh
Confidence            34677775   5667777765553  346899999999999864 3344444

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.

>CHL00181 cbbX CbbX; Provisional

Probab=95.73  E-value=0.016  Score=46.21  Aligned_cols=19  Identities=26%  Similarity=0.246  Sum_probs=16.0

Q ss_pred             CCcEEEEccCCCCcchhhh
Q 031654           66 GRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl   84 (155)
                      |.++++.+|+|||||...-
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5579999999999998653

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.73  E-value=0.017  Score=46.90  Aligned_cols=45  Identities=27%  Similarity=0.131  Sum_probs=30.1

Q ss_pred             HHhCCCCCCCHHHHHHHHHH-hcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           44 PRTYKYVKPTPVQRHATSIL-VAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        44 l~~~g~~~pt~iQ~~~i~~~-l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      +.+.|.  .++.|...+..+ ..+.+++++++||||||... -.++..+
T Consensus       123 lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i  168 (323)
T PRK13833        123 YVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEI  168 (323)
T ss_pred             HHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHH
Confidence            334443  567777766544 45689999999999999753 3344444

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.69  E-value=0.025  Score=48.77  Aligned_cols=73  Identities=12%  Similarity=0.233  Sum_probs=38.7

Q ss_pred             cCccccccCCcCcccCCC--------CCCCCCcccccCC-----HHHHHhHHhC---CCCCCCHHHHHHHHHHhcCCcEE
Q 031654            7 ADSVFASENAAPASSSTN--------TLSSPAARFAYVP-----QHLRNKPRTY---KYVKPTPVQRHATSILVAGRDLM   70 (155)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~--------~~p~~~~~f~~l~-----~~l~~~l~~~---g~~~pt~iQ~~~i~~~l~g~dvl   70 (155)
                      ..+.|.+.++-.++..+.        ..-.|-..|++++     .+.-..+++.   ..-.|--+.+..|+++   +-++
T Consensus       184 T~i~F~k~~~s~lnL~~~~~~k~~~n~ii~Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HV---KGiL  260 (744)
T KOG0741|consen  184 TQIVFEKAENSSLNLIGKSKTKPASNSIINPDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHV---KGIL  260 (744)
T ss_pred             cEEEEEeccCcceEeeccccccchhccccCCCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccce---eeEE
Confidence            344555554444443333        2224556788887     3333333221   1113333333333333   5799


Q ss_pred             EEccCCCCcchh
Q 031654           71 ACAQTGSRKTTP   82 (155)
Q Consensus        71 ~~a~TGsGKT~~   82 (155)
                      ..+|+|+|||+.
T Consensus       261 LyGPPGTGKTLi  272 (744)
T KOG0741|consen  261 LYGPPGTGKTLI  272 (744)
T ss_pred             EECCCCCChhHH
Confidence            999999999995

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=95.68  E-value=0.047  Score=47.00  Aligned_cols=43  Identities=23%  Similarity=0.095  Sum_probs=30.1

Q ss_pred             CCCCCCHHHHHHHHHHh----cCCcEEEEccCCCCcchhhhhHHHHH
Q 031654           48 KYVKPTPVQRHATSILV----AGRDLMACAQTGSRKTTPFCFPIING   90 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l----~g~dvl~~a~TGsGKT~~yllp~l~~   90 (155)
                      -|..-+|-|..=.-.+.    .+.+.++..|+|+|||.+.+--++..
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aY   59 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAY   59 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHH
Confidence            35667788876554442    44688999999999999866444443

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=95.64  E-value=0.028  Score=46.67  Aligned_cols=68  Identities=13%  Similarity=0.154  Sum_probs=39.5

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHH----cCC-----CCcccccceE
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLE----RGR-----VSLQMIIRYL  137 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~----~~~-----~~l~~l~~~l  137 (155)
                      ..+++.|++|+|||... -.+.+.+...           ..+..++..|...+...+.    .+.     -.+.++ ++|
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~-----------~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~-dlL  203 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILEN-----------NPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRSV-DLL  203 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHh-----------CCCCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHHHhC-CEE
Confidence            35899999999999743 2333333221           1235566666655433221    111     124567 899


Q ss_pred             EEEcccccccc
Q 031654          138 ALKEAADQTLD  148 (155)
Q Consensus       138 VlDEa~D~ll~  148 (155)
                      ||||+ |.+..
T Consensus       204 iiDDi-~~l~~  213 (405)
T TIGR00362       204 LIDDI-QFLAG  213 (405)
T ss_pred             EEehh-hhhcC
Confidence            99999 87653

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=95.63  E-value=0.03  Score=44.31  Aligned_cols=81  Identities=20%  Similarity=0.081  Sum_probs=44.7

Q ss_pred             cCCc-EEEEccCCCCcchhhhhHHHHHHHHhhhc-h-------HHHHHHHhcCCcEEEEChHHH----------HHHHHc
Q 031654           65 AGRD-LMACAQTGSRKTTPFCFPIINGIMREYYS-A-------RKELRELARWVDNLMATLRRL----------VNLLER  125 (155)
Q Consensus        65 ~g~d-vl~~a~TGsGKT~~yllp~l~~l~~~~~~-~-------~~~~~~l~~~~~IlI~TP~~l----------~~~l~~  125 (155)
                      ++.. +++.+|+|+|||.+... +...+...... .       ..........++++.-+|...          .++...
T Consensus        22 ~~~halL~~Gp~G~Gktt~a~~-lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~  100 (325)
T COG0470          22 RLPHALLFYGPPGVGKTTAALA-LAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEF  100 (325)
T ss_pred             CCCceeeeeCCCCCCHHHHHHH-HHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHHH
Confidence            3456 99999999999987543 22333211110 0       111122223467777776432          222222


Q ss_pred             CCCC--cccccceEEEEcccccccc
Q 031654          126 GRVS--LQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       126 ~~~~--l~~l~~~lVlDEa~D~ll~  148 (155)
                      ....  .... +.++|||| |.|-.
T Consensus       101 ~~~~~~~~~~-kviiidea-d~mt~  123 (325)
T COG0470         101 LSESPLEGGY-KVVIIDEA-DKLTE  123 (325)
T ss_pred             hccCCCCCCc-eEEEeCcH-HHHhH
Confidence            2222  2567 89999999 99864

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=95.61  E-value=0.0051  Score=49.28  Aligned_cols=79  Identities=16%  Similarity=0.142  Sum_probs=43.8

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEECh-----HHHHHH----HHc------------
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATL-----RRLVNL----LER------------  125 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP-----~~l~~~----l~~------------  125 (155)
                      .+++++|+|+.|||..     +.++........+  ..-..-|=++|-+|     .++...    +.-            
T Consensus        62 p~lLivG~snnGKT~I-----i~rF~~~hp~~~d--~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~  134 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMI-----IERFRRLHPPQSD--EDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRPRDRVAKLE  134 (302)
T ss_pred             CceEEecCCCCcHHHH-----HHHHHHHCCCCCC--CCCccccEEEEecCCCCChHHHHHHHHHHhCcccCCCCCHHHHH
Confidence            5999999999999983     4555443222110  00001133444444     122111    110            


Q ss_pred             ----CCCCcccccceEEEEcccccccccccccC
Q 031654          126 ----GRVSLQMIIRYLALKEAADQTLDMALNQK  154 (155)
Q Consensus       126 ----~~~~l~~l~~~lVlDEa~D~ll~~gf~~~  154 (155)
                          ..+.--.+ ++|||||+ |.+|.....+|
T Consensus       135 ~~~~~llr~~~v-rmLIIDE~-H~lLaGs~~~q  165 (302)
T PF05621_consen  135 QQVLRLLRRLGV-RMLIIDEF-HNLLAGSYRKQ  165 (302)
T ss_pred             HHHHHHHHHcCC-cEEEeech-HHHhcccHHHH
Confidence                11223466 99999999 99998776554

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=95.56  E-value=0.034  Score=46.88  Aligned_cols=68  Identities=16%  Similarity=0.193  Sum_probs=40.8

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHH----cCCC-----Cc-ccccce
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLE----RGRV-----SL-QMIIRY  136 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~----~~~~-----~l-~~l~~~  136 (155)
                      ..+++.||+|+|||.-. -.+.+.+.           ....+..++..|...+..-+.    .+..     .+ ..+ ++
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~-----------~~~~~~~v~yi~~~~f~~~~~~~~~~~~~~~f~~~~~~~~-dv  197 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVV-----------QNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKV-DV  197 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHH-----------HhCCCCeEEEEEHHHHHHHHHHHHhcccHHHHHHHHHhcC-CE
Confidence            46999999999999742 22222221           111245677777776544332    1211     01 257 89


Q ss_pred             EEEEcccccccc
Q 031654          137 LALKEAADQTLD  148 (155)
Q Consensus       137 lVlDEa~D~ll~  148 (155)
                      |++||+ |.+.+
T Consensus       198 LlIDDi-~~l~~  208 (440)
T PRK14088        198 LLIDDV-QFLIG  208 (440)
T ss_pred             EEEech-hhhcC
Confidence            999999 98764

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.55  E-value=0.015  Score=48.74  Aligned_cols=62  Identities=21%  Similarity=0.171  Sum_probs=39.5

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHH-----------HHHHHHcCCCCcccccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRR-----------LVNLLERGRVSLQMIIR  135 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~-----------l~~~l~~~~~~l~~l~~  135 (155)
                      +|++..+|+|+|||++.-     .            -....|-|..+.|-|-           ++.++.....+-..+  
T Consensus       385 RNilfyGPPGTGKTm~Ar-----e------------lAr~SGlDYA~mTGGDVAPlG~qaVTkiH~lFDWakkS~rGL--  445 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFAR-----E------------LARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKSRRGL--  445 (630)
T ss_pred             hheeeeCCCCCCchHHHH-----H------------HHhhcCCceehhcCCCccccchHHHHHHHHHHHHHhhcccce--
Confidence            699999999999999641     0            1112344555555432           344444444445556  


Q ss_pred             eEEEEcccccccc
Q 031654          136 YLALKEAADQTLD  148 (155)
Q Consensus       136 ~lVlDEa~D~ll~  148 (155)
                      +|.|||| |..|.
T Consensus       446 llFIDEA-DAFLc  457 (630)
T KOG0742|consen  446 LLFIDEA-DAFLC  457 (630)
T ss_pred             EEEehhh-HHHHH
Confidence            7889999 98874

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.54  E-value=0.023  Score=47.86  Aligned_cols=17  Identities=29%  Similarity=0.305  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      ..||++.+|||||||+-
T Consensus       226 KSNvLllGPtGsGKTll  242 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLL  242 (564)
T ss_pred             cccEEEECCCCCchhHH
Confidence            34899999999999984

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=95.48  E-value=0.025  Score=49.27  Aligned_cols=104  Identities=7%  Similarity=-0.151  Sum_probs=73.4

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------------   98 (155)
                      +.+.+.+..+--+....+|..++..+-+|+++.+...|.+||.++|.+.....+.......                   
T Consensus       273 E~~~~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~  352 (1034)
T KOG4150|consen  273 ESIRSLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHATNSLLPSEMVEHLRNGSKGQV  352 (1034)
T ss_pred             HHHHHHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCcccceecchhHHHHhhccCCceE
Confidence            5555666677677889999999999999999999999999999998876655443222111                   


Q ss_pred             ----------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCC----CCcccccceEEEEcc
Q 031654           99 ----------------------RKELRELARWVDNLMATLRRLVNLLERGR----VSLQMIIRYLALKEA  142 (155)
Q Consensus        99 ----------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~----~~l~~l~~~lVlDEa  142 (155)
                                            .....-.+.+..++.+.|.....-.--+.    ..+-.. .+++.||.
T Consensus       353 V~~~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~-~~~~~~~~  421 (1034)
T KOG4150|consen  353 VHVEVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEE-LCKDTNSC  421 (1034)
T ss_pred             EEEEehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHH-HHhcccce
Confidence                                  33334445688999999988765443332    223344 57788887

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=95.44  E-value=0.013  Score=47.24  Aligned_cols=18  Identities=22%  Similarity=0.163  Sum_probs=15.4

Q ss_pred             CcEEEEccCCCCcchhhh
Q 031654           67 RDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yl   84 (155)
                      ..+++.+|+|+|||....
T Consensus        52 ~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             CcEEEECCCCccHHHHHH
Confidence            579999999999998643

>PRK04296 thymidine kinase; Provisional

Probab=95.44  E-value=0.016  Score=43.22  Aligned_cols=75  Identities=11%  Similarity=0.043  Sum_probs=37.5

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---H---HH---HHHHhc--C---CcEEEEChHHHHHHHHcCCCCcc
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---R---KE---LRELAR--W---VDNLMATLRRLVNLLERGRVSLQ  131 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---~---~~---~~~l~~--~---~~IlI~TP~~l~~~l~~~~~~l~  131 (155)
                      |.=+++.+|+|+|||...+ -.+.++.......   +   +.   ...+..  +   ..+.+..+..+.+.+..   .-.
T Consensus         2 g~i~litG~~GsGKTT~~l-~~~~~~~~~g~~v~i~k~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~---~~~   77 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELL-QRAYNYEERGMKVLVFKPAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE---EGE   77 (190)
T ss_pred             cEEEEEECCCCCHHHHHHH-HHHHHHHHcCCeEEEEeccccccccCCcEecCCCCcccceEeCChHHHHHHHHh---hCC
Confidence            3346789999999997543 3333333222111   0   00   000111  1   11223445555555543   234


Q ss_pred             cccceEEEEcccccc
Q 031654          132 MIIRYLALKEAADQT  146 (155)
Q Consensus       132 ~l~~~lVlDEa~D~l  146 (155)
                      +. .+|||||| +.+
T Consensus        78 ~~-dvviIDEa-q~l   90 (190)
T PRK04296         78 KI-DCVLIDEA-QFL   90 (190)
T ss_pred             CC-CEEEEEcc-ccC
Confidence            56 78999999 543

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=95.43  E-value=0.036  Score=51.06  Aligned_cols=35  Identities=9%  Similarity=0.233  Sum_probs=25.7

Q ss_pred             CcEEEEChHHHHHHHHcC---CCCcccccceEEEEcccccc
Q 031654          109 VDNLMATLRRLVNLLERG---RVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       109 ~~IlI~TP~~l~~~l~~~---~~~l~~l~~~lVlDEa~D~l  146 (155)
                      -.|+|+|=.++-......   ...-.++  .+|+||| |+-
T Consensus       351 ~~ii~TTIQKf~~~~~~~~~~~~~~~~i--vvI~DEa-HRS  388 (962)
T COG0610         351 GKIIVTTIQKFNKAVKEDELELLKRKNV--VVIIDEA-HRS  388 (962)
T ss_pred             CcEEEEEecccchhhhcccccccCCCcE--EEEEech-hhc
Confidence            389999999988877664   1233444  7889999 873

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=95.41  E-value=0.031  Score=47.09  Aligned_cols=67  Identities=15%  Similarity=0.110  Sum_probs=39.1

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHH----cCC-----CCcccccceE
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLE----RGR-----VSLQMIIRYL  137 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~----~~~-----~~l~~l~~~l  137 (155)
                      ..+++.||+|+|||... -.+.+.+..           ...+..++..|...+...+.    .+.     -.+.++ .+|
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~-----------~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~-dlL  215 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILE-----------KNPNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYRSV-DVL  215 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHH-----------hCCCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHHhcC-CEE
Confidence            45999999999999743 222222221           11145566666655433221    111     124567 899


Q ss_pred             EEEccccccc
Q 031654          138 ALKEAADQTL  147 (155)
Q Consensus       138 VlDEa~D~ll  147 (155)
                      ||||+ |.+-
T Consensus       216 iiDDi-~~l~  224 (450)
T PRK00149        216 LIDDI-QFLA  224 (450)
T ss_pred             EEehh-hhhc
Confidence            99999 8764

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=95.41  E-value=0.044  Score=48.96  Aligned_cols=94  Identities=15%  Similarity=0.120  Sum_probs=56.3

Q ss_pred             CCCHHHHHHHHHH----hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh--ch--------------------------
Q 031654           51 KPTPVQRHATSIL----VAGRDLMACAQTGSRKTTPFCFPIINGIMREYY--SA--------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~----l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~--~~--------------------------   98 (155)
                      .+.+.|.+.+..+    -+|-|.+..-.-|-|||+-- +..+..+.....  ..                          
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQt-Is~l~yl~~~~~~~GPfLVi~P~StL~NW~~Ef~rf~P~l~~  245 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQT-ISLLGYLKGRKGIPGPFLVIAPKSTLDNWMNEFKRFTPSLNV  245 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHH-HHHHHHHHHhcCCCCCeEEEeeHhhHHHHHHHHHHhCCCcce
Confidence            4556666654433    47889999999999999753 444444433111  11                          


Q ss_pred             ------HHHHHHHh------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 ------RKELRELA------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 ------~~~~~~l~------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                            +.+...+.      ...+|+|+|-+-.+.-  ...+.--.- +|+||||| |++=+.
T Consensus       246 ~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d--k~~lk~~~W-~ylvIDEa-HRiKN~  304 (971)
T KOG0385|consen  246 VVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD--KSFLKKFNW-RYLVIDEA-HRIKNE  304 (971)
T ss_pred             EEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh--HHHHhcCCc-eEEEechh-hhhcch
Confidence                  22222222      2689999998765432  112222334 78999999 998654

>PHA02244 ATPase-like protein

Probab=95.38  E-value=0.1  Score=43.16  Aligned_cols=22  Identities=23%  Similarity=0.176  Sum_probs=18.5

Q ss_pred             HHHhcCCcEEEEccCCCCcchh
Q 031654           61 SILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        61 ~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ..+..+.++++.+|||+|||..
T Consensus       114 r~l~~~~PVLL~GppGtGKTtL  135 (383)
T PHA02244        114 KIVNANIPVFLKGGAGSGKNHI  135 (383)
T ss_pred             HHHhcCCCEEEECCCCCCHHHH
Confidence            3456779999999999999974

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.37  E-value=0.059  Score=44.82  Aligned_cols=75  Identities=11%  Similarity=0.098  Sum_probs=42.3

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHh----hhch------------HHHHHHHhc--CCcEE-EEChHHHHHHHHcC
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMRE----YYSA------------RKELRELAR--WVDNL-MATLRRLVNLLERG  126 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~----~~~~------------~~~~~~l~~--~~~Il-I~TP~~l~~~l~~~  126 (155)
                      ++.+++++|||+|||.+..--+ .++...    ....            ..|.+...+  +..+. +.++..+...+.. 
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA-~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~-  251 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLA-AIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ-  251 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHH-HHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH-
Confidence            3578999999999998754211 122111    1111            344444433  33333 3355555554442 


Q ss_pred             CCCcccccceEEEEccccccc
Q 031654          127 RVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus       127 ~~~l~~l~~~lVlDEa~D~ll  147 (155)
                         +.+. .++++|++ .++.
T Consensus       252 ---~~~~-DlVLIDTa-Gr~~  267 (388)
T PRK12723        252 ---SKDF-DLVLVDTI-GKSP  267 (388)
T ss_pred             ---hCCC-CEEEEcCC-CCCc
Confidence               3567 89999999 7765

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.34  E-value=0.028  Score=45.02  Aligned_cols=46  Identities=24%  Similarity=0.189  Sum_probs=29.5

Q ss_pred             hHHhCCCCCCCHHHHHHHHHH-hcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           43 KPRTYKYVKPTPVQRHATSIL-VAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        43 ~l~~~g~~~pt~iQ~~~i~~~-l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      .+.+.|  ..++-|...+..+ ..+++++++++||||||... -.++..+
T Consensus       110 ~l~~~g--~~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i  156 (299)
T TIGR02782       110 DYVEAG--IMTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEI  156 (299)
T ss_pred             HHHhcC--CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHh
Confidence            344445  3455566655544 45689999999999999853 3344444

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=95.34  E-value=0.029  Score=44.53  Aligned_cols=18  Identities=22%  Similarity=0.154  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      +.++++.+|+|||||...
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            458999999999999765

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=95.32  E-value=0.069  Score=44.51  Aligned_cols=72  Identities=15%  Similarity=0.207  Sum_probs=39.8

Q ss_pred             CCcEEEEccCCCCcchhhh-hHHHHHHHHhhhch------------HHHHH---HHhcCCcEEEEChHHHHHHHHcCCCC
Q 031654           66 GRDLMACAQTGSRKTTPFC-FPIINGIMREYYSA------------RKELR---ELARWVDNLMATLRRLVNLLERGRVS  129 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl-lp~l~~l~~~~~~~------------~~~~~---~l~~~~~IlI~TP~~l~~~l~~~~~~  129 (155)
                      ++-+...||||-|||..-+ |+............            .+|.+   .+.+-|=.++-+|.-|.+.+.    .
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~----~  278 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIE----A  278 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHH----H
Confidence            7889999999999998743 22222111111111            33333   333344455666666655554    4


Q ss_pred             cccccceEEEEcc
Q 031654          130 LQMIIRYLALKEA  142 (155)
Q Consensus       130 l~~l~~~lVlDEa  142 (155)
                      +.++ +++.+|=|
T Consensus       279 l~~~-d~ILVDTa  290 (407)
T COG1419         279 LRDC-DVILVDTA  290 (407)
T ss_pred             hhcC-CEEEEeCC
Confidence            5556 66666654

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=95.30  E-value=0.033  Score=43.08  Aligned_cols=60  Identities=20%  Similarity=0.134  Sum_probs=32.0

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEE----EChHHHHHHHHcCCCCcccccceEEEEcc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLM----ATLRRLVNLLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI----~TP~~l~~~l~~~~~~l~~l~~~lVlDEa  142 (155)
                      .+++..+|+|+|||.-.-      +..         ..+...+++.-    .-++.+...+.+    +..= ..|.+||+
T Consensus        51 ~h~lf~GPPG~GKTTLA~------IIA---------~e~~~~~~~~sg~~i~k~~dl~~il~~----l~~~-~ILFIDEI  110 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLAR------IIA---------NELGVNFKITSGPAIEKAGDLAAILTN----LKEG-DILFIDEI  110 (233)
T ss_dssp             -EEEEESSTTSSHHHHHH------HHH---------HHCT--EEEEECCC--SCHHHHHHHHT------TT--EEEECTC
T ss_pred             ceEEEECCCccchhHHHH------HHH---------hccCCCeEeccchhhhhHHHHHHHHHh----cCCC-cEEEEech
Confidence            369999999999997432      221         22222222222    234556666553    3444 67899999


Q ss_pred             ccccc
Q 031654          143 ADQTL  147 (155)
Q Consensus       143 ~D~ll  147 (155)
                       |+|=
T Consensus       111 -HRln  114 (233)
T PF05496_consen  111 -HRLN  114 (233)
T ss_dssp             -CC--
T ss_pred             -hhcc
Confidence             9873

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.26  E-value=0.048  Score=46.12  Aligned_cols=66  Identities=12%  Similarity=0.100  Sum_probs=41.3

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHH----cCCC-----CcccccceE
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLE----RGRV-----SLQMIIRYL  137 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~----~~~~-----~l~~l~~~l  137 (155)
                      ..+++.||+|+|||.-. -.+.+.+..             .+..++..+...+.+.+.    .+..     .+.++ .+|
T Consensus       142 npl~L~G~~G~GKTHLl-~Ai~~~l~~-------------~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~-dvL  206 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLM-QAAVHALRE-------------SGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNV-DAL  206 (445)
T ss_pred             ceEEEEcCCCCCHHHHH-HHHHHHHHH-------------cCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccC-CEE
Confidence            45999999999999742 233332221             256777777766544332    2211     14677 899


Q ss_pred             EEEcccccccc
Q 031654          138 ALKEAADQTLD  148 (155)
Q Consensus       138 VlDEa~D~ll~  148 (155)
                      ++||+ +.+-.
T Consensus       207 iIDDi-q~l~~  216 (445)
T PRK12422        207 FIEDI-EVFSG  216 (445)
T ss_pred             EEcch-hhhcC
Confidence            99999 87643

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.22  E-value=0.072  Score=51.79  Aligned_cols=32  Identities=31%  Similarity=0.264  Sum_probs=28.6

Q ss_pred             CCCHHHHHHHHHHhcC--CcEEEEccCCCCcchh
Q 031654           51 KPTPVQRHATSILVAG--RDLMACAQTGSRKTTP   82 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~   82 (155)
                      .+++.|..|+..++.+  +-+++++..|+|||..
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~ 1000 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQ 1000 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHH
Confidence            6899999999999986  5688999999999976

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.21  E-value=0.086  Score=52.00  Aligned_cols=32  Identities=22%  Similarity=0.262  Sum_probs=27.7

Q ss_pred             CCCHHHHHHHHHHhcC--CcEEEEccCCCCcchh
Q 031654           51 KPTPVQRHATSILVAG--RDLMACAQTGSRKTTP   82 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~   82 (155)
                      .+++-|+.++..++.+  +=.++.++.|+|||..
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~  462 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEI  462 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHH
Confidence            5789999999999876  5688899999999975

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=95.20  E-value=0.054  Score=43.27  Aligned_cols=16  Identities=31%  Similarity=0.414  Sum_probs=14.4

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      .+++.||+|+|||...
T Consensus        38 ~lll~Gp~GtGKT~la   53 (337)
T PRK12402         38 HLLVQGPPGSGKTAAV   53 (337)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999764

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.18  E-value=0.056  Score=53.22  Aligned_cols=34  Identities=24%  Similarity=0.241  Sum_probs=28.9

Q ss_pred             CCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhh
Q 031654           50 VKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~y   83 (155)
                      ..+++.|+.|+..++.+  +-++++++.|+|||...
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l 1053 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTML 1053 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhH
Confidence            36899999999999876  45778899999999764

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PLN03025 replication factor C subunit; Provisional

Probab=95.15  E-value=0.015  Score=46.72  Aligned_cols=17  Identities=29%  Similarity=0.468  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .+++++||+|+|||...
T Consensus        35 ~~lll~Gp~G~GKTtla   51 (319)
T PLN03025         35 PNLILSGPPGTGKTTSI   51 (319)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            47999999999999654

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=95.09  E-value=0.028  Score=50.28  Aligned_cols=44  Identities=16%  Similarity=0.069  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHhcC---C-cEEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           51 KPTPVQRHATSILVAG---R-DLMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g---~-dvl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      .+.+.|..++..+.++   . .+++.||||.|||.+.+.++...+...
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~  242 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK  242 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc
Confidence            3488999999888755   4 789999999999999999988877763

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=95.07  E-value=0.0088  Score=45.28  Aligned_cols=14  Identities=29%  Similarity=0.359  Sum_probs=12.4

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      ++|.|+.|||||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999985

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.07  E-value=0.076  Score=44.63  Aligned_cols=19  Identities=32%  Similarity=0.366  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCCCcchhhh
Q 031654           66 GRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl   84 (155)
                      |+.+++.+|||+|||....
T Consensus       221 ~~~i~~vGptGvGKTTt~~  239 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLA  239 (424)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5678999999999997644

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=95.02  E-value=0.012  Score=52.82  Aligned_cols=36  Identities=19%  Similarity=0.210  Sum_probs=24.9

Q ss_pred             CcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          109 VDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       109 ~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      .+-++..-+.|..+.   .-.+.+. ++|||||+ ...+..
T Consensus       122 ~~rLivqIdSL~R~~---~~~l~~y-DvVIIDEv-~svL~q  157 (824)
T PF02399_consen  122 YDRLIVQIDSLHRLD---GSLLDRY-DVVIIDEV-MSVLNQ  157 (824)
T ss_pred             cCeEEEEehhhhhcc---ccccccc-CEEEEehH-HHHHHH
Confidence            356677766665443   2245667 89999999 888766

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.00  E-value=0.051  Score=46.82  Aligned_cols=47  Identities=19%  Similarity=0.322  Sum_probs=35.6

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCC-CCc--chhhhhHHHHHHHHhhh
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTG-SRK--TTPFCFPIINGIMREYY   96 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TG-sGK--T~~yllp~l~~l~~~~~   96 (155)
                      ..+|+.|.+.+..+.+.+|++....|- .|+  +-.|++-+++++.+...
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~  264 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRD  264 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHH
Confidence            367999999999999999998654332 344  45689999999886543

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=94.98  E-value=0.048  Score=44.39  Aligned_cols=21  Identities=19%  Similarity=0.333  Sum_probs=18.0

Q ss_pred             HHhcCCcEEEEccCCCCcchh
Q 031654           62 ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ++..+++++++++||||||..
T Consensus       156 ~v~~~~nili~G~tgSGKTTl  176 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKTTF  176 (332)
T ss_pred             HHHcCCcEEEECCCCCCHHHH
Confidence            445679999999999999975

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=94.98  E-value=0.04  Score=45.92  Aligned_cols=51  Identities=12%  Similarity=0.149  Sum_probs=29.1

Q ss_pred             CcccccCC--HHHHHhHHhC---CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           30 AARFAYVP--QHLRNKPRTY---KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~---g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      -.+|++++  +...+.+++.   -+.+|...+..-   +..++.+++.+|+|+|||+..
T Consensus       141 ~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~G---l~~pkgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        141 DVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIG---IDPPRGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             CCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcC---CCCCceEEEECCCCCCHHHHH
Confidence            35788877  4444444332   122222222111   123578999999999999853

>TIGR01075 uvrD DNA helicase II

Probab=94.97  E-value=0.058  Score=48.11  Aligned_cols=91  Identities=24%  Similarity=0.206  Sum_probs=52.6

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------HHHHHHHhc--CCcE
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------RKELRELAR--WVDN  111 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------~~~~~~l~~--~~~I  111 (155)
                      ..+++-|.+++.+  ...+++|.|..|||||.+-.--+...+.......                .+.+..+..  ...+
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~~~~~~~   80 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLGTSARGM   80 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhcccccCc
Confidence            4689999998854  3468999999999999885444443333211111                122222211  2468


Q ss_pred             EEEChHHHHH-HHHcCC--CCcccccceEEEEccccc
Q 031654          112 LMATLRRLVN-LLERGR--VSLQMIIRYLALKEAADQ  145 (155)
Q Consensus       112 lI~TP~~l~~-~l~~~~--~~l~~l~~~lVlDEa~D~  145 (155)
                      .|+|-..+.. ++++..  ..+. - .+-|+|+. |.
T Consensus        81 ~i~TfHs~~~~iLr~~~~~~g~~-~-~f~i~d~~-d~  114 (715)
T TIGR01075        81 WIGTFHGLAHRLLRAHHLDAGLP-Q-DFQILDSD-DQ  114 (715)
T ss_pred             EEEcHHHHHHHHHHHHHHHhCCC-C-CCeecCHH-HH
Confidence            8999887654 343321  1111 1 24577887 65

Designed to identify uvrD members of the uvrD/rep subfamily.

>KOG3089 consensus Predicted DEAD-box-containing helicase [General function prediction only]

Probab=94.90  E-value=0.031  Score=42.89  Aligned_cols=42  Identities=21%  Similarity=0.360  Sum_probs=34.0

Q ss_pred             HHHHHHHh-cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEc
Q 031654           99 RKELRELA-RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKE  141 (155)
Q Consensus        99 ~~~~~~l~-~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDE  141 (155)
                      ..+...+. +..++-||||+|+..+++.+.++++.+ +++|+|=
T Consensus       186 ~~~~k~~k~~~v~~gIgTp~Ri~~lv~~~~f~~~~l-k~iIlD~  228 (271)
T KOG3089|consen  186 QAQVKLLKKRVVHLGIGTPGRIKELVKQGGFNLSPL-KFIILDW  228 (271)
T ss_pred             HHHHHHHhhcceeEeecCcHHHHHHHHhcCCCCCcc-eeEEeec
Confidence            33444443 368999999999999999999999999 9999883

>PRK04195 replication factor C large subunit; Provisional

Probab=94.79  E-value=0.097  Score=44.55  Aligned_cols=18  Identities=22%  Similarity=0.261  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.+++.||+|+|||...
T Consensus        39 ~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            468999999999999753

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=94.78  E-value=0.11  Score=46.13  Aligned_cols=28  Identities=25%  Similarity=0.336  Sum_probs=20.5

Q ss_pred             HHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           55 VQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        55 iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+.+.+..+...+-|++.+.||||||.-
T Consensus       360 ~R~~ll~~ir~n~vvvivgETGSGKTTQ  387 (1042)
T KOG0924|consen  360 CRDQLLSVIRENQVVVIVGETGSGKTTQ  387 (1042)
T ss_pred             HHHHHHHHHhhCcEEEEEecCCCCchhh
Confidence            4444444555667789999999999985

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.78  E-value=0.029  Score=45.89  Aligned_cols=22  Identities=36%  Similarity=0.528  Sum_probs=18.5

Q ss_pred             HHHhcCCcEEEEccCCCCcchh
Q 031654           61 SILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        61 ~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      -++..+++++++++||||||..
T Consensus       157 ~~v~~~~nilI~G~tGSGKTTl  178 (344)
T PRK13851        157 ACVVGRLTMLLCGPTGSGKTTM  178 (344)
T ss_pred             HHHHcCCeEEEECCCCccHHHH
Confidence            3455779999999999999975

>PF13479 AAA_24: AAA domain

Probab=94.73  E-value=0.018  Score=43.64  Aligned_cols=75  Identities=13%  Similarity=0.018  Sum_probs=48.1

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEE
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL  139 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVl  139 (155)
                      +-.+++.+++|+|||....-     +  .....      ......+.....+-|.++..+.+.+..-.-..... +.|||
T Consensus         3 ~~~~lIyG~~G~GKTt~a~~-----~--~k~l~id~E~g~~~~~~~~~~~~i~i~s~~~~~~~~~~l~~~~~~y-~tiVI   74 (213)
T PF13479_consen    3 PIKILIYGPPGSGKTTLAAS-----L--PKPLFIDTENGSDSLKFLDDGDVIPITSWEDFLEALDELEEDEADY-DTIVI   74 (213)
T ss_pred             ceEEEEECCCCCCHHHHHHh-----C--CCeEEEEeCCCccchhhhcCCCeeCcCCHHHHHHHHHHHHhccCCC-CEEEE
Confidence            34689999999999974321     1  11111      11233343556777889999988775321226678 89999


Q ss_pred             Eccccccccc
Q 031654          140 KEAADQTLDM  149 (155)
Q Consensus       140 DEa~D~ll~~  149 (155)
                      |-+ +.|.++
T Consensus        75 Dsi-s~~~~~   83 (213)
T PF13479_consen   75 DSI-SWLEDM   83 (213)
T ss_pred             ECH-HHHHHH
Confidence            999 887654

>PRK11054 helD DNA helicase IV; Provisional

Probab=94.66  E-value=0.26  Score=43.98  Aligned_cols=90  Identities=20%  Similarity=0.154  Sum_probs=50.0

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------HHHHHHHhcCCcEEE
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------RKELRELARWVDNLM  113 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------~~~~~~l~~~~~IlI  113 (155)
                      ..+++-|+.|+-  ....+++|.|..|||||.+.+--+...+.......                .+.+........|-|
T Consensus       195 ~~L~~~Q~~av~--~~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg~~~v~v  272 (684)
T PRK11054        195 SPLNPSQARAVV--NGEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLGTEDITA  272 (684)
T ss_pred             CCCCHHHHHHHh--CCCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcCCCCcEE
Confidence            468999999874  23357899999999999886544433333221111                111122122347889


Q ss_pred             EChHHHHH-HHHcCCCCcccccceEEEEcc
Q 031654          114 ATLRRLVN-LLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus       114 ~TP~~l~~-~l~~~~~~l~~l~~~lVlDEa  142 (155)
                      +|--.+.. +++...-....+ .-+..|+.
T Consensus       273 ~TFHSlal~Il~~~~~~~p~~-s~~~~d~~  301 (684)
T PRK11054        273 RTFHALALHIIQQGSKKVPVI-SKLENDSK  301 (684)
T ss_pred             EeHHHHHHHHHHHhhhcCCCc-CccccchH
Confidence            99887753 444321112233 33445554

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

Probab=94.60  E-value=0.017  Score=48.58  Aligned_cols=22  Identities=36%  Similarity=0.585  Sum_probs=20.2

Q ss_pred             CcEEEEccCCCCcchhhhhHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPII   88 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l   88 (155)
                      .++++.||||||||.+|++|.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~l   66 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNL   66 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHH
Confidence            4799999999999999999976

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

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.59  E-value=0.013  Score=48.27  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=19.4

Q ss_pred             cEEEEccCCCCcchhhhhHHHH
Q 031654           68 DLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      ++++.|+||||||.++++|-+-
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll   22 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLL   22 (384)
T ss_pred             CeeEecCCCCCCccEEEccchh
Confidence            4789999999999999999654

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=94.48  E-value=0.12  Score=42.21  Aligned_cols=32  Identities=25%  Similarity=0.125  Sum_probs=24.8

Q ss_pred             CCHHHHHHHHHHhc--C---CcEEEEccCCCCcchhh
Q 031654           52 PTPVQRHATSILVA--G---RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        52 pt~iQ~~~i~~~l~--g---~dvl~~a~TGsGKT~~y   83 (155)
                      .+|+|...|..+.+  |   +-+++.||.|.||+...
T Consensus         2 ~yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA   38 (342)
T PRK06964          2 LYPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFA   38 (342)
T ss_pred             CCcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHH
Confidence            36888888887753  3   36889999999998754

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

Probab=94.46  E-value=0.06  Score=39.85  Aligned_cols=33  Identities=27%  Similarity=0.307  Sum_probs=25.1

Q ss_pred             CCCHHHHHHHHHH-hcCCcEEEEccCCCCcchhh
Q 031654           51 KPTPVQRHATSIL-VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        51 ~pt~iQ~~~i~~~-l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..++-|...+... ..|..+++++|||||||...
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            4556666666544 46789999999999999753

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.

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=94.46  E-value=0.093  Score=46.40  Aligned_cols=29  Identities=28%  Similarity=0.328  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           54 PVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        54 ~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      +.-.+.+.++....=++|.+.||||||.-
T Consensus       268 ~ykdell~av~e~QVLiI~GeTGSGKTTQ  296 (902)
T KOG0923|consen  268 PYKDELLKAVKEHQVLIIVGETGSGKTTQ  296 (902)
T ss_pred             hhHHHHHHHHHhCcEEEEEcCCCCCcccc
Confidence            33344556666778899999999999985

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=94.42  E-value=0.091  Score=46.12  Aligned_cols=67  Identities=16%  Similarity=0.128  Sum_probs=40.6

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHH----cCC-----CCcccccceEE
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLE----RGR-----VSLQMIIRYLA  138 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~----~~~-----~~l~~l~~~lV  138 (155)
                      .+++.+++|+|||.-. -.+.+.+           .....+..++..|.+.+.+.+.    .+.     -.+.++ .+||
T Consensus       316 pL~LyG~sGsGKTHLL-~AIa~~a-----------~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y~~~-DLLl  382 (617)
T PRK14086        316 PLFIYGESGLGKTHLL-HAIGHYA-----------RRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRYREM-DILL  382 (617)
T ss_pred             cEEEECCCCCCHHHHH-HHHHHHH-----------HHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHhhcC-CEEE
Confidence            4899999999999732 2222222           2222356677777766553332    111     124567 8999


Q ss_pred             EEcccccccc
Q 031654          139 LKEAADQTLD  148 (155)
Q Consensus       139 lDEa~D~ll~  148 (155)
                      |||+ +.+..
T Consensus       383 IDDI-q~l~g  391 (617)
T PRK14086        383 VDDI-QFLED  391 (617)
T ss_pred             Eehh-ccccC
Confidence            9999 87754

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=94.40  E-value=0.12  Score=43.17  Aligned_cols=79  Identities=11%  Similarity=0.031  Sum_probs=42.4

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhh-------hchHHHHHHHhcCCcEEEEChHH-------HHHHHHcC--CCCc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREY-------YSARKELRELARWVDNLMATLRR-------LVNLLERG--RVSL  130 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~-------~~~~~~~~~l~~~~~IlI~TP~~-------l~~~l~~~--~~~l  130 (155)
                      +-+++.+|.|+|||.....- ...+....       .........-...||+.+.+|+.       +.+++..-  .-..
T Consensus        37 ha~Lf~Gp~G~GKt~lA~~l-A~~l~c~~~~~~~Cg~C~~C~~~~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~  115 (394)
T PRK07940         37 HAWLFTGPPGSGRSVAARAF-AAALQCTDPDEPGCGECRACRTVLAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPST  115 (394)
T ss_pred             eEEEEECCCCCcHHHHHHHH-HHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHHhCccc
Confidence            46899999999998654322 22222211       00011122223467887777742       22222211  1123


Q ss_pred             ccccceEEEEcccccccc
Q 031654          131 QMIIRYLALKEAADQTLD  148 (155)
Q Consensus       131 ~~l~~~lVlDEa~D~ll~  148 (155)
                      ... +.++|||+ |+|-.
T Consensus       116 ~~~-kViiIDea-d~m~~  131 (394)
T PRK07940        116 GRW-RIVVIEDA-DRLTE  131 (394)
T ss_pred             CCc-EEEEEech-hhcCH
Confidence            466 78999999 99854

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=94.35  E-value=0.024  Score=38.14  Aligned_cols=18  Identities=33%  Similarity=0.385  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      +..+++.+|+|||||...
T Consensus         2 ~~~~~l~G~~G~GKTtl~   19 (148)
T smart00382        2 GEVILIVGPPGSGKTTLA   19 (148)
T ss_pred             CCEEEEECCCCCcHHHHH
Confidence            567999999999999864

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=94.27  E-value=0.17  Score=40.98  Aligned_cols=95  Identities=15%  Similarity=0.107  Sum_probs=54.4

Q ss_pred             CCCHHHHHHHHHHh----cCC---cEEEEccCCCCcchhhhhHHHHHHHHhhh---ch----HHHHHHHhcCCcEEEECh
Q 031654           51 KPTPVQRHATSILV----AGR---DLMACAQTGSRKTTPFCFPIINGIMREYY---SA----RKELRELARWVDNLMATL  116 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l----~g~---dvl~~a~TGsGKT~~yllp~l~~l~~~~~---~~----~~~~~~l~~~~~IlI~TP  116 (155)
                      .++|+|...|..+.    +|+   -++++||.|.||+.... .+...+.....   .+    ..+.-.-...||+.+-.|
T Consensus         3 ~~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~-~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p   81 (319)
T PRK06090          3 NDYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVE-LFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKP   81 (319)
T ss_pred             cCcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHH-HHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEec
Confidence            45788888887765    343   68999999999985432 22222322111   01    222222234688888777


Q ss_pred             HH---------HHHHHHc--CCCCcccccceEEEEcccccccc
Q 031654          117 RR---------LVNLLER--GRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       117 ~~---------l~~~l~~--~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      +.         +.++...  ..-..... |.+|||+| |+|-.
T Consensus        82 ~~~~~~I~vdqiR~l~~~~~~~~~~~~~-kV~iI~~a-e~m~~  122 (319)
T PRK06090         82 EKEGKSITVEQIRQCNRLAQESSQLNGY-RLFVIEPA-DAMNE  122 (319)
T ss_pred             CcCCCcCCHHHHHHHHHHHhhCcccCCc-eEEEecch-hhhCH
Confidence            41         1111111  11234567 89999999 99854

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.25  E-value=0.19  Score=41.94  Aligned_cols=20  Identities=35%  Similarity=0.317  Sum_probs=16.5

Q ss_pred             cCCcEEEEccCCCCcchhhh
Q 031654           65 AGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yl   84 (155)
                      .++-+++++|+|+|||....
T Consensus       205 ~~~ii~lvGptGvGKTTt~a  224 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLV  224 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            45778999999999997654

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=94.23  E-value=0.047  Score=38.25  Aligned_cols=15  Identities=40%  Similarity=0.426  Sum_probs=13.0

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      +++.+++|+|||...
T Consensus         2 ~~i~G~~G~GKT~l~   16 (165)
T cd01120           2 ILVFGPTGSGKTTLA   16 (165)
T ss_pred             eeEeCCCCCCHHHHH
Confidence            678999999999854

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=94.20  E-value=0.23  Score=44.11  Aligned_cols=40  Identities=25%  Similarity=0.202  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .+++-|++++.+  ....++|.|+.|||||.+-.--+...+.
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~   41 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIR   41 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHH
Confidence            478999998864  3467889999999999986555555443

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

Probab=94.19  E-value=0.16  Score=44.61  Aligned_cols=59  Identities=10%  Similarity=0.106  Sum_probs=37.7

Q ss_pred             cCCCCCCCCCcccccCC--HHHHHhHHhC--CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           21 SSTNTLSSPAARFAYVP--QHLRNKPRTY--KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        21 ~~~~~~p~~~~~f~~l~--~~l~~~l~~~--g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      +.+...|.+-.+|++++  +..+..|.++  .+.+|-..++..   +.--+-|++++|+|+|||.-
T Consensus       177 ~~~~~~~~snv~f~diGG~d~~~~el~~li~~i~~Pe~~~~lG---v~PprGvLlHGPPGCGKT~l  239 (802)
T KOG0733|consen  177 VEGLEFPESNVSFSDIGGLDKTLAELCELIIHIKHPEVFSSLG---VRPPRGVLLHGPPGCGKTSL  239 (802)
T ss_pred             hcccCCCCCCcchhhccChHHHHHHHHHHHHHhcCchhHhhcC---CCCCCceeeeCCCCccHHHH
Confidence            34455566566899998  4444444433  255665554432   12237899999999999974

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=94.17  E-value=0.18  Score=46.69  Aligned_cols=32  Identities=25%  Similarity=0.082  Sum_probs=24.2

Q ss_pred             CCHHHHHHHHHHhc--------CCcEEEEccCCCCcchhh
Q 031654           52 PTPVQRHATSILVA--------GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        52 pt~iQ~~~i~~~l~--------g~dvl~~a~TGsGKT~~y   83 (155)
                      -..+|-.|+..+..        |--+|--|.||+|||++=
T Consensus       409 rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aN  448 (1110)
T TIGR02562       409 RFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLAN  448 (1110)
T ss_pred             CcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHH
Confidence            35689999887753        335667799999999973

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=94.16  E-value=0.043  Score=42.53  Aligned_cols=24  Identities=13%  Similarity=0.012  Sum_probs=13.2

Q ss_pred             HHHHHHhcCCcEEEEChHHHHHHHH
Q 031654          100 KELRELARWVDNLMATLRRLVNLLE  124 (155)
Q Consensus       100 ~~~~~l~~~~~IlI~TP~~l~~~l~  124 (155)
                      ++.... +..-+++.|||++.-+..
T Consensus        84 ~~i~~~-~~~y~l~DtPGQiElf~~  107 (238)
T PF03029_consen   84 EEIEKY-EDDYLLFDTPGQIELFTH  107 (238)
T ss_dssp             HHHHHH-H-SEEEEE--SSHHHHHH
T ss_pred             HHHhhc-CCcEEEEeCCCCEEEEEe
Confidence            444444 347899999999654443

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=94.13  E-value=0.033  Score=47.78  Aligned_cols=35  Identities=20%  Similarity=0.146  Sum_probs=28.4

Q ss_pred             CCCHHHHHHHHHHhcC---CcEEEEccCCCCcchhhhh
Q 031654           51 KPTPVQRHATSILVAG---RDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g---~dvl~~a~TGsGKT~~yll   85 (155)
                      .+.|-|..++..++..   +.=+++-|-|+|||+.-+-
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvT  339 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVT  339 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeee
Confidence            3678999999988743   6888899999999987543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.10  E-value=0.038  Score=49.39  Aligned_cols=16  Identities=19%  Similarity=0.314  Sum_probs=14.4

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.+++.+|+|+|||+.
T Consensus       488 ~giLL~GppGtGKT~l  503 (733)
T TIGR01243       488 KGVLLFGPPGTGKTLL  503 (733)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            5699999999999985

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.08  E-value=0.17  Score=43.54  Aligned_cols=78  Identities=15%  Similarity=-0.023  Sum_probs=39.4

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhh---ch----HHHHHHHhcCCcEEEEChH------HHHHHHHc--CCCCccc
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYY---SA----RKELRELARWVDNLMATLR------RLVNLLER--GRVSLQM  132 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~---~~----~~~~~~l~~~~~IlI~TP~------~l~~~l~~--~~~~l~~  132 (155)
                      -+++++|+|+|||.+... +...+.....   .+    ......-...++++.-.+.      .+.++...  ..-....
T Consensus        38 a~Lf~GppGtGKTTlA~~-lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~~~~  116 (504)
T PRK14963         38 AYLFSGPRGVGKTTTARL-IAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLRGG  116 (504)
T ss_pred             EEEEECCCCCCHHHHHHH-HHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhccccCC
Confidence            359999999999987542 3333332110   00    1111111224566654442      11222111  0112356


Q ss_pred             ccceEEEEcccccccc
Q 031654          133 IIRYLALKEAADQTLD  148 (155)
Q Consensus       133 l~~~lVlDEa~D~ll~  148 (155)
                      - +++||||+ |.|-.
T Consensus       117 ~-kVVIIDEa-d~ls~  130 (504)
T PRK14963        117 R-KVYILDEA-HMMSK  130 (504)
T ss_pred             C-eEEEEECc-cccCH
Confidence            7 89999999 98743

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=94.06  E-value=0.15  Score=37.05  Aligned_cols=78  Identities=15%  Similarity=0.118  Sum_probs=42.5

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhhch-------HHHHHHHhcCCcEEEEChHHH---------HHHHHcCCC--C
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYYSA-------RKELRELARWVDNLMATLRRL---------VNLLERGRV--S  129 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------~~~~~~l~~~~~IlI~TP~~l---------~~~l~~~~~--~  129 (155)
                      -+++.+|.|+||+.... ..+..+.......       ..........+|+.+..|..-         .++...-..  .
T Consensus        21 a~L~~G~~g~gk~~~a~-~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~~~   99 (162)
T PF13177_consen   21 ALLFHGPSGSGKKTLAL-AFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKSIKIDQIREIIEFLSLSPS   99 (162)
T ss_dssp             EEEEECSTTSSHHHHHH-HHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS-T
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccchhhHHHHHHHHHHHHHHHh
Confidence            57999999999876543 2333333322210       222222234688888877532         222222111  1


Q ss_pred             cccccceEEEEcccccccc
Q 031654          130 LQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       130 l~~l~~~lVlDEa~D~ll~  148 (155)
                      -..- +.+||||| |.|-.
T Consensus       100 ~~~~-KviiI~~a-d~l~~  116 (162)
T PF13177_consen  100 EGKY-KVIIIDEA-DKLTE  116 (162)
T ss_dssp             TSSS-EEEEEETG-GGS-H
T ss_pred             cCCc-eEEEeehH-hhhhH
Confidence            2457 89999999 98854

...

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.06  E-value=0.1  Score=44.45  Aligned_cols=17  Identities=24%  Similarity=0.188  Sum_probs=14.2

Q ss_pred             cEEEEccCCCCcchhhh
Q 031654           68 DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yl   84 (155)
                      .++++||+|+|||....
T Consensus        38 ~~Lf~GPpGtGKTTlA~   54 (472)
T PRK14962         38 AYIFAGPRGTGKTTVAR   54 (472)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37999999999997653

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.04  E-value=0.049  Score=42.65  Aligned_cols=26  Identities=27%  Similarity=0.220  Sum_probs=21.6

Q ss_pred             HHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           58 HATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        58 ~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ++...+..|+++++.+|+|+|||...
T Consensus        13 ~~l~~l~~g~~vLL~G~~GtGKT~lA   38 (262)
T TIGR02640        13 RALRYLKSGYPVHLRGPAGTGKTTLA   38 (262)
T ss_pred             HHHHHHhcCCeEEEEcCCCCCHHHHH
Confidence            44556678899999999999999864

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=94.02  E-value=0.13  Score=41.87  Aligned_cols=94  Identities=21%  Similarity=0.165  Sum_probs=54.6

Q ss_pred             CCHHHHHHHHHHh----cCC---cEEEEccCCCCcchhhhhHHHHHHHHhh-h---ch----HHHHHHHhcCCcEEEECh
Q 031654           52 PTPVQRHATSILV----AGR---DLMACAQTGSRKTTPFCFPIINGIMREY-Y---SA----RKELRELARWVDNLMATL  116 (155)
Q Consensus        52 pt~iQ~~~i~~~l----~g~---dvl~~a~TGsGKT~~yllp~l~~l~~~~-~---~~----~~~~~~l~~~~~IlI~TP  116 (155)
                      .+|+|...|..+.    +|+   -.++.||.|+||+.... .+...+.... .   .+    ..+.-.-...||+..-+|
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~-~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p   81 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIY-ALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTP   81 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHH-HHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEec
Confidence            4788888887764    343   57899999999986543 2223332211 1   01    222222334689988888


Q ss_pred             HH---------HHHHHHc--CCCCcccccceEEEEcccccccc
Q 031654          117 RR---------LVNLLER--GRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       117 ~~---------l~~~l~~--~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      +.         +.++.+.  ..-....- +.+|||+| |+|=.
T Consensus        82 ~~~~~~I~idqiR~l~~~~~~~~~~g~~-kV~iI~~a-e~m~~  122 (334)
T PRK07993         82 EKGKSSLGVDAVREVTEKLYEHARLGGA-KVVWLPDA-ALLTD  122 (334)
T ss_pred             ccccccCCHHHHHHHHHHHhhccccCCc-eEEEEcch-HhhCH
Confidence            52         1111111  11123566 89999999 99854

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=94.01  E-value=0.2  Score=40.65  Aligned_cols=91  Identities=13%  Similarity=0.073  Sum_probs=51.4

Q ss_pred             CHHHHHHHHHHh--cCC---cEEEEccCCCCcchhhhhHHHHHHHHhhh-----ch----HHHHHHHhcCCcEEEEChHH
Q 031654           53 TPVQRHATSILV--AGR---DLMACAQTGSRKTTPFCFPIINGIMREYY-----SA----RKELRELARWVDNLMATLRR  118 (155)
Q Consensus        53 t~iQ~~~i~~~l--~g~---dvl~~a~TGsGKT~~yllp~l~~l~~~~~-----~~----~~~~~~l~~~~~IlI~TP~~  118 (155)
                      +|+|...|..+.  .|+   -+++.||.|.|||.....- ...+.....     .+    ....-.-...||+..-+|+.
T Consensus         3 yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~~-a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~   81 (325)
T PRK08699          3 YPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARFA-AQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLS   81 (325)
T ss_pred             CCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHHH-HHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEeccc
Confidence            688888888776  332   5889999999998764322 222221111     11    22222233468998888731


Q ss_pred             ----------------HHHHHHcCC--CCcccccceEEEEcccccc
Q 031654          119 ----------------LVNLLERGR--VSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       119 ----------------l~~~l~~~~--~~l~~l~~~lVlDEa~D~l  146 (155)
                                      +.++...-.  -....- +.+|+|++ |.|
T Consensus        82 ~~~~~g~~~~~I~id~iR~l~~~~~~~p~~~~~-kV~iiEp~-~~L  125 (325)
T PRK08699         82 DEPENGRKLLQIKIDAVREIIDNVYLTSVRGGL-RVILIHPA-ESM  125 (325)
T ss_pred             ccccccccCCCcCHHHHHHHHHHHhhCcccCCc-eEEEEech-hhC
Confidence                            122221111  123556 77888888 776

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=93.99  E-value=0.16  Score=41.20  Aligned_cols=95  Identities=9%  Similarity=0.052  Sum_probs=53.1

Q ss_pred             CCHHHHHHHHHHh----cC---CcEEEEccCCCCcchhhhhHHHHHHHHhh-h---ch--HHHHHHH--hcCCcEEEECh
Q 031654           52 PTPVQRHATSILV----AG---RDLMACAQTGSRKTTPFCFPIINGIMREY-Y---SA--RKELREL--ARWVDNLMATL  116 (155)
Q Consensus        52 pt~iQ~~~i~~~l----~g---~dvl~~a~TGsGKT~~yllp~l~~l~~~~-~---~~--~~~~~~l--~~~~~IlI~TP  116 (155)
                      .+|+|...|..+.    +|   +-.++.||.|.||+..... +...+.... .   .+  -...+.+  ...||+.+-.|
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~-~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p   81 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRA-LAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEP   81 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHH-HHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEcc
Confidence            3688888887664    44   3577999999999865432 223333211 1   11  1222222  34688887777


Q ss_pred             H--------HHHHHHHc--CCCCcccccceEEEEccccccccc
Q 031654          117 R--------RLVNLLER--GRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       117 ~--------~l~~~l~~--~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      .        .+.++...  ..-.-..- +.+|||+| |+|=..
T Consensus        82 ~~~~~I~id~iR~l~~~~~~~~~~g~~-KV~iI~~a-~~m~~~  122 (325)
T PRK06871         82 IDNKDIGVDQVREINEKVSQHAQQGGN-KVVYIQGA-ERLTEA  122 (325)
T ss_pred             ccCCCCCHHHHHHHHHHHhhccccCCc-eEEEEech-hhhCHH
Confidence            3        11111111  11123466 88999999 998643

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=93.98  E-value=0.029  Score=49.70  Aligned_cols=24  Identities=17%  Similarity=0.160  Sum_probs=21.2

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIING   90 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~   90 (155)
                      .++++.||||||||.+|++|-+-.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~  163 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLT  163 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhc
Confidence            589999999999999999996543

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=93.96  E-value=0.18  Score=37.15  Aligned_cols=79  Identities=13%  Similarity=0.057  Sum_probs=40.1

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhh----ch----HHHHHHHhcCCcEEEECh-------HHHHHHHHcC--CCC
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYY----SA----RKELRELARWVDNLMATL-------RRLVNLLERG--RVS  129 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~----~~----~~~~~~l~~~~~IlI~TP-------~~l~~~l~~~--~~~  129 (155)
                      ..+++.+|+|+|||.... -+...+.....    .+    ..........+|+.+..+       +.+.+++..-  .-.
T Consensus        15 ~~~L~~G~~G~gkt~~a~-~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~~~~~   93 (188)
T TIGR00678        15 HAYLFAGPEGVGKELLAL-ALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRTPQ   93 (188)
T ss_pred             eEEEEECCCCCCHHHHHH-HHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHccCcc
Confidence            358899999999986532 22233322100    00    111111122355554443       3333333221  112


Q ss_pred             cccccceEEEEcccccccc
Q 031654          130 LQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       130 l~~l~~~lVlDEa~D~ll~  148 (155)
                      ...- +.+||||+ |.|-.
T Consensus        94 ~~~~-kviiide~-~~l~~  110 (188)
T TIGR00678        94 ESGR-RVVIIEDA-ERMNE  110 (188)
T ss_pred             cCCe-EEEEEech-hhhCH
Confidence            3566 89999999 99854

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=93.86  E-value=0.13  Score=46.02  Aligned_cols=91  Identities=22%  Similarity=0.175  Sum_probs=52.0

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------HHHHHHHhc--CCcE
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------RKELRELAR--WVDN  111 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------~~~~~~l~~--~~~I  111 (155)
                      ..+++-|.+++-+  ....++|.|..|||||.+-.--+...+.......                .+....+..  ...+
T Consensus         8 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~~~~~~~   85 (721)
T PRK11773          8 DSLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLGTSQGGM   85 (721)
T ss_pred             HhcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhccCCCCC
Confidence            3589999998853  3468999999999999885544443332211111                122222211  2357


Q ss_pred             EEEChHHHHHH-HHcCC--CCcccccceEEEEccccc
Q 031654          112 LMATLRRLVNL-LERGR--VSLQMIIRYLALKEAADQ  145 (155)
Q Consensus       112 lI~TP~~l~~~-l~~~~--~~l~~l~~~lVlDEa~D~  145 (155)
                      .|+|--.+..- ++...  ..+. - .+-|+|+. |+
T Consensus        86 ~i~TfHs~~~~iLr~~~~~~g~~-~-~f~i~d~~-d~  119 (721)
T PRK11773         86 WVGTFHGLAHRLLRAHWQDANLP-Q-DFQILDSD-DQ  119 (721)
T ss_pred             EEEcHHHHHHHHHHHHHHHhCCC-C-CCeecCHH-HH
Confidence            89998877543 33321  1111 1 35577876 64

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.82  E-value=0.17  Score=41.47  Aligned_cols=17  Identities=24%  Similarity=0.134  Sum_probs=14.1

Q ss_pred             cEEEEccCCCCcchhhh
Q 031654           68 DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yl   84 (155)
                      -+++.||.|+|||....
T Consensus        40 ~~L~~Gp~G~GKTtla~   56 (363)
T PRK14961         40 AWLLSGTRGVGKTTIAR   56 (363)
T ss_pred             EEEEecCCCCCHHHHHH
Confidence            36899999999998653

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.81  E-value=0.18  Score=43.16  Aligned_cols=81  Identities=10%  Similarity=0.024  Sum_probs=42.7

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhc-----hHHHHHHHh--cCCcEEEEChH------HHHHHHHcC-CC-Ccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYS-----ARKELRELA--RWVDNLMATLR------RLVNLLERG-RV-SLQ  131 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~-----~~~~~~~l~--~~~~IlI~TP~------~l~~~l~~~-~~-~l~  131 (155)
                      +.++.+||.|+|||.+..+-+-.........     .......+.  ..+|++-..+.      .+.+++..- .. ...
T Consensus        36 ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~~~vddIR~Iie~~~~~P~~~  115 (491)
T PRK14964         36 QSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVDDIKVILENSCYLPISS  115 (491)
T ss_pred             ceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccCCCHHHHHHHHHHHHhccccC
Confidence            3689999999999986543221111111110     022223332  35677765552      233333221 11 235


Q ss_pred             cccceEEEEccccccccc
Q 031654          132 MIIRYLALKEAADQTLDM  149 (155)
Q Consensus       132 ~l~~~lVlDEa~D~ll~~  149 (155)
                      +- +.+||||+ |.|-..
T Consensus       116 ~~-KVvIIDEa-h~Ls~~  131 (491)
T PRK14964        116 KF-KVYIIDEV-HMLSNS  131 (491)
T ss_pred             Cc-eEEEEeCh-HhCCHH
Confidence            67 89999999 876543

>TIGR00763 lon ATP-dependent protease La

Probab=93.80  E-value=0.082  Score=47.66  Aligned_cols=78  Identities=18%  Similarity=0.164  Sum_probs=40.8

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----HHHHHHHhcCCc-EEEEChHHHHHHHHcCCCCcccccceEEE
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----RKELRELARWVD-NLMATLRRLVNLLERGRVSLQMIIRYLAL  139 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----~~~~~~l~~~~~-IlI~TP~~l~~~l~~~~~~l~~l~~~lVl  139 (155)
                      .|..++..+|+|+|||...- .+...+.......    ......+..... .+=..|+++.+.+....   ..- ..+++
T Consensus       346 ~~~~lll~GppG~GKT~lAk-~iA~~l~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~g~i~~~l~~~~---~~~-~vill  420 (775)
T TIGR00763       346 KGPILCLVGPPGVGKTSLGK-SIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAK---TKN-PLFLL  420 (775)
T ss_pred             CCceEEEECCCCCCHHHHHH-HHHHHhcCCeEEEeCCCcccHHHHcCCCCceeCCCCchHHHHHHHhC---cCC-CEEEE
Confidence            34679999999999997532 2222221110000    111222222122 23345778776665321   122 46899


Q ss_pred             Ecccccccc
Q 031654          140 KEAADQTLD  148 (155)
Q Consensus       140 DEa~D~ll~  148 (155)
                      ||+ |++..
T Consensus       421 DEi-dk~~~  428 (775)
T TIGR00763       421 DEI-DKIGS  428 (775)
T ss_pred             ech-hhcCC
Confidence            999 99963

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.76  E-value=0.19  Score=42.16  Aligned_cols=19  Identities=26%  Similarity=0.286  Sum_probs=15.8

Q ss_pred             CcEEEEccCCCCcchhhhh
Q 031654           67 RDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yll   85 (155)
                      +.+++++|||+|||.....
T Consensus       242 ~vI~LVGptGvGKTTTiaK  260 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAK  260 (436)
T ss_pred             cEEEEECCCCCcHHHHHHH
Confidence            5788999999999987543

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=93.73  E-value=0.14  Score=40.82  Aligned_cols=15  Identities=27%  Similarity=0.463  Sum_probs=12.1

Q ss_pred             cEEE-EccCCCCcchh
Q 031654           68 DLMA-CAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~-~a~TGsGKT~~   82 (155)
                      ++++ .||+|+|||..
T Consensus        44 ~~lll~G~~G~GKT~l   59 (316)
T PHA02544         44 NMLLHSPSPGTGKTTV   59 (316)
T ss_pred             eEEEeeCcCCCCHHHH
Confidence            4555 89999999975

>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=93.73  E-value=0.037  Score=43.76  Aligned_cols=21  Identities=29%  Similarity=0.529  Sum_probs=18.2

Q ss_pred             HHhcCCcEEEEccCCCCcchh
Q 031654           62 ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+.+++.++++||+|+|||..
T Consensus        29 l~~~~~pvLl~G~~GtGKT~l   49 (272)
T PF12775_consen   29 LLSNGRPVLLVGPSGTGKTSL   49 (272)
T ss_dssp             HHHCTEEEEEESSTTSSHHHH
T ss_pred             HHHcCCcEEEECCCCCchhHH
Confidence            345779999999999999985

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=93.71  E-value=0.34  Score=42.75  Aligned_cols=70  Identities=19%  Similarity=0.079  Sum_probs=44.5

Q ss_pred             CCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhh--hch--------------HHHHHH-Hh--cCCcEE
Q 031654           52 PTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY--YSA--------------RKELRE-LA--RWVDNL  112 (155)
Q Consensus        52 pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~--~~~--------------~~~~~~-l~--~~~~Il  112 (155)
                      +++-|.+++..  ...+++|.|+.|||||.+-+--+...+....  +..              ...... +.  ....+-
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l~~~~~~~v~   79 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLGKGEARGLT   79 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhCccccCCeE
Confidence            68889998754  3568999999999999886655555553321  111              111211 11  134688


Q ss_pred             EEChHHHHHHH
Q 031654          113 MATLRRLVNLL  123 (155)
Q Consensus       113 I~TP~~l~~~l  123 (155)
                      |+|-.++...+
T Consensus        80 v~TfHs~a~~i   90 (664)
T TIGR01074        80 ISTFHTLGLDI   90 (664)
T ss_pred             EEeHHHHHHHH
Confidence            99998886544

Designed to identify rep members of the uvrD/rep subfamily.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=93.67  E-value=0.032  Score=48.92  Aligned_cols=24  Identities=29%  Similarity=0.306  Sum_probs=21.5

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIING   90 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~   90 (155)
                      .++++.||||||||.+|++|-+-.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~  182 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLF  182 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHh
Confidence            589999999999999999997654

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=93.66  E-value=0.094  Score=43.50  Aligned_cols=16  Identities=19%  Similarity=0.320  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.+++.||+|+|||+.
T Consensus       166 ~gvLL~GppGtGKT~l  181 (389)
T PRK03992        166 KGVLLYGPPGTGKTLL  181 (389)
T ss_pred             CceEEECCCCCChHHH
Confidence            6799999999999975

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=93.60  E-value=0.18  Score=39.92  Aligned_cols=16  Identities=31%  Similarity=0.399  Sum_probs=14.2

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      .+++.||+|+|||...
T Consensus        40 ~~ll~G~~G~GKt~~~   55 (319)
T PRK00440         40 HLLFAGPPGTGKTTAA   55 (319)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            5999999999999764

>PRK14873 primosome assembly protein PriA; Provisional

Probab=93.49  E-value=0.11  Score=46.24  Aligned_cols=22  Identities=9%  Similarity=-0.012  Sum_probs=15.0

Q ss_pred             EccCCCCcchhhhhHHHHHHHH
Q 031654           72 CAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        72 ~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .+.+|||||..|+-.+-..+..
T Consensus       166 ~~~~GSGKTevyl~~i~~~l~~  187 (665)
T PRK14873        166 QALPGEDWARRLAAAAAATLRA  187 (665)
T ss_pred             hcCCCCcHHHHHHHHHHHHHHc
Confidence            3346999999997655554443

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=93.42  E-value=0.25  Score=39.78  Aligned_cols=79  Identities=9%  Similarity=-0.001  Sum_probs=39.6

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhh----ch----HHHHHHHhcCCcEEEEChH------HHHHHHHc--CCCCc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYY----SA----RKELRELARWVDNLMATLR------RLVNLLER--GRVSL  130 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~----~~----~~~~~~l~~~~~IlI~TP~------~l~~~l~~--~~~~l  130 (155)
                      +.+++.||+|+|||... ..+...+.....    .+    ....-.....++++.-.+.      .+.+++..  ..-..
T Consensus        37 ~~~Ll~G~~G~GKt~~a-~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~  115 (355)
T TIGR02397        37 HAYLFSGPRGTGKTSIA-RIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVIEIDAASNNGVDDIREILDNVKYAPSS  115 (355)
T ss_pred             eEEEEECCCCCCHHHHH-HHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeeccccCCHHHHHHHHHHHhcCccc
Confidence            35789999999999653 223333322110    00    1111111223566654432      22333332  11123


Q ss_pred             ccccceEEEEcccccccc
Q 031654          131 QMIIRYLALKEAADQTLD  148 (155)
Q Consensus       131 ~~l~~~lVlDEa~D~ll~  148 (155)
                      ..- +.+||||| |.|-+
T Consensus       116 ~~~-~vviidea-~~l~~  131 (355)
T TIGR02397       116 GKY-KVYIIDEV-HMLSK  131 (355)
T ss_pred             CCc-eEEEEeCh-hhcCH
Confidence            455 78999999 98844

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>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=93.40  E-value=0.039  Score=43.07  Aligned_cols=29  Identities=24%  Similarity=0.297  Sum_probs=21.4

Q ss_pred             hcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           64 VAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      ..+.+++++|+||||||... -.++..+..
T Consensus       125 ~~~~~ili~G~tGSGKTT~l-~all~~i~~  153 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKTTLL-NALLEEIPP  153 (270)
T ss_dssp             HTTEEEEEEESTTSSHHHHH-HHHHHHCHT
T ss_pred             ccceEEEEECCCccccchHH-HHHhhhccc
Confidence            45689999999999999864 444444443

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 ....

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=93.32  E-value=0.13  Score=46.00  Aligned_cols=50  Identities=12%  Similarity=0.181  Sum_probs=28.6

Q ss_pred             CcccccCC--HHHHHhHHhC---CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           30 AARFAYVP--QHLRNKPRTY---KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~---g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      -.+|+++.  +..++.+.++   -+.+|.-.+..   .+..++.+++.+|+|||||..
T Consensus       174 ~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~---gi~~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHL---GIEPPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCceEEEECCCCCChHHH
Confidence            35788877  5555555432   11121111111   113457899999999999974

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=93.26  E-value=0.034  Score=49.03  Aligned_cols=23  Identities=22%  Similarity=0.289  Sum_probs=20.9

Q ss_pred             CcEEEEccCCCCcchhhhhHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      .++++.||||||||.++++|-+-
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL  198 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLL  198 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchh
Confidence            68999999999999999999764

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=93.22  E-value=0.11  Score=49.18  Aligned_cols=40  Identities=33%  Similarity=0.372  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           52 PTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        52 pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .|+-|.++|-  ..|++++|.|..|||||.+-+--++..+..
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~   41 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILR   41 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhc
Confidence            5889999996  478999999999999999876666665543

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=93.17  E-value=0.12  Score=46.67  Aligned_cols=93  Identities=19%  Similarity=0.105  Sum_probs=58.0

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      +|..+|...  .+.-...-++.-.||-|||++..+|+.-..+.+....                                
T Consensus        80 ~~~dVQliG--~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~gkgVhvVTvNdYLA~RDae~m~~l~~~LGlsvG~~~~  157 (822)
T COG0653          80 RHFDVQLLG--GIVLHLGDIAEMRTGEGKTLVATLPAYLNALAGKGVHVVTVNDYLARRDAEWMGPLYEFLGLSVGVILA  157 (822)
T ss_pred             ChhhHHHhh--hhhhcCCceeeeecCCchHHHHHHHHHHHhcCCCCcEEeeehHHhhhhCHHHHHHHHHHcCCceeeccC
Confidence            455566553  3333344567889999999999999766555444322                                


Q ss_pred             --HHHHHHHhcCCcEEEEChHHH-HHHHHcC------CCCcccccceEEEEccccccc
Q 031654           99 --RKELRELARWVDNLMATLRRL-VNLLERG------RVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --~~~~~~l~~~~~IlI~TP~~l-~~~l~~~------~~~l~~l~~~lVlDEa~D~ll  147 (155)
                        ....+.-.-.|||..+|-..+ .++++-+      ..-...+ .|-|+||+ |-+|
T Consensus       158 ~m~~~ek~~aY~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~-~faIvDEv-DSIL  213 (822)
T COG0653         158 GMSPEEKRAAYACDITYGTNNELGFDYLRDNMVTSQEEKVQRGL-NFAIVDEV-DSIL  213 (822)
T ss_pred             CCChHHHHHHHhcCceeccccccCcchhhhhhhccHHHhhhccC-CeEEEcch-hhee
Confidence              122222233589999998776 2222221      1224467 89999999 9876

>PF14516 AAA_35: AAA-like domain

Probab=93.15  E-value=0.3  Score=39.58  Aligned_cols=39  Identities=15%  Similarity=0.227  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHhc-CCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           54 PVQRHATSILVA-GRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        54 ~iQ~~~i~~~l~-g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      |+.+.++..+.+ |.-+.+.||-.+|||.. +.-+++++.+
T Consensus        18 ~~e~~~~~~i~~~G~~~~I~apRq~GKTSl-l~~l~~~l~~   57 (331)
T PF14516_consen   18 PAEQECYQEIVQPGSYIRIKAPRQMGKTSL-LLRLLERLQQ   57 (331)
T ss_pred             HHHHHHHHHHhcCCCEEEEECcccCCHHHH-HHHHHHHHHH
Confidence            588999999987 99999999999999975 3455555544

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.14  E-value=0.16  Score=43.73  Aligned_cols=81  Identities=14%  Similarity=0.062  Sum_probs=40.3

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHH-hhhc-----hHHHHHHHhc--CCcEEEEChHH------HHHHHHcCCC--Ccc
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMR-EYYS-----ARKELRELAR--WVDNLMATLRR------LVNLLERGRV--SLQ  131 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~-~~~~-----~~~~~~~l~~--~~~IlI~TP~~------l~~~l~~~~~--~l~  131 (155)
                      -.+.+||.|+|||.+..+-+ ..+.. ....     .......+..  .+|++--.+..      +.+++..-..  .-.
T Consensus        40 a~Lf~Gp~G~GKTt~A~~lA-k~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~  118 (509)
T PRK14958         40 AYLFTGTRGVGKTTISRILA-KCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKG  118 (509)
T ss_pred             eEEEECCCCCCHHHHHHHHH-HHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccC
Confidence            46899999999997654322 22211 1100     0122223322  34565555431      2222221111  123


Q ss_pred             cccceEEEEccccccccccc
Q 031654          132 MIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       132 ~l~~~lVlDEa~D~ll~~gf  151 (155)
                      +- +.+||||| |.|-...|
T Consensus       119 ~~-kV~iIDE~-~~ls~~a~  136 (509)
T PRK14958        119 RF-KVYLIDEV-HMLSGHSF  136 (509)
T ss_pred             Cc-EEEEEECh-HhcCHHHH
Confidence            56 78999999 87755443

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.11  E-value=0.28  Score=44.23  Aligned_cols=19  Identities=37%  Similarity=0.331  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCCcchhhh
Q 031654           66 GRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl   84 (155)
                      |+=+.+++|||+|||.+..
T Consensus       185 g~Vi~lVGpnGvGKTTTia  203 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTA  203 (767)
T ss_pred             CeEEEEECCCCCcHHHHHH
Confidence            3447889999999998754

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.06  E-value=0.4  Score=41.64  Aligned_cols=19  Identities=32%  Similarity=0.384  Sum_probs=16.3

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|+.+.+++|||+|||...
T Consensus       349 ~G~vIaLVGPtGvGKTTta  367 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTI  367 (559)
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678889999999999875

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=92.99  E-value=0.051  Score=48.19  Aligned_cols=24  Identities=21%  Similarity=0.256  Sum_probs=21.4

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIING   90 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~   90 (155)
                      .++++.||||||||.++++|-|-.
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~  168 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLT  168 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHh
Confidence            689999999999999999996543

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=92.98  E-value=0.096  Score=43.07  Aligned_cols=26  Identities=27%  Similarity=0.285  Sum_probs=19.5

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      .+.-+++++|||||||... -.++..+
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            5678999999999998863 3344444

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=92.91  E-value=0.16  Score=42.34  Aligned_cols=17  Identities=24%  Similarity=0.286  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      ..+++.||+|+|||...
T Consensus        37 ~~ilL~GppGtGKTtLA   53 (413)
T PRK13342         37 SSMILWGPPGTGKTTLA   53 (413)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            47999999999999754

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.87  E-value=0.23  Score=42.48  Aligned_cols=17  Identities=24%  Similarity=0.098  Sum_probs=14.5

Q ss_pred             cEEEEccCCCCcchhhh
Q 031654           68 DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yl   84 (155)
                      -++++||.|+|||.+..
T Consensus        42 a~Lf~GP~GtGKTTlAr   58 (484)
T PRK14956         42 AYIFFGPRGVGKTTIAR   58 (484)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47999999999998754

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.87  E-value=0.046  Score=48.37  Aligned_cols=31  Identities=16%  Similarity=0.186  Sum_probs=23.8

Q ss_pred             HhcCCcEEEEccCCCCcchhhhhHHHHHHHHhh
Q 031654           63 LVAGRDLMACAQTGSRKTTPFCFPIINGIMREY   95 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~   95 (155)
                      +-.|+-+-+++|.|||||.+  ..++.+++...
T Consensus       491 i~pGe~vALVGPSGsGKSTi--asLL~rfY~Pt  521 (716)
T KOG0058|consen  491 IRPGEVVALVGPSGSGKSTI--ASLLLRFYDPT  521 (716)
T ss_pred             eCCCCEEEEECCCCCCHHHH--HHHHHHhcCCC
Confidence            45688999999999999986  45666666543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.85  E-value=0.17  Score=44.93  Aligned_cols=17  Identities=24%  Similarity=0.114  Sum_probs=14.4

Q ss_pred             cEEEEccCCCCcchhhh
Q 031654           68 DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yl   84 (155)
                      -++++||.|+|||....
T Consensus        39 AyLF~GPpGvGKTTlAr   55 (702)
T PRK14960         39 AYLFTGTRGVGKTTIAR   55 (702)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            56999999999998654

>PF12846 AAA_10: AAA-like domain

Probab=92.70  E-value=0.1  Score=40.58  Aligned_cols=22  Identities=27%  Similarity=0.330  Sum_probs=17.4

Q ss_pred             CcEEEEccCCCCcchhhhhHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      +++++.|+||||||.... .++.
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~   23 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLE   23 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHH
Confidence            578999999999997755 4443

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=92.69  E-value=0.2  Score=40.91  Aligned_cols=40  Identities=23%  Similarity=0.111  Sum_probs=27.8

Q ss_pred             HHhHHhCCCCCCCHHHHHHHHHHh-cCCcEEEEccCCCCcchh
Q 031654           41 RNKPRTYKYVKPTPVQRHATSILV-AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        41 ~~~l~~~g~~~pt~iQ~~~i~~~l-~g~dvl~~a~TGsGKT~~   82 (155)
                      ++.|.+.|+  .++-+...+..+. .+.+++++++||||||..
T Consensus       154 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTl  194 (340)
T TIGR03819       154 LDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTL  194 (340)
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHH
Confidence            444555564  4556666665544 558999999999999874

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.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=92.67  E-value=0.23  Score=43.62  Aligned_cols=78  Identities=13%  Similarity=0.064  Sum_probs=42.5

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhh---h------ch--HHHHHHHhc--CCcEEEEChHH---------HHHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREY---Y------SA--RKELRELAR--WVDNLMATLRR---------LVNLLE  124 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~---~------~~--~~~~~~l~~--~~~IlI~TP~~---------l~~~l~  124 (155)
                      +.+++++|.|+|||....+-+ ..+....   .      .+  ....+.+..  .+|++...|..         +.+.+.
T Consensus        47 ha~L~~Gp~GvGKTt~Ar~lA-k~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~  125 (598)
T PRK09111         47 QAFMLTGVRGVGKTTTARILA-RALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVR  125 (598)
T ss_pred             ceEEEECCCCCCHHHHHHHHH-HhhCcCCccccCCCccccCcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHH
Confidence            368999999999998754332 2222110   0      00  122233332  46777655432         222222


Q ss_pred             cCCCCcccccceEEEEcccccccc
Q 031654          125 RGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       125 ~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      ... ....- +.+||||+ |.|-.
T Consensus       126 ~~P-~~a~~-KVvIIDEa-d~Ls~  146 (598)
T PRK09111        126 YRP-VSARY-KVYIIDEV-HMLST  146 (598)
T ss_pred             hch-hcCCc-EEEEEECh-HhCCH
Confidence            222 24566 89999999 88754

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=92.65  E-value=0.42  Score=44.14  Aligned_cols=27  Identities=15%  Similarity=0.092  Sum_probs=21.9

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .|+.+..+||||||.+|+-.++.....
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~   86 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQK   86 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHH
Confidence            489999999999999998777665443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.63  E-value=0.27  Score=42.49  Aligned_cols=17  Identities=24%  Similarity=0.120  Sum_probs=14.1

Q ss_pred             cEEEEccCCCCcchhhh
Q 031654           68 DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yl   84 (155)
                      -++++||.|+|||....
T Consensus        40 a~Lf~Gp~G~GKTt~A~   56 (527)
T PRK14969         40 AYLFTGTRGVGKTTLAR   56 (527)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            36899999999997654

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=92.63  E-value=0.2  Score=44.95  Aligned_cols=17  Identities=18%  Similarity=0.200  Sum_probs=15.3

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .|+++.+|+|+|||...
T Consensus       204 ~n~lL~G~pG~GKT~l~  220 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIA  220 (731)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            69999999999999863

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=92.56  E-value=0.65  Score=37.96  Aligned_cols=47  Identities=13%  Similarity=0.078  Sum_probs=36.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhh
Q 031654           49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY   95 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~   95 (155)
                      +.--|+.|..=+..+.+.-=+++.+|-|+|||.-.....+..+....
T Consensus       126 I~~kt~~Q~~y~eai~~~di~fGiGpAGTGKTyLava~av~al~~~~  172 (348)
T COG1702         126 IIPKTPGQNMYPEAIEEHDIVFGIGPAGTGKTYLAVAKAVDALGAGQ  172 (348)
T ss_pred             eEecChhHHHHHHHHHhcCeeeeecccccCChhhhHHhHhhhhhhcc
Confidence            44568899888777777777889999999999877666666665443

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=92.56  E-value=0.55  Score=42.02  Aligned_cols=40  Identities=30%  Similarity=0.297  Sum_probs=30.8

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      ..+++-|.+++.+  ...+++|.|+.|||||.+..--+...+
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li   42 (726)
T TIGR01073         3 AHLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLI   42 (726)
T ss_pred             cccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHH
Confidence            4589999998864  346899999999999988655554444

Designed to identify pcrA members of the uvrD/rep subfamily.

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=92.55  E-value=0.061  Score=39.34  Aligned_cols=47  Identities=23%  Similarity=0.231  Sum_probs=31.3

Q ss_pred             HHHHHHhcCCcEEEEChHHHHHHHHcCC---CCcccccceEEEEccccccccc
Q 031654          100 KELRELARWVDNLMATLRRLVNLLERGR---VSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       100 ~~~~~l~~~~~IlI~TP~~l~~~l~~~~---~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      ...+.....+||||++-..|.+-.....   +++.+  ..|||||| |.|.+.
T Consensus       111 ~~~r~~~~~adivi~~y~yl~~~~~~~~~~~~~~~~--~ivI~DEA-HNL~~~  160 (174)
T PF06733_consen  111 YLARELAKNADIVICNYNYLFDPSIRKSLFGIDLKD--NIVIFDEA-HNLEDA  160 (174)
T ss_dssp             HHHHHCGGG-SEEEEETHHHHSHHHHHHHCT--CCC--EEEEETTG-GGCGGG
T ss_pred             HHHHHhcccCCEEEeCHHHHhhHHHHhhhccccccC--cEEEEecc-cchHHH
Confidence            3445666679999999888766544332   33443  48999999 988765

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=92.55  E-value=0.21  Score=42.66  Aligned_cols=52  Identities=13%  Similarity=0.211  Sum_probs=29.0

Q ss_pred             CCCcccccCC--HHHHHhHHhCC--CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           28 SPAARFAYVP--QHLRNKPRTYK--YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        28 ~~~~~f~~l~--~~l~~~l~~~g--~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+-.+|+++.  +.+.+.+.+.-  +..|...+...   .-..+.+++.+|+|||||+.
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~l  104 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLG---AKIPKGVLLVGPPGTGKTLL  104 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcC---CCCCCcEEEECCCCCCHHHH
Confidence            3446888887  44544443320  22222222110   11225799999999999985

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>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=92.55  E-value=0.11  Score=41.80  Aligned_cols=40  Identities=25%  Similarity=0.314  Sum_probs=28.2

Q ss_pred             CCCCCHHHHH-HHHHHhcCCcEEEEccCCCCcchhhhhHHHH
Q 031654           49 YVKPTPVQRH-ATSILVAGRDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        49 ~~~pt~iQ~~-~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      +..+++.|.. .|-.+-.+++++++++||||||.. +.+++.
T Consensus       125 ~gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~-lnall~  165 (312)
T COG0630         125 YGTISPEQAAYLWLAIEARKSIIICGGTASGKTTL-LNALLD  165 (312)
T ss_pred             cCCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHH
Confidence            3455666655 455667789999999999999974 334433

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=92.52  E-value=0.54  Score=38.65  Aligned_cols=17  Identities=24%  Similarity=0.282  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      +..+++.+|-|||||.-
T Consensus        49 snsviiigprgsgkT~l   65 (408)
T KOG2228|consen   49 SNSVIIIGPRGSGKTIL   65 (408)
T ss_pred             CCceEEEccCCCCceEe
Confidence            37899999999999964

>COG1674 FtsK DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]

Probab=92.49  E-value=0.11  Score=47.30  Aligned_cols=32  Identities=19%  Similarity=0.193  Sum_probs=24.2

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhch
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSA   98 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~   98 (155)
                      -++++.+.||||||.+----+++.+....+..
T Consensus       531 ~hllv~G~tgsGKSv~lnt~i~Sll~~~~P~e  562 (858)
T COG1674         531 GHLLIAGATGSGKSVALNTMILSLLYTHSPEE  562 (858)
T ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHHHhCChhH
Confidence            58999999999999987666666666554433

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=92.41  E-value=0.19  Score=39.99  Aligned_cols=48  Identities=13%  Similarity=0.144  Sum_probs=34.0

Q ss_pred             HHHHHHHhcCCcEEEEChHHHHHHHHcC--CCCcccccceEEEEccccccccc
Q 031654           99 RKELRELARWVDNLMATLRRLVNLLERG--RVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 ~~~~~~l~~~~~IlI~TP~~l~~~l~~~--~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      ....+.....+||||++...|++-..++  ...+. - .+|||||| |.|.+.
T Consensus       202 Y~~~r~~~~~Adivi~ny~yll~~~~r~~~~~~l~-~-~~lIiDEA-HnL~d~  251 (289)
T smart00489      202 YFASRKAIEFANVVVLPYQYLLDPKIRQALSIELK-D-SIVIFDEA-HNLDNV  251 (289)
T ss_pred             hHHHHHHhhcCCEEEECHHHHhcHHHHHHhccccc-c-cEEEEeCc-cChHHH
Confidence            3444455577999999999887765332  23443 4 69999999 998764

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=92.41  E-value=0.19  Score=39.99  Aligned_cols=48  Identities=13%  Similarity=0.144  Sum_probs=34.0

Q ss_pred             HHHHHHHhcCCcEEEEChHHHHHHHHcC--CCCcccccceEEEEccccccccc
Q 031654           99 RKELRELARWVDNLMATLRRLVNLLERG--RVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 ~~~~~~l~~~~~IlI~TP~~l~~~l~~~--~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      ....+.....+||||++...|++-..++  ...+. - .+|||||| |.|.+.
T Consensus       202 Y~~~r~~~~~Adivi~ny~yll~~~~r~~~~~~l~-~-~~lIiDEA-HnL~d~  251 (289)
T smart00488      202 YFASRKAIEFANVVVLPYQYLLDPKIRQALSIELK-D-SIVIFDEA-HNLDNV  251 (289)
T ss_pred             hHHHHHHhhcCCEEEECHHHHhcHHHHHHhccccc-c-cEEEEeCc-cChHHH
Confidence            3444455577999999999887765332  23443 4 69999999 998764

>PRK10865 protein disaggregation chaperone; Provisional

Probab=92.36  E-value=0.13  Score=46.88  Aligned_cols=17  Identities=18%  Similarity=0.202  Sum_probs=15.2

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.+|+|+|||...
T Consensus       200 ~n~lL~G~pGvGKT~l~  216 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIV  216 (857)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            59999999999999864

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=92.35  E-value=0.14  Score=42.37  Aligned_cols=27  Identities=30%  Similarity=0.226  Sum_probs=19.6

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .+..+++++|||||||... -.++..+.
T Consensus       148 ~~GlilI~G~TGSGKTT~l-~al~~~i~  174 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLA-ASIYQHCG  174 (372)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            4457999999999999753 34555554

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).

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=92.32  E-value=0.14  Score=41.08  Aligned_cols=21  Identities=29%  Similarity=0.412  Sum_probs=18.0

Q ss_pred             HHhcCCcEEEEccCCCCcchh
Q 031654           62 ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..|.+++++++||||||..
T Consensus       140 ~v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       140 AIASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             HhhCCCEEEEECCCCCCHHHH
Confidence            345779999999999999985

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.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.18  E-value=0.34  Score=42.71  Aligned_cols=19  Identities=21%  Similarity=0.114  Sum_probs=15.5

Q ss_pred             CcEEEEccCCCCcchhhhh
Q 031654           67 RDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yll   85 (155)
                      ..++.++|.|+|||.+..+
T Consensus        39 ha~Lf~GPpG~GKTtiAri   57 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARI   57 (624)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            3588999999999987643

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.16  E-value=0.27  Score=40.29  Aligned_cols=15  Identities=27%  Similarity=0.412  Sum_probs=12.9

Q ss_pred             CcEEEEccCCCCcch
Q 031654           67 RDLMACAQTGSRKTT   81 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~   81 (155)
                      |=+++.+|+|+|||.
T Consensus       178 RliLlhGPPGTGKTS  192 (423)
T KOG0744|consen  178 RLILLHGPPGTGKTS  192 (423)
T ss_pred             eEEEEeCCCCCChhH
Confidence            457899999999985

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=92.10  E-value=1.1  Score=36.87  Aligned_cols=16  Identities=25%  Similarity=0.146  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      -+++.+|.|+|||...
T Consensus        47 a~L~~G~~G~GKttlA   62 (351)
T PRK09112         47 ALLFEGPEGIGKATLA   62 (351)
T ss_pred             eEeeECCCCCCHHHHH
Confidence            5899999999998653

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=92.07  E-value=0.15  Score=46.45  Aligned_cols=17  Identities=18%  Similarity=0.202  Sum_probs=15.2

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.+|+|+|||...
T Consensus       195 ~n~lL~G~pGvGKT~l~  211 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIV  211 (852)
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            69999999999999864

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=92.01  E-value=0.36  Score=36.02  Aligned_cols=25  Identities=24%  Similarity=0.179  Sum_probs=18.2

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      .|.=+.+.+++|||||...+--+.+
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~   35 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVN   35 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3456889999999999876443333

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=91.98  E-value=0.23  Score=45.18  Aligned_cols=82  Identities=15%  Similarity=0.007  Sum_probs=41.5

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhh---ch--HHHHHHHhc----CCcEEEECh------HHHHHHHHcCCC--Cc
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYY---SA--RKELRELAR----WVDNLMATL------RRLVNLLERGRV--SL  130 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~---~~--~~~~~~l~~----~~~IlI~TP------~~l~~~l~~~~~--~l  130 (155)
                      -+|+++|.|+|||.+..+-.-..+.....   .+  ....+.+..    ..|++.-..      +.+.++...-.+  ..
T Consensus        39 a~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~  118 (824)
T PRK07764         39 AYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAE  118 (824)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhc
Confidence            36899999999998765433222211110   01  122233322    245544433      122222211111  23


Q ss_pred             ccccceEEEEccccccccccc
Q 031654          131 QMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       131 ~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      .+- +.+||||+ |+|-..++
T Consensus       119 ~~~-KV~IIDEa-d~lt~~a~  137 (824)
T PRK07764        119 SRY-KIFIIDEA-HMVTPQGF  137 (824)
T ss_pred             CCc-eEEEEech-hhcCHHHH
Confidence            466 89999999 98866544

>cd01131 PilT Pilus retraction ATPase PilT

Probab=91.97  E-value=0.08  Score=39.66  Aligned_cols=23  Identities=30%  Similarity=0.416  Sum_probs=16.6

Q ss_pred             EEEEccCCCCcchhhhhHHHHHHH
Q 031654           69 LMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        69 vl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      +++++|||||||... -.++..+.
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhh
Confidence            689999999999874 33444443

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=91.96  E-value=0.14  Score=39.04  Aligned_cols=26  Identities=27%  Similarity=0.327  Sum_probs=16.8

Q ss_pred             HHHHHH-hcCCcEEEEccCCCCcchhh
Q 031654           58 HATSIL-VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        58 ~~i~~~-l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +|+... ..++++++.+|+|||||+..
T Consensus        13 rAL~iAAaG~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   13 RALEIAAAGGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             HHHHHHHHCC--EEEES-CCCTHHHHH
T ss_pred             HHHHHHHcCCCCeEEECCCCCCHHHHH
Confidence            344433 35589999999999999864

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=91.77  E-value=0.29  Score=43.68  Aligned_cols=18  Identities=22%  Similarity=0.139  Sum_probs=15.2

Q ss_pred             CcEEEEccCCCCcchhhh
Q 031654           67 RDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yl   84 (155)
                      +.++++||.|+|||....
T Consensus        39 Ha~Lf~GP~GvGKTTlAr   56 (709)
T PRK08691         39 HAYLLTGTRGVGKTTIAR   56 (709)
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            468999999999998654

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=91.74  E-value=0.15  Score=43.29  Aligned_cols=24  Identities=29%  Similarity=0.418  Sum_probs=18.9

Q ss_pred             HHHHH-hcCCcEEEEccCCCCcchh
Q 031654           59 ATSIL-VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        59 ~i~~~-l~g~dvl~~a~TGsGKT~~   82 (155)
                      |+... ..|+|+++.+|+|||||+.
T Consensus       190 AleiAAAGgHnLl~~GpPGtGKTml  214 (490)
T COG0606         190 ALEIAAAGGHNLLLVGPPGTGKTML  214 (490)
T ss_pred             HHHHHHhcCCcEEEecCCCCchHHh
Confidence            44433 4569999999999999986

>CHL00195 ycf46 Ycf46; Provisional

Probab=91.72  E-value=0.19  Score=43.10  Aligned_cols=17  Identities=24%  Similarity=0.341  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +-+++.||+|||||+..
T Consensus       260 kGILL~GPpGTGKTllA  276 (489)
T CHL00195        260 RGLLLVGIQGTGKSLTA  276 (489)
T ss_pred             ceEEEECCCCCcHHHHH
Confidence            67999999999999753

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=91.70  E-value=0.7  Score=39.85  Aligned_cols=19  Identities=21%  Similarity=0.148  Sum_probs=15.7

Q ss_pred             CcEEEEccCCCCcchhhhh
Q 031654           67 RDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yll   85 (155)
                      ..++.+||.|+|||.+..+
T Consensus        44 ~a~Lf~Gp~G~GKTT~Ari   62 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARI   62 (507)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            3689999999999987543

>CHL00095 clpC Clp protease ATP binding subunit

Probab=91.68  E-value=0.31  Score=44.27  Aligned_cols=74  Identities=9%  Similarity=0.072  Sum_probs=40.2

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHH--------------HHHHcCCCCccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLV--------------NLLERGRVSLQM  132 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~--------------~~l~~~~~~l~~  132 (155)
                      .++++.+|+|+|||...-. +...+...      +......++.++....+.++              .++..-  .-..
T Consensus       201 ~n~lL~G~pGvGKTal~~~-la~~i~~~------~vp~~l~~~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~--~~~~  271 (821)
T CHL00095        201 NNPILIGEPGVGKTAIAEG-LAQRIVNR------DVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEI--QENN  271 (821)
T ss_pred             CCeEEECCCCCCHHHHHHH-HHHHHHhC------CCChhhcCCeEEEeeHHHHhccCCCccHHHHHHHHHHHHH--HhcC
Confidence            6999999999999986422 11222111      01111234556655554433              222210  0012


Q ss_pred             ccceEEEEccccccccccc
Q 031654          133 IIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       133 l~~~lVlDEa~D~ll~~gf  151 (155)
                      - ..|++||+ |.++..|.
T Consensus       272 ~-~ILfiDEi-h~l~~~g~  288 (821)
T CHL00095        272 N-IILVIDEV-HTLIGAGA  288 (821)
T ss_pred             C-eEEEEecH-HHHhcCCC
Confidence            2 37999999 99987653

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=91.68  E-value=0.12  Score=31.82  Aligned_cols=19  Identities=26%  Similarity=0.326  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|...++.+++|||||..+
T Consensus        22 ~g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4567999999999999864

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.64  E-value=0.42  Score=41.58  Aligned_cols=17  Identities=24%  Similarity=0.063  Sum_probs=14.1

Q ss_pred             cEEEEccCCCCcchhhh
Q 031654           68 DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yl   84 (155)
                      -++++||.|+|||....
T Consensus        40 a~Lf~Gp~GvGKTTlAr   56 (546)
T PRK14957         40 AYLFTGTRGVGKTTLGR   56 (546)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37899999999998653

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=91.62  E-value=0.32  Score=42.73  Aligned_cols=18  Identities=17%  Similarity=0.076  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhhh
Q 031654           67 RDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yl   84 (155)
                      +-++++||.|+|||....
T Consensus        39 hA~Lf~GP~GvGKTTlA~   56 (605)
T PRK05896         39 HAYIFSGPRGIGKTSIAK   56 (605)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            358899999999998654

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

Probab=91.61  E-value=0.096  Score=46.15  Aligned_cols=22  Identities=27%  Similarity=0.366  Sum_probs=20.3

Q ss_pred             CcEEEEccCCCCcchhhhhHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPII   88 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l   88 (155)
                      .++++.||||||||.++++|-+
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnL  233 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTA  233 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhh
Confidence            6899999999999999999953

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.

>TIGR00767 rho transcription termination factor Rho

Probab=91.56  E-value=0.47  Score=39.81  Aligned_cols=19  Identities=21%  Similarity=0.115  Sum_probs=16.7

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      -.|+-+++.+|+|+|||..
T Consensus       166 g~Gq~~~IvG~~g~GKTtL  184 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVL  184 (415)
T ss_pred             CCCCEEEEECCCCCChhHH
Confidence            4678899999999999974

Members of this family differ in the specificity of RNA binding.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=91.53  E-value=0.49  Score=37.38  Aligned_cols=18  Identities=22%  Similarity=0.272  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCcchhhh
Q 031654           67 RDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yl   84 (155)
                      +-+++++++|+|||....
T Consensus        73 ~vi~l~G~~G~GKTTt~a   90 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIA   90 (272)
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            457788999999998644

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=91.50  E-value=0.29  Score=43.97  Aligned_cols=17  Identities=29%  Similarity=0.255  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        53 ~slLL~GPpGtGKTTLA   69 (725)
T PRK13341         53 GSLILYGPPGVGKTTLA   69 (725)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            48999999999999754

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=91.49  E-value=0.35  Score=43.67  Aligned_cols=17  Identities=24%  Similarity=0.110  Sum_probs=13.9

Q ss_pred             cEEEEccCCCCcchhhh
Q 031654           68 DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yl   84 (155)
                      -++++++.|+|||....
T Consensus        40 AyLFtGPpGvGKTTlAr   56 (830)
T PRK07003         40 AYLFTGTRGVGKTTLSR   56 (830)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            35899999999997643

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.46  E-value=0.15  Score=44.63  Aligned_cols=39  Identities=15%  Similarity=0.205  Sum_probs=27.3

Q ss_pred             cCCcEEEEChHHHHHHHHcC---CC---Ccccccc-eEEEEccccccc
Q 031654          107 RWVDNLMATLRRLVNLLERG---RV---SLQMIIR-YLALKEAADQTL  147 (155)
Q Consensus       107 ~~~~IlI~TP~~l~~~l~~~---~~---~l~~l~~-~lVlDEa~D~ll  147 (155)
                      .+..|..+|-..|...+.+.   .+   ++.+. + .++-||| |+|=
T Consensus        80 d~iei~fttiq~l~~d~~~~ken~itledl~~~-klvfl~dea-hhln  125 (812)
T COG3421          80 DAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQ-KLVFLADEA-HHLN  125 (812)
T ss_pred             CceEEEEeehHHHHHHHHhhccccccHhhHhhC-ceEEEechh-hhhh
Confidence            36789999999998777653   33   34444 3 4566999 8874

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=91.40  E-value=0.28  Score=39.88  Aligned_cols=77  Identities=18%  Similarity=0.169  Sum_probs=39.2

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChH---HHHHHHHcCCCCc--ccccceEEEEc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLR---RLVNLLERGRVSL--QMIIRYLALKE  141 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~---~l~~~l~~~~~~l--~~l~~~lVlDE  141 (155)
                      .+.+.-+|+|+|||-.-+ +....+... .........+....+-=++.+.   .+....+...+.-  ... +++|+||
T Consensus        63 Ph~L~YgPPGtGktsti~-a~a~~ly~~-~~~~~m~lelnaSd~rgid~vr~qi~~fast~~~~~fst~~~f-KlvILDE  139 (360)
T KOG0990|consen   63 PHLLFYGPPGTGKTSTIL-ANARDFYSP-HPTTSMLLELNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAF-KLVILDE  139 (360)
T ss_pred             CcccccCCCCCCCCCchh-hhhhhhcCC-CCchhHHHHhhccCccCCcchHHHHHHHHhhccceeccccCce-eEEEecc
Confidence            478888899999998743 333333331 1112233333322222222222   1222222212222  367 9999999


Q ss_pred             cccccc
Q 031654          142 AADQTL  147 (155)
Q Consensus       142 a~D~ll  147 (155)
                      | |.|-
T Consensus       140 A-DaMT  144 (360)
T KOG0990|consen  140 A-DAMT  144 (360)
T ss_pred             h-hHhh
Confidence            9 9885

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=91.40  E-value=0.21  Score=45.63  Aligned_cols=17  Identities=18%  Similarity=0.257  Sum_probs=15.2

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.+|+|+|||...
T Consensus       209 ~n~lLvG~pGvGKTal~  225 (852)
T TIGR03345       209 NNPILTGEAGVGKTAVV  225 (852)
T ss_pred             CceeEECCCCCCHHHHH
Confidence            59999999999999864

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=91.31  E-value=0.19  Score=37.29  Aligned_cols=26  Identities=31%  Similarity=0.353  Sum_probs=20.8

Q ss_pred             HHHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           58 HATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        58 ~~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .++..++.|.|  +++.++||||||.+-
T Consensus        14 ~~v~~~~~G~n~~i~~yG~tGsGKT~Tm   41 (186)
T cd01363          14 PLLQSALDGYNVCIFAYGQTGSGKTYTM   41 (186)
T ss_pred             HHHHHHhCCcceeEEEECCCCCcceEec
Confidence            56677789965  678899999999663

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

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.29  E-value=0.49  Score=39.94  Aligned_cols=18  Identities=33%  Similarity=0.401  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCcchhhh
Q 031654           67 RDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yl   84 (155)
                      .-+++++|+|+|||....
T Consensus       224 ~vi~lvGptGvGKTTtaa  241 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIA  241 (432)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            347889999999998754

>TIGR00959 ffh signal recognition particle protein

Probab=91.29  E-value=0.5  Score=39.85  Aligned_cols=16  Identities=31%  Similarity=0.339  Sum_probs=13.8

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      -+++++++|+|||...
T Consensus       101 vi~~vG~~GsGKTTta  116 (428)
T TIGR00959       101 VILMVGLQGSGKTTTC  116 (428)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            4788999999999874

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=91.29  E-value=0.26  Score=41.62  Aligned_cols=18  Identities=33%  Similarity=0.383  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhhh
Q 031654           67 RDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yl   84 (155)
                      .-+++++++|+|||....
T Consensus        96 ~vI~lvG~~GsGKTTtaa  113 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAA  113 (437)
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            468899999999998753

>CHL00176 ftsH cell division protein; Validated

Probab=91.28  E-value=0.37  Score=42.66  Aligned_cols=17  Identities=18%  Similarity=0.266  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +.+++.+|+|+|||+..
T Consensus       217 ~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            57999999999999853

>PRK13764 ATPase; Provisional

Probab=91.26  E-value=0.19  Score=44.12  Aligned_cols=28  Identities=11%  Similarity=0.107  Sum_probs=20.7

Q ss_pred             hcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           64 VAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      ..+++++++++||||||.. +-.++..+.
T Consensus       255 ~~~~~ILIsG~TGSGKTTl-l~AL~~~i~  282 (602)
T PRK13764        255 ERAEGILIAGAPGAGKSTF-AQALAEFYA  282 (602)
T ss_pred             hcCCEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            3468899999999999974 344555554

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=91.24  E-value=0.15  Score=42.49  Aligned_cols=74  Identities=14%  Similarity=0.038  Sum_probs=36.4

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCC----CcccccceEEEEcc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRV----SLQMIIRYLALKEA  142 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~----~l~~l~~~lVlDEa  142 (155)
                      +=+++.+|+|+|||+..-.- ...+...  ...-...++.   .=.+|-|++++..+-+..-    .-..- ..|.|||+
T Consensus       149 lgllL~GPPGcGKTllArai-A~elg~~--~i~vsa~eL~---sk~vGEsEk~IR~~F~~A~~~a~~~~aP-cVLFIDEI  221 (413)
T PLN00020        149 LILGIWGGKGQGKSFQCELV-FKKMGIE--PIVMSAGELE---SENAGEPGKLIRQRYREAADIIKKKGKM-SCLFINDL  221 (413)
T ss_pred             eEEEeeCCCCCCHHHHHHHH-HHHcCCC--eEEEEHHHhh---cCcCCcHHHHHHHHHHHHHHHhhccCCC-eEEEEehh
Confidence            35788999999999853211 1111000  0000001111   1134555555544433211    12245 68999999


Q ss_pred             cccccc
Q 031654          143 ADQTLD  148 (155)
Q Consensus       143 ~D~ll~  148 (155)
                       |.++-
T Consensus       222 -DA~~g  226 (413)
T PLN00020        222 -DAGAG  226 (413)
T ss_pred             -hhcCC
Confidence             98773

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.23  E-value=0.53  Score=41.17  Aligned_cols=79  Identities=15%  Similarity=0.109  Sum_probs=39.7

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhh-----ch--HHHHHHHhc--CCcEEEECh------HHHHHHHHc--CCCC
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYY-----SA--RKELRELAR--WVDNLMATL------RRLVNLLER--GRVS  129 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~-----~~--~~~~~~l~~--~~~IlI~TP------~~l~~~l~~--~~~~  129 (155)
                      +.++++||.|+|||....+- ...+.....     .+  ....+.+..  .++++--.+      +.+.+++..  ..-.
T Consensus        39 ~a~Lf~Gp~G~GKTtlA~~l-A~~l~c~~~~~~~~~c~~c~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~  117 (585)
T PRK14950         39 HAYLFTGPRGVGKTSTARIL-AKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPA  117 (585)
T ss_pred             eEEEEECCCCCCHHHHHHHH-HHHhcCCCCCCCCCCCccCHHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcc
Confidence            35689999999999875432 222221110     00  122233333  345543233      122222221  1112


Q ss_pred             cccccceEEEEcccccccc
Q 031654          130 LQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       130 l~~l~~~lVlDEa~D~ll~  148 (155)
                      ...- +.+||||+ |.|-+
T Consensus       118 ~~~~-kVvIIDEa-~~L~~  134 (585)
T PRK14950        118 LARY-KVYIIDEV-HMLST  134 (585)
T ss_pred             cCCe-EEEEEeCh-HhCCH
Confidence            3566 89999999 88754

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=91.19  E-value=0.62  Score=35.42  Aligned_cols=20  Identities=20%  Similarity=0.140  Sum_probs=16.2

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..|.-+++.|++|+|||...
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~   30 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFA   30 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHH
Confidence            45677899999999999643

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=91.12  E-value=0.25  Score=37.16  Aligned_cols=88  Identities=11%  Similarity=-0.025  Sum_probs=48.2

Q ss_pred             hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhcCCcEEEEChHH-----------HHHH
Q 031654           64 VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELARWVDNLMATLRR-----------LVNL  122 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~~~~IlI~TP~~-----------l~~~  122 (155)
                      +....+++..++|.|||.+.+--++..+.......          ......+..-+.|-+-..++           -...
T Consensus        20 ~~~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~   99 (191)
T PRK05986         20 EEKGLLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAA   99 (191)
T ss_pred             ccCCeEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHH
Confidence            45679999999999999987655555444333222          22333333211122211111           0011


Q ss_pred             ----HHc--CCCCcccccceEEEEccccccccccccc
Q 031654          123 ----LER--GRVSLQMIIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       123 ----l~~--~~~~l~~l~~~lVlDEa~D~ll~~gf~~  153 (155)
                          +..  ..+.-... ++|||||+ -..++.|+.+
T Consensus       100 ~~~~~~~a~~~l~~~~y-dlvVLDEi-~~Al~~gli~  134 (191)
T PRK05986        100 AREGWEEAKRMLADESY-DLVVLDEL-TYALKYGYLD  134 (191)
T ss_pred             HHHHHHHHHHHHhCCCC-CEEEEehh-hHHHHCCCcc
Confidence                111  11223567 89999999 8888888754

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=91.10  E-value=0.52  Score=41.07  Aligned_cols=80  Identities=8%  Similarity=0.043  Sum_probs=40.7

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHH-Hhhh---ch--HHHHHHHhc--CCcEEEEChH------HHHHHHHcCC--CCc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIM-REYY---SA--RKELRELAR--WVDNLMATLR------RLVNLLERGR--VSL  130 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~-~~~~---~~--~~~~~~l~~--~~~IlI~TP~------~l~~~l~~~~--~~l  130 (155)
                      +-.+.+||.|+|||.+.-+-+ ..+. ....   .+  ......+..  .+|++.-.+.      .+.++...-.  -..
T Consensus        39 hayLf~Gp~GtGKTt~Ak~lA-kal~c~~~~~~~pC~~C~~C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~  117 (559)
T PRK05563         39 HAYLFSGPRGTGKTSAAKIFA-KAVNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSE  117 (559)
T ss_pred             eEEEEECCCCCCHHHHHHHHH-HHhcCCCCCCCCCCCccHHHHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCccc
Confidence            347889999999998754322 1121 1100   00  122233322  4566554441      1222322211  123


Q ss_pred             ccccceEEEEccccccccc
Q 031654          131 QMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       131 ~~l~~~lVlDEa~D~ll~~  149 (155)
                      ..- +.+||||+ |.|-..
T Consensus       118 ~~~-kViIIDE~-~~Lt~~  134 (559)
T PRK05563        118 AKY-KVYIIDEV-HMLSTG  134 (559)
T ss_pred             CCe-EEEEEECc-ccCCHH
Confidence            456 78999999 887543

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.10  E-value=0.5  Score=39.25  Aligned_cols=18  Identities=22%  Similarity=0.146  Sum_probs=14.9

Q ss_pred             cEEEEccCCCCcchhhhh
Q 031654           68 DLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yll   85 (155)
                      -++.++|.|+|||.+..+
T Consensus        40 a~lf~Gp~G~GKtt~A~~   57 (397)
T PRK14955         40 GYIFSGLRGVGKTTAARV   57 (397)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            488999999999987543

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=91.10  E-value=0.29  Score=37.03  Aligned_cols=78  Identities=10%  Similarity=-0.049  Sum_probs=43.5

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhhch--------HHHHHHHh-----cCCcEEEEChHHHHHHHHcCCCCccccc
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYYSA--------RKELRELA-----RWVDNLMATLRRLVNLLERGRVSLQMII  134 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------~~~~~~l~-----~~~~IlI~TP~~l~~~l~~~~~~l~~l~  134 (155)
                      =.++++|-.||||..-+--+-+.........        .-....+.     ..+-++|-.+..+.+.+....-++. + 
T Consensus         6 l~~i~gpM~SGKT~eLl~r~~~~~~~g~~v~vfkp~iD~R~~~~~V~Sr~G~~~~A~~i~~~~~i~~~i~~~~~~~~-~-   83 (201)
T COG1435           6 LEFIYGPMFSGKTEELLRRARRYKEAGMKVLVFKPAIDTRYGVGKVSSRIGLSSEAVVIPSDTDIFDEIAALHEKPP-V-   83 (201)
T ss_pred             EEEEEccCcCcchHHHHHHHHHHHHcCCeEEEEecccccccccceeeeccCCcccceecCChHHHHHHHHhcccCCC-c-
Confidence            3578999999999954333222221111111        00111111     1345677777777777776543333 6 


Q ss_pred             ceEEEEccccccccc
Q 031654          135 RYLALKEAADQTLDM  149 (155)
Q Consensus       135 ~~lVlDEa~D~ll~~  149 (155)
                      ..+.+|||  +.++.
T Consensus        84 ~~v~IDEa--QF~~~   96 (201)
T COG1435          84 DCVLIDEA--QFFDE   96 (201)
T ss_pred             CEEEEehh--HhCCH
Confidence            78999999  55543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=91.06  E-value=0.18  Score=46.10  Aligned_cols=16  Identities=19%  Similarity=0.221  Sum_probs=13.8

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      .++.++|||+|||...
T Consensus       598 ~~lf~Gp~GvGKT~lA  613 (852)
T TIGR03345       598 VFLLVGPSGVGKTETA  613 (852)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3799999999999764

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=90.96  E-value=0.053  Score=41.66  Aligned_cols=73  Identities=11%  Similarity=0.121  Sum_probs=40.8

Q ss_pred             CcEEEEccCCCCcchhh-hhHHHHHHHHhhhch---HHHHHHHhc--CCcEEEE----ChHHHHHHHHcCCCCcccccce
Q 031654           67 RDLMACAQTGSRKTTPF-CFPIINGIMREYYSA---RKELRELAR--WVDNLMA----TLRRLVNLLERGRVSLQMIIRY  136 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y-llp~l~~l~~~~~~~---~~~~~~l~~--~~~IlI~----TP~~l~~~l~~~~~~l~~l~~~  136 (155)
                      ..+++++++|+|||... .+|       .....   ..-...+..  ..+++=.    +.+.+.+.+..-....... +.
T Consensus        13 ~~~liyG~~G~GKtt~a~~~~-------~~~~~~~~d~~~~~l~g~~~~~v~~~d~~~~~~~~~d~l~~~~~~~~~y-dt   84 (220)
T TIGR01618        13 NMYLIYGKPGTGKTSTIKYLP-------GKTLVLSFDMSSKVLIGDENVDIADHDDMPPIQAMVEFYVMQNIQAVKY-DN   84 (220)
T ss_pred             cEEEEECCCCCCHHHHHHhcC-------CCCEEEeccccchhccCCCCCceeecCCCCCHHHHHHHHHHHHhccccC-CE
Confidence            45899999999999864 222       10000   111122221  2333321    1245555555433446778 99


Q ss_pred             EEEEcccccccc
Q 031654          137 LALKEAADQTLD  148 (155)
Q Consensus       137 lVlDEa~D~ll~  148 (155)
                      ||||.+ +.|-.
T Consensus        85 VVIDsI-~~l~~   95 (220)
T TIGR01618        85 IVIDNI-SALQN   95 (220)
T ss_pred             EEEecH-HHHHH
Confidence            999999 88755

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>PF13337 Lon_2: Putative ATP-dependent Lon protease

Probab=90.95  E-value=0.29  Score=41.44  Aligned_cols=87  Identities=15%  Similarity=0.257  Sum_probs=54.9

Q ss_pred             HHHHHh-HHhCCCC--CCCHHHHH-----HHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCC
Q 031654           38 QHLRNK-PRTYKYV--KPTPVQRH-----ATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWV  109 (155)
Q Consensus        38 ~~l~~~-l~~~g~~--~pt~iQ~~-----~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~  109 (155)
                      ++.+.. |.++||+  ..+.-|+.     .+|.+-..-|++=-||-|||||..|                   ..+... 
T Consensus       172 eEWiD~LlrS~G~eP~~~~~r~Kl~~L~RLiPlVE~N~NliELgPrGTGKS~vy-------------------~eiSp~-  231 (457)
T PF13337_consen  172 EEWIDLLLRSIGYEPSGFSERQKLLLLARLIPLVERNYNLIELGPRGTGKSYVY-------------------KEISPY-  231 (457)
T ss_pred             HHHHHHHHHhcCCCccccCHHHHHHHHHhHHHhcccccceEEEcCCCCCceeeh-------------------hhcCcc-
Confidence            444444 5788987  23444443     4577777889999999999999987                   233332 


Q ss_pred             cEEE----EChHHHHHHHHcCCCC-cccccceEEEEcccccc
Q 031654          110 DNLM----ATLRRLVNLLERGRVS-LQMIIRYLALKEAADQT  146 (155)
Q Consensus       110 ~IlI----~TP~~l~~~l~~~~~~-l~~l~~~lVlDEa~D~l  146 (155)
                      -++|    +|+.+|..-..++..- ...- +.|++||+ ..+
T Consensus       232 ~~liSGG~~T~A~LFyn~~~~~~GlV~~~-D~VafDEv-~~i  271 (457)
T PF13337_consen  232 GILISGGQVTVAKLFYNMSTGQIGLVGRW-DVVAFDEV-AGI  271 (457)
T ss_pred             cEEEECCCcchHHheeeccCCcceeeeec-cEEEEEec-cCc
Confidence            3333    4666665555554332 2334 67999999 443

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=90.91  E-value=0.35  Score=43.61  Aligned_cols=18  Identities=17%  Similarity=0.195  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ..++++.+|+|+|||...
T Consensus       207 ~~n~LLvGppGvGKT~la  224 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIA  224 (758)
T ss_pred             CCCeEEECCCCCCHHHHH
Confidence            469999999999999863

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=90.90  E-value=0.23  Score=45.00  Aligned_cols=77  Identities=17%  Similarity=0.112  Sum_probs=41.2

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc-h----HHHHHHHhcCCc-EEEEChHHHHHHHHcCCCCcccccceEE
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-A----RKELRELARWVD-NLMATLRRLVNLLERGRVSLQMIIRYLA  138 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~-~----~~~~~~l~~~~~-IlI~TP~~l~~~l~~~~~~l~~l~~~lV  138 (155)
                      .|..+++.+|+|+|||...-  .+......... .    ......+...-. .+=+.||++.+.+.....   .- ..++
T Consensus       348 ~g~~i~l~GppG~GKTtl~~--~ia~~l~~~~~~i~~~~~~d~~~i~g~~~~~~g~~~G~~~~~l~~~~~---~~-~vil  421 (784)
T PRK10787        348 KGPILCLVGPPGVGKTSLGQ--SIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKVGV---KN-PLFL  421 (784)
T ss_pred             CCceEEEECCCCCCHHHHHH--HHHHHhCCCEEEEEcCCCCCHHHhccchhccCCCCCcHHHHHHHhcCC---CC-CEEE
Confidence            46679999999999996532  11211111100 0    111122221111 122468888877765321   22 4689


Q ss_pred             EEcccccccc
Q 031654          139 LKEAADQTLD  148 (155)
Q Consensus       139 lDEa~D~ll~  148 (155)
                      +||+ |++-.
T Consensus       422 lDEi-dk~~~  430 (784)
T PRK10787        422 LDEI-DKMSS  430 (784)
T ss_pred             EECh-hhccc
Confidence            9999 99864

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=90.88  E-value=0.21  Score=42.28  Aligned_cols=41  Identities=22%  Similarity=0.142  Sum_probs=33.6

Q ss_pred             CCcEEEEChHHHHHHHHc------CCCCcccccceEEEEcccccccccc
Q 031654          108 WVDNLMATLRRLVNLLER------GRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       108 ~~~IlI~TP~~l~~~l~~------~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                      .+|||||+|-.|.-.+..      ..-.|+.+ +.+|+|.| |.|+-+.
T Consensus       131 ~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSI-Ev~iiD~a-d~l~MQN  177 (442)
T PF06862_consen  131 SSDIIIASPLGLRMIIGEEGEKKRDYDFLSSI-EVLIIDQA-DVLLMQN  177 (442)
T ss_pred             cCCEEEEChHHHHHHhccccccccccchhhee-eeEeechh-hHHHHhh
Confidence            589999999998887774      12348999 99999999 9988654

; GO: 0005634 nucleus

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=90.88  E-value=0.6  Score=40.50  Aligned_cols=71  Identities=23%  Similarity=0.229  Sum_probs=45.2

Q ss_pred             CCCHHHHHHHHHHhcC-----CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHc
Q 031654           51 KPTPVQRHATSILVAG-----RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLER  125 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g-----~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~  125 (155)
                      .|+.-|-.||..+..|     +.-+.-+-||||||.+-.--               +..+ +.|-+|++-...|..-|-.
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnV---------------I~~~-~rPtLV~AhNKTLAaQLy~   75 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANV---------------IAKV-QRPTLVLAHNKTLAAQLYS   75 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHH---------------HHHh-CCCeEEEecchhHHHHHHH
Confidence            5677788888777654     57788899999999874211               1222 4577777777666555543


Q ss_pred             C---CCCcccccceEE
Q 031654          126 G---RVSLQMIIRYLA  138 (155)
Q Consensus       126 ~---~~~l~~l~~~lV  138 (155)
                      .   .+.=+.| .|+|
T Consensus        76 Efk~fFP~NaV-EYFV   90 (663)
T COG0556          76 EFKEFFPENAV-EYFV   90 (663)
T ss_pred             HHHHhCcCcce-EEEe
Confidence            2   2333455 6666

>PRK13531 regulatory ATPase RavA; Provisional

Probab=90.88  E-value=0.28  Score=42.01  Aligned_cols=45  Identities=13%  Similarity=0.160  Sum_probs=30.7

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..+.+.|.+.=+.+-.-+ ..+.-.++.|.++++.+|+|+|||...
T Consensus        12 ~~l~~~l~~~i~gre~vI-~lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         12 SRLSSALEKGLYERSHAI-RLCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             HHHHHHHhhhccCcHHHH-HHHHHHHccCCCEEEECCCChhHHHHH
Confidence            345555655444443333 334456789999999999999999864

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=90.87  E-value=0.13  Score=45.43  Aligned_cols=22  Identities=27%  Similarity=0.298  Sum_probs=20.3

Q ss_pred             CcEEEEccCCCCcchhhhhHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPII   88 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l   88 (155)
                      .++++.||||||||.++++|-+
T Consensus       225 ~H~Lv~ApTgsGKt~g~VIPnL  246 (641)
T PRK13822        225 THGLVFAGSGGFKTTSVVVPTA  246 (641)
T ss_pred             ceEEEEeCCCCCccceEehhhh
Confidence            6899999999999999999964

>PHA01747 putative ATP-dependent protease

Probab=90.81  E-value=0.39  Score=39.89  Aligned_cols=61  Identities=18%  Similarity=0.193  Sum_probs=36.7

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhc-CCcEEE---EChHHHHHHHHcCCCC-cccccceEEE
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELAR-WVDNLM---ATLRRLVNLLERGRVS-LQMIIRYLAL  139 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~-~~~IlI---~TP~~l~~~l~~~~~~-l~~l~~~lVl  139 (155)
                      ..-|++=-+|.|||||..|.-                   +.. .+..+.   +|+.+|..-...+.+- ...- +.|++
T Consensus       189 ~NyNliELgPRGTGKS~~f~e-------------------is~fsp~~iSGG~~TvA~LFyN~~t~~~GLVg~~-D~VaF  248 (425)
T PHA01747        189 RPVHIIELSNRGTGKTTTFVI-------------------LQELFNFRYYTEPPTYANLVYDAKTNALGLVFLS-NGLIF  248 (425)
T ss_pred             CCeeEEEecCCCCChhhHHHH-------------------hhhcCCceeeCCCCchHHheEecCCCceeEEeec-cEEEE
Confidence            456888889999999998731                   111 122222   3666665555544332 2233 56999


Q ss_pred             Ecccccc
Q 031654          140 KEAADQT  146 (155)
Q Consensus       140 DEa~D~l  146 (155)
                      ||+ +.+
T Consensus       249 DEV-a~i  254 (425)
T PHA01747        249 DEI-QTW  254 (425)
T ss_pred             Ecc-ccc
Confidence            999 554

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=90.79  E-value=0.81  Score=39.23  Aligned_cols=19  Identities=32%  Similarity=0.281  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCcchhhh
Q 031654           66 GRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl   84 (155)
                      |+-+.+++|||+|||.+..
T Consensus       256 g~Vi~LvGpnGvGKTTTia  274 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTA  274 (484)
T ss_pred             CcEEEEECCCCccHHHHHH
Confidence            4568899999999998854

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.78  E-value=0.19  Score=45.97  Aligned_cols=17  Identities=18%  Similarity=0.145  Sum_probs=14.1

Q ss_pred             EEEEccCCCCcchhhhh
Q 031654           69 LMACAQTGSRKTTPFCF   85 (155)
Q Consensus        69 vl~~a~TGsGKT~~yll   85 (155)
                      ++++||.|+|||....+
T Consensus        41 yLFtGPpGtGKTTLARi   57 (944)
T PRK14949         41 YLFTGTRGVGKTSLARL   57 (944)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            58999999999987543

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=90.75  E-value=0.15  Score=41.57  Aligned_cols=26  Identities=27%  Similarity=0.337  Sum_probs=19.0

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      .+..+++++|||||||... -.++..+
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i  146 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYI  146 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhh
Confidence            4678999999999999864 2334434

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.72  E-value=0.61  Score=41.49  Aligned_cols=80  Identities=14%  Similarity=0.125  Sum_probs=41.1

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhh----h-------chHHHHHHHhc--CCcEEEEChH------HHHHHHHcCCC
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREY----Y-------SARKELRELAR--WVDNLMATLR------RLVNLLERGRV  128 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~----~-------~~~~~~~~l~~--~~~IlI~TP~------~l~~~l~~~~~  128 (155)
                      -++++++.|+|||....+- ...+....    .       ........+..  .+|++--.+.      .+.+++..-..
T Consensus        40 A~LFtGP~GvGKTTLAriL-AkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~  118 (700)
T PRK12323         40 AYLFTGTRGVGKTTLSRIL-AKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVY  118 (700)
T ss_pred             EEEEECCCCCCHHHHHHHH-HHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHh
Confidence            4699999999999765432 22222110    0       00122222222  3466654442      23333332111


Q ss_pred             --CcccccceEEEEcccccccccc
Q 031654          129 --SLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       129 --~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                        ...+- +.+||||+ |+|-...
T Consensus       119 ~P~~gr~-KViIIDEa-h~Ls~~A  140 (700)
T PRK12323        119 APTAGRF-KVYMIDEV-HMLTNHA  140 (700)
T ss_pred             chhcCCc-eEEEEECh-HhcCHHH
Confidence              23456 89999999 8875443

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=90.71  E-value=0.13  Score=34.76  Aligned_cols=14  Identities=29%  Similarity=0.423  Sum_probs=12.5

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      +++.|++|||||..
T Consensus         2 I~I~G~~gsGKST~   15 (121)
T PF13207_consen    2 IIISGPPGSGKSTL   15 (121)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67899999999985

...

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

Probab=90.56  E-value=0.13  Score=35.72  Aligned_cols=16  Identities=25%  Similarity=0.289  Sum_probs=13.9

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      +|++.+|+|+|||...
T Consensus         1 ~vlL~G~~G~GKt~l~   16 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLA   16 (139)
T ss_dssp             EEEEEESSSSSHHHHH
T ss_pred             CEEEECCCCCCHHHHH
Confidence            5899999999999853

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.50  E-value=0.61  Score=41.19  Aligned_cols=79  Identities=13%  Similarity=0.098  Sum_probs=40.2

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhh--------hchHHHHHHHhc--CCcEEEEChH------HHHHHHHcCCC--
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREY--------YSARKELRELAR--WVDNLMATLR------RLVNLLERGRV--  128 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~--------~~~~~~~~~l~~--~~~IlI~TP~------~l~~~l~~~~~--  128 (155)
                      ..++++||.|+|||.....- ...+....        .......+.+..  .+|++...+.      .+.+++..-..  
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~l-Ak~L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p  117 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARIL-AKSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAP  117 (620)
T ss_pred             ceEEEECCCCCChHHHHHHH-HHHhcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhCh
Confidence            46799999999999865332 22222110        000222233332  2445433332      23333322111  


Q ss_pred             CcccccceEEEEcccccccc
Q 031654          129 SLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       129 ~l~~l~~~lVlDEa~D~ll~  148 (155)
                      ....- +.+||||| |.|=.
T Consensus       118 ~~~~~-KViIIDEa-d~Lt~  135 (620)
T PRK14948        118 VQARW-KVYVIDEC-HMLST  135 (620)
T ss_pred             hcCCc-eEEEEECc-cccCH
Confidence            13556 88999999 98743

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=90.41  E-value=0.14  Score=35.54  Aligned_cols=14  Identities=36%  Similarity=0.684  Sum_probs=12.5

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      ++++|++|||||..
T Consensus         2 ii~~G~pgsGKSt~   15 (143)
T PF13671_consen    2 IILCGPPGSGKSTL   15 (143)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            68999999999975

...

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.39  E-value=0.68  Score=39.66  Aligned_cols=17  Identities=24%  Similarity=0.198  Sum_probs=13.7

Q ss_pred             EEEEccCCCCcchhhhh
Q 031654           69 LMACAQTGSRKTTPFCF   85 (155)
Q Consensus        69 vl~~a~TGsGKT~~yll   85 (155)
                      .+++||.|+|||.+..+
T Consensus        41 yLf~Gp~G~GKTtlAr~   57 (486)
T PRK14953         41 YIFAGPRGTGKTTIARI   57 (486)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            57899999999876543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.38  E-value=0.43  Score=42.09  Aligned_cols=80  Identities=15%  Similarity=0.157  Sum_probs=40.7

Q ss_pred             EEEEccCCCCcchhhhhHHHHHHHHhh-----------hchHHHHHHHhc--CCcEEEEChH------HHHHHHHcC--C
Q 031654           69 LMACAQTGSRKTTPFCFPIINGIMREY-----------YSARKELRELAR--WVDNLMATLR------RLVNLLERG--R  127 (155)
Q Consensus        69 vl~~a~TGsGKT~~yllp~l~~l~~~~-----------~~~~~~~~~l~~--~~~IlI~TP~------~l~~~l~~~--~  127 (155)
                      ++++||.|+|||....+- ...+....           .......+.+..  .+|++.-.+.      .+.+++..-  .
T Consensus        41 ~Lf~Gp~GvGKTtlAr~l-Ak~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~  119 (618)
T PRK14951         41 YLFTGTRGVGKTTVSRIL-AKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYK  119 (618)
T ss_pred             EEEECCCCCCHHHHHHHH-HHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhC
Confidence            589999999999876442 22222110           000122222222  3455544332      223333221  1


Q ss_pred             CCcccccceEEEEccccccccccc
Q 031654          128 VSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       128 ~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      -...+. +.+||||+ |.|-...|
T Consensus       120 p~~g~~-KV~IIDEv-h~Ls~~a~  141 (618)
T PRK14951        120 PVQGRF-KVFMIDEV-HMLTNTAF  141 (618)
T ss_pred             cccCCc-eEEEEECh-hhCCHHHH
Confidence            123457 89999999 88765444

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=90.36  E-value=0.23  Score=43.09  Aligned_cols=66  Identities=12%  Similarity=0.133  Sum_probs=43.7

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcC--------C--CCcccccce
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERG--------R--VSLQMIIRY  136 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~--------~--~~l~~l~~~  136 (155)
                      ..+++.+|.|||||.-.+                ++..-..=|-|=|++|+.+.-+-+..        .  ---+.+ ..
T Consensus       539 vSvLl~Gp~~sGKTaLAA----------------~iA~~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~l-si  601 (744)
T KOG0741|consen  539 VSVLLEGPPGSGKTALAA----------------KIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPL-SI  601 (744)
T ss_pred             eEEEEecCCCCChHHHHH----------------HHHhhcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcc-eE
Confidence            479999999999997432                22222334667788887764332221        1  113566 88


Q ss_pred             EEEEcccccccccc
Q 031654          137 LALKEAADQTLDMA  150 (155)
Q Consensus       137 lVlDEa~D~ll~~g  150 (155)
                      +|+|+. .+|+|+.
T Consensus       602 ivvDdi-ErLiD~v  614 (744)
T KOG0741|consen  602 IVVDDI-ERLLDYV  614 (744)
T ss_pred             EEEcch-hhhhccc
Confidence            999999 9999974

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=90.27  E-value=0.15  Score=44.05  Aligned_cols=20  Identities=25%  Similarity=0.393  Sum_probs=16.8

Q ss_pred             HhcCCcEEEEccCCCCcchh
Q 031654           63 LVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~   82 (155)
                      +..|.-+-+++|||||||..
T Consensus       352 i~~Ge~vaiVG~sGsGKSTl  371 (567)
T COG1132         352 IEPGEKVAIVGPSGSGKSTL  371 (567)
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            56788888999999999764

>KOG2373 consensus Predicted mitochondrial DNA helicase twinkle [Replication, recombination and repair]

Probab=90.17  E-value=0.12  Score=42.65  Aligned_cols=52  Identities=17%  Similarity=0.080  Sum_probs=30.3

Q ss_pred             CCcccccCCHHHHHhHHhCCCCCCCHHHHHHHH---HHhcC----CcEEEEccCCCCcchh
Q 031654           29 PAARFAYVPQHLRNKPRTYKYVKPTPVQRHATS---ILVAG----RDLMACAQTGSRKTTP   82 (155)
Q Consensus        29 ~~~~f~~l~~~l~~~l~~~g~~~pt~iQ~~~i~---~~l~g----~dvl~~a~TGsGKT~~   82 (155)
                      .+.+|.++.+.++..|.+  .++-.-+|..-+|   .++.|    .=.+..+|||||||.-
T Consensus       231 ~i~sf~~mRe~ilseL~N--~e~v~G~~WkRFpvLNk~LkGhR~GElTvlTGpTGsGKTTF  289 (514)
T KOG2373|consen  231 GIRSFTDMREGILSELLN--TERVVGFQWKRFPVLNKYLKGHRPGELTVLTGPTGSGKTTF  289 (514)
T ss_pred             hhhhHHHHHHHHHHHHhh--hhhhhceeehhhhHHHHHhccCCCCceEEEecCCCCCceeE
Confidence            355666666555544432  2222333444444   33444    5689999999999975

>TIGR00602 rad24 checkpoint protein rad24

Probab=90.16  E-value=0.54  Score=41.64  Aligned_cols=16  Identities=25%  Similarity=0.366  Sum_probs=14.0

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      =+++.+|+|+|||...
T Consensus       112 illL~GP~GsGKTTl~  127 (637)
T TIGR00602       112 ILLITGPSGCGKSTTI  127 (637)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3899999999999864

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

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=90.16  E-value=0.39  Score=38.57  Aligned_cols=60  Identities=20%  Similarity=0.181  Sum_probs=37.1

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCC----cEEEEChHHHHHHHHcCCCCcccccceEEEEcc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWV----DNLMATLRRLVNLLERGRVSLQMIIRYLALKEA  142 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~----~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa  142 (155)
                      -+++..+|+|.|||.-..      +..         .++..++    -=++--|+-|..++.    ++..= +.|-+||.
T Consensus        53 DHvLl~GPPGlGKTTLA~------IIA---------~Emgvn~k~tsGp~leK~gDlaaiLt----~Le~~-DVLFIDEI  112 (332)
T COG2255          53 DHVLLFGPPGLGKTTLAH------IIA---------NELGVNLKITSGPALEKPGDLAAILT----NLEEG-DVLFIDEI  112 (332)
T ss_pred             CeEEeeCCCCCcHHHHHH------HHH---------HHhcCCeEecccccccChhhHHHHHh----cCCcC-CeEEEehh
Confidence            379999999999997432      222         1221111    113445777777776    34444 66889999


Q ss_pred             ccccc
Q 031654          143 ADQTL  147 (155)
Q Consensus       143 ~D~ll  147 (155)
                       |+|-
T Consensus       113 -Hrl~  116 (332)
T COG2255         113 -HRLS  116 (332)
T ss_pred             -hhcC
Confidence             8863

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=90.11  E-value=0.16  Score=34.49  Aligned_cols=14  Identities=29%  Similarity=0.394  Sum_probs=12.6

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      +++.||+|+|||..
T Consensus         1 ill~G~~G~GKT~l   14 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL   14 (132)
T ss_dssp             EEEESSTTSSHHHH
T ss_pred             CEEECcCCCCeeHH
Confidence            68899999999985

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>cd01394 radB RadB

Probab=90.07  E-value=0.42  Score=35.93  Aligned_cols=20  Identities=20%  Similarity=0.101  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCcchhhhh
Q 031654           66 GRDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yll   85 (155)
                      |.=+++.+++|||||...+-
T Consensus        19 g~i~~i~G~~GsGKT~l~~~   38 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQ   38 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            35588999999999986443

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=90.03  E-value=0.37  Score=41.10  Aligned_cols=18  Identities=28%  Similarity=0.377  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      +..+.|++.+|+|||.+-
T Consensus       175 ~gSlYVsG~PGtgkt~~l  192 (529)
T KOG2227|consen  175 SGSLYVSGQPGTGKTALL  192 (529)
T ss_pred             CcceEeeCCCCcchHHHH
Confidence            468999999999999873

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=90.02  E-value=0.25  Score=40.88  Aligned_cols=32  Identities=22%  Similarity=0.206  Sum_probs=21.6

Q ss_pred             HHhcCCcEEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           62 ILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      .-...+++++.+.||||||. ++-+++..+...
T Consensus        11 ~~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~   42 (386)
T PF10412_consen   11 KDSENRHILIIGATGSGKTQ-AIRHLLDQIRAR   42 (386)
T ss_dssp             GGGGGG-EEEEE-TTSSHHH-HHHHHHHHHHHT
T ss_pred             cchhhCcEEEECCCCCCHHH-HHHHHHHHHHHc
Confidence            33456899999999999997 445666666544

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=89.97  E-value=1.1  Score=40.36  Aligned_cols=78  Identities=10%  Similarity=0.101  Sum_probs=38.5

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHH-hhh----chHHHHHHHhcCCcEEEECh------HHHHHHHHcC-CC-Cccccc
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMR-EYY----SARKELRELARWVDNLMATL------RRLVNLLERG-RV-SLQMII  134 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~-~~~----~~~~~~~~l~~~~~IlI~TP------~~l~~~l~~~-~~-~l~~l~  134 (155)
                      -.+.+||.|+|||.+..+-+ ..+.. ...    .+..-.......++++-.-+      +.+.+++..- .. ....- 
T Consensus        42 AYLF~GP~GtGKTt~AriLA-k~LnC~~~~~~~~pC~~C~~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~-  119 (725)
T PRK07133         42 AYLFSGPRGTGKTSVAKIFA-NALNCSHKTDLLEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKY-  119 (725)
T ss_pred             EEEEECCCCCcHHHHHHHHH-HHhcccccCCCCCchhHHHHhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCC-
Confidence            36899999999998764322 22211 110    11111111233566664332      2222332211 11 23456 


Q ss_pred             ceEEEEcccccccc
Q 031654          135 RYLALKEAADQTLD  148 (155)
Q Consensus       135 ~~lVlDEa~D~ll~  148 (155)
                      +.+||||| |.|-.
T Consensus       120 KV~IIDEa-~~LT~  132 (725)
T PRK07133        120 KIYIIDEV-HMLSK  132 (725)
T ss_pred             EEEEEECh-hhCCH
Confidence            78999999 87743

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.92  E-value=0.11  Score=42.51  Aligned_cols=17  Identities=35%  Similarity=0.485  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +.++++||+|+|||...
T Consensus        40 ~~~L~~G~~G~GKt~~a   56 (367)
T PRK14970         40 QALLFCGPRGVGKTTCA   56 (367)
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            47889999999999654

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=89.92  E-value=0.48  Score=35.67  Aligned_cols=20  Identities=30%  Similarity=0.150  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCCCcchhhhh
Q 031654           66 GRDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yll   85 (155)
                      |.=+.+.+++|+|||...+-
T Consensus        19 g~v~~I~G~~GsGKT~l~~~   38 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQ   38 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHH
Confidence            45688899999999986543

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=89.90  E-value=0.16  Score=38.13  Aligned_cols=15  Identities=33%  Similarity=0.392  Sum_probs=13.2

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      +++++|||+|||.+-
T Consensus         4 i~lvGptGvGKTTt~   18 (196)
T PF00448_consen    4 IALVGPTGVGKTTTI   18 (196)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCchHhHH
Confidence            678999999999874

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=89.85  E-value=0.77  Score=37.06  Aligned_cols=48  Identities=17%  Similarity=0.210  Sum_probs=26.0

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhc--h-HHHHHHHhcCCcEEEECh
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYS--A-RKELRELARWVDNLMATL  116 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~--~-~~~~~~l~~~~~IlI~TP  116 (155)
                      .-.+++||.|+||+... ..+...+......  + .... .-.+.||+.+..|
T Consensus        27 ha~Lf~G~~G~Gk~~~A-~~~a~~llc~~~c~~c~~~~~-~~~~hPDl~~i~p   77 (314)
T PRK07399         27 PAYLFAGPEGVGRKLAA-LCFIEGLLSQGSPSKNIRRRL-EEGNHPDLLWVEP   77 (314)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHcCCCCCCCcHhccc-ccCCCCCEEEEec
Confidence            47899999999998643 2333333322211  1 1111 1123577777666

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=89.80  E-value=0.8  Score=39.74  Aligned_cols=78  Identities=14%  Similarity=0.150  Sum_probs=39.9

Q ss_pred             EEEEccCCCCcchhhhhHHHHHHHHh-hhc---h--HHHHHHHhc--CCcEEEECh------HHHHHHHHcCC--CCccc
Q 031654           69 LMACAQTGSRKTTPFCFPIINGIMRE-YYS---A--RKELRELAR--WVDNLMATL------RRLVNLLERGR--VSLQM  132 (155)
Q Consensus        69 vl~~a~TGsGKT~~yllp~l~~l~~~-~~~---~--~~~~~~l~~--~~~IlI~TP------~~l~~~l~~~~--~~l~~  132 (155)
                      .+++||.|+|||.+... +...+... ...   +  ......+..  .++++-...      ..+.+.+....  -....
T Consensus        39 yLf~Gp~G~GKTt~Ar~-LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eldaas~~gId~IRelie~~~~~P~~~~  117 (535)
T PRK08451         39 YLFSGLRGSGKTSSARI-FARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMDAASNRGIDDIRELIEQTKYKPSMAR  117 (535)
T ss_pred             EEEECCCCCcHHHHHHH-HHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEeccccccCHHHHHHHHHHHhhCcccCC
Confidence            48999999999986543 22222211 110   0  111222222  344544332      23444443211  12356


Q ss_pred             ccceEEEEccccccccc
Q 031654          133 IIRYLALKEAADQTLDM  149 (155)
Q Consensus       133 l~~~lVlDEa~D~ll~~  149 (155)
                      - +.+||||| |.|-..
T Consensus       118 ~-KVvIIDEa-d~Lt~~  132 (535)
T PRK08451        118 F-KIFIIDEV-HMLTKE  132 (535)
T ss_pred             e-EEEEEECc-ccCCHH
Confidence            7 89999999 888653

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=89.75  E-value=0.18  Score=34.07  Aligned_cols=14  Identities=36%  Similarity=0.256  Sum_probs=12.6

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      |++.|++|||||..
T Consensus         1 I~i~G~~GsGKtTi   14 (129)
T PF13238_consen    1 IGISGIPGSGKTTI   14 (129)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             CEEECCCCCCHHHH
Confidence            67899999999986

...

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=89.75  E-value=0.71  Score=41.58  Aligned_cols=65  Identities=15%  Similarity=0.153  Sum_probs=36.9

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEE
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALK  140 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlD  140 (155)
                      +-+++++|+|||||+..-      ........      ..+.-++.    +-++ +.|+.+++....-+...   .+-+|
T Consensus       345 kGvLL~GPPGTGKTLLAK------AiAGEAgVPF~svSGSEFvE~~----~g~~-asrvr~lf~~ar~~aP~---iifid  410 (774)
T KOG0731|consen  345 KGVLLVGPPGTGKTLLAK------AIAGEAGVPFFSVSGSEFVEMF----VGVG-ASRVRDLFPLARKNAPS---IIFID  410 (774)
T ss_pred             CceEEECCCCCcHHHHHH------HHhcccCCceeeechHHHHHHh----cccc-hHHHHHHHHHhhccCCe---EEEec
Confidence            689999999999998531      22221111      22222221    1222 67777777665433333   46789


Q ss_pred             cccccc
Q 031654          141 EAADQT  146 (155)
Q Consensus       141 Ea~D~l  146 (155)
                      |. |.+
T Consensus       411 ei-da~  415 (774)
T KOG0731|consen  411 EI-DAV  415 (774)
T ss_pred             cc-ccc
Confidence            98 865

>CHL00095 clpC Clp protease ATP binding subunit

Probab=89.74  E-value=0.15  Score=46.33  Aligned_cols=16  Identities=25%  Similarity=0.243  Sum_probs=13.2

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      .++.++|||+|||...
T Consensus       541 ~~lf~Gp~GvGKt~lA  556 (821)
T CHL00095        541 SFLFSGPTGVGKTELT  556 (821)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            3789999999999643

>PHA00012 I assembly protein

Probab=89.73  E-value=0.76  Score=37.61  Aligned_cols=26  Identities=15%  Similarity=0.190  Sum_probs=18.8

Q ss_pred             EEEEccCCCCcchhhhhHHHHHHHHh
Q 031654           69 LMACAQTGSRKTTPFCFPIINGIMRE   94 (155)
Q Consensus        69 vl~~a~TGsGKT~~yllp~l~~l~~~   94 (155)
                      -++.+..|||||+..+.-++..+.+.
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~G   29 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVKG   29 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHcC
Confidence            47889999999998766555544443

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.67  E-value=1.2  Score=37.46  Aligned_cols=19  Identities=32%  Similarity=0.242  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCcchhhh
Q 031654           66 GRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl   84 (155)
                      |.-+.+++|||+|||....
T Consensus       191 g~vi~lvGpnG~GKTTtla  209 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTA  209 (420)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            4568899999999998764

>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup

Probab=89.61  E-value=0.31  Score=39.73  Aligned_cols=25  Identities=28%  Similarity=0.353  Sum_probs=19.6

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||.+.
T Consensus        80 ~v~~~l~G~n~ti~aYGqtGSGKTyTm  106 (345)
T cd01368          80 LVQDLLKGKNSLLFTYGVTNSGKTYTM  106 (345)
T ss_pred             HHHHHhCCCceEEEEeCCCCCCCeEEe
Confidence            3456678865  778899999999874

Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, a

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=89.56  E-value=1.3  Score=36.57  Aligned_cols=16  Identities=19%  Similarity=0.102  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      -+++.+|.|+||+...
T Consensus        43 A~Lf~Gp~G~GK~~lA   58 (365)
T PRK07471         43 AWLIGGPQGIGKATLA   58 (365)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4899999999998653

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.49  E-value=0.68  Score=40.60  Aligned_cols=17  Identities=18%  Similarity=0.208  Sum_probs=14.4

Q ss_pred             EEEEccCCCCcchhhhh
Q 031654           69 LMACAQTGSRKTTPFCF   85 (155)
Q Consensus        69 vl~~a~TGsGKT~~yll   85 (155)
                      ++++||.|+|||.+..+
T Consensus        38 ~Lf~Gp~G~GKTt~A~~   54 (584)
T PRK14952         38 YLFSGPRGCGKTSSARI   54 (584)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            58999999999987644

>cd01370 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup

Probab=89.38  E-value=0.37  Score=39.18  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=19.8

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||.+.
T Consensus        79 lv~~~~~G~n~~i~ayGqtGSGKTyTm  105 (338)
T cd01370          79 LVDGVLNGYNATVFAYGATGAGKTHTM  105 (338)
T ss_pred             HHHHHHCCCCceEEeeCCCCCCCeEEE
Confidence            4456678865  788899999999885

The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a sec

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=89.35  E-value=0.16  Score=42.96  Aligned_cols=19  Identities=16%  Similarity=0.202  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .++.+++.+|+|||||+..
T Consensus       216 ~p~gVLL~GPPGTGKT~LA  234 (438)
T PTZ00361        216 PPKGVILYGPPGTGKTLLA  234 (438)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4478999999999999864

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=89.25  E-value=0.42  Score=36.14  Aligned_cols=23  Identities=22%  Similarity=0.088  Sum_probs=17.0

Q ss_pred             CCcEEEEccCCCCcchhhhhHHH
Q 031654           66 GRDLMACAQTGSRKTTPFCFPII   88 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l   88 (155)
                      |.-+.+.+++|+|||...+--+.
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~   45 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAV   45 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999876543333

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=89.24  E-value=0.91  Score=40.37  Aligned_cols=33  Identities=33%  Similarity=0.356  Sum_probs=27.0

Q ss_pred             CCCHHHHHHHHHHhcC-----CcEEEEccCCCCcchhh
Q 031654           51 KPTPVQRHATSILVAG-----RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g-----~dvl~~a~TGsGKT~~y   83 (155)
                      .|+..|..+|..+.+|     +..++.+-||||||+..
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~   46 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTM   46 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHH
Confidence            6889999999887554     36678999999999874

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

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=89.23  E-value=0.42  Score=36.89  Aligned_cols=33  Identities=21%  Similarity=0.257  Sum_probs=23.2

Q ss_pred             CCCHHHHHHHHHHh----cC-CcEEEEccCCCCcchhh
Q 031654           51 KPTPVQRHATSILV----AG-RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l----~g-~dvl~~a~TGsGKT~~y   83 (155)
                      .+++.+.+++..+.    .+ ..+++.|++|+|||...
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~   60 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLI   60 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            45666666666553    23 36889999999999764

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=89.22  E-value=0.65  Score=41.22  Aligned_cols=16  Identities=25%  Similarity=0.140  Sum_probs=13.7

Q ss_pred             EEEEccCCCCcchhhh
Q 031654           69 LMACAQTGSRKTTPFC   84 (155)
Q Consensus        69 vl~~a~TGsGKT~~yl   84 (155)
                      +++.||.|+|||....
T Consensus        41 yLf~Gp~GvGKTTlAr   56 (647)
T PRK07994         41 YLFSGTRGVGKTTIAR   56 (647)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6899999999998653

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=89.19  E-value=0.64  Score=33.93  Aligned_cols=23  Identities=17%  Similarity=0.157  Sum_probs=17.7

Q ss_pred             CcccccceEEEEccccccccccccc
Q 031654          129 SLQMIIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       129 ~l~~l~~~lVlDEa~D~ll~~gf~~  153 (155)
                      ..... ++|||||+ -..++.|+.+
T Consensus        92 ~~~~~-dLlVLDEi-~~a~~~gli~  114 (159)
T cd00561          92 ASGEY-DLVILDEI-NYALGYGLLD  114 (159)
T ss_pred             hcCCC-CEEEEech-HhHhhCCCCC
Confidence            34577 89999999 7777877643

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>cd01367 KISc_KIF2_like Kinesin motor domain, KIF2-like group

Probab=89.18  E-value=0.33  Score=39.16  Aligned_cols=26  Identities=31%  Similarity=0.265  Sum_probs=19.9

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPFC   84 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~yl   84 (155)
                      .+..++.|.|  +++.++||||||.+-.
T Consensus        76 lv~~~~~G~n~~i~ayGqtGSGKTyTm~  103 (322)
T cd01367          76 LIPHVFEGGVATCFAYGQTGSGKTYTML  103 (322)
T ss_pred             HHHHHhCCCceEEEeccCCCCCCceEec
Confidence            4456678865  7778999999998753

KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and lo

>cd01365 KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like proteins

Probab=89.10  E-value=0.36  Score=39.50  Aligned_cols=25  Identities=32%  Similarity=0.364  Sum_probs=19.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||.+-
T Consensus        80 ~v~~~l~G~n~~i~ayGqtGSGKT~Tm  106 (356)
T cd01365          80 LLDHAFEGYNVCLFAYGQTGSGKSYTM  106 (356)
T ss_pred             HHHHHhCCCceEEEEecCCCCCCeEEe
Confidence            3456688865  788899999999864

KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.

>cd01373 KISc_KLP2_like Kinesin motor domain, KLP2-like subgroup

Probab=89.07  E-value=0.35  Score=39.27  Aligned_cols=25  Identities=32%  Similarity=0.387  Sum_probs=19.3

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||.+-
T Consensus        66 ~v~~~~~G~n~ti~aYGqTGSGKTyTm   92 (337)
T cd01373          66 LVEDCLSGYNGSIFAYGQTGSGKTYTM   92 (337)
T ss_pred             HHHHHhCCCceeEEEeCCCCCCceEEe
Confidence            3456688965  778899999999653

Members of this subgroup seem to play a role in mitosis and meiosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=89.05  E-value=0.48  Score=43.08  Aligned_cols=44  Identities=20%  Similarity=0.127  Sum_probs=38.3

Q ss_pred             HHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          104 ELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       104 ~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      .+.....|+++||.-|..-+-.+.++++.+ ..+|+||| |++...
T Consensus         3 ~ly~~ggi~~~T~rIl~~DlL~~ri~~~~i-tgiiv~~A-hr~~~~   46 (814)
T TIGR00596         3 KVYLEGGIFSITSRILVVDLLTGIIPPELI-TGILVLRA-DRIIES   46 (814)
T ss_pred             hHhhcCCEEEEechhhHhHHhcCCCCHHHc-cEEEEeec-cccccc
Confidence            344566899999999998888999999999 99999999 998754

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

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=88.90  E-value=0.21  Score=37.25  Aligned_cols=20  Identities=25%  Similarity=0.328  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCCcchhhhh
Q 031654           66 GRDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yll   85 (155)
                      ...++++||.|||||.-|..
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~   22 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQ   22 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            46799999999999997753

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=88.84  E-value=0.26  Score=41.10  Aligned_cols=31  Identities=23%  Similarity=0.167  Sum_probs=22.1

Q ss_pred             HHHHhcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           60 TSILVAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        60 i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      +|.-...+++++.|+||||||.. +..++..+
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~   66 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQ-IRELLASI   66 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHH-HHHHHHHH
Confidence            45555668999999999999975 33344443

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.

>cd01369 KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup

Probab=88.68  E-value=0.39  Score=38.66  Aligned_cols=24  Identities=33%  Similarity=0.416  Sum_probs=19.4

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTP   82 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~   82 (155)
                      .+..++.|.|  +++.++||||||..
T Consensus        68 ~v~~~~~G~n~~i~ayG~tgSGKT~T   93 (325)
T cd01369          68 IVDDVLNGYNGTIFAYGQTGSGKTYT   93 (325)
T ss_pred             HHHHHHcCccceEEEeCCCCCCceEE
Confidence            4556688865  68889999999987

Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-c

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=88.65  E-value=0.2  Score=36.06  Aligned_cols=27  Identities=22%  Similarity=0.436  Sum_probs=14.8

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      ++.+++.|++|+|||..- --++.++..
T Consensus        24 ~~~~ll~G~~G~GKT~ll-~~~~~~~~~   50 (185)
T PF13191_consen   24 PRNLLLTGESGSGKTSLL-RALLDRLAE   50 (185)
T ss_dssp             ---EEE-B-TTSSHHHHH-HHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            378999999999999752 224444443

>PRK14530 adenylate kinase; Provisional

Probab=88.61  E-value=0.24  Score=37.39  Aligned_cols=18  Identities=17%  Similarity=0.248  Sum_probs=15.6

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..+++.+++|||||..
T Consensus         2 ~~~~I~i~G~pGsGKsT~   19 (215)
T PRK14530          2 SQPRILLLGAPGAGKGTQ   19 (215)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            567899999999999965

>cd01376 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup

Probab=88.58  E-value=0.47  Score=38.20  Aligned_cols=25  Identities=28%  Similarity=0.493  Sum_probs=20.0

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .++.++.|.|  +++.++||||||.+.
T Consensus        72 lv~~~~~G~n~~i~ayG~tgSGKTyTm   98 (319)
T cd01376          72 IVPHLLSGQNATVFAYGSTGAGKTHTM   98 (319)
T ss_pred             HHHHHhCCCceEEEEECCCCCCCcEEE
Confidence            4566788975  677899999999875

Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=88.55  E-value=0.56  Score=32.79  Aligned_cols=21  Identities=10%  Similarity=0.229  Sum_probs=16.7

Q ss_pred             HHhcCCcEEEEccCCCCcchh
Q 031654           62 ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .......|++.+++||||+.+
T Consensus        17 ~a~~~~pvli~GE~GtGK~~~   37 (138)
T PF14532_consen   17 LAKSSSPVLITGEPGTGKSLL   37 (138)
T ss_dssp             HHCSSS-EEEECCTTSSHHHH
T ss_pred             HhCCCCcEEEEcCCCCCHHHH
Confidence            344568999999999999986

>KOG0060 consensus Long-chain acyl-CoA transporter, ABC superfamily (involved in peroxisome organization and biogenesis) [Lipid transport and metabolism; General function prediction only]

Probab=88.45  E-value=0.23  Score=43.29  Aligned_cols=22  Identities=23%  Similarity=0.434  Sum_probs=18.7

Q ss_pred             HHhcCCcEEEEccCCCCcchhh
Q 031654           62 ILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+-+|++++|++|+|+|||--+
T Consensus       457 ~V~~g~~LLItG~sG~GKtSLl  478 (659)
T KOG0060|consen  457 EVPSGQNLLITGPSGCGKTSLL  478 (659)
T ss_pred             EecCCCeEEEECCCCCchhHHH
Confidence            4568999999999999999743

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=88.43  E-value=0.19  Score=40.18  Aligned_cols=84  Identities=19%  Similarity=0.086  Sum_probs=48.9

Q ss_pred             HHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCC-
Q 031654           61 SILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELARWVDNLMATLRRLVNLLERGRVS-  129 (155)
Q Consensus        61 ~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~-  129 (155)
                      |+-..|+-+++.+..|.|||.+-.    +...+++...          ...+..+  -.+..++|-+.+.+...+.... 
T Consensus        89 ~A~k~g~l~~vyg~~g~gKt~a~~----~y~~s~p~~~l~~~~p~~~a~~~i~~i--~~~~~~~~~~~~~d~~~~~~~~l  162 (297)
T COG2842          89 PASKTGSLVVVYGYAGLGKTQAAK----NYAPSNPNALLIEADPSYTALVLILII--CAAAFGATDGTINDLTERLMIRL  162 (297)
T ss_pred             hhhhcCceEEEeccccchhHHHHH----hhcccCccceeecCChhhHHHHHHHHH--HHHHhcccchhHHHHHHHHHHHH
Confidence            555678888889999999998742    1111111111          1111111  1345556666655555443222 


Q ss_pred             cccccceEEEEcccccccccccc
Q 031654          130 LQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       130 l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                      ...+ +.+++||| |+|.=.+|+
T Consensus       163 ~~~~-~~iivDEA-~~L~~~ale  183 (297)
T COG2842         163 RDTV-RLIIVDEA-DRLPYRALE  183 (297)
T ss_pred             ccCc-ceeeeehh-hccChHHHH
Confidence            4566 89999999 999766654

>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=88.32  E-value=0.41  Score=35.67  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=15.5

Q ss_pred             CcEEEEccCCCCcchhhhhHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      .++++.+.||||||.+-..-+.+
T Consensus        39 ~h~li~G~tgsGKS~~l~~ll~~   61 (205)
T PF01580_consen   39 PHLLIAGATGSGKSTLLRTLLLS   61 (205)
T ss_dssp             -SEEEE--TTSSHHHHHHHHHHH
T ss_pred             ceEEEEcCCCCCccHHHHHHHHH
Confidence            48999999999999875543333

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.

>PHA00350 putative assembly protein

Probab=88.21  E-value=0.73  Score=38.53  Aligned_cols=17  Identities=18%  Similarity=0.153  Sum_probs=13.8

Q ss_pred             EEEEccCCCCcchhhhh
Q 031654           69 LMACAQTGSRKTTPFCF   85 (155)
Q Consensus        69 vl~~a~TGsGKT~~yll   85 (155)
                      .++.+..|||||+..+-
T Consensus         4 ~l~tG~pGSGKT~~aV~   20 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVV   20 (399)
T ss_pred             EEEecCCCCchhHHHHH
Confidence            46789999999997653

>PRK04328 hypothetical protein; Provisional

Probab=88.18  E-value=1.6  Score=33.79  Aligned_cols=18  Identities=11%  Similarity=0.130  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+++.+++|+|||.-
T Consensus        22 ~gs~ili~G~pGsGKT~l   39 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIF   39 (249)
T ss_pred             CCcEEEEEcCCCCCHHHH
Confidence            457899999999999874

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=88.17  E-value=2.6  Score=38.05  Aligned_cols=107  Identities=14%  Similarity=0.186  Sum_probs=60.7

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHH--------hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----HHHHHHH
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSIL--------VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----RKELREL  105 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~--------l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----~~~~~~l  105 (155)
                      ..-.+.|.+-.| -+..+-.+.+..+        .+|+=+..++|+|-|||...- .|...+.+.-...    -....++
T Consensus       403 ~~Ak~iLdeDHY-gm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~k-SIA~ALnRkFfRfSvGG~tDvAeI  480 (906)
T KOG2004|consen  403 ARAKEILDEDHY-GMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAK-SIARALNRKFFRFSVGGMTDVAEI  480 (906)
T ss_pred             HHHHHhhccccc-chHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHH-HHHHHhCCceEEEeccccccHHhh
Confidence            444444544333 4566667777665        245678888999999997531 1222121111000    2233334


Q ss_pred             hcCC-cEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654          106 ARWV-DNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       106 ~~~~-~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                      +... --|=+-||++.+-|++-.  ..+  -++.+||+ |++= .|+.
T Consensus       481 kGHRRTYVGAMPGkiIq~LK~v~--t~N--PliLiDEv-DKlG-~g~q  522 (906)
T KOG2004|consen  481 KGHRRTYVGAMPGKIIQCLKKVK--TEN--PLILIDEV-DKLG-SGHQ  522 (906)
T ss_pred             cccceeeeccCChHHHHHHHhhC--CCC--ceEEeehh-hhhC-CCCC
Confidence            3322 345567999999987532  122  47889999 9986 4443

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=88.13  E-value=0.68  Score=33.88  Aligned_cols=44  Identities=18%  Similarity=0.164  Sum_probs=33.7

Q ss_pred             HHHHhHHhCCCCC-----CCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           39 HLRNKPRTYKYVK-----PTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        39 ~l~~~l~~~g~~~-----pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ++++..+++||.-     -+......+...+.++-+++++++|.||+.-
T Consensus         3 ~~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l~~k~~vl~G~SGvGKSSL   51 (161)
T PF03193_consen    3 ELLEQYEKLGYPVFFISAKTGEGIEELKELLKGKTSVLLGQSGVGKSSL   51 (161)
T ss_dssp             HHHHHHHHTTSEEEE-BTTTTTTHHHHHHHHTTSEEEEECSTTSSHHHH
T ss_pred             HHHHHHHHcCCcEEEEeCCCCcCHHHHHHHhcCCEEEEECCCCCCHHHH
Confidence            5566777888762     2445566777888899999999999999873

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=88.10  E-value=0.88  Score=40.72  Aligned_cols=103  Identities=17%  Similarity=0.180  Sum_probs=54.7

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHH--------hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------HHHH
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSIL--------VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------RKEL  102 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~--------l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------~~~~  102 (155)
                      ....+.|.+-.| -+-.+-.+.+..+        +.|.=++.++|+|.|||..- =.+...+.+.-...       ...+
T Consensus       315 ~~a~~iLd~dHY-GLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLg-kSIA~al~RkfvR~sLGGvrDEAEI  392 (782)
T COG0466         315 KKAEKILDKDHY-GLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLG-KSIAKALGRKFVRISLGGVRDEAEI  392 (782)
T ss_pred             HHHHHHhccccc-CchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHH-HHHHHHhCCCEEEEecCccccHHHh
Confidence            444455544433 2334444444433        24456778899999999742 12222111110000       2222


Q ss_pred             HHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          103 RELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       103 ~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      +.-++  --+=+-|||+.+-+..-..  .+  -.+++||+ |+|=..
T Consensus       393 RGHRR--TYIGamPGrIiQ~mkka~~--~N--Pv~LLDEI-DKm~ss  432 (782)
T COG0466         393 RGHRR--TYIGAMPGKIIQGMKKAGV--KN--PVFLLDEI-DKMGSS  432 (782)
T ss_pred             ccccc--cccccCChHHHHHHHHhCC--cC--CeEEeech-hhccCC
Confidence            22222  2355679999998876321  11  47899999 998643

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=88.06  E-value=0.27  Score=39.56  Aligned_cols=17  Identities=12%  Similarity=0.132  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +=+++.||||||||...
T Consensus         5 ~ii~I~GpTasGKS~LA   21 (300)
T PRK14729          5 KIVFIFGPTAVGKSNIL   21 (300)
T ss_pred             cEEEEECCCccCHHHHH
Confidence            34789999999999754

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=88.06  E-value=1.7  Score=34.81  Aligned_cols=18  Identities=17%  Similarity=0.209  Sum_probs=15.6

Q ss_pred             CcEEEEccCCCCcchhhh
Q 031654           67 RDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yl   84 (155)
                      +-++..+|+|+|||+-.-
T Consensus       206 KGvLmYGPPGTGKTlmAR  223 (424)
T KOG0652|consen  206 KGVLMYGPPGTGKTLMAR  223 (424)
T ss_pred             CceEeeCCCCCcHHHHHH
Confidence            689999999999998643

>PF00225 Kinesin: Kinesin motor domain; InterPro: IPR001752 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport

Probab=87.97  E-value=0.46  Score=38.27  Aligned_cols=27  Identities=30%  Similarity=0.336  Sum_probs=19.6

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhhhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPFCF   85 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~yll   85 (155)
                      .+..++.|.|  +++.++||||||.+..=
T Consensus        66 ~v~~~l~G~n~~i~ayG~tgSGKT~Tm~G   94 (335)
T PF00225_consen   66 LVDSVLDGYNATIFAYGQTGSGKTYTMFG   94 (335)
T ss_dssp             HHHHHHTT-EEEEEEEESTTSSHHHHHTB
T ss_pred             HHHHhhcCCceEEEeeccccccccccccc
Confidence            4556789976  77789999999966433

The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section. The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement; PDB: 3NWN_A 2Y5W_A 2Y65_C 3BFN_A 2WBE_C 2ZFL_A 2ZFI_A 1I6I_A 2ZFM_A 1IA0_K ....

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=87.91  E-value=0.31  Score=40.78  Aligned_cols=22  Identities=18%  Similarity=0.339  Sum_probs=18.5

Q ss_pred             HHHhcC-----CcEEEEccCCCCcchh
Q 031654           61 SILVAG-----RDLMACAQTGSRKTTP   82 (155)
Q Consensus        61 ~~~l~g-----~dvl~~a~TGsGKT~~   82 (155)
                      |.+++|     +-|+..+|+|||||+-
T Consensus       235 Pe~F~GirrPWkgvLm~GPPGTGKTlL  261 (491)
T KOG0738|consen  235 PEFFKGIRRPWKGVLMVGPPGTGKTLL  261 (491)
T ss_pred             HHHHhhcccccceeeeeCCCCCcHHHH
Confidence            555666     6899999999999984

>cd01375 KISc_KIF9_like Kinesin motor domain, KIF9-like subgroup; might play a role in cell shape remodeling

Probab=87.90  E-value=0.51  Score=38.29  Aligned_cols=25  Identities=28%  Similarity=0.401  Sum_probs=19.4

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||..-
T Consensus        72 ~v~~~~~G~n~~i~ayG~tgSGKTyTm   98 (334)
T cd01375          72 VVDSALDGYNGTIFAYGQTGAGKTFTM   98 (334)
T ss_pred             HHHHHhCCCccceeeecCCCCCCeEEc
Confidence            3456788854  788899999999763

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=87.83  E-value=2.4  Score=35.39  Aligned_cols=22  Identities=32%  Similarity=0.229  Sum_probs=16.5

Q ss_pred             HhcCCcEEEEccCCCCcchhhh
Q 031654           63 LVAGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~yl   84 (155)
                      +..|.=+++.|++|+|||...+
T Consensus       191 ~~~g~liviag~pg~GKT~~al  212 (421)
T TIGR03600       191 LVKGDLIVIGARPSMGKTTLAL  212 (421)
T ss_pred             CCCCceEEEEeCCCCCHHHHHH
Confidence            3445667889999999997543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=87.56  E-value=2.2  Score=33.79  Aligned_cols=21  Identities=24%  Similarity=0.207  Sum_probs=17.2

Q ss_pred             cCCcEEEEccCCCCcchhhhh
Q 031654           65 AGRDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yll   85 (155)
                      .|..+++++++|+|||..+..
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~   94 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAK   94 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHH
Confidence            346789999999999997654

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=87.47  E-value=0.33  Score=35.78  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      |..+++.+|+|||||...
T Consensus         2 g~~i~l~G~sGsGKsTl~   19 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLL   19 (186)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            567899999999999863

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=87.47  E-value=0.33  Score=40.60  Aligned_cols=17  Identities=24%  Similarity=0.301  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .+.+..+|+|+|||...
T Consensus        49 ~SmIl~GPPG~GKTTlA   65 (436)
T COG2256          49 HSMILWGPPGTGKTTLA   65 (436)
T ss_pred             ceeEEECCCCCCHHHHH
Confidence            58999999999999854

>PRK09354 recA recombinase A; Provisional

Probab=87.46  E-value=1.3  Score=36.38  Aligned_cols=80  Identities=16%  Similarity=0.046  Sum_probs=41.4

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHh-cCCcEEEEChHHHHHHHHc--CCCCcccc
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELA-RWVDNLMATLRRLVNLLER--GRVSLQMI  133 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~-~~~~IlI~TP~~l~~~l~~--~~~~l~~l  133 (155)
                      |+=+.+.+|+|||||.-.+--+.+.........         ....+.+. .--++++..|....+.+..  ..+.-..+
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~s~~~  139 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAV  139 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhcCCC
Confidence            457889999999999865444433332221111         11111110 0124777776332222211  11122467


Q ss_pred             cceEEEEccccccc
Q 031654          134 IRYLALKEAADQTL  147 (155)
Q Consensus       134 ~~~lVlDEa~D~ll  147 (155)
                       +++|+|-+ -.+.
T Consensus       140 -~lIVIDSv-aaL~  151 (349)
T PRK09354        140 -DLIVVDSV-AALV  151 (349)
T ss_pred             -CEEEEeCh-hhhc
Confidence             89999998 6655

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=87.40  E-value=0.61  Score=35.25  Aligned_cols=29  Identities=28%  Similarity=0.290  Sum_probs=20.2

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .|.-+++.+++|||||.-.+--+.+.+..
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~   46 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKN   46 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhh
Confidence            44789999999999998644334444443

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>cd01374 KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis

Probab=87.38  E-value=0.54  Score=37.82  Aligned_cols=26  Identities=27%  Similarity=0.317  Sum_probs=20.2

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPFC   84 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~yl   84 (155)
                      .+..++.|.|  +++.++||||||.+..
T Consensus        65 ~v~~~l~G~n~~i~ayG~tgSGKT~T~~   92 (321)
T cd01374          65 VVRSALEGYNGTIFAYGQTSSGKTFTMS   92 (321)
T ss_pred             HHHHHHCCCceeEEeecCCCCCCceecc
Confidence            4566688865  7788999999997753

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=87.13  E-value=1.2  Score=39.46  Aligned_cols=33  Identities=36%  Similarity=0.364  Sum_probs=27.2

Q ss_pred             CCCHHHHHHHHHHhcC-----CcEEEEccCCCCcchhh
Q 031654           51 KPTPVQRHATSILVAG-----RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g-----~dvl~~a~TGsGKT~~y   83 (155)
                      .|++.|..++..+.++     +..++.+.+||||++..
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~li   49 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTM   49 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHH
Confidence            7899999999988543     25779999999999874

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=87.09  E-value=1.6  Score=35.34  Aligned_cols=78  Identities=9%  Similarity=0.070  Sum_probs=41.5

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhh-h---ch--HHHHHHHh--cCCcEEEEChH-------HHHHHHHc--CCCCc
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREY-Y---SA--RKELRELA--RWVDNLMATLR-------RLVNLLER--GRVSL  130 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~-~---~~--~~~~~~l~--~~~~IlI~TP~-------~l~~~l~~--~~~~l  130 (155)
                      -.+..||.|+||+..... +...+.... .   .+  ....+.+.  ..+|+.+..|+       .+.++...  ..-..
T Consensus        30 a~Lf~G~~G~gk~~~a~~-la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~  108 (329)
T PRK08058         30 AYLFEGAKGTGKKATALW-LAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVE  108 (329)
T ss_pred             eEEEECCCCCCHHHHHHH-HHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcc
Confidence            358999999999764322 222222211 0   00  12222222  34678777663       23333321  11134


Q ss_pred             ccccceEEEEcccccccc
Q 031654          131 QMIIRYLALKEAADQTLD  148 (155)
Q Consensus       131 ~~l~~~lVlDEa~D~ll~  148 (155)
                      ..- +.+||||| |+|=+
T Consensus       109 ~~~-kvviI~~a-~~~~~  124 (329)
T PRK08058        109 SNK-KVYIIEHA-DKMTA  124 (329)
T ss_pred             cCc-eEEEeehH-hhhCH
Confidence            566 89999999 98854

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.96  E-value=1.3  Score=38.76  Aligned_cols=18  Identities=17%  Similarity=0.191  Sum_probs=14.6

Q ss_pred             cEEEEccCCCCcchhhhh
Q 031654           68 DLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yll   85 (155)
                      -.+++||.|+|||.+..+
T Consensus        40 ayLf~Gp~G~GKtt~A~~   57 (576)
T PRK14965         40 AFLFTGARGVGKTSTARI   57 (576)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            358999999999987543

>KOG1533 consensus Predicted GTPase [General function prediction only]

Probab=86.95  E-value=0.53  Score=36.87  Aligned_cols=27  Identities=19%  Similarity=0.185  Sum_probs=20.0

Q ss_pred             EEEEccCCCCcchhhhhHHHHHHHHhhh
Q 031654           69 LMACAQTGSRKTTPFCFPIINGIMREYY   96 (155)
Q Consensus        69 vl~~a~TGsGKT~~yllp~l~~l~~~~~   96 (155)
                      .+|.+|+|||||. |+..+.+.+....+
T Consensus         5 qvVIGPPgSGKsT-Yc~g~~~fls~~gr   31 (290)
T KOG1533|consen    5 QVVIGPPGSGKST-YCNGMSQFLSAIGR   31 (290)
T ss_pred             eEEEcCCCCCccc-hhhhHHHHHHHhCC
Confidence            4789999999985 77776666655444

>TIGR02012 tigrfam_recA protein RecA

Probab=86.83  E-value=1.3  Score=35.91  Aligned_cols=79  Identities=18%  Similarity=0.061  Sum_probs=41.8

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHh-cCCcEEEEChHHHHHHHHc--CCCCccc
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELA-RWVDNLMATLRRLVNLLER--GRVSLQM  132 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~-~~~~IlI~TP~~l~~~l~~--~~~~l~~  132 (155)
                      |+=+.+.+|+|||||.-.+- ++..........          ....+.+. .--++++..|....+.+..  ..+.-..
T Consensus        55 G~iteI~G~~GsGKTtLaL~-~~~~~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~~~~  133 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALH-AIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGA  133 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHH-HHHHHHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhccC
Confidence            46788999999999986543 333333222211          11111110 0125677777543333221  1122246


Q ss_pred             ccceEEEEccccccc
Q 031654          133 IIRYLALKEAADQTL  147 (155)
Q Consensus       133 l~~~lVlDEa~D~ll  147 (155)
                      + +++|+|-+ ..+.
T Consensus       134 ~-~lIVIDSv-~al~  146 (321)
T TIGR02012       134 V-DIIVVDSV-AALV  146 (321)
T ss_pred             C-cEEEEcch-hhhc
Confidence            7 89999999 7665

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=86.80  E-value=0.37  Score=39.95  Aligned_cols=20  Identities=30%  Similarity=0.491  Sum_probs=17.3

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +.|+-+++.+|+|||||...
T Consensus        63 ~aGrgiLi~GppgTGKTAlA   82 (450)
T COG1224          63 MAGRGILIVGPPGTGKTALA   82 (450)
T ss_pred             ccccEEEEECCCCCcHHHHH
Confidence            56789999999999999743

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=86.79  E-value=2.9  Score=37.86  Aligned_cols=45  Identities=24%  Similarity=0.329  Sum_probs=30.8

Q ss_pred             CCCHHHHHHHHHHh---cC-------CcEEEEccCCCCcchhhhhHHHHHHHHhhh
Q 031654           51 KPTPVQRHATSILV---AG-------RDLMACAQTGSRKTTPFCFPIINGIMREYY   96 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l---~g-------~dvl~~a~TGsGKT~~yllp~l~~l~~~~~   96 (155)
                      .+.|+|++.+..+.   .|       .-.++.-..|+|||+-. ++.+..+.+..+
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~-IsflwtlLrq~P  292 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQC-ISFIWTLLRQFP  292 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHH-HHHHHHHHHhCc
Confidence            56899999998774   22       23667778899999864 455555554433

>cd01372 KISc_KIF4 Kinesin motor domain, KIF4-like subfamily

Probab=86.78  E-value=0.56  Score=38.03  Aligned_cols=24  Identities=38%  Similarity=0.454  Sum_probs=19.4

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||.+.
T Consensus        66 v~~~~~G~n~~i~ayG~tgSGKT~Tm   91 (341)
T cd01372          66 VDGLFEGYNATVLAYGQTGSGKTYTM   91 (341)
T ss_pred             HHHHhCCCccceeeecCCCCCCcEEe
Confidence            455678864  788999999999885

Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain,

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=86.71  E-value=0.63  Score=37.51  Aligned_cols=25  Identities=28%  Similarity=0.242  Sum_probs=21.2

Q ss_pred             HHHHHHhcCCcEEEEccCCCCcchh
Q 031654           58 HATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        58 ~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .++-.++.|+.+++.+++|+|||..
T Consensus        35 ~~l~a~~~~~~vll~G~PG~gKT~l   59 (329)
T COG0714          35 LALLALLAGGHVLLEGPPGVGKTLL   59 (329)
T ss_pred             HHHHHHHcCCCEEEECCCCccHHHH
Confidence            3445678999999999999999985

>PLN02165 adenylate isopentenyltransferase

Probab=86.61  E-value=0.4  Score=39.12  Aligned_cols=20  Identities=20%  Similarity=0.189  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCCCcchhhh
Q 031654           65 AGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yl   84 (155)
                      .|+-+++.+|||||||....
T Consensus        42 ~g~iivIiGPTGSGKStLA~   61 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSV   61 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHH
Confidence            45679999999999997653

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=86.59  E-value=0.38  Score=39.95  Aligned_cols=20  Identities=30%  Similarity=0.517  Sum_probs=14.9

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +.|+-+++.+|+|||||...
T Consensus        48 ~aGr~iLiaGppGtGKTAlA   67 (398)
T PF06068_consen   48 IAGRAILIAGPPGTGKTALA   67 (398)
T ss_dssp             -TT-EEEEEE-TTSSHHHHH
T ss_pred             ccCcEEEEeCCCCCCchHHH
Confidence            36789999999999999753

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>TIGR03689 pup_AAA proteasome ATPase

Probab=86.55  E-value=0.27  Score=42.34  Aligned_cols=17  Identities=18%  Similarity=0.237  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      .+.+++.+|+|+|||+.
T Consensus       216 p~GILLyGPPGTGKT~L  232 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLI  232 (512)
T ss_pred             CcceEEECCCCCcHHHH
Confidence            36899999999999985

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

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

Probab=86.51  E-value=0.4  Score=36.33  Aligned_cols=18  Identities=28%  Similarity=0.412  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++++.|.|.||||||...
T Consensus        23 ~~H~~I~G~TGsGKS~~~   40 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTV   40 (229)
T ss_pred             cceEEEECCCCCCHHHHH
Confidence            579999999999999864

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

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=86.48  E-value=0.94  Score=36.68  Aligned_cols=13  Identities=15%  Similarity=0.235  Sum_probs=11.0

Q ss_pred             ceEEEEcccccccc
Q 031654          135 RYLALKEAADQTLD  148 (155)
Q Consensus       135 ~~lVlDEa~D~ll~  148 (155)
                      ..+|+||+ |+|-.
T Consensus       180 slFIFDE~-DKmp~  192 (344)
T KOG2170|consen  180 SLFIFDEV-DKLPP  192 (344)
T ss_pred             ceEEechh-hhcCH
Confidence            68999999 99853

>PRK00131 aroK shikimate kinase; Reviewed

Probab=86.42  E-value=0.34  Score=34.57  Aligned_cols=18  Identities=22%  Similarity=0.339  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..+++++++|||||..
T Consensus         3 ~~~~i~l~G~~GsGKstl   20 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTI   20 (175)
T ss_pred             CCCeEEEEcCCCCCHHHH
Confidence            567899999999999976

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

Probab=86.38  E-value=0.19  Score=39.11  Aligned_cols=45  Identities=29%  Similarity=0.249  Sum_probs=26.5

Q ss_pred             HHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           39 HLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        39 ~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +++++|...|.....+.--..+.-+..|.-+++.|++|+|||...
T Consensus         3 ~~~~~~~~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~   47 (271)
T cd01122           3 EIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFL   47 (271)
T ss_pred             hhhccccccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHH
Confidence            455555533333222222222234566788999999999999743

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

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=86.36  E-value=6  Score=35.83  Aligned_cols=64  Identities=14%  Similarity=0.116  Sum_probs=43.5

Q ss_pred             hHHhCCCCCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHH
Q 031654           43 KPRTYKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRR  118 (155)
Q Consensus        43 ~l~~~g~~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~  118 (155)
                      .+.....+.+..-|.+.+..++.+  +-+++.|.-|-|||.+.-+.+.. +           ..+....+|+|+.|..
T Consensus       206 ~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~-~-----------~~~~~~~~iiVTAP~~  271 (758)
T COG1444         206 ELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAA-A-----------ARLAGSVRIIVTAPTP  271 (758)
T ss_pred             HHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHH-H-----------HHhcCCceEEEeCCCH
Confidence            366666666677777777777766  36888999999999987766522 1           1111156888888854

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=86.33  E-value=2.7  Score=37.06  Aligned_cols=41  Identities=32%  Similarity=0.203  Sum_probs=30.6

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .+++-|.++....  ...++|.|..|||||-+-.--+...+..
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~   42 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAA   42 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHc
Confidence            5788999988665  6678889999999998865554444443

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=86.33  E-value=1.4  Score=36.94  Aligned_cols=67  Identities=13%  Similarity=0.065  Sum_probs=40.1

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHH----HcCC-----CCcccccce
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLL----ERGR-----VSLQMIIRY  136 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l----~~~~-----~~l~~l~~~  136 (155)
                      ..-+++.|++|+|||.-  +   +.+       ..........+.++-.|.+.+..-+    ..+.     -.. ++ ++
T Consensus       113 ~nplfi~G~~GlGKTHL--l---~Ai-------gn~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y-~~-dl  178 (408)
T COG0593         113 YNPLFIYGGVGLGKTHL--L---QAI-------GNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY-SL-DL  178 (408)
T ss_pred             CCcEEEECCCCCCHHHH--H---HHH-------HHHHHhhCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh-cc-Ce
Confidence            35799999999999973  2   111       1122333334577888887754222    1111     123 78 89


Q ss_pred             EEEEccccccc
Q 031654          137 LALKEAADQTL  147 (155)
Q Consensus       137 lVlDEa~D~ll  147 (155)
                      |++|++ +.+-
T Consensus       179 llIDDi-q~l~  188 (408)
T COG0593         179 LLIDDI-QFLA  188 (408)
T ss_pred             eeechH-hHhc
Confidence            999999 6554

>PRK00300 gmk guanylate kinase; Provisional

Probab=86.27  E-value=0.43  Score=35.41  Aligned_cols=18  Identities=22%  Similarity=0.307  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|+-+++.||+|||||..
T Consensus         4 ~g~~i~i~G~sGsGKstl   21 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTL   21 (205)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            567899999999999963

>PRK11823 DNA repair protein RadA; Provisional

Probab=86.26  E-value=1.8  Score=36.73  Aligned_cols=18  Identities=22%  Similarity=0.326  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      |.-+++.+++|+|||.-.
T Consensus        80 Gs~~lI~G~pG~GKTtL~   97 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLL   97 (446)
T ss_pred             CEEEEEECCCCCCHHHHH
Confidence            457889999999999853

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=86.25  E-value=0.44  Score=34.67  Aligned_cols=19  Identities=16%  Similarity=0.233  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|+-+++++++|||||...
T Consensus         1 ~~~~i~l~G~~gsGKst~a   19 (175)
T cd00227           1 TGRIIILNGGSSAGKSSIA   19 (175)
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3677999999999999763

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=86.21  E-value=0.44  Score=41.57  Aligned_cols=52  Identities=13%  Similarity=0.163  Sum_probs=29.7

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHH---HhcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSI---LVAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~---~l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .++.+.+++.+-.  .++.-.-+|.   -...+++++.|+||||||.+ +-.++..+.
T Consensus       147 ~~l~~~l~~~~~~--~~~~igg~pl~~~~~e~~h~li~G~tGsGKs~~-i~~ll~~~~  201 (566)
T TIGR02759       147 KELIKKLKKSRRA--SDIKIGGLPLIKFGSETQHILIHGTTGSGKSVA-IRKLLRWIR  201 (566)
T ss_pred             HHHHHHHHhcCCC--CceeeCCccCCCCcccccceEEEcCCCCCHHHH-HHHHHHHHH
Confidence            5566666655522  2222222343   23447999999999999963 233444443

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).

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=86.18  E-value=0.59  Score=41.38  Aligned_cols=19  Identities=21%  Similarity=0.125  Sum_probs=16.3

Q ss_pred             CcEEEEccCCCCcchhhhh
Q 031654           67 RDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yll   85 (155)
                      .++++.|+||+|||..+.+
T Consensus       177 ~H~lv~G~TGsGKT~l~~~  195 (634)
T TIGR03743       177 GHTLVLGTTGVGKTRLAEL  195 (634)
T ss_pred             CcEEEECCCCCCHHHHHHH
Confidence            6899999999999987643

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.16  E-value=1.8  Score=38.33  Aligned_cols=17  Identities=24%  Similarity=0.153  Sum_probs=14.6

Q ss_pred             cEEEEccCCCCcchhhh
Q 031654           68 DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yl   84 (155)
                      -++.+||.|+|||.+..
T Consensus        40 a~Lf~Gp~GvGKttlA~   56 (620)
T PRK14954         40 GYIFSGLRGVGKTTAAR   56 (620)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            48899999999998754

>PRK14974 cell division protein FtsY; Provisional

Probab=86.05  E-value=1.8  Score=35.40  Aligned_cols=17  Identities=24%  Similarity=0.259  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .=+++++++|+|||..-
T Consensus       141 ~vi~~~G~~GvGKTTti  157 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTI  157 (336)
T ss_pred             eEEEEEcCCCCCHHHHH
Confidence            34788999999999864

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=86.01  E-value=2.6  Score=38.07  Aligned_cols=16  Identities=38%  Similarity=0.538  Sum_probs=13.7

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +=++.|+|.|-|||..
T Consensus       327 KilLL~GppGlGKTTL  342 (877)
T KOG1969|consen  327 KILLLCGPPGLGKTTL  342 (877)
T ss_pred             ceEEeecCCCCChhHH
Confidence            3579999999999984

>PRK05973 replicative DNA helicase; Provisional

Probab=85.97  E-value=0.51  Score=36.68  Aligned_cols=39  Identities=23%  Similarity=0.152  Sum_probs=25.1

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHH
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIING   90 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~   90 (155)
                      .+||... ...-+..|.-+++.|++|+|||.-.+--+.+.
T Consensus        50 ~~~p~~~-l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~   88 (237)
T PRK05973         50 ATTPAEE-LFSQLKPGDLVLLGARPGHGKTLLGLELAVEA   88 (237)
T ss_pred             CCCCHHH-hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            4566322 33445566789999999999998654333333

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=85.96  E-value=2.1  Score=37.41  Aligned_cols=18  Identities=17%  Similarity=0.104  Sum_probs=15.0

Q ss_pred             cEEEEccCCCCcchhhhh
Q 031654           68 DLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yll   85 (155)
                      -.+++||.|+|||.+..+
T Consensus        40 ayLf~Gp~G~GKTt~Ar~   57 (563)
T PRK06647         40 AYIFSGPRGVGKTSSARA   57 (563)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478999999999987643

>cd01364 KISc_BimC_Eg5 Kinesin motor domain, BimC/Eg5 spindle pole proteins, participate in spindle assembly and chromosome segregation during cell division

Probab=85.95  E-value=0.64  Score=37.92  Aligned_cols=24  Identities=29%  Similarity=0.432  Sum_probs=18.6

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||.+.
T Consensus        74 v~~~~~G~n~~i~ayG~tgSGKTyTl   99 (352)
T cd01364          74 LDEVLMGYNCTIFAYGQTGTGKTYTM   99 (352)
T ss_pred             HHHHhCCCeEEEEECCCCCCCCcEEe
Confidence            455678876  677899999999653

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil d

>PRK07261 topology modulation protein; Provisional

Probab=85.90  E-value=0.41  Score=34.96  Aligned_cols=16  Identities=25%  Similarity=0.239  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      -++++|++|||||...
T Consensus         2 ri~i~G~~GsGKSTla   17 (171)
T PRK07261          2 KIAIIGYSGSGKSTLA   17 (171)
T ss_pred             EEEEEcCCCCCHHHHH
Confidence            3789999999999754

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=85.90  E-value=0.41  Score=33.70  Aligned_cols=14  Identities=21%  Similarity=0.349  Sum_probs=12.1

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      +++.+|||||||..
T Consensus         2 i~i~GpsGsGKstl   15 (137)
T cd00071           2 IVLSGPSGVGKSTL   15 (137)
T ss_pred             EEEECCCCCCHHHH
Confidence            57899999999973

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=85.77  E-value=0.44  Score=39.95  Aligned_cols=18  Identities=28%  Similarity=0.272  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ..++++.+|||+|||...
T Consensus       108 ~~~iLl~Gp~GtGKT~lA  125 (412)
T PRK05342        108 KSNILLIGPTGSGKTLLA  125 (412)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            367999999999999864

>cd00106 KISc Kinesin motor domain

Probab=85.77  E-value=0.99  Score=36.22  Aligned_cols=26  Identities=31%  Similarity=0.426  Sum_probs=19.9

Q ss_pred             HHHHHHHhcCCc--EEEEccCCCCcchh
Q 031654           57 RHATSILVAGRD--LMACAQTGSRKTTP   82 (155)
Q Consensus        57 ~~~i~~~l~g~d--vl~~a~TGsGKT~~   82 (155)
                      ...+..++.|.|  +++.++||||||..
T Consensus        68 ~~~v~~~~~G~~~~i~~yG~tgSGKT~t   95 (328)
T cd00106          68 KPLVESVLEGYNGTIFAYGQTGSGKTYT   95 (328)
T ss_pred             HHHHHHHhCCCceeEEEecCCCCCCeEE
Confidence            345566688865  67789999999965

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coil

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=85.66  E-value=0.66  Score=33.62  Aligned_cols=15  Identities=27%  Similarity=0.206  Sum_probs=13.1

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      +++.+++|+|||...
T Consensus         2 ~li~G~~G~GKT~l~   16 (187)
T cd01124           2 TLLSGGPGTGKTTFA   16 (187)
T ss_pred             EEEEcCCCCCHHHHH
Confidence            689999999999854

A related protein is found in archaea.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=85.66  E-value=1  Score=36.71  Aligned_cols=24  Identities=21%  Similarity=0.213  Sum_probs=19.4

Q ss_pred             HHHHHhcCCcEEEEccCCCCcchh
Q 031654           59 ATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        59 ~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+-.+..++++++.+++|+|||..
T Consensus        57 vl~~l~~~~~ilL~G~pGtGKTtl   80 (327)
T TIGR01650        57 ICAGFAYDRRVMVQGYHGTGKSTH   80 (327)
T ss_pred             HHHHHhcCCcEEEEeCCCChHHHH
Confidence            334456689999999999999985

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>cd01371 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins

Probab=85.49  E-value=0.77  Score=37.21  Aligned_cols=24  Identities=29%  Similarity=0.429  Sum_probs=18.9

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTP   82 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~   82 (155)
                      .+..++.|.|  +++.++||||||..
T Consensus        73 lv~~~~~G~n~~i~ayG~tgSGKTyT   98 (333)
T cd01371          73 LVDSVLEGYNGTIFAYGQTGTGKTFT   98 (333)
T ss_pred             HHHHHhCCCceeEEecCCCCCCCcEe
Confidence            4456688865  78889999999955

Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this group the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain

>PRK08118 topology modulation protein; Reviewed

Probab=85.47  E-value=0.45  Score=34.70  Aligned_cols=15  Identities=27%  Similarity=0.353  Sum_probs=13.2

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      -++|+|++|||||..
T Consensus         3 rI~I~G~~GsGKSTl   17 (167)
T PRK08118          3 KIILIGSGGSGKSTL   17 (167)
T ss_pred             EEEEECCCCCCHHHH
Confidence            489999999999974

>PF05729 NACHT: NACHT domain

Probab=85.46  E-value=0.49  Score=33.24  Aligned_cols=24  Identities=21%  Similarity=0.275  Sum_probs=16.6

Q ss_pred             EEEEccCCCCcchhhhhHHHHHHHH
Q 031654           69 LMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        69 vl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      +++.|++|+|||... --++..+..
T Consensus         3 l~I~G~~G~GKStll-~~~~~~~~~   26 (166)
T PF05729_consen    3 LWISGEPGSGKSTLL-RKLAQQLAE   26 (166)
T ss_pred             EEEECCCCCChHHHH-HHHHHHHHh
Confidence            789999999999853 334444433

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=85.38  E-value=0.88  Score=39.04  Aligned_cols=31  Identities=26%  Similarity=0.438  Sum_probs=25.1

Q ss_pred             CHHHHHHHHHHh-------cCCcEEEEccCCCCcchhh
Q 031654           53 TPVQRHATSILV-------AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        53 t~iQ~~~i~~~l-------~g~dvl~~a~TGsGKT~~y   83 (155)
                      ++||......+-       .|.=+.++||+|||||.--
T Consensus        12 r~Ie~~l~~vL~~Vsl~i~~GEiv~L~G~SGsGKSTLL   49 (504)
T TIGR03238        12 RKIQTDLERILVKFNKELPSSSLLFLCGSSGDGKSEIL   49 (504)
T ss_pred             hHHHHHHHHHHhCCceeecCCCEEEEECCCCCCHHHHH
Confidence            788888776663       5788999999999999853

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=85.37  E-value=1.2  Score=34.46  Aligned_cols=27  Identities=22%  Similarity=0.089  Sum_probs=17.6

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      |.=+++.|+||.|||...+ -++..+..
T Consensus        19 g~L~vi~a~pg~GKT~~~l-~ia~~~a~   45 (259)
T PF03796_consen   19 GELTVIAARPGVGKTAFAL-QIALNAAL   45 (259)
T ss_dssp             T-EEEEEESTTSSHHHHHH-HHHHHHHH
T ss_pred             CcEEEEEecccCCchHHHH-HHHHHHHH
Confidence            3457888999999998544 44444433

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=85.31  E-value=0.51  Score=36.46  Aligned_cols=19  Identities=26%  Similarity=0.314  Sum_probs=16.0

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      ..|.=+++++|+|||||.-
T Consensus        26 ~~Gevv~iiGpSGSGKSTl   44 (240)
T COG1126          26 EKGEVVVIIGPSGSGKSTL   44 (240)
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4677789999999999874

>smart00129 KISc Kinesin motor, catalytic domain

Probab=85.28  E-value=1  Score=36.37  Aligned_cols=26  Identities=31%  Similarity=0.415  Sum_probs=19.8

Q ss_pred             HHHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           58 HATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        58 ~~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      ..+..++.|.|  +++.++||||||.+.
T Consensus        70 p~v~~~~~G~~~~i~~yG~tgSGKT~tl   97 (335)
T smart00129       70 PLVDSVLEGYNATIFAYGQTGSGKTYTM   97 (335)
T ss_pred             HHHHHHhcCCceeEEEeCCCCCCCceEe
Confidence            34556788865  677899999999664

ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.

>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

Probab=85.27  E-value=0.44  Score=38.49  Aligned_cols=15  Identities=27%  Similarity=0.231  Sum_probs=12.9

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      +++++||+||||--.
T Consensus         6 i~I~GPTAsGKT~la   20 (308)
T COG0324           6 IVIAGPTASGKTALA   20 (308)
T ss_pred             EEEECCCCcCHHHHH
Confidence            789999999999743

>PLN03130 ABC transporter C family member; Provisional

Probab=85.15  E-value=0.3  Score=47.57  Aligned_cols=27  Identities=15%  Similarity=0.220  Sum_probs=19.9

Q ss_pred             hcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           64 VAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      -.|+-+-++|+||||||..  +-++.++.
T Consensus      1263 ~~GekVaIVGrSGSGKSTL--l~lL~rl~ 1289 (1622)
T PLN03130       1263 SPSEKVGIVGRTGAGKSSM--LNALFRIV 1289 (1622)
T ss_pred             cCCCEEEEECCCCCCHHHH--HHHHhCcC
Confidence            4678899999999999974  33444443

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=85.14  E-value=0.46  Score=37.94  Aligned_cols=17  Identities=18%  Similarity=0.301  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      -+||+..+|+|+|||+.
T Consensus       151 PknVLFyGppGTGKTm~  167 (368)
T COG1223         151 PKNVLFYGPPGTGKTMM  167 (368)
T ss_pred             cceeEEECCCCccHHHH
Confidence            37999999999999985

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=85.12  E-value=0.49  Score=39.74  Aligned_cols=17  Identities=29%  Similarity=0.309  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.+|||+|||...
T Consensus       117 ~~iLL~GP~GsGKT~lA  133 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLA  133 (413)
T ss_pred             ceEEEECCCCcCHHHHH
Confidence            57999999999999864

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=85.05  E-value=0.45  Score=34.96  Aligned_cols=14  Identities=21%  Similarity=0.437  Sum_probs=12.8

Q ss_pred             cEEEEccCCCCcch
Q 031654           68 DLMACAQTGSRKTT   81 (155)
Q Consensus        68 dvl~~a~TGsGKT~   81 (155)
                      +++..+|||+|||.
T Consensus         5 ~~ll~GpsGvGKT~   18 (171)
T PF07724_consen    5 NFLLAGPSGVGKTE   18 (171)
T ss_dssp             EEEEESSTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            68899999999996

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=85.02  E-value=0.52  Score=36.38  Aligned_cols=27  Identities=26%  Similarity=0.388  Sum_probs=19.6

Q ss_pred             hcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           64 VAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      -.|.-+.+.+|+|||||.-  +-++..+.
T Consensus        29 ~~Ge~vaI~GpSGSGKSTL--Lniig~ld   55 (226)
T COG1136          29 EAGEFVAIVGPSGSGKSTL--LNLLGGLD   55 (226)
T ss_pred             cCCCEEEEECCCCCCHHHH--HHHHhccc
Confidence            4678899999999999873  44444333

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=84.99  E-value=0.53  Score=32.39  Aligned_cols=18  Identities=28%  Similarity=0.322  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+.+.+++|||||.-
T Consensus        10 ~g~~~~i~G~nGsGKStL   27 (137)
T PF00005_consen   10 PGEIVAIVGPNGSGKSTL   27 (137)
T ss_dssp             TTSEEEEEESTTSSHHHH
T ss_pred             CCCEEEEEccCCCccccc
Confidence            577889999999999975

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>TIGR00957 MRP_assoc_pro multi drug resistance-associated protein (MRP)

Probab=84.94  E-value=0.43  Score=46.21  Aligned_cols=19  Identities=21%  Similarity=0.328  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      -.|+-+-++++||||||..
T Consensus      1310 ~~GekiaIVGrTGsGKSTL 1328 (1522)
T TIGR00957      1310 HGGEKVGIVGRTGAGKSSL 1328 (1522)
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3678899999999999974

This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.

>TIGR02653 Lon_rel_chp conserved hypothetical protein

Probab=84.65  E-value=0.56  Score=41.54  Aligned_cols=85  Identities=15%  Similarity=0.178  Sum_probs=54.6

Q ss_pred             HHHHHh-HHhCCCCC--CCHHHHH-----HHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCC
Q 031654           38 QHLRNK-PRTYKYVK--PTPVQRH-----ATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWV  109 (155)
Q Consensus        38 ~~l~~~-l~~~g~~~--pt~iQ~~-----~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~  109 (155)
                      ++.+.. |++.||+.  .+.-|+.     .+|.+-+.-|++=-+|-|||||..|                   +++....
T Consensus       180 dEWid~LlrSiG~eP~~~~~r~K~~~L~RliPlVE~N~Nl~ELgPrgTGKS~~y-------------------~eiSp~~  240 (675)
T TIGR02653       180 DEWIDVLLRSVGMEPTNLERRTKWHLLTRLIPLVENNYNLCELGPRGTGKSHVY-------------------KECSPNS  240 (675)
T ss_pred             HHHHHHHHHhcCCCccccCHHHHHHHHHhhhhhcccccceEEECCCCCCcceee-------------------eccCCce
Confidence            555554 46688863  3444443     4577778889999999999999987                   2333323


Q ss_pred             cEEEE----ChHHHHHHHHcCCCC-cccccceEEEEccc
Q 031654          110 DNLMA----TLRRLVNLLERGRVS-LQMIIRYLALKEAA  143 (155)
Q Consensus       110 ~IlI~----TP~~l~~~l~~~~~~-l~~l~~~lVlDEa~  143 (155)
                       ++|+    |+.+|..-+.++.+- ...- +.+++||+|
T Consensus       241 -~liSGG~~T~A~LFyn~~~~~~GlVg~~-D~VaFDEva  277 (675)
T TIGR02653       241 -ILMSGGQTTVANLFYNMSTRQIGLVGMW-DVVAFDEVA  277 (675)
T ss_pred             -EEEECCccchhHeeEEcCCCceeEEeec-cEEEEeecc
Confidence             3443    777766555555432 3344 679999993

This model describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to Pfam model pfam05362, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of E. coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST].

>TIGR03263 guanyl_kin guanylate kinase

Probab=84.60  E-value=0.55  Score=34.04  Aligned_cols=17  Identities=24%  Similarity=0.304  Sum_probs=14.2

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      |+=+++.+|+|||||..
T Consensus         1 g~ii~l~G~~GsGKsTl   17 (180)
T TIGR03263         1 GLLIVISGPSGVGKSTL   17 (180)
T ss_pred             CcEEEEECCCCCCHHHH
Confidence            45578999999999984

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=84.56  E-value=0.53  Score=37.97  Aligned_cols=17  Identities=24%  Similarity=0.190  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +=+++++|||||||...
T Consensus         5 ~~i~i~GptgsGKt~la   21 (307)
T PRK00091          5 KVIVIVGPTASGKTALA   21 (307)
T ss_pred             eEEEEECCCCcCHHHHH
Confidence            34789999999999764

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=84.50  E-value=1.2  Score=36.79  Aligned_cols=19  Identities=21%  Similarity=0.300  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCCcchhhh
Q 031654           66 GRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl   84 (155)
                      |.=+++.+++|+|||.-.+
T Consensus        82 GslvLI~G~pG~GKStLll  100 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLL  100 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHH
Confidence            4678899999999998543

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=84.43  E-value=0.55  Score=34.08  Aligned_cols=17  Identities=24%  Similarity=0.341  Sum_probs=14.4

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +-+++.+|+|||||...
T Consensus         2 ~~~~i~G~sGsGKttl~   18 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLL   18 (179)
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            45789999999999865

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=84.43  E-value=0.53  Score=36.70  Aligned_cols=23  Identities=22%  Similarity=0.244  Sum_probs=16.9

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIING   90 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~   90 (155)
                      -.+++.|++|||||. +++-++..
T Consensus        14 fr~viIG~sGSGKT~-li~~lL~~   36 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTT-LIKSLLYY   36 (241)
T ss_pred             ceEEEECCCCCCHHH-HHHHHHHh
Confidence            378999999999997 44444433

This is thought to be an ATPase involved in viral DNA packaging [].

>cd01366 KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins

Probab=84.40  E-value=0.95  Score=36.50  Aligned_cols=26  Identities=31%  Similarity=0.369  Sum_probs=20.5

Q ss_pred             HHHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           58 HATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        58 ~~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      ..+..++.|.|  +++.++||||||.+.
T Consensus        68 p~v~~~~~G~~~~i~ayG~tgSGKT~tl   95 (329)
T cd01366          68 PLVQSALDGYNVCIFAYGQTGSGKTYTM   95 (329)
T ss_pred             HHHHHHhCCCceEEEEeCCCCCCCcEEe
Confidence            35566778965  778899999999875

Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found at the C-terminus (C-type). C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for mi

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=84.28  E-value=1  Score=38.12  Aligned_cols=17  Identities=24%  Similarity=0.331  Sum_probs=15.1

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +++++.+|||+|||...
T Consensus        48 ~~ILLiGppG~GKT~lA   64 (441)
T TIGR00390        48 KNILMIGPTGVGKTEIA   64 (441)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            68999999999999753

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein

Probab=84.19  E-value=0.44  Score=42.52  Aligned_cols=19  Identities=26%  Similarity=0.305  Sum_probs=16.7

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      -.|+-+.+++|+|||||..
T Consensus       505 ~~Ge~vaIvG~SGsGKSTL  523 (711)
T TIGR00958       505 HPGEVVALVGPSGSGKSTV  523 (711)
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4678899999999999975

>PRK06620 hypothetical protein; Validated

Probab=84.10  E-value=0.55  Score=35.71  Aligned_cols=16  Identities=25%  Similarity=0.104  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.++++||+|||||.-
T Consensus        45 ~~l~l~Gp~G~GKThL   60 (214)
T PRK06620         45 FTLLIKGPSSSGKTYL   60 (214)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            4589999999999985

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=84.06  E-value=0.9  Score=34.85  Aligned_cols=27  Identities=15%  Similarity=0.119  Sum_probs=19.3

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      .|..+++.+++|+|||.-.+--+.+.+
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~   46 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGL   46 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            357899999999999985443344444

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	155
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-14
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-11
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		1e-09
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		1e-05
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		2e-05
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		2e-05
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-05
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-04
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		4e-04

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

Iteration: 1
 Score = 74.7 bits (182), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 54/162 (33%), Positives = 72/162 (44%), Gaps = 59/162 (36%)
Query: 48  KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI-----------MRE-- 94
           +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I           M+E  
Sbjct: 34  RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENG 93
Query: 95  ------------------------YYSARK--------------------ELRELARWVD 110
                                   Y  ARK                    ++R+L R   
Sbjct: 94  RYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCH 153
Query: 111 NLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN 152
            L+AT  RLV+++ERG++ L    +YL L E AD+ LDM   
Sbjct: 154 LLVATPGRLVDMMERGKIGLDF-CKYLVLDE-ADRMLDMGFE 193

>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 = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 46/160 (28%), Positives = 71/160 (44%), Gaps = 50/160 (31%)
Query: 40  LRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM-----RE 94
           +RN      Y +PTP+Q++A   ++  RD+MACAQTGS KT  F  PIIN ++     ++
Sbjct: 34  IRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQ 93
Query: 95  YYS-------------------------------------------ARKELRELARWVDN 111
            YS                                              ++RE+      
Sbjct: 94  RYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHL 153
Query: 112 LMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL 151
           L+AT  RLV+ +E+ ++SL+   +Y+ L E AD+ LDM  
Sbjct: 154 LVATPGRLVDFIEKNKISLEF-CKYIVLDE-ADRMLDMGF 191

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 49/199 (24%), Positives = 87/199 (43%), Gaps = 48/199 (24%)
Query: 1   MSASWAADSVFASENAAPASSSTNTLSSPAARF--AYVPQHLRNKPRTYKYVKPTPVQRH 58
            S+  A+   F+  N  P   + + +  P   F  A +   + +      Y  PTP+Q+ 
Sbjct: 26  FSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKC 85
Query: 59  ATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS---ARKEL------RELARWV 109
           +  ++ +GRDLMACAQTGS KT  F  PI++ ++ + +     R ++      RELA  +
Sbjct: 86  SIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQI 145
Query: 110 DN-----------------------------------LMATLRRLVNLLERGRVSLQMII 134
            N                                   ++AT  RL++ ++R  ++ +   
Sbjct: 146 FNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFED-T 204
Query: 135 RYLALKEAADQTLDMALNQ 153
           R++ L E AD+ LDM  ++
Sbjct: 205 RFVVLDE-ADRMLDMGFSE 222

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR 93
           + KPT +Q  A  + + GRD++  A+TGS KT  F  PI+N ++ 
Sbjct: 63  WTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLE 107

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 41/86 (47%), Gaps = 9/86 (10%)
Query: 26  LSSPAARFAYVPQHLRNKPRTYK------YVKPTPVQRHATSILVAGRDLMACAQTGSRK 79
           L  P A F  + Q  +   R  +      +  PTP+Q  A  +++ GR+L+A A TGS K
Sbjct: 20  LPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGK 79
Query: 80  TTPFCFPIINGIMREYYSARKELREL 105
           T  F  PI   +M+    A K  R L
Sbjct: 80  TLAFSIPI---LMQLKQPANKGFRAL 102

>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 = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/148 (25%), Positives = 59/148 (39%), Gaps = 46/148 (31%)
Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKE------- 101
           + +PT +Q     + ++G D++  AQTGS KT  +  P I  I  + +  R +       
Sbjct: 63  FTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVL 122
Query: 102 -------------------------------------LRELARWVDNLMATLRRLVNLLE 124
                                                +R+L R V+  +AT  RL++ LE
Sbjct: 123 APTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLE 182
Query: 125 RGRVSLQMIIRYLALKEAADQTLDMALN 152
            G+ +L+    YL L E AD+ LDM   
Sbjct: 183 CGKTNLRRTT-YLVLDE-ADRMLDMGFE 208

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 37/148 (25%), Positives = 59/148 (39%), Gaps = 46/148 (31%)
Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKE------- 101
           + +PT +Q     + ++G D++  AQTGS KT  +  P I  I  + +  R +       
Sbjct: 49  FTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVL 108
Query: 102 -------------------------------------LRELARWVDNLMATLRRLVNLLE 124
                                                +R+L R V+  +AT  RL++ LE
Sbjct: 109 APTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLE 168
Query: 125 RGRVSLQMIIRYLALKEAADQTLDMALN 152
            G+ +L+    YL L E AD+ LDM   
Sbjct: 169 CGKTNLRRTT-YLVLDE-ADRMLDMGFE 194

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/164 (26%), Positives = 66/164 (40%), Gaps = 47/164 (28%)
Query: 33  FAYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPII---- 88
           F   P  L++  R    +KPTP+Q  A  I++ G DL+  AQTG+ KT  +  P      
Sbjct: 25  FQQYPDLLKSIIRV-GILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLD 83
Query: 89  -NGIMRE------------------------------------YYSARK---ELRELARW 108
              I RE                                     Y  R    ++ ++++ 
Sbjct: 84  SQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDISKG 143
Query: 109 VDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN 152
           VD ++AT  RL +L     V+L+  I YL + E AD+ LDM   
Sbjct: 144 VDIIIATPGRLNDLQMNNSVNLRS-ITYLVIDE-ADKMLDMEFE 185

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 26/43 (60%)
Query: 49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI 91
          + KP+P+Q  A  + + GRD++A A+ G+ KT  F  P +  +
Sbjct: 41 FEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKV 83

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	155
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-29
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	4e-28
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	4e-26
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-24
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-22
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	2e-22
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	6e-17
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-15
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	6e-15
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	4e-14
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-13
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	6e-13
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	1e-11
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	4e-11
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-10
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-09
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	2e-09
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	6e-09
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	8e-09
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-08
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-08
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	2e-08
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	2e-08
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-08
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	9e-08
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	8e-07
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-06
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	5e-06
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	5e-06
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	7e-06
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-04

>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 =  107 bits (269), Expect = 1e-29
 Identities = 47/161 (29%), Positives = 72/161 (44%), Gaps = 50/161 (31%)

Query: 37  PQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM---- 92
              +RN      Y +PTP+Q++A   ++  RD+MACAQTGS KT  F  PIIN ++    
Sbjct: 31  DPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDL 90

Query: 93  -------------------RE-----YYSARK--------------------ELRELARW 108
                              RE        ++K                    ++RE+   
Sbjct: 91  NQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMG 150

Query: 109 VDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM 149
              L+AT  RLV+ +E+ ++SL+   +Y+ L E AD+ LDM
Sbjct: 151 CHLLVATPGRLVDFIEKNKISLEF-CKYIVLDE-ADRMLDM 189

>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 =  106 bits (267), Expect = 4e-28
 Identities = 44/167 (26%), Positives = 72/167 (43%), Gaps = 48/167 (28%)

Query: 29  PAARF--AYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFP 86
           P   F  A +   + +      Y  PTP+Q+ +  ++ +GRDLMACAQTGS KT  F  P
Sbjct: 54  PIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLP 113

Query: 87  IINGIM-------------------RE-----YYSARK--------------------EL 102
           I++ ++                   RE     +  ARK                    + 
Sbjct: 114 ILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQN 173

Query: 103 RELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM 149
             + R    ++AT  RL++ ++R  ++ +   R++ L E AD+ LDM
Sbjct: 174 ECITRGCHVVIATPGRLLDFVDRTFITFED-TRFVVLDE-ADRMLDM 218

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  101 bits (253), Expect = 4e-26
 Identities = 54/173 (31%), Positives = 74/173 (42%), Gaps = 59/173 (34%)

Query: 34  AYVPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM- 92
             + + +       +Y +PTPVQ+HA  I+   RDLMACAQTGS KT  F  PI++ I  
Sbjct: 20  VEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYS 79

Query: 93  -------------------------------RE-----YYSARK---------------- 100
                                          RE     Y  ARK                
Sbjct: 80  DGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGA 139

Query: 101 ----ELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM 149
               ++R+L R    L+AT  RLV+++ERG++ L    +YL L E AD+ LDM
Sbjct: 140 DIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDF-CKYLVLDE-ADRMLDM 190

>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 = 94.1 bits (235), Expect = 1e-24
 Identities = 42/167 (25%), Positives = 66/167 (39%), Gaps = 48/167 (28%)

Query: 29  PAARFAYV--PQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFP 86
           P   F     P ++ +      + +PT +Q     + ++G D++  AQTGS KT  +  P
Sbjct: 27  PVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLP 86

Query: 87  IINGIM-------------------RE-----YYSARK--------------------EL 102
            I  I                    RE        A +                    ++
Sbjct: 87  AIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQI 146

Query: 103 RELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM 149
           R+L R V+  +AT  RL++ LE G+ +L+    YL L E AD+ LDM
Sbjct: 147 RDLERGVEICIATPGRLIDFLECGKTNLRR-TTYLVLDE-ADRMLDM 191

>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 = 88.4 bits (220), Expect = 1e-22
 Identities = 38/146 (26%), Positives = 59/146 (40%), Gaps = 46/146 (31%)

Query: 48  KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM--------------- 92
             +KPTP+Q  A  I++ G DL+  AQTG+ KT  +  P    +                
Sbjct: 39  GILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGML 98

Query: 93  -----RE-----YYSARK-------------------ELRELARWVDNLMATLRRLVNLL 123
                RE          K                   ++ ++++ VD ++AT  RL +L 
Sbjct: 99  VLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQ 158

Query: 124 ERGRVSLQMIIRYLALKEAADQTLDM 149
               V+L+  I YL + E AD+ LDM
Sbjct: 159 MNNSVNLRS-ITYLVIDE-ADKMLDM 182

>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 = 88.8 bits (221), Expect = 2e-22
 Identities = 33/158 (20%), Positives = 58/158 (36%), Gaps = 45/158 (28%)

Query: 36  VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM--- 92
           +   L        +  PTP+Q  A  +++ GR+L+A A TGS KT  F  PI+  +    
Sbjct: 36  INSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA 95

Query: 93  ------------RE-----YYSARK---------------------ELRELARWVDNLMA 114
                       RE     +    K                        + ++  D L+ 
Sbjct: 96  NKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVT 155

Query: 115 TLRRLVNLLERGR--VSLQMIIRYLALKEAADQTLDMA 150
           T  RL+ LL++    + L   + +L + E +D+  +  
Sbjct: 156 TPNRLIYLLKQDPPGIDLAS-VEWLVVDE-SDKLFEDG 191

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 75.5 bits (186), Expect = 6e-17
 Identities = 19/140 (13%), Positives = 36/140 (25%), Gaps = 43/140 (30%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM-----------RE--- 94
               T  QR     +V G+     A TG  KTT      +                    
Sbjct: 19  GKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVK 78

Query: 95  ------------------YYSA------RKELRELAR-WVDNLMATLRRLVNLLERGRVS 129
                             +YS+       K  +         L+ + + +     R ++S
Sbjct: 79  QTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSK--NREKLS 136

Query: 130 LQMIIRYLALKEAADQTLDM 149
            +    ++ + +  D  L  
Sbjct: 137 QKR-FDFVFVDD-VDAVLKA 154

>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 = 69.6 bits (171), Expect = 3e-15
 Identities = 36/141 (25%), Positives = 62/141 (43%), Gaps = 42/141 (29%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM--------------RE 94
           + KPT +Q  A  + + GRD++  A+TGS KT  F  PI+N ++              RE
Sbjct: 63  WTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRE 122

Query: 95  ----------YYSARKELR---------------ELARWVDNLMATLRRLVNLLERGR-V 128
                        +   ++                LA+    ++AT  RL++ LE  +  
Sbjct: 123 LAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGF 182

Query: 129 SLQMIIRYLALKEAADQTLDM 149
           +L+  ++YL + E AD+ L+M
Sbjct: 183 NLRA-LKYLVMDE-ADRILNM 201

>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 = 67.9 bits (167), Expect = 6e-15
 Identities = 35/141 (24%), Positives = 51/141 (36%), Gaps = 42/141 (29%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARK-------- 100
              PTP+Q  A  + + G+DL+  A+TG+ KT  F  PI   +       RK        
Sbjct: 21  LTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTP 80

Query: 101 --EL------------------------------RELARWVDNLMATLRRLVNLLERGRV 128
             EL                                L R  D ++AT  R ++ L +G +
Sbjct: 81  TRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVL 140

Query: 129 SLQMIIRYLALKEAADQTLDM 149
            L   +    L E AD+ L M
Sbjct: 141 DLSR-VEVAVLDE-ADEMLSM 159

>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 = 66.6 bits (163), Expect = 4e-14
 Identities = 28/106 (26%), Positives = 45/106 (42%), Gaps = 14/106 (13%)

Query: 14  ENAAPASSSTNTLSSPAARFAYVPQHLRNKP-----RTYKYVKPTPVQRHATSILVAGRD 68
           E+  P+     T +     FA +   + N+      +   +   T +Q  +   L+ GRD
Sbjct: 35  ESEVPSLPLGLTGAFEDTSFASLCNLV-NENTLKAIKEMGFTNMTEIQHKSIRPLLEGRD 93

Query: 69  LMACAQTGSRKTTPFCFPIINGIMREYYSARKEL--------RELA 106
           L+A A+TGS KT  F  P +  I++  +  R           RELA
Sbjct: 94  LLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELA 139

>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 = 65.6 bits (161), Expect = 1e-13
 Identities = 26/133 (19%), Positives = 49/133 (36%), Gaps = 34/133 (25%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR--------------- 93
           +   T VQ     +++ G++++  A+TGS KT  +  PI+   M+               
Sbjct: 14  FKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTRELTRQVA 73

Query: 94  ---EYYSARKELRELA--------------RWVDNLMATLRRLVNLLERGRVSLQMIIRY 136
                     + +                 R  D ++AT  RL++L  +G + L      
Sbjct: 74  SHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWSKGVIDLSS-FEI 132

Query: 137 LALKEAADQTLDM 149
           + + E AD   +M
Sbjct: 133 VIIDE-ADLMFEM 144

>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 = 63.0 bits (154), Expect = 6e-13
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 8/67 (11%)

Query: 48  KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKEL----- 102
           +Y   T +Q+    + + G+D++  A+TGS KT  F  P++  + R  +++   L     
Sbjct: 44  QYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLII 103

Query: 103 ---RELA 106
              RELA
Sbjct: 104 SPTRELA 110

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 59.1 bits (144), Expect = 1e-11
 Identities = 27/144 (18%), Positives = 46/144 (31%), Gaps = 45/144 (31%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM--------------RE 94
           + KPT +Q       + G  ++  +QTG+ KT  +  PI+  I               RE
Sbjct: 24  FYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE 83

Query: 95  --------------------------YY---SARKELRELARWVDNLMATLRRLVNLLER 125
                                            +K L +L      ++ T  R+ + +  
Sbjct: 84  LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIRE 143

Query: 126 GRVSLQMIIRYLALKEAADQTLDM 149
             + +      L + E AD  LDM
Sbjct: 144 QALDVHT-AHILVVDE-ADLMLDM 165

>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 = 57.5 bits (140), Expect = 4e-11
 Identities = 26/141 (18%), Positives = 58/141 (41%), Gaps = 42/141 (29%)

Query: 49  YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI----------------- 91
           + KP+P+Q  +  I ++GRD++A A+ G+ K+  +  P++  +                 
Sbjct: 23  WEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE 82

Query: 92  --------MREY------------Y---SARKELRELARWVDNLMATLRRLVNLLERGRV 128
                     +                 + R ++  L   V  ++AT  R+++L+++G  
Sbjct: 83  LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVA 142

Query: 129 SLQMIIRYLALKEAADQTLDM 149
            +   ++ + L E AD+ L  
Sbjct: 143 KVDH-VQMIVLDE-ADKLLSQ 161

>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 = 57.1 bits (138), Expect = 2e-10
 Identities = 29/152 (19%), Positives = 57/152 (37%), Gaps = 51/152 (33%)

Query: 48  KYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKEL--- 102
           ++   TPVQ+     +++    D++A A+TG+ KT  F  PI   ++   + ++  +   
Sbjct: 91  EFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAV 150

Query: 103 -----RELA----------------------------------------RWVDNLMATLR 117
                R+LA                                           + ++AT  
Sbjct: 151 IVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPG 210

Query: 118 RLVNLLERGRVSLQMIIRYLALKEAADQTLDM 149
           RL+++LE+        + Y  L E AD+ L++
Sbjct: 211 RLIDVLEKYSNKFFRFVDYKVLDE-ADRLLEI 241

>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 = 54.8 bits (132), Expect = 1e-09
 Identities = 29/152 (19%), Positives = 57/152 (37%), Gaps = 51/152 (33%)

Query: 48  KYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKEL--- 102
           ++   TPVQ+     +++    D++A A+TG+ KT  F  PI   ++   + ++  +   
Sbjct: 40  EFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAV 99

Query: 103 -----RELA----------------------------------------RWVDNLMATLR 117
                R+LA                                           + ++AT  
Sbjct: 100 IVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPG 159

Query: 118 RLVNLLERGRVSLQMIIRYLALKEAADQTLDM 149
           RL+++LE+        + Y  L E AD+ L++
Sbjct: 160 RLIDVLEKYSNKFFRFVDYKVLDE-ADRLLEI 190

>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 = 53.7 bits (130), Expect = 2e-09
 Identities = 29/142 (20%), Positives = 50/142 (35%), Gaps = 41/142 (28%)

Query: 47  YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI--------------- 91
             + KP+P+Q  A  + + GRD++A A+ G+ KT  F  P +  +               
Sbjct: 39  AGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPT 98

Query: 92  ----------MREY--------------YSARKELRELARWVDNLMATLRRLVNLLERGR 127
                     +R                 + R ++  L   V  L+ T  R+++L  R  
Sbjct: 99  RELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKV 158

Query: 128 VSLQMIIRYLALKEAADQTLDM 149
             L        + E AD+ L  
Sbjct: 159 ADLSD-CSLFIMDE-ADKMLSR 178

>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 = 52.5 bits (127), Expect = 6e-09
 Identities = 30/139 (21%), Positives = 56/139 (40%), Gaps = 40/139 (28%)

Query: 49  YVKPTPVQRHATSILVAGR-DLMACAQTGSRKTTPFCFPIINGI-------------MRE 94
           + KPT +Q     + +    +++A A+TGS KT  F  P+I  +              RE
Sbjct: 26  FEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRE 85

Query: 95  ----------YYSARKELRELA--------------RWVDNLMATLRRLVNLLERGRVSL 130
                          K L+                 +  + ++ T  R+++ + RG ++L
Sbjct: 86  LAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNL 145

Query: 131 QMIIRYLALKEAADQTLDM 149
           +  ++Y  L E AD+ L+M
Sbjct: 146 KN-VKYFILDE-ADEMLNM 162

>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 = 51.5 bits (124), Expect = 8e-09
 Identities = 27/142 (19%), Positives = 49/142 (34%), Gaps = 41/142 (28%)

Query: 47  YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI--------------M 92
             + +P+PVQ  A  +   G DL+  A++G+ KT  F    ++ +               
Sbjct: 42  AGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPT 101

Query: 93  REY-YSARKELRELARWVDNL--------------MATLR----------RLVNLLERGR 127
           RE        +  +   ++ L                 L+          R+  L+E   
Sbjct: 102 REIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDY 161

Query: 128 VSLQMIIRYLALKEAADQTLDM 149
           ++    IR   L E AD+ L+ 
Sbjct: 162 LNPGS-IRLFILDE-ADKLLEE 181

>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 = 51.5 bits (124), Expect = 1e-08
 Identities = 15/45 (33%), Positives = 26/45 (57%)

Query: 47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI 91
          Y + KP+ +Q+ A    + G D++A AQ+G+ KT  F   I+  +
Sbjct: 48 YGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQL 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 = 51.0 bits (123), Expect = 1e-08
 Identities = 14/45 (31%), Positives = 26/45 (57%)

Query: 47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI 91
          Y + +P+ +Q+ A   ++ G D++A AQ+G+ KT  F    +  I
Sbjct: 32 YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI 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 = 51.0 bits (123), Expect = 2e-08
 Identities = 29/145 (20%), Positives = 50/145 (34%), Gaps = 48/145 (33%)

Query: 47  YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKEL---- 102
           Y + +P+ +Q+ A   ++ G D++A AQ+G+ KT  F    +  I        K      
Sbjct: 39  YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS----VKAPQALM 94

Query: 103 ----RELARWVDNLMATLR----------------------------------RLVNLLE 124
               RELA  +  ++  L                                   R+ + ++
Sbjct: 95  LAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQ 154

Query: 125 RGRVSLQMIIRYLALKEAADQTLDM 149
           R R      I+   L E AD+ L  
Sbjct: 155 RRRFRTDK-IKMFILDE-ADEMLSS 177

>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 = 51.0 bits (123), Expect = 2e-08
 Identities = 26/142 (18%), Positives = 56/142 (39%), Gaps = 41/142 (28%)

Query: 47  YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI--------------- 91
           Y + KP+ +Q+ A   ++ GRD++A +Q+G+ KT  F   ++  +               
Sbjct: 55  YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPT 114

Query: 92  ----------MREY-----------Y---SARKELRELARWVDNLMATLRRLVNLLERGR 127
                     +                  +  +++R+L      +  T  R+ +++ R  
Sbjct: 115 RELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRS 174

Query: 128 VSLQMIIRYLALKEAADQTLDM 149
           +  +  I+ L L E AD+ L+ 
Sbjct: 175 LRTRA-IKMLVLDE-ADEMLNK 194

>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 = 50.6 bits (122), Expect = 2e-08
 Identities = 16/45 (35%), Positives = 26/45 (57%)

Query: 47  YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI 91
           Y + KP+ +Q+ A    + G D++A AQ+G+ KT  F   I+  I
Sbjct: 58  YGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQI 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 = 48.4 bits (116), Expect = 9e-08
 Identities = 24/143 (16%), Positives = 49/143 (34%), Gaps = 43/143 (30%)

Query: 47  YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI--------------M 92
             +  P+ VQ       + G D++  A++G  KT  F    +  +               
Sbjct: 32  CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHT 91

Query: 93  REY-YSARKELRELARWVDNL--------------MATLR------------RLVNLLER 125
           RE  +   KE    ++++ N+                 L+            R++ L   
Sbjct: 92  RELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN 151

Query: 126 GRVSLQMIIRYLALKEAADQTLD 148
             ++L+  I++  L E  D+ L+
Sbjct: 152 KSLNLKH-IKHFILDE-CDKMLE 172

>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 = 46.4 bits (111), Expect = 8e-07
 Identities = 10/45 (22%), Positives = 19/45 (42%)

Query: 47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI 91
            +  P+ VQ       + G D++  A++G  KT  F    +  +
Sbjct: 26 CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQL 70

>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 = 44.7 bits (106), Expect = 2e-06
 Identities = 11/47 (23%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 47  YKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGI 91
             + +P+ +Q +A  +++A   ++L+A +Q+G+ KT  F   +++ +
Sbjct: 110 MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

>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 = 44.1 bits (105), Expect = 5e-06
 Identities = 11/47 (23%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 47 YKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGI 91
            + +P+ +Q +A  +++A   ++L+A +Q+G+ KT  F   +++ +
Sbjct: 43 MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 89

>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 = 44.1 bits (105), Expect = 5e-06
 Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 47 YKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGI 91
           K+ KP+ +Q  A  +L+    R+++A +Q+G+ KT  F   ++  +
Sbjct: 23 MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69

>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 = 43.5 bits (103), Expect = 7e-06
 Identities = 11/47 (23%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 47  YKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGI 91
             + +P+ +Q +A  +++A   ++L+A +Q+G+ KT  F   +++ +
Sbjct: 110 MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	155
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.97
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.97
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.96
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.96
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.96
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.96
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.95
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.95
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.95
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.95
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.95
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.95
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.95
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.95
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.95
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.94
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.94
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.92
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.91
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.91
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.91
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.9
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.9
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.9
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.9
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.89
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.89
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.88
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.83
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.83
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.83
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.83
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.83
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.83
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.82
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.81
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.81
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.81
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.8
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.79
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.79
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.78
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.78
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.78
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.78
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.78
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.77
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.77
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.73
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.73
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.72
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.71
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.71
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.71
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.67
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.64
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.57
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.55
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.54
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.5
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.49
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.49
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.49
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.48
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.47
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.44
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.35
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.34
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.34
3h1t_A	590	Type I site-specific restriction-modification syst	99.32
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.29
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.28
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.13
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.01
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.0
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.72
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.68
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.54
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.49
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.43
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.13
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.86
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.84
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.73
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.08
3bos_A	242	Putative DNA replication factor; P-loop containing	97.02
3co5_A	143	Putative two-component system transcriptional RES	96.7
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.68
2qgz_A	308	Helicase loader, putative primosome component; str	96.68
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.64
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.54
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.46
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.45
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.4
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.31
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.12
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.09
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.0
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.0
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	95.97
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	95.88
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.81
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	95.75
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	95.72
2chg_A	226	Replication factor C small subunit; DNA-binding pr	95.65
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	95.59
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.55
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	95.43
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.35
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.32
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	95.01
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	94.93
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.8
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	94.77
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.75
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	94.22
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	94.21
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	94.1
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	94.08
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	93.94
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	93.93
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	92.62
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	92.49
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	92.36
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	92.3
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	92.24
3pvs_A	447	Replication-associated recombination protein A; ma	92.23
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	92.23
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	92.17
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	92.16
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	92.13
1xp8_A	366	RECA protein, recombinase A; recombination, radior	92.02
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	91.98
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	91.59
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	91.55
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	91.29
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	91.26
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	90.82
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	90.72
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	90.7
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	90.37
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	90.31
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	90.21
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	90.19
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	90.14
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	89.85
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	89.82
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	89.73
2r44_A	331	Uncharacterized protein; putative ATPase, structur	89.71
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	89.62
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	89.6
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	89.51
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	89.45
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	89.41
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	89.37
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	89.34
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	89.33
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	89.28
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	89.28
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	89.27
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	89.24
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	89.21
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	89.16
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	89.16
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	89.08
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	89.02
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	88.97
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	88.9
3u06_A	412	Protein claret segregational; motor domain, stalk	88.89
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	88.81
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	88.76
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	88.75
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	88.62
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	88.53
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	88.44
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	88.33
2eyu_A	261	Twitching motility protein PILT; pilus retraction	88.29
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	88.23
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	88.17
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	88.16
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	88.15
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	88.15
1p9r_A	418	General secretion pathway protein E; bacterial typ	88.13
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	88.07
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	88.01
2r6a_A	454	DNAB helicase, replicative helicase; replication,	88.0
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	87.98
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	87.95
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	87.93
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	87.9
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	87.84
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	87.8
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	87.57
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	87.56
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	87.44
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	87.42
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	87.32
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	87.25
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	87.18
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	87.17
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	86.92
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	86.73
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	86.7
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	86.55
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	86.53
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	86.53
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	86.41
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	86.23
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	86.17
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	86.16
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	86.13
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	86.05
2ewv_A	372	Twitching motility protein PILT; pilus retraction	85.89
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	85.75
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	85.72
1u94_A	356	RECA protein, recombinase A; homologous recombinat	85.63
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	85.52
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	85.5
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	85.41
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	85.33
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	85.22
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	85.21
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	85.13
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	85.1
1tue_A	212	Replication protein E1; helicase, replication, E1E	85.1
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	85.05
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	84.87
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	84.8
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	84.79
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	84.69
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	84.63
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	84.62
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	84.44
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	84.43
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	84.31
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	84.25
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	84.17
4h1g_A	715	Maltose binding protein-cakar3 motor domain fusio;	83.9
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	83.8
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	83.63
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	83.4
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	83.37
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	83.35
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	83.25
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	83.13
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	83.13
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	83.05
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	83.01
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	82.82
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	82.63
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	82.48
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	82.26
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	82.21
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	82.15
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	82.01
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	81.99
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	81.81
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	81.77
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	81.74
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	81.48
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	81.32
3io5_A	333	Recombination and repair protein; storage dimer, i	81.26
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	81.12
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	81.04
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	80.82
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	80.7
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	80.63
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	80.6
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	80.44
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	80.34
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	80.15
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	80.1
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	80.09
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	80.03

>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=100.00  E-value=5.2e-34  Score=234.98  Aligned_cols=149  Identities=29%  Similarity=0.514  Sum_probs=134.2

Q ss_pred             CCcccCccccccCCcCcccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcc
Q 031654            3 ASWAADSVFASENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKT   80 (155)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT   80 (155)
                      ....++.+|+.++++++.+.|.+.|.++.+|++++  +.++++|+++||.+|||+|+++||.+++|+|++++||||||||
T Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT  107 (434)
T 2db3_A           28 SGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKT  107 (434)
T ss_dssp             CCCCCCTTGGGGGGSCEEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHH
T ss_pred             cCcccccChhhhcCceeEecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCch
Confidence            34566788999999999999999999999999987  9999999999999999999999999999999999999999999


Q ss_pred             hhhhhHHHHHHHHhhhc-------h-------------------------------------HHHHHHHhcCCcEEEECh
Q 031654           81 TPFCFPIINGIMREYYS-------A-------------------------------------RKELRELARWVDNLMATL  116 (155)
Q Consensus        81 ~~yllp~l~~l~~~~~~-------~-------------------------------------~~~~~~l~~~~~IlI~TP  116 (155)
                      ++|++|+++++......       .                                     ..+...+..+++|+|+||
T Consensus       108 ~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp  187 (434)
T 2db3_A          108 AAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATP  187 (434)
T ss_dssp             HHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECH
T ss_pred             HHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEECh
Confidence            99999999998764321       1                                     345566667899999999


Q ss_pred             HHHHHHHHcCCCCcccccceEEEEccccccccccccc
Q 031654          117 RRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       117 ~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~~  153 (155)
                      ++|.+++.++.+.++++ +++|+||| |+|+++||.+
T Consensus       188 ~~l~~~l~~~~~~l~~~-~~lVlDEa-h~~~~~gf~~  222 (434)
T 2db3_A          188 GRLLDFVDRTFITFEDT-RFVVLDEA-DRMLDMGFSE  222 (434)
T ss_dssp             HHHHHHHHTTSCCCTTC-CEEEEETH-HHHTSTTTHH
T ss_pred             HHHHHHHHhCCcccccC-CeEEEccH-hhhhccCcHH
Confidence            99999999999999999 99999999 9999999875

>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=99.97  E-value=1.1e-31  Score=205.26  Aligned_cols=136  Identities=28%  Similarity=0.426  Sum_probs=119.8

Q ss_pred             CcCcccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           16 AAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        16 ~~~~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      +..+.+.|.+.|.++.+|++++  +.+++++.++||..|+++|.++|+.+++|+|++++||||||||++|++|++.++..
T Consensus        14 ~~~i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~   93 (242)
T 3fe2_A           14 SKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINH   93 (242)
T ss_dssp             HHTEEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             cCceEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHh
Confidence            3466778889999999999987  99999999999999999999999999999999999999999999999999998874


Q ss_pred             hh-------hch-------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCC
Q 031654           94 EY-------YSA-------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVS  129 (155)
Q Consensus        94 ~~-------~~~-------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~  129 (155)
                      ..       ...                                     ..+...+..+++|+|+||++|.+++.++...
T Consensus        94 ~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~  173 (242)
T 3fe2_A           94 QPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTN  173 (242)
T ss_dssp             SCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCC
T ss_pred             ccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCC
Confidence            32       001                                     3444556667999999999999999999899


Q ss_pred             cccccceEEEEccccccccccccc
Q 031654          130 LQMIIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       130 l~~l~~~lVlDEa~D~ll~~gf~~  153 (155)
                      ++++ +++|+||| |+|+++||.+
T Consensus       174 ~~~~-~~lViDEa-h~l~~~~~~~  195 (242)
T 3fe2_A          174 LRRT-TYLVLDEA-DRMLDMGFEP  195 (242)
T ss_dssp             CTTC-CEEEETTH-HHHHHTTCHH
T ss_pred             cccc-cEEEEeCH-HHHhhhCcHH
Confidence            9999 99999999 9999999864

>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=99.97  E-value=6.6e-32  Score=207.29  Aligned_cols=141  Identities=35%  Similarity=0.577  Sum_probs=123.8

Q ss_pred             ccccCCcCcccCCCCCCC--CCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhH
Q 031654           11 FASENAAPASSSTNTLSS--PAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFP   86 (155)
Q Consensus        11 ~~~~~~~~~~~~~~~~p~--~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp   86 (155)
                      |..|+++++.+.|...|.  ++.+|++++  +.++++|.++||..|+++|.++|+.+++|+|+++++|||||||++|++|
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~   80 (253)
T 1wrb_A            1 FDKYDSIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIP   80 (253)
T ss_dssp             --CCCCCCCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHH
T ss_pred             CcchhhCceeeeCCCCCCCCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHH
Confidence            678899999999999887  889999987  9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhh-----------ch-------------------------------------HHHHHHHhcCCcEEEEChHH
Q 031654           87 IINGIMREYY-----------SA-------------------------------------RKELRELARWVDNLMATLRR  118 (155)
Q Consensus        87 ~l~~l~~~~~-----------~~-------------------------------------~~~~~~l~~~~~IlI~TP~~  118 (155)
                      ++..+.....           ..                                     ..+...+..+++|+|+||++
T Consensus        81 ~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~  160 (253)
T 1wrb_A           81 IINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGR  160 (253)
T ss_dssp             HHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHH
T ss_pred             HHHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHH
Confidence            9998864321           11                                     34445556678999999999


Q ss_pred             HHHHHHcCCCCcccccceEEEEccccccccccccc
Q 031654          119 LVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       119 l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~~  153 (155)
                      |.+++..+.+.++++ +++|+||| |+|+++||.+
T Consensus       161 l~~~l~~~~~~~~~~-~~lViDEa-h~~~~~~~~~  193 (253)
T 1wrb_A          161 LVDFIEKNKISLEFC-KYIVLDEA-DRMLDMGFEP  193 (253)
T ss_dssp             HHHHHHTTSBCCTTC-CEEEEETH-HHHHHTTCHH
T ss_pred             HHHHHHcCCCChhhC-CEEEEeCH-HHHHhCchHH
Confidence            999999988899999 99999999 9999999864

>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=99.96  E-value=2.5e-30  Score=195.48  Aligned_cols=131  Identities=30%  Similarity=0.441  Sum_probs=111.2

Q ss_pred             cCCCCCCCCCccccc-CC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhh--
Q 031654           21 SSTNTLSSPAARFAY-VP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY--   95 (155)
Q Consensus        21 ~~~~~~p~~~~~f~~-l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~--   95 (155)
                      ..+...|.+..+|++ ++  ++++++|.++||..|+++|.++|+.+++|+|+++++|||||||++|++|++..+....  
T Consensus         9 ~~~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~   88 (228)
T 3iuy_A            9 GEKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPIS   88 (228)
T ss_dssp             SSCCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-----
T ss_pred             CccCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccch
Confidence            345667899999999 45  9999999999999999999999999999999999999999999999999998775321  


Q ss_pred             ------hch------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccc
Q 031654           96 ------YSA------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMI  133 (155)
Q Consensus        96 ------~~~------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l  133 (155)
                            ...                                    ..+...+.++++|+|+||+++.+++..+.+.++++
T Consensus        89 ~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           89 REQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             ----CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             hhccCCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccc
Confidence                  000                                    23334555678999999999999999998999999


Q ss_pred             cceEEEEccccccccccccc
Q 031654          134 IRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       134 ~~~lVlDEa~D~ll~~gf~~  153 (155)
                       +++|+||| |+|+++||.+
T Consensus       169 -~~lViDEa-h~~~~~~~~~  186 (228)
T 3iuy_A          169 -TYLVIDEA-DKMLDMEFEP  186 (228)
T ss_dssp             -CEEEECCH-HHHHHTTCHH
T ss_pred             -eEEEEECH-HHHhccchHH
Confidence             99999999 9999999854

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

Probab=99.96  E-value=4.5e-29  Score=202.12  Aligned_cols=133  Identities=38%  Similarity=0.629  Sum_probs=117.2

Q ss_pred             cccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh
Q 031654           19 ASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY   96 (155)
Q Consensus        19 ~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~   96 (155)
                      +.+.|.+.|.++.+|++++  +.++++|+.+||..|||+|.++||.++.|+|++++||||||||++|++|++..+.....
T Consensus         3 ~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~   82 (417)
T 2i4i_A            3 VEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGP   82 (417)
T ss_dssp             EEEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCC
T ss_pred             cccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccc
Confidence            4567888999999999987  99999999999999999999999999999999999999999999999999998875431


Q ss_pred             c--------------------h-------------------------------------HHHHHHHhcCCcEEEEChHHH
Q 031654           97 S--------------------A-------------------------------------RKELRELARWVDNLMATLRRL  119 (155)
Q Consensus        97 ~--------------------~-------------------------------------~~~~~~l~~~~~IlI~TP~~l  119 (155)
                      .                    .                                     ..+...+..+++|+|+||++|
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l  162 (417)
T 2i4i_A           83 GEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRL  162 (417)
T ss_dssp             CHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHH
T ss_pred             cchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHH
Confidence            1                    1                                     234445556789999999999


Q ss_pred             HHHHHcCCCCcccccceEEEEccccccccccccc
Q 031654          120 VNLLERGRVSLQMIIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       120 ~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~~  153 (155)
                      .+++..+.+.++++ +++|+||| |++++.+|.+
T Consensus       163 ~~~l~~~~~~~~~~-~~iViDEa-h~~~~~~~~~  194 (417)
T 2i4i_A          163 VDMMERGKIGLDFC-KYLVLDEA-DRMLDMGFEP  194 (417)
T ss_dssp             HHHHHTTSBCCTTC-CEEEESSH-HHHHHTTCHH
T ss_pred             HHHHHcCCcChhhC-cEEEEECh-hHhhccCcHH
Confidence            99999988899999 99999999 9999998754

>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=99.96  E-value=4.2e-30  Score=203.12  Aligned_cols=123  Identities=16%  Similarity=0.280  Sum_probs=103.4

Q ss_pred             CCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------
Q 031654           29 PAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------   98 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------   98 (155)
                      ...+|++++  +.++++|.++||..||++|.++||.++.|  +|++++||||||||++|++|+++++.......      
T Consensus        90 ~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~  169 (300)
T 3fmo_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  169 (300)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             CcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEc
Confidence            467899987  99999999999999999999999999998  99999999999999999999999886543321      


Q ss_pred             ---------HHHHHHHh----------------------cCCcEEEEChHHHHHHHHc-CCCCcccccceEEEEcccccc
Q 031654           99 ---------RKELRELA----------------------RWVDNLMATLRRLVNLLER-GRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ---------~~~~~~l~----------------------~~~~IlI~TP~~l~~~l~~-~~~~l~~l~~~lVlDEa~D~l  146 (155)
                               ......+.                      .+++|+|+||++|.+++.+ +.++++++ ++|||||| |+|
T Consensus       170 PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l-~~lVlDEa-d~l  247 (300)
T 3fmo_B          170 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI-KVFVLDEA-DVM  247 (300)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTTCCCCGGGC-SEEEETTH-HHH
T ss_pred             CcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhhcCCCCEEEECHHHHHHHHHhcCCCChhhc-eEEEEeCH-HHH
Confidence                     11122221                      2468999999999999976 57889999 99999999 999


Q ss_pred             cc-ccccc
Q 031654          147 LD-MALNQ  153 (155)
Q Consensus       147 l~-~gf~~  153 (155)
                      ++ .||.+
T Consensus       248 ~~~~~~~~  255 (300)
T 3fmo_B          248 IATQGHQD  255 (300)
T ss_dssp             HHSTTHHH
T ss_pred             hhccCcHH
Confidence            98 57754

>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=99.96  E-value=9e-30  Score=194.34  Aligned_cols=131  Identities=28%  Similarity=0.461  Sum_probs=110.0

Q ss_pred             cCcccCCCCCCCCCcccccC----C--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHH
Q 031654           17 APASSSTNTLSSPAARFAYV----P--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIING   90 (155)
Q Consensus        17 ~~~~~~~~~~p~~~~~f~~l----~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~   90 (155)
                      ..+.+.+...|.++.+|+++    +  +.++++|.++||..|+++|.++|+.+++|+|+++++|||||||++|++|++..
T Consensus        11 ~~i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~   90 (245)
T 3dkp_A           11 HKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQ   90 (245)
T ss_dssp             TTEEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CceEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHH
Confidence            45667888999999999986    3  99999999999999999999999999999999999999999999999999988


Q ss_pred             HHHhhhc---h-------------HHHHHHH-------------------------hcCCcEEEEChHHHHHHHHcC--C
Q 031654           91 IMREYYS---A-------------RKELREL-------------------------ARWVDNLMATLRRLVNLLERG--R  127 (155)
Q Consensus        91 l~~~~~~---~-------------~~~~~~l-------------------------~~~~~IlI~TP~~l~~~l~~~--~  127 (155)
                      +......   .             .+....+                         ..+++|+|+||++|.+++..+  .
T Consensus        91 l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~  170 (245)
T 3dkp_A           91 LKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPG  170 (245)
T ss_dssp             HCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCS
T ss_pred             HhhcccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCC
Confidence            8542111   1             1111111                         235799999999999999886  5


Q ss_pred             CCcccccceEEEEccccccccc
Q 031654          128 VSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       128 ~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      ++++++ +++|+||| |+|++.
T Consensus       171 ~~~~~~-~~lViDEa-h~~~~~  190 (245)
T 3dkp_A          171 IDLASV-EWLVVDES-DKLFED  190 (245)
T ss_dssp             CCCTTC-CEEEESSH-HHHHHH
T ss_pred             cccccC-cEEEEeCh-HHhccc
Confidence            789999 99999999 999984

>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=99.95  E-value=3.1e-29  Score=191.18  Aligned_cols=131  Identities=24%  Similarity=0.380  Sum_probs=104.0

Q ss_pred             cCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch
Q 031654           21 SSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA   98 (155)
Q Consensus        21 ~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~   98 (155)
                      +...+.|.+..+|++++  +.++++|.++||..|+++|.++|+.+++|+|+++++|||||||++|++|++..+.......
T Consensus        20 ~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~   99 (237)
T 3bor_A           20 VIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKET   99 (237)
T ss_dssp             -------CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSC
T ss_pred             cccCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCc
Confidence            44556677889999988  9999999999999999999999999999999999999999999999999998765322111


Q ss_pred             ---------------------------------------HHHHHHHhcC-CcEEEEChHHHHHHHHcCCCCcccccceEE
Q 031654           99 ---------------------------------------RKELRELARW-VDNLMATLRRLVNLLERGRVSLQMIIRYLA  138 (155)
Q Consensus        99 ---------------------------------------~~~~~~l~~~-~~IlI~TP~~l~~~l~~~~~~l~~l~~~lV  138 (155)
                                                             ..+...+..+ ++|+|+||++|.+++.++.+.+.++ +++|
T Consensus       100 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~-~~lV  178 (237)
T 3bor_A          100 QALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWI-KMFV  178 (237)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTC-CEEE
T ss_pred             eEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccC-cEEE
Confidence                                                   1111222223 8999999999999999988889999 9999


Q ss_pred             EEccccccccccccc
Q 031654          139 LKEAADQTLDMALNQ  153 (155)
Q Consensus       139 lDEa~D~ll~~gf~~  153 (155)
                      +||| |+|++.||..
T Consensus       179 iDEa-h~~~~~~~~~  192 (237)
T 3bor_A          179 LDEA-DEMLSRGFKD  192 (237)
T ss_dssp             EESH-HHHHHTTCHH
T ss_pred             ECCc-hHhhccCcHH
Confidence            9999 9999998854

>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=99.95  E-value=1.1e-28  Score=187.16  Aligned_cols=131  Identities=22%  Similarity=0.308  Sum_probs=103.2

Q ss_pred             cCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch
Q 031654           21 SSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA   98 (155)
Q Consensus        21 ~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~   98 (155)
                      ..++..|.+..+|++++  +.++++|+++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.......
T Consensus        14 ~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~   93 (230)
T 2oxc_A           14 RTGDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLST   93 (230)
T ss_dssp             ----------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSC
T ss_pred             ccCCCCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCc
Confidence            34566677788999987  9999999999999999999999999999999999999999999999999998775432111


Q ss_pred             ---------------H------------------------HHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEE
Q 031654           99 ---------------R------------------------KELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL  139 (155)
Q Consensus        99 ---------------~------------------------~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVl  139 (155)
                                     .                        ........+++|+|+||+++.+++..+.+.+.++ +++|+
T Consensus        94 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~-~~lVi  172 (230)
T 2oxc_A           94 QILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSI-RLFIL  172 (230)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTTSCSEEEECHHHHHHHHHTTSSCGGGC-CEEEE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhccCCCEEEECHHHHHHHHhcCCcccccC-CEEEe
Confidence                           1                        1111122358999999999999999988899999 99999


Q ss_pred             Ecccccccccc-ccc
Q 031654          140 KEAADQTLDMA-LNQ  153 (155)
Q Consensus       140 DEa~D~ll~~g-f~~  153 (155)
                      ||| |+|+++| |.+
T Consensus       173 DEa-h~~~~~~~~~~  186 (230)
T 2oxc_A          173 DEA-DKLLEEGSFQE  186 (230)
T ss_dssp             SSH-HHHHSTTSSHH
T ss_pred             CCc-hHhhcCcchHH
Confidence            999 9999987 653

>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=99.95  E-value=3.1e-28  Score=187.36  Aligned_cols=124  Identities=29%  Similarity=0.450  Sum_probs=107.8

Q ss_pred             CCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------
Q 031654           28 SPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------   98 (155)
Q Consensus        28 ~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------   98 (155)
                      .+..+|++++  +.++++|+++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.......       
T Consensus        40 ~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~P  119 (249)
T 3ber_A           40 EETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTP  119 (249)
T ss_dssp             HHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECS
T ss_pred             cccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeC
Confidence            4467899988  9999999999999999999999999999999999999999999999999999887653221       


Q ss_pred             --------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHc-CCCCcccccceEEEEccccc
Q 031654           99 --------------------------------RKELRELARWVDNLMATLRRLVNLLER-GRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 --------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~-~~~~l~~l~~~lVlDEa~D~  145 (155)
                                                      ..+...+..+++|+|+||++|.+++.+ +.+.+.++ +++|+||| |+
T Consensus       120 tr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~-~~lViDEa-h~  197 (249)
T 3ber_A          120 TRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRAL-KYLVMDEA-DR  197 (249)
T ss_dssp             SHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTC-CEEEECSH-HH
T ss_pred             CHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCcccc-CEEEEcCh-hh
Confidence                                            233444556899999999999999887 56789999 99999999 99


Q ss_pred             cccccccc
Q 031654          146 TLDMALNQ  153 (155)
Q Consensus       146 ll~~gf~~  153 (155)
                      |++++|..
T Consensus       198 l~~~~~~~  205 (249)
T 3ber_A          198 ILNMDFET  205 (249)
T ss_dssp             HHHTTCHH
T ss_pred             hhccChHH
Confidence            99998854

>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=99.95  E-value=3.1e-28  Score=180.89  Aligned_cols=121  Identities=24%  Similarity=0.417  Sum_probs=104.2

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      .+|++++  ++++++|.++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.......          
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~   82 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHH
Confidence            4688887  9999999999999999999999999999999999999999999999999998764322111          


Q ss_pred             ------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 ------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 ------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                                    ..+...+..+++|+|+||+++.+.+.++...++++ +++|+||| |+|++
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~-~~lViDEa-h~~~~  160 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHV-QMIVLDEA-DKLLS  160 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTC-CEEEEETH-HHHTS
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccC-CEEEEECh-HHhHh
Confidence                                          23334445678999999999999999988889999 99999999 99999


Q ss_pred             ccccc
Q 031654          149 MALNQ  153 (155)
Q Consensus       149 ~gf~~  153 (155)
                      .+|..
T Consensus       161 ~~~~~  165 (206)
T 1vec_A          161 QDFVQ  165 (206)
T ss_dssp             TTTHH
T ss_pred             hCcHH
Confidence            88753

>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=99.95  E-value=6.3e-28  Score=186.91  Aligned_cols=115  Identities=25%  Similarity=0.398  Sum_probs=100.1

Q ss_pred             CHHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhh------hch------------
Q 031654           37 PQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY------YSA------------   98 (155)
Q Consensus        37 ~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~------~~~------------   98 (155)
                      +++++++|+++||..|+++|.++++.++.|+|++++||||||||++|++|++..+....      ...            
T Consensus        62 ~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q  141 (262)
T 3ly5_A           62 NENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQ  141 (262)
T ss_dssp             CHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHH
T ss_pred             CHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHH
Confidence            39999999999999999999999999999999999999999999999999999887622      111            


Q ss_pred             -------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEEcccccccccccc
Q 031654           99 -------------------------RKELRELARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus        99 -------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                                               ..+...+..+++|+|+||+++.+++... .+.++++ +++|+||| |+|+++||.
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l-~~lViDEa-h~l~~~~~~  219 (262)
T 3ly5_A          142 TFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNL-QCLVIDEA-DRILDVGFE  219 (262)
T ss_dssp             HHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTC-CEEEECSH-HHHHHTTCH
T ss_pred             HHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccC-CEEEEcCh-HHHhhhhHH
Confidence                                     3444555567999999999999988875 4789999 99999999 999999986


Q ss_pred             c
Q 031654          153 Q  153 (155)
Q Consensus       153 ~  153 (155)
                      +
T Consensus       220 ~  220 (262)
T 3ly5_A          220 E  220 (262)
T ss_dssp             H
T ss_pred             H
Confidence            4

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.95  E-value=1.3e-28  Score=185.30  Aligned_cols=122  Identities=22%  Similarity=0.358  Sum_probs=102.6

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      ..+|++++  +.++++|+++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.......         
T Consensus         3 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   82 (219)
T 1q0u_A            3 ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTR   82 (219)
T ss_dssp             -CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcH
Confidence            45799987  9999999999999999999999999999999999999999999999999998875432211         


Q ss_pred             ------HHHHHHH----------------------------hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccc
Q 031654           99 ------RKELREL----------------------------ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        99 ------~~~~~~l----------------------------~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D  144 (155)
                            .+....+                            ..+++|+|+||+++.+++.++.+.+.++ +++|+||| |
T Consensus        83 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~-~~lViDEa-h  160 (219)
T 1q0u_A           83 ELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTA-HILVVDEA-D  160 (219)
T ss_dssp             HHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGC-CEEEECSH-H
T ss_pred             HHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcc-eEEEEcCc-h
Confidence                  1111111                            1257899999999999999988899999 99999999 9


Q ss_pred             ccccccccc
Q 031654          145 QTLDMALNQ  153 (155)
Q Consensus       145 ~ll~~gf~~  153 (155)
                      +++++||..
T Consensus       161 ~~~~~~~~~  169 (219)
T 1q0u_A          161 LMLDMGFIT  169 (219)
T ss_dssp             HHHHTTCHH
T ss_pred             HHhhhChHH
Confidence            999988753

>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=99.95  E-value=1.2e-27  Score=177.71  Aligned_cols=120  Identities=29%  Similarity=0.444  Sum_probs=103.9

Q ss_pred             ccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHh-----hhch------
Q 031654           32 RFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE-----YYSA------   98 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~-----~~~~------   98 (155)
                      +|++++  ++++++|+++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+...     ....      
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~   81 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPT   81 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSS
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECC
Confidence            588877  999999999999999999999999999999999999999999999999999877531     1111      


Q ss_pred             -----------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 -----------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 -----------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                                   ..+...+..+++|+|+||+++.+++..+.+.+.++ +++|+||| |+|++.
T Consensus        82 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~-~~iViDEa-h~~~~~  159 (207)
T 2gxq_A           82 RELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRV-EVAVLDEA-DEMLSM  159 (207)
T ss_dssp             HHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTC-SEEEEESH-HHHHHT
T ss_pred             HHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhc-eEEEEECh-hHhhcc
Confidence                                         23344455679999999999999999988899999 99999999 999998


Q ss_pred             cccc
Q 031654          150 ALNQ  153 (155)
Q Consensus       150 gf~~  153 (155)
                      +|..
T Consensus       160 ~~~~  163 (207)
T 2gxq_A          160 GFEE  163 (207)
T ss_dssp             TCHH
T ss_pred             chHH
Confidence            8753

>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=99.95  E-value=1.2e-27  Score=179.88  Aligned_cols=128  Identities=23%  Similarity=0.353  Sum_probs=107.0

Q ss_pred             CCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---
Q 031654           24 NTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---   98 (155)
Q Consensus        24 ~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---   98 (155)
                      .+.+.++.+|++++  +.++++|+++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.......   
T Consensus         7 ~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~l   86 (224)
T 1qde_A            7 TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQAL   86 (224)
T ss_dssp             BSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEE
T ss_pred             cccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEE
Confidence            34566778999988  9999999999999999999999999999999999999999999999999998775432211   


Q ss_pred             ------------HHHHHHH-----------------------hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccc
Q 031654           99 ------------RKELREL-----------------------ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAA  143 (155)
Q Consensus        99 ------------~~~~~~l-----------------------~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~  143 (155)
                                  .+....+                       ...++|+|+||+++.+.+.++...++++ +++|+||| 
T Consensus        87 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~-~~iViDEa-  164 (224)
T 1qde_A           87 MLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKI-KMFILDEA-  164 (224)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTTCSEEEECHHHHHHHHHTTSSCCTTC-CEEEEETH-
T ss_pred             EEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCCCCEEEECHHHHHHHHHhCCcchhhC-cEEEEcCh-
Confidence                        1111111                       1238999999999999999988899999 99999999 


Q ss_pred             cccccccccc
Q 031654          144 DQTLDMALNQ  153 (155)
Q Consensus       144 D~ll~~gf~~  153 (155)
                      |++++.+|..
T Consensus       165 h~~~~~~~~~  174 (224)
T 1qde_A          165 DEMLSSGFKE  174 (224)
T ss_dssp             HHHHHTTCHH
T ss_pred             hHHhhhhhHH
Confidence            9999988753

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.95  E-value=1.9e-27  Score=180.49  Aligned_cols=124  Identities=24%  Similarity=0.412  Sum_probs=104.6

Q ss_pred             CCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhh-----h-ch
Q 031654           27 SSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY-----Y-SA   98 (155)
Q Consensus        27 p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~-----~-~~   98 (155)
                      +.++.+|++++  +.++++|+++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+....     . ..
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~  100 (236)
T 2pl3_A           21 VNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGV  100 (236)
T ss_dssp             GGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCE
T ss_pred             CcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceE
Confidence            34567899988  9999999999999999999999999999999999999999999999999999886521     1 11


Q ss_pred             -------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEE
Q 031654           99 -------------------------------------RKELRELARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALK  140 (155)
Q Consensus        99 -------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlD  140 (155)
                                                           ..+...+ .+++|+|+||+++.+++... .+.+.++ +++|+|
T Consensus       101 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~-~~lViD  178 (236)
T 2pl3_A          101 LIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDL-QMLVLD  178 (236)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTC-CEEEET
T ss_pred             EEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccc-cEEEEe
Confidence                                                 1122222 46899999999999998775 5778999 999999


Q ss_pred             ccccccccccccc
Q 031654          141 EAADQTLDMALNQ  153 (155)
Q Consensus       141 Ea~D~ll~~gf~~  153 (155)
                      || |+|+++||.+
T Consensus       179 Ea-h~~~~~~~~~  190 (236)
T 2pl3_A          179 EA-DRILDMGFAD  190 (236)
T ss_dssp             TH-HHHHHTTTHH
T ss_pred             Ch-HHHhcCCcHH
Confidence            99 9999998753

>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=99.94  E-value=5e-27  Score=190.10  Aligned_cols=138  Identities=22%  Similarity=0.373  Sum_probs=114.3

Q ss_pred             cCCcCcccCCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           14 ENAAPASSSTNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        14 ~~~~~~~~~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      ++...+.......+.+..+|++++  +.++++|.++||..|+|+|.++|+.+++|+|+++++|||||||++|++|++..+
T Consensus        20 ~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l   99 (410)
T 2j0s_A           20 EDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCL   99 (410)
T ss_dssp             CCSSSCCCCCCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTC
T ss_pred             ccCcccccCCCCCccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHH
Confidence            333444445555556677899988  999999999999999999999999999999999999999999999999999876


Q ss_pred             HHhhhch---------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCccc
Q 031654           92 MREYYSA---------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQM  132 (155)
Q Consensus        92 ~~~~~~~---------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~  132 (155)
                      .......                                       ..+...+..+++|+|+||++|.+++.++.+.+.+
T Consensus       100 ~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~  179 (410)
T 2j0s_A          100 DIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA  179 (410)
T ss_dssp             CTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             hhccCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhh
Confidence            4221111                                       3344455567899999999999999999889999


Q ss_pred             ccceEEEEccccccccccccc
Q 031654          133 IIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       133 l~~~lVlDEa~D~ll~~gf~~  153 (155)
                      + +++|+||| |+|++.+|.+
T Consensus       180 ~-~~vViDEa-h~~~~~~~~~  198 (410)
T 2j0s_A          180 I-KMLVLDEA-DEMLNKGFKE  198 (410)
T ss_dssp             C-CEEEEETH-HHHTSTTTHH
T ss_pred             e-eEEEEccH-HHHHhhhhHH
Confidence            9 99999999 9999998753

>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=99.94  E-value=7.9e-27  Score=175.23  Aligned_cols=128  Identities=19%  Similarity=0.268  Sum_probs=101.3

Q ss_pred             CCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc--h
Q 031654           23 TNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS--A   98 (155)
Q Consensus        23 ~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~--~   98 (155)
                      +...+.+..+|++++  +.++++|+++||+.|+++|.++++.+++|+|+++++|||||||++|++|++..+......  .
T Consensus         6 ~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~   85 (220)
T 1t6n_A            6 GSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV   85 (220)
T ss_dssp             --------CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCE
T ss_pred             CCcccccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEE
Confidence            334445556799987  999999999999999999999999999999999999999999999999999876432221  1


Q ss_pred             --------------------------------------HHHHHHHh-cCCcEEEEChHHHHHHHHcCCCCcccccceEEE
Q 031654           99 --------------------------------------RKELRELA-RWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL  139 (155)
Q Consensus        99 --------------------------------------~~~~~~l~-~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVl  139 (155)
                                                            ..+...+. ..++|+|+||+++.+++..+.+.+.++ +++|+
T Consensus        86 lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~-~~lVi  164 (220)
T 1t6n_A           86 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHI-KHFIL  164 (220)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTC-CEEEE
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccC-CEEEE
Confidence                                                  12222222 246999999999999999988899999 99999


Q ss_pred             Ecccccccc-cccc
Q 031654          140 KEAADQTLD-MALN  152 (155)
Q Consensus       140 DEa~D~ll~-~gf~  152 (155)
                      ||| |++++ .+|.
T Consensus       165 DEa-h~~~~~~~~~  177 (220)
T 1t6n_A          165 DEC-DKMLEQLDMR  177 (220)
T ss_dssp             ESH-HHHHSSHHHH
T ss_pred             cCH-HHHhcccCcH
Confidence            999 99997 4654

>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=99.92  E-value=4.7e-25  Score=178.10  Aligned_cols=129  Identities=25%  Similarity=0.377  Sum_probs=108.9

Q ss_pred             CCCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-
Q 031654           22 STNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-   98 (155)
Q Consensus        22 ~~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-   98 (155)
                      ...+.+....+|++++  +.+++.|+++||..|+++|.++|+.+++|+|+++++|||||||++|++|+++.+....... 
T Consensus        31 ~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~  110 (414)
T 3eiq_A           31 IESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQ  110 (414)
T ss_dssp             CCCCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCC
T ss_pred             cCCCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCcee
Confidence            3444566778899987  9999999999999999999999999999999999999999999999999998765421111 


Q ss_pred             --------------------------------------HHHHHHHh-cCCcEEEEChHHHHHHHHcCCCCcccccceEEE
Q 031654           99 --------------------------------------RKELRELA-RWVDNLMATLRRLVNLLERGRVSLQMIIRYLAL  139 (155)
Q Consensus        99 --------------------------------------~~~~~~l~-~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVl  139 (155)
                                                            ..+...+. .+++|+|+||++|.+++..+.+.+.++ +++|+
T Consensus       111 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~-~~vVi  189 (414)
T 3eiq_A          111 ALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYI-KMFVL  189 (414)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTC-CEEEE
T ss_pred             EEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccC-cEEEE
Confidence                                                  22222332 578999999999999999998899999 99999


Q ss_pred             Ecccccccccccc
Q 031654          140 KEAADQTLDMALN  152 (155)
Q Consensus       140 DEa~D~ll~~gf~  152 (155)
                      ||| |++++.+|.
T Consensus       190 DEa-h~~~~~~~~  201 (414)
T 3eiq_A          190 DEA-DEMLSRGFK  201 (414)
T ss_dssp             CSH-HHHHHTTTH
T ss_pred             ECH-HHhhccCcH
Confidence            999 999998875

>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=99.91  E-value=8.7e-25  Score=176.21  Aligned_cols=123  Identities=25%  Similarity=0.392  Sum_probs=103.3

Q ss_pred             CCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc--h-----
Q 031654           28 SPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS--A-----   98 (155)
Q Consensus        28 ~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~--~-----   98 (155)
                      ....+|++++  +.++++|.++||+.|+|+|.++++.+++|+|+++++|||||||++|++|++..+......  .     
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   97 (400)
T 1s2m_A           18 TKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVP   97 (400)
T ss_dssp             ---CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             cccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcC
Confidence            3456899988  999999999999999999999999999999999999999999999999999876432111  1     


Q ss_pred             --------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 --------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 --------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                      ..+...+..+++|+|+||+++.+++.++...+.++ +++|+||| |++
T Consensus        98 ~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~-~~vIiDEa-H~~  175 (400)
T 1s2m_A           98 TRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDC-SLFIMDEA-DKM  175 (400)
T ss_dssp             SHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTC-CEEEEESH-HHH
T ss_pred             CHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccC-CEEEEeCc-hHh
Confidence                                            22333444678999999999999999888889999 99999999 999


Q ss_pred             cccccc
Q 031654          147 LDMALN  152 (155)
Q Consensus       147 l~~gf~  152 (155)
                      ++.+|.
T Consensus       176 ~~~~~~  181 (400)
T 1s2m_A          176 LSRDFK  181 (400)
T ss_dssp             SSHHHH
T ss_pred             hhhchH
Confidence            887654

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.91  E-value=3.8e-25  Score=187.69  Aligned_cols=116  Identities=24%  Similarity=0.440  Sum_probs=97.7

Q ss_pred             CCHHHHHhHHhCCCCCCCHHHHHHHHHHh--cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc------h---------
Q 031654           36 VPQHLRNKPRTYKYVKPTPVQRHATSILV--AGRDLMACAQTGSRKTTPFCFPIINGIMREYYS------A---------   98 (155)
Q Consensus        36 l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l--~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~------~---------   98 (155)
                      |+++++++|+++||..|+|+|.++|+.++  .|+|++++||||||||++|++|+++.+......      .         
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~L  107 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  107 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHH
Confidence            34999999999999999999999999999  789999999999999999999999988765311      1         


Q ss_pred             --------------------------------HHHHHHH-hcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEEcccc
Q 031654           99 --------------------------------RKELREL-ARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        99 --------------------------------~~~~~~l-~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlDEa~D  144 (155)
                                                      ..+...+ ..+++|+|+||++|.+++.+. ...++.+ ++||+||| |
T Consensus       108 a~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~-~~lViDEa-h  185 (579)
T 3sqw_A          108 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFV-DYKVLDEA-D  185 (579)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTC-CEEEEETH-H
T ss_pred             HHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccC-CEEEEECh-H
Confidence                                            1122222 236899999999999998875 4567889 99999999 9


Q ss_pred             ccccccccc
Q 031654          145 QTLDMALNQ  153 (155)
Q Consensus       145 ~ll~~gf~~  153 (155)
                      +|+++||.+
T Consensus       186 ~l~~~gf~~  194 (579)
T 3sqw_A          186 RLLEIGFRD  194 (579)
T ss_dssp             HHTSTTTHH
T ss_pred             HhhcCCCHH
Confidence            999999865

>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=99.91  E-value=5.1e-25  Score=185.61  Aligned_cols=116  Identities=24%  Similarity=0.440  Sum_probs=97.4

Q ss_pred             CCHHHHHhHHhCCCCCCCHHHHHHHHHHh--cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc------h---------
Q 031654           36 VPQHLRNKPRTYKYVKPTPVQRHATSILV--AGRDLMACAQTGSRKTTPFCFPIINGIMREYYS------A---------   98 (155)
Q Consensus        36 l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l--~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~------~---------   98 (155)
                      ++++++++|.++||..|+|+|.++|+.++  .|+|++++||||||||++|++|+++.+......      .         
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~L  158 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  158 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHH
Confidence            44999999999999999999999999999  678999999999999999999999998765411      1         


Q ss_pred             --------------------------------HHHHHHH-hcCCcEEEEChHHHHHHHHcC-CCCcccccceEEEEcccc
Q 031654           99 --------------------------------RKELREL-ARWVDNLMATLRRLVNLLERG-RVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        99 --------------------------------~~~~~~l-~~~~~IlI~TP~~l~~~l~~~-~~~l~~l~~~lVlDEa~D  144 (155)
                                                      ..+...+ ..+++|+|+||++|.+++.+. ...++.+ ++||+||| |
T Consensus       159 a~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~-~~lViDEa-h  236 (563)
T 3i5x_A          159 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFV-DYKVLDEA-D  236 (563)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTC-CEEEEETH-H
T ss_pred             HHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccc-eEEEEeCH-H
Confidence                                            1122222 337899999999999998875 3467889 99999999 9


Q ss_pred             ccccccccc
Q 031654          145 QTLDMALNQ  153 (155)
Q Consensus       145 ~ll~~gf~~  153 (155)
                      +|+++||.+
T Consensus       237 ~l~~~~f~~  245 (563)
T 3i5x_A          237 RLLEIGFRD  245 (563)
T ss_dssp             HHTSTTTHH
T ss_pred             HHhccchHH
Confidence            999999864

>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=99.90  E-value=8.9e-24  Score=170.30  Aligned_cols=124  Identities=15%  Similarity=0.262  Sum_probs=102.4

Q ss_pred             CCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch----
Q 031654           27 SSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA----   98 (155)
Q Consensus        27 p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----   98 (155)
                      ...+.+|++++  +.++++|.++||..|+|+|.++|+.++.|  +|+++++|||||||++|++|++..+.......    
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~li  100 (412)
T 3fht_A           21 LYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLC  100 (412)
T ss_dssp             TCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEE
T ss_pred             ccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEE
Confidence            35678899987  99999999999999999999999999998  99999999999999999999998876443221    


Q ss_pred             --------HHH---HHHHh----------------------cCCcEEEEChHHHHHHHHc-CCCCcccccceEEEEcccc
Q 031654           99 --------RKE---LRELA----------------------RWVDNLMATLRRLVNLLER-GRVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        99 --------~~~---~~~l~----------------------~~~~IlI~TP~~l~~~l~~-~~~~l~~l~~~lVlDEa~D  144 (155)
                              .+.   ...+.                      .+++|+|+||+++.+++.+ +.+.+.++ +++|+||| |
T Consensus       101 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~-~~iViDEa-h  178 (412)
T 3fht_A          101 LSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI-KVFVLDEA-D  178 (412)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCSSCGGGC-CEEEEETH-H
T ss_pred             ECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhhcCCCCEEEECchHHHHHHHhcCCcChhhC-cEEEEeCH-H
Confidence                    111   22221                      1369999999999999966 56788999 99999999 9


Q ss_pred             cccc-cccc
Q 031654          145 QTLD-MALN  152 (155)
Q Consensus       145 ~ll~-~gf~  152 (155)
                      ++++ .+|.
T Consensus       179 ~~~~~~~~~  187 (412)
T 3fht_A          179 VMIATQGHQ  187 (412)
T ss_dssp             HHHSTTTTH
T ss_pred             HHhhcCCcH
Confidence            9987 4553

>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=99.90  E-value=5.9e-24  Score=170.07  Aligned_cols=121  Identities=27%  Similarity=0.422  Sum_probs=101.0

Q ss_pred             CCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------
Q 031654           29 PAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------   98 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------   98 (155)
                      ...+|++++  +.++++|.++||..|+|+|.++++.++.|  +|+++++|||||||++|++|++..+.......      
T Consensus         3 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~   82 (395)
T 3pey_A            3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLA   82 (395)
T ss_dssp             -CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             cccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEEC
Confidence            357899988  99999999999999999999999999998  99999999999999999999998775432211      


Q ss_pred             ------HHH---HHHHh--------------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc-
Q 031654           99 ------RKE---LRELA--------------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD-  148 (155)
Q Consensus        99 ------~~~---~~~l~--------------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~-  148 (155)
                            .+.   ...+.                    .+++|+|+||+++.+++.++...+.++ +++|+||| |++.+ 
T Consensus        83 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~-~~iIiDEa-h~~~~~  160 (395)
T 3pey_A           83 PSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKI-KIFVLDEA-DNMLDQ  160 (395)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTTSCBCCSEEEECHHHHHHHHHTTCBCCTTC-CEEEEETH-HHHHHS
T ss_pred             CCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhhccCCCCEEEEcHHHHHHHHHcCCcccccC-CEEEEECh-hhhcCc
Confidence                  111   22211                    157999999999999999988899999 99999999 99987 


Q ss_pred             ccc
Q 031654          149 MAL  151 (155)
Q Consensus       149 ~gf  151 (155)
                      .+|
T Consensus       161 ~~~  163 (395)
T 3pey_A          161 QGL  163 (395)
T ss_dssp             TTH
T ss_pred             ccc
Confidence            454

>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=99.90  E-value=5.3e-24  Score=176.41  Aligned_cols=122  Identities=16%  Similarity=0.277  Sum_probs=100.8

Q ss_pred             CCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------
Q 031654           29 PAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------   98 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------   98 (155)
                      +..+|++++  +.++++|.++||..|+|+|.++||.++.|  +|++++||||||||++|++|++..+.......      
T Consensus        90 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  169 (479)
T 3fmp_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  169 (479)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEEC
T ss_pred             CcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEe
Confidence            356888887  99999999999999999999999999987  99999999999999999999998876544221      


Q ss_pred             ------HHH---HHHHh----------------------cCCcEEEEChHHHHHHHHc-CCCCcccccceEEEEcccccc
Q 031654           99 ------RKE---LRELA----------------------RWVDNLMATLRRLVNLLER-GRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ------~~~---~~~l~----------------------~~~~IlI~TP~~l~~~l~~-~~~~l~~l~~~lVlDEa~D~l  146 (155)
                            .+.   ...+.                      .+++|+|+||++|.+++.+ +.+.+.++ ++||+||| |+|
T Consensus       170 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~-~~iViDEa-h~~  247 (479)
T 3fmp_B          170 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI-KVFVLDEA-DVM  247 (479)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCCCCGGGC-CEEEECCH-HHH
T ss_pred             ChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccccCCCCEEEECchHHHHHHHhcCCcCcccC-CEEEEECH-HHH
Confidence                  111   22221                      1358999999999999966 56789999 99999999 999


Q ss_pred             cc-cccc
Q 031654          147 LD-MALN  152 (155)
Q Consensus       147 l~-~gf~  152 (155)
                      ++ .+|.
T Consensus       248 ~~~~~~~  254 (479)
T 3fmp_B          248 IATQGHQ  254 (479)
T ss_dssp             HTSTTHH
T ss_pred             hhcCCcH
Confidence            97 4654

>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=99.90  E-value=3.2e-24  Score=171.98  Aligned_cols=123  Identities=23%  Similarity=0.356  Sum_probs=103.4

Q ss_pred             CCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------
Q 031654           27 SSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------   98 (155)
Q Consensus        27 p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------   98 (155)
                      ..+..+|++++  +.+.++|..+||..|+|+|.++++.+++|+|+++++|||||||++|++|++..+.......      
T Consensus        17 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~   96 (394)
T 1fuu_A           17 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLA   96 (394)
T ss_dssp             CCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             ccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEc
Confidence            34556799887  9999999999999999999999999999999999999999999999999998765432211      


Q ss_pred             ---------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654           99 ---------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 ---------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                                                       ..+...+ .+++|+|+||+++.+.+..+.+.+.++ +++|+||| |+
T Consensus        97 P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~i~v~T~~~l~~~~~~~~~~~~~~-~~vIiDEa-h~  173 (394)
T 1fuu_A           97 PTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKI-KMFILDEA-DE  173 (394)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHH-HHCSEEEECHHHHHHHHHTTSSCCTTC-CEEEEETH-HH
T ss_pred             CCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhc-CCCCEEEECHHHHHHHHHhCCcchhhC-cEEEEECh-HH
Confidence                                             1111111 257999999999999999988889999 99999999 99


Q ss_pred             ccccccc
Q 031654          146 TLDMALN  152 (155)
Q Consensus       146 ll~~gf~  152 (155)
                      +++.+|.
T Consensus       174 ~~~~~~~  180 (394)
T 1fuu_A          174 MLSSGFK  180 (394)
T ss_dssp             HHHTTCH
T ss_pred             hhCCCcH
Confidence            9988775

>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=99.89  E-value=1.4e-23  Score=168.31  Aligned_cols=119  Identities=19%  Similarity=0.276  Sum_probs=98.5

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc--h--------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS--A--------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~--~--------   98 (155)
                      .+|++++  +.++++|.++||+.|+|+|.++++.++.|+|+++++|||+|||++|++|++..+......  .        
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~   87 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   87 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHH
Confidence            4688877  999999999999999999999999999999999999999999999999998875432211  1        


Q ss_pred             ------------------------------HHHHHHHh-cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccc
Q 031654           99 ------------------------------RKELRELA-RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 ------------------------------~~~~~~l~-~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                                                    ..+...+. ..++|+|+||+++.+++..+...+.++ +++|+||| |+++
T Consensus        88 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~-~~vViDEa-H~~~  165 (391)
T 1xti_A           88 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHI-KHFILDEC-DKML  165 (391)
T ss_dssp             HHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTC-SEEEECSH-HHHT
T ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccc-CEEEEeCH-HHHh
Confidence                                          11112222 237999999999999999988889999 99999999 9998


Q ss_pred             cc-cc
Q 031654          148 DM-AL  151 (155)
Q Consensus       148 ~~-gf  151 (155)
                      +. +|
T Consensus       166 ~~~~~  170 (391)
T 1xti_A          166 EQLDM  170 (391)
T ss_dssp             SSHHH
T ss_pred             hccch
Confidence            73 54

>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=99.89  E-value=3.1e-23  Score=164.35  Aligned_cols=120  Identities=25%  Similarity=0.437  Sum_probs=100.7

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------   98 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------   98 (155)
                      ..+|++++  +.++++|+++||..|+|+|.++++.+++| +++++++|||||||++|++|++..+.......        
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~   84 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTR   84 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCH
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCH
Confidence            35788877  99999999999999999999999999998 79999999999999999999987664322111        


Q ss_pred             ------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 ------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 ------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                                    ..+...+ .+++|+|+||+++.+.+..+.+.+.++ +++|+||| |++.+
T Consensus        85 ~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~-~~~~iiv~T~~~l~~~~~~~~~~~~~~-~~iIiDEa-h~~~~  161 (367)
T 1hv8_A           85 ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNV-KYFILDEA-DEMLN  161 (367)
T ss_dssp             HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHTTCSCTTSC-CEEEEETH-HHHHT
T ss_pred             HHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhc-CCCCEEEecHHHHHHHHHcCCcccccC-CEEEEeCc-hHhhh
Confidence                                          1111222 268999999999999999988889999 99999999 99998


Q ss_pred             cccc
Q 031654          149 MALN  152 (155)
Q Consensus       149 ~gf~  152 (155)
                      .+|.
T Consensus       162 ~~~~  165 (367)
T 1hv8_A          162 MGFI  165 (367)
T ss_dssp             TTTH
T ss_pred             hchH
Confidence            8764

>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=99.88  E-value=2.5e-22  Score=157.72  Aligned_cols=111  Identities=24%  Similarity=0.428  Sum_probs=93.8

Q ss_pred             CCHHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-----------------
Q 031654           36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-----------------   98 (155)
Q Consensus        36 l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-----------------   98 (155)
                      |++++.++|+++||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..   .....                 
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~---~~~~liv~P~~~L~~q~~~~~~   77 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL---GMKSLVVTPTRELTRQVASHIR   77 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH---TCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh---cCCEEEEeCCHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999999999999999998763   11110                 


Q ss_pred             -------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654           99 -------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus        99 -------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                                         ..+...+ ..++|+|+||++|.+++..+.+.+.++ +++|+||| |++.+.+|.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~v~T~~~l~~~~~~~~~~~~~~-~~iViDEa-h~~~~~~~~  147 (337)
T 2z0m_A           78 DIGRYMDTKVAEVYGGMPYKAQINRV-RNADIVVATPGRLLDLWSKGVIDLSSF-EIVIIDEA-DLMFEMGFI  147 (337)
T ss_dssp             HHTTTSCCCEEEECTTSCHHHHHHHH-TTCSEEEECHHHHHHHHHTTSCCGGGC-SEEEEESH-HHHHHTTCH
T ss_pred             HHhhhcCCcEEEEECCcchHHHHhhc-CCCCEEEECHHHHHHHHHcCCcchhhC-cEEEEECh-HHhhccccH
Confidence                               1122222 348999999999999999888889999 99999999 999988874

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

Probab=99.83  E-value=1.9e-20  Score=162.11  Aligned_cols=119  Identities=20%  Similarity=0.185  Sum_probs=99.3

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHH-HhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSI-LVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~-~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      .+|++++  +++.+.+++.||..|+|+|.++++. +.+|+|++++||||||||++|.+|+++.+.......         
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~L   87 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRAL   87 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHH
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHH
Confidence            4688886  9999999999999999999999999 788999999999999999999999998876433222         


Q ss_pred             -HHHHHHHh-----------------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654           99 -RKELRELA-----------------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 -~~~~~~l~-----------------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                       .+....+.                       ..++|+|+||+++..++.++...++++ +++|+||| |.+.+.++
T Consensus        88 a~q~~~~~~~~~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~-~~vIiDE~-H~l~~~~~  162 (715)
T 2va8_A           88 TNEKYLTFKDWELIGFKVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLNEV-NYFVLDEL-HYLNDPER  162 (715)
T ss_dssp             HHHHHHHHGGGGGGTCCEEECCSCSSSCCGGGGGCSEEEECHHHHHHHHHHCCGGGGGE-EEEEECSG-GGGGCTTT
T ss_pred             HHHHHHHHHHhhcCCCEEEEEeCCCCCchhhcCCCCEEEEcHHHHHHHHhCChhHhhcc-CEEEEech-hhcCCccc
Confidence             22222221                       147999999999999998877779999 99999999 99876554

>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=99.83  E-value=2e-21  Score=163.74  Aligned_cols=115  Identities=16%  Similarity=0.126  Sum_probs=89.9

Q ss_pred             cccccCC--HHHHHhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           31 ARFAYVP--QHLRNKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      .+|++++  +.+.+.|++ +||..|+|+|.++|+.+++|+|+++++|||+|||++|++|++..   .....         
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~---~g~~lvi~P~~aL~   78 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL---NGLTVVVSPLISLM   78 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS---SSEEEEECSCHHHH
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh---CCCEEEECChHHHH
Confidence            5789998  889999998 79999999999999999999999999999999999999998742   11000         


Q ss_pred             -----------------------H---HHHHHH-hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccc
Q 031654           99 -----------------------R---KELREL-ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus        99 -----------------------~---~~~~~l-~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                             .   .....+ ...++|+++||++|......+.+...++ .++|+||| |++.++|
T Consensus        79 ~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~-~~vViDEa-H~i~~~g  155 (523)
T 1oyw_A           79 KDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNP-VLLAVDEA-HCISQWG  155 (523)
T ss_dssp             HHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCE-EEEEESSG-GGGCTTS
T ss_pred             HHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCC-CEEEEeCc-cccCcCC
Confidence                                   1   111222 3468999999999853222222345788 99999999 9999988

>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=99.83  E-value=3.3e-20  Score=158.42  Aligned_cols=124  Identities=16%  Similarity=0.265  Sum_probs=91.6

Q ss_pred             CCCCccccc--CC--HHHHHhHHh-CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHH-----------
Q 031654           27 SSPAARFAY--VP--QHLRNKPRT-YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIING-----------   90 (155)
Q Consensus        27 p~~~~~f~~--l~--~~l~~~l~~-~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~-----------   90 (155)
                      +....+|..  ++  +.+.+.|++ +||..|+|+|.++|+.+++|+|+++++|||+|||++|++|++..           
T Consensus        15 ~~~~~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~~g~~lVisP~~   94 (591)
T 2v1x_A           15 DSSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLI   94 (591)
T ss_dssp             -CCGGGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTSSSEEEEECSCH
T ss_pred             CcchhccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHcCCcEEEEeCHH
Confidence            334455554  55  889999998 69999999999999999999999999999999999999999752           


Q ss_pred             -HHHhhhch--------------------HHHHHHH---hcCCcEEEEChHHHH------HHHHcCCCCcccccceEEEE
Q 031654           91 -IMREYYSA--------------------RKELREL---ARWVDNLMATLRRLV------NLLERGRVSLQMIIRYLALK  140 (155)
Q Consensus        91 -l~~~~~~~--------------------~~~~~~l---~~~~~IlI~TP~~l~------~~l~~~~~~l~~l~~~lVlD  140 (155)
                       |.......                    ......+   ...++|+|+||++|.      +.+. +...+.++ .++|||
T Consensus        95 ~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~-~~~~~~~i-~~iViD  172 (591)
T 2v1x_A           95 SLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLE-KAYEARRF-TRIAVD  172 (591)
T ss_dssp             HHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHH-HHHHTTCE-EEEEEE
T ss_pred             HHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHH-hhhhccCC-cEEEEE
Confidence             11000000                    1111222   357899999999874      2232 23456789 999999


Q ss_pred             cccccccccc--ccc
Q 031654          141 EAADQTLDMA--LNQ  153 (155)
Q Consensus       141 Ea~D~ll~~g--f~~  153 (155)
                      || |++.++|  |.+
T Consensus       173 EA-H~is~~g~dfr~  186 (591)
T 2v1x_A          173 EV-HCCSQWGHDFRP  186 (591)
T ss_dssp             TG-GGGSTTCTTCCG
T ss_pred             Cc-ccccccccccHH
Confidence            99 9999998  654

>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=99.83  E-value=2.2e-20  Score=162.08  Aligned_cols=118  Identities=17%  Similarity=0.196  Sum_probs=98.6

Q ss_pred             ccccCC--HHHHHhHHhCCCCCCCHHHHHHHHH-HhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           32 RFAYVP--QHLRNKPRTYKYVKPTPVQRHATSI-LVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~-~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      +|++++  +++.+.+++.||..|+|+|.++++. +.+|+|++++||||||||++|.+|++..+.......          
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raLa   81 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALA   81 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGGH
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHH
Confidence            477776  9999999999999999999999998 889999999999999999999999998887433222          


Q ss_pred             HHHHHHHh-----------------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654           99 RKELRELA-----------------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 ~~~~~~l~-----------------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      .+....+.                       ..++|+|+||+++..++.++...++++ +++|+||| |.+.+.++
T Consensus        82 ~q~~~~~~~l~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~-~~vIiDE~-H~l~~~~r  155 (720)
T 2zj8_A           82 EEKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDV-KILVADEI-HLIGSRDR  155 (720)
T ss_dssp             HHHHHHTGGGGGGTCCEEEECSCSSCCCGGGGGCSEEEECHHHHHHHHHHTCTTGGGE-EEEEEETG-GGGGCTTT
T ss_pred             HHHHHHHHHHHhcCCEEEEecCCCCccccccCCCCEEEECHHHHHHHHHcChhhhhcC-CEEEEECC-cccCCCcc
Confidence            22222221                       247999999999999998877778999 99999999 98887554

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.83  E-value=3.5e-21  Score=156.57  Aligned_cols=106  Identities=19%  Similarity=0.120  Sum_probs=82.4

Q ss_pred             HHHHHhHHhC-CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------------
Q 031654           38 QHLRNKPRTY-KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------------   98 (155)
Q Consensus        38 ~~l~~~l~~~-g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------------   98 (155)
                      +++.+.+++. || .|+|+|.++|+.+++|+|+++++|||||||++|++|++..+.......                  
T Consensus         8 ~~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~   86 (414)
T 3oiy_A            8 EDFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQK   86 (414)
T ss_dssp             HHHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHHHHHH
Confidence            4566666654 66 899999999999999999999999999999999999887652221111                  


Q ss_pred             --------------------HHHHHHHhcC-CcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 --------------------RKELRELARW-VDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 --------------------~~~~~~l~~~-~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                          ..+...+..+ ++|+|+||++|.+++..  +.+.++ +++|+||| |++.+
T Consensus        87 ~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~-~~iViDEa-H~~~~  153 (414)
T 3oiy_A           87 LADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRF-DFVFVDDV-DAVLK  153 (414)
T ss_dssp             HCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCC-SEEEESCH-HHHHH
T ss_pred             HccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccc-cEEEEeCh-Hhhhh
Confidence                                1123344444 99999999999888874  667799 99999999 86553

>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=99.83  E-value=7.9e-21  Score=166.23  Aligned_cols=102  Identities=22%  Similarity=0.199  Sum_probs=81.1

Q ss_pred             hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------------------------
Q 031654           46 TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------------------------   98 (155)
Q Consensus        46 ~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------------------------   98 (155)
                      .+|| +||++|..++|.++.|+  ++.++||||||++|++|++..........                           
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~g~~vlVltptreLA~qd~e~~~~l~~~lgl~v  155 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTV  155 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCE
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHHhhcCCeE
Confidence            5799 99999999999999999  99999999999999999985433221111                           


Q ss_pred             -------HHHHHHHhcCCcEEEEChHHH-HHHHHcC------CCCcccccceEEEEccccccc-ccccc
Q 031654           99 -------RKELRELARWVDNLMATLRRL-VNLLERG------RVSLQMIIRYLALKEAADQTL-DMALN  152 (155)
Q Consensus        99 -------~~~~~~l~~~~~IlI~TP~~l-~~~l~~~------~~~l~~l~~~lVlDEa~D~ll-~~gf~  152 (155)
                             ..+.+....+|||+||||++| .+++..+      .+.++.+ +++||||| |.|| |+++.
T Consensus       156 ~~i~gg~~~~~r~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~-~~lVlDEa-D~mLiDea~t  222 (844)
T 1tf5_A          156 GLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPL-HFAVIDEV-DSILIDEART  222 (844)
T ss_dssp             EECCTTSCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCC-CEEEEETH-HHHHTTTTTC
T ss_pred             EEEeCCCCHHHHHHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCC-CEEEECch-hhhhhhcccc
Confidence                   223344445799999999999 6766543      3678899 99999999 9999 88754

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

Probab=99.82  E-value=2.7e-20  Score=160.13  Aligned_cols=105  Identities=21%  Similarity=0.256  Sum_probs=83.7

Q ss_pred             HHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh----ch------------------
Q 031654           41 RNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY----SA------------------   98 (155)
Q Consensus        41 ~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~----~~------------------   98 (155)
                      .++|..+||..|+++|.++++.++.|+|+++++|||||||++|++|+++.+.....    ..                  
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~   82 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFS   82 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999998875431    11                  


Q ss_pred             -------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCC-CcccccceEEEEccccccc
Q 031654           99 -------------------RKELRELARWVDNLMATLRRLVNLLERGRV-SLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 -------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~-~l~~l~~~lVlDEa~D~ll  147 (155)
                                         ..+...+..+++|+|+||++|.+.+..+.+ .+.++ +++||||| |++.
T Consensus        83 ~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~-~~vViDEa-H~~~  149 (696)
T 2ykg_A           83 KYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIF-TLMIFDEC-HNTS  149 (696)
T ss_dssp             HHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGC-SEEEEETG-GGCS
T ss_pred             HHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccc-cEEEEeCC-Cccc
Confidence                               111222334689999999999999998877 79999 99999999 9953

>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=99.81  E-value=1.1e-20  Score=163.66  Aligned_cols=118  Identities=12%  Similarity=0.089  Sum_probs=94.7

Q ss_pred             ccccCC----HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           32 RFAYVP----QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        32 ~f~~l~----~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      +|++++    +.+.+.+++.||+.|+|+|.++++.+++|+|++++||||||||++|.+|++..+.......         
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~P~r~La   81 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALA   81 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHH
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEeCcHHHH
Confidence            456644    7889999999999999999999999999999999999999999999999998876432221         


Q ss_pred             HHHHHHHh-----------------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654           99 RKELRELA-----------------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 ~~~~~~l~-----------------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      .+..+.+.                       .+++|+|+||+++..++.++...++++ +++|+||| |.+.+.++
T Consensus        82 ~q~~~~~~~~~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~-~~vIiDE~-H~l~~~~r  155 (702)
T 2p6r_A           82 GEKYESFKKWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAV-SCLVVDEI-HLLDSEKR  155 (702)
T ss_dssp             HHHHHHHTTTTTTTCCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGC-CEEEETTG-GGGGCTTT
T ss_pred             HHHHHHHHHHHhcCCEEEEEeCCCCcchhhccCCCEEEECHHHHHHHHHcChhHHhhc-CEEEEeee-eecCCCCc
Confidence            33333331                       157999999999999999877779999 99999999 99887654

>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=99.81  E-value=4.1e-20  Score=154.18  Aligned_cols=103  Identities=20%  Similarity=0.208  Sum_probs=82.8

Q ss_pred             CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh---ch-------------------------
Q 031654           47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY---SA-------------------------   98 (155)
Q Consensus        47 ~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~---~~-------------------------   98 (155)
                      ++.-.|+|+|.++++.+++|+|+++++|||||||++|++|++..+.....   ..                         
T Consensus         3 ~~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~   82 (556)
T 4a2p_A            3 METKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ   82 (556)
T ss_dssp             -----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGG
T ss_pred             CCCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            45568999999999999999999999999999999999999998876431   11                         


Q ss_pred             -------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCC-CcccccceEEEEccccccccccc
Q 031654           99 -------------RKELRELARWVDNLMATLRRLVNLLERGRV-SLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus        99 -------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~-~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                                   ..+...+..+++|+|+||++|.+++..+.+ .+.++ +++|+||| |++.+.++
T Consensus        83 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~-~~vViDEa-h~~~~~~~  147 (556)
T 4a2p_A           83 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIF-TLMIFDEC-HNTTGNHP  147 (556)
T ss_dssp             TCCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTC-SEEEEETG-GGCSTTSH
T ss_pred             CceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccC-CEEEEECC-cccCCcch
Confidence                         122233445689999999999999999887 89999 99999999 99987763

>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=99.80  E-value=1.9e-20  Score=169.23  Aligned_cols=119  Identities=21%  Similarity=0.267  Sum_probs=97.3

Q ss_pred             ccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HH
Q 031654           32 RFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RK  100 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~  100 (155)
                      .|..++  +.+...+...++..|+|+|.++|+.+++|+|++++||||||||++|++|++..+.......         .+
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~rvlvl~PtraLa~Q  242 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQ  242 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEESSHHHHHH
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEcCcHHHHHH
Confidence            455555  6666667777777899999999999999999999999999999999999998875443222         22


Q ss_pred             HHHHHh----------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654          101 ELRELA----------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       101 ~~~~l~----------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                      +.+.+.                .+++|+|+||++|.+++.++...+.++ ++|||||| |+|.+.+|.
T Consensus       243 ~~~~l~~~~~~VglltGd~~~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l-~lVVIDEa-H~l~d~~rg  308 (1108)
T 3l9o_A          243 KYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREV-AWVIFDEV-HYMRDKERG  308 (1108)
T ss_dssp             HHHHHHHHTSSEEEECSSCBCCCSCSEEEEEHHHHHHHHHHCSSHHHHE-EEEEEETG-GGTTSHHHH
T ss_pred             HHHHHHHHhCCccEEeCccccCCCCCEEEeChHHHHHHHHcCccccccC-CEEEEhhh-hhccccchH
Confidence            333322                248999999999999999988889999 99999999 999998764

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

Probab=99.79  E-value=1.1e-19  Score=151.24  Aligned_cols=98  Identities=21%  Similarity=0.224  Sum_probs=82.4

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh---ch-----------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY---SA-----------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~---~~-----------------------------   98 (155)
                      .|+|+|.++++.++.|+|+++++|||||||++|++|++..+.....   ..                             
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~   83 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNI   83 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEE
Confidence            6999999999999999999999999999999999999998876431   11                             


Q ss_pred             ---------HHHHHHHhcCCcEEEEChHHHHHHHHcCCC-CcccccceEEEEcccccccccc
Q 031654           99 ---------RKELRELARWVDNLMATLRRLVNLLERGRV-SLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus        99 ---------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~-~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                               ..+...+..+++|+|+||++|.+++..+.+ .+.++ +++|+||| |++.+.+
T Consensus        84 ~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~-~~vViDEa-h~~~~~~  143 (555)
T 3tbk_A           84 ASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVF-TLMIFDEC-HNTSKNH  143 (555)
T ss_dssp             EEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGC-SEEEETTG-GGCSTTC
T ss_pred             EEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccC-CEEEEECc-cccCCcc
Confidence                     111222334589999999999999998877 89999 99999999 9998764

>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=99.79  E-value=5.3e-20  Score=160.90  Aligned_cols=100  Identities=19%  Similarity=0.127  Sum_probs=80.3

Q ss_pred             CCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------------------
Q 031654           47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------------------   98 (155)
Q Consensus        47 ~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------------------   98 (155)
                      +|. +|+++|..++|.++.|+  ++.++||||||++|++|++..........                            
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~g~~vlVltPTreLA~Q~~e~~~~l~~~lgl~v~  147 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVG  147 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTTSSCCEEEESSHHHHHHHHHHHHHHHHHTTCCEE
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHcCCcEEEEcCCHHHHHHHHHHHHHHHHhcCCeEE
Confidence            464 99999999999999998  99999999999999999986543321111                            


Q ss_pred             ------HHHHHHHhcCCcEEEEChHHH-HHHHHcCC------CCcccccceEEEEccccccc-cccc
Q 031654           99 ------RKELRELARWVDNLMATLRRL-VNLLERGR------VSLQMIIRYLALKEAADQTL-DMAL  151 (155)
Q Consensus        99 ------~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~------~~l~~l~~~lVlDEa~D~ll-~~gf  151 (155)
                            ..+.+.+..+|||+||||++| .++++.+.      +.++.+ +++||||| |+|| |+|+
T Consensus       148 ~i~GG~~~~~r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l-~~lVlDEa-D~mLiD~a~  212 (853)
T 2fsf_A          148 INLPGMPAPAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKL-HYALVDEV-DSILIDEAR  212 (853)
T ss_dssp             ECCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSC-CEEEESCH-HHHTTTTTT
T ss_pred             EEeCCCCHHHHHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCC-cEEEECch-HHHHHhcCc
Confidence                  223444555799999999999 78887653      668999 99999999 9999 7664

>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=99.78  E-value=1.6e-19  Score=133.87  Aligned_cols=109  Identities=17%  Similarity=0.230  Sum_probs=78.2

Q ss_pred             HhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh----ch----------HHH-H----
Q 031654           42 NKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY----SA----------RKE-L----  102 (155)
Q Consensus        42 ~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~----~~----------~~~-~----  102 (155)
                      ......+...|+++|.++++.+++|+++++++|||+|||++|+++++..+.....    ..          ..| .    
T Consensus        24 ~~~~~~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~  103 (216)
T 3b6e_A           24 ARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEF  103 (216)
T ss_dssp             HHTCCSCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTH
T ss_pred             cccCccCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHH
Confidence            3334445668999999999999999999999999999999999999887765431    11          112 1    


Q ss_pred             HHH-----------------------hcCCcEEEEChHHHHHHHHcCC------CCcccccceEEEEcccccccccccc
Q 031654          103 REL-----------------------ARWVDNLMATLRRLVNLLERGR------VSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       103 ~~l-----------------------~~~~~IlI~TP~~l~~~l~~~~------~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                      ..+                       ..+++|+|+||+++.+.+....      ..+.++ +++|+||| |++.+.++.
T Consensus       104 ~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~-~~iIiDEa-h~~~~~~~~  180 (216)
T 3b6e_A          104 QPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDF-SLIIIDEC-HHTNKEAVY  180 (216)
T ss_dssp             HHHHTTTSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGC-SEEEETTC--------CH
T ss_pred             HHHhccCceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcc-cEEEEECc-hhhccCCcH
Confidence            111                       1238999999999999988753      678899 99999999 999877653

>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=99.78  E-value=4.1e-19  Score=155.74  Aligned_cols=104  Identities=21%  Similarity=0.237  Sum_probs=83.3

Q ss_pred             HhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh---c-h----------------------
Q 031654           45 RTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY---S-A----------------------   98 (155)
Q Consensus        45 ~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~---~-~----------------------   98 (155)
                      ..+|+..|+|+|.++++.++.|+|+++++|||||||++|++|++..+.....   . .                      
T Consensus       242 ~~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~  321 (797)
T 4a2q_A          242 PVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFE  321 (797)
T ss_dssp             ------CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             hhcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhcc
Confidence            3558999999999999999999999999999999999999999998876421   1 1                      


Q ss_pred             ---------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCC-CcccccceEEEEcccccccccc
Q 031654           99 ---------------RKELRELARWVDNLMATLRRLVNLLERGRV-SLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus        99 ---------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~-~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                     ..+...+..+++|+|+||++|.+++..+.+ .+.++ ++||+||| |++.+.+
T Consensus       322 ~~~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~-~~iViDEa-H~~~~~~  387 (797)
T 4a2q_A          322 RQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIF-TLMIFDEC-HNTTGNH  387 (797)
T ss_dssp             GGTCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGC-SEEEETTG-GGCSTTS
T ss_pred             cCCceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccC-CEEEEECc-cccCCCc
Confidence                           122334445789999999999999998877 89999 99999999 9988764

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.78  E-value=2.2e-19  Score=162.36  Aligned_cols=110  Identities=18%  Similarity=0.141  Sum_probs=85.3

Q ss_pred             HHHhHH-hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------
Q 031654           40 LRNKPR-TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------   98 (155)
Q Consensus        40 l~~~l~-~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------   98 (155)
                      +.+.++ .+|| .|||+|.++||.+++|+|++++||||||||++|++|++..+.......                    
T Consensus        67 ~~~~~~~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~l~  145 (1104)
T 4ddu_A           67 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLA  145 (1104)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHHhh
Confidence            334443 4688 699999999999999999999999999999999888877653222111                    


Q ss_pred             ------------------HHHHHHHhcC-CcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc----------cc-
Q 031654           99 ------------------RKELRELARW-VDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT----------LD-  148 (155)
Q Consensus        99 ------------------~~~~~~l~~~-~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l----------l~-  148 (155)
                                        ..+...+..+ ++|+|+||++|.+++..  +.++++ ++||+||| |++          ++ 
T Consensus       146 ~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l-~~lViDEa-H~l~~~~r~~Dr~L~~  221 (1104)
T 4ddu_A          146 DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRF-DFVFVDDV-DAVLKASRNIDTLLMM  221 (1104)
T ss_dssp             CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCC-SEEEESCH-HHHTTSSHHHHHHHHT
T ss_pred             CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCc-CEEEEeCC-CccccccccchhhhHh
Confidence                              2344455555 99999999999888874  677899 99999999 764          45 


Q ss_pred             cccccC
Q 031654          149 MALNQK  154 (155)
Q Consensus       149 ~gf~~~  154 (155)
                      +||.++
T Consensus       222 ~gf~~~  227 (1104)
T 4ddu_A          222 VGIPEE  227 (1104)
T ss_dssp             SSCCHH
T ss_pred             cCCCHH
Confidence            788653

>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=99.78  E-value=3.9e-19  Score=135.19  Aligned_cols=100  Identities=14%  Similarity=0.161  Sum_probs=80.0

Q ss_pred             CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------HHHHHHHh-------
Q 031654           48 KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------RKELRELA-------  106 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------~~~~~~l~-------  106 (155)
                      +...++++|.++++.+..|++++++||||||||++|.++++..+.......              ......+.       
T Consensus        58 ~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~  137 (235)
T 3llm_A           58 ELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEP  137 (235)
T ss_dssp             HTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCT
T ss_pred             hcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhcccc
Confidence            344579999999999999999999999999999999999988776543311              11112221       


Q ss_pred             ----------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc-cccccc
Q 031654          107 ----------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT-LDMALN  152 (155)
Q Consensus       107 ----------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l-l~~gf~  152 (155)
                                      .+++|+|+||++|.+++..   .++++ ++||+||| |++ ++++|.
T Consensus       138 ~~~~g~~~~~~~~~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~-~~lVlDEa-h~~~~~~~~~  195 (235)
T 3llm_A          138 GKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEA---GIRGI-SHVIVDEI-HERDINTDFL  195 (235)
T ss_dssp             TSSEEEEETTEEECCCSSSEEEEEEHHHHHHHHHH---CCTTC-CEEEECCT-TSCCHHHHHH
T ss_pred             CceEEEeechhhccCCCCCeEEEECHHHHHHHHHh---hhcCC-cEEEEECC-ccCCcchHHH
Confidence                            3478999999999999976   48999 99999999 997 888775

>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=99.78  E-value=7.4e-19  Score=164.09  Aligned_cols=110  Identities=17%  Similarity=0.110  Sum_probs=87.3

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------------   98 (155)
                      +...+++...+|+.++|+|.++++.++.+ +|++++||||||||++|.+|++..+.......                  
T Consensus       913 ~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P~raLa~q~~~~~  992 (1724)
T 4f92_B          913 NSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDW  992 (1724)
T ss_dssp             CHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHH
T ss_pred             CHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcChHHHHHHHHHHH
Confidence            56778888889999999999999999865 78999999999999999999999987654322                  


Q ss_pred             ------------------HHHHHHHhcCCcEEEEChHHHHHHHHcC--CCCcccccceEEEEccccccccc
Q 031654           99 ------------------RKELRELARWVDNLMATLRRLVNLLERG--RVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 ------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~--~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                        .........+++|+|+||+++..++++.  ...++++ ++||+||+ |.|-+.
T Consensus       993 ~~~f~~~~g~~V~~ltGd~~~~~~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v-~lvViDE~-H~l~d~ 1061 (1724)
T 4f92_B          993 YEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNI-NLFVVDEV-HLIGGE 1061 (1724)
T ss_dssp             HHHHTTTSCCCEEECCSCHHHHHHHHHHCSEEEECHHHHHHHHTTTTTCHHHHSC-SEEEECCG-GGGGST
T ss_pred             HHHhchhcCCEEEEEECCCCcchhhcCCCCEEEECHHHHHHHHhCccccccccee-eEEEeech-hhcCCC
Confidence                              1111122235899999999987777653  3358899 99999999 877653

>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=99.77  E-value=2.4e-19  Score=161.55  Aligned_cols=101  Identities=15%  Similarity=0.151  Sum_probs=80.8

Q ss_pred             HHHHHhHH-hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------H----
Q 031654           38 QHLRNKPR-TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------R----   99 (155)
Q Consensus        38 ~~l~~~l~-~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------~----   99 (155)
                      +.+.+.+. .+||. | ++|.++||.++.|+|++++||||||||+ |++|++..+.......             .    
T Consensus        44 ~~~~~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~  120 (1054)
T 1gku_B           44 KEFVEFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIR  120 (1054)
T ss_dssp             HHHHHHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHH
Confidence            44455554 57999 9 9999999999999999999999999998 9999988776433222             0    


Q ss_pred             ------------------------H---HHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654          100 ------------------------K---ELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       100 ------------------------~---~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                              .   +...+.+ ++|+|+||++|.+++.+    ++++ +++|+||| |+|++
T Consensus       121 ~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l-~~lViDEa-h~~l~  189 (1054)
T 1gku_B          121 KYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHF-DFIFVDDV-DAILK  189 (1054)
T ss_dssp             HHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCC-SEEEESCH-HHHHT
T ss_pred             HHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccC-CEEEEeCh-hhhhh
Confidence                                    1   1222334 89999999999988765    6789 99999999 99999

>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=99.77  E-value=2.8e-19  Score=156.95  Aligned_cols=105  Identities=23%  Similarity=0.238  Sum_probs=82.1

Q ss_pred             HHhH-HhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------------------
Q 031654           41 RNKP-RTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------------------   98 (155)
Q Consensus        41 ~~~l-~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------------------   98 (155)
                      .++. +.+|+ +||++|..++|.++.|+  ++.++||+|||++|++|++..........                     
T Consensus       101 rEa~~R~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g~~v~VvTpTreLA~Qdae~m~~l~~  177 (922)
T 1nkt_A          101 REAAWRVLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVHR  177 (922)
T ss_dssp             HHHHHHHHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTTSCEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhCCCeEEEeCCHHHHHHHHHHHHHHHh
Confidence            3444 34698 99999999999999998  99999999999999999975443322111                     


Q ss_pred             -------------HHHHHHHhcCCcEEEEChHHH-HHHHHcC------CCCcccccceEEEEccccccc-ccc
Q 031654           99 -------------RKELRELARWVDNLMATLRRL-VNLLERG------RVSLQMIIRYLALKEAADQTL-DMA  150 (155)
Q Consensus        99 -------------~~~~~~l~~~~~IlI~TP~~l-~~~l~~~------~~~l~~l~~~lVlDEa~D~ll-~~g  150 (155)
                                   ..+.+....+|||++|||++| .++++.+      .+.++.+ +++||||| |.|| |.+
T Consensus       178 ~lGLsv~~i~gg~~~~~r~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l-~~lIVDEa-DsmLiDea  248 (922)
T 1nkt_A          178 FLGLQVGVILATMTPDERRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGH-HYAIVDEV-DSILIDEA  248 (922)
T ss_dssp             HTTCCEEECCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCC-CEEEETTH-HHHHTTGG
T ss_pred             hcCCeEEEEeCCCCHHHHHHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCC-CEEEEeCh-HHHHHhcC
Confidence                         233344445699999999999 7888765      3678899 99999999 9999 654

>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=99.73  E-value=3.6e-18  Score=152.28  Aligned_cols=103  Identities=21%  Similarity=0.243  Sum_probs=81.4

Q ss_pred             hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhh---hc-h-----------------------
Q 031654           46 TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY---YS-A-----------------------   98 (155)
Q Consensus        46 ~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~---~~-~-----------------------   98 (155)
                      -.|+..|+++|.++++.+++|+|+++++|||||||++|++|++..+....   .. .                       
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~  322 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHT
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            44788999999999999999999999999999999999999998876532   11 1                       


Q ss_pred             --------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCC-CcccccceEEEEcccccccccc
Q 031654           99 --------------RKELRELARWVDNLMATLRRLVNLLERGRV-SLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus        99 --------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~-~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                    ..+...+..+++|+|+||++|.+++..+.+ .+.++ +++|+||| |++.+.+
T Consensus       323 ~~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~-~liViDEa-H~~~~~~  387 (936)
T 4a2w_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIF-TLMIFDEC-HNTTGNH  387 (936)
T ss_dssp             TTCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGC-SEEEEETG-GGCSTTC
T ss_pred             cCceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCC-CEEEEECc-cccCCCc
Confidence                          111223334589999999999999998877 79999 99999999 9988753

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.73  E-value=3.7e-18  Score=149.94  Aligned_cols=101  Identities=22%  Similarity=0.195  Sum_probs=80.9

Q ss_pred             hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------------------------
Q 031654           46 TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------------------------   98 (155)
Q Consensus        46 ~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------------------------   98 (155)
                      .+|+ +||++|..++|.++.|+  +++++||||||++|++|++..........                           
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G~qv~VvTPTreLA~Qdae~m~~l~~~lGLsv  151 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTGKGVHVVTVNDYLARRDAEWMGPVYRGLGLSV  151 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTCSCCEEEESSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeE
Confidence            4799 99999999999999998  99999999999999999965443322111                           


Q ss_pred             -------HHHHHHHhcCCcEEEEChHHH-HHHHHcCC------CCcc---cccceEEEEccccccc-cccc
Q 031654           99 -------RKELRELARWVDNLMATLRRL-VNLLERGR------VSLQ---MIIRYLALKEAADQTL-DMAL  151 (155)
Q Consensus        99 -------~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~------~~l~---~l~~~lVlDEa~D~ll-~~gf  151 (155)
                             ..+.+....+|||+||||++| .++++.+.      +.++   .+ +++||||| |.|| |.+.
T Consensus       152 ~~i~Gg~~~~~r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l-~~lIIDEa-DsmLiDear  220 (997)
T 2ipc_A          152 GVIQHASTPAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPL-HYAIIDEV-DSILIDEAR  220 (997)
T ss_dssp             EECCTTCCHHHHHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSS-CEEEETTH-HHHTTSSTT
T ss_pred             EEEeCCCCHHHHHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCc-ceEEEech-HHHHHhCCC
Confidence                   233444455799999999999 88888763      5677   89 99999999 9998 4454

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

Probab=99.72  E-value=9.9e-18  Score=150.47  Aligned_cols=105  Identities=23%  Similarity=0.297  Sum_probs=86.6

Q ss_pred             HHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHh--------
Q 031654           44 PRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELA--------  106 (155)
Q Consensus        44 l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~--------  106 (155)
                      ...++|+ |+++|.++++.+.+|+|+++++|||||||++|.+|++..+.......         .+..+.+.        
T Consensus        80 ~~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~g~rvL~l~PtkaLa~Q~~~~l~~~~~~vgl  158 (1010)
T 2xgj_A           80 ARTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGL  158 (1010)
T ss_dssp             SCCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHHHHHSCEEE
T ss_pred             HHhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhccCCeEEEECChHHHHHHHHHHHHHHhCCEEE
Confidence            4556786 99999999999999999999999999999999999988775432221         23333322        


Q ss_pred             --------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654          107 --------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       107 --------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                              ..++|+|+||++|.+++.++...+.++ ++|||||| |+|.+.++
T Consensus       159 ltGd~~~~~~~~IvV~Tpe~L~~~L~~~~~~l~~l-~lVViDEa-H~l~d~~r  209 (1010)
T 2xgj_A          159 MTGDITINPDAGCLVMTTEILRSMLYRGSEVMREV-AWVIFDEV-HYMRDKER  209 (1010)
T ss_dssp             ECSSCEECTTCSEEEEEHHHHHHHHHHTCTTGGGE-EEEEEETG-GGGGCTTT
T ss_pred             EeCCCccCCCCCEEEEcHHHHHHHHHcCcchhhcC-CEEEEech-hhhcccch
Confidence                    147999999999999999888889999 99999999 99998754

>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=99.71  E-value=1.1e-17  Score=156.38  Aligned_cols=133  Identities=12%  Similarity=0.133  Sum_probs=90.7

Q ss_pred             cccccCCcCcccCCCCC---CCCCcccccCCHHHHHhHHhCCCCCCCHHHHHHHHHHhc-CCcEEEEccCCCCcchhhhh
Q 031654           10 VFASENAAPASSSTNTL---SSPAARFAYVPQHLRNKPRTYKYVKPTPVQRHATSILVA-GRDLMACAQTGSRKTTPFCF   85 (155)
Q Consensus        10 ~~~~~~~~~~~~~~~~~---p~~~~~f~~l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~-g~dvl~~a~TGsGKT~~yll   85 (155)
                      .+..|+++.+.......   ......+.+||+....++.  ||++++++|++++|.++. ++|++++||||||||++|.+
T Consensus        37 ~~~~~eei~vp~~~~~~~~~~~~l~~i~~Lp~~~~~~f~--g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l  114 (1724)
T 4f92_B           37 QRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFE--GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALM  114 (1724)
T ss_dssp             ECSSEEEEEECCCCCCCCCSSCCCCBTTTSCGGGSTTCT--TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHH
T ss_pred             ccCCcceEecCCCCCCCCCCcCCccchHhcCHHHHHhcC--CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHH
Confidence            45556665554322111   1233456667755544432  899999999999998875 68999999999999999999


Q ss_pred             HHHHHHHHhhhc----------h----------HHHHHHHh------------------------cCCcEEEEChHHHHH
Q 031654           86 PIINGIMREYYS----------A----------RKELRELA------------------------RWVDNLMATLRRLVN  121 (155)
Q Consensus        86 p~l~~l~~~~~~----------~----------~~~~~~l~------------------------~~~~IlI~TP~~l~~  121 (155)
                      |++..+.+....          .          .+..+.+.                        .+++|+|+||+++..
T Consensus       115 ~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~~~~~~~gi~V~~~tGd~~~~~~~~~~~~IlVtTpEkld~  194 (1724)
T 4f92_B          115 CMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDI  194 (1724)
T ss_dssp             HHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHHHHHTTTTCCEEECCSSCSSCCTTGGGCSEEEECHHHHHH
T ss_pred             HHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHHHHHhhCCCEEEEEECCCCCCccccCCCCEEEECHHHHHH
Confidence            999998753211          0          22222211                        248999999999755


Q ss_pred             HHHcCC--CCcccccceEEEEcccccc
Q 031654          122 LLERGR--VSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       122 ~l~~~~--~~l~~l~~~lVlDEa~D~l  146 (155)
                      ++++..  -.++++ ++||+||+ |.+
T Consensus       195 llr~~~~~~~l~~v-~~vIiDEv-H~l  219 (1724)
T 4f92_B          195 ITRKGGERTYTQLV-RLIILDEI-HLL  219 (1724)
T ss_dssp             HTTSSTTHHHHTTE-EEEEETTG-GGG
T ss_pred             HHcCCccchhhcCc-CEEEEecc-hhc
Confidence            555432  237889 99999999 644

>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=99.71  E-value=1.5e-17  Score=143.15  Aligned_cols=99  Identities=20%  Similarity=0.272  Sum_probs=79.8

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhh----ch-----------HHH-H------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYY----SA-----------RKE-L------------  102 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~----~~-----------~~~-~------------  102 (155)
                      .|+|+|.++++.+++|+|+++++|||+|||++|++|++..+.....    ..           .++ .            
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~~~~   86 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYR   86 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTTTSC
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCcCce
Confidence            7899999999999999999999999999999999999998876533    11           222 1            


Q ss_pred             --------------HHHhcCCcEEEEChHHHHHHH------HcCCCCcccccceEEEEccccccccccc
Q 031654          103 --------------RELARWVDNLMATLRRLVNLL------ERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       103 --------------~~l~~~~~IlI~TP~~l~~~l------~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                                    ..+...++|+|+||++|.+.+      ....+.+.++ ++||+||| |++...++
T Consensus        87 v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~-~lvViDEa-H~~~~~~~  153 (699)
T 4gl2_A           87 VIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDF-SLIIIDEC-HHTNKEAV  153 (699)
T ss_dssp             EEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGC-SEEEEESG-GGCBTTBS
T ss_pred             EEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccC-cEEEEECc-cccCccch
Confidence                          122246899999999999988      4556789999 99999999 99866543

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

Probab=99.71  E-value=3.2e-17  Score=146.99  Aligned_cols=106  Identities=18%  Similarity=0.225  Sum_probs=87.0

Q ss_pred             HhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHhc--------
Q 031654           45 RTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELAR--------  107 (155)
Q Consensus        45 ~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~~--------  107 (155)
                      ..++|+ |+++|.++|+.+++|+|+++++|||||||++|++|+...+.......         .++...+..        
T Consensus        34 ~~~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~g~~vlvl~PtraLa~Q~~~~l~~~~~~~~v~  112 (997)
T 4a4z_A           34 RSWPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIG  112 (997)
T ss_dssp             CCCSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHTTCEEEEEESCGGGHHHHHHHHHTTC--CCEE
T ss_pred             HhCCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhcCCeEEEEeCCHHHHHHHHHHHHHHcCCCeEE
Confidence            355774 89999999999999999999999999999999999887654332211         344443332        


Q ss_pred             ----------CCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccccccc
Q 031654          108 ----------WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALNQ  153 (155)
Q Consensus       108 ----------~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~~  153 (155)
                                .++|+|+||++|.+++..+...+.++ .+||+||| |++.+++|..
T Consensus       113 ~l~G~~~~~~~~~IlV~Tpe~L~~~l~~~~~~l~~l-~lvViDEa-H~l~d~~~g~  166 (997)
T 4a4z_A          113 LITGDVQINPDANCLIMTTEILRSMLYRGADLIRDV-EFVIFDEV-HYVNDQDRGV  166 (997)
T ss_dssp             EECSSCEECTTSSEEEEEHHHHHHHHHHTCSGGGGE-EEEEECCT-TCCCTTCTTC
T ss_pred             EEeCCCccCCCCCEEEECHHHHHHHHHhCchhhcCC-CEEEEECc-ccccccchHH
Confidence                      37999999999999999888889999 99999999 9999988754

>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=99.67  E-value=2.1e-16  Score=138.64  Aligned_cols=101  Identities=16%  Similarity=0.182  Sum_probs=80.4

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcC------CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAG------RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g------~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------   98 (155)
                      +.+.+.++.++| .||++|.++|+.++++      .|++++++||||||++|++|++..+.......             
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~  434 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHY  434 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHH
Confidence            455566788999 9999999999999876      59999999999999999999998876443221             


Q ss_pred             --------------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 --------------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 --------------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                ..+...+.. .++|+|+||+.+.+     .+.+.++ +++|+||+ |++
T Consensus       435 ~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l-~lVVIDEa-Hr~  502 (780)
T 1gm5_A          435 RRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNL-GLVIIDEQ-HRF  502 (780)
T ss_dssp             HHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCC-CEEEEESC-CCC
T ss_pred             HHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCC-ceEEeccc-chh
Confidence                                      122334444 49999999988743     4678999 99999999 986

>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=99.64  E-value=8.9e-16  Score=124.50  Aligned_cols=96  Identities=18%  Similarity=0.111  Sum_probs=78.6

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      .|+|+|.++++.++.+ ++++++|||+|||++++++++..+.......                                
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~   87 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALT   87 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEEC
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEee
Confidence            6899999999999999 9999999999999999999988765222111                                


Q ss_pred             ----HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 ----RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 ----~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                          .........+++|+|+||+.+...+..+.+.+.++ +++|+||| |++.+.
T Consensus        88 g~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~-~~vIiDEa-H~~~~~  140 (494)
T 1wp9_A           88 GEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDV-SLIVFDEA-HRAVGN  140 (494)
T ss_dssp             SCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSC-SEEEEETG-GGCSTT
T ss_pred             CCcchhhhhhhccCCCEEEecHHHHHHHHhcCCcchhhc-eEEEEECC-cccCCC
Confidence                11122223357999999999999999888889999 99999999 998754

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.57  E-value=9.8e-16  Score=126.72  Aligned_cols=95  Identities=12%  Similarity=0.039  Sum_probs=74.7

Q ss_pred             CCCCCCHHHHHHHHHHhcCCcE-EEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHh----------
Q 031654           48 KYVKPTPVQRHATSILVAGRDL-MACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELA----------  106 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l~g~dv-l~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~----------  106 (155)
                      |+..|+|+|+ +||.+++|+|+ +++||||||||++|++|++..+.......          .+....+.          
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g~~v~~~~~~   79 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPA   79 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCEEECCTT
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHhcCceeeeeecc
Confidence            7899999986 79999999887 99999999999999999998876544322          22222221          


Q ss_pred             ------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654          107 ------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       107 ------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                            .+..|.++|++.+...+.+. ..+.++ +++|+||| |++
T Consensus        80 ~~~~~~~~~~i~~~t~~~l~~~l~~~-~~l~~~-~~iViDEa-h~~  122 (451)
T 2jlq_A           80 VKSDHTGREIVDLMCHATFTTRLLSS-TRVPNY-NLIVMDEA-HFT  122 (451)
T ss_dssp             CSCCCCSSCCEEEEEHHHHHHHHHHC-SCCCCC-SEEEEETT-TCC
T ss_pred             ccccCCCCceEEEEChHHHHHHhhCc-ccccCC-CEEEEeCC-ccC
Confidence                  12368899999998877654 568899 99999999 976

>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=99.55  E-value=1.4e-17  Score=142.97  Aligned_cols=110  Identities=12%  Similarity=0.003  Sum_probs=75.8

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhc
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELAR  107 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~  107 (155)
                      +.+++++... ...|+|+|+.++|.+++|+|++++||||||||++|++|++..+.......          .+....+..
T Consensus       159 ~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~PtreLa~Qi~~~l~~  237 (618)
T 2whx_A          159 GDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRG  237 (618)
T ss_dssp             ---CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT
T ss_pred             HHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcChHHHHHHHHHHhcC
Confidence            6666666654 58999999999999999999999999999999999999999887643222          233333311


Q ss_pred             ----------------CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654          108 ----------------WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       108 ----------------~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                                      +..+.+.|.+.+...+... ..++++ ++||+||| |+| +++|.
T Consensus       238 ~~v~~~~~~l~~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~-~~iViDEa-h~~-~~~~~  294 (618)
T 2whx_A          238 LPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSS-TRVPNY-NLIVMDEA-HFT-DPCSV  294 (618)
T ss_dssp             SCEEECCTTSSCCCCSSSCEEEEEHHHHHHHHHHC-SSCCCC-SEEEEEST-TCC-SHHHH
T ss_pred             CceeEecccceeccCCCceEEEEChHHHHHHHhcc-ccccCC-eEEEEECC-CCC-CccHH
Confidence                            1123333444444333322 358899 99999999 998 76664

>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=99.54  E-value=9.7e-15  Score=113.38  Aligned_cols=95  Identities=8%  Similarity=-0.009  Sum_probs=72.0

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------HHHHHHHh-----------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------RKELRELA-----------  106 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------~~~~~~l~-----------  106 (155)
                      .|+++|.++++.++.+++.++++|||+|||+++++++...+.......             .+......           
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~~~  192 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIG  192 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECS
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHHHHhcccccceEEEEe
Confidence            799999999999999989999999999999999988877665432122             12222221           


Q ss_pred             ----------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccc
Q 031654          107 ----------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       107 ----------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                .+++|+|+||+++..   .....+.++ +++|+||| |++.+..
T Consensus       193 ~~~~~~~~~~~~~~I~v~T~~~l~~---~~~~~~~~~-~~vIiDEa-H~~~~~~  241 (282)
T 1rif_A          193 GGASKDDKYKNDAPVVVGTWQTVVK---QPKEWFSQF-GMMMNDEC-HLATGKS  241 (282)
T ss_dssp             TTCSSTTCCCTTCSEEEECHHHHTT---SCGGGGGGE-EEEEEETG-GGCCHHH
T ss_pred             CCCcchhhhccCCcEEEEchHHHHh---hHHHHHhhC-CEEEEECC-ccCCccc
Confidence                      358999999988643   233457889 99999999 9987643

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.50  E-value=3.5e-17  Score=141.61  Aligned_cols=103  Identities=10%  Similarity=0.022  Sum_probs=72.6

Q ss_pred             HhHHhCCCC-----CCCHHHH-----HHHHHHh------cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------
Q 031654           42 NKPRTYKYV-----KPTPVQR-----HATSILV------AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------   98 (155)
Q Consensus        42 ~~l~~~g~~-----~pt~iQ~-----~~i~~~l------~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------   98 (155)
                      .+|..+||.     .||++|+     ++||.++      +|+|++++||||||||++|++|++..+.......       
T Consensus       201 ~~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr  280 (673)
T 2wv9_A          201 IGLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTR  280 (673)
T ss_dssp             EEEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             EEeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHH
Confidence            366777888     9999999     9999988      8999999999999999999999998876544322       


Q ss_pred             ---HHHHHHHhc------CCcE-EEEChHHHHHHHHcC--------CCCcccccceEEEEcccccc
Q 031654           99 ---RKELRELAR------WVDN-LMATLRRLVNLLERG--------RVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ---~~~~~~l~~------~~~I-lI~TP~~l~~~l~~~--------~~~l~~l~~~lVlDEa~D~l  146 (155)
                         .+....+..      ...+ .++||+++++++..+        ...++++ ++||+||| |+|
T Consensus       281 ~La~Q~~~~l~~~~i~~~~~~l~~v~tp~~ll~~l~~~~l~~~l~~~~~l~~l-~lvViDEa-H~~  344 (673)
T 2wv9_A          281 VVAAEMAEALRGLPVRYLTPAVQREHSGNEIVDVMCHATLTHRLMSPLRVPNY-NLFVMDEA-HFT  344 (673)
T ss_dssp             HHHHHHHHHTTTSCCEECCC---CCCCSCCCEEEEEHHHHHHHHHSSSCCCCC-SEEEEEST-TCC
T ss_pred             HHHHHHHHHHhcCCeeeecccccccCCHHHHHHHHHhhhhHHHHhcccccccc-eEEEEeCC-ccc
Confidence               233333321      1111 177887765433322        2368899 99999999 998

>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=99.49  E-value=1e-13  Score=125.90  Aligned_cols=101  Identities=20%  Similarity=0.234  Sum_probs=74.6

Q ss_pred             HHHHHhH-HhCCCCCCCHHHHHHHHHHhc----CC--cEEEEccCCCCcchhhhhHHHHHHHHhhhch------------
Q 031654           38 QHLRNKP-RTYKYVKPTPVQRHATSILVA----GR--DLMACAQTGSRKTTPFCFPIINGIMREYYSA------------   98 (155)
Q Consensus        38 ~~l~~~l-~~~g~~~pt~iQ~~~i~~~l~----g~--dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------   98 (155)
                      +...+.+ ..++|+ |||+|.++|+.++.    |+  |++++++||||||++|+++++..+.......            
T Consensus       590 ~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~  668 (1151)
T 2eyq_A          590 REQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQH  668 (1151)
T ss_dssp             HHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHH
T ss_pred             HHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHH
Confidence            3344444 566886 69999999999986    66  9999999999999999988876544322111            


Q ss_pred             ---------------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 ---------------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 ---------------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                 ......+.. .++|+|+||+.+     .+.+.+.++ +++|+||+ |++
T Consensus       669 ~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll-----~~~~~~~~l-~lvIiDEa-H~~  737 (1151)
T 2eyq_A          669 YDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLL-----QSDVKFKDL-GLLIVDEE-HRF  737 (1151)
T ss_dssp             HHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHH-----HSCCCCSSE-EEEEEESG-GGS
T ss_pred             HHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHH-----hCCcccccc-ceEEEech-Hhc
Confidence                                       122233444 499999999765     245678999 99999999 985

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.49  E-value=7.3e-14  Score=118.15  Aligned_cols=41  Identities=22%  Similarity=0.001  Sum_probs=35.8

Q ss_pred             CCCCCCHHHHHHHHH----HhcCCcEEEEccCCCCcchhhhhHHHH
Q 031654           48 KYVKPTPVQRHATSI----LVAGRDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~----~l~g~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      || .|+|.|.+++..    +..|+|+++.||||||||++|++|++.
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~   45 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE   45 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh
Confidence            34 689999997764    468999999999999999999999986

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

Probab=99.49  E-value=5.3e-14  Score=117.03  Aligned_cols=96  Identities=8%  Similarity=-0.006  Sum_probs=73.8

Q ss_pred             CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------HHHHHHH----------
Q 031654           49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------RKELREL----------  105 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------~~~~~~l----------  105 (155)
                      ...|++.|.++++.+++++|++++++||||||++|++|+...+.......             .+.....          
T Consensus       111 ~~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~  190 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (510)
T ss_dssp             EECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEE
T ss_pred             CCCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHHHHHHhhcCCccceEE
Confidence            34899999999999999999999999999999999999888775433222             1111111          


Q ss_pred             -----------hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          106 -----------ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       106 -----------~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                 ..+++|+|+||+.|.   ......+.++ .++|+||| |++...
T Consensus       191 ~~~~~~~~~~~~~~~~I~i~T~~~l~---~~~~~~~~~~-~liIiDE~-H~~~~~  240 (510)
T 2oca_A          191 IGGGASKDDKYKNDAPVVVGTWQTVV---KQPKEWFSQF-GMMMNDEC-HLATGK  240 (510)
T ss_dssp             CGGGCCTTGGGCTTCSEEEEEHHHHT---TSCGGGGGGE-EEEEEETG-GGCCHH
T ss_pred             EecCCccccccccCCcEEEEeHHHHh---hchhhhhhcC-CEEEEECC-cCCCcc
Confidence                       135799999999754   3344668899 99999999 998753

>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=99.48  E-value=1.4e-13  Score=113.49  Aligned_cols=107  Identities=12%  Similarity=-0.052  Sum_probs=79.6

Q ss_pred             HHHHHhHHhCCCC------------------CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-
Q 031654           38 QHLRNKPRTYKYV------------------KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~------------------~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-   98 (155)
                      +.+.+.|...|+.                  .|+|.|.++++.++.++++++++|||+|||++|+.++...   ..... 
T Consensus        62 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~---~~~~Lv  138 (472)
T 2fwr_A           62 RDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL---STPTLI  138 (472)
T ss_dssp             HHHHHHHHHTTCCEEEESCCCCCCCCCCCCCCBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH---CSCEEE
T ss_pred             HHHHHHHHHcCCCcccccccccCcccccCCCCcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc---CCCEEE
Confidence            6677777766654                  5899999999999999999999999999999999988753   11110 


Q ss_pred             --------HHHHHHHh---------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654           99 --------RKELRELA---------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus        99 --------~~~~~~l~---------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                              .+....+.               ..++|+|+||+.+...+..   ...++ .++|+||| |++.+.+|.
T Consensus       139 l~P~~~L~~Q~~~~~~~~~~~~v~~~~g~~~~~~~Ivv~T~~~l~~~~~~---~~~~~-~liIvDEa-H~~~~~~~~  210 (472)
T 2fwr_A          139 VVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEK---LGNRF-MLLIFDEV-HHLPAESYV  210 (472)
T ss_dssp             EESSHHHHHHHHHHGGGGCGGGEEEBSSSCBCCCSEEEEEHHHHHHTHHH---HTTTC-SEEEEETG-GGTTSTTTH
T ss_pred             EECCHHHHHHHHHHHHhCCCcceEEECCCcCCcCCEEEEEcHHHHHHHHH---hcCCC-CEEEEECC-cCCCChHHH
Confidence                    22222221               1468999999998776542   12458 99999999 999887764

>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=99.47  E-value=2.1e-13  Score=103.99  Aligned_cols=94  Identities=14%  Similarity=-0.038  Sum_probs=69.5

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHh---------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELA---------------  106 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~---------------  106 (155)
                      .|+++|.+++..++.++++++++|||+|||.+++.++...   .....         .+..+.+.               
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~---~~~~liv~P~~~L~~q~~~~~~~~~~~~v~~~~g~~~  169 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL---STPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIK  169 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS---CSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSCB
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHhCCCCeEEEEeCCCC
Confidence            6899999999999999999999999999999998876543   11110         22222222               


Q ss_pred             cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654          107 RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       107 ~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                      ...+|+|+||+.+......   ...++ ++||+||| |++.+.+|.
T Consensus       170 ~~~~i~v~T~~~l~~~~~~---~~~~~-~llIiDEa-H~l~~~~~~  210 (237)
T 2fz4_A          170 ELKPLTVSTYDSAYVNAEK---LGNRF-MLLIFDEV-HHLPAESYV  210 (237)
T ss_dssp             CCCSEEEEEHHHHHHTHHH---HTTTC-SEEEEECS-SCCCTTTHH
T ss_pred             CcCCEEEEeHHHHHhhHHH---hcccC-CEEEEECC-ccCCChHHH
Confidence            1468999999998765542   12457 99999999 999877654

>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=99.44  E-value=1.7e-13  Score=120.22  Aligned_cols=116  Identities=18%  Similarity=0.067  Sum_probs=85.8

Q ss_pred             CCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcC-CcEEEEccCCCCcchhhhhHHHHHHHHhh---hc-h--
Q 031654           28 SPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAG-RDLMACAQTGSRKTTPFCFPIINGIMREY---YS-A--   98 (155)
Q Consensus        28 ~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~---~~-~--   98 (155)
                      .++.+|++++  +.+.+.++..+ ..|+++|+.+|+.++.+ ++++++||||||||+  ++|++.......   .. .  
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~~~~g~~ilv  145 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMPHLENTQVAC  145 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCGGGGTCEEEE
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccccCCCceEEe
Confidence            3466799987  99999999888 89999999999988755 689999999999999  577663222111   11 1  


Q ss_pred             --------HHHHHHHh----------------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc-cc
Q 031654           99 --------RKELRELA----------------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ-TL  147 (155)
Q Consensus        99 --------~~~~~~l~----------------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~-ll  147 (155)
                              .+....+.                      ...+|+++|||++.+.+..+ ..+.++ ++|||||+ |. ++
T Consensus       146 l~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~~~~~~~~I~v~T~G~l~r~l~~~-~~l~~~-~~lIlDEa-h~R~l  222 (773)
T 2xau_A          146 TQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMED-HDLSRY-SCIILDEA-HERTL  222 (773)
T ss_dssp             EESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEEECCTTCSEEEEEHHHHHHHHHHS-TTCTTE-EEEEECSG-GGCCH
T ss_pred             cCchHHHHHHHHHHHHHHhCCchhheecceeccccccCCCCCEEEECHHHHHHHHhhC-ccccCC-CEEEecCc-ccccc
Confidence                    11111111                      24689999999999887664 468899 99999999 95 77


Q ss_pred             cc
Q 031654          148 DM  149 (155)
Q Consensus       148 ~~  149 (155)
                      +.
T Consensus       223 d~  224 (773)
T 2xau_A          223 AT  224 (773)
T ss_dssp             HH
T ss_pred             ch
Confidence            63

>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=99.35  E-value=5.1e-14  Score=121.48  Aligned_cols=91  Identities=14%  Similarity=0.029  Sum_probs=65.6

Q ss_pred             CHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------HHHH-HHH-----------------h
Q 031654           53 TPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------RKEL-REL-----------------A  106 (155)
Q Consensus        53 t~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------~~~~-~~l-----------------~  106 (155)
                      .+.|..+++.+.+++|++++||||||||.+|.+|+++.   .....        ..|. +.+                 .
T Consensus       219 ~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~---g~~vLVl~PTReLA~Qia~~l~~~~g~~vg~~vG~~~~~  295 (666)
T 3o8b_A          219 FTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ---GYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRTIT  295 (666)
T ss_dssp             CCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT---TCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCEEC
T ss_pred             HHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC---CCeEEEEcchHHHHHHHHHHHHHHhCCCeeEEECcEecc
Confidence            34444445555678899999999999999999998762   11111        1111 111                 2


Q ss_pred             cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654          107 RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       107 ~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                      .+++|+|+||++|   +....+.++++ ++||||||  +|++++|.
T Consensus       296 ~~~~IlV~TPGrL---l~~~~l~l~~l-~~lVlDEA--H~l~~~~~  335 (666)
T 3o8b_A          296 TGAPVTYSTYGKF---LADGGCSGGAY-DIIICDEC--HSTDSTTI  335 (666)
T ss_dssp             CCCSEEEEEHHHH---HHTTSCCTTSC-SEEEETTT--TCCSHHHH
T ss_pred             CCCCEEEECcHHH---HhCCCcccCcc-cEEEEccc--hhcCccHH
Confidence            3689999999997   56778889999 99999999  67788774

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.34  E-value=8.5e-13  Score=111.44  Aligned_cols=42  Identities=21%  Similarity=0.140  Sum_probs=33.1

Q ss_pred             CCCCCCCHHHHHHHH----HHhcCCcEEEEccCCCCcchhhhhHHHH
Q 031654           47 YKYVKPTPVQRHATS----ILVAGRDLMACAQTGSRKTTPFCFPIIN   89 (155)
Q Consensus        47 ~g~~~pt~iQ~~~i~----~~l~g~dvl~~a~TGsGKT~~yllp~l~   89 (155)
                      .|| .|+|+|.+++.    .+..|+++++.||||||||++|++|++.
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~   49 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQ   49 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            477 89999999865    4568899999999999999999999865

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.34  E-value=2.3e-14  Score=118.31  Aligned_cols=83  Identities=13%  Similarity=0.095  Sum_probs=59.7

Q ss_pred             HHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhc------CCcE-EEEChHHHHHHHH
Q 031654           62 ILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELAR------WVDN-LMATLRRLVNLLE  124 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~------~~~I-lI~TP~~l~~~l~  124 (155)
                      .+++|+|++++||||||||++|++|+++.+.......          .+....+..      ...+ .|+||+++.+++.
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~~~lil~Ptr~La~Q~~~~l~~~~v~~~~~~~~~v~Tp~~l~~~l~   83 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMC   83 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCEEEESSCCCCCCCSSCCEEEEE
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcCCeEEEEcchHHHHHHHHHHHhcCCeEEecccceeccCCccceeeec
Confidence            3578999999999999999999999999887654322          333333321      1122 4899987765444


Q ss_pred             cC--------CCCcccccceEEEEcccccc
Q 031654          125 RG--------RVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       125 ~~--------~~~l~~l~~~lVlDEa~D~l  146 (155)
                      .+        ...+.++ +++|+||| |+|
T Consensus        84 ~~~l~~~~~~~~~~~~l-~~vViDEa-h~~  111 (440)
T 1yks_A           84 HATLTYRMLEPTRVVNW-EVIIMDEA-HFL  111 (440)
T ss_dssp             HHHHHHHHTSSSCCCCC-SEEEETTT-TCC
T ss_pred             ccchhHhhhCcccccCc-cEEEEECc-ccc
Confidence            33        2348899 99999999 998

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.32  E-value=9.8e-13  Score=111.52  Aligned_cols=96  Identities=14%  Similarity=0.132  Sum_probs=60.7

Q ss_pred             CCCHHHHHHHHHHhc----C-CcEEEEccCCCCcchhhhhHHHHHHHHhh-------hch-----------HHHHH----
Q 031654           51 KPTPVQRHATSILVA----G-RDLMACAQTGSRKTTPFCFPIINGIMREY-------YSA-----------RKELR----  103 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~----g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~-------~~~-----------~~~~~----  103 (155)
                      .|+++|.++++.++.    | ++++++++||||||++++ +++..+....       ...           ..|..    
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~-~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAF-QISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHH-HHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            799999999998876    5 679999999999999964 4555554432       111           22222    


Q ss_pred             -------------HHhcCCcEEEEChHHHHHHHHc----CCCCcccccceEEEEccccccccc
Q 031654          104 -------------ELARWVDNLMATLRRLVNLLER----GRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       104 -------------~l~~~~~IlI~TP~~l~~~l~~----~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                   ....+.+|+|+||++|......    +.+....+ .+||+||| |++...
T Consensus       257 ~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~-~lvIiDEa-H~~~~~  317 (590)
T 3h1t_A          257 TPFGDARHKIEGGKVVKSREIYFAIYQSIASDERRPGLYKEFPQDFF-DLIIIDEC-HRGSAR  317 (590)
T ss_dssp             TTTCSSEEECCC--CCSSCSEEEEEGGGC------CCGGGGSCTTSC-SEEEESCC-C-----
T ss_pred             HhcchhhhhhhccCCCCCCcEEEEEhhhhccccccccccccCCCCcc-CEEEEECC-cccccc
Confidence                         1223689999999999887652    23566788 99999999 999864

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.29  E-value=1.3e-12  Score=108.19  Aligned_cols=89  Identities=13%  Similarity=0.019  Sum_probs=61.6

Q ss_pred             HHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHh----------------cCCcEEEE
Q 031654           61 SILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELA----------------RWVDNLMA  114 (155)
Q Consensus        61 ~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~----------------~~~~IlI~  114 (155)
                      ..+.+|+|+++++|||||||++|++|++..+.......          .+....+.                .+.-+.+.
T Consensus        16 ~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g~~v~~~~~~~~~~~t~~~~i~~~   95 (459)
T 2z83_A           16 NMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMAEALRGLPVRYQTSAVQREHQGNEIVDVM   95 (459)
T ss_dssp             GGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSHHHHHHHHHHTTTSCEEECC--------CCCSEEEE
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchHHHHHHHHHHhcCceEeEEecccccCCCCCcEEEEE
Confidence            34567899999999999999999999999886543322          22222221                12335566


Q ss_pred             ChHHHHHHHHcCCCCcccccceEEEEccccc-----ccccccc
Q 031654          115 TLRRLVNLLERGRVSLQMIIRYLALKEAADQ-----TLDMALN  152 (155)
Q Consensus       115 TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~-----ll~~gf~  152 (155)
                      |.+.+...+... ..++++ ++||+||| |+     +++.||.
T Consensus        96 ~~~~l~~~l~~~-~~l~~~-~~iViDEa-H~~~~~~~~~~~~~  135 (459)
T 2z83_A           96 CHATLTHRLMSP-NRVPNY-NLFVMDEA-HFTDPASIAARGYI  135 (459)
T ss_dssp             EHHHHHHHHHSC-C-CCCC-SEEEESST-TCCSHHHHHHHHHH
T ss_pred             chHHHHHHhhcc-ccccCC-cEEEEECC-ccCCchhhHHHHHH
Confidence            777665555443 568899 99999999 98     6777764

>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=99.28  E-value=6e-12  Score=113.29  Aligned_cols=110  Identities=18%  Similarity=0.099  Sum_probs=79.3

Q ss_pred             HHHHHhHHhCC-------CCCCCHHHHHHHHHHhc--------------CCcEEEEccCCCCcchhhhhHHHHHHHHhhh
Q 031654           38 QHLRNKPRTYK-------YVKPTPVQRHATSILVA--------------GRDLMACAQTGSRKTTPFCFPIINGIMREYY   96 (155)
Q Consensus        38 ~~l~~~l~~~g-------~~~pt~iQ~~~i~~~l~--------------g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~   96 (155)
                      +.+++.+...-       ...|+|+|..|++.++.              +++.+++++||||||+++ ++++..+.....
T Consensus       251 ~~ll~~l~~f~~~~~~~~~~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~  329 (1038)
T 2w00_A          251 HTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDF  329 (1038)
T ss_dssp             HHHHHHHHHSEEECTTCCEEECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTT
T ss_pred             HHHHHHHHhheeeccccccccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCC
Confidence            66666665542       23599999999999875              378999999999999997 676654432111


Q ss_pred             --ch-------------------------------HHHHHHHh-cCCcEEEEChHHHHHHHHcCC--CCcccccceEEEE
Q 031654           97 --SA-------------------------------RKELRELA-RWVDNLMATLRRLVNLLERGR--VSLQMIIRYLALK  140 (155)
Q Consensus        97 --~~-------------------------------~~~~~~l~-~~~~IlI~TP~~l~~~l~~~~--~~l~~l~~~lVlD  140 (155)
                        ..                               ......+. .+++|+|+||++|..++....  ..++.. .+||+|
T Consensus       330 ~~rvLvlvpr~eL~~Q~~~~f~~f~~~~v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~-~lvIiD  408 (1038)
T 2w00_A          330 IDKVFFVVDRKDLDYQTMKEYQRFSPDSVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQ-VVFIFD  408 (1038)
T ss_dssp             CCEEEEEECGGGCCHHHHHHHHTTSTTCSSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSC-EEEEEE
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHhcccccccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccc-cEEEEE
Confidence              11                               23333443 468999999999999887542  246678 899999


Q ss_pred             cccccccccc
Q 031654          141 EAADQTLDMA  150 (155)
Q Consensus       141 Ea~D~ll~~g  150 (155)
                      || |++...+
T Consensus       409 EA-Hrs~~~~  417 (1038)
T 2w00_A          409 EC-HRSQFGE  417 (1038)
T ss_dssp             SC-CTTHHHH
T ss_pred             cc-chhcchH
Confidence            99 9987543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.13  E-value=5.1e-11  Score=97.94  Aligned_cols=79  Identities=13%  Similarity=0.023  Sum_probs=53.7

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHhc-----------------CCcEEEEChHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELAR-----------------WVDNLMATLRR  118 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~~-----------------~~~IlI~TP~~  118 (155)
                      +|+|+++++|||||||++|++|+++.+.......         ..|......                 +.-+.+.|.+.
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~~La~Q~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~   80 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVVASEMYEALRGEPIRYMTPAVQSERTGNEIVDFMCHST   80 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCEEEC---------CCCSEEEEEHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHHHHHHHHHHHhCCCeEEEEecCccccCCCCceEEEEchHH
Confidence            4789999999999999999999997776544322         222222221                 22344445555


Q ss_pred             HHHHHHcCCCCcccccceEEEEcccccc
Q 031654          119 LVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       119 l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                      +...+.. ...+.++ +++|+||| |++
T Consensus        81 l~~~l~~-~~~~~~l-~~vViDEa-H~~  105 (431)
T 2v6i_A           81 FTMKLLQ-GVRVPNY-NLYIMDEA-HFL  105 (431)
T ss_dssp             HHHHHHH-TCCCCCC-SEEEEEST-TCC
T ss_pred             HHHHHhc-CccccCC-CEEEEeCC-ccC
Confidence            5444444 4558899 99999999 987

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.01  E-value=2.3e-11  Score=105.34  Aligned_cols=105  Identities=10%  Similarity=-0.026  Sum_probs=63.5

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHhc-
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELAR-  107 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~~-  107 (155)
                      .+-++++..++  .|  .|.......++|+|++++||||||||+    +++..+.......         .+....+.. 
T Consensus       131 ~d~l~~i~dl~--~p--~~~~p~ar~l~rk~vlv~apTGSGKT~----~al~~l~~~~~gl~l~PtR~LA~Qi~~~l~~~  202 (677)
T 3rc3_A          131 KDDLRKISDLR--IP--PNWYPDARAMQRKIIFHSGPTNSGKTY----HAIQKYFSAKSGVYCGPLKLLAHEIFEKSNAA  202 (677)
T ss_dssp             HHHHHHHTBCC--CG--GGGCHHHHTSCCEEEEEECCTTSSHHH----HHHHHHHHSSSEEEEESSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhcc--Ch--hhhCHHHHhcCCCEEEEEcCCCCCHHH----HHHHHHHhcCCeEEEeCHHHHHHHHHHHHHhc
Confidence            44445554443  33  333444566799999999999999998    4444444432211         222222221 


Q ss_pred             ---------CCcEEEEChHHHHHHHHcC--CC-CcccccceEEEEcccccccccccc
Q 031654          108 ---------WVDNLMATLRRLVNLLERG--RV-SLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus       108 ---------~~~IlI~TP~~l~~~l~~~--~~-~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                               +.+++++||+++.+++...  .. ....+ +++|+||| |+|++.+|.
T Consensus       203 g~~v~lltG~~~~iv~TpGr~~~il~~T~e~~~l~~~v-~lvVIDEa-H~l~d~~~g  257 (677)
T 3rc3_A          203 GVPCDLVTGEERVTVQPNGKQASHVSCTVEMCSVTTPY-EVAVIDEI-QMIRDPARG  257 (677)
T ss_dssp             TCCEEEECSSCEECCSTTCCCCSEEEEEGGGCCSSSCE-EEEEECSG-GGGGCTTTH
T ss_pred             CCcEEEEECCeeEEecCCCcccceeEecHhHhhhcccC-CEEEEecc-eecCCccch
Confidence                     3455666776655555432  12 24677 99999999 999988764

>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=99.00  E-value=5.6e-10  Score=92.47  Aligned_cols=95  Identities=18%  Similarity=0.168  Sum_probs=65.5

Q ss_pred             CCCCHHHHHHHHHH----hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc-h-------------HHHHHHHh-----
Q 031654           50 VKPTPVQRHATSIL----VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-A-------------RKELRELA-----  106 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~----l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~-~-------------~~~~~~l~-----  106 (155)
                      ..|+|+|.+++..+    ..|++.+++.+||+|||+..+. ++..+...... .             ..+.....     
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~-~i~~~~~~~~~~~~LIv~P~~l~~qw~~e~~~~~~~~~v  114 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRF  114 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTTCCSSEEEEECSTTHHHHHHHHHHHCTTSCE
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHH-HHHHHHhcCCCCCEEEEccHHHHHHHHHHHHHHCCCceE
Confidence            37999999999876    4678999999999999999654 44444332211 1             22222221     


Q ss_pred             ------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccc
Q 031654          107 ------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       107 ------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                  ..++|+|+|++.+.....   +..... .++|+||| |++-+.+
T Consensus       115 ~~~~g~~~~~~~~~~~ivi~t~~~l~~~~~---l~~~~~-~~vIvDEa-H~~kn~~  165 (500)
T 1z63_A          115 AVFHEDRSKIKLEDYDIILTTYAVLLRDTR---LKEVEW-KYIVIDEA-QNIKNPQ  165 (500)
T ss_dssp             EECSSSTTSCCGGGSSEEEEEHHHHTTCHH---HHTCCE-EEEEEETG-GGGSCTT
T ss_pred             EEEecCchhccccCCcEEEeeHHHHhccch---hcCCCc-CEEEEeCc-cccCCHh
Confidence                        246899999999865433   333456 88999999 9987643

>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=98.72  E-value=1.1e-08  Score=91.63  Aligned_cols=98  Identities=12%  Similarity=0.033  Sum_probs=66.8

Q ss_pred             CCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHH-------------
Q 031654           51 KPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELREL-------------  105 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l-------------  105 (155)
                      .|+|+|..++..++..  .+++++.+||+|||+.++..+...+.......          .+....+             
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~sLl~Qw~~E~~~~f~l~v~v~~~  232 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALFDD  232 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCTTTHHHHHHHHHHHSCCCCEECCH
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCHHHHHHHHHHHHHHhCCCEEEEcc
Confidence            6899999999988764  58999999999999999877766554433111          1111111             


Q ss_pred             -------------hcCCcEEEEChHHHHHHHHc-CCCCcccccceEEEEcccccccccc
Q 031654          106 -------------ARWVDNLMATLRRLVNLLER-GRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       106 -------------~~~~~IlI~TP~~l~~~l~~-~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                   ....+|+|+|++.+...... ..+...+. .+||+||| |++-+.+
T Consensus       233 ~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~-dlVIvDEA-H~~kn~~  289 (968)
T 3dmq_A          233 ERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEW-DLLVVDEA-HHLVWSE  289 (968)
T ss_dssp             HHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCC-CEEEECCS-SCCCCBT
T ss_pred             chhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCC-CEEEehhh-HhhcCCC
Confidence                         12469999999886532111 11334577 89999999 9986544

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.68  E-value=1.2e-08  Score=87.62  Aligned_cols=43  Identities=19%  Similarity=0.012  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHH----HHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           51 KPTPVQRHATS----ILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        51 ~pt~iQ~~~i~----~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .|+|.|.+.+.    .+.+|+|+++.||||||||++|++|++..+..
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~   49 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSE   49 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh
Confidence            67999998875    55689999999999999999999999988753

>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=98.54  E-value=4.4e-08  Score=83.84  Aligned_cols=39  Identities=15%  Similarity=0.150  Sum_probs=34.8

Q ss_pred             CHHHHHHHHHHhcCCcEEEEccCCCCcc--hhhhhHHHHHH
Q 031654           53 TPVQRHATSILVAGRDLMACAQTGSRKT--TPFCFPIINGI   91 (155)
Q Consensus        53 t~iQ~~~i~~~l~g~dvl~~a~TGsGKT--~~yllp~l~~l   91 (155)
                      ++.|+.+++.++.+++++++|++|||||  ++++++.+..+
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~  191 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQM  191 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            7899999999999999999999999999  77777776543

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

Probab=98.49  E-value=2.6e-07  Score=81.18  Aligned_cols=94  Identities=16%  Similarity=0.138  Sum_probs=62.8

Q ss_pred             CCCHHHHHHHHHHh----cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------------------
Q 031654           51 KPTPVQRHATSILV----AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l----~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------------------   98 (155)
                      .++|.|..++..++    .|++.+++.++|+|||+..+..+...+.......                            
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P~sll~qW~~E~~~~~p~~~v~  315 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCI  315 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECCTTTHHHHHHHHHHHSTTCCEE
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEECchHHHHHHHHHHHHCCCceEE
Confidence            67899999998665    8899999999999999987655544333221111                            


Q ss_pred             --------HHHHHH------------HhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 --------RKELRE------------LARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 --------~~~~~~------------l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                              ....+.            ....++|+|+|++.+......  +.-... .+||+||| |++-+
T Consensus       316 ~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w-~~vIvDEa-H~lkn  381 (800)
T 3mwy_W          316 CYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKW-QFMAVDEA-HRLKN  381 (800)
T ss_dssp             ECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEE-EEEEETTG-GGGCC
T ss_pred             EEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCc-ceeehhhh-hhhcC
Confidence                    111111            112578999999998654321  122246 78999999 99854

>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=98.43  E-value=7e-07  Score=76.73  Aligned_cols=95  Identities=13%  Similarity=0.024  Sum_probs=63.6

Q ss_pred             CCCHHHHHHHHHHh---------cCCcEEEEccCCCCcchhhhhHHHHHHHHhhh---c---h------------HHH--
Q 031654           51 KPTPVQRHATSILV---------AGRDLMACAQTGSRKTTPFCFPIINGIMREYY---S---A------------RKE--  101 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l---------~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~---~---~------------~~~--  101 (155)
                      .+.|+|.+++..+.         .++..++..++|+|||+..+..+...+.....   .   .            ..+  
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~sll~qW~~E~~  134 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVG  134 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecHHHHHHHHHHHH
Confidence            68999999998774         45789999999999999876665554432210   0   0            000  


Q ss_pred             -----------------------HHHHh------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          102 -----------------------LRELA------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       102 -----------------------~~~l~------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                             .....      ..++|+|+|++.+....  ..+..... .++|+||| |++-+.
T Consensus       135 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~--~~l~~~~~-~~vI~DEa-H~ikn~  207 (644)
T 1z3i_X          135 KWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA--EVLHKGKV-GLVICDEG-HRLKNS  207 (644)
T ss_dssp             HHHGGGCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT--TTTTTSCC-CEEEETTG-GGCCTT
T ss_pred             HHcCCCeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhH--HHhhcCCc-cEEEEECc-eecCCh
Confidence                                   11111      13789999999876542  33444567 88999999 998543

>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=98.13  E-value=2.4e-06  Score=74.47  Aligned_cols=45  Identities=29%  Similarity=0.305  Sum_probs=38.1

Q ss_pred             hCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           46 TYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        46 ~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .+|. +|+++|....-.+..|+  ++...||+|||+++.+|++-....
T Consensus        71 ~lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~  115 (822)
T 3jux_A           71 TLGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI  115 (822)
T ss_dssp             HTSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT
T ss_pred             HhCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc
Confidence            3355 78999999999999888  889999999999999998755443

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.86  E-value=9.9e-06  Score=69.53  Aligned_cols=33  Identities=18%  Similarity=0.227  Sum_probs=28.4

Q ss_pred             CCCHHHHHHHHHHhcCCc-EEEEccCCCCcchhh
Q 031654           51 KPTPVQRHATSILVAGRD-LMACAQTGSRKTTPF   83 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~d-vl~~a~TGsGKT~~y   83 (155)
                      .+++-|.+|+..++..++ .+|+||+|||||.+-
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti  222 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTV  222 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHH
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHH
Confidence            468899999999988776 688999999999864

>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=97.84  E-value=1.1e-05  Score=66.57  Aligned_cols=48  Identities=19%  Similarity=0.192  Sum_probs=34.2

Q ss_pred             HHhCCCCCCCHHHHHHHHHHhcC-----CcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           44 PRTYKYVKPTPVQRHATSILVAG-----RDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        44 l~~~g~~~pt~iQ~~~i~~~l~g-----~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      ..-+.|..+++-|+.++..++..     ..+++.|+.|||||... ..++..+.
T Consensus        18 ~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~   70 (459)
T 3upu_A           18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALI   70 (459)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHH
T ss_pred             cCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHH
Confidence            34567899999999999877543     38999999999999643 33444443

>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=97.73  E-value=2.2e-05  Score=66.76  Aligned_cols=32  Identities=19%  Similarity=0.154  Sum_probs=29.7

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+++.|..++..++.++.+++.|++|||||..
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~  220 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTT  220 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHH
Confidence            47899999999999999999999999999975

>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=97.08  E-value=0.001  Score=47.41  Aligned_cols=31  Identities=23%  Similarity=0.187  Sum_probs=22.3

Q ss_pred             CHHHHHHHHHHh---------cCCcEEEEccCCCCcchhh
Q 031654           53 TPVQRHATSILV---------AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        53 t~iQ~~~i~~~l---------~g~dvl~~a~TGsGKT~~y   83 (155)
                      ++.|..++..+.         .|+.+++.+|+|+|||...
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHH
Confidence            445555554442         4789999999999999753

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=97.02  E-value=0.00055  Score=50.21  Aligned_cols=68  Identities=7%  Similarity=-0.004  Sum_probs=38.8

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccc
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAAD  144 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D  144 (155)
                      .++.+++.||+|+|||.... .+...+.             ..+..++..+...+...+....-.+... ..+||||+ |
T Consensus        51 ~~~~~ll~G~~G~GKT~la~-~l~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~vliiDe~-~  114 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIH-AACARAN-------------ELERRSFYIPLGIHASISTALLEGLEQF-DLICIDDV-D  114 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHH-HHHHHHH-------------HTTCCEEEEEGGGGGGSCGGGGTTGGGS-SEEEEETG-G
T ss_pred             CCCeEEEECCCCCCHHHHHH-HHHHHHH-------------HcCCeEEEEEHHHHHHHHHHHHHhccCC-CEEEEecc-c
Confidence            46899999999999998532 1111111             1134555555433322211111124556 78999999 9


Q ss_pred             cccc
Q 031654          145 QTLD  148 (155)
Q Consensus       145 ~ll~  148 (155)
                      .+..
T Consensus       115 ~~~~  118 (242)
T 3bos_A          115 AVAG  118 (242)
T ss_dssp             GGTT
T ss_pred             cccC
Confidence            8754

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.70  E-value=0.00074  Score=46.67  Aligned_cols=20  Identities=15%  Similarity=0.072  Sum_probs=17.2

Q ss_pred             HhcCCcEEEEccCCCCcchh
Q 031654           63 LVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ...+.++++.+++|+|||..
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            45668999999999999975

>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=96.68  E-value=0.0027  Score=54.26  Aligned_cols=42  Identities=14%  Similarity=0.063  Sum_probs=33.0

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      ..+++-|..|+..++.+.-+++.||+|||||.... .++..+.
T Consensus       179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~-~~i~~l~  220 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLA  220 (624)
T ss_dssp             CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHH-HHHHHHH
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHH-HHHHHHH
Confidence            35689999999999988889999999999998642 3344443

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.68  E-value=0.01  Score=46.28  Aligned_cols=66  Identities=9%  Similarity=0.146  Sum_probs=38.5

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHcCC--------C-Ccccccce
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLERGR--------V-SLQMIIRY  136 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~~~--------~-~l~~l~~~  136 (155)
                      ++++++.||+|+|||.... .+...+.            ...+..++..+...+...+....        + .+.+. .+
T Consensus       152 ~~~lll~G~~GtGKT~La~-aia~~~~------------~~~g~~v~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~-~l  217 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA-AMAHELS------------EKKGVSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKNV-PV  217 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH-HHHHHHH------------HHSCCCEEEEEHHHHHHHHHCCCC----CCTTHHHHTS-SE
T ss_pred             CceEEEECCCCCCHHHHHH-HHHHHHH------------HhcCCcEEEEEHHHHHHHHHHHhccchHHHHHHHhcCC-CE
Confidence            6899999999999997532 2222221            02345565444444444443211        1 14567 89


Q ss_pred             EEEEcccccc
Q 031654          137 LALKEAADQT  146 (155)
Q Consensus       137 lVlDEa~D~l  146 (155)
                      |||||+ +..
T Consensus       218 LiiDdi-g~~  226 (308)
T 2qgz_A          218 LILDDI-GAE  226 (308)
T ss_dssp             EEEETC-CC-
T ss_pred             EEEcCC-CCC
Confidence            999999 754

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.64  E-value=0.006  Score=48.18  Aligned_cols=19  Identities=11%  Similarity=-0.001  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.++++.||+|+|||+..
T Consensus        44 ~~~~lli~GpPGTGKT~~v   62 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLV   62 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3468999999999999864

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.54  E-value=0.011  Score=42.49  Aligned_cols=16  Identities=25%  Similarity=0.183  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.+++.+|+|+|||..
T Consensus        55 ~~~~l~G~~GtGKT~l   70 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYL   70 (202)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            7899999999999985

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.46  E-value=0.0028  Score=44.40  Aligned_cols=17  Identities=18%  Similarity=0.173  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      +.++++.+|+|+|||..
T Consensus        43 ~~~vll~G~~G~GKT~l   59 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAI   59 (187)
T ss_dssp             SCEEEEESCGGGCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            46899999999999975

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.45  E-value=0.0046  Score=43.20  Aligned_cols=18  Identities=17%  Similarity=0.171  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++.+++.||+|+|||...
T Consensus        43 ~~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            368999999999999753

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.40  E-value=0.0052  Score=54.17  Aligned_cols=34  Identities=18%  Similarity=0.108  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..+++-|..|+..++.+.-+++.||+|||||...
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i  392 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTS  392 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHH
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            3568999999999988878899999999999764

>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=96.31  E-value=0.0061  Score=53.74  Aligned_cols=41  Identities=15%  Similarity=0.057  Sum_probs=32.9

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      .+++-|..|+..++.+.-.++.||+|||||... ..++..+.
T Consensus       356 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti-~~~i~~l~  396 (800)
T 2wjy_A          356 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLA  396 (800)
T ss_dssp             CCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHH-HHHHHHHH
T ss_pred             CCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHH-HHHHHHHH
Confidence            468999999999998888999999999999864 33444444

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=96.12  E-value=0.0063  Score=46.08  Aligned_cols=17  Identities=18%  Similarity=0.018  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      ..+++.+|+|+|||...
T Consensus        65 ~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            57999999999999853

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=96.09  E-value=0.0075  Score=47.36  Aligned_cols=94  Identities=17%  Similarity=0.109  Sum_probs=50.6

Q ss_pred             CCHHHHHHHHHHh----cCC---cEEEEccCCCCcchhhhhHHHHHHHHhhhc----h----HHHHHHHhcCCcEEEECh
Q 031654           52 PTPVQRHATSILV----AGR---DLMACAQTGSRKTTPFCFPIINGIMREYYS----A----RKELRELARWVDNLMATL  116 (155)
Q Consensus        52 pt~iQ~~~i~~~l----~g~---dvl~~a~TGsGKT~~yllp~l~~l~~~~~~----~----~~~~~~l~~~~~IlI~TP  116 (155)
                      .+|+|..++..+.    +|+   -+++.||.|+|||.... .+...+......    +    ......-...+++..-.|
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~-~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~   81 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIY-ALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAP   81 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHH-HHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECC
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHH-HHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEec
Confidence            3677777776553    443   48999999999997643 222333221110    0    111111223467776655


Q ss_pred             H---------HHHHHHHcCC--CCcccccceEEEEcccccccc
Q 031654          117 R---------RLVNLLERGR--VSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       117 ~---------~l~~~l~~~~--~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      +         .+.+++..-.  -....- +.+||||| |.|-.
T Consensus        82 ~~~~~~~~i~~ir~l~~~~~~~~~~~~~-kvviIdea-d~l~~  122 (334)
T 1a5t_A           82 EKGKNTLGVDAVREVTEKLNEHARLGGA-KVVWVTDA-ALLTD  122 (334)
T ss_dssp             CTTCSSBCHHHHHHHHHHTTSCCTTSSC-EEEEESCG-GGBCH
T ss_pred             cccCCCCCHHHHHHHHHHHhhccccCCc-EEEEECch-hhcCH
Confidence            3         2223332211  123456 88999999 98854

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.00  E-value=0.0062  Score=47.71  Aligned_cols=19  Identities=21%  Similarity=0.188  Sum_probs=16.1

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+..+++.||+|+|||...
T Consensus        43 ~~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHH
Confidence            3578999999999999853

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=96.00  E-value=0.0078  Score=46.71  Aligned_cols=67  Identities=12%  Similarity=0.164  Sum_probs=37.6

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHH----HcCCC-----Ccccccce
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLL----ERGRV-----SLQMIIRY  136 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l----~~~~~-----~l~~l~~~  136 (155)
                      +..+++.||+|+|||...- .+...+..             .+..++..+...+...+    .....     .+.+. .+
T Consensus        37 ~~~lll~G~~GtGKT~la~-~i~~~~~~-------------~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~v  101 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQ-AAGNEAKK-------------RGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSV-DL  101 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHH-HHHHHHHH-------------TTCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHHTC-SE
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHH-------------CCCEEEEEEHHHHHHHHHHHHHcCcHHHHHHHhcCC-CE
Confidence            4689999999999997532 22222211             13445555544432221    11110     12346 78


Q ss_pred             EEEEcccccccc
Q 031654          137 LALKEAADQTLD  148 (155)
Q Consensus       137 lVlDEa~D~ll~  148 (155)
                      |+|||+ |.+..
T Consensus       102 L~iDEi-~~l~~  112 (324)
T 1l8q_A          102 LLLDDV-QFLSG  112 (324)
T ss_dssp             EEEECG-GGGTT
T ss_pred             EEEcCc-ccccC
Confidence            999999 98763

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=95.97  E-value=0.0094  Score=45.66  Aligned_cols=17  Identities=24%  Similarity=0.184  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        68 ~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            57999999999999854

>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=95.88  E-value=0.012  Score=45.51  Aligned_cols=51  Identities=10%  Similarity=0.156  Sum_probs=29.4

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHH-HHHH--HhcCCcEEEEccCCCCcchhh
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRH-ATSI--LVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~-~i~~--~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      -.+|+++.  +..++.|.+.- .  .|.... .+..  +..++.+++.+|+|+|||+..
T Consensus        11 ~~~~~di~G~~~~~~~l~~~v-~--~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           11 QVTWEDIGGLEDVKRELQELV-Q--YPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHH-H--HHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHH-H--HHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            35788887  66666665420 0  011100 0001  124578999999999999853

>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=95.81  E-value=0.053  Score=42.12  Aligned_cols=48  Identities=13%  Similarity=0.162  Sum_probs=29.4

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHh-----cCCcEEEEccCCCCcchhh
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILV-----AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l-----~g~dvl~~a~TGsGKT~~y   83 (155)
                      -.+|+++.  +..++.|.+.-.   .|.   ..|.++     ..+.+++.+|+|+|||...
T Consensus        14 ~~~~~di~G~~~~~~~l~~~i~---~~~---~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           14 NVKWEDVAGLEGAKEALKEAVI---LPV---KFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTH---HHH---HCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCHHHhcChHHHHHHHHHHHH---HHH---hCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            35788887  777777665310   011   111111     1357999999999999853

>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=95.75  E-value=0.02  Score=48.39  Aligned_cols=41  Identities=24%  Similarity=0.180  Sum_probs=31.1

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      ..+++-|.+++.  ..+..++|.|+.|||||.+-+--+...+.
T Consensus         8 ~~Ln~~Q~~av~--~~~~~~lV~a~aGsGKT~~l~~ri~~l~~   48 (647)
T 3lfu_A            8 DSLNDKQREAVA--APRSNLLVLAGAGSGKTRVLVHRIAWLMS   48 (647)
T ss_dssp             TTCCHHHHHHHT--CCSSCEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHh--CCCCCEEEEECCCCCHHHHHHHHHHHHHH
Confidence            468999999996  33578999999999999876544444443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=95.72  E-value=0.0077  Score=47.30  Aligned_cols=18  Identities=33%  Similarity=0.503  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++.+++.||+|+|||...
T Consensus        70 ~~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             TCEEEEEESTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            368999999999999853

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=95.65  E-value=0.05  Score=38.64  Aligned_cols=16  Identities=25%  Similarity=0.376  Sum_probs=14.2

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      ..+++.||+|+|||..
T Consensus        39 ~~~ll~G~~G~GKT~l   54 (226)
T 2chg_A           39 PHLLFSGPPGTGKTAT   54 (226)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4699999999999974

>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=95.59  E-value=0.12  Score=39.21  Aligned_cols=19  Identities=21%  Similarity=0.279  Sum_probs=16.1

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.++++.||+|+|||...
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            3578999999999999753

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=95.55  E-value=0.036  Score=42.97  Aligned_cols=59  Identities=19%  Similarity=0.070  Sum_probs=34.8

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEE-----EChHHHHHHHHcCCCCcccccceEEEEc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLM-----ATLRRLVNLLERGRVSLQMIIRYLALKE  141 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI-----~TP~~l~~~l~~~~~~l~~l~~~lVlDE  141 (155)
                      .++++.+|+|+|||...-     .+..          .+ ..+-+.+     ..++.+...+..    ...- ..|+|||
T Consensus        56 ~~vll~G~~GtGKT~la~-----~ia~----------~~-~~~~~~~~~~~~~~~~~~~~~~~~----~~~~-~vl~lDE  114 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLAN-----IISY----------EM-SANIKTTAAPMIEKSGDLAAILTN----LSEG-DILFIDE  114 (338)
T ss_dssp             CCEEEECSTTSSHHHHHH-----HHHH----------HT-TCCEEEEEGGGCCSHHHHHHHHHT----CCTT-CEEEEET
T ss_pred             CeEEEECcCCCCHHHHHH-----HHHH----------Hh-CCCeEEecchhccchhHHHHHHHh----ccCC-CEEEEec
Confidence            589999999999998532     1111          11 1111111     234555555543    3355 6899999


Q ss_pred             cccccc
Q 031654          142 AADQTL  147 (155)
Q Consensus       142 a~D~ll  147 (155)
                      + |.|-
T Consensus       115 i-~~l~  119 (338)
T 3pfi_A          115 I-HRLS  119 (338)
T ss_dssp             G-GGCC
T ss_pred             h-hhcC
Confidence            9 9874

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=95.43  E-value=0.026  Score=43.37  Aligned_cols=18  Identities=28%  Similarity=0.163  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ...+++.||+|+|||...
T Consensus        38 ~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCCEEECCTTCCCHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            378999999999999753

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=95.35  E-value=0.027  Score=46.04  Aligned_cols=69  Identities=14%  Similarity=0.191  Sum_probs=39.0

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHH----HHHcCCC-----Ccc-cccc
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVN----LLERGRV-----SLQ-MIIR  135 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~----~l~~~~~-----~l~-~l~~  135 (155)
                      +..+++.||+|+|||...- .+...+..           ...+..++..+...+..    .+.....     .+. .. .
T Consensus       130 ~~~lll~Gp~G~GKTtLa~-aia~~l~~-----------~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  196 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQ-SIGNYVVQ-----------NEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKV-D  196 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHH-HHHHHHHH-----------HCCSSCEEEEEHHHHHHHHHHHHHTTCHHHHHHHHTTTC-S
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHH-----------hCCCCeEEEeeHHHHHHHHHHHHHcccHHHHHHHhcCCC-C
Confidence            3689999999999998532 22222211           11234555555444322    2222211     123 56 7


Q ss_pred             eEEEEcccccccc
Q 031654          136 YLALKEAADQTLD  148 (155)
Q Consensus       136 ~lVlDEa~D~ll~  148 (155)
                      .|+|||+ |.+.+
T Consensus       197 vL~IDEi-~~l~~  208 (440)
T 2z4s_A          197 ILLIDDV-QFLIG  208 (440)
T ss_dssp             EEEEECG-GGGSS
T ss_pred             EEEEeCc-ccccC
Confidence            9999999 98875

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=95.32  E-value=0.027  Score=43.43  Aligned_cols=16  Identities=19%  Similarity=0.011  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.+++.+|+|+|||..
T Consensus        37 ~~lLl~GppGtGKT~l   52 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQ   52 (293)
T ss_dssp             SEEEEEECTTSCHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            5789999999999985

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=95.01  E-value=0.021  Score=44.50  Aligned_cols=19  Identities=21%  Similarity=0.295  Sum_probs=16.1

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+..+++.||+|+|||...
T Consensus        44 ~~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           44 KPNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             CCCCEEEEECTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3578999999999999853

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=94.93  E-value=0.064  Score=46.40  Aligned_cols=74  Identities=19%  Similarity=0.159  Sum_probs=47.8

Q ss_pred             CCCHHHHHHHHHHhcC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEECh-----HHHHHHH
Q 031654           51 KPTPVQRHATSILVAG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATL-----RRLVNLL  123 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP-----~~l~~~l  123 (155)
                      .+|.-|++++..++.-  .-.++.|+-|.|||.+.-+.+-               .+.  ..++|+.|     ..|..+.
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a---------------~~~--~~~~vtAP~~~a~~~l~~~~  237 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLIS---------------RIA--GRAIVTAPAKASTDVLAQFA  237 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHH---------------HSS--SCEEEECSSCCSCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHH---------------HHH--hCcEEECCCHHHHHHHHHHh
Confidence            6799999999988763  3478899999999965433321               111  13577777     3344443


Q ss_pred             HcC--CC-------CcccccceEEEEcc
Q 031654          124 ERG--RV-------SLQMIIRYLALKEA  142 (155)
Q Consensus       124 ~~~--~~-------~l~~l~~~lVlDEa  142 (155)
                      ...  .+       .+... ++||||||
T Consensus       238 ~~~i~~~~Pd~~~~~~~~~-dlliVDEA  264 (671)
T 2zpa_A          238 GEKFRFIAPDALLASDEQA-DWLVVDEA  264 (671)
T ss_dssp             GGGCCBCCHHHHHHSCCCC-SEEEEETG
T ss_pred             hCCeEEeCchhhhhCcccC-CEEEEEch
Confidence            321  11       23447 89999999

>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=94.80  E-value=0.073  Score=41.96  Aligned_cols=19  Identities=26%  Similarity=0.267  Sum_probs=16.3

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+..+++.+|+|+|||...
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

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=94.77  E-value=0.015  Score=41.94  Aligned_cols=20  Identities=25%  Similarity=0.177  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCCCcchhhh
Q 031654           65 AGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yl   84 (155)
                      .|+=.++.++.|+|||...+
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll   21 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELL   21 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHH
T ss_pred             ccEEEEEECCCCCCHHHHHH
Confidence            45667889999999998753

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=94.75  E-value=0.12  Score=39.42  Aligned_cols=17  Identities=29%  Similarity=0.309  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      ..+++.||+|+|||...
T Consensus        47 ~~~ll~G~~G~GKT~la   63 (327)
T 1iqp_A           47 PHLLFAGPPGVGKTTAA   63 (327)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            36999999999999753

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=94.22  E-value=0.055  Score=42.37  Aligned_cols=16  Identities=19%  Similarity=0.256  Sum_probs=14.4

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      .+++.||+|+|||...
T Consensus        46 ~~li~G~~G~GKTtl~   61 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL   61 (389)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999864

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=94.21  E-value=0.049  Score=44.51  Aligned_cols=18  Identities=17%  Similarity=0.189  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.+++.||+|+|||+..
T Consensus       167 ~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          167 WRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CSEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            368999999999999853

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=94.10  E-value=0.023  Score=45.01  Aligned_cols=17  Identities=12%  Similarity=0.188  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +.+++.+|+|+|||+..
T Consensus        85 ~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCEEEECSTTSCHHHHH
T ss_pred             ceEEEECCCCCcHHHHH
Confidence            57999999999999853

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=94.08  E-value=0.034  Score=38.11  Aligned_cols=20  Identities=10%  Similarity=0.059  Sum_probs=17.2

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..+.++++.+++|||||...
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            45689999999999999864

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=93.94  E-value=0.045  Score=40.93  Aligned_cols=77  Identities=6%  Similarity=-0.010  Sum_probs=42.7

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------HHHHH--HHhc-----CCcEEEEChHHHHHHHHcCCCCcc
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------RKELR--ELAR-----WVDNLMATLRRLVNLLERGRVSLQ  131 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------~~~~~--~l~~-----~~~IlI~TP~~l~~~l~~~~~~l~  131 (155)
                      .|.=+++.+++|+|||.+.+ -++.++.......      .+...  .+..     ...+-+.+...+.+.+.... .-.
T Consensus        11 ~G~i~litG~mGsGKTT~ll-~~~~r~~~~g~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~-~~~   88 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELI-RRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNS-FND   88 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHH-HHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTT-SCT
T ss_pred             CcEEEEEECCCCCcHHHHHH-HHHHHHHhcCCEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHHh-hCC
Confidence            45667888999999998753 3333333322111      11000  1111     12455666677777665432 223


Q ss_pred             cccceEEEEccccc
Q 031654          132 MIIRYLALKEAADQ  145 (155)
Q Consensus       132 ~l~~~lVlDEa~D~  145 (155)
                      .. .+|||||| ..
T Consensus        89 ~~-dvViIDEa-Q~  100 (223)
T 2b8t_A           89 ET-KVIGIDEV-QF  100 (223)
T ss_dssp             TC-CEEEECSG-GG
T ss_pred             CC-CEEEEecC-cc
Confidence            46 89999999 54

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=93.93  E-value=0.11  Score=44.44  Aligned_cols=41  Identities=24%  Similarity=0.189  Sum_probs=31.3

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .+++-|.+++..  .+..++|.|+.|||||.+-+--+...+..
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~   42 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRG   42 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHh
Confidence            478999999864  36789999999999998765445444443

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=92.62  E-value=0.071  Score=41.10  Aligned_cols=14  Identities=14%  Similarity=0.211  Sum_probs=12.1

Q ss_pred             cccceEEEEccccccc
Q 031654          132 MIIRYLALKEAADQTL  147 (155)
Q Consensus       132 ~l~~~lVlDEa~D~ll  147 (155)
                      .. +.++|||+ |.|-
T Consensus       105 ~~-~vliiDEi-~~l~  118 (324)
T 3u61_B          105 RQ-KVIVIDEF-DRSG  118 (324)
T ss_dssp             CE-EEEEEESC-CCGG
T ss_pred             CC-eEEEEECC-cccC
Confidence            56 79999999 9885

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=92.49  E-value=0.077  Score=41.41  Aligned_cols=48  Identities=13%  Similarity=0.195  Sum_probs=29.0

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhc-----CCcEEEEccCCCCcchhh
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVA-----GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~-----g~dvl~~a~TGsGKT~~y   83 (155)
                      -.+|+++.  +.+++.|.+.=.   .|.+   .|.++.     .+.+++.+|+|+|||+..
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v~---~p~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAVI---LPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHH---HHHH---CGGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHH---HHHh---CHHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            35799987  666666654200   0110   112222     268999999999999853

>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=92.36  E-value=0.12  Score=44.88  Aligned_cols=41  Identities=22%  Similarity=0.156  Sum_probs=31.5

Q ss_pred             CCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           50 VKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        50 ~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      ..+++-|.+++..  .+..++|.|+.|||||.+-.--+...+.
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~   50 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMA   50 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHH
Confidence            4689999999865  3578999999999999876544444443

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=92.30  E-value=0.026  Score=42.68  Aligned_cols=49  Identities=12%  Similarity=0.182  Sum_probs=29.2

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHH-HHHHHH--HhcCCcEEEEccCCCCcchh
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQ-RHATSI--LVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ-~~~i~~--~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+|+++.  +..++.|.+.- .  .+.+ ...+..  +..++.+++.||+|+|||..
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~-~--~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~l   67 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVV-E--LPLKHPELFEKVGIEPPKGILLYGPPGTGKTLL   67 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHT-H--HHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHH-H--HHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHH
Confidence            4788887  66666665431 0  1111 111111  13457899999999999975

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=92.24  E-value=0.11  Score=42.78  Aligned_cols=16  Identities=19%  Similarity=0.204  Sum_probs=13.5

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      =.++.|+.|||||...
T Consensus       163 v~~I~G~aGsGKTt~I  178 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEI  178 (446)
T ss_dssp             EEEEEECTTSCHHHHH
T ss_pred             EEEEEcCCCCCHHHHH
Confidence            4678999999999864

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=92.23  E-value=0.059  Score=44.24  Aligned_cols=17  Identities=24%  Similarity=0.301  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      ..+++.+|+|+|||...
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            47999999999999853

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=92.23  E-value=0.11  Score=43.35  Aligned_cols=39  Identities=13%  Similarity=-0.138  Sum_probs=25.7

Q ss_pred             HhHHhCCCCCCCHHHHHHHH-HHhcCCcEEEEccCCCCcchh
Q 031654           42 NKPRTYKYVKPTPVQRHATS-ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        42 ~~l~~~g~~~pt~iQ~~~i~-~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ..|.+.|.  +++.+..-+. .+-.|..+++++|||||||..
T Consensus       237 ~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          237 IDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHH
T ss_pred             hhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            34455562  2343333333 456788999999999999975

>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=92.17  E-value=0.087  Score=48.41  Aligned_cols=41  Identities=29%  Similarity=0.292  Sum_probs=32.8

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      .+|+-|.++|-.  .+++++|.|..|||||.+-+--++..+..
T Consensus        10 ~~t~eQ~~~i~~--~~~~~~v~a~AGSGKT~vl~~ri~~ll~~   50 (1232)
T 3u4q_A           10 TWTDDQWNAIVS--TGQDILVAAAAGSGKTAVLVERMIRKITA   50 (1232)
T ss_dssp             CCCHHHHHHHHC--CSSCEEEEECTTCCHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhc
Confidence            579999999864  38899999999999999865555555544

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=92.16  E-value=0.12  Score=43.36  Aligned_cols=19  Identities=26%  Similarity=0.204  Sum_probs=16.4

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|..+++.+|+|+|||...
T Consensus       107 ~g~~vll~Gp~GtGKTtla  125 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLA  125 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999753

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=92.13  E-value=0.19  Score=44.27  Aligned_cols=16  Identities=19%  Similarity=0.212  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      .+++++||+|+|||..
T Consensus       192 ~~vlL~G~pG~GKT~l  207 (854)
T 1qvr_A          192 NNPVLIGEPGVGKTAI  207 (854)
T ss_dssp             CCCEEEECTTSCHHHH
T ss_pred             CceEEEcCCCCCHHHH
Confidence            5899999999999974

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=92.02  E-value=0.16  Score=40.70  Aligned_cols=85  Identities=14%  Similarity=0.123  Sum_probs=45.2

Q ss_pred             HHHHHhc------CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhcC-CcEEEECh---HH
Q 031654           59 ATSILVA------GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELARW-VDNLMATL---RR  118 (155)
Q Consensus        59 ~i~~~l~------g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~~-~~IlI~TP---~~  118 (155)
                      .+..++.      |.-+++.+++|+|||. +++.++..+.......          ......+.-. -+++|..|   +.
T Consensus        61 ~LD~~Lg~GGl~~G~li~I~G~pGsGKTt-lal~la~~~~~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~  139 (366)
T 1xp8_A           61 SLDLALGVGGIPRGRITEIYGPESGGKTT-LALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQ  139 (366)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHH-HHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHH
T ss_pred             HHHHHhCCCCccCCcEEEEEcCCCCChHH-HHHHHHHHHHHCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHH
Confidence            4455555      3678999999999996 4445544443322221          1111122111 13444443   44


Q ss_pred             HHHHHHcCCCCcccccceEEEEccccccc
Q 031654          119 LVNLLERGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus       119 l~~~l~~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                      +.+.+.. .+.-..+ ++||||.+ ..|.
T Consensus       140 ~l~~l~~-l~~~~~~-~lVVIDsl-~~l~  165 (366)
T 1xp8_A          140 ALEIMEL-LVRSGAI-DVVVVDSV-AALT  165 (366)
T ss_dssp             HHHHHHH-HHTTTCC-SEEEEECT-TTCC
T ss_pred             HHHHHHH-HHhcCCC-CEEEEeCh-HHhc
Confidence            4444431 1112357 89999999 8776

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.98  E-value=0.029  Score=46.05  Aligned_cols=52  Identities=12%  Similarity=0.106  Sum_probs=31.9

Q ss_pred             CCCcccccCC--HHHHHhHHhCC---CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           28 SPAARFAYVP--QHLRNKPRTYK---YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        28 ~~~~~f~~l~--~~l~~~l~~~g---~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .|-.+|++++  ++..+.|.+.=   +.+|.-.+...+   --.+.+++.||+|||||+.
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLL  231 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHH
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHH
Confidence            4556899998  77777665421   112222221111   1237899999999999985

>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=91.59  E-value=0.29  Score=37.61  Aligned_cols=44  Identities=9%  Similarity=-0.031  Sum_probs=33.1

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHH-HHHHhcCC-----cEEEEccCCCCcchhhh
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHA-TSILVAGR-----DLMACAQTGSRKTTPFC   84 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~-i~~~l~g~-----dvl~~a~TGsGKT~~yl   84 (155)
                      ..+.+.|+..||.   |++... +-..+.|+     .+++.+|+|||||+.+.
T Consensus        73 n~i~~~l~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           73 NRIYKILELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             CHHHHHHHHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            5888999988885   666544 44555553     49999999999998764

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=91.55  E-value=0.2  Score=41.81  Aligned_cols=44  Identities=11%  Similarity=0.093  Sum_probs=30.1

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ..+.+.+... +-.-..+=..+.-.+..|.++++.||+|+|||..
T Consensus        14 ~~l~~~l~~~-ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           14 SRLSSSLEKG-LYERSHAIRLCLLAALSGESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             HHHHHHHHTT-CSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHH
T ss_pred             HHHHHHHHhh-hHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHH
Confidence            4455555543 3333344455666778889999999999999985

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=91.29  E-value=0.26  Score=36.63  Aligned_cols=19  Identities=21%  Similarity=0.209  Sum_probs=13.6

Q ss_pred             CCcEEEEccCCCCcchhhh
Q 031654           66 GRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl   84 (155)
                      |+=.+++++-|||||.+.+
T Consensus        28 G~l~vitG~MgsGKTT~lL   46 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELI   46 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHH
T ss_pred             CEEEEEECCCCCcHHHHHH
Confidence            3434577888999998753

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=91.26  E-value=0.22  Score=36.46  Aligned_cols=35  Identities=20%  Similarity=0.089  Sum_probs=28.2

Q ss_pred             CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +..-+.-|..++.-+..|.-+.+.+|+|||||.-.
T Consensus         5 i~pk~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            5 IRPKTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CCCCSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             cccCCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            44445667778888889999999999999999854

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=90.82  E-value=0.22  Score=34.41  Aligned_cols=18  Identities=17%  Similarity=0.287  Sum_probs=16.4

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|+.+++.+|+|+|||..
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            688999999999999875

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=90.72  E-value=0.16  Score=40.71  Aligned_cols=25  Identities=32%  Similarity=0.437  Sum_probs=19.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||..-
T Consensus        96 lv~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           96 VVSQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhCCCCEEEEEeCCCCCCccEEe
Confidence            3455688976  778899999999764

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.70  E-value=0.055  Score=44.07  Aligned_cols=48  Identities=17%  Similarity=0.254  Sum_probs=31.3

Q ss_pred             CCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHh------cCCcEEEEccCCCCcchh
Q 031654           29 PAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILV------AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l------~g~dvl~~a~TGsGKT~~   82 (155)
                      |-.+|++++  ++..+.|++. +.  .|+..   |.++      -.+.++..||+|+|||+.
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~-v~--~Pl~~---pe~f~~~gi~~prGvLL~GPPGTGKTll  198 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEV-IE--LPVKH---PELFESLGIAQPKGVILYGPPGTGKTLL  198 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHH-TH--HHHHC---HHHHHHHTCCCCCCEEEESCSSSSHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHH-HH--HHHhC---HHHHHhCCCCCCCceEEeCCCCCCHHHH
Confidence            446899998  7777777653 11  12111   2222      237899999999999985

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=90.37  E-value=0.12  Score=41.07  Aligned_cols=21  Identities=33%  Similarity=0.362  Sum_probs=18.4

Q ss_pred             HHhcCCcEEEEccCCCCcchh
Q 031654           62 ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..|..+++++|||||||..
T Consensus       171 ~i~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          171 AVQLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HHHTTCCEEEEESSSSCHHHH
T ss_pred             HHhcCCEEEEECCCCCCHHHH
Confidence            456889999999999999975

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=90.31  E-value=0.21  Score=39.59  Aligned_cols=78  Identities=13%  Similarity=0.061  Sum_probs=39.8

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhc-CCcEEEECh---HHHHHHHHcCCCCcc
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELAR-WVDNLMATL---RRLVNLLERGRVSLQ  131 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~-~~~IlI~TP---~~l~~~l~~~~~~l~  131 (155)
                      |+-+++.+++|||||...+ -++..+.......          ....+.+.- .-++.+..|   +.+++.+.. .+.-.
T Consensus        61 G~iv~I~G~pGsGKTtLal-~la~~~~~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~-l~~~~  138 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVAL-HAVANAQAAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEIADM-LVRSG  138 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHH-HHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHH-HHTTT
T ss_pred             CeEEEEECCCCCCHHHHHH-HHHHHHHhCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHHHHH-HHhcC
Confidence            4678999999999997543 3333333222111          111122211 113444444   333333321 01113


Q ss_pred             cccceEEEEccccccc
Q 031654          132 MIIRYLALKEAADQTL  147 (155)
Q Consensus       132 ~l~~~lVlDEa~D~ll  147 (155)
                      .. ++||||++ ..++
T Consensus       139 ~~-~lIVIDsl-~~l~  152 (349)
T 2zr9_A          139 AL-DIIVIDSV-AALV  152 (349)
T ss_dssp             CC-SEEEEECG-GGCC
T ss_pred             CC-CEEEEcCh-Hhhc
Confidence            47 89999999 8877

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=90.21  E-value=0.18  Score=37.65  Aligned_cols=18  Identities=11%  Similarity=0.222  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..+++.+++|+|||..
T Consensus        28 ~~~~vll~G~~GtGKt~l   45 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELI   45 (265)
T ss_dssp             SCSCEEEECCTTSCHHHH
T ss_pred             CCCCEEEECCCCCcHHHH
Confidence            468999999999999975

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=90.19  E-value=0.19  Score=39.66  Aligned_cols=25  Identities=28%  Similarity=0.359  Sum_probs=19.8

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||.+-
T Consensus        69 lv~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           69 IVKDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             hHHHHhCCCeEEEEEECCCCCCCceEe
Confidence            3455688976  788899999999875

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=90.14  E-value=0.1  Score=36.97  Aligned_cols=20  Identities=10%  Similarity=0.049  Sum_probs=16.7

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +.|+-+++++|+|||||...
T Consensus         3 ~~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            45778899999999999853

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=89.85  E-value=0.18  Score=40.13  Aligned_cols=24  Identities=29%  Similarity=0.412  Sum_probs=19.0

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||.+.
T Consensus        87 v~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           87 VDKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hhHhhCCCceEEEEecCCCCCCCeEE
Confidence            445678976  678899999999874

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=89.82  E-value=0.55  Score=39.10  Aligned_cols=17  Identities=18%  Similarity=0.237  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +.+++.+|+|+|||+..
T Consensus        65 ~GvLL~GppGtGKTtLa   81 (499)
T 2dhr_A           65 KGVLLVGPPGVGKTHLA   81 (499)
T ss_dssp             SEEEEECSSSSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            45999999999999853

>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=89.73  E-value=0.18  Score=40.67  Aligned_cols=27  Identities=19%  Similarity=0.212  Sum_probs=20.2

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      ...++++.|+||||||... -+++..+.
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~   78 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGL   78 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHH
Confidence            4579999999999999974 34444444

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=89.71  E-value=0.12  Score=40.01  Aligned_cols=25  Identities=16%  Similarity=0.141  Sum_probs=19.9

Q ss_pred             HHHHHHhcCCcEEEEccCCCCcchh
Q 031654           58 HATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        58 ~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ...-.+..|.++++.+|+|+|||..
T Consensus        38 ~l~~~l~~~~~vll~G~pGtGKT~l   62 (331)
T 2r44_A           38 RLLIGICTGGHILLEGVPGLAKTLS   62 (331)
T ss_dssp             HHHHHHHHTCCEEEESCCCHHHHHH
T ss_pred             HHHHHHHcCCeEEEECCCCCcHHHH
Confidence            3334556789999999999999974

>4a14_A Kinesin, kinesin-like protein KIF7; motor protein, motor domain; HET: ADP; 1.60A {Homo sapiens} SCOP: c.37.1.0 PDB: 2xt3_A*

Probab=89.62  E-value=0.22  Score=39.54  Aligned_cols=25  Identities=32%  Similarity=0.387  Sum_probs=19.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||..-
T Consensus        75 lv~~~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           75 LLEAFFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHhhcCeeEEEecccCCCceEee
Confidence            3456678976  677899999999874

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=89.60  E-value=0.22  Score=39.91  Aligned_cols=24  Identities=33%  Similarity=0.437  Sum_probs=19.2

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||..-
T Consensus        77 v~~~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           77 VTDVLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCceEEEeecCCCCCCceEE
Confidence            345678976  677899999999875

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=89.51  E-value=0.23  Score=39.61  Aligned_cols=24  Identities=29%  Similarity=0.430  Sum_probs=19.0

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||..-
T Consensus        82 v~~~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           82 IDAVLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCceeEEeecCCCCCCCEEe
Confidence            345678976  677899999999874

>3b6u_A Kinesin-like protein KIF3B; structural genomics consortium, motor domain, ADP, SGC, ATP-binding, coiled coil, microtubule, motor protein; HET: ADP; 1.80A {Homo sapiens} PDB: 3b6v_A*

Probab=89.45  E-value=0.23  Score=39.96  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=19.3

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||..-
T Consensus        93 lv~~~l~G~n~tifAYGqTGSGKTyTM  119 (372)
T 3b6u_A           93 LVDSVLQGFNGTIFAYGQTGTGKTYTM  119 (372)
T ss_dssp             HHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhCCCeeeEEeecCCCCCCCEeE
Confidence            3455688976  677899999999763

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=89.41  E-value=0.23  Score=39.18  Aligned_cols=25  Identities=28%  Similarity=0.396  Sum_probs=20.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus        72 lv~~~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           72 LVTSCIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHhCCCEEEEEeECCCCCCCcEEE
Confidence            5567789976  678899999999775

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=89.37  E-value=0.047  Score=41.76  Aligned_cols=50  Identities=18%  Similarity=0.262  Sum_probs=24.8

Q ss_pred             CcccccCC--HHHHHhHHhCCCCCCCHHHH-HHHHHH--hcCCcEEEEccCCCCcchh
Q 031654           30 AARFAYVP--QHLRNKPRTYKYVKPTPVQR-HATSIL--VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        30 ~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~-~~i~~~--l~g~dvl~~a~TGsGKT~~   82 (155)
                      -.+|++++  +++.+.|++.= .  .|... ..+..+  .-.+.+++.+|+|+|||+.
T Consensus         6 ~~~~~di~g~~~~~~~l~~~i-~--~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtL   60 (274)
T 2x8a_A            6 NVTWADIGALEDIREELTMAI-L--APVRNPDQFKALGLVTPAGVLLAGPPGCGKTLL   60 (274)
T ss_dssp             ------CCHHHHHHHHHHHHH-T--HHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHH-H--HHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHH
Confidence            45899998  77777776521 1  11111 112111  1123499999999999985

>2zfi_A Kinesin-like protein KIF1A, kinesin heavy chain isoform 5C; alpha and beta protein, enzyme, ATPase, P-loop, motor protein, ATP-binding, coiled coil; HET: ADP; 1.55A {Mus musculus} SCOP: c.37.1.9 PDB: 1vfw_A* 1vfx_A* 1vfz_A* 1vfv_A* 2zfj_A* 2zfk_A* 2zfl_A* 2zfm_A* 1i5s_A* 1i6i_A* 2hxf_C* 1ia0_K* 2hxh_C*

Probab=89.34  E-value=0.24  Score=39.72  Aligned_cols=25  Identities=24%  Similarity=0.336  Sum_probs=19.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus        81 lv~~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           81 MLQHAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcCCeeEEEEeCCCCCCCceEe
Confidence            3455688976  677899999999764

>3gbj_A KIF13B protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, ATP-binding, microtubule, motor protein; HET: ADP; 2.10A {Homo sapiens} SCOP: c.37.1.9

Probab=89.33  E-value=0.24  Score=39.55  Aligned_cols=25  Identities=28%  Similarity=0.337  Sum_probs=19.9

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus        84 lv~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           84 ILQNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHHHhCCceeEEEeeCCCCCCCceEE
Confidence            3456678976  677899999999885

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=89.28  E-value=0.23  Score=39.68  Aligned_cols=24  Identities=25%  Similarity=0.421  Sum_probs=19.1

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||..-
T Consensus        73 v~~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           73 VDDILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCcceEEEECCCCCCcceEe
Confidence            345678976  777899999999875

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=89.27  E-value=0.24  Score=40.22  Aligned_cols=25  Identities=32%  Similarity=0.383  Sum_probs=20.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||.+-
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEe
Confidence            5567789977  677899999999875

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=89.24  E-value=0.15  Score=40.15  Aligned_cols=21  Identities=38%  Similarity=0.634  Sum_probs=18.0

Q ss_pred             HHhcCCcEEEEccCCCCcchh
Q 031654           62 ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..|..+.+.+|||||||..
T Consensus       167 ~i~~g~~v~i~G~~GsGKTTl  187 (330)
T 2pt7_A          167 GIAIGKNVIVCGGTGSGKTTY  187 (330)
T ss_dssp             HHHHTCCEEEEESTTSCHHHH
T ss_pred             hccCCCEEEEECCCCCCHHHH
Confidence            345789999999999999984

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=89.21  E-value=0.23  Score=39.62  Aligned_cols=24  Identities=25%  Similarity=0.422  Sum_probs=19.1

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||..-
T Consensus        98 v~~~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A           98 LRSFLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HHHHTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhCCCceEEEEeCCCCCCceeee
Confidence            345678976  678899999999874

>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker, cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A* 2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A* 2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A* 1q0b_A* ...

Probab=89.16  E-value=0.23  Score=39.70  Aligned_cols=25  Identities=28%  Similarity=0.417  Sum_probs=19.4

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus        80 lv~~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           80 ILDEVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHHHHhCCCceEEEEeCCCCCCCceEE
Confidence            3455678976  677899999999764

>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP complex, stranded beta-sheet core with solvent exposed alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}

Probab=89.16  E-value=0.25  Score=39.37  Aligned_cols=25  Identities=28%  Similarity=0.337  Sum_probs=19.8

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus        69 lv~~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           69 IIDSAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHHcCCccceeeecCCCCCCCeEE
Confidence            3456688976  677899999999875

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=89.08  E-value=0.33  Score=38.73  Aligned_cols=79  Identities=15%  Similarity=0.109  Sum_probs=42.0

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhcC-CcEEEEChHHH---HHHHHcCCCCcc
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELARW-VDNLMATLRRL---VNLLERGRVSLQ  131 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~~-~~IlI~TP~~l---~~~l~~~~~~l~  131 (155)
                      |.-+++.+|+|+|||. +++.++..+.......          ....+.+.-. -++.+..|..+   +..+.. .+.-.
T Consensus        61 G~i~~I~GppGsGKST-Lal~la~~~~~~gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~-l~~~~  138 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTT-LALHAIAEAQKMGGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDE-LVRSG  138 (356)
T ss_dssp             TEEEEEEESTTSSHHH-HHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHH-HHHTS
T ss_pred             CcEEEEECCCCCCHHH-HHHHHHHHHHhcCCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHH-Hhhhc
Confidence            4578999999999997 4455554443322211          2222222211 23555554333   222221 01114


Q ss_pred             cccceEEEEcccccccc
Q 031654          132 MIIRYLALKEAADQTLD  148 (155)
Q Consensus       132 ~l~~~lVlDEa~D~ll~  148 (155)
                      .. +++|||.+ ..++.
T Consensus       139 ~~-dlvVIDSi-~~l~~  153 (356)
T 3hr8_A          139 VV-DLIVVDSV-AALVP  153 (356)
T ss_dssp             CC-SEEEEECT-TTCCC
T ss_pred             CC-CeEEehHh-hhhcC
Confidence            57 89999999 77764

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=89.02  E-value=0.74  Score=35.65  Aligned_cols=67  Identities=7%  Similarity=0.051  Sum_probs=37.7

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHh-cCCcEEEEChH-------HHHHHHHc--CCCCcccccceE
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELA-RWVDNLMATLR-------RLVNLLER--GRVSLQMIIRYL  137 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~-~~~~IlI~TP~-------~l~~~l~~--~~~~l~~l~~~l  137 (155)
                      ..++.||.|+|||..... +....           .... ..++++.-.|.       .+.+++..  ..-....- +.+
T Consensus        20 ~~Lf~Gp~G~GKtt~a~~-la~~~-----------~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~~~~~-kvv   86 (305)
T 2gno_A           20 SILINGEDLSYPREVSLE-LPEYV-----------EKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTR-KYV   86 (305)
T ss_dssp             EEEEECSSSSHHHHHHHH-HHHHH-----------HTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSS-EEE
T ss_pred             EEEEECCCCCCHHHHHHH-HHHhC-----------chhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhccccCCc-eEE
Confidence            689999999999875422 11100           0000 34677766653       12232221  11123567 899


Q ss_pred             EEEcccccccc
Q 031654          138 ALKEAADQTLD  148 (155)
Q Consensus       138 VlDEa~D~ll~  148 (155)
                      ||||| |.|-.
T Consensus        87 iIdea-d~lt~   96 (305)
T 2gno_A           87 IVHDC-ERMTQ   96 (305)
T ss_dssp             EETTG-GGBCH
T ss_pred             EeccH-HHhCH
Confidence            99999 98853

>3cob_A Kinesin heavy chain-like protein; motor, switch II, loop L11, conformation, nucleotide, ATP-binding, microtubule, motor protein; HET: ADP; 2.20A {Solanum tuberosum} SCOP: c.37.1.9 PDB: 3cnz_A* 1sdm_A* 3h4s_A*

Probab=88.97  E-value=0.21  Score=40.10  Aligned_cols=25  Identities=36%  Similarity=0.408  Sum_probs=20.4

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||.+.
T Consensus        71 lv~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           71 LVQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hhHhhhcCCceEEEEECCCCCCCeEee
Confidence            5567789976  677899999999875

>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P; HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB: 1v8j_A* 2gry_A*

Probab=88.90  E-value=0.24  Score=40.33  Aligned_cols=24  Identities=33%  Similarity=0.434  Sum_probs=19.1

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||.+.
T Consensus       147 V~~~l~G~N~tifAYGQTGSGKTyTM  172 (410)
T 1v8k_A          147 VQTIFEGGKATCFAYGQTGSGKTHTM  172 (410)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHhcCCceeEEeecCCCCCCCeEe
Confidence            445678976  777899999999874

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=88.89  E-value=0.23  Score=40.47  Aligned_cols=25  Identities=32%  Similarity=0.391  Sum_probs=20.6

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus       130 lv~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          130 LIQSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHCCCceEEEEecCCCCCCeeEe
Confidence            5677789976  677899999999874

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=88.81  E-value=0.15  Score=35.50  Aligned_cols=18  Identities=11%  Similarity=0.113  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .++-+++++++|||||..
T Consensus         2 ~~~~i~l~G~~GsGKST~   19 (178)
T 1qhx_A            2 TTRMIILNGGSSAGKSGI   19 (178)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CceEEEEECCCCCCHHHH
Confidence            356789999999999976

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=88.76  E-value=0.093  Score=36.84  Aligned_cols=20  Identities=20%  Similarity=0.120  Sum_probs=17.0

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..++.+++++++|||||...
T Consensus         9 ~~~~~i~i~G~~GsGKst~~   28 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLG   28 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHH
Confidence            45788999999999999853

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.75  E-value=0.078  Score=43.96  Aligned_cols=51  Identities=18%  Similarity=0.209  Sum_probs=31.0

Q ss_pred             CCcccccCC--HHHHHhHHhCCCCCCCHHHH-HHHHHH--hcCCcEEEEccCCCCcchh
Q 031654           29 PAARFAYVP--QHLRNKPRTYKYVKPTPVQR-HATSIL--VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~-~~i~~~--l~g~dvl~~a~TGsGKT~~   82 (155)
                      |-.+|++++  ++..+.|++.= .  .|... ..+..+  --.+-+++.+|+|+|||+.
T Consensus       204 P~vt~~DIgGl~~~k~~L~e~V-~--~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlL  259 (467)
T 4b4t_H          204 PDVTYSDVGGCKDQIEKLREVV-E--LPLLSPERFATLGIDPPKGILLYGPPGTGKTLC  259 (467)
T ss_dssp             CSCCCSSCTTCHHHHHHHHHHT-H--HHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHH-H--HHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHH
Confidence            346899998  77777776531 1  11111 111111  1237899999999999975

>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis, GTP-binding, motor protein, cell division, cell cycle, microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A {Drosophila melanogaster}

Probab=88.62  E-value=0.25  Score=39.74  Aligned_cols=24  Identities=29%  Similarity=0.451  Sum_probs=18.8

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||...
T Consensus        93 v~~~l~G~n~tifAYGqTGSGKTyTm  118 (373)
T 2wbe_C           93 IEEVLNGYNCTVFAYGQTGTGKTHTM  118 (373)
T ss_dssp             HHHHHHTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCceEEEEeecCCCCCcceec
Confidence            345678876  677899999999774

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=88.53  E-value=0.17  Score=36.24  Aligned_cols=20  Identities=25%  Similarity=0.047  Sum_probs=16.7

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..|+.+++++++|||||...
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~   42 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLG   42 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHH
Confidence            36789999999999999763

>2heh_A KIF2C protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, structural protein; HET: ADP; 2.15A {Homo sapiens} PDB: 3edl_D*

Probab=88.44  E-value=0.28  Score=39.69  Aligned_cols=24  Identities=33%  Similarity=0.434  Sum_probs=19.1

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||.+.
T Consensus       127 v~~~l~G~N~tifAYGQTGSGKTyTM  152 (387)
T 2heh_A          127 VQTIFEGGKATCFAYGQTGSGKTHTM  152 (387)
T ss_dssp             HHHHHTTCEEEEEEESCTTSSHHHHH
T ss_pred             HHHHhcCCceEEEEecCCCCCCCeEe
Confidence            445688976  778899999999874

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=88.33  E-value=0.45  Score=47.83  Aligned_cols=48  Identities=17%  Similarity=0.240  Sum_probs=33.5

Q ss_pred             CCHHHHHhHHhCCCCCCCHHH-HHHHH---HHhcCCcEEEEccCCCCcchhhh
Q 031654           36 VPQHLRNKPRTYKYVKPTPVQ-RHATS---ILVAGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        36 l~~~l~~~l~~~g~~~pt~iQ-~~~i~---~~l~g~dvl~~a~TGsGKT~~yl   84 (155)
                      |...+.+.++++|+.. ++.+ .+++.   .+...+-++++||||||||.+|-
T Consensus       873 l~~ai~~~~~~~~L~~-~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          873 LRKKIQEIAKQRHLVT-KQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             HHHHHHHHHHHTTCCC-CHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCcc-CHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHH
Confidence            3377778888888854 4433 33443   22344679999999999999974

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=88.29  E-value=0.14  Score=38.87  Aligned_cols=21  Identities=24%  Similarity=0.181  Sum_probs=17.6

Q ss_pred             HhcCCcEEEEccCCCCcchhh
Q 031654           63 LVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +..|.-+.+++|||||||...
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll   42 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTI   42 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHH
Confidence            456778999999999999753

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=88.23  E-value=0.21  Score=39.76  Aligned_cols=25  Identities=32%  Similarity=0.387  Sum_probs=20.2

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||..-
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEe
Confidence            4566789976  677899999999875

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=88.17  E-value=0.14  Score=36.88  Aligned_cols=21  Identities=24%  Similarity=0.317  Sum_probs=17.1

Q ss_pred             HHhcCCcEEEEccCCCCcchh
Q 031654           62 ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ++..|+-+++++|+|||||..
T Consensus         8 ~~~~~~~i~l~G~sGsGKsTl   28 (204)
T 2qor_A            8 HMARIPPLVVCGPSGVGKGTL   28 (204)
T ss_dssp             -CCCCCCEEEECCTTSCHHHH
T ss_pred             ccccCCEEEEECCCCCCHHHH
Confidence            345678899999999999874

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.16  E-value=0.07  Score=43.85  Aligned_cols=49  Identities=12%  Similarity=0.140  Sum_probs=29.9

Q ss_pred             CCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHh------cCCcEEEEccCCCCcchhh
Q 031654           29 PAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILV------AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l------~g~dvl~~a~TGsGKT~~y   83 (155)
                      |-.+|++++  ++..+.|++. +.  .|+..   |.++      -.+-+++.||+|||||+..
T Consensus       176 p~v~~~digGl~~~k~~l~e~-v~--~pl~~---p~~f~~~g~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          176 GEITFDGIGGLTEQIRELREV-IE--LPLKN---PEIFQRVGIKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CSSCSGGGCSCHHHHHHHHHH-HH--HHHHC---HHHHHHHCCCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCChhHhCChHHHHHHHHHH-HH--HHHhC---HHHHHhCCCCCCCeEEEECCCCCcHHHHH
Confidence            445799988  6666666542 00  11111   1121      2378999999999999853

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=88.15  E-value=0.17  Score=36.03  Aligned_cols=20  Identities=20%  Similarity=0.129  Sum_probs=16.4

Q ss_pred             HhcCCcEEEEccCCCCcchh
Q 031654           63 LVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~   82 (155)
                      +..|.-+++.||+|||||..
T Consensus         3 i~~g~~i~l~G~~GsGKSTl   22 (207)
T 2j41_A            3 NEKGLLIVLSGPSGVGKGTV   22 (207)
T ss_dssp             -CCCCEEEEECSTTSCHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHH
Confidence            34678899999999999875

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=88.15  E-value=0.18  Score=36.33  Aligned_cols=19  Identities=21%  Similarity=0.363  Sum_probs=15.1

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|+-+.+++|+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778999999999999853

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=88.13  E-value=0.13  Score=41.95  Aligned_cols=36  Identities=19%  Similarity=0.189  Sum_probs=23.8

Q ss_pred             HHhCCCCCCCHHHHHHHHHHh--cCCcEEEEccCCCCcchh
Q 031654           44 PRTYKYVKPTPVQRHATSILV--AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        44 l~~~g~~~pt~iQ~~~i~~~l--~g~dvl~~a~TGsGKT~~   82 (155)
                      +.++|+   .+-+..++..++  .|.-+++.+|||||||..
T Consensus       146 l~~Lg~---~~~~~~~L~~l~~~~ggii~I~GpnGSGKTTl  183 (418)
T 1p9r_A          146 LHSLGM---TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTT  183 (418)
T ss_dssp             GGGSCC---CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHH
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHH
Confidence            455554   334445555444  345689999999999975

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.07  E-value=0.075  Score=43.53  Aligned_cols=52  Identities=17%  Similarity=0.222  Sum_probs=29.7

Q ss_pred             CCcccccCC--HHHHHhHHhCC---CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           29 PAARFAYVP--QHLRNKPRTYK---YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~g---~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      |-.+|++++  +...+.|.+.=   +.+|--.+...   +--.+-+++.||+|||||+..
T Consensus       167 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g---~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          167 PDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG---IDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCceEEEECCCCCCHHHHH
Confidence            345899988  66666665420   11111111100   112367999999999999853

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=88.01  E-value=0.32  Score=39.98  Aligned_cols=24  Identities=29%  Similarity=0.329  Sum_probs=19.0

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  |++.++||||||...
T Consensus       129 v~~~l~GyN~tIfAYGQTGSGKTyTM  154 (443)
T 2owm_A          129 LDHNFEGYHTCIFAYGQTGSGKSYTM  154 (443)
T ss_dssp             HHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHhhcCCceEEEEeCCCCCCCCEEe
Confidence            345578976  778899999999875

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=88.00  E-value=1.6  Score=35.41  Aligned_cols=26  Identities=15%  Similarity=0.162  Sum_probs=18.0

Q ss_pred             cCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           65 AGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      .|.=+++.|++|+|||... +-++..+
T Consensus       202 ~G~liiI~G~pG~GKTtl~-l~ia~~~  227 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFA-LNIAQNV  227 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            3466889999999999744 3333333

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=87.98  E-value=0.34  Score=35.50  Aligned_cols=19  Identities=21%  Similarity=0.104  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|+=.++.++.|||||.-.
T Consensus        19 ~g~l~fiyG~MgsGKTt~L   37 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTEL   37 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHH
T ss_pred             ceEEEEEECCCCCcHHHHH
Confidence            4667889999999999643

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=87.95  E-value=0.18  Score=38.21  Aligned_cols=18  Identities=22%  Similarity=0.276  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++.+++.||+|+|||...
T Consensus        54 ~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CSEEEEESSSSSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            578999999999999853

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=87.93  E-value=0.19  Score=37.07  Aligned_cols=17  Identities=18%  Similarity=0.165  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      .+.+++.+|+|+|||..
T Consensus        39 ~~~vll~G~~GtGKT~l   55 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLL   55 (262)
T ss_dssp             CCEEEEESCTTSSHHHH
T ss_pred             CceEEEECCCCCCHHHH
Confidence            46899999999999975

>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural genomics consortium domain, ADP, SGC, ATP-binding, DNA-binding, microtubule, MO protein; HET: ADP; 2.30A {Homo sapiens}

Probab=87.90  E-value=0.26  Score=39.88  Aligned_cols=32  Identities=25%  Similarity=0.401  Sum_probs=23.0

Q ss_pred             CCHHHHHHH--------HHHhcCCc--EEEEccCCCCcchhh
Q 031654           52 PTPVQRHAT--------SILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        52 pt~iQ~~~i--------~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..-|...+        ..++.|.|  +++.++||||||...
T Consensus        75 ~~~tQ~~Vy~~~~~plv~~~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           75 ERSTQQDIYAGSVQPILRHLLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             TTCCHHHHHHHHTGGGHHHHTTTCCEEEEEESCTTSSHHHHH
T ss_pred             CCCCHhHHHHHHHHHHHHHhhcCceeeEeeecCCCCCCCeEe
Confidence            444555554        34678876  677899999999875

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=87.84  E-value=0.19  Score=35.16  Aligned_cols=18  Identities=17%  Similarity=0.224  Sum_probs=15.1

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+++.+++|||||..
T Consensus         2 ~~~~I~i~G~~GsGKsT~   19 (192)
T 1kht_A            2 KNKVVVVTGVPGVGSTTS   19 (192)
T ss_dssp             -CCEEEEECCTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            466799999999999975

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=87.80  E-value=0.88  Score=44.03  Aligned_cols=85  Identities=15%  Similarity=0.067  Sum_probs=45.2

Q ss_pred             HHHHhc------CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhc-CCcEEEEChH---HH
Q 031654           60 TSILVA------GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELAR-WVDNLMATLR---RL  119 (155)
Q Consensus        60 i~~~l~------g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~-~~~IlI~TP~---~l  119 (155)
                      +..++.      |+++++.+|+|+|||...+--+.+ ........          ....+.+-- --++.|..|.   ++
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~e-a~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~ 1493 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAA-AQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQA 1493 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHH-HHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHH
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHH-HHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHH
Confidence            566666      689999999999999865433322 22221111          111222110 0124555553   33


Q ss_pred             HHHHHcCCCCcccccceEEEEcccccccc
Q 031654          120 VNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       120 ~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      ...+.. .+.-..+ +.|||||+ +-++.
T Consensus      1494 l~~~~~-lvr~~~~-~lVVIDsi-~al~p 1519 (2050)
T 3cmu_A         1494 LEICDA-LARSGAV-DVIVVDSV-AALTP 1519 (2050)
T ss_dssp             HHHHHH-HHHHTCC-SEEEESCG-GGCCC
T ss_pred             HHHHHH-HHhcCCC-CEEEEcCh-hHhcc
Confidence            333321 1112467 89999999 86664

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=87.57  E-value=0.21  Score=35.03  Aligned_cols=18  Identities=17%  Similarity=0.060  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++.+++++++|||||...
T Consensus         5 ~~~i~l~G~~GsGKst~a   22 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVG   22 (185)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            568999999999999753

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=87.56  E-value=0.21  Score=36.18  Aligned_cols=19  Identities=21%  Similarity=0.162  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|+=+++++|+|+|||...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            4677899999999999753

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.44  E-value=0.068  Score=43.95  Aligned_cols=51  Identities=10%  Similarity=0.202  Sum_probs=31.0

Q ss_pred             CCcccccCC--HHHHHhHHhC---CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           29 PAARFAYVP--QHLRNKPRTY---KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        29 ~~~~f~~l~--~~l~~~l~~~---g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      |-.+|++++  ++..+.|++.   -+.+|--.+...   +--.+-++..+|+|+|||+.
T Consensus       177 p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~G---i~~prGvLLyGPPGTGKTlL  232 (437)
T 4b4t_I          177 PTESYSDIGGLESQIQEIKESVELPLTHPELYEEMG---IKPPKGVILYGAPGTGKTLL  232 (437)
T ss_dssp             CCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHT---CCCCSEEEEESSTTTTHHHH
T ss_pred             CCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCCCceECCCCchHHHH
Confidence            446899998  6666666542   111222111111   11237899999999999985

>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=87.42  E-value=0.23  Score=42.66  Aligned_cols=36  Identities=31%  Similarity=0.283  Sum_probs=28.8

Q ss_pred             CCCCCCHHHHHHHHHHhc----C-CcEEEEccCCCCcchhhh
Q 031654           48 KYVKPTPVQRHATSILVA----G-RDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l~----g-~dvl~~a~TGsGKT~~yl   84 (155)
                      +| .|++.|..+|..+..    | +..++.+.||||||+.+.
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a   46 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA   46 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHH
Confidence            67 899999999986653    3 357788999999998764

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=87.32  E-value=0.2  Score=34.27  Aligned_cols=15  Identities=20%  Similarity=0.215  Sum_probs=13.0

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      -++++|++|||||..
T Consensus         3 ~I~l~G~~GsGKsT~   17 (179)
T 3lw7_A            3 VILITGMPGSGKSEF   17 (179)
T ss_dssp             EEEEECCTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999974

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=87.25  E-value=0.14  Score=38.25  Aligned_cols=19  Identities=16%  Similarity=-0.006  Sum_probs=14.8

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|.=.+++++-|||||...
T Consensus        27 ~G~I~vitG~M~sGKTT~L   45 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEEL   45 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHH
T ss_pred             CceEEEEECCCCCCHHHHH
Confidence            4555688898999999754

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=87.18  E-value=0.32  Score=37.56  Aligned_cols=18  Identities=11%  Similarity=0.244  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .+.++++.+++|+|||..
T Consensus        24 ~~~~vLi~Ge~GtGKt~l   41 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELV   41 (304)
T ss_dssp             TTSCEEEESCTTSCHHHH
T ss_pred             CCCcEEEECCCCchHHHH
Confidence            457999999999999985

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=87.17  E-value=0.24  Score=39.45  Aligned_cols=25  Identities=32%  Similarity=0.383  Sum_probs=19.6

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus        76 lv~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           76 LVQSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhcCCceeEEEEECCCCCCCcEec
Confidence            4455678976  678899999999875

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=86.92  E-value=0.19  Score=35.40  Aligned_cols=19  Identities=32%  Similarity=0.445  Sum_probs=16.1

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      ..|.-+++.+++|||||..
T Consensus         7 ~~g~~i~l~G~~GsGKSTl   25 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTI   25 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHH
T ss_pred             CCCeEEEEECCCCCCHHHH
Confidence            3567799999999999975

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=86.73  E-value=0.25  Score=34.91  Aligned_cols=18  Identities=22%  Similarity=0.423  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..+++++++|||||..
T Consensus         9 ~~~~I~l~G~~GsGKSTv   26 (184)
T 1y63_A            9 KGINILITGTPGTGKTSM   26 (184)
T ss_dssp             SSCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467899999999999985

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=86.70  E-value=0.25  Score=35.09  Aligned_cols=18  Identities=22%  Similarity=0.289  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.=+.+.||+|||||..
T Consensus         6 ~g~ii~l~Gp~GsGKSTl   23 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSL   23 (205)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCcEEEEECcCCCCHHHH
Confidence            577788999999999975

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=86.55  E-value=0.34  Score=41.11  Aligned_cols=58  Identities=17%  Similarity=0.154  Sum_probs=32.9

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHhcCCcE---EEEChHHHHHHH
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELARWVDN---LMATLRRLVNLL  123 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~~~~~I---lI~TP~~l~~~l  123 (155)
                      +.+++|.+.||||||.+.-.-+++.+.......         ......+..-+|+   +++.|......|
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpKg~eLs~~~~lPHl~~~Vvtd~~~a~~~L  283 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPKMLELSIYEGIPHLLCPVVTDMKEAANAL  283 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSSSHHHHTTTTCTTBSSSCBCCHHHHHHHH
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCChhhhHhhcCCCcccceeeCCHHHHHHHH
Confidence            468999999999999875444444333222111         2223333344555   567777654443

>2rep_A Kinesin-like protein KIFC1; structural genomics consortium, motor domain, ADP, binding, cell cycle, cell division, endosome, microtubule; HET: ADP; 2.60A {Homo sapiens}

Probab=86.53  E-value=0.31  Score=39.19  Aligned_cols=25  Identities=32%  Similarity=0.356  Sum_probs=19.4

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus       107 lv~~~l~G~N~tifAYGqTGSGKTyTM  133 (376)
T 2rep_A          107 LVQSALDGYPVCIFAYGQTGSGKTFTM  133 (376)
T ss_dssp             HHHGGGGTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCCceEEEEeCCCCCCCceEe
Confidence            3455678876  677899999999875

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=86.53  E-value=0.25  Score=35.69  Aligned_cols=16  Identities=25%  Similarity=0.449  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      |-++++||+|+|||..
T Consensus         2 RpIVi~GPSG~GK~Tl   17 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            5689999999999884

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=86.41  E-value=0.28  Score=33.90  Aligned_cols=17  Identities=24%  Similarity=0.393  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      +..+++.+++|||||..
T Consensus         4 ~~~i~l~G~~GsGKSTl   20 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTI   20 (173)
T ss_dssp             CCCEEEECCTTSCHHHH
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            56799999999999875

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=86.23  E-value=0.22  Score=39.65  Aligned_cols=20  Identities=30%  Similarity=0.365  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..|.-+++++|||||||...
T Consensus       121 ~~~g~i~I~GptGSGKTTlL  140 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTL  140 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            45568999999999999753

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=86.17  E-value=0.26  Score=36.07  Aligned_cols=19  Identities=11%  Similarity=0.207  Sum_probs=16.7

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      +.|+-+++++|+|+|||..
T Consensus        17 ~~g~~ivl~GPSGaGKsTL   35 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHI   35 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHH
T ss_pred             CCCCEEEEECcCCCCHHHH
Confidence            4788899999999999984

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=86.16  E-value=0.25  Score=36.68  Aligned_cols=18  Identities=17%  Similarity=0.231  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.+++.+|+|+|||...
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            357999999999999753

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=86.13  E-value=0.22  Score=39.61  Aligned_cols=18  Identities=22%  Similarity=0.200  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++-+++.+|||||||...
T Consensus        40 ~~lIvI~GPTgsGKTtLa   57 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLS   57 (339)
T ss_dssp             CEEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            346899999999999753

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=86.05  E-value=0.53  Score=33.47  Aligned_cols=15  Identities=20%  Similarity=0.220  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      .+++.||+|+|||..
T Consensus        47 ~~ll~G~~G~GKT~l   61 (250)
T 1njg_A           47 AYLFSGTRGVGKTSI   61 (250)
T ss_dssp             EEEEECSTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            689999999999975

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=85.89  E-value=0.22  Score=39.72  Aligned_cols=21  Identities=24%  Similarity=0.181  Sum_probs=17.3

Q ss_pred             HhcCCcEEEEccCCCCcchhh
Q 031654           63 LVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +..|..+++++|||||||...
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll  153 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTI  153 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHH
Confidence            346778999999999999853

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=85.75  E-value=0.43  Score=38.17  Aligned_cols=19  Identities=42%  Similarity=0.391  Sum_probs=16.1

Q ss_pred             cCCc--EEEEccCCCCcchhh
Q 031654           65 AGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .|.+  +++.++||||||.+.
T Consensus        82 ~G~n~tifAYGqTGSGKTyTM  102 (360)
T 1ry6_A           82 NGCVCSCFAYGQTGSGKTYTM  102 (360)
T ss_dssp             HCCEEEEEEECCTTSSHHHHH
T ss_pred             CCceeEEEeeCCCCCCCCEEE
Confidence            5877  689999999999764

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=85.72  E-value=0.26  Score=36.99  Aligned_cols=16  Identities=25%  Similarity=-0.027  Sum_probs=13.2

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      -+++++|+|||||...
T Consensus         3 li~I~G~~GSGKSTla   18 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMA   18 (253)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCcCHHHHH
Confidence            3688999999998753

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=85.63  E-value=0.63  Score=36.97  Aligned_cols=78  Identities=15%  Similarity=0.097  Sum_probs=40.0

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhc-CCcEEEECh---HHHHHHHHcCCCCcc
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELAR-WVDNLMATL---RRLVNLLERGRVSLQ  131 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~-~~~IlI~TP---~~l~~~l~~~~~~l~  131 (155)
                      |+-+++.+++|+|||...+ .++..+.......          ......+.- ..++.+..|   +.+.+.+.. ...-.
T Consensus        63 G~ii~I~G~pGsGKTtLal-~la~~~~~~g~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~-l~~~~  140 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTL-QVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDA-LARSG  140 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHH-HHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHH-HHHHT
T ss_pred             CeEEEEECCCCCCHHHHHH-HHHHHHHHCCCeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHHHHHHHHH-HHhcc
Confidence            4678999999999998553 3333333222111          111112211 113444444   333333321 01123


Q ss_pred             cccceEEEEccccccc
Q 031654          132 MIIRYLALKEAADQTL  147 (155)
Q Consensus       132 ~l~~~lVlDEa~D~ll  147 (155)
                      .+ ++||||.+ ..|.
T Consensus       141 ~~-~lVVIDsl-~~l~  154 (356)
T 1u94_A          141 AV-DVIVVDSV-AALT  154 (356)
T ss_dssp             CC-SEEEEECG-GGCC
T ss_pred             CC-CEEEEcCH-HHhc
Confidence            57 89999999 7776

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

Probab=85.52  E-value=0.67  Score=45.95  Aligned_cols=48  Identities=13%  Similarity=0.198  Sum_probs=33.5

Q ss_pred             CCHHHHHhHHhCCCCCCCHHH-HHHH---HHHhcCCcEEEEccCCCCcchhhh
Q 031654           36 VPQHLRNKPRTYKYVKPTPVQ-RHAT---SILVAGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        36 l~~~l~~~l~~~g~~~pt~iQ-~~~i---~~~l~g~dvl~~a~TGsGKT~~yl   84 (155)
                      +...+.+.+.+.|+. +++.+ .+++   ..+...+.|+++||||||||.++-
T Consensus       890 l~~~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~  941 (2695)
T 4akg_A          890 IVQCLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWK  941 (2695)
T ss_dssp             HHHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHH
Confidence            336777888888875 45544 3333   233456789999999999999864

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=85.50  E-value=0.34  Score=35.44  Aligned_cols=20  Identities=25%  Similarity=0.306  Sum_probs=16.2

Q ss_pred             HhcCCcEEEEccCCCCcchh
Q 031654           63 LVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~   82 (155)
                      +-.|+-+.+.+|+|+|||..
T Consensus        20 i~~G~~~~lvGpsGsGKSTL   39 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTL   39 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHH
Confidence            35688899999999999975

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=85.41  E-value=0.31  Score=35.93  Aligned_cols=22  Identities=18%  Similarity=0.318  Sum_probs=16.8

Q ss_pred             HHhcCCcEEEEccCCCCcchhh
Q 031654           62 ILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ++-.|+=+++.+|+|+|||...
T Consensus        12 ~~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           12 HMAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             ---CCCEEEEECCTTSCHHHHH
T ss_pred             cCCCCcEEEEECCCCCCHHHHH
Confidence            4567888999999999999853

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=85.33  E-value=0.33  Score=41.39  Aligned_cols=48  Identities=19%  Similarity=0.133  Sum_probs=32.2

Q ss_pred             HHHHHHHhcCCcEEEEChHHHHHHHHcC------CCCcccccceEEEEccccccccc
Q 031654           99 RKELRELARWVDNLMATLRRLVNLLERG------RVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 ~~~~~~l~~~~~IlI~TP~~l~~~l~~~------~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      ....+.....+||||++...|.+...+.      .+++.+  ..+||||| |.|.|.
T Consensus       166 y~~aR~~~~~ADvVV~ny~ylld~~~r~~~~~~~~i~p~~--~ivI~DEA-HNL~d~  219 (620)
T 4a15_A          166 YESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQ--IVIILDEA-HNLPDI  219 (620)
T ss_dssp             HHHHHHHGGGCSEEEEEHHHHTCHHHHHHHHHHHTCCGGG--EEEEETTG-GGHHHH
T ss_pred             cHHHHHHhhcCCEEEeCchhhcCHHHHHHHHHhhccCcCC--eEEEEECC-CchHHH
Confidence            3444555667999999997766554322      123333  48999999 999874

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=85.22  E-value=0.27  Score=38.65  Aligned_cols=16  Identities=25%  Similarity=0.173  Sum_probs=13.3

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      =+++++|||||||...
T Consensus        12 ~i~i~GptgsGKt~la   27 (316)
T 3foz_A           12 AIFLMGPTASGKTALA   27 (316)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCccCHHHHH
Confidence            3788999999999753

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=85.21  E-value=0.29  Score=33.80  Aligned_cols=15  Identities=27%  Similarity=0.213  Sum_probs=13.0

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      -++++|++|||||..
T Consensus         4 ~I~i~G~~GsGKST~   18 (181)
T 1ly1_A            4 IILTIGCPGSGKSTW   18 (181)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEecCCCCCHHHH
Confidence            478999999999975

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=85.13  E-value=0.4  Score=36.35  Aligned_cols=17  Identities=24%  Similarity=0.176  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      ..+++.+|+|+|||...
T Consensus        48 ~~~ll~G~~GtGKt~la   64 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELA   64 (311)
T ss_dssp             EEEEEESCSSSSHHHHH
T ss_pred             eEEEEECCCCcCHHHHH
Confidence            37999999999999754

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=85.10  E-value=0.26  Score=38.03  Aligned_cols=18  Identities=17%  Similarity=0.268  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ..++++.||+|+|||...
T Consensus        45 ~~~vLl~G~~GtGKT~la   62 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAV   62 (350)
T ss_dssp             GCCEEEECCGGGCTTHHH
T ss_pred             CceEEEECCCCccHHHHH
Confidence            457999999999999853

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=85.10  E-value=0.54  Score=34.87  Aligned_cols=44  Identities=14%  Similarity=0.043  Sum_probs=29.4

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhcC----CcEEEEccCCCCcchhh
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVAG----RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g----~dvl~~a~TGsGKT~~y   83 (155)
                      ..+.+.|+-.|++ +... ..++..++++    +.+++.+|+|+|||...
T Consensus        28 ~~I~~~l~yq~~~-~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a   75 (212)
T 1tue_A           28 RPIVQFLRYQQIE-FITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG   75 (212)
T ss_dssp             HHHHHHHHHTTCC-HHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH
T ss_pred             HHHHHHHHHcCcC-HHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH
Confidence            5777777766643 2233 3345555555    25999999999999754

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=85.05  E-value=0.31  Score=33.41  Aligned_cols=15  Identities=13%  Similarity=-0.048  Sum_probs=13.1

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      -+++.|+.|||||..
T Consensus         3 ~i~l~G~~GsGKsT~   17 (173)
T 3kb2_A            3 LIILEGPDCCFKSTV   17 (173)
T ss_dssp             EEEEECSSSSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999975

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=84.87  E-value=0.28  Score=34.40  Aligned_cols=20  Identities=20%  Similarity=0.016  Sum_probs=16.3

Q ss_pred             cCCcEEEEccCCCCcchhhh
Q 031654           65 AGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yl   84 (155)
                      .|.=+.+++|+|||||...-
T Consensus         8 ~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            45668899999999998654

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=84.80  E-value=0.37  Score=37.94  Aligned_cols=18  Identities=28%  Similarity=0.270  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ..++++.+|+|+|||...
T Consensus        72 ~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEECCCCCCHHHHH
Confidence            468999999999999753

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=84.79  E-value=0.37  Score=34.48  Aligned_cols=18  Identities=33%  Similarity=0.386  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+++.+++|||||..
T Consensus        28 ~g~~i~l~G~~GsGKSTl   45 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTI   45 (200)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            467899999999999975

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=84.69  E-value=0.3  Score=38.52  Aligned_cols=18  Identities=17%  Similarity=0.051  Sum_probs=14.2

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++-+++.||||||||...
T Consensus         3 ~~~i~i~GptgsGKt~la   20 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTS   20 (322)
T ss_dssp             CEEEEEECCTTSCHHHHH
T ss_pred             CcEEEEECCCcCCHHHHH
Confidence            344788999999999753

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=84.63  E-value=3.5  Score=33.32  Aligned_cols=26  Identities=19%  Similarity=0.151  Sum_probs=17.7

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      |.=+++.|++|+|||.. ++-++..+.
T Consensus       200 G~l~ii~G~pg~GKT~l-al~ia~~~a  225 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAF-ALTIAQNAA  225 (444)
T ss_dssp             TCEEEEEECTTSCHHHH-HHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHH-HHHHHHHHH
Confidence            35688899999999964 444444333

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=84.62  E-value=0.34  Score=39.53  Aligned_cols=18  Identities=28%  Similarity=0.447  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++.+++.+|+|+|||...
T Consensus        63 ~~~iLl~GppGtGKT~la   80 (456)
T 2c9o_A           63 GRAVLLAGPPGTGKTALA   80 (456)
T ss_dssp             TCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEECCCcCCHHHHH
Confidence            468999999999999764

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=84.44  E-value=0.24  Score=34.65  Aligned_cols=18  Identities=22%  Similarity=0.370  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|..+++.+++|||||..
T Consensus         3 ~g~~I~l~G~~GsGKST~   20 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQ   20 (186)
T ss_dssp             CEEEEEEECCTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            456789999999999975

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=84.31  E-value=0.38  Score=34.61  Aligned_cols=22  Identities=18%  Similarity=0.197  Sum_probs=16.9

Q ss_pred             HHhcCCcEEEEccCCCCcchhh
Q 031654           62 ILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+-.|+=+.+.+|+|+|||...
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl   37 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVV   37 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHH
Confidence            5677888999999999999753

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=84.25  E-value=0.089  Score=45.23  Aligned_cols=21  Identities=14%  Similarity=0.107  Sum_probs=17.4

Q ss_pred             HHHHHhHHhCCCCCCCHHHHH
Q 031654           38 QHLRNKPRTYKYVKPTPVQRH   58 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~   58 (155)
                      ..+.+.|.++||++...++..
T Consensus       170 ~~l~~~L~~~GY~r~~~V~~~  190 (661)
T 2d7d_A          170 NELLRKLVDIQYARNDIDFQR  190 (661)
T ss_dssp             HHHHHHHHHTTCEECSSSCCT
T ss_pred             HHHHHHHHHcCCeeCCcCCCC
Confidence            889999999999987776554

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=84.17  E-value=0.31  Score=33.80  Aligned_cols=19  Identities=16%  Similarity=0.074  Sum_probs=15.6

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|.-+++++++|||||...
T Consensus         7 ~g~~i~l~G~~GsGKSTl~   25 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVA   25 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            3567899999999998753

>4h1g_A Maltose binding protein-cakar3 motor domain fusio; kinesin motor domain, motor protein, chimera; HET: MTT ADP EDO; 2.15A {Escherichia coli}

Probab=83.90  E-value=0.65  Score=40.18  Aligned_cols=25  Identities=32%  Similarity=0.392  Sum_probs=20.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..+++|.|  |++.++||||||.+-
T Consensus       454 ~v~~~~~G~n~~i~ayGqtgsGKT~Tm  480 (715)
T 4h1g_A          454 LIQCSLDGTNVCVFAYGQTGSGKTFTM  480 (715)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHhCCceEEEEccCCCCCchhhcc
Confidence            5678899976  677799999999764

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=83.80  E-value=0.56  Score=36.06  Aligned_cols=17  Identities=18%  Similarity=0.356  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        59 ~~~ll~G~~G~GKT~la   75 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTI   75 (353)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46999999999999753

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=83.63  E-value=0.58  Score=33.67  Aligned_cols=31  Identities=19%  Similarity=0.045  Sum_probs=22.9

Q ss_pred             CCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           52 PTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        52 pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      .++.++.. ..+..|.-+++.+++|||||...
T Consensus        12 ~~~~~r~~-~~~~~~~~i~~~G~~GsGKsT~~   42 (211)
T 1m7g_A           12 LTRSERTE-LRNQRGLTIWLTGLSASGKSTLA   42 (211)
T ss_dssp             CCHHHHHH-HHTSSCEEEEEECSTTSSHHHHH
T ss_pred             cCHHHhhc-ccCCCCCEEEEECCCCCCHHHHH
Confidence            35565555 45567788999999999998753

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=83.37  E-value=0.4  Score=38.06  Aligned_cols=18  Identities=28%  Similarity=0.325  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++.+++.+|+|+|||...
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999853

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=83.35  E-value=0.22  Score=37.10  Aligned_cols=18  Identities=17%  Similarity=0.222  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.+++.||+|+|||...
T Consensus        44 ~~~vll~G~~GtGKT~la   61 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLA   61 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            357999999999999853

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=83.25  E-value=0.35  Score=33.80  Aligned_cols=18  Identities=17%  Similarity=0.099  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      +.-+++.+++|||||...
T Consensus         3 ~~~I~l~G~~GsGKsT~a   20 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQC   20 (196)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            456899999999999753

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=83.13  E-value=0.43  Score=35.22  Aligned_cols=18  Identities=17%  Similarity=0.331  Sum_probs=14.7

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|+-+++.+|||+|||..
T Consensus        33 ~g~~ilI~GpsGsGKStL   50 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSET   50 (205)
T ss_dssp             TTEEEEEECCCTTTTHHH
T ss_pred             CCEEEEEECCCCCCHHHH
Confidence            356689999999999753

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=83.13  E-value=0.42  Score=37.59  Aligned_cols=18  Identities=17%  Similarity=0.167  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.+++.+|+|+|||...
T Consensus       117 ~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CSEEEEESSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            468999999999999853

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=83.05  E-value=0.45  Score=34.74  Aligned_cols=20  Identities=30%  Similarity=0.278  Sum_probs=12.6

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..|+=+.+.+|+|||||...
T Consensus        25 ~~G~ii~l~Gp~GsGKSTl~   44 (231)
T 3lnc_A           25 SVGVILVLSSPSGCGKTTVA   44 (231)
T ss_dssp             ECCCEEEEECSCC----CHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35677889999999999763

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=83.01  E-value=0.4  Score=35.45  Aligned_cols=16  Identities=19%  Similarity=0.299  Sum_probs=13.9

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.+++.+|+|+|||..
T Consensus        50 ~g~ll~G~~G~GKTtl   65 (254)
T 1ixz_A           50 KGVLLVGPPGVGKTHL   65 (254)
T ss_dssp             SEEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4599999999999974

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=82.82  E-value=0.57  Score=35.33  Aligned_cols=22  Identities=32%  Similarity=0.305  Sum_probs=18.4

Q ss_pred             HHhcCCcEEEEccCCCCcchhh
Q 031654           62 ILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        62 ~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..+.|+.+++.+++|||||...
T Consensus        44 ~~l~g~~i~l~G~~GsGKSTl~   65 (250)
T 3nwj_A           44 PYLNGRSMYLVGMMGSGKTTVG   65 (250)
T ss_dssp             HHHTTCCEEEECSTTSCHHHHH
T ss_pred             hhcCCCEEEEECCCCCCHHHHH
Confidence            3345999999999999999863

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=82.63  E-value=0.51  Score=33.11  Aligned_cols=19  Identities=21%  Similarity=0.171  Sum_probs=16.2

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      ..+.-+++.+++|||||..
T Consensus         7 ~~~~~I~l~G~~GsGKsT~   25 (196)
T 2c95_A            7 KKTNIIFVVGGPGSGKGTQ   25 (196)
T ss_dssp             TTSCEEEEEECTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4567899999999999975

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=82.48  E-value=0.49  Score=33.90  Aligned_cols=19  Identities=21%  Similarity=0.125  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|.-+++.+|+|+|||...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~   40 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFS   40 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            4677899999999999643

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=82.26  E-value=0.52  Score=33.33  Aligned_cols=18  Identities=28%  Similarity=0.141  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+++.++.|||||..
T Consensus         3 ~~~~I~l~G~~GsGKsT~   20 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQ   20 (204)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCcEEEEEcCCCCCHHHH
Confidence            467899999999999975

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=82.21  E-value=0.94  Score=34.08  Aligned_cols=20  Identities=20%  Similarity=0.084  Sum_probs=15.0

Q ss_pred             cCCcEEEEccCCCCcchhhh
Q 031654           65 AGRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~yl   84 (155)
                      .|+=.+++++-|||||.+.+
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL   37 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELM   37 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHH
T ss_pred             ceEEEEEECCCCCcHHHHHH
Confidence            45656777888999998754

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=82.15  E-value=0.44  Score=37.51  Aligned_cols=17  Identities=18%  Similarity=0.112  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +-+++++|||||||...
T Consensus         6 ~~i~i~GptGsGKTtla   22 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLA   22 (323)
T ss_dssp             EEEEEECCTTSCHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            35889999999999753

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=82.01  E-value=0.47  Score=34.14  Aligned_cols=18  Identities=22%  Similarity=0.189  Sum_probs=14.8

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+.+.+|+|||||..
T Consensus        21 ~g~~v~I~G~sGsGKSTl   38 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTL   38 (208)
T ss_dssp             SCEEEEEECCTTSCTHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            456788899999999874

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=81.99  E-value=0.46  Score=37.73  Aligned_cols=16  Identities=25%  Similarity=0.098  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      -++++||||||||...
T Consensus         9 lI~I~GptgSGKTtla   24 (340)
T 3d3q_A            9 LIVIVGPTASGKTELS   24 (340)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             eEEEECCCcCcHHHHH
Confidence            5789999999999753

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=81.81  E-value=0.85  Score=33.04  Aligned_cols=19  Identities=16%  Similarity=0.092  Sum_probs=16.1

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|.-+++.+++|+|||...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~   40 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFS   40 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4578899999999999864

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=81.77  E-value=0.93  Score=32.87  Aligned_cols=19  Identities=32%  Similarity=0.361  Sum_probs=15.6

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|.-+++.|++|+|||.-.
T Consensus        29 ~G~l~~i~G~pG~GKT~l~   47 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFA   47 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHH
Confidence            3567899999999999743

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=81.74  E-value=0.45  Score=33.32  Aligned_cols=17  Identities=18%  Similarity=0.147  Sum_probs=14.5

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      +.-++++++.|||||..
T Consensus         5 ~~~I~l~G~~GsGKST~   21 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTL   21 (193)
T ss_dssp             CEEEEEEESTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45689999999999975

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=81.48  E-value=0.56  Score=36.53  Aligned_cols=18  Identities=22%  Similarity=-0.005  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ++.+++.||+|+|||...
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            357999999999999853

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=81.32  E-value=0.56  Score=35.89  Aligned_cols=16  Identities=31%  Similarity=0.358  Sum_probs=13.8

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      .-++++||+|||||..
T Consensus        34 ~livl~G~sGsGKSTl   49 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTSL   49 (287)
T ss_dssp             EEEEEECCTTSCTHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4689999999999875

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=81.26  E-value=2.3  Score=33.67  Aligned_cols=77  Identities=12%  Similarity=0.087  Sum_probs=43.6

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHh--hhch----------HHHHHHHhc-CCcEEEEChHHHHHH-HH---c-CCCC
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMRE--YYSA----------RKELRELAR-WVDNLMATLRRLVNL-LE---R-GRVS  129 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~--~~~~----------~~~~~~l~~-~~~IlI~TP~~l~~~-l~---~-~~~~  129 (155)
                      -+.+.+|+|+|||... +.++......  ....          ....+.+.- .-++++..|..+.+. +.   . ..+.
T Consensus        30 iteI~G~pGsGKTtL~-Lq~~~~~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l~~i~  108 (333)
T 3io5_A           30 LLILAGPSKSFKSNFG-LTMVSSYMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQLDAIE  108 (333)
T ss_dssp             EEEEEESSSSSHHHHH-HHHHHHHHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHHHHTCC
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHHHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHHHHHhh
Confidence            4789999999999754 4444444432  1111          222233321 235778776554433 21   1 1123


Q ss_pred             cccccceEEEEccccccc
Q 031654          130 LQMIIRYLALKEAADQTL  147 (155)
Q Consensus       130 l~~l~~~lVlDEa~D~ll  147 (155)
                      -..+ +++|+|-+ ..|.
T Consensus       109 ~~~~-~lvVIDSI-~aL~  124 (333)
T 3io5_A          109 RGEK-VVVFIDSL-GNLA  124 (333)
T ss_dssp             TTCC-EEEEEECS-TTCB
T ss_pred             ccCc-eEEEEecc-cccc
Confidence            3467 89999999 8776

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=81.12  E-value=0.5  Score=33.72  Aligned_cols=31  Identities=23%  Similarity=0.178  Sum_probs=20.7

Q ss_pred             CCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           52 PTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        52 pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+..+.... ..-.|.-+++.+++|||||...
T Consensus        12 ~~~~~~~~~-~~~~g~~i~l~G~sGsGKSTl~   42 (200)
T 3uie_A           12 VEKVDRQRL-LDQKGCVIWVTGLSGSGKSTLA   42 (200)
T ss_dssp             CCHHHHHHH-HTSCCEEEEEECSTTSSHHHHH
T ss_pred             cCHHHHHHh-cCCCCeEEEEECCCCCCHHHHH
Confidence            444444322 2245678899999999999753

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=81.04  E-value=0.45  Score=33.75  Aligned_cols=18  Identities=22%  Similarity=0.176  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+++.|+.|||||..
T Consensus         3 ~~~~I~i~G~~GsGKsT~   20 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQ   20 (213)
T ss_dssp             CCEEEEEECCTTSSHHHH
T ss_pred             CCeEEEEEcCCCCCHHHH
Confidence            466789999999999975

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=80.82  E-value=0.56  Score=33.39  Aligned_cols=17  Identities=18%  Similarity=0.210  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .-++++|++|||||...
T Consensus        19 ~~I~l~G~~GsGKSTla   35 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVG   35 (202)
T ss_dssp             SCEEEECSTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            47999999999999853

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=80.70  E-value=0.55  Score=32.68  Aligned_cols=15  Identities=20%  Similarity=0.060  Sum_probs=13.0

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      -+++.++.|||||..
T Consensus         3 ~I~i~G~~GsGKsT~   17 (194)
T 1nks_A            3 IGIVTGIPGVGKSTV   17 (194)
T ss_dssp             EEEEEECTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999974

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=80.63  E-value=0.64  Score=33.59  Aligned_cols=18  Identities=17%  Similarity=0.211  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .+..+++.++.|||||..
T Consensus         3 ~~~~I~l~G~~GsGKsT~   20 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQ   20 (220)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            356799999999999975

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=80.60  E-value=0.97  Score=36.99  Aligned_cols=18  Identities=17%  Similarity=0.126  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      ..++++.||+|+|||...
T Consensus       201 ~~~~LL~G~pG~GKT~la  218 (468)
T 3pxg_A          201 KNNPVLIGEPGVGKTAIA  218 (468)
T ss_dssp             SCEEEEESCTTTTTHHHH
T ss_pred             CCCeEEECCCCCCHHHHH
Confidence            368999999999999864

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=80.44  E-value=5.2  Score=31.47  Aligned_cols=19  Identities=21%  Similarity=0.212  Sum_probs=15.1

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|.=+++.|++|+|||...
T Consensus        45 ~G~LiiIaG~pG~GKTt~a   63 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLM   63 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHH
Confidence            3456888999999999754

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=80.34  E-value=1.1  Score=35.52  Aligned_cols=19  Identities=16%  Similarity=0.184  Sum_probs=16.4

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.++++.++||||||...
T Consensus        34 ~~~~~~i~G~~G~GKs~~~   52 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTA   52 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHH
Confidence            5679999999999999753

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=80.15  E-value=0.42  Score=33.61  Aligned_cols=16  Identities=19%  Similarity=0.266  Sum_probs=13.5

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      .-+++.+|+|||||..
T Consensus         3 ~ii~l~G~~GaGKSTl   18 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTT   18 (189)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             eEEEEECCCCCcHHHH
Confidence            4578899999999985

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=80.10  E-value=0.66  Score=34.44  Aligned_cols=18  Identities=28%  Similarity=0.290  Sum_probs=15.5

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+.+.+|+|||||.-
T Consensus        30 ~Ge~~~iiG~nGsGKSTL   47 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTM   47 (235)
T ss_dssp             TTCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCcHHHH
Confidence            567788999999999974

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=80.09  E-value=0.57  Score=32.66  Aligned_cols=18  Identities=28%  Similarity=0.305  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.-+++.++.|||||..
T Consensus         4 ~g~~i~l~G~~GsGKST~   21 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTV   21 (179)
T ss_dssp             CCEEEEEECCTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            466789999999999875

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=80.03  E-value=0.57  Score=38.15  Aligned_cols=15  Identities=20%  Similarity=0.253  Sum_probs=12.7

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      +++.||||||||...
T Consensus         5 i~i~GptgsGKttla   19 (409)
T 3eph_A            5 IVIAGTTGVGKSQLS   19 (409)
T ss_dssp             EEEEECSSSSHHHHH
T ss_pred             EEEECcchhhHHHHH
Confidence            678999999999653

---

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	155
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	6e-08
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	1e-07
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	7e-07
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	8e-07
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-06
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	2e-06
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	2e-06
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	3e-06
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	4e-06
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	5e-06
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	1e-05
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	5e-05

>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 = 48.0 bits (113), Expect = 6e-08
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 5/88 (5%)

Query: 12 ASENAAPASSSTNTLSSPAARFAYVPQHLRNKPRT----YKYVKPTPVQRHATSILVAGR 67
          A+  AA A+++    ++ AA     P+    K           +P  +Q+     ++   
Sbjct: 1  AAAAAAAAAAAAAAAAA-AASLCLFPEDFLLKEFVEFFRKCVGEPRAIQKMWAKRILRKE 59

Query: 68 DLMACAQTGSRKTTPFCFPIINGIMREY 95
             A A TG  KT+      +   ++  
Sbjct: 60 SFAATAPTGVGKTSFGLAMSLFLALKGK 87

>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 = 47.2 bits (111), Expect = 1e-07
 Identities = 25/68 (36%), Positives = 41/68 (60%)

Query: 36  VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY 95
           +   +RN      Y +PTP+Q++A   ++  RD+MACAQTGS KT  F  PIIN ++ + 
Sbjct: 28  LDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQD 87

Query: 96  YSARKELR 103
            + ++  +
Sbjct: 88  LNQQRYSK 95

>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 = 44.6 bits (104), Expect = 7e-07
 Identities = 11/49 (22%), Positives = 20/49 (40%)

Query: 45 RTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMR 93
           T+ Y +  P Q      +++GRD +    TG  K+  +  P +     
Sbjct: 19 ETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGL 67

>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 = 44.5 bits (104), Expect = 8e-07
 Identities = 17/64 (26%), Positives = 32/64 (50%)

Query: 36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY 95
          + + L      Y + KP+ +Q+ A    + G D++A AQ+G+ KT  F   I+  I  + 
Sbjct: 19 LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL 78

Query: 96 YSAR 99
           + +
Sbjct: 79 KATQ 82

>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 = 43.7 bits (102), Expect = 2e-06
 Identities = 10/53 (18%), Positives = 19/53 (35%)

Query: 47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSAR 99
            +  P+ VQ       + G D++  A++G  KT  F    +  +        
Sbjct: 19 CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVS 71

>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 = 43.8 bits (102), Expect = 2e-06
 Identities = 15/53 (28%), Positives = 28/53 (52%)

Query: 47 YKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSAR 99
            + KP+P+Q  A  + + GRD++A A+ G+ KT  F  P +  +  +    +
Sbjct: 19 AGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQ 71

>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 = 43.1 bits (101), Expect = 2e-06
 Identities = 29/153 (18%), Positives = 61/153 (39%), Gaps = 42/153 (27%)

Query: 36  VPQHLRNKPRTYKYVKPTPVQRHATSILVAGR-DLMACAQTGSRKTTPFCFPIINGIMRE 94
           +  ++ N  R   + KPT +Q     + +    +++A A+TGS KT  F  P+I  +   
Sbjct: 11  LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN 70

Query: 95  YY--------------------------------------SARKELRELARWVDNLMATL 116
                                                   +   +++ L +  + ++ T 
Sbjct: 71  NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTP 129

Query: 117 RRLVNLLERGRVSLQMIIRYLALKEAADQTLDM 149
            R+++ + RG ++L+  ++Y  L E AD+ L+M
Sbjct: 130 GRILDHINRGTLNLKN-VKYFILDE-ADEMLNM 160

>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 = 43.0 bits (100), Expect = 3e-06
 Identities = 14/61 (22%), Positives = 32/61 (52%)

Query: 36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY 95
          + + L        + KP+P+Q  +  I ++GRD++A A+ G+ K+  +  P++  +  + 
Sbjct: 10 LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK 69

Query: 96 Y 96
           
Sbjct: 70 D 70

>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 = 42.9 bits (100), Expect = 4e-06
 Identities = 15/64 (23%), Positives = 33/64 (51%)

Query: 36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY 95
          + + L      Y + KP+ +Q+ A   ++ GRD++A +Q+G+ KT  F   ++  +  + 
Sbjct: 24 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 83

Query: 96 YSAR 99
             +
Sbjct: 84 RETQ 87

>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 = 42.3 bits (98), Expect = 5e-06
 Identities = 8/61 (13%), Positives = 22/61 (36%)

Query: 36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY 95
          +  +     +     +  P Q  A   + +G++L+    T + KT      ++   ++  
Sbjct: 10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG 69

Query: 96 Y 96
           
Sbjct: 70 K 70

>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 = 41.2 bits (95), Expect = 1e-05
 Identities = 15/61 (24%), Positives = 27/61 (44%)

Query: 36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREY 95
              +    +T ++ KPT +Q       + G  ++  +QTG+ KT  +  PI+  I  E 
Sbjct: 8  FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER 67

Query: 96 Y 96
           
Sbjct: 68 A 68

>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 = 39.4 bits (91), Expect = 5e-05
 Identities = 15/59 (25%), Positives = 30/59 (50%)

Query: 36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMRE 94
          + ++L      Y + +P+ +Q+ A   ++ G D++A AQ+G+ KT  F    +  I   
Sbjct: 17 LDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS 75

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	155
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.97
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.87
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.86
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.84
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.69
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.42
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.1
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.93
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.92
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	98.87
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.84
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.49
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.3
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.06
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.95
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.56
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.33
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.01
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.92
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.75
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.49
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.2
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.17
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.96
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	95.84
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	95.8
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	95.72
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	95.71
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	95.67
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	95.56
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	95.4
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.13
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.95
d1okkd2	207	GTPase domain of the signal recognition particle r	94.94
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.66
d1vmaa2	213	GTPase domain of the signal recognition particle r	94.55
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	94.45
d2qy9a2	211	GTPase domain of the signal recognition particle r	94.32
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.26
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	93.77
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.51
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.1
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	92.83
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	92.34
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	92.31
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	92.18
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	92.18
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	92.16
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	92.02
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	91.69
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	91.24
d1ls1a2	207	GTPase domain of the signal sequence recognition p	91.21
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	91.02
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	90.94
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.79
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	90.59
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	90.52
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	90.43
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	90.37
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	89.5
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	89.49
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	89.19
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	89.13
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	89.11
d1j8yf2	211	GTPase domain of the signal sequence recognition p	89.1
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	89.09
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	88.95
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	88.82
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	88.72
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	88.63
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	88.43
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	88.34
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	88.22
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	88.05
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	87.68
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	87.56
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	86.7
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	86.69
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	86.55
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	86.46
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	86.21
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	86.19
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	86.01
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	86.0
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	85.96
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	85.93
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	85.82
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	85.78
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	85.66
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	85.64
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	85.56
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	85.3
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	85.0
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	84.82
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	84.65
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	84.62
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	84.59
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	84.53
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	84.36
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	84.11
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	83.57
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	83.54
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	83.3
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	83.12
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	82.71
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	82.69
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	82.58
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	82.57
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	82.45
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	81.96
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	81.8
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	81.79
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	81.43
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	80.8
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	80.2

>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=100.00  E-value=4.8e-38  Score=237.87  Aligned_cols=124  Identities=23%  Similarity=0.409  Sum_probs=113.0

Q ss_pred             CCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------
Q 031654           28 SPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------   98 (155)
Q Consensus        28 ~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------   98 (155)
                      +...+|++|+  ++++++|+++||++|||+|++|||.+++|+|++++||||||||+||++|+++++.......       
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~P   93 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAP   93 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECS
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecc
Confidence            4456899988  9999999999999999999999999999999999999999999999999999886554332       


Q ss_pred             --------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 --------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 --------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                      ..+...+..++||+|+||+||.+++.++.++++++ +++|+||| |+|
T Consensus        94 treLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l-~~lVlDEa-D~l  171 (222)
T d2j0sa1          94 TRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAI-KMLVLDEA-DEM  171 (222)
T ss_dssp             SHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTC-CEEEEETH-HHH
T ss_pred             hHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccc-eeeeecch-hHh
Confidence                                            56667777899999999999999999999999999 99999999 999


Q ss_pred             ccccccc
Q 031654          147 LDMALNQ  153 (155)
Q Consensus       147 l~~gf~~  153 (155)
                      +++||.+
T Consensus       172 l~~~f~~  178 (222)
T d2j0sa1         172 LNKGFKE  178 (222)
T ss_dssp             TSTTTHH
T ss_pred             hhcCcHH
Confidence            9999975

>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=100.00  E-value=6.4e-38  Score=234.45  Aligned_cols=122  Identities=24%  Similarity=0.408  Sum_probs=111.2

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      .+|++++  ++++++|+++||++|||+|++|||.+++|+|++++||||||||+||++|+++++.......          
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~e   82 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecch
Confidence            5899988  9999999999999999999999999999999999999999999999999999876444322          


Q ss_pred             ------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654           99 ------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus        99 ------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                                    ..+...+..++||+|+||+|+.+++..+.++++++ ++||+||| |+|++
T Consensus        83 l~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l-~~lVlDEa-D~ll~  160 (206)
T d1veca_          83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHV-QMIVLDEA-DKLLS  160 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTC-CEEEEETH-HHHTS
T ss_pred             hhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhcccccc-ceEEEecc-ccccc
Confidence                                          56666777899999999999999999999999999 99999999 99999


Q ss_pred             cccccC
Q 031654          149 MALNQK  154 (155)
Q Consensus       149 ~gf~~~  154 (155)
                      .||.++
T Consensus       161 ~~f~~~  166 (206)
T d1veca_         161 QDFVQI  166 (206)
T ss_dssp             TTTHHH
T ss_pred             cchHHH
Confidence            999753

>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=100.00  E-value=1e-37  Score=238.11  Aligned_cols=140  Identities=34%  Similarity=0.567  Sum_probs=124.1

Q ss_pred             ccCCcCcccCCCCC--CCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHH
Q 031654           13 SENAAPASSSTNTL--SSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPII   88 (155)
Q Consensus        13 ~~~~~~~~~~~~~~--p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l   88 (155)
                      +|+.+++...+...  |.++.+|++|+  ++++++|+++||++|||+|+++||.+++|+|++++||||||||+||++|++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l   80 (238)
T d1wrba1           1 KYDSIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPII   80 (238)
T ss_dssp             CCCCCCCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcccceeeeCCCCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHH
Confidence            47788887766654  56789999988  999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhch------------------------------------------------HHHHHHHhcCCcEEEEChHHHH
Q 031654           89 NGIMREYYSA------------------------------------------------RKELRELARWVDNLMATLRRLV  120 (155)
Q Consensus        89 ~~l~~~~~~~------------------------------------------------~~~~~~l~~~~~IlI~TP~~l~  120 (155)
                      +++.......                                                ..+.+....++||+|+||++|.
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~  160 (238)
T d1wrba1          81 NHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLV  160 (238)
T ss_dssp             HHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHH
T ss_pred             HHHHhcccccccccCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHH
Confidence            9986542111                                                5566777789999999999999


Q ss_pred             HHHHcCCCCcccccceEEEEcccccccccccccC
Q 031654          121 NLLERGRVSLQMIIRYLALKEAADQTLDMALNQK  154 (155)
Q Consensus       121 ~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~~~  154 (155)
                      +++..+.+.+.++ +++|+||| |+|++.||.++
T Consensus       161 ~~~~~~~~~l~~v-~~lViDEa-D~ll~~~f~~~  192 (238)
T d1wrba1         161 DFIEKNKISLEFC-KYIVLDEA-DRMLDMGFEPQ  192 (238)
T ss_dssp             HHHHTTSBCCTTC-CEEEEETH-HHHHHTTCHHH
T ss_pred             hHHccCceecccc-ceeeeehh-hhhhhhccHHH
Confidence            9999999999999 99999999 99999999753

>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=100.00  E-value=7.5e-37  Score=229.66  Aligned_cols=129  Identities=21%  Similarity=0.337  Sum_probs=112.1

Q ss_pred             CCCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--
Q 031654           23 TNTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--   98 (155)
Q Consensus        23 ~~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--   98 (155)
                      +.+.|+++.+|++|+  ++++++|+++||++|||+|+++||.++.|+|++++||||||||+||++|+++++.......  
T Consensus         2 ~~~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~   81 (212)
T d1qdea_           2 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQA   81 (212)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCE
T ss_pred             CCCCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcce
Confidence            346688899999998  9999999999999999999999999999999999999999999999999999886544332  


Q ss_pred             -------------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEc
Q 031654           99 -------------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKE  141 (155)
Q Consensus        99 -------------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDE  141 (155)
                                                           ..+... .+++||+|+||+++.+++..+.++++++ +++|+||
T Consensus        82 lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~IvI~TP~~l~~~~~~~~~~l~~l-~~lVlDE  159 (212)
T d1qdea_          82 LMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG-LRDAQIVVGTPGRVFDNIQRRRFRTDKI-KMFILDE  159 (212)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-----------CTTCSEEEECHHHHHHHHHTTSSCCTTC-CEEEEET
T ss_pred             EEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHH-hcCCcEEEECCCccccccccCceecCcc-eEEeehh
Confidence                                                 222222 2468999999999999999999999999 9999999


Q ss_pred             ccccccccccccC
Q 031654          142 AADQTLDMALNQK  154 (155)
Q Consensus       142 a~D~ll~~gf~~~  154 (155)
                      | |+|+|+||.++
T Consensus       160 a-d~lld~~f~~~  171 (212)
T d1qdea_         160 A-DEMLSSGFKEQ  171 (212)
T ss_dssp             H-HHHHHTTCHHH
T ss_pred             h-hhhcccchHHH
Confidence            9 99999999753

>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=100.00  E-value=3.5e-37  Score=232.39  Aligned_cols=128  Identities=23%  Similarity=0.340  Sum_probs=111.2

Q ss_pred             CCCCCCCcccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---
Q 031654           24 NTLSSPAARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---   98 (155)
Q Consensus        24 ~~~p~~~~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---   98 (155)
                      .+.|+++.+|++++  ++++++|+++||++|||+|++|||.++.|+|++++||||||||+||++|+++++.......   
T Consensus         5 ~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~al   84 (218)
T d2g9na1           5 SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQAL   84 (218)
T ss_dssp             CCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEE
T ss_pred             CCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEE
Confidence            34678899999988  9999999999999999999999999999999999999999999999999999986443322   


Q ss_pred             ------------HHHHH-------------------------HHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEc
Q 031654           99 ------------RKELR-------------------------ELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKE  141 (155)
Q Consensus        99 ------------~~~~~-------------------------~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDE  141 (155)
                                  .....                         ...+++||+|+||+++.+++.++...++++ +++|+||
T Consensus        85 il~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l-~~lVlDE  163 (218)
T d2g9na1          85 VLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYI-KMFVLDE  163 (218)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTC-CEEEEES
T ss_pred             EEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccc-eEEEeee
Confidence                        11111                         112368999999999999999999999999 9999999


Q ss_pred             cccccccccccc
Q 031654          142 AADQTLDMALNQ  153 (155)
Q Consensus       142 a~D~ll~~gf~~  153 (155)
                      | |+|++.||.+
T Consensus       164 a-D~ll~~~f~~  174 (218)
T d2g9na1         164 A-DEMLSRGFKD  174 (218)
T ss_dssp             H-HHHHHTTCHH
T ss_pred             c-chhhcCchHH
Confidence            9 9999999975

>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=100.00  E-value=2.1e-36  Score=225.80  Aligned_cols=121  Identities=25%  Similarity=0.386  Sum_probs=110.2

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      .||++|+  +.++++|+++||++|||+|+++||.+++|+|+++.||||||||+||++|+++++.......          
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~   80 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE   80 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchh
Confidence            3799987  9999999999999999999999999999999999999999999999999998875443322          


Q ss_pred             -----------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 -----------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 -----------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                                   ..+...+..++||+|+||++|.++++.+.++++++ +++|+||| |+|++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l-~~lV~DEa-D~l~~~  158 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDC-SLFIMDEA-DKMLSR  158 (206)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTC-CEEEEESH-HHHSSH
T ss_pred             hhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccc-eEEEeech-hhhhhh
Confidence                                         56666777899999999999999999999999999 99999999 999999


Q ss_pred             cccc
Q 031654          150 ALNQ  153 (155)
Q Consensus       150 gf~~  153 (155)
                      ||.+
T Consensus       159 ~f~~  162 (206)
T d1s2ma1         159 DFKT  162 (206)
T ss_dssp             HHHH
T ss_pred             hhHH
Confidence            9875

>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=100.00  E-value=4.2e-36  Score=224.66  Aligned_cols=121  Identities=19%  Similarity=0.277  Sum_probs=106.5

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      .+|++|+  ++++++|+++||++|||+|++|||.+++|+|++++||||||||+||++|+++++.......          
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~Ptre   80 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   80 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccch
Confidence            3689887  9999999999999999999999999999999999999999999999999998875443222          


Q ss_pred             ------------------------------HHHHHHH-hcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccc
Q 031654           99 ------------------------------RKELREL-ARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 ------------------------------~~~~~~l-~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                                                    ..+...+ ..++||+|+||+++.++++++.++++++ +++|+||| |+|+
T Consensus        81 L~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l-~~lVlDEa-D~ll  158 (207)
T d1t6na_          81 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHI-KHFILDEC-DKML  158 (207)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTC-CEEEEESH-HHHH
T ss_pred             hhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceecccc-ceeehhhh-hhhh
Confidence                                          3444444 4679999999999999999999999999 99999999 9999


Q ss_pred             cc-cccc
Q 031654          148 DM-ALNQ  153 (155)
Q Consensus       148 ~~-gf~~  153 (155)
                      +. ||.+
T Consensus       159 ~~~~~~~  165 (207)
T d1t6na_         159 EQLDMRR  165 (207)
T ss_dssp             SSHHHHH
T ss_pred             hcCCcHH
Confidence            84 7764

>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=100.00  E-value=9e-36  Score=221.94  Aligned_cols=121  Identities=24%  Similarity=0.392  Sum_probs=106.6

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      ++|++++  ++++++|+++||++|||+|++|||.+++|+|++++||||||||+||++|+++.+.......          
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~   80 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   80 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccc
Confidence            4799988  9999999999999999999999999999999999999999999999999998776443322          


Q ss_pred             ---------------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654           99 ---------------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 ---------------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                                                       ..+......+++|+|+||+++.+++.++...++++ +++|+||| |+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l-~~lViDEa-d~  158 (209)
T d1q0ua_          81 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTA-HILVVDEA-DL  158 (209)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGC-CEEEECSH-HH
T ss_pred             hhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccc-eEEEEeec-cc
Confidence                                             22223344579999999999999999999999999 99999999 99


Q ss_pred             cccccccc
Q 031654          146 TLDMALNQ  153 (155)
Q Consensus       146 ll~~gf~~  153 (155)
                      |++.||.+
T Consensus       159 ll~~~f~~  166 (209)
T d1q0ua_         159 MLDMGFIT  166 (209)
T ss_dssp             HHHTTCHH
T ss_pred             ccccccHH
Confidence            99999875

>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=99.97  E-value=7.3e-33  Score=206.88  Aligned_cols=120  Identities=25%  Similarity=0.453  Sum_probs=104.7

Q ss_pred             cccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCC-cEEEEccCCCCcchhhhhHHHHHHHHhhhch---------
Q 031654           31 ARFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGR-DLMACAQTGSRKTTPFCFPIINGIMREYYSA---------   98 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~-dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------   98 (155)
                      .+|++|+  ++++++|+++||++|||+|+++||.+++|+ |++++||||||||++|++|++++........         
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~   83 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRE   83 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHH
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccccCcceEEEeeccc
Confidence            5899876  999999999999999999999999999985 9999999999999999999988654332211         


Q ss_pred             -----------------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 -----------------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 -----------------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                                   ..+.+.+ +++||+||||++|.++++++.++++++ +++|+||| |+|++.
T Consensus        84 l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-~~~~IlV~TP~~l~~~l~~~~~~~~~l-~~lViDEa-d~l~~~  160 (208)
T d1hv8a1          84 LAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNV-KYFILDEA-DEMLNM  160 (208)
T ss_dssp             HHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHTTCSCTTSC-CEEEEETH-HHHHTT
T ss_pred             cchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc-CCCCEEEEChHHHHHHHHcCCCCcccC-cEEEEECh-HHhhcC
Confidence                                         3444444 479999999999999999999999999 99999999 999999


Q ss_pred             cccc
Q 031654          150 ALNQ  153 (155)
Q Consensus       150 gf~~  153 (155)
                      +|.+
T Consensus       161 ~~~~  164 (208)
T d1hv8a1         161 GFIK  164 (208)
T ss_dssp             TTHH
T ss_pred             CChH
Confidence            8864

>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=99.87  E-value=1.1e-22  Score=153.20  Aligned_cols=103  Identities=14%  Similarity=0.052  Sum_probs=80.0

Q ss_pred             HHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------------------
Q 031654           41 RNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------------------   98 (155)
Q Consensus        41 ~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------------------   98 (155)
                      .+++.+.++.+|+++|+.+|+.++.|+|++++||||||||++|++|++.....+....                      
T Consensus        33 ~~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt~~La~Q~~~~l~~~~~~  112 (237)
T d1gkub1          33 FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEK  112 (237)
T ss_dssp             HHHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEeccHHHHHHHHHHHHHHHHH
Confidence            4555566899999999999999999999999999999999999999887665433222                      


Q ss_pred             --------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 --------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 --------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                          ..+.......++|+|+||++|.+    ....++++ +++|+||| |.|++.
T Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~----~~~~~~~~-~~vVvDE~-d~~l~~  177 (237)
T d1gkub1         113 AGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSK----HYRELGHF-DFIFVDDV-DAILKA  177 (237)
T ss_dssp             TCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHH----CSTTSCCC-SEEEESCH-HHHHTS
T ss_pred             cCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHH----hhhhcCCC-CEEEEECh-hhhhhc
Confidence                                11111122357999999998754    34467889 99999999 999874

>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=99.86  E-value=5.7e-23  Score=151.59  Aligned_cols=119  Identities=14%  Similarity=0.040  Sum_probs=91.8

Q ss_pred             ccccCC--HHHHHhHHhC-CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------
Q 031654           32 RFAYVP--QHLRNKPRTY-KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------   98 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~-g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------   98 (155)
                      .++.++  +.+.+.|++. ||+.++|.|.+||+.+++|+|+++++|||||||++|.+|++.+........          
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~~~~~~~v~P~~~L~~q~~   82 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQV   82 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSSSEEEEECSCHHHHHHHH
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhccCceEEeccchhhhhhHH
Confidence            345666  7788888877 999999999999999999999999999999999999999876432110000          


Q ss_pred             -----------------------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccccc
Q 031654           99 -----------------------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMALN  152 (155)
Q Consensus        99 -----------------------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf~  152 (155)
                                             ...........+|+++||.++.............+ +++|+||| |.+.+.|+.
T Consensus        83 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v-~~lviDEa-H~~~~~~~~  157 (206)
T d1oywa2          83 DQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNP-VLLAVDEA-HCISQWGHD  157 (206)
T ss_dssp             HHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCE-EEEEESSG-GGGCTTSSC
T ss_pred             HHHHhhcccccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhhee-eeeeeeee-eeeeccccc
Confidence                                   22222334568999999999765555555667789 99999999 999988753

>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=99.84  E-value=9.2e-22  Score=144.85  Aligned_cols=113  Identities=12%  Similarity=0.103  Sum_probs=92.8

Q ss_pred             CCHHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch---------HHHHHHHh
Q 031654           36 VPQHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA---------RKELRELA  106 (155)
Q Consensus        36 l~~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~---------~~~~~~l~  106 (155)
                      +++.+...|++.||++|+|+|.++++.+++|+|+++++|||||||.+|.++++..+.......         .++...+.
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~~~L~~q~~~~~~   89 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFK   89 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHT
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhccCcceeecccHHHHHHHHHHHH
Confidence            458889999999999999999999999999999999999999999999999988776543322         33333332


Q ss_pred             -----------------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccccc
Q 031654          107 -----------------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       107 -----------------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~g  150 (155)
                                             ..++|+++||..+..++......+..+ +++|+||+ |.+.+.+
T Consensus        90 ~~~~~~~~v~~~~~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~-~~ii~DE~-h~~~~~~  154 (202)
T d2p6ra3          90 KWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAV-SCLVVDEI-HLLDSEK  154 (202)
T ss_dssp             TTTTTTCCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGC-CEEEETTG-GGGGCTT
T ss_pred             HHhhccccceeeccCcccccccccccceeeeccHHHHHHHhccchhhhhh-hhccccHH-HHhcccc
Confidence                                   247999999999999998888889999 99999999 9887765

>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=99.69  E-value=5.6e-17  Score=118.01  Aligned_cols=98  Identities=17%  Similarity=0.119  Sum_probs=78.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch------------------------------
Q 031654           49 YVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA------------------------------   98 (155)
Q Consensus        49 ~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------------------------------   98 (155)
                      +-.|++.|.+++..+. ++|+++++|||||||+++++++...+.......                              
T Consensus         7 ~~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (200)
T d1wp9a1           7 LIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (200)
T ss_dssp             HHCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CCCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHHHHHHHHHHHHhhcccccceee
Confidence            3479999999998765 668999999999999999988877665543222                              


Q ss_pred             ------HHHHHHHhcCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654           99 ------RKELRELARWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus        99 ------~~~~~~l~~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                            ..........++++++||+++...+..+.+.++++ +++|+||| |.+.+.
T Consensus        86 ~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~-~~vIiDE~-H~~~~~  140 (200)
T d1wp9a1          86 LTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDV-SLIVFDEA-HRAVGN  140 (200)
T ss_dssp             ECSCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSC-SEEEEETG-GGCSTT
T ss_pred             eecccchhHHHHhhhcccccccccchhHHHHhhhhhhcccc-ceEEEEeh-hhhhcc
Confidence                  22333333457899999999999999998999999 99999999 987654

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

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]

Probab=99.42  E-value=6.8e-14  Score=106.83  Aligned_cols=86  Identities=12%  Similarity=0.047  Sum_probs=63.5

Q ss_pred             HhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHH----------------hcCCcEEEECh
Q 031654           63 LVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELREL----------------ARWVDNLMATL  116 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l----------------~~~~~IlI~TP  116 (155)
                      +.+|+++++.||||||||++|++|++..........          .+..+.+                .....++++||
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~t~   85 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCH   85 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHTTTSCCBCCC--------CCCSEEEEEH
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEeecccCccccccCCc
Confidence            457899999999999999999989887766544322          2222222                22468999999


Q ss_pred             HHHHHHHHcCCCCcccccceEEEEccccccccccc
Q 031654          117 RRLVNLLERGRVSLQMIIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       117 ~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~gf  151 (155)
                      +.+..++. ....+.++ +++|+||| |++.+.++
T Consensus        86 ~~l~~~~~-~~~~~~~~-~~vViDE~-H~~~~~~~  117 (305)
T d2bmfa2          86 ATFTMRLL-SPIRVPNY-NLIIMDEA-HFTDPASI  117 (305)
T ss_dssp             HHHHHHHT-SSSCCCCC-SEEEEEST-TCCSHHHH
T ss_pred             HHHHHHHh-cCccccce-eEEEeeee-eecchhhH
Confidence            98877665 44567889 99999999 99876653

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

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: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.10  E-value=9.3e-11  Score=78.93  Aligned_cols=83  Identities=12%  Similarity=-0.018  Sum_probs=56.9

Q ss_pred             hcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHhc----------------CCcEEEEChH
Q 031654           64 VAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELAR----------------WVDNLMATLR  117 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~~----------------~~~IlI~TP~  117 (155)
                      .+|+++++++|||||||..++..++..........          .+..+.+..                ...+.+.|..
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHA   84 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCEEEESSCCCCCCCSSCCEEEEEHH
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecchhHHHHHHHHhhhhhhhhcccccccccccccchhhhhHH
Confidence            46899999999999999998777777665544322          222222221                2467777777


Q ss_pred             HHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          118 RLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       118 ~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                      .+.... .....+.++ +++|+||| |++-..
T Consensus        85 ~l~~~~-~~~~~~~~~-~lvIiDEa-H~~~~~  113 (140)
T d1yksa1          85 TLTYRM-LEPTRVVNW-EVIIMDEA-HFLDPA  113 (140)
T ss_dssp             HHHHHH-TSSSCCCCC-SEEEETTT-TCCSHH
T ss_pred             HHHHHH-hccccccce-eEEEEccc-cccChh
Confidence            765543 445678899 99999999 977433

>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=98.93  E-value=1.7e-09  Score=82.08  Aligned_cols=101  Identities=16%  Similarity=0.174  Sum_probs=73.0

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHhc----C--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILVA----G--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l~----g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------   98 (155)
                      +...+.++++.| .+|.-|.+|+..+..    +  .+-+++|.||||||..|+..++..+..+....             
T Consensus        71 ~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~  149 (264)
T d1gm5a3          71 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHY  149 (264)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHH
T ss_pred             HHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHHH
Confidence            333444566667 689999999998853    3  47899999999999999999988776654333             


Q ss_pred             --------------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccc
Q 031654           99 --------------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus        99 --------------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                                                .+....+.+ .++|+|||..-+.     ..+.++++ .++|+||- |+.
T Consensus       150 ~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~-----~~~~f~~L-glviiDEq-H~f  217 (264)
T d1gm5a3         150 RRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQ-----EDVHFKNL-GLVIIDEQ-HRF  217 (264)
T ss_dssp             HHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHH-----HCCCCSCC-CEEEEESC-CCC
T ss_pred             HHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhc-----CCCCcccc-ceeeeccc-ccc
Confidence                                      222333333 6899999975432     34567899 99999998 754

>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=98.92  E-value=1.9e-09  Score=78.50  Aligned_cols=101  Identities=14%  Similarity=0.003  Sum_probs=68.9

Q ss_pred             HHHHHhHHhCCCC------------------CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch-
Q 031654           38 QHLRNKPRTYKYV------------------KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA-   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~------------------~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-   98 (155)
                      +.+.+.+++.|+.                  .+++.|.+++..+++++..++.+|||+|||+..+..+ ..+.   ... 
T Consensus        39 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~~~---~~~L  114 (206)
T d2fz4a1          39 RDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NELS---TPTL  114 (206)
T ss_dssp             HHHHHHHHHTTCCEEEESCCCCCCCCCCCCCCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HHSC---SCEE
T ss_pred             HHHHHHHHHCCCceeeccccccCCCCCCCCCCcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HHhc---Ccee
Confidence            5666777666542                  5889999999999999999999999999998765433 2221   111 


Q ss_pred             ---------HHHHHHHh---------------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccc
Q 031654           99 ---------RKELRELA---------------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 ---------~~~~~~l~---------------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll  147 (155)
                               .+....+.               ....|+|+|...+......   ..++. .+||+||| |++-
T Consensus       115 iv~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~---~~~~~-~lvIiDEa-H~~~  182 (206)
T d2fz4a1         115 IVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEK---LGNRF-MLLIFDEV-HHLP  182 (206)
T ss_dssp             EEESSHHHHHHHHHHHGGGCGGGEEEESSSCBCCCSEEEEEHHHHHHTHHH---HTTTC-SEEEEECS-SCCC
T ss_pred             EEEcccchHHHHHHHHHhhcccchhhcccccccccccccceehhhhhhhHh---hCCcC-CEEEEECC-eeCC
Confidence                     22222222               1357899998886554332   23467 89999999 9874

>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=98.87  E-value=8.6e-09  Score=76.73  Aligned_cols=101  Identities=20%  Similarity=0.170  Sum_probs=71.4

Q ss_pred             HHHHHhHHhCCCCCCCHHHHHHHHHHh----cC--CcEEEEccCCCCcchhhhhHHHHHHHHhhhch-------------
Q 031654           38 QHLRNKPRTYKYVKPTPVQRHATSILV----AG--RDLMACAQTGSRKTTPFCFPIINGIMREYYSA-------------   98 (155)
Q Consensus        38 ~~l~~~l~~~g~~~pt~iQ~~~i~~~l----~g--~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~-------------   98 (155)
                      .+..+.+.+.---.+|+-|..++..+.    ++  .+.+++|.||||||..|+..+...+..+....             
T Consensus        42 ~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~  121 (233)
T d2eyqa3          42 REQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHY  121 (233)
T ss_dssp             HHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHH
T ss_pred             HHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHH
Confidence            455555544333478999999998774    33  47899999999999999998887665433222             


Q ss_pred             --------------------------HHHHHHHhc-CCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccc
Q 031654           99 --------------------------RKELRELAR-WVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQ  145 (155)
Q Consensus        99 --------------------------~~~~~~l~~-~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~  145 (155)
                                                ......+.. .++|||||-..+.     ..+.++++ .++|+||= |+
T Consensus       122 ~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~L-gLiIiDEe-H~  188 (233)
T d2eyqa3         122 DNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDL-GLLIVDEE-HR  188 (233)
T ss_dssp             HHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSE-EEEEEESG-GG
T ss_pred             HHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccc-cceeeech-hh
Confidence                                      222233333 5899999976543     45678899 99999999 75

>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=98.84  E-value=5.7e-10  Score=85.28  Aligned_cols=92  Identities=10%  Similarity=0.049  Sum_probs=63.2

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhc-h----------HHHHHHHh-------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYS-A----------RKELRELA-------------  106 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~-~----------~~~~~~l~-------------  106 (155)
                      .|.+.|..|+..++..+..++.+|||+|||+....- +..+...... .          .+....+.             
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i-~~~~~~~~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~~  191 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALL-ARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKI  191 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHH-HHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEEC
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHH-HHHhhhcccceEEEEEcCchhHHHHHHHHHHhhccccccceee
Confidence            699999999999999999999999999999876543 3333332221 1          11111111             


Q ss_pred             -----------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEcccccccc
Q 031654          107 -----------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       107 -----------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                                 ...+|+|+|+..+...   ....++++ .++|+||| |++-.
T Consensus       192 ~~g~~~~~~~~~~~~i~i~t~qs~~~~---~~~~~~~f-~~VIvDEa-H~~~a  239 (282)
T d1rifa_         192 GGGASKDDKYKNDAPVVVGTWQTVVKQ---PKEWFSQF-GMMMNDEC-HLATG  239 (282)
T ss_dssp             STTCSSTTCCCTTCSEEEECHHHHTTS---CGGGGGGE-EEEEEETG-GGCCH
T ss_pred             cceecccccccccceEEEEeeehhhhh---cccccCCC-CEEEEECC-CCCCc
Confidence                       1357999999775432   33456788 99999999 87653

>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=98.49  E-value=1.7e-07  Score=63.09  Aligned_cols=71  Identities=17%  Similarity=0.036  Sum_probs=43.9

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhch----------HHHHHHHh-----------------cCCcEEEEChHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSA----------RKELRELA-----------------RWVDNLMATLRRL  119 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~----------~~~~~~l~-----------------~~~~IlI~TP~~l  119 (155)
                      +..++.+|||||||..+...+    .......          .+..+.+.                 ....++++|.+.+
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~----~~~~~~vli~~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAY----AAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKF   84 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHH----HTTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCEECCCCSEEEEEHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHH----HHcCCcEEEEcChHHHHHHHHHHHHHHhhccccccccccccccccceEEEeeeee
Confidence            567999999999997542222    1212111          22222221                 1357888898775


Q ss_pred             HHHHHcCCCCcccccceEEEEcccccc
Q 031654          120 VNLLERGRVSLQMIIRYLALKEAADQT  146 (155)
Q Consensus       120 ~~~l~~~~~~l~~l~~~lVlDEa~D~l  146 (155)
                      .   ......++++ +++|+||+ |++
T Consensus        85 ~---~~~~~~~~~~-~~vIiDE~-H~~  106 (136)
T d1a1va1          85 L---ADGGCSGGAY-DIIICDEC-HST  106 (136)
T ss_dssp             H---HTTGGGGCCC-SEEEEETT-TCC
T ss_pred             c---cccchhhhcC-CEEEEecc-ccc
Confidence            3   3344567899 99999999 865

>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=98.30  E-value=6.1e-07  Score=67.56  Aligned_cols=93  Identities=22%  Similarity=0.206  Sum_probs=68.0

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------------------------
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------------------------   98 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------------------------   98 (155)
                      +|+++|...--.+..|+  ++.-.||-|||++..+|++-.........                                
T Consensus        80 RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~g~~vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~~~~  157 (273)
T d1tf5a3          80 FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLN  157 (273)
T ss_dssp             CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCT
T ss_pred             EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcCCCceEEecCccccchhhhHHhHHHHHcCCCcccccc
Confidence            78999999887888885  88999999999999999876666544332                                


Q ss_pred             --HHHHHHHhcCCcEEEEChHHH-HHHHHcCC------CCcccccceEEEEccccccc
Q 031654           99 --RKELRELARWVDNLMATLRRL-VNLLERGR------VSLQMIIRYLALKEAADQTL  147 (155)
Q Consensus        99 --~~~~~~l~~~~~IlI~TP~~l-~~~l~~~~------~~l~~l~~~lVlDEa~D~ll  147 (155)
                        ....+.-.-.|||+.+|...+ .|+|+.+.      ...+.+ .+.|+||+ |.||
T Consensus       158 ~~~~~~r~~~Y~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~-~~aIvDEv-Dsil  213 (273)
T d1tf5a3         158 SMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPL-HFAVIDEV-DSIL  213 (273)
T ss_dssp             TSCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCC-CEEEEETH-HHHH
T ss_pred             ccCHHHHHHHhhCCceecchhhhhhhhcchhhhcChhhhccCCC-CEEEEEcc-hhhh
Confidence              112222223589999999887 45555432      234567 89999999 9887

>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=97.95  E-value=1.8e-05  Score=61.69  Aligned_cols=33  Identities=21%  Similarity=0.219  Sum_probs=29.5

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..+..|..|+..++.++-+++++|+|||||...
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            456789999999999999999999999999873

>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=97.56  E-value=8.5e-05  Score=53.68  Aligned_cols=93  Identities=18%  Similarity=0.182  Sum_probs=57.0

Q ss_pred             CCCHHHHHHHHHHh----cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhch--------------HHHHHHHh------
Q 031654           51 KPTPVQRHATSILV----AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSA--------------RKELRELA------  106 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l----~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------------~~~~~~l~------  106 (155)
                      .+.|.|.+++..+.    .+...++.-+.|.|||+..+ .++..+.......              .++.....      
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i-~~~~~~~~~~~~~~~LIv~p~~l~~~W~~e~~~~~~~~~~~   90 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFA   90 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHTTCCSSEEEEECSTTHHHHHHHHHHHCTTSCEE
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHH-HhhhhhhhcccccccceecchhhhhHHHHHHHhhcccccce
Confidence            57899999987543    45678999999999999864 3444443332211              22222221      


Q ss_pred             -----------cCCcEEEEChHHHHHHHHcCCCCcccccceEEEEccccccccc
Q 031654          107 -----------RWVDNLMATLRRLVNLLERGRVSLQMIIRYLALKEAADQTLDM  149 (155)
Q Consensus       107 -----------~~~~IlI~TP~~l~~~l~~~~~~l~~l~~~lVlDEa~D~ll~~  149 (155)
                                 ...+|+|+|.+.+...-.   +.--.. .++|+||| +.+-+.
T Consensus        91 ~~~~~~~~~~~~~~~vvi~~~~~~~~~~~---l~~~~~-~~vI~DEa-h~~k~~  139 (230)
T d1z63a1          91 VFHEDRSKIKLEDYDIILTTYAVLLRDTR---LKEVEW-KYIVIDEA-QNIKNP  139 (230)
T ss_dssp             ECSSSTTSCCGGGSSEEEEEHHHHTTCHH---HHTCCE-EEEEEETG-GGGSCT
T ss_pred             eeccccchhhccCcCEEEeeHHHHHhHHH---Hhcccc-eEEEEEhh-hccccc
Confidence                       235888998877543221   111133 56999999 887653

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

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

Probab=97.33  E-value=0.00058  Score=51.07  Aligned_cols=33  Identities=21%  Similarity=0.195  Sum_probs=26.1

Q ss_pred             CCCHHHHHHHHHHh---------cCCcEEEEccCCCCcchhh
Q 031654           51 KPTPVQRHATSILV---------AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l---------~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+.|+|..++..+.         .+...+++-..|.|||+..
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qa   96 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQC   96 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHH
Confidence            57899999997653         3456888899999999753

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [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: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=97.01  E-value=0.00019  Score=53.09  Aligned_cols=34  Identities=24%  Similarity=0.215  Sum_probs=27.0

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhH
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFP   86 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp   86 (155)
                      +++|-|.+++..  ....++|.|+.|||||.+.+--
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~r   34 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNK   34 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHH
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHH
Confidence            478999999954  3467999999999999875433

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.92  E-value=0.001  Score=47.23  Aligned_cols=94  Identities=16%  Similarity=0.083  Sum_probs=50.9

Q ss_pred             CCHHHHHHHHHH----hcCC---cEEEEccCCCCcchhhhhHHHHHHHHhhhch--------HHHHHHHhcCCcEEEECh
Q 031654           52 PTPVQRHATSIL----VAGR---DLMACAQTGSRKTTPFCFPIINGIMREYYSA--------RKELRELARWVDNLMATL  116 (155)
Q Consensus        52 pt~iQ~~~i~~~----l~g~---dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------~~~~~~l~~~~~IlI~TP  116 (155)
                      .+|+|..++..+    .+++   -+++.||+|+|||..... ++..+.......        ......-...+++....+
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~-~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~   81 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA-LSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAP   81 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH-HHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECC
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHH-HHHhcccccccccccccccchhhhhhhccccccchhhh
Confidence            357887777755    3443   389999999999986432 222232111100        111122223456666654


Q ss_pred             H---------HHHHHHHcC--CCCcccccceEEEEcccccccc
Q 031654          117 R---------RLVNLLERG--RVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       117 ~---------~l~~~l~~~--~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      +         .+.++...-  .-....- +++|+||| |.|-.
T Consensus        82 ~~~~~~i~~~~ir~l~~~~~~~~~~~~~-kviIide~-d~l~~  122 (207)
T d1a5ta2          82 EKGKNTLGVDAVREVTEKLNEHARLGGA-KVVWVTDA-ALLTD  122 (207)
T ss_dssp             CTTCSSBCHHHHHHHHHHTTSCCTTSSC-EEEEESCG-GGBCH
T ss_pred             hhcccccccchhhHHhhhhhhccccCcc-ceEEechh-hhhhh
Confidence            2         222233321  1223456 79999999 99864

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.75  E-value=0.0048  Score=44.33  Aligned_cols=77  Identities=17%  Similarity=0.160  Sum_probs=40.3

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhhch------HHHHHHH--hcCCcEEEECh------HHHHHHHHcCCC--Ccc
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYYSA------RKELREL--ARWVDNLMATL------RRLVNLLERGRV--SLQ  131 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~------~~~~~~l--~~~~~IlI~TP------~~l~~~l~~~~~--~l~  131 (155)
                      .+++.||+|+|||.... -++..+.......      ......+  ...++++....      +.+.+++..-..  .-.
T Consensus        36 ~~Ll~Gp~G~GKtt~a~-~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~  114 (239)
T d1njfa_          36 AYLFSGTRGVGKTSIAR-LLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARG  114 (239)
T ss_dssp             EEEEECSTTSSHHHHHH-HHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSS
T ss_pred             eEEEECCCCCcHHHHHH-HHHHHhcCccccccCccccchHHHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccC
Confidence            48999999999998643 3334443221111      1111222  22345554333      223344443221  123


Q ss_pred             cccceEEEEccccccc
Q 031654          132 MIIRYLALKEAADQTL  147 (155)
Q Consensus       132 ~l~~~lVlDEa~D~ll  147 (155)
                      .. +.+||||| |.|-
T Consensus       115 ~~-kviiIde~-d~l~  128 (239)
T d1njfa_         115 RF-KVYLIDEV-HMLS  128 (239)
T ss_dssp             SS-EEEEEETG-GGSC
T ss_pred             CC-EEEEEECc-ccCC
Confidence            45 78999999 9984

>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=96.49  E-value=0.0023  Score=50.06  Aligned_cols=45  Identities=16%  Similarity=0.155  Sum_probs=31.8

Q ss_pred             HHhCCCCCCCHHHHHHHHHHhcCC--cEEEEccCCCCcchhhhhHHHHHHH
Q 031654           44 PRTYKYVKPTPVQRHATSILVAGR--DLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        44 l~~~g~~~pt~iQ~~~i~~~l~g~--dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      +..+||   .+-|...+..++...  =+++++|||||||.... .+++.+.
T Consensus       137 l~~LG~---~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~-~~l~~~~  183 (401)
T d1p9ra_         137 LHSLGM---TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLY-AGLQELN  183 (401)
T ss_dssp             GGGSCC---CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHH-HHHHHHC
T ss_pred             hhhhcc---cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHH-HHhhhhc
Confidence            456665   577777787777554  48999999999998743 3455553

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

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: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=96.20  E-value=0.0019  Score=47.13  Aligned_cols=17  Identities=18%  Similarity=0.018  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +.+++.||+|+|||...
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46999999999999863

>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=96.17  E-value=0.015  Score=41.05  Aligned_cols=17  Identities=29%  Similarity=0.309  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        46 ~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            46999999999998764

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

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: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.96  E-value=0.0046  Score=44.04  Aligned_cols=65  Identities=12%  Similarity=0.113  Sum_probs=39.9

Q ss_pred             cEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHc----CC-----CCcccccceEE
Q 031654           68 DLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLER----GR-----VSLQMIIRYLA  138 (155)
Q Consensus        68 dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~----~~-----~~l~~l~~~lV  138 (155)
                      .+++.||+|+|||.-. -++.+.+             ...+..++..+...+.+.+..    +.     -.+..+ .+|+
T Consensus        38 ~l~l~G~~G~GKTHLl-~A~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-dll~  102 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLL-QAAGNEA-------------KKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSV-DLLL  102 (213)
T ss_dssp             SEEEECSSSSSHHHHH-HHHHHHH-------------HHTTCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHHTC-SEEE
T ss_pred             cEEEECCCCCcHHHHH-HHHHHHh-------------ccCccceEEechHHHHHHHHHHHHccchhhHHHHHhhc-cchh
Confidence            4899999999999521 1222222             123456666666555443322    11     125678 9999


Q ss_pred             EEcccccccc
Q 031654          139 LKEAADQTLD  148 (155)
Q Consensus       139 lDEa~D~ll~  148 (155)
                      ||++ |.+..
T Consensus       103 iDDi-~~i~~  111 (213)
T d1l8qa2         103 LDDV-QFLSG  111 (213)
T ss_dssp             EECG-GGGTT
T ss_pred             hhhh-hhhcC
Confidence            9999 88754

>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=95.84  E-value=0.0041  Score=45.99  Aligned_cols=39  Identities=23%  Similarity=0.169  Sum_probs=29.7

Q ss_pred             CCCHHHHHHHHHHhcCCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           51 KPTPVQRHATSILVAGRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        51 ~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      .+++-|.+++..  .+..++|.|+.|||||.+.+--+...+
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll   49 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLM   49 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHH
Confidence            478999999974  356799999999999997654444333

>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=95.80  E-value=0.0016  Score=46.45  Aligned_cols=17  Identities=24%  Similarity=0.227  Sum_probs=15.2

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        36 ~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            57999999999999964

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.72  E-value=0.0096  Score=41.86  Aligned_cols=79  Identities=10%  Similarity=0.061  Sum_probs=46.4

Q ss_pred             HHHHHHHHh---cCCcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChH-------HHHH---H
Q 031654           56 QRHATSILV---AGRDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLR-------RLVN---L  122 (155)
Q Consensus        56 Q~~~i~~~l---~g~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~-------~l~~---~  122 (155)
                      |.+.+..+.   .+..+++.+|.|+|||.....-. ..+.          ..-...+|++.-.|+       .+.+   .
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~-~~i~----------~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~   70 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELP-EYVE----------KFPPKASDVLEIDPEGENIGIDDIRTIKDF   70 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHH-HHHH----------TSCCCTTTEEEECCSSSCBCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH-HHHh----------ccccCCCCEEEEeCCcCCCCHHHHHHHHHH
Confidence            344444443   34689999999999998653221 2111          111234788888773       2222   2


Q ss_pred             HHcCCCCcccccceEEEEcccccccc
Q 031654          123 LERGRVSLQMIIRYLALKEAADQTLD  148 (155)
Q Consensus       123 l~~~~~~l~~l~~~lVlDEa~D~ll~  148 (155)
                      +.... ....- +.+|+||| |+|=.
T Consensus        71 ~~~~~-~~~~~-KviIId~a-d~l~~   93 (198)
T d2gnoa2          71 LNYSP-ELYTR-KYVIVHDC-ERMTQ   93 (198)
T ss_dssp             HTSCC-SSSSS-EEEEETTG-GGBCH
T ss_pred             HhhCc-ccCCC-EEEEEeCc-cccch
Confidence            22222 23566 89999999 99854

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {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 C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.71  E-value=0.0072  Score=42.66  Aligned_cols=16  Identities=25%  Similarity=0.358  Sum_probs=14.4

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      ++++.||+|+|||.+.
T Consensus        38 ~~ll~Gp~G~GKTt~a   53 (224)
T d1sxjb2          38 HMIISGMPGIGKTTSV   53 (224)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECCCCCCchhhH
Confidence            6999999999999864

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=95.67  E-value=0.0051  Score=44.85  Aligned_cols=47  Identities=13%  Similarity=0.196  Sum_probs=27.5

Q ss_pred             cccccCC--HHHHHhHHhC-C-CCCCCHHHHHHHHHH--hcCCcEEEEccCCCCcchh
Q 031654           31 ARFAYVP--QHLRNKPRTY-K-YVKPTPVQRHATSIL--VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~-g-~~~pt~iQ~~~i~~~--l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+|+++.  ++..+.|++. . +..|     ..+...  ...+.+++.||+|||||+.
T Consensus         6 ~~~~di~G~~~~k~~l~~~i~~l~~~-----~~~~~~g~~~~~giLl~GppGtGKT~l   58 (247)
T d1ixza_           6 VTFKDVAGAEEAKEELKEIVEFLKNP-----SRFHEMGARIPKGVLLVGPPGVGKTHL   58 (247)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCH-----HHHHHTTCCCCSEEEEECCTTSSHHHH
T ss_pred             CcHHHHccHHHHHHHHHHHHHHHHCH-----HHHHHcCCCCCceEEEecCCCCChhHH
Confidence            5899986  6666655431 0 1111     111111  1125699999999999985

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=95.56  E-value=0.0019  Score=47.50  Aligned_cols=49  Identities=16%  Similarity=0.174  Sum_probs=26.8

Q ss_pred             cccccCC--HHHHHhHHhC--CCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchh
Q 031654           31 ARFAYVP--QHLRNKPRTY--KYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        31 ~~f~~l~--~~l~~~l~~~--g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      .+|+|+.  +...+.|.+.  -+..|...|..   .+-..+.+++.+|+|||||+.
T Consensus         9 ~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~---g~~~~~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_           9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHH
T ss_pred             CCHHHHhchHHHHHHHHHHHHHHHCHHHHHHc---CCCCCCeEEeeCCCCCCccHH
Confidence            4788887  5555444321  01122112211   111236799999999999985

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

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-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=95.40  E-value=0.0025  Score=45.78  Aligned_cols=15  Identities=27%  Similarity=0.133  Sum_probs=12.3

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      ++++||+|+|||...
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            456799999999874

>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=95.13  E-value=0.017  Score=40.54  Aligned_cols=16  Identities=25%  Similarity=0.422  Sum_probs=13.9

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      ++++.||+|+|||...
T Consensus        37 ~lLl~Gp~G~GKttl~   52 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTI   52 (227)
T ss_dssp             CEEEECSSSSSHHHHH
T ss_pred             eEEEECCCCCChhHHH
Confidence            6999999999999643

>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=94.95  E-value=0.0048  Score=46.87  Aligned_cols=29  Identities=31%  Similarity=0.426  Sum_probs=21.4

Q ss_pred             HHHHHHHH-HHhcCCcEEEEccCCCCcchh
Q 031654           54 PVQRHATS-ILVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        54 ~iQ~~~i~-~~l~g~dvl~~a~TGsGKT~~   82 (155)
                      +-+...+. .+..+++++++++||||||..
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~  182 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTY  182 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHH
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHH
Confidence            33444443 446779999999999999985

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=94.94  E-value=0.03  Score=39.70  Aligned_cols=19  Identities=32%  Similarity=0.475  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCCcchhhh
Q 031654           66 GRDLMACAQTGSRKTTPFC   84 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yl   84 (155)
                      ++=+++++|||+|||.+-.
T Consensus         6 ~~vi~lvGptGvGKTTTia   24 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIA   24 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            3457789999999998843

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {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: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.66  E-value=0.0099  Score=39.57  Aligned_cols=26  Identities=19%  Similarity=0.212  Sum_probs=19.5

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHH
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMR   93 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~   93 (155)
                      |+|++.+|+|||||. .+--++..+..
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHH
Confidence            789999999999998 33445555544

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=94.55  E-value=0.036  Score=39.46  Aligned_cols=16  Identities=31%  Similarity=0.410  Sum_probs=13.3

Q ss_pred             EEEEccCCCCcchhhh
Q 031654           69 LMACAQTGSRKTTPFC   84 (155)
Q Consensus        69 vl~~a~TGsGKT~~yl   84 (155)
                      ++.++|||+|||.+-.
T Consensus        14 i~lvGptGvGKTTTiA   29 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCG   29 (213)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5678999999998743

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=94.32  E-value=0.063  Score=38.09  Aligned_cols=16  Identities=25%  Similarity=0.341  Sum_probs=13.2

Q ss_pred             EEEEccCCCCcchhhh
Q 031654           69 LMACAQTGSRKTTPFC   84 (155)
Q Consensus        69 vl~~a~TGsGKT~~yl   84 (155)
                      +++++|||+|||.+-.
T Consensus        12 i~lvGptGvGKTTTiA   27 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIG   27 (211)
T ss_dssp             EEEECCTTSCHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5679999999998743

>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=94.26  E-value=0.0067  Score=48.00  Aligned_cols=17  Identities=24%  Similarity=0.345  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      .+|+++.+|||||||+-
T Consensus        49 ksNILliGPTGvGKTlL   65 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCCEEEECCTTSSHHHH
T ss_pred             cccEEEECCCCCCHHHH
Confidence            46999999999999985

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {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: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=93.77  E-value=0.047  Score=38.35  Aligned_cols=74  Identities=16%  Similarity=0.127  Sum_probs=41.0

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHH------cC---CC-Cc----cc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLE------RG---RV-SL----QM  132 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~------~~---~~-~l----~~  132 (155)
                      .|+++++++|.|||..-- -+..++...      +...-..+.+|+-..+++|+.-..      .+   .+ .+    .+
T Consensus        44 ~n~lLvG~pGVGKTalv~-~LA~ri~~~------~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~  116 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVE-GLAQRIING------EVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGN  116 (195)
T ss_dssp             CEEEEECCTTSCHHHHHH-HHHHHHHHT------CSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTT
T ss_pred             CCeEEEecCCcccHHHHH-HHHHHHHhC------CCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCc
Confidence            599999999999997521 112222211      111122346788888777653111      10   00 11    12


Q ss_pred             ccceEEEEcccccccccc
Q 031654          133 IIRYLALKEAADQTLDMA  150 (155)
Q Consensus       133 l~~~lVlDEa~D~ll~~g  150 (155)
                      +  .|++||+ +.++..|
T Consensus       117 i--ILfIDei-h~l~~~g  131 (195)
T d1jbka_         117 V--ILFIDEL-HTMVGAG  131 (195)
T ss_dssp             E--EEEEETG-GGGTT--
T ss_pred             E--EEEcchH-HHHhcCC
Confidence            3  7899999 9998764

>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=93.51  E-value=0.048  Score=40.56  Aligned_cols=19  Identities=21%  Similarity=0.279  Sum_probs=16.5

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      ..+.++.++|||+|||...
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3589999999999999854

>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=93.10  E-value=0.023  Score=40.24  Aligned_cols=17  Identities=18%  Similarity=0.223  Sum_probs=15.1

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        44 ~~lll~GppGtGKT~l~   60 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL   60 (276)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CceEEECCCCCCHHHHH
Confidence            68999999999999763

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=92.83  E-value=0.018  Score=37.37  Aligned_cols=18  Identities=22%  Similarity=0.276  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      .+++++.|++|||||...
T Consensus         2 ~k~I~l~G~~GsGKSTva   19 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIG   19 (169)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            468999999999999753

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=92.34  E-value=0.016  Score=38.48  Aligned_cols=19  Identities=32%  Similarity=0.445  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      +.|+-+++.+++|||||..
T Consensus         2 ~~g~iI~l~G~~GsGKSTi   20 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKSTI   20 (176)
T ss_dssp             CTTEEEEEEECTTSCHHHH
T ss_pred             CCCeEEEEECCCCCCHHHH
Confidence            4677789999999999985

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=92.31  E-value=0.023  Score=37.62  Aligned_cols=17  Identities=24%  Similarity=0.456  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      +.++++.|++|||||..
T Consensus         5 ~~~I~i~G~~GsGKTT~   21 (174)
T d1y63a_           5 GINILITGTPGTGKTSM   21 (174)
T ss_dssp             SCEEEEECSTTSSHHHH
T ss_pred             CCEEEEEeCCCCCHHHH
Confidence            56799999999999985

>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=92.18  E-value=0.024  Score=40.09  Aligned_cols=17  Identities=29%  Similarity=0.259  Sum_probs=15.1

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        36 ~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            58999999999999864

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {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: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=92.18  E-value=0.022  Score=37.10  Aligned_cols=14  Identities=29%  Similarity=0.318  Sum_probs=12.4

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      ++++|++|||||..
T Consensus         5 Iii~G~pGsGKTTl   18 (152)
T d1ly1a_           5 ILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEECCTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67899999999884

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {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: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=92.16  E-value=0.049  Score=40.06  Aligned_cols=74  Identities=14%  Similarity=0.067  Sum_probs=38.6

Q ss_pred             CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHH--------------HHHcCCCCccc
Q 031654           67 RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVN--------------LLERGRVSLQM  132 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~--------------~l~~~~~~l~~  132 (155)
                      .|++++|++|.|||..-- -+..++....      ......+.+|+.-.+++|+.              ++..- ....+
T Consensus        40 ~n~lLVG~~GvGKTalv~-~la~ri~~~~------vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~-~~~~~  111 (268)
T d1r6bx2          40 NNPLLVGESGVGKTAIAE-GLAWRIVQGD------VPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQL-EQDTN  111 (268)
T ss_dssp             CEEEEECCTTSSHHHHHH-HHHHHHHHTC------SCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHH-SSSSC
T ss_pred             CCcEEECCCCCcHHHHHH-HHHHHHHhCC------cccccccceeEEeeechHhccCccchhHHHHHHHHHHHh-hccCC
Confidence            689999999999997521 1222222211      11112234555555544432              22110 01223


Q ss_pred             ccceEEEEccccccccccc
Q 031654          133 IIRYLALKEAADQTLDMAL  151 (155)
Q Consensus       133 l~~~lVlDEa~D~ll~~gf  151 (155)
                      +  .+++||+ |.|+..|-
T Consensus       112 i--IlfiDei-h~l~~~g~  127 (268)
T d1r6bx2         112 S--ILFIDEI-HTIIGAGA  127 (268)
T ss_dssp             E--EEEETTT-TTTTTSCC
T ss_pred             c--eEEecch-HHHhcCCC
Confidence            3  7889999 99987653

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {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: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=92.02  E-value=0.015  Score=38.58  Aligned_cols=16  Identities=13%  Similarity=0.104  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.|++.|++|||||..
T Consensus         8 K~I~i~G~~GsGKTTl   23 (192)
T d1lw7a2           8 KTVAILGGESSGKSVL   23 (192)
T ss_dssp             EEEEEECCTTSHHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            6799999999999975

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=91.69  E-value=0.028  Score=37.07  Aligned_cols=16  Identities=25%  Similarity=0.341  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      .+++++|++|||||..
T Consensus         5 ~~I~i~G~pGsGKTTi   20 (173)
T d1rkba_           5 PNILLTGTPGVGKTTL   20 (173)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4789999999999974

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=91.24  E-value=0.033  Score=36.51  Aligned_cols=15  Identities=20%  Similarity=0.224  Sum_probs=13.2

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      =+++.|++|||||..
T Consensus         4 lI~i~G~~GsGKTTv   18 (176)
T d2bdta1           4 LYIITGPAGVGKSTT   18 (176)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            378899999999985

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=91.21  E-value=0.079  Score=37.34  Aligned_cols=18  Identities=33%  Similarity=0.368  Sum_probs=13.7

Q ss_pred             Cc-EEEEccCCCCcchhhh
Q 031654           67 RD-LMACAQTGSRKTTPFC   84 (155)
Q Consensus        67 ~d-vl~~a~TGsGKT~~yl   84 (155)
                      ++ +++++|||+|||.+-.
T Consensus        10 ~~vi~lvGp~GvGKTTTia   28 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAA   28 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            45 4568999999987743

>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=91.02  E-value=0.067  Score=39.97  Aligned_cols=25  Identities=28%  Similarity=0.359  Sum_probs=20.3

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..+++|.|  +++.|+||||||...
T Consensus        67 lv~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          67 IVKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHcCCCcceeeecccCCCCceec
Confidence            3566789975  788899999999874

>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=90.94  E-value=0.11  Score=39.62  Aligned_cols=17  Identities=29%  Similarity=0.307  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .+++.++|||+|||...
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            68999999999999753

>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=90.79  E-value=0.053  Score=41.49  Aligned_cols=28  Identities=18%  Similarity=0.205  Sum_probs=20.5

Q ss_pred             hcCCcEEEEccCCCCcchhhhhHHHHHHH
Q 031654           64 VAGRDLMACAQTGSRKTTPFCFPIINGIM   92 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~yllp~l~~l~   92 (155)
                      ...+++++.|+||||||.+. ..++..+.
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l-~~li~~~~   75 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLL-RELAYTGL   75 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHH
T ss_pred             cccceEEEEeCCCCcHHHHH-HHHHHHHH
Confidence            44579999999999999764 44444444

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=90.59  E-value=0.043  Score=38.95  Aligned_cols=15  Identities=33%  Similarity=0.386  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      .+++.||+|||||..
T Consensus        34 ~ilL~GpPGtGKT~l   48 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSL   48 (273)
T ss_dssp             EEEEECCTTSCTHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            599999999999985

>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=90.52  E-value=0.04  Score=38.96  Aligned_cols=17  Identities=35%  Similarity=0.319  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +.+++.||+|+|||.+.
T Consensus        53 ~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            47999999999999764

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=90.43  E-value=0.11  Score=39.99  Aligned_cols=82  Identities=15%  Similarity=0.164  Sum_probs=35.0

Q ss_pred             HHHHHh-cC-CcEEEEccCCCCcchhhhhHHHHHHHHhhhchHHHHHHHhcCCcEEEEChHHHHHHHHc-CCC-------
Q 031654           59 ATSILV-AG-RDLMACAQTGSRKTTPFCFPIINGIMREYYSARKELRELARWVDNLMATLRRLVNLLER-GRV-------  128 (155)
Q Consensus        59 ~i~~~l-~g-~dvl~~a~TGsGKT~~yllp~l~~l~~~~~~~~~~~~~l~~~~~IlI~TP~~l~~~l~~-~~~-------  128 (155)
                      .+..+. ++ .|++++|++|.|||...- -+..++...      +......+.+|+-..+++|+.-... +.+       
T Consensus        34 ~~~~L~r~~k~n~llvG~~GvGKtaiv~-~la~~i~~~------~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i  106 (387)
T d1qvra2          34 VIQILLRRTKNNPVLIGEPGVGKTAIVE-GLAQRIVKG------DVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAV  106 (387)
T ss_dssp             HHHHHHCSSCCCCEEEECTTSCHHHHHH-HHHHHHHHT------CSCTTSTTCEEEEECC-----------CHHHHHHHH
T ss_pred             HHHHHhcCCCCCCeEECCCCCCHHHHHH-HHHHHHHhC------CCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHH
Confidence            444444 23 689999999999997521 122222221      1111122456777777776554332 111       


Q ss_pred             --Cc---c-cccceEEEEcccccccccc
Q 031654          129 --SL---Q-MIIRYLALKEAADQTLDMA  150 (155)
Q Consensus       129 --~l---~-~l~~~lVlDEa~D~ll~~g  150 (155)
                        .+   . ++  .|++||+ |.|+..|
T Consensus       107 ~~~~~~~~~~~--ilfide~-h~l~~~g  131 (387)
T d1qvra2         107 IQEVVQSQGEV--ILFIDEL-HTVVGAG  131 (387)
T ss_dssp             HHHHHTTCSSE--EEEECCC--------
T ss_pred             HHHhccCCCce--EEEeccH-HHHhcCC
Confidence              01   1 22  6899999 9998764

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=90.37  E-value=0.048  Score=36.39  Aligned_cols=16  Identities=25%  Similarity=0.333  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +++++.+++|+|||..
T Consensus         1 k~I~liG~~GsGKsTi   16 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTL   16 (161)
T ss_dssp             CCEEEECCTTSCHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            5899999999999965

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=89.50  E-value=0.029  Score=37.07  Aligned_cols=20  Identities=15%  Similarity=0.079  Sum_probs=16.9

Q ss_pred             hcCCcEEEEccCCCCcchhh
Q 031654           64 VAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~y   83 (155)
                      .+|.-|+++|++|||||...
T Consensus         4 ~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            46778999999999999754

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

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: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=89.49  E-value=0.064  Score=39.92  Aligned_cols=18  Identities=17%  Similarity=0.276  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .|.++++.+++|+|||+.
T Consensus        27 ~~h~vLl~G~pG~GKT~l   44 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTA   44 (333)
T ss_dssp             GGCCEEEECCGGGCTTHH
T ss_pred             CCCeEEEECCCCccHHHH
Confidence            457999999999999975

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

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: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=89.19  E-value=0.12  Score=39.05  Aligned_cols=25  Identities=24%  Similarity=0.336  Sum_probs=20.0

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..+++|.|  +++.++||||||...
T Consensus        78 lv~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          78 MLQHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHhccCceeeeeccCCCCCceee
Confidence            3456689965  788899999999875

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

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: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=89.13  E-value=0.11  Score=39.54  Aligned_cols=24  Identities=33%  Similarity=0.434  Sum_probs=18.8

Q ss_pred             HHHHhcCCc--EEEEccCCCCcchhh
Q 031654           60 TSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        60 i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      +..++.|.|  +++.++||||||...
T Consensus       106 v~~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         106 VQTIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhccCceEEeeccCCCCCceee
Confidence            456688976  667799999999764

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {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 C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.11  E-value=0.063  Score=37.43  Aligned_cols=17  Identities=18%  Similarity=0.356  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      .++++.||+|+|||...
T Consensus        34 ~~lll~Gp~G~GKTtl~   50 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTSTI   50 (237)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCChHHHH
Confidence            35999999999998753

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=89.10  E-value=0.065  Score=37.97  Aligned_cols=15  Identities=27%  Similarity=0.359  Sum_probs=8.9

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      ++.++|||+|||.+-
T Consensus        15 i~lvGptGvGKTTTi   29 (211)
T d1j8yf2          15 IMLVGVQGTGKATTA   29 (211)
T ss_dssp             EEEECSCCC----HH
T ss_pred             EEEECCCCCCHHHHH
Confidence            566899999999874

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

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: Neurospora crassa [TaxId: 5141]

Probab=89.09  E-value=0.11  Score=39.23  Aligned_cols=25  Identities=24%  Similarity=0.412  Sum_probs=19.7

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.|+||||||...
T Consensus        71 lv~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          71 TVDDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhhccCceeEEecccCCCCcceee
Confidence            4556689976  778899999999663

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

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 heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=88.95  E-value=0.1  Score=39.75  Aligned_cols=25  Identities=36%  Similarity=0.408  Sum_probs=20.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.|+||||||.+.
T Consensus        66 lv~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          66 LVQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcCCceeeeccccCCCCccccc
Confidence            3677789976  677899999999874

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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 motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=88.82  E-value=0.1  Score=39.73  Aligned_cols=25  Identities=32%  Similarity=0.391  Sum_probs=20.5

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus       116 lv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         116 LIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcccceeEEeeccCCCccceEe
Confidence            5677889976  788899999999774

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=88.72  E-value=0.072  Score=34.93  Aligned_cols=18  Identities=11%  Similarity=0.113  Sum_probs=14.8

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      +.+=|+++|++|||||..
T Consensus         2 ~~kiI~l~G~~GsGKsTv   19 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGI   19 (178)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            456688899999999965

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

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: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=88.63  E-value=0.068  Score=35.43  Aligned_cols=15  Identities=27%  Similarity=0.386  Sum_probs=13.1

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      .+++.+|+|+|||.-
T Consensus         2 ki~I~G~~G~GKSTL   16 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL   16 (178)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCcHHHHH
Confidence            378999999999983

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [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), mitotic kinesin eg5 [TaxId: 9606]

Probab=88.43  E-value=0.13  Score=38.67  Aligned_cols=24  Identities=29%  Similarity=0.412  Sum_probs=19.4

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTP   82 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~   82 (155)
                      .+..++.|.|  +++.++||||||..
T Consensus        72 lv~~~l~G~n~~i~aYGqtgSGKTyT   97 (345)
T d1x88a1          72 ILDEVIMGYNCTIFAYGQTGTGKTFT   97 (345)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHH
T ss_pred             hHHHHhccCCceEEeeeeccccceEE
Confidence            4567789976  67889999999965

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.34  E-value=0.079  Score=36.09  Aligned_cols=16  Identities=25%  Similarity=0.449  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      |-|+++||+|+|||..
T Consensus         2 rpIvl~GpsG~GK~tl   17 (186)
T d1gkya_           2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5689999999999983

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {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: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=88.22  E-value=0.075  Score=34.92  Aligned_cols=15  Identities=20%  Similarity=0.202  Sum_probs=13.0

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      +++.|++|||||...
T Consensus         9 ivl~G~~GsGKsT~a   23 (171)
T d1knqa_           9 YVLMGVSGSGKSAVA   23 (171)
T ss_dssp             EEEECSTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999864

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=88.05  E-value=0.089  Score=35.61  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      |-.+++.+|+|||||..
T Consensus         3 ~~riil~G~pGSGKsT~   19 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQ   19 (190)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             ccEEEEECCCCCCHHHH
Confidence            56788999999999975

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {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 C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.68  E-value=0.089  Score=36.94  Aligned_cols=40  Identities=18%  Similarity=0.218  Sum_probs=26.9

Q ss_pred             ccccCC--HHHHHhHHhCCCCCCCHHHHHHHHHHhcCCcEEEEccCCCCcchhh
Q 031654           32 RFAYVP--QHLRNKPRTYKYVKPTPVQRHATSILVAGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        32 ~f~~l~--~~l~~~l~~~g~~~pt~iQ~~~i~~~l~g~dvl~~a~TGsGKT~~y   83 (155)
                      +|+++-  +.+.+.|+.+- ...           ....++++.||+|+|||...
T Consensus         9 ~~~diig~~~~~~~L~~~~-~~~-----------~~~~~lll~Gp~G~GKTt~~   50 (252)
T d1sxje2           9 SLNALSHNEELTNFLKSLS-DQP-----------RDLPHLLLYGPNGTGKKTRC   50 (252)
T ss_dssp             SGGGCCSCHHHHHHHHTTT-TCT-----------TCCCCEEEECSTTSSHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHH-HcC-----------CCCCeEEEECCCCCCHHHHH
Confidence            577765  77777776541 110           01236999999999999864

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.56  E-value=0.087  Score=35.64  Aligned_cols=15  Identities=27%  Similarity=0.246  Sum_probs=12.9

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      =++++|++|||||..
T Consensus        16 liil~G~pGsGKST~   30 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTF   30 (172)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999974

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=86.70  E-value=0.1  Score=34.80  Aligned_cols=16  Identities=25%  Similarity=0.283  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCcchhh
Q 031654           68 DLMACAQTGSRKTTPF   83 (155)
Q Consensus        68 dvl~~a~TGsGKT~~y   83 (155)
                      .+++.||+|||||...
T Consensus         2 ~I~i~G~pGSGKsT~a   17 (182)
T d1zina1           2 NLVLMGLPGAGKGTQA   17 (182)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4889999999998753

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=86.69  E-value=0.1  Score=35.30  Aligned_cols=15  Identities=27%  Similarity=0.277  Sum_probs=13.0

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      .+++.||+|||||..
T Consensus         5 ~I~i~GppGsGKsT~   19 (189)
T d1zaka1           5 KVMISGAPASGKGTQ   19 (189)
T ss_dssp             CEEEEESTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            588999999999764

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.55  E-value=0.1  Score=34.98  Aligned_cols=15  Identities=20%  Similarity=0.293  Sum_probs=13.3

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      ++++.||+|||||..
T Consensus         2 ~I~i~G~pGsGKsT~   16 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQ   16 (181)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            578999999999975

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.46  E-value=0.12  Score=35.37  Aligned_cols=16  Identities=25%  Similarity=0.412  Sum_probs=13.8

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      |-++++||+|||||..
T Consensus         1 rpIvl~GPsGsGK~tl   16 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTL   16 (190)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4589999999999984

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

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: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.21  E-value=0.12  Score=37.29  Aligned_cols=16  Identities=25%  Similarity=0.376  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.+++.+|+|||||+.
T Consensus        39 ~giLL~GppGtGKT~l   54 (258)
T d1e32a2          39 RGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             ceeEEecCCCCCchHH
Confidence            6799999999999974

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=86.19  E-value=0.22  Score=32.70  Aligned_cols=75  Identities=9%  Similarity=0.114  Sum_probs=41.3

Q ss_pred             EEEEccCCCCcchhhhhHHHHHHHHhhhch--------HHHHHHHh-----cCCcEEEEChHHHHHHHHcCCCCcccccc
Q 031654           69 LMACAQTGSRKTTPFCFPIINGIMREYYSA--------RKELRELA-----RWVDNLMATLRRLVNLLERGRVSLQMIIR  135 (155)
Q Consensus        69 vl~~a~TGsGKT~~yllp~l~~l~~~~~~~--------~~~~~~l~-----~~~~IlI~TP~~l~~~l~~~~~~l~~l~~  135 (155)
                      -++.+|-.||||.-. +-.+.+........        .+....+.     .-..+.+.+...+.+.+..... ..+. +
T Consensus         5 ~~i~GpMfsGKTteL-i~~~~~~~~~~~kv~~ikp~~D~R~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~-~~~~-d   81 (139)
T d2b8ta1           5 EFITGPMFAGKTAEL-IRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSF-NDET-K   81 (139)
T ss_dssp             EEEECSTTSCHHHHH-HHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTS-CTTC-C
T ss_pred             EEEEccccCHHHHHH-HHHHHHHHHCCCcEEEEEEcccccccceEEcccCceeeeEEeccchhhHHHHHhhcc-ccCc-C
Confidence            467899999999854 33344433222222        11000010     1234556666666666654432 3577 8


Q ss_pred             eEEEEcccccccc
Q 031654          136 YLALKEAADQTLD  148 (155)
Q Consensus       136 ~lVlDEa~D~ll~  148 (155)
                      ++.+|||  ++++
T Consensus        82 vI~IDE~--QFf~   92 (139)
T d2b8ta1          82 VIGIDEV--QFFD   92 (139)
T ss_dssp             EEEECSG--GGSC
T ss_pred             EEEechh--hhcc
Confidence            9999999  5553

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=86.01  E-value=0.13  Score=35.86  Aligned_cols=19  Identities=21%  Similarity=0.356  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      +|+=++++||+|+|||...
T Consensus         1 ~G~livi~GPSG~GK~tl~   19 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLI   19 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4677899999999999853

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

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: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=86.00  E-value=0.21  Score=37.99  Aligned_cols=36  Identities=22%  Similarity=0.013  Sum_probs=24.4

Q ss_pred             CCCCCCHHHHHHHHHHhcC----CcEEEEccCCCCcchhh
Q 031654           48 KYVKPTPVQRHATSILVAG----RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        48 g~~~pt~iQ~~~i~~~l~g----~dvl~~a~TGsGKT~~y   83 (155)
                      ++......-..++..++.|    +.+++.||+|+|||+..
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~  171 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLA  171 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHH
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHH
Confidence            4554444444455555655    57999999999999853

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=85.96  E-value=0.12  Score=34.02  Aligned_cols=16  Identities=19%  Similarity=0.252  Sum_probs=13.5

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +=|++.|++|||||..
T Consensus         2 kiI~i~G~~GsGKsT~   17 (190)
T d1khta_           2 KVVVVTGVPGVGSTTS   17 (190)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4478899999999875

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=85.93  E-value=0.13  Score=34.59  Aligned_cols=17  Identities=24%  Similarity=0.323  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      |+=++++||+|+|||..
T Consensus         2 G~iivl~GpsG~GK~tl   18 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTV   18 (182)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            66789999999999984

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal 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: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.82  E-value=0.47  Score=30.69  Aligned_cols=25  Identities=16%  Similarity=0.064  Sum_probs=16.5

Q ss_pred             CCcEEEEccCCCCcchhhhhHHHHHH
Q 031654           66 GRDLMACAQTGSRKTTPFCFPIINGI   91 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~yllp~l~~l   91 (155)
                      |.=-++++|-.||||.- |+-.+.+.
T Consensus         2 G~L~li~GpMfsGKTt~-Li~~~~~~   26 (133)
T d1xbta1           2 GQIQVILGPMFSGKSTE-LMRRVRRF   26 (133)
T ss_dssp             CEEEEEECCTTSCHHHH-HHHHHHHH
T ss_pred             cEEEEEEecccCHHHHH-HHHHHHHH
Confidence            33357889999999984 44444433

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=85.78  E-value=0.12  Score=34.61  Aligned_cols=15  Identities=13%  Similarity=0.089  Sum_probs=13.2

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      .+++.+|+|||||..
T Consensus         2 ~I~i~G~pGSGKsT~   16 (179)
T d1e4va1           2 RIILLGAPVAGKGTQ   16 (179)
T ss_dssp             EEEEEESTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999985

>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=85.66  E-value=0.15  Score=34.01  Aligned_cols=17  Identities=18%  Similarity=0.010  Sum_probs=14.6

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      |+=+++.+|+|||||..
T Consensus        23 G~v~~i~G~~GsGKT~l   39 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQI   39 (242)
T ss_dssp             TSEEEEECCTTSSHHHH
T ss_pred             CEEEEEEeCCCCCHHHH
Confidence            46789999999999964

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=85.64  E-value=0.13  Score=33.55  Aligned_cols=14  Identities=43%  Similarity=0.375  Sum_probs=12.1

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      +.++++.|||||.-
T Consensus         5 i~itG~~GSGKTTL   18 (170)
T d1np6a_           5 LAFAAWSGTGKTTL   18 (170)
T ss_dssp             EEEECCTTSCHHHH
T ss_pred             EEEEcCCCCCHHHH
Confidence            67899999999983

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=85.56  E-value=0.13  Score=34.86  Aligned_cols=15  Identities=27%  Similarity=0.244  Sum_probs=12.8

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      -+++.||+|||||..
T Consensus         8 iI~i~G~pGSGKsT~   22 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQ   22 (194)
T ss_dssp             EEEEEESTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            368899999999974

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {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: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.30  E-value=0.13  Score=34.84  Aligned_cols=14  Identities=21%  Similarity=0.328  Sum_probs=12.1

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      +++.||+|||||..
T Consensus        11 I~i~GppGSGKsT~   24 (196)
T d1ukza_          11 IFVLGGPGAGKGTQ   24 (196)
T ss_dssp             EEEECSTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            78889999999764

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=85.00  E-value=0.14  Score=34.33  Aligned_cols=15  Identities=20%  Similarity=0.326  Sum_probs=13.1

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      .+++.+|+|||||..
T Consensus         2 ~I~i~G~pGSGKsT~   16 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQ   16 (182)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            378999999999975

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

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 motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=84.82  E-value=0.17  Score=37.96  Aligned_cols=25  Identities=32%  Similarity=0.383  Sum_probs=19.9

Q ss_pred             HHHHHhcCCc--EEEEccCCCCcchhh
Q 031654           59 ATSILVAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        59 ~i~~~l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+..++.|.|  +++.++||||||...
T Consensus        74 ~v~~~l~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          74 LVQSSLDGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             hhcchhcccccceeeeeccCCcccccc
Confidence            4566688975  677899999999775

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=84.65  E-value=0.19  Score=34.10  Aligned_cols=20  Identities=25%  Similarity=0.293  Sum_probs=16.5

Q ss_pred             HhcCCcEEEEccCCCCcchh
Q 031654           63 LVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~   82 (155)
                      +..++-+++.||+||||+..
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~   24 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQ   24 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHH
Confidence            45567789999999999974

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {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: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=84.62  E-value=0.45  Score=32.99  Aligned_cols=18  Identities=6%  Similarity=-0.051  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCCCcchh
Q 031654           65 AGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~   82 (155)
                      .++.+++.||.|+|||..
T Consensus        28 ~~~~i~i~G~~G~GKTsL   45 (283)
T d2fnaa2          28 RAPITLVLGLRRTGKSSI   45 (283)
T ss_dssp             CSSEEEEEESTTSSHHHH
T ss_pred             cCCEEEEEcCCCCcHHHH
Confidence            346799999999999974

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {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: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.59  E-value=0.065  Score=35.99  Aligned_cols=18  Identities=28%  Similarity=0.265  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCCCcchhh
Q 031654           66 GRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~y   83 (155)
                      |.-++++|++|||||...
T Consensus        19 g~vI~L~G~pGSGKTTiA   36 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVS   36 (195)
T ss_dssp             CEEEEEESSCHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456778999999999853

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=84.53  E-value=0.17  Score=33.55  Aligned_cols=16  Identities=19%  Similarity=0.231  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +.+++.|++|||||..
T Consensus         3 ~~Iil~G~~GsGKSTi   18 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTV   18 (170)
T ss_dssp             CCEEEESCTTSSHHHH
T ss_pred             CCEEEECCCCCCHHHH
Confidence            5788999999999875

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.36  E-value=0.18  Score=34.66  Aligned_cols=17  Identities=12%  Similarity=-0.013  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      |+-+++.+++|||||..
T Consensus        34 G~~~li~G~pGsGKT~l   50 (251)
T d1szpa2          34 GSITELFGEFRTGKSQL   50 (251)
T ss_dssp             SSEEEEEESTTSSHHHH
T ss_pred             CeEEEEEcCCCCCHHHH
Confidence            46799999999999974

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.11  E-value=0.16  Score=34.02  Aligned_cols=15  Identities=20%  Similarity=0.297  Sum_probs=13.1

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      -+++.||+|||||..
T Consensus         4 rIvl~G~pGSGKtT~   18 (180)
T d1akya1           4 RMVLIGPPGAGKGTQ   18 (180)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999975

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

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: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.57  E-value=0.17  Score=36.61  Aligned_cols=17  Identities=18%  Similarity=0.260  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCcchh
Q 031654           66 GRDLMACAQTGSRKTTP   82 (155)
Q Consensus        66 g~dvl~~a~TGsGKT~~   82 (155)
                      .+.+++.||+|||||..
T Consensus        41 ~~giLL~Gp~GtGKT~l   57 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLL   57 (265)
T ss_dssp             CCEEEEBCCTTSSHHHH
T ss_pred             CCeEEEECCCCCcchhH
Confidence            36799999999999985

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {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: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.54  E-value=0.18  Score=34.00  Aligned_cols=14  Identities=21%  Similarity=0.304  Sum_probs=12.3

Q ss_pred             EEEEccCCCCcchh
Q 031654           69 LMACAQTGSRKTTP   82 (155)
Q Consensus        69 vl~~a~TGsGKT~~   82 (155)
                      +++.+|+|||||..
T Consensus         4 I~i~GppGSGKsT~   17 (194)
T d1teva_           4 VFVLGGPGAGKGTQ   17 (194)
T ss_dssp             EEEECCTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            68899999999865

>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=83.30  E-value=0.17  Score=35.13  Aligned_cols=17  Identities=24%  Similarity=0.012  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCCcchhh
Q 031654           67 RDLMACAQTGSRKTTPF   83 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~y   83 (155)
                      +=+++.+++|||||.-.
T Consensus        37 ~~~li~G~pGsGKT~~~   53 (254)
T d1pzna2          37 AITEVFGEFGSGKTQLA   53 (254)
T ss_dssp             EEEEEEESTTSSHHHHH
T ss_pred             EEEEEEcCCCCCHHHHH
Confidence            57899999999999854

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=83.12  E-value=0.19  Score=34.27  Aligned_cols=16  Identities=25%  Similarity=0.104  Sum_probs=13.8

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      -.+++.+|+|||||..
T Consensus         7 mrIiliG~PGSGKtT~   22 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTV   22 (189)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             eeEEEECCCCCCHHHH
Confidence            3688999999999875

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {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: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=82.71  E-value=0.76  Score=35.33  Aligned_cols=34  Identities=32%  Similarity=0.371  Sum_probs=21.5

Q ss_pred             CCCCCH--HHHHHHHHH----hcCC-cEEEEccCCCCcchh
Q 031654           49 YVKPTP--VQRHATSIL----VAGR-DLMACAQTGSRKTTP   82 (155)
Q Consensus        49 ~~~pt~--iQ~~~i~~~----l~g~-dvl~~a~TGsGKT~~   82 (155)
                      |..|||  =|-+||..+    -.|. .+.+.+-+||+|++.
T Consensus         4 ~~~~~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~   44 (408)
T d1c4oa1           4 YRGPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVT   44 (408)
T ss_dssp             CCSCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHH
T ss_pred             ccCCCCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHH
Confidence            444444  444456544    4454 578899999999854

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

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: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=82.69  E-value=0.31  Score=36.30  Aligned_cols=20  Identities=40%  Similarity=0.340  Sum_probs=16.1

Q ss_pred             hcCCc--EEEEccCCCCcchhh
Q 031654           64 VAGRD--LMACAQTGSRKTTPF   83 (155)
Q Consensus        64 l~g~d--vl~~a~TGsGKT~~y   83 (155)
                      .+|.|  +++.++||||||.+-
T Consensus        81 ~~G~n~~i~aYGqTGSGKTyTm  102 (330)
T d1ry6a_          81 ENGCVCSCFAYGQTGSGKTYTM  102 (330)
T ss_dssp             HHCCEEEEEEECCTTSSHHHHH
T ss_pred             hcCCCeEEEeeeccccccceee
Confidence            36876  677899999999874

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=82.58  E-value=0.2  Score=32.99  Aligned_cols=15  Identities=20%  Similarity=0.189  Sum_probs=12.4

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      +++.|++|||||...
T Consensus         4 ivi~G~~GsGKTT~~   18 (194)
T d1nksa_           4 GIVTGIPGVGKSTVL   18 (194)
T ss_dssp             EEEEECTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            567899999999753

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=82.57  E-value=0.2  Score=33.29  Aligned_cols=13  Identities=31%  Similarity=-0.023  Sum_probs=11.1

Q ss_pred             EEEccCCCCcchh
Q 031654           70 MACAQTGSRKTTP   82 (155)
Q Consensus        70 l~~a~TGsGKT~~   82 (155)
                      -+.|++|||||..
T Consensus        26 gI~G~~GSGKSTl   38 (198)
T d1rz3a_          26 GIDGLSRSGKTTL   38 (198)
T ss_dssp             EEEECTTSSHHHH
T ss_pred             EEECCCCCCHHHH
Confidence            3789999999974

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

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: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=82.45  E-value=0.41  Score=34.14  Aligned_cols=20  Identities=15%  Similarity=0.160  Sum_probs=16.6

Q ss_pred             HhcCCcEEEEccCCCCcchh
Q 031654           63 LVAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        63 ~l~g~dvl~~a~TGsGKT~~   82 (155)
                      ......|++.|++||||+..
T Consensus        20 a~~~~pvlI~Ge~GtGK~~~   39 (247)
T d1ny5a2          20 SCAECPVLITGESGVGKEVV   39 (247)
T ss_dssp             TTCCSCEEEECSTTSSHHHH
T ss_pred             hCCCCCEEEECCCCcCHHHH
Confidence            34567899999999999864

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.96  E-value=0.25  Score=33.48  Aligned_cols=16  Identities=13%  Similarity=0.206  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCcchh
Q 031654           67 RDLMACAQTGSRKTTP   82 (155)
Q Consensus        67 ~dvl~~a~TGsGKT~~   82 (155)
                      +-++++||+|+||+..
T Consensus         4 k~ivl~Gpsg~GK~tl   19 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHI   19 (178)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            5689999999999985

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=81.80  E-value=0.24  Score=33.42  Aligned_cols=15  Identities=13%  Similarity=0.011  Sum_probs=12.9

Q ss_pred             EEEEccCCCCcchhh
Q 031654           69 LMACAQTGSRKTTPF   83 (155)
Q Consensus        69 vl~~a~TGsGKT~~y   83 (155)
                      ++++|.+|||||..+
T Consensus         5 i~l~GlpgsGKSTla   19 (213)
T d1bifa1           5 IVMVGLPARGKTYIS   19 (213)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678899999999865

>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=81.79  E-value=0.48  Score=32.12  Aligned_cols=19  Identities=26%  Similarity=0.345  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCCCcchhh
Q 031654           65 AGRDLMACAQTGSRKTTPF   83 (155)
Q Consensus        65 ~g~dvl~~a~TGsGKT~~y   83 (155)
                      .|.-+++.|++|+|||.-.
T Consensus        25 ~G~~~~I~G~~G~GKT~la   43 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFS   43 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHH
Confidence            4578999999999999643

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.43  E-value=0.26  Score=32.48  Aligned_cols=15  Identities=27%  Similarity=0.248  Sum_probs=13.2

Q ss_pred             cEEEEccCCCCcchh
Q 031654           68 DLMACAQTGSRKTTP   82 (155)
Q Consensus        68 dvl~~a~TGsGKT~~   82 (155)
                      .+++.|+.|+|||..
T Consensus         3 ~IvliG~~G~GKSTi   17 (165)
T d2iyva1           3 KAVLVGLPGSGKSTI   17 (165)
T ss_dssp             SEEEECSTTSSHHHH
T ss_pred             cEEEECCCCCCHHHH
Confidence            578889999999975

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {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: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=80.80  E-value=0.29  Score=35.11  Aligned_cols=19  Identities=26%  Similarity=0.298  Sum_probs=16.1

Q ss_pred             hcCCcEEEEccCCCCcchh
Q 031654           64 VAGRDLMACAQTGSRKTTP   82 (155)
Q Consensus        64 l~g~dvl~~a~TGsGKT~~   82 (155)
                      -.|.-+.+++++|||||.-
T Consensus        27 ~~Ge~vaIvG~sGsGKSTL   45 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKSTL   45 (241)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3578899999999999963

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {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: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.20  E-value=0.28  Score=33.60  Aligned_cols=13  Identities=23%  Similarity=0.125  Sum_probs=10.8

Q ss_pred             EEEccCCCCcchh
Q 031654           70 MACAQTGSRKTTP   82 (155)
Q Consensus        70 l~~a~TGsGKT~~   82 (155)
                      -+.|++|||||..
T Consensus         6 gI~G~~gSGKSTl   18 (213)
T d1uj2a_           6 GVSGGTASGKSSV   18 (213)
T ss_dssp             EEECSTTSSHHHH
T ss_pred             EEECCCCCCHHHH
Confidence            4679999999964