Psyllid ID: psy7786

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250--
Protein Sequence
MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF
Secondary Structure (PSIPRED)
cccccccccEEEEEccccccHHHHHHHHHHHHHHcccccccccccccEEEEEcccHHHHHHHHHHHHHHHHHccccccEEEEEccccccccHHHHHcccccccccccccccccccccccHHHHHHHHHHcccEEEcccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHHHHcccccccccccccEEEEEcccHHHHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cccEEccccEEEEEccccHHHHHHHHHHHHHHHccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHHcccccEEEEEEccccccHHHHHHHccccccccEcccccccHHHHHccHHHHHHHHHHcEEEEEccccccccccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEEcccHHHHHHHHHHHHHHHccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mvtyrnsrDIIGIaftgsgktLVFVLPILMFCLeqetklpflpgegpygliicpsrelaRQTHDIIQYYCaalpiplrtclaiggvpmnqsldvikkgiqyndpiktswraprcilslpdqVHDIIRRNLRilvegddvppaccsfrlmkLPESLVRALEakgikkptpiqvqgipaalsgrdiigiaftgsgktLVFVLPILMFCLeqetklpflpgegpygliicpsrelaRQTHDIIQYYCAALPIGSF
Flexible Loop (DISEMBL)
mvtyrnsrdiigiaftgsgktlVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNdpiktswraprCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEakgikkptpiqVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF
Low Complexity Region (SEG)
MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF
Disordered region (IsUnstruct)
*******RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI***
Disordered Region (DISOPRED)
MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQE******PGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL********************NDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETK****PGEGPYGLIICPSRELARQTHDIIQYYCAALPIG**
Disordered Region (DISEMBL)
MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF
Disordered Region (DISPRO)
MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI***
Transmembrane Helix (TMHMM)
iiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	252	2.2.26 [Sep-21-2011]
Q9UJV9	622	Probable ATP-dependent RN	yes	N/A	0.607	0.245	0.636	4e-56
Q91VN6	622	Probable ATP-dependent RN	yes	N/A	0.607	0.245	0.636	9e-56
Q9V3C0	619	ATP-dependent RNA helicas	yes	N/A	0.591	0.240	0.627	3e-52
Q5Z6G5	619	DEAD-box ATP-dependent RN	yes	N/A	0.722	0.294	0.515	1e-50
Q0E3X4	627	DEAD-box ATP-dependent RN	no	N/A	0.626	0.251	0.549	2e-48
Q54KG1	671	Probable ATP-dependent RN	yes	N/A	0.579	0.217	0.569	5e-48
Q9LU46	591	DEAD-box ATP-dependent RN	yes	N/A	0.607	0.258	0.515	2e-43
Q9SZB4	542	Putative DEAD-box ATP-dep	no	N/A	0.607	0.282	0.503	2e-42
Q0J7Y8	947	DEAD-box ATP-dependent RN	no	N/A	0.476	0.126	0.455	2e-23
Q7ZY47	947	ATP-dependent RNA helicas	N/A	N/A	0.456	0.121	0.445	8e-23

>sp|Q9UJV9|DDX41_HUMAN Probable ATP-dependent RNA helicase DDX41 OS=Homo sapiens GN=DDX41 PE=1 SV=2

 Score =  218 bits (554), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query: 91  SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
           S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct: 128 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 187

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
            P +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct: 188 FPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 247

Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
            +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct: 248 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 284

Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q91VN6|DDX41_MOUSE Probable ATP-dependent RNA helicase DDX41 OS=Mus musculus GN=Ddx41 PE=1 SV=2

 Score =  216 bits (551), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query: 91  SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
           S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct: 128 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 187

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
            P +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct: 188 FPAAILRGLKKKGILHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 247

Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
            +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct: 248 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 284

Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9V3C0|DDX41_DROME ATP-dependent RNA helicase abstrakt OS=Drosophila melanogaster GN=abs PE=1 SV=1

 Score =  205 bits (521), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 96/153 (62%), Positives = 116/153 (75%)

Query: 95  IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
           + KGIQY  PIKT+W+ PR I  + ++  + +R  LRILVEG+   P   SFR MK P+ 
Sbjct: 128 LAKGIQYEQPIKTAWKPPRYIREMSEEEREAVRHELRILVEGETPSPPIRSFREMKFPKG 187

Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           ++  L AKGIK PTPIQVQG+P  L+GRD+IGIAFTGSGKTLVFVLP++MF LEQE  LP
Sbjct: 188 ILNGLAAKGIKNPTPIQVQGLPTVLAGRDLIGIAFTGSGKTLVFVLPVIMFALEQEYSLP 247

Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
           F   EGPYGLIICPSRELA+QTH+IIQ+Y   L
Sbjct: 248 FERNEGPYGLIICPSRELAKQTHEIIQHYSKHL 280

ATP-dependent RNA helicase. Is essential for the directed and fasciculated early outgrowth of the bolwig nerves, as well as for its navigation at later stages. Is required during post-transcriptional gene expression. Plays a role during morphogenetic process, apoptosis and the establishment of cell polarity.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5Z6G5|RH35B_ORYSJ DEAD-box ATP-dependent RNA helicase 35B OS=Oryza sativa subsp. japonica GN=Os06g0697200 PE=3 SV=1

 Score =  200 bits (508), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 101/196 (51%), Positives = 137/196 (69%), Gaps = 14/196 (7%)

Query: 52  ICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRA 111
           + P+  L +Q  ++I++         R  L    +P+ +    I KGI Y++PI T WR 
Sbjct: 95  VTPAERLLQQEREMIEHLSD------RKAL----MPVGE----IAKGISYSEPITTGWRP 140

Query: 112 PRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQ 171
           P  +  +P    D +RR+  ILV+GDDVPP   SF  ++LPE ++RAL  KGI+KPTPIQ
Sbjct: 141 PLRLRRMPRSRADALRRSWHILVDGDDVPPPSRSFGDLRLPEPILRALRGKGIEKPTPIQ 200

Query: 172 VQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE 231
           VQG+P ALSGRD+IGIAFTGSGKTLVFVLP++M  L++E  +P +PGEGP+GLI+CPSRE
Sbjct: 201 VQGLPVALSGRDMIGIAFTGSGKTLVFVLPLIMAALQEEILMPIVPGEGPFGLIVCPSRE 260

Query: 232 LARQTHDIIQYYCAAL 247
           LARQTH++I+ + A L
Sbjct: 261 LARQTHEVIEMFLAPL 276

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0E3X4|RH35A_ORYSJ DEAD-box ATP-dependent RNA helicase 35A OS=Oryza sativa subsp. japonica GN=Os02g0150100 PE=2 SV=2

 Score =  192 bits (488), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 89/162 (54%), Positives = 119/162 (73%)

Query: 91  SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
           S+  + KGI Y+DP+KT W+ P  +  +P    D +RR   ILV+GDDVPP    FR ++
Sbjct: 129 SVRELAKGITYSDPLKTGWKPPLRLRRMPRAKADELRRKWHILVDGDDVPPPARDFRDLR 188

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           LPE ++R L  KGI +PTPIQVQG+P  LSGRD+IGIAFTGSGKTLVFVLP++M  L++E
Sbjct: 189 LPEPMLRKLREKGIVQPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPLIMVALQEE 248

Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF 252
             +P +PGEGP+G+IICPSRELA+QT+D+I+ +   L    +
Sbjct: 249 MMMPIVPGEGPFGMIICPSRELAKQTYDVIEQFLVPLKEAGY 290

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q54KG1|DDX41_DICDI Probable ATP-dependent RNA helicase ddx41 OS=Dictyostelium discoideum GN=ddx41 PE=1 SV=1

 Score =  191 bits (485), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 86/151 (56%), Positives = 116/151 (76%)

Query: 97  KGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLV 156
           K + Y D IKT+WRAPR IL   ++ H  +R  L I+ +G+D+PP   +F+ MK+P+ ++
Sbjct: 175 KDVIYTDSIKTNWRAPRYILERDEKDHQKVRDQLNIITDGEDIPPPITTFKEMKIPKPVI 234

Query: 157 RALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL 216
             L  KGIKKP+PIQVQG+P  LSGRD+IGIA+TGSGKTLVF LP+++F LE+E KLP +
Sbjct: 235 DVLLEKGIKKPSPIQVQGLPVILSGRDMIGIAYTGSGKTLVFTLPMVLFALEEECKLPII 294

Query: 217 PGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
            GEGP+GLI+CPSRELARQT+D++  +  AL
Sbjct: 295 QGEGPFGLILCPSRELARQTYDLVNSFTNAL 325

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9LU46|RH35_ARATH DEAD-box ATP-dependent RNA helicase 35 OS=Arabidopsis thaliana GN=RH35 PE=2 SV=1

 Score =  176 bits (446), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 81/157 (51%), Positives = 113/157 (71%)

Query: 91  SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
           S+  + KGI Y +P+ T W+ P  I  +  +  D+IR+   I+V GDD+PP   +F+ MK
Sbjct: 93  SVRELAKGITYTEPLLTGWKPPLHIRKMSSKQRDLIRKQWHIIVNGDDIPPPIKNFKDMK 152

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
            P  ++  L+ KGI +PTPIQVQG+P  L+GRD+IGIAFTGSGKTLVFVLP++M  L++E
Sbjct: 153 FPRPVLDTLKEKGIVQPTPIQVQGLPVILAGRDMIGIAFTGSGKTLVFVLPMIMIALQEE 212

Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
             +P   GEGP GLI+CPSRELARQT+++++ + A L
Sbjct: 213 MMMPIAAGEGPIGLIVCPSRELARQTYEVVEQFVAPL 249

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9SZB4|RH43_ARATH Putative DEAD-box ATP-dependent RNA helicase 43 OS=Arabidopsis thaliana GN=RH43 PE=3 SV=1

 Score =  172 bits (436), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 79/157 (50%), Positives = 111/157 (70%)

Query: 91  SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
           S+  + +GI Y +P+ T W+ P  +  +  +  D+IR+   I V G+D+PP   +F  MK
Sbjct: 44  SVGELARGITYTEPLSTWWKPPLHVRKMSTKQMDLIRKQWHITVNGEDIPPPIKNFMDMK 103

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
            P  L+R L+ KGI  PTPIQVQG+P  LSGRD+IGIAFTGSGKTLVFVLP+++  L++E
Sbjct: 104 FPSPLLRMLKDKGIMHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPMIILALQEE 163

Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
             +P   GEGP  L+ICPSRELA+QT+D+++ + A+L
Sbjct: 164 IMMPIAAGEGPIALVICPSRELAKQTYDVVEQFVASL 200

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0J7Y8|RH45_ORYSJ DEAD-box ATP-dependent RNA helicase 45 OS=Oryza sativa subsp. japonica GN=Os08g0154200 PE=3 SV=2

 Score =  109 bits (272), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 56/123 (45%), Positives = 75/123 (60%), Gaps = 3/123 (2%)

Query: 127 RRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIG 186
           R+NL + V G DVP    ++    L   L+  ++  G +KP PIQ Q +P  +SGRD IG
Sbjct: 268 RKNLELKVHGKDVPKPIKTWVQSGLTSKLLDTIKKLGFEKPMPIQAQALPIIMSGRDCIG 327

Query: 187 IAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA 246
           IA TGSGKTL FVLP+L    +Q    P +PG+GP GLI+ P+REL  Q H  I+ +  +
Sbjct: 328 IAKTGSGKTLAFVLPMLRHVKDQP---PVVPGDGPIGLIMAPTRELVVQIHSDIKKFAKS 384

Query: 247 LPI 249
           L I
Sbjct: 385 LGI 387

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q7ZY47|DDX42_XENLA ATP-dependent RNA helicase DDX42 OS=Xenopus laevis GN=ddx42 PE=2 SV=1

 Score =  107 bits (267), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 53/119 (44%), Positives = 71/119 (59%), Gaps = 4/119 (3%)

Query: 119 PDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAA 178
           P Q+ ++ R  L + V G   P  C SF      E L+  +      +PTPIQ QGIP A
Sbjct: 226 PQQITEL-RHKLNLRVSGAAPPRLCSSFAHFGFDEQLLHQIRKSEYTQPTPIQCQGIPVA 284

Query: 179 LSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH 237
           LSGRD+IGIA TGSGKT  F+ PIL+  ++Q+      P +GP  +I+CP+REL +Q H
Sbjct: 285 LSGRDMIGIAKTGSGKTAAFIWPILVHIMDQKE---LQPADGPIAVIVCPTRELCQQIH 340

ATP-dependent RNA helicase. Binds to RNA. May be involved in the survival of cells.

Xenopus laevis (taxid: 8355)

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	252
157130314	619	DEAD box ATP-dependent RNA helicase [Aed	0.603	0.245	0.692	2e-59
270014204	619	hypothetical protein TcasGA2_TC016289 [T	0.583	0.237	0.701	1e-58
158298027	613	AGAP004711-PA [Anopheles gambiae str. PE	0.583	0.239	0.712	2e-58
193683780	615	PREDICTED: ATP-dependent RNA helicase ab	0.603	0.247	0.679	3e-57
170059153	619	ATP-dependent RNA helicase abstrakt [Cul	0.583	0.237	0.673	7e-57
357623365	613	putative ATP-dependent RNA helicase abst	0.611	0.251	0.664	7e-57
383858565	625	PREDICTED: ATP-dependent RNA helicase ab	0.591	0.238	0.686	2e-56
47222980	509	unnamed protein product [Tetraodon nigro	0.607	0.300	0.662	2e-56
340725455	625	PREDICTED: ATP-dependent RNA helicase ab	0.591	0.238	0.692	3e-56
350415294	625	PREDICTED: ATP-dependent RNA helicase ab	0.591	0.238	0.692	3e-56

>gi|157130314|ref|XP_001661885.1| DEAD box ATP-dependent RNA helicase [Aedes aegypti] gi|108871945|gb|EAT36170.1| AAEL011744-PA [Aedes aegypti]

 Score =  235 bits (599), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 108/156 (69%), Positives = 129/156 (82%)

Query: 95  IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
           + KGIQY DPIKTSW+ PR ILS  D  H+ +R  +RILV+G++VPP  CSFR MK P++
Sbjct: 131 LAKGIQYEDPIKTSWKPPRYILSRTDASHERVREKMRILVDGENVPPPICSFREMKFPKA 190

Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           ++ ALE + I+KP+PIQVQGIPA LSGRD+IGIAFTGSGKTLVFVLPI+MF LEQE +LP
Sbjct: 191 ILAALEKRNIRKPSPIQVQGIPAVLSGRDLIGIAFTGSGKTLVFVLPIVMFSLEQELRLP 250

Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG 250
           F+  EGPYGLIICPSRELA+QTHDIIQYYC  L + 
Sbjct: 251 FISKEGPYGLIICPSRELAKQTHDIIQYYCQHLQMS 286

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270014204|gb|EFA10652.1| hypothetical protein TcasGA2_TC016289 [Tribolium castaneum]

 Score =  232 bits (591), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 106/151 (70%), Positives = 127/151 (84%)

Query: 97  KGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLV 156
           KGIQY+DPIKTSWR PR +L++P+  H+ IR  LRILVEG+D+PP   +FR MKL E ++
Sbjct: 131 KGIQYSDPIKTSWRPPRYVLAMPENRHEKIRNELRILVEGEDIPPPLKTFREMKLHEGII 190

Query: 157 RALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL 216
             L+ K IKKPTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVFVLP++MFCLEQE KLPF+
Sbjct: 191 SGLKEKKIKKPTPIQIQGIPTVLSGRDMIGIAFTGSGKTLVFVLPLIMFCLEQEVKLPFI 250

Query: 217 PGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
             EGPYGLIICPSRELA+QT DIIQ++C +L
Sbjct: 251 KNEGPYGLIICPSRELAKQTFDIIQHFCNSL 281

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158298027|ref|XP_318117.4| AGAP004711-PA [Anopheles gambiae str. PEST] gi|157014611|gb|EAA13218.5| AGAP004711-PA [Anopheles gambiae str. PEST]

 Score =  231 bits (590), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 109/153 (71%), Positives = 127/153 (83%)

Query: 95  IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
           + KGIQY DPIKTSW  PR ILS P+  H+ IR  LRIL EG++VPP   +FR MKLP++
Sbjct: 125 LAKGIQYEDPIKTSWTPPRYILSKPESRHEKIREKLRILTEGENVPPPLRTFREMKLPKA 184

Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           ++ AL  + IKKP+PIQVQGIPA L+GRD+IGIAFTGSGKTLVFVLPI+MFCLEQE +LP
Sbjct: 185 VLAALAKRNIKKPSPIQVQGIPAVLAGRDLIGIAFTGSGKTLVFVLPIIMFCLEQELRLP 244

Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
           F+  EGPYGLIICPSRELA+QTHDIIQYYC  L
Sbjct: 245 FIKREGPYGLIICPSRELAKQTHDIIQYYCRHL 277

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193683780|ref|XP_001952119.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Acyrthosiphon pisum]

 Score =  227 bits (579), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 106/156 (67%), Positives = 127/156 (81%)

Query: 97  KGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLV 156
           KGIQY+DPIKTSW APR IL++P++ H+ +R  LRILVEG+++PP   SF+ MKL + ++
Sbjct: 127 KGIQYDDPIKTSWTAPRYILAMPEERHENVRLKLRILVEGEEIPPPLKSFKEMKLNKGIM 186

Query: 157 RALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL 216
             L  KGIKKPTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVFVLP+LMFCLEQE KLPF 
Sbjct: 187 AGLSQKGIKKPTPIQIQGIPTVLSGRDMIGIAFTGSGKTLVFVLPLLMFCLEQEIKLPFK 246

Query: 217 PGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF 252
           P EGPYGLIICPSRELA+QT DII +Y   L   ++
Sbjct: 247 PNEGPYGLIICPSRELAKQTFDIINHYMTFLERSNY 282

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170059153|ref|XP_001865238.1| ATP-dependent RNA helicase abstrakt [Culex quinquefasciatus] gi|167878066|gb|EDS41449.1| ATP-dependent RNA helicase abstrakt [Culex quinquefasciatus]

 Score =  226 bits (576), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 103/153 (67%), Positives = 126/153 (82%)

Query: 95  IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
           + KGIQY DPIKTSW+ PR IL+  D  H+ +R  +RILV+G++VPP  C+FR MK P+S
Sbjct: 131 LAKGIQYEDPIKTSWKPPRYILARADVSHEKVRERMRILVDGENVPPPICTFREMKFPKS 190

Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           ++  LE + I+KP+PIQVQGIPA L+GRD+IGIAFTGSGKTLVFVLPI+MF LEQE +LP
Sbjct: 191 ILAGLEKRNIRKPSPIQVQGIPAVLAGRDLIGIAFTGSGKTLVFVLPIVMFSLEQEIRLP 250

Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
           F+  EGPYGLIICPSRELA+QT DI+QYYC  L
Sbjct: 251 FMAKEGPYGLIICPSRELAKQTFDIVQYYCQHL 283

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357623365|gb|EHJ74551.1| putative ATP-dependent RNA helicase abstrakt [Danaus plexippus]

 Score =  226 bits (576), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 105/158 (66%), Positives = 128/158 (81%)

Query: 95  IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
           + KGIQY++PIKTSW+ P CI SLP + H+ +RR LRI VEG++VPP   +FR MK P+ 
Sbjct: 126 LAKGIQYSEPIKTSWKPPGCISSLPPERHERVRRELRIQVEGENVPPPIRTFRHMKFPKG 185

Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           +++ LEAKGIKKPTPIQVQGIPA LSGRD+IGIAFTGSGKTLVF LPI+M CLEQE ++P
Sbjct: 186 ILQGLEAKGIKKPTPIQVQGIPAVLSGRDMIGIAFTGSGKTLVFTLPIIMMCLEQEIEMP 245

Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF 252
           F+  EGPYGLIICPSRELA+QTHDII ++   L +   
Sbjct: 246 FIRNEGPYGLIICPSRELAKQTHDIIMHFVKHLKMAGH 283

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858565|ref|XP_003704771.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Megachile rotundata]

 Score =  225 bits (573), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 105/153 (68%), Positives = 124/153 (81%)

Query: 95  IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
           + KGIQY DPIKTSWR PR +L+L +  H+ +RR LRILVEGDD+PP   SF+ MK    
Sbjct: 135 LAKGIQYEDPIKTSWRPPRAVLALGEARHERVRRKLRILVEGDDIPPPLKSFKEMKFHRG 194

Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           ++  LE KGI KPTPIQVQGIP  LSGRD+IGIAFTGSGKTLVFVLPI+MFCLEQE  +P
Sbjct: 195 ILNGLEQKGIIKPTPIQVQGIPTVLSGRDMIGIAFTGSGKTLVFVLPIIMFCLEQEVAMP 254

Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
           F+  EGPYGLIICPSRELA+QT+DII++Y  +L
Sbjct: 255 FVRNEGPYGLIICPSRELAKQTYDIIRHYTNSL 287

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|47222980|emb|CAF99136.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  224 bits (572), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 104/157 (66%), Positives = 127/157 (80%)

Query: 91  SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
           S+  + KGI Y+DPIKTSW+APR IL++PD  H+ +R+   ILV+GD++PP   SFR MK
Sbjct: 47  SVKEMAKGIIYDDPIKTSWKAPRYILNMPDTRHERVRKKFHILVDGDNIPPPIKSFREMK 106

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           LP ++++ L+ KGI  PTPIQ+QG+P  LSGRD+IGIAFTGSGKTLVF LPI+MFCLEQE
Sbjct: 107 LPPAILKGLKKKGIVHPTPIQIQGMPTVLSGRDMIGIAFTGSGKTLVFTLPIIMFCLEQE 166

Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
            +LPF   EGPYGLIICPSRELARQTH II+YYC  L
Sbjct: 167 KRLPFCKREGPYGLIICPSRELARQTHGIIEYYCKLL 203

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|340725455|ref|XP_003401085.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Bombus terrestris]

 Score =  224 bits (570), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 106/153 (69%), Positives = 122/153 (79%)

Query: 95  IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
           + KGIQY DPIKTSWR PR +L+  +  H+ IRR LRILVEGDDVPP   SF+ MK    
Sbjct: 135 LAKGIQYEDPIKTSWRPPRAVLAAGEARHERIRRKLRILVEGDDVPPPLKSFKEMKFHRG 194

Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           ++  LE KGI KPTPIQVQGIP  LSGRD+IGIAFTGSGKTLVFVLPI+MFCLEQE  +P
Sbjct: 195 ILNGLEQKGIVKPTPIQVQGIPTVLSGRDMIGIAFTGSGKTLVFVLPIIMFCLEQEVAMP 254

Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
           F+  EGPYGLIICPSRELA+QT+DII++Y   L
Sbjct: 255 FVRNEGPYGLIICPSRELAKQTYDIIRHYTNTL 287

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350415294|ref|XP_003490595.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Bombus impatiens]

 Score =  224 bits (570), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 106/153 (69%), Positives = 122/153 (79%)

Query: 95  IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
           + KGIQY DPIKTSWR PR +L+  +  H+ IRR LRILVEGDDVPP   SF+ MK    
Sbjct: 135 LAKGIQYEDPIKTSWRPPRAVLAAGEARHERIRRKLRILVEGDDVPPPLKSFKEMKFHRG 194

Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           ++  LE KGI KPTPIQVQGIP  LSGRD+IGIAFTGSGKTLVFVLPI+MFCLEQE  +P
Sbjct: 195 ILNGLEQKGIVKPTPIQVQGIPTVLSGRDMIGIAFTGSGKTLVFVLPIIMFCLEQEVAMP 254

Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
           F+  EGPYGLIICPSRELA+QT+DII++Y   L
Sbjct: 255 FVRNEGPYGLIICPSRELAKQTYDIIRHYTNTL 287

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	252
UNIPROTKB|F1NAH6	607	LOC100859810 "Uncharacterized	0.623	0.258	0.649	2.4e-53
RGD|1311758	622	Ddx41 "DEAD (Asp-Glu-Ala-Asp)	0.623	0.252	0.643	6.3e-53
RGD|1559513	621	RGD1559513 "similar to DEAD (A	0.623	0.252	0.643	6.3e-53
UNIPROTKB|A3KN07	622	DDX41 "Uncharacterized protein	0.623	0.252	0.636	1.3e-52
UNIPROTKB|E2R052	622	DDX41 "Uncharacterized protein	0.623	0.252	0.636	1.3e-52
UNIPROTKB|J9NZF6	649	DDX41 "Uncharacterized protein	0.623	0.241	0.636	1.3e-52
UNIPROTKB|J3KNN5	640	DDX41 "Probable ATP-dependent	0.623	0.245	0.636	1.3e-52
UNIPROTKB|Q9UJV9	622	DDX41 "Probable ATP-dependent	0.623	0.252	0.636	1.3e-52
MGI|MGI:1920185	622	Ddx41 "DEAD (Asp-Glu-Ala-Asp)	0.623	0.252	0.636	1.7e-52
FB|FBgn0015331	619	abs "abstrakt" [Drosophila mel	0.591	0.240	0.637	1.1e-48

UNIPROTKB|F1NAH6 LOC100859810 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 552 (199.4 bits), Expect = 2.4e-53, P = 2.4e-53
 Identities = 102/157 (64%), Positives = 126/157 (80%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSWRAPR IL++ +  H+ +R+   ILVEG+ +PP   SF+ MK
Sbjct:   124 SVKEMAKGITYDDPIKTSWRAPRYILAMSEARHNRVRKKYHILVEGEGIPPPIKSFKEMK 183

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
              P +++R L+ KGI++PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   184 FPAAILRGLKKKGIQQPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 243

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH II+YYC  L
Sbjct:   244 KRLPFSKREGPYGLIICPSRELARQTHGIIEYYCRLL 280

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA

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

GO:0051607 "defense response to virus" evidence=IEA

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

RGD|1311758 Ddx41 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Rattus norvegicus (taxid:10116)]

 Score = 548 (198.0 bits), Expect = 6.3e-53, P = 6.3e-53
 Identities = 101/157 (64%), Positives = 124/157 (78%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct:   128 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 187

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
             LP +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   188 LPAAILRGLKKKGILHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 247

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct:   248 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 284

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005783 "endoplasmic reticulum" evidence=IEA;ISO

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA;ISO

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

GO:0051607 "defense response to virus" evidence=IEA;ISO

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

GO:0005730 "nucleolus" evidence=ISO

RGD|1559513 RGD1559513 "similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Rattus norvegicus (taxid:10116)]

 Score = 548 (198.0 bits), Expect = 6.3e-53, P = 6.3e-53
 Identities = 101/157 (64%), Positives = 124/157 (78%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct:   127 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 186

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
             LP +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   187 LPAAILRGLKKKGILHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 246

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct:   247 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 283

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|A3KN07 DDX41 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct:   128 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 187

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
              P +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   188 FPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 247

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct:   248 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 284

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0051607 "defense response to virus" evidence=IEA

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

GO:0035458 "cellular response to interferon-beta" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

UNIPROTKB|E2R052 DDX41 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct:   128 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 187

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
              P +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   188 FPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 247

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct:   248 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 284

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

GO:0051607 "defense response to virus" evidence=IEA

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

GO:0035458 "cellular response to interferon-beta" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|J9NZF6 DDX41 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct:   155 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 214

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
              P +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   215 FPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 274

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct:   275 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 311

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J3KNN5 DDX41 "Probable ATP-dependent RNA helicase DDX41" [Homo sapiens (taxid:9606)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct:   146 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 205

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
              P +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   206 FPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 265

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct:   266 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 302

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q9UJV9 DDX41 "Probable ATP-dependent RNA helicase DDX41" [Homo sapiens (taxid:9606)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct:   128 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 187

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
              P +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   188 FPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 247

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct:   248 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 284

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA

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

GO:0051607 "defense response to virus" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:1920185 Ddx41 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Mus musculus (taxid:10090)]

 Score = 544 (196.6 bits), Expect = 1.7e-52, P = 1.7e-52
 Identities = 100/157 (63%), Positives = 123/157 (78%)

Query:    91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK 150
             S+  + KGI Y+DPIKTSW  PR +LS+ ++ H+ +R+   ILVEGD +PP   SF+ MK
Sbjct:   128 SVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMK 187

Query:   151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
              P +++R L+ KGI  PTPIQ+QGIP  LSGRD+IGIAFTGSGKTLVF LP++MFCLEQE
Sbjct:   188 FPAAILRGLKKKGILHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQE 247

Query:   211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL 247
              +LPF   EGPYGLIICPSRELARQTH I++YYC  L
Sbjct:   248 KRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL 284

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IMP

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0051607 "defense response to virus" evidence=IMP

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

FB|FBgn0015331 abs "abstrakt" [Drosophila melanogaster (taxid:7227)]

 Score = 508 (183.9 bits), Expect = 1.1e-48, P = 1.1e-48
 Identities = 95/149 (63%), Positives = 115/149 (77%)

Query:    95 IKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES 154
             + KGIQY  PIKT+W+ PR I  + ++  + +R  LRILVEG+   P   SFR MK P+ 
Sbjct:   128 LAKGIQYEQPIKTAWKPPRYIREMSEEEREAVRHELRILVEGETPSPPIRSFREMKFPKG 187

Query:   155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
             ++  L AKGIK PTPIQVQG+P  L+GRD+IGIAFTGSGKTLVFVLP++MF LEQE  LP
Sbjct:   188 ILNGLAAKGIKNPTPIQVQGLPTVLAGRDLIGIAFTGSGKTLVFVLPVIMFALEQEYSLP 247

Query:   215 FLPGEGPYGLIICPSRELARQTHDIIQYY 243
             F   EGPYGLIICPSRELA+QTH+IIQ+Y
Sbjct:   248 FERNEGPYGLIICPSRELAKQTHEIIQHY 276

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

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

GO:0004386 "helicase activity" evidence=ISS

GO:0030010 "establishment of cell polarity" evidence=NAS

GO:0007399 "nervous system development" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

GO:0009653 "anatomical structure morphogenesis" evidence=NAS

GO:0006915 "apoptotic process" evidence=NAS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9LU46	RH35_ARATH	3, ., 6, ., 4, ., 1, 3	0.5159	0.6071	0.2588	yes	N/A
Q5Z6G5	RH35B_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5153	0.7222	0.2940	yes	N/A
Q91VN6	DDX41_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6369	0.6071	0.2459	yes	N/A
Q9V3C0	DDX41_DROME	3, ., 6, ., 4, ., 1, 3	0.6274	0.5912	0.2407	yes	N/A
Q54KG1	DDX41_DICDI	3, ., 6, ., 4, ., 1, 3	0.5695	0.5793	0.2175	yes	N/A
Q9UJV9	DDX41_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6369	0.6071	0.2459	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	252
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-31
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-30
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-28
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	8e-25
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-20
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	5e-19
cd00268	203	cd00268, DEADc, DEAD-box helicases	2e-18
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	4e-18
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	6e-18
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	2e-16
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	4e-16
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	9e-15
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	7e-14
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-13
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	5e-13
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	9e-12
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-11
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-10
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	3e-10
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	8e-10
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-09
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	4e-09
COG1205	851	COG1205, COG1205, Distinct helicase family with a	2e-08
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-07
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-07
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	3e-07
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	8e-07
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-05
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	3e-05
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	4e-05
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	2e-04
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	3e-04
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	5e-04
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	6e-04
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	0.001
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	0.002
COG1205	851	COG1205, COG1205, Distinct helicase family with a	0.004

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

 Score =  121 bits (304), Expect = 2e-31
 Identities = 54/114 (47%), Positives = 74/114 (64%), Gaps = 6/114 (5%)

Query: 124 DIIRRNLRI-LVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGR 182
           D IR+   I ++ G++VP    SF     P+ ++++L+  G  +PTPIQVQG P ALSGR
Sbjct: 109 DEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGR 168

Query: 183 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL-PGEGPYGLIICPSRELARQ 235
           D+IGIA TGSGKTL F+LP ++    Q    P L  G+GP  L++ P+RELA Q
Sbjct: 169 DMIGIAETGSGKTLAFLLPAIVHINAQ----PLLRYGDGPIVLVLAPTRELAEQ 218

Length = 545

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

 Score =  112 bits (283), Expect = 1e-30
 Identities = 44/96 (45%), Positives = 58/96 (60%), Gaps = 6/96 (6%)

Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
           F  + L   L+R + A G +KPTPIQ + IP  LSGRD+IG A TGSGKT  F++PIL  
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPIL-- 58

Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
               E   P    +GP  LI+ P+RELA Q  ++ +
Sbjct: 59  ----EKLDPSPKKDGPQALILAPTRELALQIAEVAR 90

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 =  112 bits (283), Expect = 1e-28
 Identities = 38/104 (36%), Positives = 59/104 (56%), Gaps = 6/104 (5%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F  + L   L++AL+  G ++PTPIQ+  IP  L+GRD++G A TG+GKT  F+LP+L 
Sbjct: 30  EFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLL- 88

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
                +  L  +  +    LI+ P+RELA Q  + ++     L 
Sbjct: 89  -----QKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLG 127

Length = 513

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

 Score =  102 bits (255), Expect = 8e-25
 Identities = 53/133 (39%), Positives = 72/133 (54%), Gaps = 1/133 (0%)

Query: 116 LSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGI 175
             L     +++RR L I V+G+ VPP   SF    LP  L+  LE  G + PTPIQ+Q I
Sbjct: 93  SGLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAI 152

Query: 176 PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
           PAALSGR ++  A TGSGKT  F++PI+  C    +  P      P  +++ P+REL  Q
Sbjct: 153 PAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHP-SEQRNPLAMVLTPTRELCVQ 211

Query: 236 THDIIQYYCAALP 248
             D  +     LP
Sbjct: 212 VEDQAKVLGKGLP 224

Length = 518

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

 Score = 90.0 bits (224), Expect = 1e-20
 Identities = 42/89 (47%), Positives = 54/89 (60%), Gaps = 6/89 (6%)

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           L ESL+ AL+ KG  +PT IQ + IP AL GRD++G A TG+GKT  F+LP L   L+  
Sbjct: 8   LDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFP 67

Query: 211 TKLPFLPGEGPYG-LIICPSRELARQTHD 238
            +       GP   LI+ P+RELA Q  D
Sbjct: 68  RRKS-----GPPRILILTPTRELAMQVAD 91

Length = 434

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

 Score = 85.6 bits (212), Expect = 5e-19
 Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 7/96 (7%)

Query: 6   NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI 65
             RD++G A TG+GKT  F+LP+L      +  L  +  +    LI+ P+RELA Q  + 
Sbjct: 65  AGRDVLGQAQTGTGKTAAFLLPLL------QKILKSVERKYVSALILAPTRELAVQIAEE 118

Query: 66  IQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQY 101
           ++     L   LR  +  GGV + + ++ +K+G+  
Sbjct: 119 LRKLGKNLG-GLRVAVVYGGVSIRKQIEALKRGVDI 153

Length = 513

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

 Score = 80.2 bits (199), Expect = 2e-18
 Identities = 31/93 (33%), Positives = 49/93 (52%), Gaps = 8/93 (8%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           RD+IG A TGSGKT  F++PIL      E   P    +GP  LI+ P+RELA Q  ++ +
Sbjct: 37  RDVIGQAQTGSGKTAAFLIPIL------EKLDPSPKKDGPQALILAPTRELALQIAEVAR 90

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
                  +  +  +  GG  +++ +  +K+G  
Sbjct: 91  KLGKHTNL--KVVVIYGGTSIDKQIRKLKRGPH 121

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|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score = 78.8 bits (195), Expect = 4e-18
 Identities = 36/82 (43%), Positives = 50/82 (60%), Gaps = 8/82 (9%)

Query: 168 TPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC 227
           TPIQ Q IPA LSG+D++  A TGSGKTL F+LPIL   L ++         GP  L++ 
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKG--------GPQALVLA 52

Query: 228 PSRELARQTHDIIQYYCAALPI 249
           P+RELA Q ++ ++     L +
Sbjct: 53  PTRELAEQIYEELKKLFKILGL 74

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

 Score = 82.2 bits (203), Expect = 6e-18
 Identities = 44/108 (40%), Positives = 63/108 (58%), Gaps = 4/108 (3%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           SF  + L   ++RA+  +G ++PTPIQ Q IPA L GRD++  A TG+GKT  F LP+L 
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 205 FCLEQETKLPFLPGEGPY-GLIICPSRELARQTHDIIQYYCAALPIGS 251
             + ++   P   G  P   LI+ P+RELA Q  + ++ Y   L I S
Sbjct: 62  HLITRQ---PHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRS 106

Length = 456

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

 Score = 74.8 bits (184), Expect = 2e-16
 Identities = 33/92 (35%), Positives = 47/92 (51%), Gaps = 10/92 (10%)

Query: 159 LEAKGIKKPTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLP 217
           +E  G +   P Q + I A LSG RD+I  A TGSGKTL  +LP L              
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEA---------LKR 51

Query: 218 GEGPYGLIICPSRELARQTHDIIQYYCAALPI 249
           G+G   L++ P+RELA Q  + ++    +L +
Sbjct: 52  GKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

Length = 201

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

 Score = 73.1 bits (180), Expect = 4e-16
 Identities = 40/134 (29%), Positives = 65/134 (48%), Gaps = 29/134 (21%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           +D++  A TGSGKTL F+LPIL   L ++         GP  L++ P+RELA Q ++ ++
Sbjct: 15  KDVLVQAPTGSGKTLAFLLPILQALLPKKG--------GPQALVLAPTRELAEQIYEELK 66

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIR 127
                L +  R  L  GG  + +    +KKG                ++  P ++ D++R
Sbjct: 67  KLFKILGL--RVALLTGGTSLKEQARKLKKG------------KADILVGTPGRLLDLLR 112

Query: 128 R-------NLRILV 134
           R       NL++LV
Sbjct: 113 RGKLKLLKNLKLLV 126

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

 Score = 73.0 bits (179), Expect = 9e-15
 Identities = 39/91 (42%), Positives = 56/91 (61%), Gaps = 8/91 (8%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F  + L   ++ AL   G +KP+PIQ + IP  L+GRD++G+A TGSGKT  F LP L+
Sbjct: 7   TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLP-LL 65

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
             L+ E K P +       L++ P+RELA Q
Sbjct: 66  HNLDPELKAPQI-------LVLAPTRELAVQ 89

Length = 629

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

 Score = 70.2 bits (172), Expect = 7e-14
 Identities = 38/94 (40%), Positives = 56/94 (59%), Gaps = 7/94 (7%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL-PGEGPYGLIICPSRELARQTHDII 66
           RD+IGIA TGSGKTL F+LP ++    Q    P L  G+GP  L++ P+RELA Q  +  
Sbjct: 168 RDMIGIAETGSGKTLAFLLPAIVHINAQ----PLLRYGDGPIVLVLAPTRELAEQIREQC 223

Query: 67  QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
             + A+  I  R  +A GGVP    +  +++G++
Sbjct: 224 NKFGASSKI--RNTVAYGGVPKRGQIYALRRGVE 255

Length = 545

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

 Score = 68.4 bits (167), Expect = 4e-13
 Identities = 39/100 (39%), Positives = 54/100 (54%), Gaps = 1/100 (1%)

Query: 138 DVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLV 197
           D P    +F    L  +L+  LE+ G  + TPIQ   +P AL G D+ G A TG+GKTL 
Sbjct: 3   DKPLTDLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLA 62

Query: 198 FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH 237
           F++ ++   L +       P E P  LI+ P+RELA Q H
Sbjct: 63  FLVAVMNRLLSRPALADRKP-EDPRALILAPTRELAIQIH 101

Length = 572

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

 Score = 67.9 bits (167), Expect = 5e-13
 Identities = 38/94 (40%), Positives = 51/94 (54%), Gaps = 14/94 (14%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F  + LP +L+  L   G  + TPIQ Q +PA L+G+D+I  A TGSGKT  F L +L 
Sbjct: 5   AFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL- 63

Query: 205 FCLEQETKL---PFLPGEGPYGLIICPSRELARQ 235
                  KL    F        L++CP+RELA Q
Sbjct: 64  ------QKLDVKRF----RVQALVLCPTRELADQ 87

Length = 460

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

 Score = 62.1 bits (151), Expect = 9e-12
 Identities = 28/95 (29%), Positives = 42/95 (44%), Gaps = 11/95 (11%)

Query: 4   YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH 63
               RD+I  A TGSGKTL  +LP L              G+G   L++ P+RELA Q  
Sbjct: 21  LSGLRDVILAAPTGSGKTLAALLPALEA---------LKRGKGGRVLVLVPTRELAEQWA 71

Query: 64  DIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKG 98
           + ++       + L+     GG    + L  ++ G
Sbjct: 72  EELKKLGP--SLGLKVVGLYGGDSKREQLRKLESG 104

Length = 201

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

 Score = 63.5 bits (155), Expect = 1e-11
 Identities = 35/87 (40%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           L   +V ALE KG    TPIQ   +P  L+GRD+ G A TG+GKT+ F+     + L   
Sbjct: 15  LHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHP 74

Query: 211 TKLPFLPGEGPYGLIICPSRELARQTH 237
                   + P  LI+ P+RELA Q H
Sbjct: 75  APEDRKVNQ-PRALIMAPTRELAVQIH 100

Length = 423

>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score = 59.5 bits (144), Expect = 3e-10
 Identities = 36/96 (37%), Positives = 52/96 (54%), Gaps = 8/96 (8%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           SF  +KL E L+R + + G +KP+ IQ +GI   L G D IG A +G+GKT  FV+  L 
Sbjct: 29  SFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAAL- 87

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
               Q         +    LI+ P+RELA+Q   ++
Sbjct: 88  ----QLIDYDLNACQ---ALILAPTRELAQQIQKVV 116

Length = 401

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

 Score = 59.2 bits (143), Expect = 3e-10
 Identities = 35/90 (38%), Positives = 45/90 (50%), Gaps = 1/90 (1%)

Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
           F    L   L+ A+   G    TPIQ Q +   L+G D IG A TG+GKT  F++ I+  
Sbjct: 89  FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148

Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQ 235
            L+         GE P  LII P+REL  Q
Sbjct: 149 LLQTPPPKERYMGE-PRALIIAPTRELVVQ 177

Length = 475

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

 Score = 55.4 bits (134), Expect = 8e-10
 Identities = 26/93 (27%), Positives = 41/93 (44%), Gaps = 12/93 (12%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           RD++  A TGSGKTL  +LPIL               +G   L++ P+RELA Q  + ++
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILEL---------LDSLKGGQVLVLAPTRELANQVAERLK 51

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
                    ++    IGG  + Q   ++     
Sbjct: 52  ---ELFGEGIKVGYLIGGTSIKQQEKLLSGKTD 81

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

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

 Score = 57.5 bits (139), Expect = 1e-09
 Identities = 31/93 (33%), Positives = 48/93 (51%), Gaps = 3/93 (3%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           R ++  A TGSGKT  F++PI+  C    +  P      P  +++ P+REL  Q  D  Q
Sbjct: 159 RSLLVSADTGSGKTASFLVPIISRCCTIRSGHP-SEQRNPLAMVLTPTRELCVQVED--Q 215

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
                  +P +T L +GG  M Q L  I++G++
Sbjct: 216 AKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVE 248

Length = 518

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

 Score = 56.5 bits (137), Expect = 4e-09
 Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 4/84 (4%)

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           L   +    + K     TP Q   IP   SG +++ IA TGSGKT    LP++   L   
Sbjct: 8   LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLS-L 65

Query: 211 TKLPFLPGEGPYGLIICPSRELAR 234
            K      +G Y L I P + L  
Sbjct: 66  GKGK--LEDGIYALYISPLKALNN 87

Length = 814

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

 Score = 54.3 bits (131), Expect = 2e-08
 Identities = 25/72 (34%), Positives = 33/72 (45%)

Query: 140 PPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFV 199
            P   S       ESL  AL   GI++    QV  +     GR+++    TGSGKT  F+
Sbjct: 44  RPGKTSEFPELRDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFL 103

Query: 200 LPILMFCLEQET 211
           LPIL   L   +
Sbjct: 104 LPILDHLLRDPS 115

Length = 851

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

 Score = 50.7 bits (122), Expect = 2e-07
 Identities = 32/87 (36%), Positives = 41/87 (47%), Gaps = 13/87 (14%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG-LIICPSRELARQTHDII 66
           RD++G A TG+GKT  F+LP L   L+   +       GP   LI+ P+RELA Q  D  
Sbjct: 39  RDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKS-----GPPRILILTPTRELAMQVAD-- 91

Query: 67  QYYCAALPIPLRTCLAI--GGVP-MNQ 90
                 L       +A   GGV  MN 
Sbjct: 92  --QARELAKHTHLDIATITGGVAYMNH 116

Length = 434

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

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 9/60 (15%)

Query: 182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           RD++  A TGSGKTL  +LPIL               +G   L++ P+RELA Q  + ++
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILEL---------LDSLKGGQVLVLAPTRELANQVAERLK 51

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

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

 Score = 50.6 bits (121), Expect = 3e-07
 Identities = 32/93 (34%), Positives = 51/93 (54%), Gaps = 6/93 (6%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY-GLIICPSRELARQTHDII 66
           RD++  A TG+GKT  F LP+L   + ++   P   G  P   LI+ P+RELA Q  + +
Sbjct: 39  RDLMASAQTGTGKTAGFTLPLLQHLITRQ---PHAKGRRPVRALILTPTRELAAQIGENV 95

Query: 67  QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGI 99
           + Y   L I  R+ +  GGV +N  +  ++ G+
Sbjct: 96  RDYSKYLNI--RSLVVFGGVSINPQMMKLRGGV 126

Length = 456

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

 Score = 49.2 bits (117), Expect = 8e-07
 Identities = 32/92 (34%), Positives = 50/92 (54%), Gaps = 3/92 (3%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D+ G A TG+GKTL F++ ++   L +       P E P  LI+ P+RELA Q H    
Sbjct: 47  GDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKP-EDPRALILAPTRELAIQIHKDAV 105

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGI 99
            + A L   LR  L  GGV  ++  +++++G+
Sbjct: 106 KFGADL--GLRFALVYGGVDYDKQRELLQQGV 135

Length = 572

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

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 26/56 (46%), Positives = 35/56 (62%), Gaps = 8/56 (14%)

Query: 6  NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 61
          N RD++G+A TGSGKT  F LP L+  L+ E K P +       L++ P+RELA Q
Sbjct: 42 NGRDVLGMAQTGSGKTAAFSLP-LLHNLDPELKAPQI-------LVLAPTRELAVQ 89

Length = 629

>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase

 Score = 44.3 bits (105), Expect = 3e-05
 Identities = 20/52 (38%), Positives = 29/52 (55%)

Query: 152 PESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL 203
              +V ALEA GI +P   Q +    A +GR ++    T SGK+L + LP+L
Sbjct: 22  HPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVL 73

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. Length = 742

>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]

 Score = 44.0 bits (104), Expect = 4e-05
 Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 11/89 (12%)

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAAL-SGRDIIGIAFTGSGKTLVFVLPILMFCLEQ 209
           +PE   R L+ +GI++  P+QV  + A L  G +++ ++ T SGKTL+  L  +   L  
Sbjct: 201 IPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSG 260

Query: 210 ETKLPFLPGEGPYGLIICPSRELARQTHD 238
             K+ FL           P   LA Q ++
Sbjct: 261 GKKMLFL----------VPLVALANQKYE 279

Length = 830

>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated

 Score = 41.8 bits (99), Expect = 2e-04
 Identities = 29/72 (40%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI 225
            P P Q++   AAL GR  + IA TGSGKTL   LP L+     E      P +G + L 
Sbjct: 13  TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEK-----PKKGLHTLY 67

Query: 226 ICPSRELARQTH 237
           I P R LA    
Sbjct: 68  ITPLRALAVDIA 79

Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H. Length = 803

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

 Score = 41.1 bits (97), Expect = 3e-04
 Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 11/98 (11%)

Query: 6   NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI 65
             RD+ G A TG+GKT+ F+     + L           + P  LI+ P+RELA      
Sbjct: 44  AGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQ-PRALIMAPTRELA------ 96

Query: 66  IQYYCAALPIP----LRTCLAIGGVPMNQSLDVIKKGI 99
           +Q +  A P+     L+  LA GG   ++ L V++ G+
Sbjct: 97  VQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGV 134

Length = 423

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

 Score = 40.6 bits (96), Expect = 5e-04
 Identities = 23/59 (38%), Positives = 29/59 (49%), Gaps = 14/59 (23%)

Query: 6  NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKL---PFLPGEGPYGLIICPSRELARQ 61
            +D+I  A TGSGKT  F L +L        KL    F        L++CP+RELA Q
Sbjct: 40 AGKDVIAQAKTGSGKTAAFGLGLL-------QKLDVKRF----RVQALVLCPTRELADQ 87

Length = 460

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

 Score = 40.4 bits (95), Expect = 6e-04
 Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 11/88 (12%)

Query: 150 KLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLPILMFCLE 208
           KL + ++  L+  GI +    Q + +    LS  +++  A TGSGKTL+ +L IL   LE
Sbjct: 15  KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLE 74

Query: 209 QETKLPFLPGEGPYGLIICPSRELARQT 236
              K+          + I P + LA + 
Sbjct: 75  GGGKV----------VYIVPLKALAEEK 92

Length = 766

>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 14/35 (40%), Positives = 22/35 (62%)

Query: 171 QVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
           Q + I A LSG+D + +  TG GK+L + +P L+ 
Sbjct: 22  QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL 56

Length = 590

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

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 23/54 (42%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 61
            D IG A TG+GKT  F++ I+   L+         GE P  LII P+REL  Q
Sbjct: 125 HDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGE-PRALIIAPTRELVVQ 177

Length = 475

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

 Score = 37.8 bits (88), Expect = 0.004
 Identities = 33/144 (22%), Positives = 56/144 (38%), Gaps = 32/144 (22%)

Query: 1   MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR 60
           +   R  R+++    TGSGKT  F+LPIL   L   +            L++ P+  LA 
Sbjct: 79  LRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA---------RALLLYPTNALAN 129

Query: 61  QTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPD 120
              + ++   + LP  +      G  P  +   +I+               P  +L+ PD
Sbjct: 130 DQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRN-------------PPDILLTNPD 176

Query: 121 QVHDIIRR----------NLRILV 134
            +H ++ R          NL+ LV
Sbjct: 177 MLHYLLLRNHDAWLWLLRNLKYLV 200

Length = 851

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	252
KOG0331|consensus	519		100.0
KOG0330|consensus	476		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0342|consensus	543		99.97
KOG0335|consensus	482		99.97
KOG0348|consensus	708		99.97
KOG0338|consensus	691		99.97
KOG0345|consensus	567		99.97
KOG0328|consensus	400		99.97
KOG0343|consensus	758		99.96
KOG0341|consensus	610		99.96
KOG0346|consensus	569		99.96
KOG0333|consensus	673		99.96
KOG0340|consensus	442		99.96
KOG0326|consensus	459		99.96
PTZ00110	545	helicase; Provisional	99.95
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.95
KOG0339|consensus	731		99.95
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.95
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.95
KOG0336|consensus	629		99.94
KOG0334|consensus	997		99.94
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.94
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.94
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.94
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.94
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.94
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.94
KOG0337|consensus	529		99.93
KOG0347|consensus	731		99.93
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.92
KOG0350|consensus	620		99.92
KOG0341|consensus	610		99.9
KOG0327|consensus	397		99.9
PRK13767	876	ATP-dependent helicase; Provisional	99.89
PTZ00424	401	helicase 45; Provisional	99.88
KOG0332|consensus	477		99.88
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.87
KOG4284|consensus	980		99.87
KOG0329|consensus	387		99.86
COG1205	851	Distinct helicase family with a unique C-terminal	99.86
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.85
PRK09401	1176	reverse gyrase; Reviewed	99.82
PRK02362	737	ski2-like helicase; Provisional	99.8
PRK14701	1638	reverse gyrase; Provisional	99.8
KOG0344|consensus	593		99.8
PRK00254	720	ski2-like helicase; Provisional	99.8
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.79
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.78
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.76
PRK01172	674	ski2-like helicase; Provisional	99.76
PTZ00110	545	helicase; Provisional	99.76
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.74
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.74
KOG0330|consensus	476		99.73
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.73
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.72
KOG0333|consensus	673		99.72
KOG0349|consensus	725		99.71
COG1204	766	Superfamily II helicase [General function predicti	99.71
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.7
KOG0346|consensus	569		99.7
KOG0331|consensus	519		99.7
KOG0339|consensus	731		99.69
KOG0334|consensus	997		99.69
PRK10689	1147	transcription-repair coupling factor; Provisional	99.68
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.68
KOG0340|consensus	442		99.68
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.67
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.67
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.66
KOG0338|consensus	691		99.66
PHA02653	675	RNA helicase NPH-II; Provisional	99.65
COG1202	830	Superfamily II helicase, archaea-specific [General	99.65
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.63
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.61
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.61
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.59
KOG0348|consensus	708		99.59
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.59
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.57
KOG0335|consensus	482		99.57
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.57
KOG0952|consensus	1230		99.56
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.56
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.55
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.55
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.54
KOG0347|consensus	731		99.53
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.53
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.52
KOG0345|consensus	567		99.52
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.51
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.51
KOG0328|consensus	400		99.51
KOG0342|consensus	543		99.49
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.49
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.47
KOG0343|consensus	758		99.44
KOG0344|consensus	593		99.44
KOG0326|consensus	459		99.42
PTZ00424	401	helicase 45; Provisional	99.42
KOG0337|consensus	529		99.41
KOG0336|consensus	629		99.36
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.35
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.34
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.33
KOG0329|consensus	387		99.29
KOG0332|consensus	477		99.28
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.28
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.27
PRK05580	679	primosome assembly protein PriA; Validated	99.26
KOG0327|consensus	397		99.25
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.19
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.19
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.17
PHA02558	501	uvsW UvsW helicase; Provisional	99.17
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.13
KOG0951|consensus	1674		99.09
PRK02362	737	ski2-like helicase; Provisional	99.09
PRK13766	773	Hef nuclease; Provisional	99.06
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.04
PRK00254	720	ski2-like helicase; Provisional	99.04
KOG0352|consensus	641		99.02
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.01
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.01
KOG0350|consensus	620		99.0
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.99
PRK13767	876	ATP-dependent helicase; Provisional	98.96
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.94
KOG4284|consensus	980		98.93
PRK09694	878	helicase Cas3; Provisional	98.93
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.92
PRK01172	674	ski2-like helicase; Provisional	98.9
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	98.89
KOG0354|consensus	746		98.87
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.86
KOG0351|consensus	941		98.85
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.84
PRK09401	1176	reverse gyrase; Reviewed	98.82
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.8
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.77
PRK14701	1638	reverse gyrase; Provisional	98.76
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.76
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.73
COG1205	851	Distinct helicase family with a unique C-terminal	98.69
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	98.69
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.66
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.65
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.65
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	98.65
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	98.62
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.56
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.46
PRK10689	1147	transcription-repair coupling factor; Provisional	98.44
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.43
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.4
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.39
KOG0353|consensus	695		98.36
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.31
PRK09200	790	preprotein translocase subunit SecA; Reviewed	98.3
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.3
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.28
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.27
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.25
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.23
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.2
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.18
KOG0948|consensus	1041		98.18
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.15
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.15
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.14
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.1
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.09
KOG0950|consensus	1008		98.02
PHA02558	501	uvsW UvsW helicase; Provisional	98.01
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.01
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.0
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.96
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.89
KOG0951|consensus	1674		97.86
PF13245	76	AAA_19: Part of AAA domain	97.85
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.85
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.84
PHA02653	675	RNA helicase NPH-II; Provisional	97.82
COG1204	766	Superfamily II helicase [General function predicti	97.81
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	97.8
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	97.79
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	97.78
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	97.75
PRK05580	679	primosome assembly protein PriA; Validated	97.73
COG1202	830	Superfamily II helicase, archaea-specific [General	97.69
KOG0952|consensus	1230		97.67
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.66
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	97.6
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	97.57
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.53
KOG0349|consensus	725		97.52
KOG0947|consensus	1248		97.37
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	97.31
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	97.3
PRK13766	773	Hef nuclease; Provisional	97.3
KOG0353|consensus	695		97.27
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	97.23
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	97.23
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.22
PRK12904	830	preprotein translocase subunit SecA; Reviewed	97.16
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	97.16
PRK13107	908	preprotein translocase subunit SecA; Reviewed	97.15
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.08
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.04
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	96.97
PRK14873	665	primosome assembly protein PriA; Provisional	96.95
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	96.9
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	96.83
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	96.72
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.61
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	96.61
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	96.59
PRK09694	878	helicase Cas3; Provisional	96.52
KOG0354|consensus	746		96.51
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	96.42
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	96.35
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	96.24
KOG0949|consensus	1330		96.07
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.04
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.95
PF13245	76	AAA_19: Part of AAA domain	95.95
PRK13851	344	type IV secretion system protein VirB11; Provision	95.87
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	95.85
KOG0352|consensus	641		95.82
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	95.79
KOG4150|consensus	1034		95.79
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.78
PRK15483	986	type III restriction-modification system StyLTI en	95.71
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.67
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.65
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	95.59
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	95.55
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	95.54
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	95.42
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	95.39
KOG1803|consensus	649		95.24
PRK12326	764	preprotein translocase subunit SecA; Reviewed	95.15
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	95.1
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	95.08
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.08
TIGR00376	637	DNA helicase, putative. The gene product may repre	95.06
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	95.02
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	95.0
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.95
COG0610	962	Type I site-specific restriction-modification syst	94.9
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.81
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.8
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	94.76
PRK13897	606	type IV secretion system component VirD4; Provisio	94.64
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	94.58
KOG0922|consensus	674		94.43
CHL00122	870	secA preprotein translocase subunit SecA; Validate	94.43
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	94.39
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	94.37
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	94.29
COG4096	875	HsdR Type I site-specific restriction-modification	94.28
PRK11054	684	helD DNA helicase IV; Provisional	94.22
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	94.1
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	94.07
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	94.06
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	93.96
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	93.93
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	93.9
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	93.81
PF12846	304	AAA_10: AAA-like domain	93.71
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	93.69
PRK08181	269	transposase; Validated	93.66
PRK13850	670	type IV secretion system protein VirD4; Provisiona	93.61
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	93.59
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	93.57
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	93.52
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	93.35
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	93.35
KOG0953|consensus	700		93.31
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	93.29
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.22
PRK13876	663	conjugal transfer coupling protein TraG; Provision	93.15
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	93.11
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	93.09
COG3973	747	Superfamily I DNA and RNA helicases [General funct	93.06
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	93.04
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	92.98
COG1484	254	DnaC DNA replication protein [DNA replication, rec	92.91
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	92.9
COG1198	730	PriA Primosomal protein N' (replication factor Y)	92.87
PRK04914	956	ATP-dependent helicase HepA; Validated	92.81
smart00382	148	AAA ATPases associated with a variety of cellular	92.75
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	92.68
PRK06921	266	hypothetical protein; Provisional	92.67
PRK13880	636	conjugal transfer coupling protein TraG; Provision	92.5
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	92.49
PRK13764	602	ATPase; Provisional	92.47
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	92.39
PRK10536	262	hypothetical protein; Provisional	92.26
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	92.22
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	92.2
PRK13822	641	conjugal transfer coupling protein TraG; Provision	92.15
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	92.12
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.11
KOG0351|consensus	941		92.07
PRK12377	248	putative replication protein; Provisional	91.98
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	91.97
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	91.81
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	91.78
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	91.76
PRK06526	254	transposase; Provisional	91.73
PRK05973	237	replicative DNA helicase; Provisional	91.72
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	91.7
COG3587	985	Restriction endonuclease [Defense mechanisms]	91.68
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	91.65
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	91.65
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	91.4
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	91.35
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	91.33
PF13555	62	AAA_29: P-loop containing region of AAA domain	91.32
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	91.27
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	91.23
PRK08533	230	flagellar accessory protein FlaH; Reviewed	91.21
PRK06835	329	DNA replication protein DnaC; Validated	91.16
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	91.15
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	91.09
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	91.07
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	91.04
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	91.03
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	91.03
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	91.0
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	90.87
PRK09183	259	transposase/IS protein; Provisional	90.84
PRK04328	249	hypothetical protein; Provisional	90.76
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	90.75
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	90.72
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	90.44
PRK10875	615	recD exonuclease V subunit alpha; Provisional	90.38
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	90.27
PRK08116	268	hypothetical protein; Validated	89.96
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	89.95
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	89.91
PRK08727	233	hypothetical protein; Validated	89.88
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	89.86
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	89.67
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	89.49
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	89.47
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	89.33
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	89.3
PF09439	181	SRPRB: Signal recognition particle receptor beta s	89.23
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	89.2
TIGR00376	637	DNA helicase, putative. The gene product may repre	89.11
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	89.06
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	89.01
KOG1802|consensus	935		89.01
PRK05298	652	excinuclease ABC subunit B; Provisional	88.99
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	88.91
COG3973	747	Superfamily I DNA and RNA helicases [General funct	88.7
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	88.66
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	88.56
KOG1133|consensus	821		88.34
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	88.3
KOG1942|consensus	456		88.24
PTZ00301	210	uridine kinase; Provisional	88.24
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	88.24
PF02500	284	DNA_pack_N: Probable DNA packing protein, N-termin	88.19
PRK07952	244	DNA replication protein DnaC; Validated	88.14
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	87.87
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	87.83
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	87.56
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	87.51
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	87.45
TIGR00665	434	DnaB replicative DNA helicase. This model describe	87.38
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	87.33
KOG0745|consensus	564		87.15
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	87.06
PF00004	132	AAA: ATPase family associated with various cellula	86.97
KOG2340|consensus	698		86.9
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	86.84
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	86.81
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	86.8
KOG1132|consensus	945		86.75
PRK10436	462	hypothetical protein; Provisional	86.61
cd01394	218	radB RadB. The archaeal protein radB shares simila	86.55
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	86.53
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	86.47
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	86.32
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	86.23
KOG0060|consensus	659		86.16
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	86.14
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	86.12
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	86.07
KOG0389|consensus	941		85.81
KOG1533|consensus	290		85.75
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	85.58
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	85.36
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	85.36
TIGR02237	209	recomb_radB DNA repair and recombination protein R	85.32
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	85.28
PRK04296	190	thymidine kinase; Provisional	85.18
PRK13700	732	conjugal transfer protein TraD; Provisional	85.18
PRK05595	444	replicative DNA helicase; Provisional	85.17
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	85.13
PHA00729	226	NTP-binding motif containing protein	85.11
KOG0385|consensus	971		84.99
PRK07004	460	replicative DNA helicase; Provisional	84.9
PRK05748	448	replicative DNA helicase; Provisional	84.87
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	84.85
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	84.73
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	84.55
PRK08939	306	primosomal protein DnaI; Reviewed	84.55
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	84.53
PRK11823	446	DNA repair protein RadA; Provisional	84.45
PRK08506	472	replicative DNA helicase; Provisional	84.44
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	84.29
PF05729	166	NACHT: NACHT domain	84.14
COG4889	1518	Predicted helicase [General function prediction on	84.12
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	84.09
PLN02165	334	adenylate isopentenyltransferase	84.06
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	84.01
KOG1802|consensus	935		83.99
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	83.95
COG0606	490	Predicted ATPase with chaperone activity [Posttran	83.95
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	83.92
cd01918	149	HprK_C HprK/P, the bifunctional histidine-containi	83.75
PRK11054	684	helD DNA helicase IV; Provisional	83.69
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	83.66
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	83.63
KOG0924|consensus	1042		83.46
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	83.44
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	83.44
PRK06067	234	flagellar accessory protein FlaH; Validated	83.41
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	83.34
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	83.19
PRK05642	234	DNA replication initiation factor; Validated	83.08
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	83.03
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	83.01
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	82.8
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	82.74
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	82.72
CHL00181	287	cbbX CbbX; Provisional	82.44
PHA02244	383	ATPase-like protein	82.43
TIGR02533	486	type_II_gspE general secretory pathway protein E.	82.41
PHA02542	473	41 41 helicase; Provisional	82.4
PRK06904	472	replicative DNA helicase; Validated	82.38
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	82.1
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	81.99
PRK14530	215	adenylate kinase; Provisional	81.93
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	81.79
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	81.76
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	81.7
PRK08840	464	replicative DNA helicase; Provisional	81.68
PRK09302	509	circadian clock protein KaiC; Reviewed	81.68
PRK13531	498	regulatory ATPase RavA; Provisional	81.5
PRK00771	437	signal recognition particle protein Srp54; Provisi	81.46
PRK00149	450	dnaA chromosomal replication initiation protein; R	81.44
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	81.42
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	81.42
PRK14087	450	dnaA chromosomal replication initiation protein; P	81.41
PF00005	137	ABC_tran: ABC transporter This structure is on hol	81.34
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	81.32
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	81.28
PRK08903	227	DnaA regulatory inactivator Hda; Validated	81.28
KOG1002|consensus	791		81.19
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	81.11
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	81.03
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	80.99
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	80.88
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	80.87
PRK08006	471	replicative DNA helicase; Provisional	80.87
PRK00300	205	gmk guanylate kinase; Provisional	80.78
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	80.69
PRK00131	175	aroK shikimate kinase; Reviewed	80.62
KOG1131|consensus	755		80.62
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	80.39
PRK08084	235	DNA replication initiation factor; Provisional	80.21
KOG1803|consensus	649		80.17
PRK07261	171	topology modulation protein; Provisional	80.07
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	80.06
PF00735	281	Septin: Septin; InterPro: IPR000038 Septins consti	80.02

>KOG0331|consensus

Probab=100.00  E-value=3.1e-37  Score=264.07  Aligned_cols=221  Identities=23%  Similarity=0.287  Sum_probs=168.6

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|||++.+|.||||||+||+||+++++....  ......++|++||++||||||+||.+++.++++.++  +++.
T Consensus       122 wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~--~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~--~~~~  197 (519)
T KOG0331|consen  122 WPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQ--GKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLR--LRST  197 (519)
T ss_pred             cceeccCCceEEEeccCCcchhhhhhHHHHHHHhcc--ccccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCC--ccEE
Confidence            799999999999999999999999999999998731  122344689999999999999999999999999887  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      +++||.++..|...+++++||+  |+|    |||+.++.++....+++ +.++|+||+     |+|.+|||.+++.+++.
T Consensus       198 cvyGG~~~~~Q~~~l~~gvdiv--iaT----PGRl~d~le~g~~~l~~-v~ylVLDEA-----DrMldmGFe~qI~~Il~  265 (519)
T KOG0331|consen  198 CVYGGAPKGPQLRDLERGVDVV--IAT----PGRLIDLLEEGSLNLSR-VTYLVLDEA-----DRMLDMGFEPQIRKILS  265 (519)
T ss_pred             EEeCCCCccHHHHHHhcCCcEE--EeC----ChHHHHHHHcCCccccc-eeEEEeccH-----HhhhccccHHHHHHHHH
Confidence            9999999999999999999984  555    99999999999999998 999999998     99999999999999998


Q ss_pred             HCCCCCChHHHHhhhhhhhcC-----------C--cEEEEccC----------------CCchhHHhHHHHHHHHHhhhc
Q psy7786         161 AKGIKKPTPIQVQGIPAALSG-----------R--DIIGIAFT----------------GSGKTLVFVLPILMFCLEQET  211 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~-----------~--~~~~~~~~----------------g~gKt~~~~~~~l~~i~~~~~  211 (252)
                      +..-.   ..|..+++++.++           .  .+.+....                ...| ..-+.++|..++    
T Consensus       266 ~i~~~---~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K-~~~l~~lL~~~~----  337 (519)
T KOG0331|consen  266 QIPRP---DRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAK-LRKLGKLLEDIS----  337 (519)
T ss_pred             hcCCC---cccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHH-HHHHHHHHHHHh----
Confidence            86311   1133333333221           1  11111100                1111 111122222222    


Q ss_pred             cCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH-hhCCCC
Q psy7786         212 KLPFLPGEGPYGLIICPSRELARQTHDIIQYYC-AALPIG  250 (252)
Q Consensus       212 ~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~-~~~~i~  250 (252)
                           .+...++||||+|+..|++++..+++.+ +...+|
T Consensus       338 -----~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iH  372 (519)
T KOG0331|consen  338 -----SDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIH  372 (519)
T ss_pred             -----ccCCCcEEEEecchhhHHHHHHHHHhcCcceeeec
Confidence                 2346789999999999999999998853 444443

>KOG0330|consensus

Probab=100.00  E-value=1.4e-34  Score=235.18  Aligned_cols=205  Identities=23%  Similarity=0.311  Sum_probs=154.3

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||+++.|+|+|+.|+||||||.||+||++++++.+++        .++|||++||||||.||.+.++.|+..+|  +++.
T Consensus        92 iP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~--------~~~~lVLtPtRELA~QI~e~fe~Lg~~ig--lr~~  161 (476)
T KOG0330|consen   92 IPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPK--------LFFALVLTPTRELAQQIAEQFEALGSGIG--LRVA  161 (476)
T ss_pred             cchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCC--------CceEEEecCcHHHHHHHHHHHHHhccccC--eEEE
Confidence            7999999999999999999999999999999998663        58999999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCCh-hHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPD-QVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~-~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      +++||.++..|...+.+.+||.  |+|    ||+|.++.+ .....+++ ++++|.||+     +++.++.|.+.+-.++
T Consensus       162 ~lvGG~~m~~q~~~L~kkPhil--VaT----PGrL~dhl~~Tkgf~le~-lk~LVlDEA-----DrlLd~dF~~~ld~IL  229 (476)
T KOG0330|consen  162 VLVGGMDMMLQANQLSKKPHIL--VAT----PGRLWDHLENTKGFSLEQ-LKFLVLDEA-----DRLLDMDFEEELDYIL  229 (476)
T ss_pred             EEecCchHHHHHHHhhcCCCEE--EeC----cHHHHHHHHhccCccHHH-hHHHhhchH-----HhhhhhhhHHHHHHHH
Confidence            9999999999988888887773  444    777777766 34555555 999999998     8999999999987777


Q ss_pred             HHCCCCCChHHHHhhhhhhhcCC----------cEEEEc-----------------cCCCchhHHhHHHHHHHHHhhhcc
Q psy7786         160 EAKGIKKPTPIQVQGIPAALSGR----------DIIGIA-----------------FTGSGKTLVFVLPILMFCLEQETK  212 (252)
Q Consensus       160 ~~~~~~~p~~iQ~~~~p~~~~~~----------~~~~~~-----------------~~g~gKt~~~~~~~l~~i~~~~~~  212 (252)
                      ...-    ..-|...+++++..+          +..-++                 .++..| .+|++.++..       
T Consensus       230 k~ip----~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K-~~yLV~ll~e-------  297 (476)
T KOG0330|consen  230 KVIP----RERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDK-DTYLVYLLNE-------  297 (476)
T ss_pred             HhcC----ccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEecccccc-chhHHHHHHh-------
Confidence            6642    222222222222210          111011                 111222 2333433332       


Q ss_pred             CCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         213 LPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       213 ~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                           ..+..+||||+|...+++++-.|+.++
T Consensus       298 -----~~g~s~iVF~~t~~tt~~la~~L~~lg  324 (476)
T KOG0330|consen  298 -----LAGNSVIVFCNTCNTTRFLALLLRNLG  324 (476)
T ss_pred             -----hcCCcEEEEEeccchHHHHHHHHHhcC
Confidence                 124569999999999999999988765

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

Probab=100.00  E-value=3.6e-33  Score=246.41  Aligned_cols=217  Identities=22%  Similarity=0.273  Sum_probs=159.4

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.++.|+|++++|+||||||+||++|+++.+......      ....+||++||||||.|+++.+++++++++ ++++.
T Consensus        60 IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~------~~~~aLil~PTRELA~Qi~~~~~~~~~~~~-~~~~~  132 (513)
T COG0513          60 IPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVER------KYVSALILAPTRELAVQIAEELRKLGKNLG-GLRVA  132 (513)
T ss_pred             HHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhccccc------CCCceEEECCCHHHHHHHHHHHHHHHhhcC-CccEE
Confidence            78999999999999999999999999999997643110      112299999999999999999999999983 38999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      +++||.++..|.+.+++++||+  |+|    |||++++.++....+.+ ++++|.||+     +.|.++||.+++...+.
T Consensus       133 ~i~GG~~~~~q~~~l~~~~~iv--VaT----PGRllD~i~~~~l~l~~-v~~lVlDEA-----DrmLd~Gf~~~i~~I~~  200 (513)
T COG0513         133 VVYGGVSIRKQIEALKRGVDIV--VAT----PGRLLDLIKRGKLDLSG-VETLVLDEA-----DRMLDMGFIDDIEKILK  200 (513)
T ss_pred             EEECCCCHHHHHHHHhcCCCEE--EEC----ccHHHHHHHcCCcchhh-cCEEEeccH-----hhhhcCCCHHHHHHHHH
Confidence            9999999999999999988884  555    99999999999777777 999999998     99999999999988887


Q ss_pred             HCCC---------CCChHHHHhhhhhhhcCCcEEEEccCC--C-chh---------HHhHHHHHHHHHhhhccCCCCCCC
Q psy7786         161 AKGI---------KKPTPIQVQGIPAALSGRDIIGIAFTG--S-GKT---------LVFVLPILMFCLEQETKLPFLPGE  219 (252)
Q Consensus       161 ~~~~---------~~p~~iQ~~~~p~~~~~~~~~~~~~~g--~-gKt---------~~~~~~~l~~i~~~~~~~~~~~~~  219 (252)
                      ....         ..|..+.......+.+...+.+.....  . .+.         ...-...+..++...        .
T Consensus       201 ~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~--------~  272 (513)
T COG0513         201 ALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDE--------D  272 (513)
T ss_pred             hCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcC--------C
Confidence            7531         112222222221111111122211110  0 000         001144555555432        2


Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..++||||+|+..|+.++..|++.+
T Consensus       273 ~~~~IVF~~tk~~~~~l~~~l~~~g  297 (513)
T COG0513         273 EGRVIVFVRTKRLVEELAESLRKRG  297 (513)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHCC
Confidence            3379999999999999999998775

>KOG0342|consensus

Probab=99.97  E-value=1.6e-31  Score=223.11  Aligned_cols=210  Identities=22%  Similarity=0.293  Sum_probs=161.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||+++.|+|++++|.||||||+||++|.++.+.....    .+.++..++|++||||||.|++.+++.+.++.. .+.+.
T Consensus       113 i~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~----~~r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~-~~~v~  187 (543)
T KOG0342|consen  113 IPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKF----KPRNGTGVLIICPTRELAMQIFAEAKELLKYHE-SITVG  187 (543)
T ss_pred             cCccCCCccceeeeccCCCceeeehhHHHHHHHhccc----CCCCCeeEEEecccHHHHHHHHHHHHHHHhhCC-CcceE
Confidence            6899999999999999999999999999999876543    334789999999999999999999999999984 38999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .+.||++.....+.+.+++.|.  |+|    ||||+++.++....+.+.++++|+||+     ++..++||..++.+++.
T Consensus       188 ~viGG~~~~~e~~kl~k~~nil--iAT----PGRLlDHlqNt~~f~~r~~k~lvlDEA-----DrlLd~GF~~di~~Ii~  256 (543)
T KOG0342|consen  188 IVIGGNNFSVEADKLVKGCNIL--IAT----PGRLLDHLQNTSGFLFRNLKCLVLDEA-----DRLLDIGFEEDVEQIIK  256 (543)
T ss_pred             EEeCCccchHHHHHhhccccEE--EeC----CchHHhHhhcCCcchhhccceeEeecc-----hhhhhcccHHHHHHHHH
Confidence            9999999998889999998885  666    999999999988877777999999998     99999999999988887


Q ss_pred             HCCCCCChHHHHhhhhhhhcC-----------CcEEEEccC--C----------------CchhHHhHHHHHHHHHhhhc
Q psy7786         161 AKGIKKPTPIQVQGIPAALSG-----------RDIIGIAFT--G----------------SGKTLVFVLPILMFCLEQET  211 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~-----------~~~~~~~~~--g----------------~gKt~~~~~~~l~~i~~~~~  211 (252)
                      -..    ...|...++++...           +|.......  +                +.+.+..++.++.   ++. 
T Consensus       257 ~lp----k~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~~~LK---k~~-  328 (543)
T KOG0342|consen  257 ILP----KQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLYTFLK---KNI-  328 (543)
T ss_pred             hcc----ccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHHHHHHHHH---Hhc-
Confidence            643    33333333333211           122222211  1                1121233333332   221 


Q ss_pred             cCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         212 KLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       212 ~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                             ...+++|||+|-..+..+++.|+
T Consensus       329 -------~~~KiiVF~sT~~~vk~~~~lL~  351 (543)
T KOG0342|consen  329 -------KRYKIIVFFSTCMSVKFHAELLN  351 (543)
T ss_pred             -------CCceEEEEechhhHHHHHHHHHh
Confidence                   12579999999999999998887

>KOG0335|consensus

Probab=99.97  E-value=6.2e-31  Score=222.10  Aligned_cols=230  Identities=20%  Similarity=0.263  Sum_probs=171.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCC--CCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcc
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPG--EGPYGLIICPSRELARQTHDIIQYYCAALPIPLR   78 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~--~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~   78 (252)
                      ||.+..|+|++++|+||||||.||++|++.+++...........  .+|++||++||||||.|++++++++.-..+  ++
T Consensus       105 ip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~--~~  182 (482)
T KOG0335|consen  105 IPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSG--MK  182 (482)
T ss_pred             cceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhccccc--ce
Confidence            78999999999999999999999999999999987654333333  369999999999999999999999987776  89


Q ss_pred             eeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-CCCCHHHHH
Q psy7786          79 TCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLVR  157 (252)
Q Consensus        79 ~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~~  157 (252)
                      +..+|||.+...+.+...+++||.  ++|    ||+|.++.++....+.+ ++++|+||+     ++|.+ |+|.+++.+
T Consensus       183 ~~~~ygg~~~~~q~~~~~~gcdIl--vaT----pGrL~d~~e~g~i~l~~-~k~~vLDEA-----DrMlD~mgF~p~Ir~  250 (482)
T KOG0335|consen  183 SVVVYGGTDLGAQLRFIKRGCDIL--VAT----PGRLKDLIERGKISLDN-CKFLVLDEA-----DRMLDEMGFEPQIRK  250 (482)
T ss_pred             eeeeeCCcchhhhhhhhccCccEE--Eec----Cchhhhhhhcceeehhh-CcEEEecch-----HHhhhhccccccHHH
Confidence            999999999999999999999995  555    99999999999999998 999999998     89998 999999988


Q ss_pred             HHHHCCC-------------CCChHHHHhhhhhhhcCCcEEEEccCCCch-----hHHh-----HHHHHHHHHhhhccC-
Q psy7786         158 ALEAKGI-------------KKPTPIQVQGIPAALSGRDIIGIAFTGSGK-----TLVF-----VLPILMFCLEQETKL-  213 (252)
Q Consensus       158 ~l~~~~~-------------~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gK-----t~~~-----~~~~l~~i~~~~~~~-  213 (252)
                      ++...+.             ..|..+|........+....+.....|+..     ...|     ..+.+..++.....- 
T Consensus       251 iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~  330 (482)
T KOG0335|consen  251 IVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEMEKRSKLLDLLNKDDGPP  330 (482)
T ss_pred             HhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecchhhHHHHHHHhhcccCCc
Confidence            8877754             235566664333333333344333333221     0111     122233222211100 


Q ss_pred             CCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         214 PFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       214 ~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      .......-.++|||.|++.|.+++..+...+
T Consensus       331 ~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~  361 (482)
T KOG0335|consen  331 SDGEPKWEKTLVFVETKRGADELAAFLSSNG  361 (482)
T ss_pred             ccCCcccceEEEEeeccchhhHHHHHHhcCC
Confidence            0011112379999999999999999987543

>KOG0348|consensus

Probab=99.97  E-value=8.2e-31  Score=220.79  Aligned_cols=166  Identities=28%  Similarity=0.389  Sum_probs=138.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|||++|.|+||||||+||++|+++.+..-..+..  ..+|+.||||+||||||.|+|+.+.+|.+...+ |-..
T Consensus       168 IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~--Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hW-IVPg  244 (708)
T KOG0348|consen  168 IPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQ--RSDGPYALVIVPTRELALQIYETVQKLLKPFHW-IVPG  244 (708)
T ss_pred             hhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCcccc--ccCCceEEEEechHHHHHHHHHHHHHHhcCceE-Eeec
Confidence            7999999999999999999999999999999976543322  446999999999999999999999999988775 5556


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .+.||...+...+.+++|++|.  |.|    ||||+++...-...-...++++|.||+     +++.++||..++-.++.
T Consensus       245 ~lmGGEkkKSEKARLRKGiNIL--IgT----PGRLvDHLknT~~i~~s~LRwlVlDEa-----DrlleLGfekdit~Il~  313 (708)
T KOG0348|consen  245 VLMGGEKKKSEKARLRKGINIL--IGT----PGRLVDHLKNTKSIKFSRLRWLVLDEA-----DRLLELGFEKDITQILK  313 (708)
T ss_pred             eeecccccccHHHHHhcCceEE--EcC----chHHHHHHhccchheeeeeeEEEecch-----hHHHhccchhhHHHHHH
Confidence            7899999999999999999984  554    999999998865554455999999998     99999999999966664


Q ss_pred             HC---------CCCCChHHHHhhhhhhhc
Q psy7786         161 AK---------GIKKPTPIQVQGIPAALS  180 (252)
Q Consensus       161 ~~---------~~~~p~~iQ~~~~p~~~~  180 (252)
                      ..         ..+.|...|...+++++.
T Consensus       314 ~v~~~~~~e~~~~~lp~q~q~mLlSATLt  342 (708)
T KOG0348|consen  314 AVHSIQNAECKDPKLPHQLQNMLLSATLT  342 (708)
T ss_pred             HHhhccchhcccccccHHHHhHhhhhhhH
Confidence            43         133455677777787764

>KOG0338|consensus

Probab=99.97  E-value=6e-32  Score=226.51  Aligned_cols=157  Identities=24%  Similarity=0.290  Sum_probs=130.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||..+-|||+++||-||||||.||.+|++.+++..+++     ....++||++||||||.|++++.++++.++.  +.++
T Consensus       212 IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~-----~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~--I~~~  284 (691)
T KOG0338|consen  212 IPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK-----VAATRVLVLVPTRELAIQVHSVTKQLAQFTD--ITVG  284 (691)
T ss_pred             ccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc-----CcceeEEEEeccHHHHHHHHHHHHHHHhhcc--ceee
Confidence            79999999999999999999999999999999987653     2457899999999999999999999999998  9999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||-+.+.|-+.|+..|||+  |+|    |||++++...-...-..++.++|.||+     ++|.+-+|..++-+++.
T Consensus       285 L~vGGL~lk~QE~~LRs~PDIV--IAT----PGRlIDHlrNs~sf~ldsiEVLvlDEA-----DRMLeegFademnEii~  353 (691)
T KOG0338|consen  285 LAVGGLDLKAQEAVLRSRPDIV--IAT----PGRLIDHLRNSPSFNLDSIEVLVLDEA-----DRMLEEGFADEMNEIIR  353 (691)
T ss_pred             eeecCccHHHHHHHHhhCCCEE--Eec----chhHHHHhccCCCccccceeEEEechH-----HHHHHHHHHHHHHHHHH
Confidence            9999999999999999999995  666    999999887754443444999999998     77777777777655554


Q ss_pred             HCCCCCChHHHHhhhhhhh
Q psy7786         161 AKGIKKPTPIQVQGIPAAL  179 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~  179 (252)
                      -    .|..-|...+++++
T Consensus       354 l----cpk~RQTmLFSATM  368 (691)
T KOG0338|consen  354 L----CPKNRQTMLFSATM  368 (691)
T ss_pred             h----ccccccceeehhhh
Confidence            4    35555555555544

>KOG0345|consensus

Probab=99.97  E-value=1.3e-30  Score=216.63  Aligned_cols=224  Identities=25%  Similarity=0.367  Sum_probs=156.6

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++++|+++.|+||||||+||++|++..+.....+.+.   ..+.||||+||||||.||.+++..|.+++. ++.+.
T Consensus        37 IPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~---~~vgalIIsPTRELa~QI~~V~~~F~~~l~-~l~~~  112 (567)
T KOG0345|consen   37 IPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPP---GQVGALIISPTRELARQIREVAQPFLEHLP-NLNCE  112 (567)
T ss_pred             hHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCc---cceeEEEecCcHHHHHHHHHHHHHHHHhhh-ccceE
Confidence            79999999999999999999999999999998665443222   268899999999999999999999999875 49999


Q ss_pred             eeeCCcccCcchhhhhh-cccccCCccccccCCccccCCChhHHHHHh-hhhceeeccCCCCCcccccccCCCCHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKK-GIQYNDPIKTSWRAPRCILSLPDQVHDIIR-RNLRILVEGDDVPPACCSFRLMKLPESLVRA  158 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~-~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~-~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~  158 (252)
                      +++||.+.++....+++ ++.|.  |+|    ||||.++..+....+. +.+.++|+||+     +++.+|||...+..+
T Consensus       113 l~vGG~~v~~Di~~fkee~~nIl--VgT----PGRL~di~~~~~~~l~~rsLe~LVLDEA-----DrLldmgFe~~~n~I  181 (567)
T KOG0345|consen  113 LLVGGRSVEEDIKTFKEEGPNIL--VGT----PGRLLDILQREAEKLSFRSLEILVLDEA-----DRLLDMGFEASVNTI  181 (567)
T ss_pred             EEecCccHHHHHHHHHHhCCcEE--EeC----chhHHHHHhchhhhccccccceEEecch-----HhHhcccHHHHHHHH
Confidence            99999999988888865 56663  444    9999998887544443 34999999998     999999999999888


Q ss_pred             HHHCCCCCCh----HHHHhhhhhh-hcC-CcEEEEccCC-------CchhHHhH-------HHHHHHHHhhhccCCCCCC
Q psy7786         159 LEAKGIKKPT----PIQVQGIPAA-LSG-RDIIGIAFTG-------SGKTLVFV-------LPILMFCLEQETKLPFLPG  218 (252)
Q Consensus       159 l~~~~~~~p~----~iQ~~~~p~~-~~~-~~~~~~~~~g-------~gKt~~~~-------~~~l~~i~~~~~~~~~~~~  218 (252)
                      +....=..-|    .-|.....-+ ..| +|-+-+....       ++-...|+       ...+.+++.+.        
T Consensus       182 Ls~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~~--------  253 (567)
T KOG0345|consen  182 LSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNN--------  253 (567)
T ss_pred             HHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhcc--------
Confidence            7765211111    1111111111 011 2222111111       11111111       22333333332        


Q ss_pred             CCcEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         219 EGPYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       219 ~~~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ...++|||.||..-++.-...+..+....
T Consensus       254 ~~kK~iVFF~TCasVeYf~~~~~~~l~~~  282 (567)
T KOG0345|consen  254 KDKKCIVFFPTCASVEYFGKLFSRLLKKR  282 (567)
T ss_pred             ccccEEEEecCcchHHHHHHHHHHHhCCC
Confidence            23579999999999999998888774443

>KOG0328|consensus

Probab=99.97  E-value=4.1e-32  Score=212.70  Aligned_cols=203  Identities=19%  Similarity=0.221  Sum_probs=160.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||++++|||++++|++|+|||.+|.+.+++.+....        +..+|||++||||||.|+.+++..++.+++  +.+.
T Consensus        58 i~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~--------r~tQ~lilsPTRELa~Qi~~vi~alg~~mn--vq~h  127 (400)
T KOG0328|consen   58 IPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISV--------RETQALILSPTRELAVQIQKVILALGDYMN--VQCH  127 (400)
T ss_pred             hhhhhcccceEEEecCCCCceEEEEeeeeeeccccc--------ceeeEEEecChHHHHHHHHHHHHHhccccc--ceEE
Confidence            689999999999999999999999999999887655        368999999999999999999999999999  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .+.||.+..+.++.+..|+++      +.++||++.++.++.....+. ++.+|+||+     +.|.+-||..++.+.+.
T Consensus       128 acigg~n~gedikkld~G~hv------VsGtPGrv~dmikr~~L~tr~-vkmlVLDEa-----DemL~kgfk~Qiydiyr  195 (400)
T KOG0328|consen  128 ACIGGKNLGEDIKKLDYGQHV------VSGTPGRVLDMIKRRSLRTRA-VKMLVLDEA-----DEMLNKGFKEQIYDIYR  195 (400)
T ss_pred             EEecCCccchhhhhhcccceE------eeCCCchHHHHHHhccccccc-eeEEEeccH-----HHHHHhhHHHHHHHHHH
Confidence            999999999999999988887      336699999999999988888 999999998     77777788888877776


Q ss_pred             HCCCCCChHHHHhhhhhhhcC----------------------------CcEEEEccCCCchhHHhHHHHHHHHHhhhcc
Q psy7786         161 AKGIKKPTPIQVQGIPAALSG----------------------------RDIIGIAFTGSGKTLVFVLPILMFCLEQETK  212 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~----------------------------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~  212 (252)
                      ..    |...|...++++++.                            +.+++......+|     ...+..+++..  
T Consensus       196 ~l----p~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewK-----fdtLcdLYd~L--  264 (400)
T KOG0328|consen  196 YL----PPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWK-----FDTLCDLYDTL--  264 (400)
T ss_pred             hC----CCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhh-----HhHHHHHhhhh--
Confidence            53    434444444443321                            1222222222333     44444444432  


Q ss_pred             CCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         213 LPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       213 ~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                            .-.|++||||||..++++.+.++.
T Consensus       265 ------tItQavIFcnTk~kVdwLtekm~~  288 (400)
T KOG0328|consen  265 ------TITQAVIFCNTKRKVDWLTEKMRE  288 (400)
T ss_pred             ------ehheEEEEecccchhhHHHHHHHh
Confidence                  235899999999999999999875

>KOG0343|consensus

Probab=99.96  E-value=1.3e-30  Score=220.44  Aligned_cols=217  Identities=22%  Similarity=0.281  Sum_probs=163.3

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||..|.|+|++..|.||||||+||++|+++++.+...    .+.+|..||||+||||||.|+++++.+.+++.+  +.+.
T Consensus       100 Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kW----s~~DGlGalIISPTRELA~QtFevL~kvgk~h~--fSaG  173 (758)
T KOG0343|consen  100 IPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKW----SPTDGLGALIISPTRELALQTFEVLNKVGKHHD--FSAG  173 (758)
T ss_pred             cchhccCcccccccccCCCceeeehHHHHHHHHHcCC----CCCCCceeEEecchHHHHHHHHHHHHHHhhccc--cccc
Confidence            7999999999999999999999999999999987654    345799999999999999999999999999988  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .+.||.+.+.....+.+ ++|.  |+|    ||||+.+.++...+-..++.++|+||+     +++.+|||..++-.++.
T Consensus       174 LiiGG~~~k~E~eRi~~-mNIL--VCT----PGRLLQHmde~~~f~t~~lQmLvLDEA-----DR~LDMGFk~tL~~Ii~  241 (758)
T KOG0343|consen  174 LIIGGKDVKFELERISQ-MNIL--VCT----PGRLLQHMDENPNFSTSNLQMLVLDEA-----DRMLDMGFKKTLNAIIE  241 (758)
T ss_pred             eeecCchhHHHHHhhhc-CCeE--Eec----hHHHHHHhhhcCCCCCCcceEEEeccH-----HHHHHHhHHHHHHHHHH
Confidence            99999888777666654 3442  444    999999988877666667999999998     99999999999877776


Q ss_pred             HCCCCCChHHHHhhhhhhhc------------CCcEEEEccC---C-------------CchhHHhHHHHHHHHHhhhcc
Q psy7786         161 AKGIKKPTPIQVQGIPAALS------------GRDIIGIAFT---G-------------SGKTLVFVLPILMFCLEQETK  212 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~------------~~~~~~~~~~---g-------------~gKt~~~~~~~l~~i~~~~~~  212 (252)
                      ..    |..-|...++++..            ....+-....   +             .+.-+.+++..+    ...  
T Consensus       242 ~l----P~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI----~sh--  311 (758)
T KOG0343|consen  242 NL----PKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFI----KSH--  311 (758)
T ss_pred             hC----ChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHHHH----Hhc--
Confidence            63    44444444433321            1111111111   1             112233333333    222  


Q ss_pred             CCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCCC
Q psy7786         213 LPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGS  251 (252)
Q Consensus       213 ~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~~  251 (252)
                            ...+.|||..|...+..+++.++++-+.+++-+
T Consensus       312 ------lk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~  344 (758)
T KOG0343|consen  312 ------LKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLA  344 (758)
T ss_pred             ------cccceEEEEehhhHHHHHHHHHHhcCCCCceee
Confidence                  134689999999999999999999988877644

>KOG0341|consensus

Probab=99.96  E-value=3.8e-30  Score=209.63  Aligned_cols=225  Identities=37%  Similarity=0.576  Sum_probs=176.7

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC----CC
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP----IP   76 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~----~~   76 (252)
                      ||.+++|||.+.+|-||||||+.|+||++-..+......|+....||.+|||||+||||.|+++.+..+...+.    ..
T Consensus       201 lPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~  280 (610)
T KOG0341|consen  201 LPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPE  280 (610)
T ss_pred             cceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChh
Confidence            68999999999999999999999999999999999999999999999999999999999999999998877653    24


Q ss_pred             cceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHH
Q psy7786          77 LRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLV  156 (252)
Q Consensus        77 ~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~  156 (252)
                      +|+..+.||.+..+|.+.+++|++|.  ++|    ||||.++..+....+.- +++++.||+     ++|.+|||..++.
T Consensus       281 lRs~LciGG~~v~eql~~v~~GvHiv--VAT----PGRL~DmL~KK~~sLd~-CRyL~lDEA-----DRmiDmGFEddir  348 (610)
T KOG0341|consen  281 LRSLLCIGGVPVREQLDVVRRGVHIV--VAT----PGRLMDMLAKKIMSLDA-CRYLTLDEA-----DRMIDMGFEDDIR  348 (610)
T ss_pred             hhhhhhhcCccHHHHHHHHhcCeeEE--EcC----cchHHHHHHHhhccHHH-HHHhhhhhH-----HHHhhccchhhHH
Confidence            89999999999999999999999984  555    99999999998888887 899999998     9999999999998


Q ss_pred             HHHHHCC---------CCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccC---CCCCCCCcEEE
Q psy7786         157 RALEAKG---------IKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKL---PFLPGEGPYGL  224 (252)
Q Consensus       157 ~~l~~~~---------~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~---~~~~~~~~~~L  224 (252)
                      ..+....         ...|..+|.-+-+++....-+   .....|-..--.+.-+..+....+..   .+.....|.+|
T Consensus       349 ~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtv---NVGRAGAAsldViQevEyVkqEaKiVylLeCLQKT~PpVL  425 (610)
T KOG0341|consen  349 TIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTV---NVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQKTSPPVL  425 (610)
T ss_pred             HHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEE---ecccccccchhHHHHHHHHHhhhhhhhHHHHhccCCCceE
Confidence            7776553         346777877666655543211   11112221122222232222221111   12334568899


Q ss_pred             EEcCcHHHHHHHHHHH
Q psy7786         225 IICPSRELARQTHDII  240 (252)
Q Consensus       225 If~~tr~~a~~i~~~l  240 (252)
                      |||..+..++.|+++|
T Consensus       426 IFaEkK~DVD~IhEYL  441 (610)
T KOG0341|consen  426 IFAEKKADVDDIHEYL  441 (610)
T ss_pred             EEeccccChHHHHHHH
Confidence            9999999999999987

>KOG0346|consensus

Probab=99.96  E-value=2.7e-29  Score=207.28  Aligned_cols=214  Identities=19%  Similarity=0.188  Sum_probs=153.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|||+++.|.||||||+||++|++|.++......  ....++.|+|++||||||.|+++++.+|..+.+..+++.
T Consensus        50 IplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~--~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~  127 (569)
T KOG0346|consen   50 IPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTN--DGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAI  127 (569)
T ss_pred             cchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcc--cccccceeEEEechHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            799999999999999999999999999999999876543  345689999999999999999999999999988668888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      -+..+.+.......+...+||+  +.    ||++++.+...........++++|.||+     +-+...|..+++.....
T Consensus       128 nl~s~~sdsv~~~~L~d~pdIv--V~----TP~~ll~~~~~~~~~~~~~l~~LVvDEA-----DLllsfGYeedlk~l~~  196 (569)
T KOG0346|consen  128 NLASSMSDSVNSVALMDLPDIV--VA----TPAKLLRHLAAGVLEYLDSLSFLVVDEA-----DLLLSFGYEEDLKKLRS  196 (569)
T ss_pred             hhhcccchHHHHHHHccCCCeE--Ee----ChHHHHHHHhhccchhhhheeeEEechh-----hhhhhcccHHHHHHHHH
Confidence            7777766666667777778873  33    4888888877776555556999999997     66777777777654444


Q ss_pred             HCCCCCChHHHHhhhhhhhcC-------------------------Cc----EEEEccCCCchhHHhHHHHHHHHHhhhc
Q psy7786         161 AKGIKKPTPIQVQGIPAALSG-------------------------RD----IIGIAFTGSGKTLVFVLPILMFCLEQET  211 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~-------------------------~~----~~~~~~~g~gKt~~~~~~~l~~i~~~~~  211 (252)
                      .    .|...|.-.+++++..                         .|    ..+. .....| +..+..++..-+-   
T Consensus       197 ~----LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~-cse~DK-flllyallKL~LI---  267 (569)
T KOG0346|consen  197 H----LPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVK-CSEEDK-FLLLYALLKLRLI---  267 (569)
T ss_pred             h----CCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEE-eccchh-HHHHHHHHHHHHh---
Confidence            3    3555555555555432                         01    1111 112333 2222333322111   


Q ss_pred             cCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         212 KLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       212 ~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                              ..+.|||+||.+.|..+.-.|+.||
T Consensus       268 --------~gKsliFVNtIdr~YrLkLfLeqFG  292 (569)
T KOG0346|consen  268 --------RGKSLIFVNTIDRCYRLKLFLEQFG  292 (569)
T ss_pred             --------cCceEEEEechhhhHHHHHHHHHhC
Confidence                    3468999999999998877765543

>KOG0333|consensus

Probab=99.96  E-value=3.3e-30  Score=216.68  Aligned_cols=151  Identities=26%  Similarity=0.357  Sum_probs=134.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCC-CCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcce
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP-FLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRT   79 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~-~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~   79 (252)
                      ||..++.+|+|..|.||||||+||++|++..+...+.-.. ..+-.+|+|+|++||||||+||.++-.+|++.++  +++
T Consensus       276 ipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg--~r~  353 (673)
T KOG0333|consen  276 IPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLG--IRT  353 (673)
T ss_pred             ccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhccccc--ceE
Confidence            7889999999999999999999999999988876553222 1334699999999999999999999999999998  899


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      +.++||.+.++|--++..+|+|+  |+|    ||+|++-.++....+.. +.++|+||+     ++|.+|||.+++.+.|
T Consensus       354 vsvigg~s~EEq~fqls~gceiv--iat----PgrLid~Lenr~lvl~q-ctyvvldea-----drmiDmgfE~dv~~iL  421 (673)
T KOG0333|consen  354 VSVIGGLSFEEQGFQLSMGCEIV--IAT----PGRLIDSLENRYLVLNQ-CTYVVLDEA-----DRMIDMGFEPDVQKIL  421 (673)
T ss_pred             EEEecccchhhhhhhhhccceee--ecC----chHHHHHHHHHHHHhcc-CceEeccch-----hhhhcccccHHHHHHH
Confidence            99999999999988999999985  666    99999999998888887 999999998     9999999999999999


Q ss_pred             HHCCCC
Q psy7786         160 EAKGIK  165 (252)
Q Consensus       160 ~~~~~~  165 (252)
                      ..+...
T Consensus       422 ~~mPss  427 (673)
T KOG0333|consen  422 EQMPSS  427 (673)
T ss_pred             HhCCcc
Confidence            887533

>KOG0340|consensus

Probab=99.96  E-value=3.1e-29  Score=201.96  Aligned_cols=209  Identities=23%  Similarity=0.255  Sum_probs=154.5

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+|+|+|++.+|+||||||.||.+|+++++..++.        +..++|++||||||.|+.+.+..+++.++  +++.
T Consensus        38 IpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~--------giFalvlTPTrELA~QiaEQF~alGk~l~--lK~~  107 (442)
T KOG0340|consen   38 IPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPY--------GIFALVLTPTRELALQIAEQFIALGKLLN--LKVS  107 (442)
T ss_pred             hHHHhcccccccccccCCCcchhhhHHHHHhhccCCC--------cceEEEecchHHHHHHHHHHHHHhccccc--ceEE
Confidence            7999999999999999999999999999999988774        88999999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhH----HHHHhhhhceeeccCCCCCcccccccCCCCHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQV----HDIIRRNLRILVEGDDVPPACCSFRLMKLPESLV  156 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~----~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~  156 (252)
                      +++||++.-.+...|.+.+|++  ++|    ||++-++....    ...+++ ++++|.||+     +++++-.|.+.+.
T Consensus       108 vivGG~d~i~qa~~L~~rPHvV--vat----PGRlad~l~sn~~~~~~~~~r-lkflVlDEA-----DrvL~~~f~d~L~  175 (442)
T KOG0340|consen  108 VIVGGTDMIMQAAILSDRPHVV--VAT----PGRLADHLSSNLGVCSWIFQR-LKFLVLDEA-----DRVLAGCFPDILE  175 (442)
T ss_pred             EEEccHHHhhhhhhcccCCCeE--ecC----ccccccccccCCccchhhhhc-eeeEEecch-----hhhhccchhhHHh
Confidence            9999999999999999988873  444    99998887665    334454 999999998     7788777877764


Q ss_pred             HHHHHCCCCCChHHHHhhhhhhhcC-----------C--cEEEEccCCC----------------chhHHhHHHHHHHHH
Q psy7786         157 RALEAKGIKKPTPIQVQGIPAALSG-----------R--DIIGIAFTGS----------------GKTLVFVLPILMFCL  207 (252)
Q Consensus       157 ~~l~~~~~~~p~~iQ~~~~p~~~~~-----------~--~~~~~~~~g~----------------gKt~~~~~~~l~~i~  207 (252)
                      ..+..    .|.+-|...+++++..           +  -.......+.                +| .+|+...+....
T Consensus       176 ~i~e~----lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vk-daYLv~~Lr~~~  250 (442)
T KOG0340|consen  176 GIEEC----LPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVK-DAYLVHLLRDFE  250 (442)
T ss_pred             hhhcc----CCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhh-HHHHHHHHhhhh
Confidence            44433    3444444444444321           1  1111111111                11 223333332211


Q ss_pred             hhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         208 EQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       208 ~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                               ++....++||++|...|+.++..|+.+.-
T Consensus       251 ---------~~~~~simIFvnttr~cQ~l~~~l~~le~  279 (442)
T KOG0340|consen  251 ---------NKENGSIMIFVNTTRECQLLSMTLKNLEV  279 (442)
T ss_pred             ---------hccCceEEEEeehhHHHHHHHHHHhhhce
Confidence                     12345699999999999999999887653

>KOG0326|consensus

Probab=99.96  E-value=1e-29  Score=202.40  Aligned_cols=205  Identities=19%  Similarity=0.223  Sum_probs=156.7

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.++.|+|+++.|+.|+|||.||++|+++.+....        ...+++|++||||||.|+...++.++++++  +++.
T Consensus       116 IPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~--------~~IQ~~ilVPtrelALQtSqvc~~lskh~~--i~vm  185 (459)
T KOG0326|consen  116 IPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKK--------NVIQAIILVPTRELALQTSQVCKELSKHLG--IKVM  185 (459)
T ss_pred             cceeecchhhhhhccCCCCCccceechhhhhcCccc--------cceeEEEEeecchhhHHHHHHHHHHhcccC--eEEE
Confidence            799999999999999999999999999999987655        578999999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      +.+||++..+.+-.+.+++++.  ++|    |||++++.++....++. ..++|.||+     +.+.+..|.+.+.+.+.
T Consensus       186 vttGGT~lrDDI~Rl~~~VH~~--vgT----PGRIlDL~~KgVa~ls~-c~~lV~DEA-----DKlLs~~F~~~~e~li~  253 (459)
T KOG0326|consen  186 VTTGGTSLRDDIMRLNQTVHLV--VGT----PGRILDLAKKGVADLSD-CVILVMDEA-----DKLLSVDFQPIVEKLIS  253 (459)
T ss_pred             EecCCcccccceeeecCceEEE--EcC----ChhHHHHHhcccccchh-ceEEEechh-----hhhhchhhhhHHHHHHH
Confidence            9999999999999999998873  444    99999999999999988 899999997     66665555555544443


Q ss_pred             HCCCCCChHHHHhhhhhhhc--------------------------CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCC
Q psy7786         161 AKGIKKPTPIQVQGIPAALS--------------------------GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP  214 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~--------------------------~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~  214 (252)
                      .    .|..-|....+++++                          |.-........+-|     +..+..++.      
T Consensus       254 ~----lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~eLtl~GvtQyYafV~e~qK-----vhCLntLfs------  318 (459)
T KOG0326|consen  254 F----LPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEELTLKGVTQYYAFVEERQK-----VHCLNTLFS------  318 (459)
T ss_pred             h----CCccceeeEEecccchhHHHHHHHhccCcceeehhhhhhhcchhhheeeechhhh-----hhhHHHHHH------
Confidence            3    344444444433332                          21222222233333     222222222      


Q ss_pred             CCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         215 FLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       215 ~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                        +.+-.|++||||+...++.+++.+.++|
T Consensus       319 --kLqINQsIIFCNS~~rVELLAkKITelG  346 (459)
T KOG0326|consen  319 --KLQINQSIIFCNSTNRVELLAKKITELG  346 (459)
T ss_pred             --HhcccceEEEeccchHhHHHHHHHHhcc
Confidence              2345689999999999999999887665

>PTZ00110 helicase; Provisional

Probab=99.95  E-value=4.5e-28  Score=215.87  Aligned_cols=145  Identities=29%  Similarity=0.454  Sum_probs=122.5

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|++.+++.....   ....++++|||+||||||.|+.+.+++++...+  +++.
T Consensus       161 ip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~---~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~--i~~~  235 (545)
T PTZ00110        161 WPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLL---RYGDGPIVLVLAPTRELAEQIREQCNKFGASSK--IRNT  235 (545)
T ss_pred             HHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccc---cCCCCcEEEEECChHHHHHHHHHHHHHHhcccC--ccEE
Confidence            58899999999999999999999999999988754321   123578999999999999999999999988776  8899


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      +++||.+...+...+.++++|.  |.    ||+++.++..+....+++ +.++|.||+     +.+.+++|.+++.+.+.
T Consensus       236 ~~~gg~~~~~q~~~l~~~~~Il--Va----TPgrL~d~l~~~~~~l~~-v~~lViDEA-----d~mld~gf~~~i~~il~  303 (545)
T PTZ00110        236 VAYGGVPKRGQIYALRRGVEIL--IA----CPGRLIDFLESNVTNLRR-VTYLVLDEA-----DRMLDMGFEPQIRKIVS  303 (545)
T ss_pred             EEeCCCCHHHHHHHHHcCCCEE--EE----CHHHHHHHHHcCCCChhh-CcEEEeehH-----HhhhhcchHHHHHHHHH
Confidence            9999999888888888888873  44    499998887766666666 899999998     88999999998877776


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       304 ~~  305 (545)
T PTZ00110        304 QI  305 (545)
T ss_pred             hC
Confidence            54

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=2.2e-28  Score=212.88  Aligned_cols=147  Identities=23%  Similarity=0.312  Sum_probs=119.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.++..... ......++++|||+||||||.|+++.++.+++..+  +++.
T Consensus        39 ip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~-~~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~--~~v~  115 (423)
T PRK04837         39 LPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAP-EDRKVNQPRALIMAPTRELAVQIHADAEPLAQATG--LKLG  115 (423)
T ss_pred             HHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccc-cccccCCceEEEECCcHHHHHHHHHHHHHHhccCC--ceEE
Confidence            57899999999999999999999999999999765421 11112468999999999999999999999999887  8899


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+...+.+.++++++|.  |.    ||+++.++..+....+.+ ++++|.||+     +.+.+.+|..++...+.
T Consensus       116 ~~~gg~~~~~~~~~l~~~~~Il--V~----TP~~l~~~l~~~~~~l~~-v~~lViDEa-----d~l~~~~f~~~i~~i~~  183 (423)
T PRK04837        116 LAYGGDGYDKQLKVLESGVDIL--IG----TTGRLIDYAKQNHINLGA-IQVVVLDEA-----DRMFDLGFIKDIRWLFR  183 (423)
T ss_pred             EEECCCCHHHHHHHhcCCCCEE--EE----CHHHHHHHHHcCCccccc-ccEEEEecH-----HHHhhcccHHHHHHHHH
Confidence            9999998888888888877773  33    488887776655555555 899999997     77888888888766665


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       184 ~~  185 (423)
T PRK04837        184 RM  185 (423)
T ss_pred             hC
Confidence            43

>KOG0339|consensus

Probab=99.95  E-value=4e-28  Score=203.59  Aligned_cols=144  Identities=29%  Similarity=0.438  Sum_probs=130.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      +|..++|+|++-+|.||||||.||+.|++.+++.++.-   .++++|.+||++||||||.||+.++++|++..|  ++++
T Consensus       254 lptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL---~~g~gPi~vilvPTrela~Qi~~eaKkf~K~yg--l~~v  328 (731)
T KOG0339|consen  254 LPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPEL---KPGEGPIGVILVPTRELASQIFSEAKKFGKAYG--LRVV  328 (731)
T ss_pred             cccccccccchheeeccCcchhHHHHHHHHHhcchhhh---cCCCCCeEEEEeccHHHHHHHHHHHHHhhhhcc--ceEE
Confidence            58899999999999999999999999999999876642   345799999999999999999999999999888  9999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ++|||.+.-+|...|+.++.|+  ++|    |+||+++.......+.+ +.++|.||+     ++|.++||.+++..+..
T Consensus       329 ~~ygGgsk~eQ~k~Lk~g~Eiv--VaT----PgRlid~VkmKatn~~r-vS~LV~DEa-----drmfdmGfe~qVrSI~~  396 (731)
T KOG0339|consen  329 AVYGGGSKWEQSKELKEGAEIV--VAT----PGRLIDMVKMKATNLSR-VSYLVLDEA-----DRMFDMGFEPQVRSIKQ  396 (731)
T ss_pred             EeecCCcHHHHHHhhhcCCeEE--Eec----hHHHHHHHHhhccccee-eeEEEEech-----hhhhccccHHHHHHHHh
Confidence            9999999999999999999884  565    99999999999999998 999999998     99999999999855444


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       397 h  397 (731)
T KOG0339|consen  397 H  397 (731)
T ss_pred             h
Confidence            3

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=1.1e-27  Score=214.28  Aligned_cols=147  Identities=25%  Similarity=0.329  Sum_probs=117.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|++++++..... .......+++|||+||||||.|+++.+++++..++  +++.
T Consensus        40 ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~-~~~~~~~~raLIl~PTreLa~Qi~~~~~~l~~~~~--i~v~  116 (572)
T PRK04537         40 LPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPAL-ADRKPEDPRALILAPTRELAIQIHKDAVKFGADLG--LRFA  116 (572)
T ss_pred             HHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccc-cccccCCceEEEEeCcHHHHHHHHHHHHHHhccCC--ceEE
Confidence            68899999999999999999999999999998764311 11122368999999999999999999999998877  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHH-HHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVH-DIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~-~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      .++||.++..+.+.++++++|.  |.    ||+++.++..+.. ..+. .++++|.||+     +.+.+.+|..++...+
T Consensus       117 ~l~Gg~~~~~q~~~l~~~~dIi--V~----TP~rL~~~l~~~~~~~l~-~v~~lViDEA-----h~lld~gf~~~i~~il  184 (572)
T PRK04537        117 LVYGGVDYDKQRELLQQGVDVI--IA----TPGRLIDYVKQHKVVSLH-ACEICVLDEA-----DRMFDLGFIKDIRFLL  184 (572)
T ss_pred             EEECCCCHHHHHHHHhCCCCEE--EE----CHHHHHHHHHhccccchh-heeeeEecCH-----HHHhhcchHHHHHHHH
Confidence            9999999988888888877773  33    4888877665533 2344 4889999997     7788888888876666


Q ss_pred             HHC
Q psy7786         160 EAK  162 (252)
Q Consensus       160 ~~~  162 (252)
                      ...
T Consensus       185 ~~l  187 (572)
T PRK04537        185 RRM  187 (572)
T ss_pred             Hhc
Confidence            543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.95  E-value=1.3e-27  Score=210.17  Aligned_cols=206  Identities=21%  Similarity=0.273  Sum_probs=148.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|.+|+++.+....        ..+++||++||||||.|+.+.++.+++... ++++.
T Consensus        35 i~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~--------~~~~~lil~PtreLa~Q~~~~~~~~~~~~~-~~~v~  105 (460)
T PRK11776         35 LPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKR--------FRVQALVLCPTRELADQVAKEIRRLARFIP-NIKVL  105 (460)
T ss_pred             HHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhcc--------CCceEEEEeCCHHHHHHHHHHHHHHHhhCC-CcEEE
Confidence            577899999999999999999999999999885432        357899999999999999999999988764 38899


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+...+.+.+.++++|.  |.    ||+++.++..+....+.+ ++++|.||+     +.+.+++|..++...+.
T Consensus       106 ~~~Gg~~~~~~~~~l~~~~~Iv--V~----Tp~rl~~~l~~~~~~l~~-l~~lViDEa-----d~~l~~g~~~~l~~i~~  173 (460)
T PRK11776        106 TLCGGVPMGPQIDSLEHGAHII--VG----TPGRILDHLRKGTLDLDA-LNTLVLDEA-----DRMLDMGFQDAIDAIIR  173 (460)
T ss_pred             EEECCCChHHHHHHhcCCCCEE--EE----ChHHHHHHHHcCCccHHH-CCEEEEECH-----HHHhCcCcHHHHHHHHH
Confidence            9999999988888888888773  33    488888877665555665 899999997     78889999888877776


Q ss_pred             HCCCCCChHHHHhhhhhhhc-----------CCcEEEEc---------------cCCCchhHHhHHHHHHHHHhhhccCC
Q psy7786         161 AKGIKKPTPIQVQGIPAALS-----------GRDIIGIA---------------FTGSGKTLVFVLPILMFCLEQETKLP  214 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~-----------~~~~~~~~---------------~~g~gKt~~~~~~~l~~i~~~~~~~~  214 (252)
                      ...    ...|...+++++.           .....+..               .....|     ...+..++...    
T Consensus       174 ~~~----~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~i~~~~~~~~~~~k-----~~~l~~ll~~~----  240 (460)
T PRK11776        174 QAP----ARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPAIEQRFYEVSPDER-----LPALQRLLLHH----  240 (460)
T ss_pred             hCC----cccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCCCCCCeeEEEEEeCcHHH-----HHHHHHHHHhc----
Confidence            542    2222211221111           11111111               111112     33344444322    


Q ss_pred             CCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         215 FLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       215 ~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                          ...++||||||++.|+.+++.|++.+
T Consensus       241 ----~~~~~lVF~~t~~~~~~l~~~L~~~~  266 (460)
T PRK11776        241 ----QPESCVVFCNTKKECQEVADALNAQG  266 (460)
T ss_pred             ----CCCceEEEECCHHHHHHHHHHHHhCC
Confidence                23469999999999999999997654

>KOG0336|consensus

Probab=99.94  E-value=1.6e-27  Score=195.51  Aligned_cols=211  Identities=24%  Similarity=0.313  Sum_probs=160.6

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+|+|+|++..|+||+|||++|++|-+.++...+....  +..++.+|+++||||||.|+..++++++ +-|  .+..
T Consensus       251 WPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~--qr~~p~~lvl~ptreLalqie~e~~kys-yng--~ksv  325 (629)
T KOG0336|consen  251 WPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRRE--QRNGPGVLVLTPTRELALQIEGEVKKYS-YNG--LKSV  325 (629)
T ss_pred             cceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhh--ccCCCceEEEeccHHHHHHHHhHHhHhh-hcC--cceE
Confidence            7999999999999999999999999999988877665433  4568999999999999999999998875 334  7889


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      +++||.+..+|.+.++++.+|.  ++|    |+++.++.-.....++. +.++|+||+     ++|.+|+|.+++.++|-
T Consensus       326 c~ygggnR~eqie~lkrgveii--iat----PgrlndL~~~n~i~l~s-iTYlVlDEA-----DrMLDMgFEpqIrkill  393 (629)
T KOG0336|consen  326 CVYGGGNRNEQIEDLKRGVEII--IAT----PGRLNDLQMDNVINLAS-ITYLVLDEA-----DRMLDMGFEPQIRKILL  393 (629)
T ss_pred             EEecCCCchhHHHHHhcCceEE--eeC----CchHhhhhhcCeeeeee-eEEEEecch-----hhhhcccccHHHHHHhh
Confidence            9999999999999999999874  555    99999998888888888 999999998     99999999999998887


Q ss_pred             HCCCCCChHHHHhhhhhhhc---------------C-CcEE--------EEccCCCchhHHhHHHHHHHHHhhhccCCCC
Q psy7786         161 AKGIKKPTPIQVQGIPAALS---------------G-RDII--------GIAFTGSGKTLVFVLPILMFCLEQETKLPFL  216 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~---------------~-~~~~--------~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~  216 (252)
                      ..--...+..-+.+||....               | -|+.        +...+.+.|     +..+.....+.      
T Consensus       394 diRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k-----~~~~~~f~~~m------  462 (629)
T KOG0336|consen  394 DIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEK-----LEIVQFFVANM------  462 (629)
T ss_pred             hcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHH-----HHHHHHHHHhc------
Confidence            65433222222233332221               1 1111        122334444     33343333332      


Q ss_pred             CCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         217 PGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       217 ~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                       ....++||||..+..|+.+...+
T Consensus       463 -s~ndKvIiFv~~K~~AD~LSSd~  485 (629)
T KOG0336|consen  463 -SSNDKVIIFVSRKVMADHLSSDF  485 (629)
T ss_pred             -CCCceEEEEEechhhhhhccchh
Confidence             23568999999999999888765

>KOG0334|consensus

Probab=99.94  E-value=3.9e-27  Score=212.26  Aligned_cols=214  Identities=27%  Similarity=0.378  Sum_probs=156.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||++++|||+|.+|.||||||++|+||++-+++.++   +....+||-++|++||||||.|+++.+++|++.++  ++++
T Consensus       396 iP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr---~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~--ir~v  470 (997)
T KOG0334|consen  396 IPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQR---PLEEGDGPIALILAPTRELAMQIHREVRKFLKLLG--IRVV  470 (997)
T ss_pred             cchhccCcceEEeeccCCccchhhhcchhhhhhcCC---ChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcC--ceEE
Confidence            799999999999999999999999999995554433   34455799999999999999999999999999987  9999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHH---HHHhhhhceeeccCCCCCcccccccCCCCHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVH---DIIRRNLRILVEGDDVPPACCSFRLMKLPESLVR  157 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~---~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~  157 (252)
                      ++|||+...++++.++++..|.  |.|    ||+.++..-...   -++++ ..++|.||+     ++|.+++|.+++..
T Consensus       471 ~vygg~~~~~qiaelkRg~eIv--V~t----pGRmiD~l~~n~grvtnlrR-~t~lv~dea-----DrmfdmgfePq~~~  538 (997)
T KOG0334|consen  471 CVYGGSGISQQIAELKRGAEIV--VCT----PGRMIDILCANSGRVTNLRR-VTYLVLDEA-----DRMFDMGFEPQITR  538 (997)
T ss_pred             EecCCccHHHHHHHHhcCCceE--Eec----cchhhhhHhhcCCccccccc-cceeeechh-----hhhheeccCcccch
Confidence            9999999999999999998874  565    999887765433   34444 669999998     88889999999988


Q ss_pred             HHHHCCCCCChHHHHhhhhhhh----------------cCC---------cEEEEccCCCchhHHhHHHHHHHHHhhhcc
Q psy7786         158 ALEAKGIKKPTPIQVQGIPAAL----------------SGR---------DIIGIAFTGSGKTLVFVLPILMFCLEQETK  212 (252)
Q Consensus       158 ~l~~~~~~~p~~iQ~~~~p~~~----------------~~~---------~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~  212 (252)
                      ++....-...+..-+.++|..+                .++         ++.++ .....| +.-+..+|.....    
T Consensus       539 Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~-~~e~eK-f~kL~eLl~e~~e----  612 (997)
T KOG0334|consen  539 ILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVC-AIENEK-FLKLLELLGERYE----  612 (997)
T ss_pred             HHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEe-cCchHH-HHHHHHHHHHHhh----
Confidence            7777643222222222222221                111         11111 112222 3334444433222    


Q ss_pred             CCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         213 LPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       213 ~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                             ..++||||...+.|+.+.+.|.+-+
T Consensus       613 -------~~~tiiFv~~qe~~d~l~~~L~~ag  637 (997)
T KOG0334|consen  613 -------DGKTIIFVDKQEKADALLRDLQKAG  637 (997)
T ss_pred             -------cCCEEEEEcCchHHHHHHHHHHhcC
Confidence                   4579999999999999999987543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.94  E-value=3.1e-27  Score=207.16  Aligned_cols=146  Identities=26%  Similarity=0.388  Sum_probs=117.6

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+......  ......+++|||+||||||.|+.+.++.+.++++  +++.
T Consensus        32 i~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~--~~~~~~~~aLil~PtreLa~Qi~~~~~~~~~~~~--~~~~  107 (456)
T PRK10590         32 IPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPH--AKGRRPVRALILTPTRELAAQIGENVRDYSKYLN--IRSL  107 (456)
T ss_pred             HHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccc--cccCCCceEEEEeCcHHHHHHHHHHHHHHhccCC--CEEE
Confidence            57889999999999999999999999999998764321  1112356899999999999999999999998887  8888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+.+.+...+..+++|.  |.    ||+++.++.......+.+ +.++|.||+     +.+.+.++..++...+.
T Consensus       108 ~~~gg~~~~~~~~~l~~~~~Ii--V~----TP~rL~~~~~~~~~~l~~-v~~lViDEa-----h~ll~~~~~~~i~~il~  175 (456)
T PRK10590        108 VVFGGVSINPQMMKLRGGVDVL--VA----TPGRLLDLEHQNAVKLDQ-VEILVLDEA-----DRMLDMGFIHDIRRVLA  175 (456)
T ss_pred             EEECCcCHHHHHHHHcCCCcEE--EE----ChHHHHHHHHcCCccccc-ceEEEeecH-----HHHhccccHHHHHHHHH
Confidence            9999999888877887777773  33    488887776655555555 899999997     77888888777766665


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       176 ~l  177 (456)
T PRK10590        176 KL  177 (456)
T ss_pred             hC
Confidence            54

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

Probab=99.94  E-value=6.1e-27  Score=211.17  Aligned_cols=229  Identities=15%  Similarity=0.147  Sum_probs=155.2

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+.+|+|++++||||||||+|.+||+++.+....   +....+++++|||+|.|+|++++..+++.+++.+|  +.+.
T Consensus        31 ~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~---~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~~~G--~~v~  105 (814)
T COG1201          31 IPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG---KGKLEDGIYALYISPLKALNNDIRRRLEEPLRELG--IEVA  105 (814)
T ss_pred             HHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhcc---CCCCCCceEEEEeCcHHHHHHHHHHHHHHHHHHcC--Cccc
Confidence            578899999999999999999999999999998874   12234689999999999999999999999999999  6778


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCC--hhHHHHHhhhhceeeccCC------------------CC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLP--DQVHDIIRRNLRILVEGDD------------------VP  140 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~--~~~~~~l~~~~~~~V~de~------------------~~  140 (252)
                      +.+|+++..++.+..++++||   +.   |||+.+.-+.  .+....|++ ++++|.||-                  +.
T Consensus       106 vRhGDT~~~er~r~~~~PPdI---Li---TTPEsL~lll~~~~~r~~l~~-vr~VIVDEiHel~~sKRG~~Lsl~LeRL~  178 (814)
T COG1201         106 VRHGDTPQSEKQKMLKNPPHI---LI---TTPESLAILLNSPKFRELLRD-VRYVIVDEIHALAESKRGVQLALSLERLR  178 (814)
T ss_pred             eecCCCChHHhhhccCCCCcE---EE---eChhHHHHHhcCHHHHHHhcC-CcEEEeehhhhhhccccchhhhhhHHHHH
Confidence            999999999998988988887   33   3466543332  234444555 899998884                  11


Q ss_pred             CcccccccCCCCHHHHHHHHHCCCCCChH-HHHhhhhhhhcCCcEEEEccCCC----chhHHhHHHHHHHHHhhhccCCC
Q psy7786         141 PACCSFRLMKLPESLVRALEAKGIKKPTP-IQVQGIPAALSGRDIIGIAFTGS----GKTLVFVLPILMFCLEQETKLPF  215 (252)
Q Consensus       141 ~~~~~~~~~~l~~~l~~~l~~~~~~~p~~-iQ~~~~p~~~~~~~~~~~~~~g~----gKt~~~~~~~l~~i~~~~~~~~~  215 (252)
                      .....|+.+|+|+++-..-.-..|..+.. .....-.......++-+..+...    |.....++..+..+.++.     
T Consensus       179 ~l~~~~qRIGLSATV~~~~~varfL~g~~~~~~Iv~~~~~k~~~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~~-----  253 (814)
T COG1201         179 ELAGDFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELWAALYERIAELVKKH-----  253 (814)
T ss_pred             hhCcccEEEeehhccCCHHHHHHHhcCCCCceEEEEcccCCcceEEEEecCCccccccchhHHHHHHHHHHHhhc-----
Confidence            11125666666666521111000001110 00000011111223444443333    556677777777776654     


Q ss_pred             CCCCCcEEEEEcCcHHHHHHHHHHHHHHH-hhCCCCC
Q psy7786         216 LPGEGPYGLIICPSRELARQTHDIIQYYC-AALPIGS  251 (252)
Q Consensus       216 ~~~~~~~~LIf~~tr~~a~~i~~~l~~l~-~~~~i~~  251 (252)
                           ..+|||+|||..|+.++..|+++. ..+.+||
T Consensus       254 -----~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HH  285 (814)
T COG1201         254 -----RTTLIFTNTRSGAERLAFRLKKLGPDIIEVHH  285 (814)
T ss_pred             -----CcEEEEEeChHHHHHHHHHHHHhcCCceeeec
Confidence                 259999999999999999999887 4444443

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.94  E-value=7.2e-27  Score=210.33  Aligned_cols=141  Identities=25%  Similarity=0.339  Sum_probs=118.2

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||+||.+|+++.+....        .++++||++||||||.|+.+.++++.+.+. ++++.
T Consensus        37 i~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~--------~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~-~i~v~  107 (629)
T PRK11634         37 IPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPEL--------KAPQILVLAPTRELAVQVAEAMTDFSKHMR-GVNVV  107 (629)
T ss_pred             HHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhcc--------CCCeEEEEeCcHHHHHHHHHHHHHHHhhcC-CceEE
Confidence            578899999999999999999999999999886533        367899999999999999999999988774 48889


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+++.+.+.++++++|+  |    +||+++.++..+....+.+ ++++|.||+     +.|.+++|..++...+.
T Consensus       108 ~~~gG~~~~~q~~~l~~~~~IV--V----gTPgrl~d~l~r~~l~l~~-l~~lVlDEA-----d~ml~~gf~~di~~Il~  175 (629)
T PRK11634        108 ALYGGQRYDVQLRALRQGPQIV--V----GTPGRLLDHLKRGTLDLSK-LSGLVLDEA-----DEMLRMGFIEDVETIMA  175 (629)
T ss_pred             EEECCcCHHHHHHHhcCCCCEE--E----ECHHHHHHHHHcCCcchhh-ceEEEeccH-----HHHhhcccHHHHHHHHH
Confidence            9999999988888888887772  3    3488888776665555555 899999997     78889999888877776


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       176 ~l  177 (629)
T PRK11634        176 QI  177 (629)
T ss_pred             hC
Confidence            54

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.94  E-value=8.9e-27  Score=203.53  Aligned_cols=213  Identities=21%  Similarity=0.231  Sum_probs=148.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+.....    .....+++||++||+|||.|+++.+..+++..+  +++.
T Consensus        32 i~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~----~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~--~~v~  105 (434)
T PRK11192         32 IPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPR----RKSGPPRILILTPTRELAMQVADQARELAKHTH--LDIA  105 (434)
T ss_pred             HHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccc----cCCCCceEEEECCcHHHHHHHHHHHHHHHccCC--cEEE
Confidence            4678999999999999999999999999999875322    112357899999999999999999999999887  8899


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+...+...+..+++|.  |.    ||+++.++..+....+++ +.++|.||+     +.+.+++|...+.....
T Consensus       106 ~~~gg~~~~~~~~~l~~~~~Il--V~----Tp~rl~~~~~~~~~~~~~-v~~lViDEa-----h~~l~~~~~~~~~~i~~  173 (434)
T PRK11192        106 TITGGVAYMNHAEVFSENQDIV--VA----TPGRLLQYIKEENFDCRA-VETLILDEA-----DRMLDMGFAQDIETIAA  173 (434)
T ss_pred             EEECCCCHHHHHHHhcCCCCEE--EE----ChHHHHHHHHcCCcCccc-CCEEEEECH-----HHHhCCCcHHHHHHHHH
Confidence            9999999888877777777763  33    488887776655555555 889999997     78888999888866655


Q ss_pred             HCCCCCChHHHHhhhhhhhcC------------CcEEEE-ccCCCch-----------hHHhHHHHHHHHHhhhccCCCC
Q psy7786         161 AKGIKKPTPIQVQGIPAALSG------------RDIIGI-AFTGSGK-----------TLVFVLPILMFCLEQETKLPFL  216 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~------------~~~~~~-~~~g~gK-----------t~~~~~~~l~~i~~~~~~~~~~  216 (252)
                      ....    ..|...+++++.+            ....+. .+.....           ........+..+...       
T Consensus       174 ~~~~----~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~-------  242 (434)
T PRK11192        174 ETRW----RKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQ-------  242 (434)
T ss_pred             hCcc----ccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHhc-------
Confidence            4322    1122222222110            111111 1111000           011123344444432       


Q ss_pred             CCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         217 PGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       217 ~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                       ....++||||+|++.|+.+++.|+..
T Consensus       243 -~~~~~~lVF~~s~~~~~~l~~~L~~~  268 (434)
T PRK11192        243 -PEVTRSIVFVRTRERVHELAGWLRKA  268 (434)
T ss_pred             -CCCCeEEEEeCChHHHHHHHHHHHhC
Confidence             13468999999999999999999763

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

Probab=99.94  E-value=8.3e-27  Score=207.05  Aligned_cols=147  Identities=24%  Similarity=0.378  Sum_probs=119.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++++...... ......++++||++||||||.|+++.++.+++.++  +++.
T Consensus       152 ip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~-~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~--~~~~  228 (518)
T PLN00206        152 IPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSG-HPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLP--FKTA  228 (518)
T ss_pred             HHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccc-cccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCC--ceEE
Confidence            57889999999999999999999999999988753221 11223578999999999999999999999988876  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.....+...+.++++|.  |.    ||+++.++..+....+.+ +.++|.||+     +.+.+.+|.+.+.+.+.
T Consensus       229 ~~~gG~~~~~q~~~l~~~~~Ii--V~----TPgrL~~~l~~~~~~l~~-v~~lViDEa-----d~ml~~gf~~~i~~i~~  296 (518)
T PLN00206        229 LVVGGDAMPQQLYRIQQGVELI--VG----TPGRLIDLLSKHDIELDN-VSVLVLDEV-----DCMLERGFRDQVMQIFQ  296 (518)
T ss_pred             EEECCcchHHHHHHhcCCCCEE--EE----CHHHHHHHHHcCCccchh-eeEEEeecH-----HHHhhcchHHHHHHHHH
Confidence            8999998888888888888773  33    488888877666555555 899999997     78888899888877665


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       297 ~l  298 (518)
T PLN00206        297 AL  298 (518)
T ss_pred             hC
Confidence            54

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=2e-26  Score=203.19  Aligned_cols=147  Identities=20%  Similarity=0.223  Sum_probs=114.5

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+...... .....+.+++|||+||||||.|+++.++.+.+.++  +++.
T Consensus       118 i~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~-~~~~~~~~~aLil~PtreLa~Q~~~~~~~l~~~~~--~~v~  194 (475)
T PRK01297        118 LGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPP-KERYMGEPRALIIAPTRELVVQIAKDAAALTKYTG--LNVM  194 (475)
T ss_pred             HHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcc-cccccCCceEEEEeCcHHHHHHHHHHHHHhhccCC--CEEE
Confidence            46789999999999999999999999999998765321 11112357999999999999999999999998887  7888


Q ss_pred             eeeCCcccCcchhhhhh-cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKK-GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~-~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      .++||.+...+.+.+.+ .++|.  |    ++|+++.++..+....+++ ++++|.||.     +.+.+.++...+.+.+
T Consensus       195 ~~~gg~~~~~~~~~~~~~~~~Ii--v----~TP~~Ll~~~~~~~~~l~~-l~~lViDEa-----h~l~~~~~~~~l~~i~  262 (475)
T PRK01297        195 TFVGGMDFDKQLKQLEARFCDIL--V----ATPGRLLDFNQRGEVHLDM-VEVMVLDEA-----DRMLDMGFIPQVRQII  262 (475)
T ss_pred             EEEccCChHHHHHHHhCCCCCEE--E----ECHHHHHHHHHcCCccccc-CceEEechH-----HHHHhcccHHHHHHHH
Confidence            89999888877777654 46662  2    3588887665554444554 899999997     6777778877776666


Q ss_pred             HHC
Q psy7786         160 EAK  162 (252)
Q Consensus       160 ~~~  162 (252)
                      ...
T Consensus       263 ~~~  265 (475)
T PRK01297        263 RQT  265 (475)
T ss_pred             HhC
Confidence            554

>KOG0337|consensus

Probab=99.93  E-value=2e-26  Score=189.55  Aligned_cols=207  Identities=22%  Similarity=0.296  Sum_probs=162.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++..|.||||||.||++|+++++.....       .+.++++++||||||.|+.++++.+++.++  +++.
T Consensus        52 ipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~-------~g~RalilsptreLa~qtlkvvkdlgrgt~--lr~s  122 (529)
T KOG0337|consen   52 IPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQ-------TGLRALILSPTRELALQTLKVVKDLGRGTK--LRQS  122 (529)
T ss_pred             ccceeeccccceeeecCCcchhhHHHHHHHHHhhccc-------cccceeeccCcHHHHHHHHHHHHHhccccc--hhhh
Confidence            7999999999999999999999999999999976543       588999999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      +.+||.+.++|...+..++|++  ++|    ||++..+.-+....++. ++|+|-||+     +++.+|||-+++.+.+.
T Consensus       123 ~~~ggD~~eeqf~~l~~npDii--~AT----pgr~~h~~vem~l~l~s-veyVVfdEa-----drlfemgfqeql~e~l~  190 (529)
T KOG0337|consen  123 LLVGGDSIEEQFILLNENPDII--IAT----PGRLLHLGVEMTLTLSS-VEYVVFDEA-----DRLFEMGFQEQLHEILS  190 (529)
T ss_pred             hhcccchHHHHHHHhccCCCEE--Eec----Cceeeeeehheeccccc-eeeeeehhh-----hHHHhhhhHHHHHHHHH
Confidence            9999999999999999889884  555    99999888777767777 999999997     89999999999999998


Q ss_pred             HCCCCCChHHHHhhhhhhhcC-----------CcEEEEcc--C--------------CCchhHHhHHHHHHHHHhhhccC
Q psy7786         161 AKGIKKPTPIQVQGIPAALSG-----------RDIIGIAF--T--------------GSGKTLVFVLPILMFCLEQETKL  213 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~-----------~~~~~~~~--~--------------g~gKt~~~~~~~l~~i~~~~~~~  213 (252)
                      +.    |...|...+++++..           ..+++.-.  +              ...| .++++..+.....     
T Consensus       191 rl----~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~K-~aaLl~il~~~~~-----  260 (529)
T KOG0337|consen  191 RL----PESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEK-EAALLSILGGRIK-----  260 (529)
T ss_pred             hC----CCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHHH-HHHHHHHHhcccc-----
Confidence            84    444465555555431           22333211  1              1112 2333333332211     


Q ss_pred             CCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         214 PFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       214 ~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                            ..++++||+|+..++.+...++..+
T Consensus       261 ------~~~t~vf~~tk~hve~~~~ll~~~g  285 (529)
T KOG0337|consen  261 ------DKQTIVFVATKHHVEYVRGLLRDFG  285 (529)
T ss_pred             ------ccceeEEecccchHHHHHHHHHhcC
Confidence                  3469999999999999988887654

>KOG0347|consensus

Probab=99.93  E-value=4.9e-26  Score=192.70  Aligned_cols=150  Identities=23%  Similarity=0.292  Sum_probs=120.0

Q ss_pred             CCcccCC-CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCC---CCCCCcE--EEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           1 MVTYRNS-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPF---LPGEGPY--GLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         1 i~~~~~g-~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~---~~~~~~~--~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      ||++..| .|++..|.||||||+||-+|++.++.........   ....+++  +||++||||||.||.+.+..++.+.+
T Consensus       212 lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~  291 (731)
T KOG0347|consen  212 LPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQ  291 (731)
T ss_pred             ccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCcceeEEecChHHHHHHHHHHHHHhccccC
Confidence            5788888 7999999999999999999999976643221110   1123455  99999999999999999999999988


Q ss_pred             CCcceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhh--hhceeeccCCCCCcccccccCCCC
Q psy7786          75 IPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRR--NLRILVEGDDVPPACCSFRLMKLP  152 (252)
Q Consensus        75 ~~~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~--~~~~~V~de~~~~~~~~~~~~~l~  152 (252)
                        +++..++||.+...|.+.+++.++|+  |+|    |||+..++.+...++.+  .++++|.||+     ++|.+-|-=
T Consensus       292 --i~v~si~GGLavqKQqRlL~~~p~IV--VAT----PGRlweli~e~n~~l~~~k~vkcLVlDEa-----DRmvekghF  358 (731)
T KOG0347|consen  292 --IRVASITGGLAVQKQQRLLNQRPDIV--VAT----PGRLWELIEEDNTHLGNFKKVKCLVLDEA-----DRMVEKGHF  358 (731)
T ss_pred             --eEEEEeechhHHHHHHHHHhcCCCEE--Eec----chHHHHHHHhhhhhhhhhhhceEEEEccH-----HHHhhhccH
Confidence              99999999999999999999988884  565    89988888887765543  4889999998     788877766


Q ss_pred             HHHHHHHHHCC
Q psy7786         153 ESLVRALEAKG  163 (252)
Q Consensus       153 ~~l~~~l~~~~  163 (252)
                      +++...|...+
T Consensus       359 ~Els~lL~~L~  369 (731)
T KOG0347|consen  359 EELSKLLKHLN  369 (731)
T ss_pred             HHHHHHHHHhh
Confidence            66655555554

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

Probab=99.92  E-value=4.4e-25  Score=202.30  Aligned_cols=130  Identities=18%  Similarity=0.239  Sum_probs=98.7

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||+||.+|+++.+..+         .++++|||+||||||+|+.+.+++++ ..+  +++.
T Consensus        45 i~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~---------~~~~aL~l~PtraLa~q~~~~l~~l~-~~~--i~v~  112 (742)
T TIGR03817        45 AELAHAGRHVVVATGTASGKSLAYQLPVLSALADD---------PRATALYLAPTKALAADQLRAVRELT-LRG--VRPA  112 (742)
T ss_pred             HHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC---------CCcEEEEEcChHHHHHHHHHHHHHhc-cCC--eEEE
Confidence            57889999999999999999999999999998753         26789999999999999999999997 334  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCC---ChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSL---PDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESL  155 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~---~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l  155 (252)
                      .+.|+++. ++.+.++++++|   +.   ++|+++...   ....|..+.++++++|.||+     +.+.+ .|...+
T Consensus       113 ~~~Gdt~~-~~r~~i~~~~~I---iv---tTPd~L~~~~L~~~~~~~~~l~~l~~vViDEa-----h~~~g-~fg~~~  177 (742)
T TIGR03817       113 TYDGDTPT-EERRWAREHARY---VL---TNPDMLHRGILPSHARWARFLRRLRYVVIDEC-----HSYRG-VFGSHV  177 (742)
T ss_pred             EEeCCCCH-HHHHHHhcCCCE---EE---EChHHHHHhhccchhHHHHHHhcCCEEEEeCh-----hhccC-ccHHHH
Confidence            88888764 444566667776   22   458887521   12234444456999999997     66655 355554

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.

>KOG0350|consensus

Probab=99.92  E-value=1.4e-25  Score=188.06  Aligned_cols=123  Identities=24%  Similarity=0.319  Sum_probs=102.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      |....++|+++.||||||||+||++|++|.+.....       +..||+||+|||+|+.||++++++++.+.|  +.++.
T Consensus       178 p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v-------~~LRavVivPtr~L~~QV~~~f~~~~~~tg--L~V~~  248 (620)
T KOG0350|consen  178 PPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPV-------KRLRAVVIVPTRELALQVYDTFKRLNSGTG--LAVCS  248 (620)
T ss_pred             CCCCCCCceEEecCCCCCceeeehhHHHHHHccCCc-------cceEEEEEeeHHHHHHHHHHHHHHhccCCc--eEEEe
Confidence            556679999999999999999999999999876543       478999999999999999999999999988  78999


Q ss_pred             eeCCcccCcchhhhhhc-c--cccCCccccccCCccccCCChh-HHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKG-I--QYNDPIKTSWRAPRCILSLPDQ-VHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~-~--~i~~~i~t~~~~p~~l~~~~~~-~~~~l~~~~~~~V~de~  138 (252)
                      +.|..+.+....+|... +  .++..|    +|||||+++... ....+++ ++|+|.||+
T Consensus       249 ~sgq~sl~~E~~qL~~~~~~~~~DIlV----aTPGRLVDHl~~~k~f~Lk~-LrfLVIDEA  304 (620)
T KOG0350|consen  249 LSGQNSLEDEARQLASDPPECRIDILV----ATPGRLVDHLNNTKSFDLKH-LRFLVIDEA  304 (620)
T ss_pred             cccccchHHHHHHHhcCCCccccceEE----cCchHHHHhccCCCCcchhh-ceEEEechH
Confidence            99999998887777653 2  222113    459999999985 4555665 999999997

>KOG0341|consensus

Probab=99.90  E-value=9.3e-24  Score=172.51  Aligned_cols=158  Identities=65%  Similarity=1.126  Sum_probs=150.6

Q ss_pred             cchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChH
Q psy7786          90 QSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTP  169 (252)
Q Consensus        90 ~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~  169 (252)
                      ...+.+.+|..+..+|.|.|.||.-+..+..+..+..++.++++|+++++|.|+.+|.+|-|+..+++.+++.|+..||+
T Consensus       116 msV~ElakGi~Y~ePi~T~WkPP~hir~mS~e~~e~vRk~~~I~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTp  195 (610)
T KOG0341|consen  116 MSVAELAKGITYEEPIKTAWKPPRHIRKMSEEQRELVRKQLHILVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTP  195 (610)
T ss_pred             eeHHHHhCCCcccCcchhccCCcHHHHHhhHHHHHHHHHhheEEeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCc
Confidence            34677888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         170 IQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       170 iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      +|.+.+|..++|+|++.++.||||||+.|.+|++...++++.+.++....+|..||.||+|++|.|.++.+..+...+
T Consensus       196 IQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L  273 (610)
T KOG0341|consen  196 IQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAAL  273 (610)
T ss_pred             eeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999988777654

>KOG0327|consensus

Probab=99.90  E-value=5.3e-24  Score=173.63  Aligned_cols=209  Identities=18%  Similarity=0.275  Sum_probs=155.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+++..|+|+.+++++|||||.||++++++.+..+.+        ..+|++++||||||.|+.++.+.++..++  +++.
T Consensus        57 I~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~k--------e~qalilaPtreLa~qi~~v~~~lg~~~~--~~v~  126 (397)
T KOG0327|consen   57 ILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVK--------ETQALILAPTRELAQQIQKVVRALGDHMD--VSVH  126 (397)
T ss_pred             ccccccCCceeEeeeccccchhhhHHHHHhhcCcchH--------HHHHHHhcchHHHHHHHHHHHHhhhcccc--eeee
Confidence            6789999999999999999999999999999866543        67899999999999999999999999988  8899


Q ss_pred             eeeCCcccCcchhhhhh-cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKK-GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~-~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      .+.||.+...+-+.+.. ++++.  +    ++||++.++.++. ....+.++++|.||+     +.|...||.+.+...+
T Consensus       127 ~~igg~~~~~~~~~i~~~~~hiv--v----GTpgrV~dml~~~-~l~~~~iKmfvlDEa-----DEmLs~gfkdqI~~if  194 (397)
T KOG0327|consen  127 ACIGGTNVRREDQALLKDKPHIV--V----GTPGRVFDMLNRG-SLSTDGIKMFVLDEA-----DEMLSRGFKDQIYDIF  194 (397)
T ss_pred             eecCcccchhhhhhhhccCceee--c----CCchhHHHhhccc-cccccceeEEeecch-----HhhhccchHHHHHHHH
Confidence            99999988755555544 46662  2    5599999999888 444445999999997     7899999999998887


Q ss_pred             HHCCCCCChHHHHhhhhhhhcC----------CcEEEEccCCCchhHHhH------------HHHHHHHHhhhccCCCCC
Q psy7786         160 EAKGIKKPTPIQVQGIPAALSG----------RDIIGIAFTGSGKTLVFV------------LPILMFCLEQETKLPFLP  217 (252)
Q Consensus       160 ~~~~~~~p~~iQ~~~~p~~~~~----------~~~~~~~~~g~gKt~~~~------------~~~l~~i~~~~~~~~~~~  217 (252)
                      ..    .|..+|...++++...          ++.........++|..+.            ++.+..+.+ +       
T Consensus       195 ~~----lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l~dl~~-~-------  262 (397)
T KOG0327|consen  195 QE----LPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCDLYR-R-------  262 (397)
T ss_pred             HH----cCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccccccHHHHHHH-h-------
Confidence            77    4566666655555421          222222222223333221            233333333 1       


Q ss_pred             CCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         218 GEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       218 ~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                        -.+++||||||+-+.++...|.+.+.
T Consensus       263 --~~q~~if~nt~r~v~~l~~~L~~~~~  288 (397)
T KOG0327|consen  263 --VTQAVIFCNTRRKVDNLTDKLRAHGF  288 (397)
T ss_pred             --hhcceEEecchhhHHHHHHHHhhCCc
Confidence              34799999999999999999965543

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.89  E-value=6.5e-23  Score=191.43  Aligned_cols=129  Identities=17%  Similarity=0.237  Sum_probs=95.5

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH-------HHHhC
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY-------YCAAL   73 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~-------l~~~~   73 (252)
                      ||.+++|+|++++||||||||+||.+|+++.+......  ....+++++||++||||||+|+++.+..       +++..
T Consensus        41 i~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~--~~~~~~~~~LyIsPtraLa~di~~~L~~~l~~i~~~~~~~  118 (876)
T PRK13767         41 IPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGRE--GELEDKVYCLYVSPLRALNNDIHRNLEEPLTEIREIAKER  118 (876)
T ss_pred             HHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccc--cCCCCCeEEEEEcCHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            46789999999999999999999999999998764321  1113478999999999999999886653       23222


Q ss_pred             CC---CcceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHH--HHHhhhhceeeccCC
Q psy7786          74 PI---PLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVH--DIIRRNLRILVEGDD  138 (252)
Q Consensus        74 ~~---~~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~--~~l~~~~~~~V~de~  138 (252)
                      |.   ++++..++|+++..++.+.++++++|   +.   +||+++..+.....  ..++ +++++|.||.
T Consensus       119 g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~I---lV---tTPE~L~~ll~~~~~~~~l~-~l~~VVIDE~  181 (876)
T PRK13767        119 GEELPEIRVAIRTGDTSSYEKQKMLKKPPHI---LI---TTPESLAILLNSPKFREKLR-TVKWVIVDEI  181 (876)
T ss_pred             CCCcCCeeEEEEcCCCCHHHHHHHHhCCCCE---EE---ecHHHHHHHhcChhHHHHHh-cCCEEEEech
Confidence            21   47888999999888887777877777   22   35887755543322  2344 4899999996

>PTZ00424 helicase 45; Provisional

Probab=99.88  E-value=8.5e-23  Score=176.87  Aligned_cols=139  Identities=21%  Similarity=0.352  Sum_probs=106.3

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|++++||||||||++|++|+++.+....        .+.++||++||||||.|+.+.++.++...+  +.+.
T Consensus        59 i~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~--------~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~--~~~~  128 (401)
T PTZ00424         59 IKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDL--------NACQALILAPTRELAQQIQKVVLALGDYLK--VRCH  128 (401)
T ss_pred             HHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCC--------CCceEEEECCCHHHHHHHHHHHHHHhhhcC--ceEE
Confidence            467899999999999999999999999998774322        367899999999999999999999988766  7788


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++|+....++...+.++++|.  |.    +|+++.++..+.+..+.+ +.++|.||+     +.+.+.++...+.+.+.
T Consensus       129 ~~~g~~~~~~~~~~~~~~~~Iv--v~----Tp~~l~~~l~~~~~~l~~-i~lvViDEa-----h~~~~~~~~~~~~~i~~  196 (401)
T PTZ00424        129 ACVGGTVVRDDINKLKAGVHMV--VG----TPGRVYDMIDKRHLRVDD-LKLFILDEA-----DEMLSRGFKGQIYDVFK  196 (401)
T ss_pred             EEECCcCHHHHHHHHcCCCCEE--EE----CcHHHHHHHHhCCccccc-ccEEEEecH-----HHHHhcchHHHHHHHHh
Confidence            8899988777777777766662  33    377776665554444554 899999996     55555555555555554


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       197 ~  197 (401)
T PTZ00424        197 K  197 (401)
T ss_pred             h
Confidence            4

>KOG0332|consensus

Probab=99.88  E-value=5.5e-23  Score=167.05  Aligned_cols=206  Identities=19%  Similarity=0.255  Sum_probs=139.5

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCc
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGV   86 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~   86 (252)
                      .+|+|++|++|||||.||+|.++.++....        ..|++++|+||||||.|+.+++.+++++.+  +++.....|.
T Consensus       129 p~nlIaQsqsGtGKTaaFvL~MLsrvd~~~--------~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~--ita~yair~s  198 (477)
T KOG0332|consen  129 PQNLIAQSQSGTGKTAAFVLTMLSRVDPDV--------VVPQCICLAPTRELAPQTGEVVEEMGKFTE--LTASYAIRGS  198 (477)
T ss_pred             chhhhhhhcCCCchhHHHHHHHHHhcCccc--------cCCCceeeCchHHHHHHHHHHHHHhcCcee--eeEEEEecCc
Confidence            368999999999999999999999997766        378999999999999999999999999987  7777766664


Q ss_pred             ccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccc--------------------
Q psy7786          87 PMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSF--------------------  146 (252)
Q Consensus        87 ~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~--------------------  146 (252)
                             ...+|..+..+|+.  ++||.+.++..+.....-+.++++|.||+     +.|                    
T Consensus       199 -------k~~rG~~i~eqIvi--GTPGtv~Dlm~klk~id~~kikvfVlDEA-----D~Mi~tqG~~D~S~rI~~~lP~~  264 (477)
T KOG0332|consen  199 -------KAKRGNKLTEQIVI--GTPGTVLDLMLKLKCIDLEKIKVFVLDEA-----DVMIDTQGFQDQSIRIMRSLPRN  264 (477)
T ss_pred             -------ccccCCcchhheee--CCCccHHHHHHHHHhhChhhceEEEecch-----hhhhhcccccccchhhhhhcCCc
Confidence                   22334333333443  56999999999977777777999999997     222                    


Q ss_pred             -ccCCCCHHHHHH---HHHCCCCCChHHHHhhhhhhhcC-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCc
Q psy7786         147 -RLMKLPESLVRA---LEAKGIKKPTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP  221 (252)
Q Consensus       147 -~~~~l~~~l~~~---l~~~~~~~p~~iQ~~~~p~~~~~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~  221 (252)
                       +-+.||++..+.   +......+|..+-...-...+.+ +...+.......|     +..+..++.-.        .-.
T Consensus       265 ~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K-----~~~l~~lyg~~--------tig  331 (477)
T KOG0332|consen  265 QQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDK-----YQALVNLYGLL--------TIG  331 (477)
T ss_pred             ceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccchhhH-----HHHHHHHHhhh--------hhh
Confidence             222333333222   22222333332222111122222 3444444445555     44444443321        135


Q ss_pred             EEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         222 YGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       222 ~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      +++|||.||..|.+++..+++-|+.+.+
T Consensus       332 qsiIFc~tk~ta~~l~~~m~~~Gh~V~~  359 (477)
T KOG0332|consen  332 QSIIFCHTKATAMWLYEEMRAEGHQVSL  359 (477)
T ss_pred             heEEEEeehhhHHHHHHHHHhcCceeEE
Confidence            7999999999999999999998887653

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.87  E-value=9.5e-22  Score=187.81  Aligned_cols=120  Identities=18%  Similarity=0.201  Sum_probs=89.0

Q ss_pred             EEcCCCchHHHHhHHHHHHHHHHhhcCC--CCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHh----------CCCCcce
Q psy7786          12 GIAFTGSGKTLVFVLPILMFCLEQETKL--PFLPGEGPYGLIICPSRELARQTHDIIQYYCAA----------LPIPLRT   79 (252)
Q Consensus        12 ~~a~tgsGKT~a~~lp~~~~~~~~~~~~--~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~----------~~~~~~~   79 (252)
                      ++||||||||+||.||++++++.+....  ......++++|||+|||||++|+++.++.....          ...++++
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            4799999999999999999998653110  011124689999999999999999998753221          1124899


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHH-HHHhhhhceeeccCC
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVH-DIIRRNLRILVEGDD  138 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~-~~l~~~~~~~V~de~  138 (252)
                      ..++|+++.+++.+.+++++||   +.   +||+++..+..+.. ..+++ ++++|.||.
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdI---LV---TTPEsL~~LLtsk~r~~L~~-Vr~VIVDE~  133 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDI---LI---TTPESLYLMLTSRARETLRG-VETVIIDEV  133 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCE---EE---ecHHHHHHHHhhhhhhhhcc-CCEEEEecH
Confidence            9999999998888888888887   33   35888876654433 34444 999999995

>KOG4284|consensus

Probab=99.87  E-value=2.3e-23  Score=179.55  Aligned_cols=208  Identities=19%  Similarity=0.206  Sum_probs=155.2

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.++.|.|+|++|++|||||+.|.+-+++.+....        ..++++|++||||+|.||.+.+.+++..+. +.+|.
T Consensus        56 IP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~--------~~~q~~Iv~PTREiaVQI~~tv~~v~~sf~-g~~cs  126 (980)
T KOG4284|consen   56 IPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRS--------SHIQKVIVTPTREIAVQIKETVRKVAPSFT-GARCS  126 (980)
T ss_pred             hhhhhcccceEEEecCCCCceEEEEeeeehhcCccc--------CcceeEEEecchhhhhHHHHHHHHhccccc-CcceE
Confidence            799999999999999999999999999998886654        488999999999999999999999988654 49999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-CCCCHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLVRAL  159 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~~~l  159 (252)
                      +++||++....+..+++.. |.  |    ++||||.-+.+-+..+... ++++|+||+     +.+.+ -.|-.++-.++
T Consensus       127 vfIGGT~~~~d~~rlk~~r-Iv--I----GtPGRi~qL~el~~~n~s~-vrlfVLDEA-----DkL~~t~sfq~~In~ii  193 (980)
T KOG4284|consen  127 VFIGGTAHKLDLIRLKQTR-IV--I----GTPGRIAQLVELGAMNMSH-VRLFVLDEA-----DKLMDTESFQDDINIII  193 (980)
T ss_pred             EEecCchhhhhhhhhhhce-EE--e----cCchHHHHHHHhcCCCccc-eeEEEeccH-----HhhhchhhHHHHHHHHH
Confidence            9999999988888877643 31  3    4599999888888878777 999999997     55444 44666665555


Q ss_pred             HHCCCCCChHHHHhhhhhhhcC--------------------Cc----------EEEEccCCCchhHHhHHHHHHHHHhh
Q psy7786         160 EAKGIKKPTPIQVQGIPAALSG--------------------RD----------IIGIAFTGSGKTLVFVLPILMFCLEQ  209 (252)
Q Consensus       160 ~~~~~~~p~~iQ~~~~p~~~~~--------------------~~----------~~~~~~~g~gKt~~~~~~~l~~i~~~  209 (252)
                      ..    .|..-|..+.+++-+.                    .|          ..++.+.-+-+.....+..|.+++..
T Consensus       194 ~s----lP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~  269 (980)
T KOG4284|consen  194 NS----LPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKS  269 (980)
T ss_pred             Hh----cchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhh
Confidence            44    3555555444433211                    11          11122223444445556667666654


Q ss_pred             hccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         210 ETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       210 ~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      -        ...|+||||+....|+-++..|..
T Consensus       270 i--------py~QAlVF~~~~sra~~~a~~L~s  294 (980)
T KOG4284|consen  270 I--------PYVQALVFCDQISRAEPIATHLKS  294 (980)
T ss_pred             C--------chHHHHhhhhhhhhhhHHHHHhhc
Confidence            3        245799999999999999998864

>KOG0329|consensus

Probab=99.86  E-value=5e-23  Score=159.80  Aligned_cols=208  Identities=20%  Similarity=0.194  Sum_probs=148.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||...-|.|++++|++|.|||..|++..+|.+-+..        +.+.+|++|.|||||.|+.++..+|++|++ ++++.
T Consensus        73 ipqailgmdvlcqaksgmgktavfvl~tlqqiepv~--------g~vsvlvmchtrelafqi~~ey~rfskymP-~vkva  143 (387)
T KOG0329|consen   73 IPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVD--------GQVSVLVMCHTRELAFQISKEYERFSKYMP-SVKVS  143 (387)
T ss_pred             hhHHhhcchhheecccCCCceeeeehhhhhhcCCCC--------CeEEEEEEeccHHHHHHHHHHHHHHHhhCC-CceEE
Confidence            678888999999999999999999999999885543        478899999999999999999999999998 69999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccc-cCCCCHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFR-LMKLPESLVRAL  159 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~-~~~l~~~l~~~l  159 (252)
                      +++||.+.++..+.+++.++|.  +    ++|||++++.......+++ ++.+|+||.     +.|. ++....++++.+
T Consensus       144 VFfGG~~Ikkdee~lk~~Phiv--V----gTPGrilALvr~k~l~lk~-vkhFvlDEc-----dkmle~lDMrRDvQEif  211 (387)
T KOG0329|consen  144 VFFGGLFIKKDEELLKNCPHIV--V----GTPGRILALVRNRSLNLKN-VKHFVLDEC-----DKMLEQLDMRRDVQEIF  211 (387)
T ss_pred             EEEcceeccccHHHHhCCCeEE--E----cCcHHHHHHHHhccCchhh-cceeehhhH-----HHHHHHHHHHHHHHHHh
Confidence            9999999999999999988873  3    4599999999999999998 888888885     4333 344555555444


Q ss_pred             HHCCCCCChHHHHhhhhhhhcCC----------cEEEEccCCC-chhHHhHHHHHHHHHhhhccCCC----CCCCCcEEE
Q psy7786         160 EAKGIKKPTPIQVQGIPAALSGR----------DIIGIAFTGS-GKTLVFVLPILMFCLEQETKLPF----LPGEGPYGL  224 (252)
Q Consensus       160 ~~~~~~~p~~iQ~~~~p~~~~~~----------~~~~~~~~g~-gKt~~~~~~~l~~i~~~~~~~~~----~~~~~~~~L  224 (252)
                      ..    .|..-|..+++++++..          |-+-+..... .-|+.-+.....++.++++..+.    ......|++
T Consensus       212 r~----tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~LeFNQVv  287 (387)
T KOG0329|consen  212 RM----TPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLEFNQVV  287 (387)
T ss_pred             hc----CcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhhhccee
Confidence            32    45555555556555431          1111111111 22333333333344444333222    122346899


Q ss_pred             EEcCcHHHH
Q psy7786         225 IICPSRELA  233 (252)
Q Consensus       225 If~~tr~~a  233 (252)
                      ||+.+....
T Consensus       288 IFvKsv~Rl  296 (387)
T KOG0329|consen  288 IFVKSVQRL  296 (387)
T ss_pred             Eeeehhhhh
Confidence            999886653

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

Probab=99.86  E-value=7e-21  Score=175.80  Aligned_cols=121  Identities=25%  Similarity=0.335  Sum_probs=102.1

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+.+|||++++++||||||++|.+|+++.++.+..         -+||+|+||++||+++.+.++++...++.++++...
T Consensus        81 ~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~---------a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~~y  151 (851)
T COG1205          81 LIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPS---------ARALLLYPTNALANDQAERLRELISDLPGKVTFGRY  151 (851)
T ss_pred             HHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcC---------ccEEEEechhhhHhhHHHHHHHHHHhCCCcceeeee
Confidence            46799999999999999999999999999998764         289999999999999999999999998867888899


Q ss_pred             eCCcccCcchhhhhhcccccCCccccccCCccccC---CChhHHHHHhhhhceeeccCC
Q psy7786          83 IGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILS---LPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~---~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +|++..+++.+..+++++|   +.|   .|.+|--   .....|..+.++++++|.||.
T Consensus       152 ~Gdt~~~~r~~~~~~pp~I---llT---NpdMLh~~llr~~~~~~~~~~~Lk~lVvDEl  204 (851)
T COG1205         152 TGDTPPEERRAIIRNPPDI---LLT---NPDMLHYLLLRNHDAWLWLLRNLKYLVVDEL  204 (851)
T ss_pred             cCCCChHHHHHHHhCCCCE---EEe---CHHHHHHHhccCcchHHHHHhcCcEEEEecc
Confidence            9998888887888888898   554   4666544   333456666666999999995

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

Probab=99.85  E-value=2.6e-21  Score=175.84  Aligned_cols=212  Identities=16%  Similarity=0.108  Sum_probs=132.3

Q ss_pred             CCcccCCC-cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEE-EcCcHHHHHHHHHHHHHHHHhCC----
Q psy7786           1 MVTYRNSR-DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI-ICPSRELARQTHDIIQYYCAALP----   74 (252)
Q Consensus         1 i~~~~~g~-d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~li-l~ptreLa~q~~~~~~~l~~~~~----   74 (252)
                      ||.+++|+ +++++||||||||.+|.++.+.. ...        ...+++|| ++||||||.|+++.++++++.++    
T Consensus        24 i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~--------~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l~~~~~   94 (844)
T TIGR02621        24 AERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIG--------AKVPRRLVYVVNRRTVVDQVTEEAEKIGERLPDVPE   94 (844)
T ss_pred             HHHHHcCCCcceEecCCCCcccHHHHHhhccc-ccc--------ccccceEEEeCchHHHHHHHHHHHHHHHHHhcccch
Confidence            46788998 68888999999999776665522 111        13567777 55999999999999999998762    


Q ss_pred             -----------------CCcceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCC--------hhH---HHHH
Q psy7786          75 -----------------IPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLP--------DQV---HDII  126 (252)
Q Consensus        75 -----------------~~~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~--------~~~---~~~l  126 (252)
                                       .++++..++||.+.+.+.+.+.++++|+  |+|    ++.+.+-.        ...   ..-+
T Consensus        95 ~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~II--VgT----~D~i~sr~L~~gYg~~~~~~pi~ag~  168 (844)
T TIGR02621        95 VEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVI--VGT----VDMIGSRLLFSGYGCGFKSRPLHAGF  168 (844)
T ss_pred             hhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEE--EEC----HHHHcCCccccccccccccccchhhh
Confidence                             1388999999999999999999888874  444    43222111        000   0002


Q ss_pred             hhhhceeeccCCCCCcccccccCCCCHHHHHHHHHCC-CCCChHHHHhhhhhhhcC-----------CcEEE--------
Q psy7786         127 RRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKG-IKKPTPIQVQGIPAALSG-----------RDIIG--------  186 (252)
Q Consensus       127 ~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~-~~~p~~iQ~~~~p~~~~~-----------~~~~~--------  186 (252)
                      .++++++|.||+     +  .+++|.+++...+.... .....+.|...+++++..           .+...        
T Consensus       169 L~~v~~LVLDEA-----D--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~  241 (844)
T TIGR02621       169 LGQDALIVHDEA-----H--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLA  241 (844)
T ss_pred             hccceEEEEehh-----h--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeeccccccc
Confidence            344899999997     4  67889998877777531 110111344444444321           11100        


Q ss_pred             ------EccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         187 ------IAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       187 ------~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                            .......+....++..+..+..         ..+.++||||||++.|+.+++.|++.
T Consensus       242 a~ki~q~v~v~~e~Kl~~lv~~L~~ll~---------e~g~~vLVF~NTv~~Aq~L~~~L~~~  295 (844)
T TIGR02621       242 AKKIVKLVPPSDEKFLSTMVKELNLLMK---------DSGGAILVFCRTVKHVRKVFAKLPKE  295 (844)
T ss_pred             ccceEEEEecChHHHHHHHHHHHHHHHh---------hCCCcEEEEECCHHHHHHHHHHHHhc
Confidence                  0000011111122222222211         23567999999999999999999764

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.82  E-value=8.2e-20  Score=173.53  Aligned_cols=132  Identities=17%  Similarity=0.221  Sum_probs=92.4

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++|||||||| +|.+|+...+..          .+.+++||+||||||.|+++.++.++...+  +.+.
T Consensus        89 i~~il~g~dv~i~ApTGsGKT-~f~l~~~~~l~~----------~g~~alIL~PTreLa~Qi~~~l~~l~~~~~--~~~~  155 (1176)
T PRK09401         89 AKRLLLGESFAIIAPTGVGKT-TFGLVMSLYLAK----------KGKKSYIIFPTRLLVEQVVEKLEKFGEKVG--CGVK  155 (1176)
T ss_pred             HHHHHCCCcEEEEcCCCCCHH-HHHHHHHHHHHh----------cCCeEEEEeccHHHHHHHHHHHHHHhhhcC--ceEE
Confidence            467899999999999999999 577777665532          267899999999999999999999999877  6777


Q ss_pred             eeeCCccc-Cc----chhhhhh-cccccCCccccccCCccccCCChhHHHHHh-hhhceeeccCCCCCccccccc-----
Q psy7786          81 LAIGGVPM-NQ----SLDVIKK-GIQYNDPIKTSWRAPRCILSLPDQVHDIIR-RNLRILVEGDDVPPACCSFRL-----  148 (252)
Q Consensus        81 ~~~g~~~~-~~----~~~~l~~-~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~-~~~~~~V~de~~~~~~~~~~~-----  148 (252)
                      .++|+.+. ..    +.+.+.+ .++|.  |    +||+++..+..    .+. ..+.++|.||+     ++|.+     
T Consensus       156 ~~~g~~~~~~~ek~~~~~~l~~~~~~Il--V----~Tp~rL~~~~~----~l~~~~~~~lVvDEa-----D~~L~~~k~i  220 (1176)
T PRK09401        156 ILYYHSSLKKKEKEEFLERLKEGDFDIL--V----TTSQFLSKNFD----ELPKKKFDFVFVDDV-----DAVLKSSKNI  220 (1176)
T ss_pred             EEEccCCcchhHHHHHHHHHhcCCCCEE--E----ECHHHHHHHHH----hccccccCEEEEECh-----HHhhhcccch
Confidence            77777553 12    2233333 35552  2    34777765433    222 23889999986     55553     


Q ss_pred             ------CCCCH-HHHHHHH
Q psy7786         149 ------MKLPE-SLVRALE  160 (252)
Q Consensus       149 ------~~l~~-~l~~~l~  160 (252)
                            +||+. ++...+.
T Consensus       221 d~~l~~lGF~~~~i~~i~~  239 (1176)
T PRK09401        221 DKLLYLLGFSEEDIEKAME  239 (1176)
T ss_pred             hhHHHhCCCCHHHHHHHHH
Confidence                  78974 4544443

>PRK02362 ski2-like helicase; Provisional

Probab=99.80  E-value=1.7e-19  Score=166.79  Aligned_cols=128  Identities=18%  Similarity=0.202  Sum_probs=90.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +++|+|++++||||||||++|.+|+++.+..           +.+++|++||||||.|+++.+++++. .|  +++..++
T Consensus        36 ~~~g~nvlv~APTGSGKTlia~lail~~l~~-----------~~kal~i~P~raLa~q~~~~~~~~~~-~g--~~v~~~t  101 (737)
T PRK02362         36 LLDGKNLLAAIPTASGKTLIAELAMLKAIAR-----------GGKALYIVPLRALASEKFEEFERFEE-LG--VRVGIST  101 (737)
T ss_pred             HhCCCcEEEECCCcchHHHHHHHHHHHHHhc-----------CCcEEEEeChHHHHHHHHHHHHHhhc-CC--CEEEEEe
Confidence            6789999999999999999999999998842           45799999999999999999998764 35  8888899


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      |+.+...+  .+. ..+|.  |.    ||+++..+.......+. .+.++|.||.     +.+.+..+.+.+...+.
T Consensus       102 Gd~~~~~~--~l~-~~~Ii--V~----Tpek~~~llr~~~~~l~-~v~lvViDE~-----H~l~d~~rg~~le~il~  163 (737)
T PRK02362        102 GDYDSRDE--WLG-DNDII--VA----TSEKVDSLLRNGAPWLD-DITCVVVDEV-----HLIDSANRGPTLEVTLA  163 (737)
T ss_pred             CCcCcccc--ccC-CCCEE--EE----CHHHHHHHHhcChhhhh-hcCEEEEECc-----cccCCCcchHHHHHHHH
Confidence            98654332  222 23441  22    36665544433223333 4899999996     45555555555533333

>PRK14701 reverse gyrase; Provisional

Probab=99.80  E-value=1.6e-19  Score=175.19  Aligned_cols=132  Identities=16%  Similarity=0.218  Sum_probs=98.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||+.+.++.+... .          .+.++||++|||||+.|+.+.++.+++.++.++++.
T Consensus        88 i~~il~G~d~li~APTGsGKTl~~~~~al~~~-~----------~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~  156 (1638)
T PRK14701         88 AKRILRGKSFSIVAPTGMGKSTFGAFIALFLA-L----------KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLV  156 (1638)
T ss_pred             HHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHH-h----------cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEE
Confidence            47889999999999999999995555544321 1          266899999999999999999999999887668888


Q ss_pred             eeeCCcccCcchh---hhhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc--------
Q psy7786          81 LAIGGVPMNQSLD---VIKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL--------  148 (252)
Q Consensus        81 ~~~g~~~~~~~~~---~l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~--------  148 (252)
                      .++|+.+..++.+   .+.++ ++|.  +    +||+++.......   ....+.++|.||+     +.|.+        
T Consensus       157 ~~~g~~s~~e~~~~~~~l~~g~~dIL--V----~TPgrL~~~~~~l---~~~~i~~iVVDEA-----D~ml~~~knid~~  222 (1638)
T PRK14701        157 YYHSNLRKKEKEEFLERIENGDFDIL--V----TTAQFLARNFPEM---KHLKFDFIFVDDV-----DAFLKASKNIDRS  222 (1638)
T ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCEE--E----ECCchhHHhHHHH---hhCCCCEEEEECc-----eeccccccccchh
Confidence            8999988776643   34444 6662  2    3588887654432   2255889999986     44432        


Q ss_pred             ---CCCCHHHHH
Q psy7786         149 ---MKLPESLVR  157 (252)
Q Consensus       149 ---~~l~~~l~~  157 (252)
                         +||.+++.+
T Consensus       223 L~llGF~~e~~~  234 (1638)
T PRK14701        223 LQLLGFYEEIIE  234 (1638)
T ss_pred             hhcCCChHHHHH
Confidence               799999865

>KOG0344|consensus

Probab=99.80  E-value=1.8e-19  Score=154.35  Aligned_cols=215  Identities=22%  Similarity=0.181  Sum_probs=130.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH--HhCCCCcc
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC--AALPIPLR   78 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~--~~~~~~~~   78 (252)
                      ||.+++++|+++|||||||||+||.+|+++++.....   .....+.+++|+.||||||.|++.++.++.  +.++  .+
T Consensus       167 ipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~---~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~--~~  241 (593)
T KOG0344|consen  167 IPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQ---EKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTS--LR  241 (593)
T ss_pred             hhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhc---ccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCc--hh
Confidence            6889999999999999999999999999999876552   122358999999999999999999999998  5555  66


Q ss_pred             eeeeeCCcccCcchhhh-hhcccccCCccccccCCccccCCChhHH--HHHhhhhceeeccCCCCCcccccccC-CCCHH
Q psy7786          79 TCLAIGGVPMNQSLDVI-KKGIQYNDPIKTSWRAPRCILSLPDQVH--DIIRRNLRILVEGDDVPPACCSFRLM-KLPES  154 (252)
Q Consensus        79 ~~~~~g~~~~~~~~~~l-~~~~~i~~~i~t~~~~p~~l~~~~~~~~--~~l~~~~~~~V~de~~~~~~~~~~~~-~l~~~  154 (252)
                      +..+....-..+..+.+ ....|+.  +    ++|-+|....+...  ..+++ ++.+|.||+     +...+- .|-.+
T Consensus       242 a~~~~~~~~~~qk~a~~~~~k~dil--i----~TP~ri~~~~~~~~~~idl~~-V~~lV~dEa-----D~lfe~~~f~~Q  309 (593)
T KOG0344|consen  242 AAQFSKPAYPSQKPAFLSDEKYDIL--I----STPMRIVGLLGLGKLNIDLSK-VEWLVVDEA-----DLLFEPEFFVEQ  309 (593)
T ss_pred             hhhcccccchhhccchhHHHHHHHH--h----cCHHHHHHHhcCCCccchhhe-eeeEeechH-----HhhhChhhHHHH
Confidence            66555443333222222 2223331  2    33666655555433  45555 888888885     332222 33333


Q ss_pred             HHHHHHHCC----------CCCChHHHHhhhhhhhcCCcEEEEcc-----------CCCchhHHhHHHHHHHHHhhhccC
Q psy7786         155 LVRALEAKG----------IKKPTPIQVQGIPAALSGRDIIGIAF-----------TGSGKTLVFVLPILMFCLEQETKL  213 (252)
Q Consensus       155 l~~~l~~~~----------~~~p~~iQ~~~~p~~~~~~~~~~~~~-----------~g~gKt~~~~~~~l~~i~~~~~~~  213 (252)
                      +-..+..+.          ...+..+..++.-.......+++-..           ...|++..-++.+...+ ..    
T Consensus       310 la~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v-~~----  384 (593)
T KOG0344|consen  310 LADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQLV-AS----  384 (593)
T ss_pred             HHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHHHH-hc----
Confidence            333332221          33344444433222211122222111           12333333333333322 22    


Q ss_pred             CCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         214 PFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       214 ~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                          +-.|-+|||+-+.+.|.+++..|.
T Consensus       385 ----g~~PP~lIfVQs~eRak~L~~~L~  408 (593)
T KOG0344|consen  385 ----GFKPPVLIFVQSKERAKQLFEELE  408 (593)
T ss_pred             ----cCCCCeEEEEecHHHHHHHHHHhh
Confidence                235779999999999999999985

>PRK00254 ski2-like helicase; Provisional

Probab=99.80  E-value=1.1e-18  Score=161.09  Aligned_cols=131  Identities=18%  Similarity=0.182  Sum_probs=93.4

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +++|+|++++||||||||++|.+|+++.+...          +.++||++|||+||.|+++.++.+.+ .+  +++..++
T Consensus        36 ~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~----------~~~~l~l~P~~aLa~q~~~~~~~~~~-~g--~~v~~~~  102 (720)
T PRK00254         36 VLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE----------GGKAVYLVPLKALAEEKYREFKDWEK-LG--LRVAMTT  102 (720)
T ss_pred             HhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc----------CCeEEEEeChHHHHHHHHHHHHHHhh-cC--CEEEEEe
Confidence            68999999999999999999999999887642          45799999999999999999988753 45  8888999


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHHC
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAK  162 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~  162 (252)
                      |+.+...+  .+ ..++|.  |.    ||+++..+.......++ ++.++|.||.     +.+.+......+...+.+.
T Consensus       103 Gd~~~~~~--~~-~~~~Ii--V~----Tpe~~~~ll~~~~~~l~-~l~lvViDE~-----H~l~~~~rg~~le~il~~l  166 (720)
T PRK00254        103 GDYDSTDE--WL-GKYDII--IA----TAEKFDSLLRHGSSWIK-DVKLVVADEI-----HLIGSYDRGATLEMILTHM  166 (720)
T ss_pred             CCCCCchh--hh-ccCCEE--EE----cHHHHHHHHhCCchhhh-cCCEEEEcCc-----CccCCccchHHHHHHHHhc
Confidence            98765322  22 234441  22    36666555443333344 4899999996     4555555556655555543

>TIGR01054 rgy reverse gyrase

Probab=99.79  E-value=5.2e-19  Score=168.28  Aligned_cols=129  Identities=19%  Similarity=0.201  Sum_probs=94.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcc-e
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLR-T   79 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~-~   79 (252)
                      ||.++.|+|++++||||||||+ |.+|+...+..          .+++++|++||||||.|+++.++.+++.++.... +
T Consensus        87 i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~----------~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i  155 (1171)
T TIGR01054        87 AKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK----------KGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNI  155 (1171)
T ss_pred             HHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh----------cCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeee
Confidence            4678999999999999999996 88888776532          2678999999999999999999999998773221 2


Q ss_pred             eeeeCCcccCcchh---hhhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-------
Q psy7786          80 CLAIGGVPMNQSLD---VIKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-------  148 (252)
Q Consensus        80 ~~~~g~~~~~~~~~---~l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-------  148 (252)
                      ..++||.+..++.+   .+.++ ++|.  |    +||+++..+..+    +...++++|.||+     ++|.+       
T Consensus       156 ~~~~Gg~~~~e~~~~~~~l~~~~~dIl--V----~Tp~rL~~~~~~----l~~~~~~iVvDEa-----D~~L~~~k~vd~  220 (1171)
T TIGR01054       156 GAYHSRLPTKEKKEFMERIENGDFDIL--I----TTTMFLSKNYDE----LGPKFDFIFVDDV-----DALLKASKNVDK  220 (1171)
T ss_pred             eeecCCCCHHHHHHHHHHHhcCCCCEE--E----ECHHHHHHHHHH----hcCCCCEEEEeCh-----HhhhhccccHHH
Confidence            34678887765433   33333 5652  2    347776554332    2225889999997     67766       


Q ss_pred             ----CCCCHHH
Q psy7786         149 ----MKLPESL  155 (252)
Q Consensus       149 ----~~l~~~l  155 (252)
                          +||.++.
T Consensus       221 il~llGF~~e~  231 (1171)
T TIGR01054       221 LLKLLGFSEEL  231 (1171)
T ss_pred             HHHHcCCCHHH
Confidence                8899864

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.78  E-value=2.4e-18  Score=151.67  Aligned_cols=119  Identities=18%  Similarity=0.237  Sum_probs=81.4

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++++|||||||++|.+|++..              +..+||++|||||+.|+.+.++.    .+  +.+.
T Consensus        20 i~~~l~g~dvlv~apTGsGKTl~y~lp~l~~--------------~~~~lVi~P~~~L~~dq~~~l~~----~g--i~~~   79 (470)
T TIGR00614        20 INAVLLGRDCFVVMPTGGGKSLCYQLPALCS--------------DGITLVISPLISLMEDQVLQLKA----SG--IPAT   79 (470)
T ss_pred             HHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc--------------CCcEEEEecHHHHHHHHHHHHHH----cC--CcEE
Confidence            4678999999999999999999999998741              23599999999999998887764    34  6666


Q ss_pred             eeeCCcccCcchhhh---hhc-ccccCCccccccCCccccCCChhHHHH-HhhhhceeeccCCCCCcccccccCC
Q psy7786          81 LAIGGVPMNQSLDVI---KKG-IQYNDPIKTSWRAPRCILSLPDQVHDI-IRRNLRILVEGDDVPPACCSFRLMK  150 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l---~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~-l~~~~~~~V~de~~~~~~~~~~~~~  150 (252)
                      .+.|+.+..++...+   .++ .++      ++.+|+++.......... ....+.++|.||+     +.+.+.|
T Consensus        80 ~l~~~~~~~~~~~i~~~~~~~~~~i------l~~TPe~l~~~~~~~~~l~~~~~i~~iViDEa-----H~i~~~g  143 (470)
T TIGR00614        80 FLNSSQSKEQQKNVLTDLKDGKIKL------LYVTPEKCSASNRLLQTLEERKGITLIAVDEA-----HCISQWG  143 (470)
T ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCE------EEECHHHHcCchhHHHHHHhcCCcCEEEEeCC-----cccCccc
Confidence            677765544333222   222 333      334588876544222221 3445899999997     5555544

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

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.76  E-value=5.3e-19  Score=160.76  Aligned_cols=117  Identities=15%  Similarity=0.182  Sum_probs=95.5

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.++.|+|++++++||||||+||++|+++.++..           ..++||+||||||.|+.+++..+.+++|  +++.
T Consensus       101 I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g-----------~~v~IVTpTrELA~Qdae~m~~L~k~lG--LsV~  167 (970)
T PRK12899        101 LGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG-----------KPVHLVTVNDYLAQRDCEWVGSVLRWLG--LTTG  167 (970)
T ss_pred             hhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc-----------CCeEEEeCCHHHHHHHHHHHHHHHhhcC--CeEE
Confidence            57889999999999999999999999999887642           1389999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccc-cCCChhHHHHH------hhhhceeeccCC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCI-LSLPDQVHDII------RRNLRILVEGDD  138 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l-~~~~~~~~~~l------~~~~~~~V~de~  138 (252)
                      +++||.+..++.+.+  ++||      +|+||+++ .++.......+      .+.++++|.||+
T Consensus       168 ~i~GG~~~~eq~~~y--~~DI------VygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~IIDEA  224 (970)
T PRK12899        168 VLVSGSPLEKRKEIY--QCDV------VYGTASEFGFDYLRDNSIATRKEEQVGRGFYFAIIDEV  224 (970)
T ss_pred             EEeCCCCHHHHHHHc--CCCE------EEECCChhHHHHhhCCCCCcCHHHhhcccccEEEEech
Confidence            999999988877665  4777      34569999 77665542222      234689998885

>PRK01172 ski2-like helicase; Provisional

Probab=99.76  E-value=4.2e-18  Score=156.34  Aligned_cols=129  Identities=23%  Similarity=0.206  Sum_probs=90.5

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|++++||||||||++|.+++++.+..           +.+++|++|+|+||.|+++.++++. ..|  +++..
T Consensus        32 ~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~-----------~~k~v~i~P~raLa~q~~~~~~~l~-~~g--~~v~~   97 (674)
T PRK01172         32 EQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA-----------GLKSIYIVPLRSLAMEKYEELSRLR-SLG--MRVKI   97 (674)
T ss_pred             HHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh-----------CCcEEEEechHHHHHHHHHHHHHHh-hcC--CeEEE
Confidence            456889999999999999999999999987753           3469999999999999999998875 345  78888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      .+|+.+...  +.+ +..++.  +.    ||+++..+..+....+.+ +.++|.||.     +.+.+....+.+...+
T Consensus        98 ~~G~~~~~~--~~~-~~~dIi--v~----Tpek~~~l~~~~~~~l~~-v~lvViDEa-----H~l~d~~rg~~le~ll  160 (674)
T PRK01172         98 SIGDYDDPP--DFI-KRYDVV--IL----TSEKADSLIHHDPYIIND-VGLIVADEI-----HIIGDEDRGPTLETVL  160 (674)
T ss_pred             EeCCCCCCh--hhh-ccCCEE--EE----CHHHHHHHHhCChhHHhh-cCEEEEecc-----hhccCCCccHHHHHHH
Confidence            888865432  222 334542  33    376655554443334444 899999996     4555445555543333

>PTZ00110 helicase; Provisional

Probab=99.76  E-value=1.2e-17  Score=149.16  Aligned_cols=136  Identities=40%  Similarity=0.664  Sum_probs=116.9

Q ss_pred             CccccCCChhHHHHHhhhhceee-ccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccC
Q psy7786         112 PRCILSLPDQVHDIIRRNLRILV-EGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFT  190 (252)
Q Consensus       112 p~~l~~~~~~~~~~l~~~~~~~V-~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~  190 (252)
                      +..+..+..+....++...++.| .++++|++..+|.+++|++.+++.+.+.++..|+++|.+++|..+.|+|++++++|
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~i~~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApT  176 (545)
T PTZ00110         97 HPEVSALSSKEVDEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAET  176 (545)
T ss_pred             ChhhhcCCHHHHHHHHHhcCcEEecCCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCC
Confidence            34556677777777777666665 68889999999999999999999999999999999999999999999999999999


Q ss_pred             CCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         191 GSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       191 g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |+|||++|++|.+.++..+..   .....++++||++|||+||.|+.+.+++++...+++
T Consensus       177 GSGKTlaylLP~l~~i~~~~~---~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~  233 (545)
T PTZ00110        177 GSGKTLAFLLPAIVHINAQPL---LRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIR  233 (545)
T ss_pred             CChHHHHHHHHHHHHHHhccc---ccCCCCcEEEEECChHHHHHHHHHHHHHHhcccCcc
Confidence            999999999999988875431   122346899999999999999999999999877654

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

Probab=99.74  E-value=1.3e-17  Score=154.67  Aligned_cols=124  Identities=15%  Similarity=0.207  Sum_probs=86.3

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++++|||+|||++|.+|++..              ...+|||+|++||+.++...+..    .+  +++.
T Consensus       469 I~aiL~GrDVLVimPTGSGKSLcYQLPAL~~--------------~GiTLVISPLiSLmqDQV~~L~~----~G--I~Aa  528 (1195)
T PLN03137        469 INATMSGYDVFVLMPTGGGKSLTYQLPALIC--------------PGITLVISPLVSLIQDQIMNLLQ----AN--IPAA  528 (1195)
T ss_pred             HHHHHcCCCEEEEcCCCccHHHHHHHHHHHc--------------CCcEEEEeCHHHHHHHHHHHHHh----CC--CeEE
Confidence            5678999999999999999999999999842              23599999999999855443332    34  7888


Q ss_pred             eeeCCcccCcchhhhhh------cccccCCccccccCCccccCCC--hhHHHHH--hhhhceeeccCCCCCcccccccCC
Q psy7786          81 LAIGGVPMNQSLDVIKK------GIQYNDPIKTSWRAPRCILSLP--DQVHDII--RRNLRILVEGDDVPPACCSFRLMK  150 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~------~~~i~~~i~t~~~~p~~l~~~~--~~~~~~l--~~~~~~~V~de~~~~~~~~~~~~~  150 (252)
                      .+.|+.+..++.+.+++      .+++      +|.+|+++....  .+....+  ...+.++|.||+     +.+.+.|
T Consensus       529 ~L~s~~s~~eq~~ilr~l~s~~g~~~I------LyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEA-----HcVSqWG  597 (1195)
T PLN03137        529 SLSAGMEWAEQLEILQELSSEYSKYKL------LYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEA-----HCVSQWG  597 (1195)
T ss_pred             EEECCCCHHHHHHHHHHHHhcCCCCCE------EEEChHHhhcchHHHHHHHhhhhccccceeccCcc-----hhhhhcc
Confidence            89999888777666654      2333      345588876432  1111111  234778899997     5566665


Q ss_pred             --CCHHH
Q psy7786         151 --LPESL  155 (252)
Q Consensus       151 --l~~~l  155 (252)
                        |.++.
T Consensus       598 hDFRpdY  604 (1195)
T PLN03137        598 HDFRPDY  604 (1195)
T ss_pred             cchHHHH
Confidence              55554

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

Probab=99.74  E-value=3e-17  Score=146.16  Aligned_cols=136  Identities=38%  Similarity=0.595  Sum_probs=118.3

Q ss_pred             cccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCc
Q psy7786         114 CILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSG  193 (252)
Q Consensus       114 ~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~g  193 (252)
                      ...++.......+++...+.|.++++|+++.+|.++++++.+++.+.+.|+..|+++|.+++|..+.|+|++++++||+|
T Consensus        91 ~~~~~~~~~~~~~r~~~~i~~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSG  170 (518)
T PLN00206         91 STSGLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSG  170 (518)
T ss_pred             hhccCCHHHHHHHHHHCCCEecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCC
Confidence            33456777888888888999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         194 KTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       194 Kt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ||++|++|++.++...... ......++++||++|||+||.|+.+.++.++..++++
T Consensus       171 KTlayllPil~~l~~~~~~-~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~  226 (518)
T PLN00206        171 KTASFLVPIISRCCTIRSG-HPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFK  226 (518)
T ss_pred             ccHHHHHHHHHHHHhhccc-cccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCce
Confidence            9999999999887753211 1122356899999999999999999999998877654

>KOG0330|consensus

Probab=99.73  E-value=1.5e-17  Score=136.30  Aligned_cols=99  Identities=40%  Similarity=0.588  Sum_probs=93.7

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++.+++++.+.+.+++.|++||+.++|..+.|+|++..+.||+|||.+|++|++++++.+.        .-+++
T Consensus        61 ~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p--------~~~~~  132 (476)
T KOG0330|consen   61 KSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEP--------KLFFA  132 (476)
T ss_pred             cchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCC--------CCceE
Confidence            6899999999999999999999999999999999999999999999999999999999999999753        34789


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      +|++||||+|.||++.+..++..+|++
T Consensus       133 lVLtPtRELA~QI~e~fe~Lg~~iglr  159 (476)
T KOG0330|consen  133 LVLTPTRELAQQIAEQFEALGSGIGLR  159 (476)
T ss_pred             EEecCcHHHHHHHHHHHHHhccccCeE
Confidence            999999999999999999999999875

>cd00268 DEADc DEAD-box helicases

Probab=99.73  E-value=6.8e-18  Score=132.86  Aligned_cols=139  Identities=27%  Similarity=0.420  Sum_probs=103.6

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+.+|+|+++.+|||+|||++|++|+++.+.....      ..+++++|++||++|+.|+.+.++.+....+  +.+..
T Consensus        31 ~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~------~~~~~viii~p~~~L~~q~~~~~~~~~~~~~--~~~~~  102 (203)
T cd00268          31 PPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPK------KDGPQALILAPTRELALQIAEVARKLGKHTN--LKVVV  102 (203)
T ss_pred             HHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcc------cCCceEEEEcCCHHHHHHHHHHHHHHhccCC--ceEEE
Confidence            456789999999999999999999999998877521      1378999999999999999999999987765  78888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .+|+.+..+....+..++++.  +    ++|+.+.....+....+.. +.++|.||.     +.+.+.++...+...+.
T Consensus       103 ~~~~~~~~~~~~~~~~~~~ii--v----~T~~~l~~~l~~~~~~~~~-l~~lIvDE~-----h~~~~~~~~~~~~~~~~  169 (203)
T cd00268         103 IYGGTSIDKQIRKLKRGPHIV--V----ATPGRLLDLLERGKLDLSK-VKYLVLDEA-----DRMLDMGFEDQIREILK  169 (203)
T ss_pred             EECCCCHHHHHHHhcCCCCEE--E----EChHHHHHHHHcCCCChhh-CCEEEEeCh-----HHhhccChHHHHHHHHH
Confidence            999987766666665555552  2    3466665554444434444 788998986     55666666666654444

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.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.72  E-value=1.1e-16  Score=149.23  Aligned_cols=107  Identities=19%  Similarity=0.222  Sum_probs=79.7

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCc
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGV   86 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~   86 (252)
                      ++|.+++|+||||||++|++|++..+..           +.+++|++||++||.|+++.++++....+  +++..++|+.
T Consensus       472 ~~d~Ll~adTGsGKT~val~a~l~al~~-----------g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~--i~v~~Lsg~~  538 (926)
T TIGR00580       472 PMDRLVCGDVGFGKTEVAMRAAFKAVLD-----------GKQVAVLVPTTLLAQQHFETFKERFANFP--VTIELLSRFR  538 (926)
T ss_pred             cCCEEEECCCCccHHHHHHHHHHHHHHh-----------CCeEEEEeCcHHHHHHHHHHHHHHhccCC--cEEEEEeccc
Confidence            3799999999999999999999987743           46899999999999999999999877666  8888888887


Q ss_pred             ccCcchhhh---hhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          87 PMNQSLDVI---KKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        87 ~~~~~~~~l---~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +..++.+.+   .++ ++|.  |.    ||..+.     ....+++ +.++|.||.
T Consensus       539 ~~~e~~~~~~~l~~g~~dIV--IG----Tp~ll~-----~~v~f~~-L~llVIDEa  582 (926)
T TIGR00580       539 SAKEQNEILKELASGKIDIL--IG----THKLLQ-----KDVKFKD-LGLLIIDEE  582 (926)
T ss_pred             cHHHHHHHHHHHHcCCceEE--Ec----hHHHhh-----CCCCccc-CCEEEeecc
Confidence            765544433   333 5552  23    353221     1123444 899999996

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.

>KOG0333|consensus

Probab=99.72  E-value=1.5e-17  Score=140.99  Aligned_cols=138  Identities=33%  Similarity=0.565  Sum_probs=125.1

Q ss_pred             ccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCC
Q psy7786         113 RCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGS  192 (252)
Q Consensus       113 ~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~  192 (252)
                      ..+..|.+++|..|+....+.+.+.++|+|+.+|.+.+|+.++++.+.+.++..|++||..++|..+..+|++..+.||+
T Consensus       214 k~l~Em~~rdwri~redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgs  293 (673)
T KOG0333|consen  214 KVLAEMTERDWRIFREDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGS  293 (673)
T ss_pred             hhHHhcCCccceeeecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccC
Confidence            45777888889999998899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHhHHHHHHHHHhhhccCCC-CCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         193 GKTLVFVLPILMFCLEQETKLPF-LPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       193 gKt~~~~~~~l~~i~~~~~~~~~-~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |||.+|++|++.++........+ ....+|+++|++|||++|+||.++-.+|++.++++
T Consensus       294 Gktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r  352 (673)
T KOG0333|consen  294 GKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIR  352 (673)
T ss_pred             CccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccce
Confidence            99999999999998865544333 34568999999999999999999999999998864

>KOG0349|consensus

Probab=99.71  E-value=5.4e-18  Score=140.85  Aligned_cols=96  Identities=25%  Similarity=0.298  Sum_probs=80.7

Q ss_pred             EEEEEcCcHHHHHHHHHHHHHHHHhCC-CCcceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHH
Q psy7786          48 YGLIICPSRELARQTHDIIQYYCAALP-IPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDII  126 (252)
Q Consensus        48 ~~lil~ptreLa~q~~~~~~~l~~~~~-~~~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l  126 (252)
                      +++|+-|.||||.|+++.+++|-.++. ..+|.....||...+.|..++.++.+|+  +    ++|+|+..++......+
T Consensus       288 ~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~iv--v----GtpgRl~~~is~g~~~l  361 (725)
T KOG0349|consen  288 EAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIV--V----GTPGRLLQPISKGLVTL  361 (725)
T ss_pred             ceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceee--e----cCchhhhhhhhccceee
Confidence            799999999999999999999988874 3478888999999999999999999983  3    45999999999888888


Q ss_pred             hhhhceeeccCCCCCcccccccCCCCHHH
Q psy7786         127 RRNLRILVEGDDVPPACCSFRLMKLPESL  155 (252)
Q Consensus       127 ~~~~~~~V~de~~~~~~~~~~~~~l~~~l  155 (252)
                      .. .+|+|.||+     +.+...+.++.+
T Consensus       362 t~-crFlvlDea-----d~lL~qgy~d~I  384 (725)
T KOG0349|consen  362 TH-CRFLVLDEA-----DLLLGQGYDDKI  384 (725)
T ss_pred             ee-eEEEEecch-----hhhhhcccHHHH
Confidence            87 899999997     555555555544

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.71  E-value=9.3e-17  Score=146.86  Aligned_cols=113  Identities=24%  Similarity=0.304  Sum_probs=82.4

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+.+|+|+++++|||||||+...+.+++.+...          +-+++|++|+|+||.+.++.++++.. .|  +++...
T Consensus        43 ~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~----------~~k~vYivPlkALa~Ek~~~~~~~~~-~G--irV~~~  109 (766)
T COG1204          43 GLLSDENVLISAPTGSGKTLIALLAILSTLLEG----------GGKVVYIVPLKALAEEKYEEFSRLEE-LG--IRVGIS  109 (766)
T ss_pred             cccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc----------CCcEEEEeChHHHHHHHHHHhhhHHh-cC--CEEEEe
Confidence            456689999999999999999999999988764          34699999999999999999996643 45  899999


Q ss_pred             eCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          83 IGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +|+.+...  +.+. +.+|   ++   +||..+.+.......... .+..+|.||.
T Consensus       110 TgD~~~~~--~~l~-~~~V---iV---tT~EK~Dsl~R~~~~~~~-~V~lvViDEi  155 (766)
T COG1204         110 TGDYDLDD--ERLA-RYDV---IV---TTPEKLDSLTRKRPSWIE-EVDLVVIDEI  155 (766)
T ss_pred             cCCcccch--hhhc-cCCE---EE---EchHHhhHhhhcCcchhh-cccEEEEeee
Confidence            99966443  2222 2333   11   235555554444444333 4888888884

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.70  E-value=2.8e-17  Score=150.33  Aligned_cols=106  Identities=21%  Similarity=0.251  Sum_probs=82.4

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcc
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVP   87 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~   87 (252)
                      +|.+++|+||||||++|++|+++.+.           .+.+++|++||++||.|+++.++++...++  +++..++|+.+
T Consensus       283 ~~~Ll~~~TGSGKT~va~~~il~~~~-----------~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~--i~v~ll~G~~~  349 (681)
T PRK10917        283 MNRLLQGDVGSGKTVVAALAALAAIE-----------AGYQAALMAPTEILAEQHYENLKKLLEPLG--IRVALLTGSLK  349 (681)
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHHHH-----------cCCeEEEEeccHHHHHHHHHHHHHHHhhcC--cEEEEEcCCCC
Confidence            48999999999999999999998763           267899999999999999999999998887  89999999988


Q ss_pred             cCcchhh---hhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          88 MNQSLDV---IKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        88 ~~~~~~~---l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      ..++.+.   +.++ +++.  |    +||+++.+     ...+.+ +.++|.||.
T Consensus       350 ~~~r~~~~~~l~~g~~~Iv--V----gT~~ll~~-----~v~~~~-l~lvVIDE~  392 (681)
T PRK10917        350 GKERREILEAIASGEADIV--I----GTHALIQD-----DVEFHN-LGLVIIDEQ  392 (681)
T ss_pred             HHHHHHHHHHHhCCCCCEE--E----chHHHhcc-----cchhcc-cceEEEech
Confidence            6554443   3333 5552  2    23665543     123444 899999996

>KOG0346|consensus

Probab=99.70  E-value=6.5e-17  Score=134.49  Aligned_cols=103  Identities=34%  Similarity=0.536  Sum_probs=95.2

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++.+.+++.+.+.||..||.+|+.++|..+.|+|++..+.||||||.+|++|+++.++......  ..+.++.+
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~--~~e~~~sa   96 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTN--DGEQGPSA   96 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcc--ccccccee
Confidence            4799999999999999999999999999999999999999999999999999999999999999765433  55778999


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      +|++||||+|.|++..+.++..+.+
T Consensus        97 ~iLvPTkEL~qQvy~viekL~~~c~  121 (569)
T KOG0346|consen   97 VILVPTKELAQQVYKVIEKLVEYCS  121 (569)
T ss_pred             EEEechHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999887764

>KOG0331|consensus

Probab=99.70  E-value=7.8e-17  Score=139.05  Aligned_cols=105  Identities=44%  Similarity=0.730  Sum_probs=95.4

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      .|+++++++++...+...++..|++||.+.||..+.|+|++.++.||+|||++|++|.+.++...  ........+|++|
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~--~~~~~~~~~P~vL  169 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNE--QGKLSRGDGPIVL  169 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhc--cccccCCCCCeEE
Confidence            79999999999999999999999999999999999999999999999999999999999998863  1123446689999


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhhCCCCC
Q psy7786         225 IICPSRELARQTHDIIQYYCAALPIGS  251 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~~~~~i~~  251 (252)
                      |++||||||.|+.+.++++++.+++++
T Consensus       170 VL~PTRELA~QV~~~~~~~~~~~~~~~  196 (519)
T KOG0331|consen  170 VLAPTRELAVQVQAEAREFGKSLRLRS  196 (519)
T ss_pred             EEcCcHHHHHHHHHHHHHHcCCCCccE
Confidence            999999999999999999999887643

>KOG0339|consensus

Probab=99.69  E-value=7.4e-17  Score=136.33  Aligned_cols=139  Identities=37%  Similarity=0.588  Sum_probs=124.8

Q ss_pred             cCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEcc
Q psy7786         110 RAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAF  189 (252)
Q Consensus       110 ~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~  189 (252)
                      ..|..+-.+-.+....++..+.+-|.+-..++++.+|...+|...+...+.+.-++.|+++|.+.+|..+.|+|++.++.
T Consensus       189 ~e~esI~gl~~~d~~~~r~~Lnlrv~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAk  268 (731)
T KOG0339|consen  189 EEHESIEGLTKMDVIDLRLTLNLRVSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAK  268 (731)
T ss_pred             cChhhhhccccccchhhHhhhcceeccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheee
Confidence            33555666666666677777889999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCCC
Q psy7786         190 TGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGS  251 (252)
Q Consensus       190 ~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~~  251 (252)
                      +|+|||.+|++|++.+++++...   ..+.+|-.+|+||||++|.||+.++++|++..+++.
T Consensus       269 tgSgktaAfi~pm~~himdq~eL---~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~  327 (731)
T KOG0339|consen  269 TGSGKTAAFIWPMIVHIMDQPEL---KPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRV  327 (731)
T ss_pred             ccCcchhHHHHHHHHHhcchhhh---cCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceE
Confidence            99999999999999999987633   346789999999999999999999999999999875

>KOG0334|consensus

Probab=99.69  E-value=9.1e-17  Score=145.88  Aligned_cols=134  Identities=41%  Similarity=0.657  Sum_probs=117.6

Q ss_pred             cccCCChhHHHHHhhhhc-eeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCC
Q psy7786         114 CILSLPDQVHDIIRRNLR-ILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGS  192 (252)
Q Consensus       114 ~l~~~~~~~~~~l~~~~~-~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~  192 (252)
                      -+..+.......++..+. +.|.+-++|.++.+|.+.|++..+++.+.++++..|++||.++||+++.|+|++.++.||+
T Consensus       334 di~~ms~~eV~~yr~~l~~i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgS  413 (997)
T KOG0334|consen  334 DIKRMSAAEVDEYRCELDGIKVKGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGS  413 (997)
T ss_pred             hHHHHHHHHHHHhhcCccceeeccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCC
Confidence            344444445555666666 8888889999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         193 GKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       193 gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |||++|++|++.+++.+.   +.....+|-+||+||||++|.||.++++.|+..+++.
T Consensus       414 GKT~af~LPmirhi~dQr---~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir  468 (997)
T KOG0334|consen  414 GKTLAFLLPMIRHIKDQR---PLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIR  468 (997)
T ss_pred             ccchhhhcchhhhhhcCC---ChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCce
Confidence            999999999998887764   3345668999999999999999999999999988765

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.68  E-value=2.1e-16  Score=150.28  Aligned_cols=106  Identities=18%  Similarity=0.172  Sum_probs=78.9

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcc
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVP   87 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~   87 (252)
                      +|++++++||||||.+|+.+++..+.           ++.+++|++||++||.|+++.+++.....+  +++.+++|+.+
T Consensus       622 ~d~Ll~a~TGsGKT~val~aa~~~~~-----------~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~--v~i~~l~g~~s  688 (1147)
T PRK10689        622 MDRLVCGDVGFGKTEVAMRAAFLAVE-----------NHKQVAVLVPTTLLAQQHYDNFRDRFANWP--VRIEMLSRFRS  688 (1147)
T ss_pred             CCEEEEcCCCcCHHHHHHHHHHHHHH-----------cCCeEEEEeCcHHHHHHHHHHHHHhhccCC--ceEEEEECCCC
Confidence            89999999999999999998876642           267899999999999999999998665555  78888889888


Q ss_pred             cCcchhhhhh----cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          88 MNQSLDVIKK----GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        88 ~~~~~~~l~~----~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .+++.+.+.+    .++|.  |.    ||..+..     ...+. .+.++|.||+
T Consensus       689 ~~e~~~il~~l~~g~~dIV--Vg----Tp~lL~~-----~v~~~-~L~lLVIDEa  731 (1147)
T PRK10689        689 AKEQTQILAEAAEGKIDIL--IG----THKLLQS-----DVKWK-DLGLLIVDEE  731 (1147)
T ss_pred             HHHHHHHHHHHHhCCCCEE--EE----CHHHHhC-----CCCHh-hCCEEEEech
Confidence            7777655542    35552  22    3543321     11233 4889999986

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.68  E-value=8e-16  Score=139.34  Aligned_cols=123  Identities=18%  Similarity=0.250  Sum_probs=81.7

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++.+|||||||++|.+|++..              ...+||++||+||+.|+.+.++.+    +  +.+.
T Consensus        34 i~~il~g~dvlv~apTGsGKTl~y~lpal~~--------------~g~tlVisPl~sL~~dqv~~l~~~----g--i~~~   93 (607)
T PRK11057         34 IDAVLSGRDCLVVMPTGGGKSLCYQIPALVL--------------DGLTLVVSPLISLMKDQVDQLLAN----G--VAAA   93 (607)
T ss_pred             HHHHHcCCCEEEEcCCCchHHHHHHHHHHHc--------------CCCEEEEecHHHHHHHHHHHHHHc----C--CcEE
Confidence            4678999999999999999999999998842              225899999999999998877653    4  6666


Q ss_pred             eeeCCcccCcchhhhh---hc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCC--CCHH
Q psy7786          81 LAIGGVPMNQSLDVIK---KG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK--LPES  154 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~---~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~--l~~~  154 (252)
                      .+.++.+.+++...+.   .+ .++      +|.+|+++....-.. ......+.++|.||+     +.+.+.|  |.++
T Consensus        94 ~~~s~~~~~~~~~~~~~~~~g~~~i------l~~tPe~l~~~~~~~-~l~~~~l~~iVIDEa-----H~i~~~G~~fr~~  161 (607)
T PRK11057         94 CLNSTQTREQQLEVMAGCRTGQIKL------LYIAPERLMMDNFLE-HLAHWNPALLAVDEA-----HCISQWGHDFRPE  161 (607)
T ss_pred             EEcCCCCHHHHHHHHHHHhCCCCcE------EEEChHHhcChHHHH-HHhhCCCCEEEEeCc-----cccccccCcccHH
Confidence            6777655554433322   22 222      234577775421111 112235788999997     5555544  5544


Q ss_pred             H
Q psy7786         155 L  155 (252)
Q Consensus       155 l  155 (252)
                      .
T Consensus       162 y  162 (607)
T PRK11057        162 Y  162 (607)
T ss_pred             H
Confidence            3

>KOG0340|consensus

Probab=99.68  E-value=1.1e-16  Score=129.91  Aligned_cols=100  Identities=45%  Similarity=0.601  Sum_probs=93.8

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      ...|..+|+++++.+.+..++++.||++|..++|..+.|+|++.++.||+|||.+|.+|.++++.++        .++..
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsed--------P~giF   77 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSED--------PYGIF   77 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccC--------CCcce
Confidence            3679999999999999999999999999999999999999999999999999999999999988765        35788


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ++||+|||++|.|+++.+..+++.++++
T Consensus        78 alvlTPTrELA~QiaEQF~alGk~l~lK  105 (442)
T KOG0340|consen   78 ALVLTPTRELALQIAEQFIALGKLLNLK  105 (442)
T ss_pred             EEEecchHHHHHHHHHHHHHhcccccce
Confidence            9999999999999999999999988875

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.67  E-value=9.5e-16  Score=138.87  Aligned_cols=111  Identities=16%  Similarity=0.235  Sum_probs=78.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++++|||+|||++|.+|++..              +-.++|++|+++|+.|+.+.++.+    |  +.+.
T Consensus        22 i~~il~g~dvlv~~PTG~GKTl~y~lpal~~--------------~g~~lVisPl~sL~~dq~~~l~~~----g--i~~~   81 (591)
T TIGR01389        22 ISHVLDGRDVLVVMPTGGGKSLCYQVPALLL--------------KGLTVVISPLISLMKDQVDQLRAA----G--VAAA   81 (591)
T ss_pred             HHHHHcCCCEEEEcCCCccHhHHHHHHHHHc--------------CCcEEEEcCCHHHHHHHHHHHHHc----C--CcEE
Confidence            4678999999999999999999999998731              224899999999999998877753    4  6777


Q ss_pred             eeeCCcccCcchhhhhh----cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          81 LAIGGVPMNQSLDVIKK----GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~----~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .+.|+.+..++.+.+..    ..++      ++.+|+++....-..... ...+.++|.||+
T Consensus        82 ~~~s~~~~~~~~~~~~~l~~~~~~i------l~~tpe~l~~~~~~~~l~-~~~l~~iViDEa  136 (591)
T TIGR01389        82 YLNSTLSAKEQQDIEKALVNGELKL------LYVAPERLEQDYFLNMLQ-RIPIALVAVDEA  136 (591)
T ss_pred             EEeCCCCHHHHHHHHHHHhCCCCCE------EEEChhHhcChHHHHHHh-cCCCCEEEEeCC
Confidence            78888776654433322    2333      234588776432222222 235889999996

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.

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

Probab=99.67  E-value=1.5e-17  Score=126.97  Aligned_cols=137  Identities=25%  Similarity=0.339  Sum_probs=98.9

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+.+|+|+++.||||||||++|.+|+++.+....         ..++++++|+++|+.|+.+.++.+....+  +++..
T Consensus         9 ~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~---------~~~~lii~P~~~l~~q~~~~~~~~~~~~~--~~~~~   77 (169)
T PF00270_consen    9 EAIISGKNVLISAPTGSGKTLAYILPALNRLQEGK---------DARVLIIVPTRALAEQQFERLRKFFSNTN--VRVVL   77 (169)
T ss_dssp             HHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTS---------SSEEEEEESSHHHHHHHHHHHHHHTTTTT--SSEEE
T ss_pred             HHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCC---------CceEEEEeecccccccccccccccccccc--ccccc
Confidence            45668999999999999999999999999887652         23799999999999999999999887755  78888


Q ss_pred             eeCCcccC-cchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          82 AIGGVPMN-QSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        82 ~~g~~~~~-~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ++|+.+.. .....+..++++.  +    ++|+++..........+.+ +.++|.||.     +.+....+...+...+.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~il--v----~T~~~l~~~~~~~~~~~~~-~~~iViDE~-----h~l~~~~~~~~~~~i~~  145 (169)
T PF00270_consen   78 LHGGQSISEDQREVLSNQADIL--V----TTPEQLLDLISNGKINISR-LSLIVIDEA-----HHLSDETFRAMLKSILR  145 (169)
T ss_dssp             ESTTSCHHHHHHHHHHTTSSEE--E----EEHHHHHHHHHTTSSTGTT-ESEEEEETH-----HHHHHTTHHHHHHHHHH
T ss_pred             cccccccccccccccccccccc--c----cCcchhhcccccccccccc-ceeeccCcc-----cccccccHHHHHHHHHH
Confidence            89987644 3334444456652  2    3366666555543224445 889999985     55555555555544444


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       146 ~  146 (169)
T PF00270_consen  146 R  146 (169)
T ss_dssp             H
T ss_pred             H
Confidence            4

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 ....

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.66  E-value=1.4e-15  Score=138.41  Aligned_cols=105  Identities=22%  Similarity=0.296  Sum_probs=79.6

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCccc
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPM   88 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~   88 (252)
                      +.+++++||||||++|++|++..+..           +.+++|++||++||.|+++.++++...++  +++..++|+.+.
T Consensus       258 ~~Ll~g~TGSGKT~va~l~il~~~~~-----------g~qvlilaPT~~LA~Q~~~~~~~l~~~~g--i~v~lltg~~~~  324 (630)
T TIGR00643       258 NRLLQGDVGSGKTLVAALAMLAAIEA-----------GYQVALMAPTEILAEQHYNSLRNLLAPLG--IEVALLTGSLKG  324 (630)
T ss_pred             cEEEECCCCCcHHHHHHHHHHHHHHc-----------CCcEEEECCHHHHHHHHHHHHHHHhcccC--cEEEEEecCCCH
Confidence            68999999999999999999987642           56899999999999999999999988777  899999999877


Q ss_pred             Ccchhhhh---hc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          89 NQSLDVIK---KG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        89 ~~~~~~l~---~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .++...+.   ++ +++.  |    +||+++.+     ...+.+ +.++|.||.
T Consensus       325 ~~r~~~~~~i~~g~~~Ii--V----gT~~ll~~-----~~~~~~-l~lvVIDEa  366 (630)
T TIGR00643       325 KRRKELLETIASGQIHLV--V----GTHALIQE-----KVEFKR-LALVIIDEQ  366 (630)
T ss_pred             HHHHHHHHHHhCCCCCEE--E----ecHHHHhc-----cccccc-cceEEEech
Confidence            65444333   22 3431  2    23554432     123444 899999996

>KOG0338|consensus

Probab=99.66  E-value=2.1e-16  Score=133.74  Aligned_cols=101  Identities=44%  Similarity=0.576  Sum_probs=92.4

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|++|.+|..+++.+..+||..|++||..++|..+-|+|+..++.||+|||.+|++|.|.+++....     +-...++
T Consensus       181 ~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk-----~~~~TRV  255 (691)
T KOG0338|consen  181 ESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPK-----KVAATRV  255 (691)
T ss_pred             hhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcc-----cCcceeE
Confidence            48999999999999999999999999999999999999999999999999999999999998876432     2335689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      ||+||||+||-|++...++++....|
T Consensus       256 LVL~PTRELaiQv~sV~~qlaqFt~I  281 (691)
T KOG0338|consen  256 LVLVPTRELAIQVHSVTKQLAQFTDI  281 (691)
T ss_pred             EEEeccHHHHHHHHHHHHHHHhhccc
Confidence            99999999999999999999988765

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.65  E-value=6.2e-16  Score=139.71  Aligned_cols=118  Identities=11%  Similarity=0.010  Sum_probs=75.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHH---------hHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHH
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLV---------FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA   71 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a---------~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~   71 (252)
                      +|.+++|+|++++|+||||||.+         |++|.+..+..-.     .+..+.+++|+.||||||.|+...+.+...
T Consensus       173 l~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~-----~~~~~~~ilvt~PrreLa~qi~~~i~~~vg  247 (675)
T PHA02653        173 FEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID-----PNFIERPIVLSLPRVALVRLHSITLLKSLG  247 (675)
T ss_pred             HHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc-----cccCCcEEEEECcHHHHHHHHHHHHHHHhC
Confidence            35688999999999999999997         6667666553211     011356899999999999999988877654


Q ss_pred             hCC-CCcceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          72 ALP-IPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        72 ~~~-~~~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +.. .++.+...+||.+. .+.....++.++             ++.++.-....+.+ +.++|.||+
T Consensus       248 ~~~~~g~~v~v~~Gg~~~-~~~~t~~k~~~I-------------lv~T~~L~l~~L~~-v~~VVIDEa  300 (675)
T PHA02653        248 FDEIDGSPISLKYGSIPD-ELINTNPKPYGL-------------VFSTHKLTLNKLFD-YGTVIIDEV  300 (675)
T ss_pred             ccccCCceEEEEECCcch-HHhhcccCCCCE-------------EEEeCccccccccc-CCEEEcccc
Confidence            421 12667788999662 111111123333             33322211123444 899999997

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

Probab=99.65  E-value=7.4e-16  Score=132.23  Aligned_cols=207  Identities=16%  Similarity=0.126  Sum_probs=133.0

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +++|+|.++.++|+||||+.--+.-+++++...          -+.|+++|..+||||-|+.++.=-..+|  +++..-+
T Consensus       229 LLeG~nllVVSaTasGKTLIgElAGi~~~l~~g----------~KmlfLvPLVALANQKy~dF~~rYs~Lg--lkvairV  296 (830)
T COG1202         229 LLEGENLLVVSATASGKTLIGELAGIPRLLSGG----------KKMLFLVPLVALANQKYEDFKERYSKLG--LKVAIRV  296 (830)
T ss_pred             cccCCceEEEeccCCCcchHHHhhCcHHHHhCC----------CeEEEEehhHHhhcchHHHHHHHhhccc--ceEEEEe
Confidence            689999999999999999999999999888743          3599999999999999999976656666  7777777


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhh-----hhceeeccCCCCCcccccccCCCCHHHHHH
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRR-----NLRILVEGDDVPPACCSFRLMKLPESLVRA  158 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~-----~~~~~V~de~~~~~~~~~~~~~l~~~l~~~  158 (252)
                      |-...+...+...    .    .|. .-.++++.+.+.....++.     ++.++|.||-     +++.+---.+.+--.
T Consensus       297 G~srIk~~~~pv~----~----~t~-~dADIIVGTYEGiD~lLRtg~~lgdiGtVVIDEi-----HtL~deERG~RLdGL  362 (830)
T COG1202         297 GMSRIKTREEPVV----V----DTS-PDADIIVGTYEGIDYLLRTGKDLGDIGTVVIDEI-----HTLEDEERGPRLDGL  362 (830)
T ss_pred             chhhhcccCCccc----c----CCC-CCCcEEEeechhHHHHHHcCCcccccceEEeeee-----eeccchhcccchhhH
Confidence            7755544322111    1    110 0146788888888777765     4678888773     333322211211111


Q ss_pred             HHHCCCCCChHHHHhhhhhhhcC----------------------CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCC
Q psy7786         159 LEAKGIKKPTPIQVQGIPAALSG----------------------RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL  216 (252)
Q Consensus       159 l~~~~~~~p~~iQ~~~~p~~~~~----------------------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~  216 (252)
                      +.+..+..| ..|...++++..+                      ...++.+..++.|     ...+..+.+.+.....+
T Consensus       363 I~RLr~l~~-~AQ~i~LSATVgNp~elA~~l~a~lV~y~~RPVplErHlvf~~~e~eK-----~~ii~~L~k~E~~~~ss  436 (830)
T COG1202         363 IGRLRYLFP-GAQFIYLSATVGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEK-----WDIIARLVKREFSTESS  436 (830)
T ss_pred             HHHHHHhCC-CCeEEEEEeecCChHHHHHHhCCeeEeecCCCCChhHeeeeecCchHH-----HHHHHHHHHHHHhhhhc
Confidence            111111011 1222222222211                      1245556667777     45555555555555556


Q ss_pred             CCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         217 PGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       217 ~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .+...|+|||+++|..|+.+++.|..
T Consensus       437 kg~rGQtIVFT~SRrr~h~lA~~L~~  462 (830)
T COG1202         437 KGYRGQTIVFTYSRRRCHELADALTG  462 (830)
T ss_pred             cCcCCceEEEecchhhHHHHHHHhhc
Confidence            67788999999999999999999874

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.63  E-value=6.9e-16  Score=142.63  Aligned_cols=109  Identities=10%  Similarity=0.072  Sum_probs=76.7

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH-HHHHhCCCCcceee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ-YYCAALPIPLRTCL   81 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~-~l~~~~~~~~~~~~   81 (252)
                      .+.+++|++++|+||||||.+|.+|+++...           ...+++|+.|||++|.|+.+.+. .++...|  ..+..
T Consensus        16 ~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~-----------~~~~ilvlqPrR~aA~qia~rva~~l~~~~g--~~VGy   82 (812)
T PRK11664         16 ALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG-----------INGKIIMLEPRRLAARNVAQRLAEQLGEKPG--ETVGY   82 (812)
T ss_pred             HHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC-----------cCCeEEEECChHHHHHHHHHHHHHHhCcccC--ceEEE
Confidence            3567899999999999999999999986531           12479999999999999988874 4444444  56666


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .+++.+...+      ..+|.  +    .|||++..+..... .+. ++.++|.||.
T Consensus        83 ~vr~~~~~~~------~t~I~--v----~T~G~Llr~l~~d~-~L~-~v~~IIlDEa  125 (812)
T PRK11664         83 RMRAESKVGP------NTRLE--V----VTEGILTRMIQRDP-ELS-GVGLVILDEF  125 (812)
T ss_pred             EecCccccCC------CCcEE--E----EChhHHHHHHhhCC-CcC-cCcEEEEcCC
Confidence            6666443221      12231  3    34999877665422 334 4899999996

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.61  E-value=5.1e-15  Score=129.12  Aligned_cols=106  Identities=35%  Similarity=0.483  Sum_probs=93.0

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++.+++.+...|+..|+++|..++|..+.|+|++++++||+|||++|++|++..+....... .....++++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~-~~~~~~~~~   86 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPE-DRKVNQPRA   86 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhccccc-ccccCCceE
Confidence            5799999999999999999999999999999999999999999999999999999999999887543210 111345799


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ||++|||++|.|+++.++.+++..+++
T Consensus        87 lil~PtreLa~Qi~~~~~~l~~~~~~~  113 (423)
T PRK04837         87 LIMAPTRELAVQIHADAEPLAQATGLK  113 (423)
T ss_pred             EEECCcHHHHHHHHHHHHHHhccCCce
Confidence            999999999999999999999887653

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

Probab=99.61  E-value=5.4e-15  Score=131.19  Aligned_cols=101  Identities=38%  Similarity=0.584  Sum_probs=89.2

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ..|.++++++++++.+.+.+|..|++||..++|..+.|+|+++.+.||+|||.+|++|++..+.... .     .....+
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~-~-----~~~~~a  102 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSV-E-----RKYVSA  102 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhccc-c-----cCCCce
Confidence            5699999999999999999999999999999999999999999999999999999999999866421 0     111129


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhC-CCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAAL-PIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~-~i~  250 (252)
                      ||++||||||.|+++.++.++.+. ++.
T Consensus       103 Lil~PTRELA~Qi~~~~~~~~~~~~~~~  130 (513)
T COG0513         103 LILAPTRELAVQIAEELRKLGKNLGGLR  130 (513)
T ss_pred             EEECCCHHHHHHHHHHHHHHHhhcCCcc
Confidence            999999999999999999999987 443

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.59  E-value=1.6e-14  Score=123.40  Aligned_cols=52  Identities=23%  Similarity=0.080  Sum_probs=45.7

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      |+++.||||||||++|.+|++..+...         .+.+++|++|||+|+.|+++.++.+
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~---------~~~~ii~v~P~~~L~~q~~~~l~~~   52 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ---------KADRVIIALPTRATINAMYRRAKEL   52 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC---------CCCeEEEEeehHHHHHHHHHHHHHH
Confidence            689999999999999999999876432         2568999999999999999999886

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.

>KOG0348|consensus

Probab=99.59  E-value=6.3e-15  Score=125.48  Aligned_cols=103  Identities=40%  Similarity=0.594  Sum_probs=92.3

Q ss_pred             cccccCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         144 CSFRLMKLPESLVRALEA-KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~-~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      ..|..+|+.+.+...+.. +++..||.+|.+++|.++.|+|.++.+.||+|||++|++|+++.+...+....  ...|+.
T Consensus       136 ~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~--Rs~G~~  213 (708)
T KOG0348|consen  136 AAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQ--RSDGPY  213 (708)
T ss_pred             ccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCcccc--ccCCce
Confidence            578999999999888854 58999999999999999999999999999999999999999999887665433  566889


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      +||++||||+|.|+++.++++.+.+.
T Consensus       214 ALVivPTREL~~Q~y~~~qKLl~~~h  239 (708)
T KOG0348|consen  214 ALVIVPTRELALQIYETVQKLLKPFH  239 (708)
T ss_pred             EEEEechHHHHHHHHHHHHHHhcCce
Confidence            99999999999999999999987754

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.59  E-value=8.2e-15  Score=135.40  Aligned_cols=109  Identities=13%  Similarity=0.109  Sum_probs=75.4

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH-HHHHhCCCCcceee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ-YYCAALPIPLRTCL   81 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~-~l~~~~~~~~~~~~   81 (252)
                      .+.++.+++++|+||||||.+|.+|+++...           .+.+++|+.|||++|.|+.+.+. .++...|  ..+..
T Consensus        13 ~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~-----------~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g--~~VGy   79 (819)
T TIGR01970        13 ALAAHPQVVLEAPPGAGKSTAVPLALLDAPG-----------IGGKIIMLEPRRLAARSAAQRLASQLGEAVG--QTVGY   79 (819)
T ss_pred             HHHcCCcEEEECCCCCCHHHHHHHHHHHhhc-----------cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcC--cEEEE
Confidence            3567899999999999999999999997652           24589999999999999998774 4444333  44544


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .+++.+.      ..+..+|.  +    .|||++..+.... ..+. ++.++|.||.
T Consensus        80 ~vr~~~~------~s~~t~I~--v----~T~G~Llr~l~~d-~~L~-~v~~VIiDEa  122 (819)
T TIGR01970        80 RVRGENK------VSRRTRLE--V----VTEGILTRMIQDD-PELD-GVGALIFDEF  122 (819)
T ss_pred             EEccccc------cCCCCcEE--E----ECCcHHHHHHhhC-cccc-cCCEEEEecc
Confidence            4444221      12233442  3    3489888665542 2344 4899999996

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.57  E-value=5.2e-14  Score=119.85  Aligned_cols=69  Identities=19%  Similarity=0.290  Sum_probs=53.9

Q ss_pred             cccCCCc--EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC--CCcc
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP--IPLR   78 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~--~~~~   78 (252)
                      .+.++.+  ++++||||||||++|++|++..              ..++++++||++|++|+++.++.+...++  .++.
T Consensus         8 ~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~--------------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~   73 (357)
T TIGR03158         8 ALQSKDADIIFNTAPTGAGKTLAWLTPLLHG--------------ENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVN   73 (357)
T ss_pred             HHHcCCCCEEEEECCCCCCHHHHHHHHHHHc--------------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCce
Confidence            4566664  7889999999999999999841              23589999999999999999998876542  2356


Q ss_pred             eeeeeCC
Q psy7786          79 TCLAIGG   85 (252)
Q Consensus        79 ~~~~~g~   85 (252)
                      +....|.
T Consensus        74 v~~~~g~   80 (357)
T TIGR03158        74 LLHVSKA   80 (357)
T ss_pred             EEEecCC
Confidence            6666665

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.

>KOG0335|consensus

Probab=99.57  E-value=5.7e-15  Score=125.78  Aligned_cols=120  Identities=35%  Similarity=0.532  Sum_probs=106.1

Q ss_pred             eeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhc
Q psy7786         132 ILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQET  211 (252)
Q Consensus       132 ~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~  211 (252)
                      +-+.+.++|.++..|.+..+.+.+...+.+.++..|+++|...+|....|++.+++++||+|||.+|++|++..++++..
T Consensus        62 v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~  141 (482)
T KOG0335|consen   62 VKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGP  141 (482)
T ss_pred             eeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCc
Confidence            33466778888889999999999999999999999999999999999999999999999999999999999999998877


Q ss_pred             cCCCCCCC--CcEEEEEcCcHHHHHHHHHHHHHHHhhCCCCC
Q psy7786         212 KLPFLPGE--GPYGLIICPSRELARQTHDIIQYYCAALPIGS  251 (252)
Q Consensus       212 ~~~~~~~~--~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~~  251 (252)
                      ..+.....  .|+++|++|||++|.|++++.+++.-...+.+
T Consensus       142 ~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~  183 (482)
T KOG0335|consen  142 EDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKS  183 (482)
T ss_pred             ccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhccccccee
Confidence            65554444  59999999999999999999999887665543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.57  E-value=2.5e-14  Score=128.55  Aligned_cols=105  Identities=36%  Similarity=0.528  Sum_probs=91.9

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      +|.++++++++++.|.+.++..|+++|..++|..+.|+|++++++||+|||.+|++|++..+...... ......++++|
T Consensus        10 ~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~-~~~~~~~~raL   88 (572)
T PRK04537         10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPAL-ADRKPEDPRAL   88 (572)
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccc-cccccCCceEE
Confidence            58999999999999999999999999999999999999999999999999999999999988753211 01122357999


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         225 IICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |++|||+||.|+++.+++++..++++
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~~i~  114 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADLGLR  114 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCce
Confidence            99999999999999999999887754

>KOG0952|consensus

Probab=99.56  E-value=3.8e-14  Score=128.81  Aligned_cols=124  Identities=21%  Similarity=0.209  Sum_probs=86.0

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      +..+..|.+||||||||||-.|.|.+++.+.... ...-..++..+.+||+|+|+||..+.+.+.+--..+|  +++..+
T Consensus       122 aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~-~~~~i~k~~fKiVYIaPmKALa~Em~~~~~kkl~~~g--i~v~EL  198 (1230)
T KOG0952|consen  122 AYKSNENMLICAPTGSGKTVLAELCILRTIKEHE-EQGDIAKDDFKIVYIAPMKALAAEMVDKFSKKLAPLG--ISVREL  198 (1230)
T ss_pred             hhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhc-cccccccCCceEEEEechHHHHHHHHHHHhhhccccc--ceEEEe
Confidence            4567889999999999999999999999887622 2223445688999999999999988776654434444  899999


Q ss_pred             eCCcccCcchhhhhhcccccCCccccccCCccccCCChhHH--HHHhhhhceeeccCC
Q psy7786          83 IGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVH--DIIRRNLRILVEGDD  138 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~--~~l~~~~~~~V~de~  138 (252)
                      +|++...+..  . ..++|   |.   |||....-...+..  ..|.+.++.++.||-
T Consensus       199 TGD~ql~~te--i-~~tqi---iV---TTPEKwDvvTRk~~~d~~l~~~V~LviIDEV  247 (1230)
T KOG0952|consen  199 TGDTQLTKTE--I-ADTQI---IV---TTPEKWDVVTRKSVGDSALFSLVRLVIIDEV  247 (1230)
T ss_pred             cCcchhhHHH--H-HhcCE---EE---ecccceeeeeeeeccchhhhhheeeEEeeee
Confidence            9996654322  2 23444   33   34655433333322  456666899998883

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.56  E-value=2.2e-14  Score=126.11  Aligned_cols=104  Identities=38%  Similarity=0.596  Sum_probs=90.9

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      +|.++++++++.+.+.+.++..|+++|..++|..+.++|++++++||+|||.+|++|++..+......  .......++|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~--~~~~~~~~aL   79 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPH--AKGRRPVRAL   79 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccc--cccCCCceEE
Confidence            68899999999999999999999999999999999999999999999999999999999987654211  0112235899


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         225 IICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |++|||+||.|+.+.++.+.+++++.
T Consensus        80 il~PtreLa~Qi~~~~~~~~~~~~~~  105 (456)
T PRK10590         80 ILTPTRELAAQIGENVRDYSKYLNIR  105 (456)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCCE
Confidence            99999999999999999998887654

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.55  E-value=8.4e-15  Score=130.94  Aligned_cols=84  Identities=21%  Similarity=0.183  Sum_probs=72.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      +|.+++|+  +++++||+|||++|.+|++.....           +.+++|++||++||.|.++++..+.+.+|  +++.
T Consensus       112 ~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~-----------G~~v~VvTptreLA~qdae~~~~l~~~lG--lsv~  176 (656)
T PRK12898        112 GLALLSGR--LAEMQTGEGKTLTATLPAGTAALA-----------GLPVHVITVNDYLAERDAELMRPLYEALG--LTVG  176 (656)
T ss_pred             HHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc-----------CCeEEEEcCcHHHHHHHHHHHHHHHhhcC--CEEE
Confidence            46788999  999999999999999999976542           66899999999999999999999999988  8999


Q ss_pred             eeeCCcccCcchhhhhhcccc
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQY  101 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i  101 (252)
                      +++||.+.  +.+....++||
T Consensus       177 ~i~gg~~~--~~r~~~y~~dI  195 (656)
T PRK12898        177 CVVEDQSP--DERRAAYGADI  195 (656)
T ss_pred             EEeCCCCH--HHHHHHcCCCE
Confidence            99999653  34445567777

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.55  E-value=1.4e-14  Score=132.10  Aligned_cols=115  Identities=18%  Similarity=0.188  Sum_probs=86.1

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+.+|+  ++.++||+|||++|++|++...+.           |.+++|++||++||.|.++.+..+.+.+|  +++.+
T Consensus        88 ~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~-----------G~~v~VvTpt~~LA~qd~e~~~~l~~~lG--l~v~~  152 (790)
T PRK09200         88 LVLHEGN--IAEMQTGEGKTLTATMPLYLNALE-----------GKGVHLITVNDYLAKRDAEEMGQVYEFLG--LTVGL  152 (790)
T ss_pred             HHHcCCc--eeeecCCCcchHHHHHHHHHHHHc-----------CCCeEEEeCCHHHHHHHHHHHHHHHhhcC--CeEEE
Confidence            3456776  999999999999999999865553           66799999999999999999999999998  89999


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccc-----cCCC-hhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCI-----LSLP-DQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l-----~~~~-~~~~~~l~~~~~~~V~de~  138 (252)
                      .+||.+..++.+. ..++||      +|+||+++     .+.. ........+.++++|.||+
T Consensus       153 i~g~~~~~~~r~~-~y~~dI------vygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEa  208 (790)
T PRK09200        153 NFSDIDDASEKKA-IYEADI------IYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEI  208 (790)
T ss_pred             EeCCCCcHHHHHH-hcCCCE------EEECCccccchhHHhccccchhhhcccccceEEEecc
Confidence            9999874333332 345776      45668887     2222 1222233345888888875

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.54  E-value=6e-14  Score=123.70  Aligned_cols=96  Identities=38%  Similarity=0.535  Sum_probs=87.6

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++++.+.+...|+..|+++|..++|..+.|+|++++++||+|||.+|++|++..+...        ...+++
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~--------~~~~~~   75 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVK--------RFRVQA   75 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhc--------cCCceE
Confidence            579999999999999999999999999999999999999999999999999999999999876432        125689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ||++|||++|.|+++.+++++...
T Consensus        76 lil~PtreLa~Q~~~~~~~~~~~~   99 (460)
T PRK11776         76 LVLCPTRELADQVAKEIRRLARFI   99 (460)
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhC
Confidence            999999999999999999998754

>KOG0347|consensus

Probab=99.53  E-value=6.8e-15  Score=125.66  Aligned_cols=109  Identities=35%  Similarity=0.495  Sum_probs=91.8

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCC---CC
Q psy7786         142 ACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPF---LP  217 (252)
Q Consensus       142 ~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~---~~  217 (252)
                      .++.|.++.++.++++.|..+||..|++||..++|+...| .|++..+.||||||++|-+|++..+.......+.   ..
T Consensus       179 DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~  258 (731)
T KOG0347|consen  179 DVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTS  258 (731)
T ss_pred             ChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHH
Confidence            3567899999999999999999999999999999999999 8999999999999999999999955532211111   11


Q ss_pred             CCCcE--EEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         218 GEGPY--GLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       218 ~~~~~--~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ..+++  +|||+||||+|.|+...+..++++.+++
T Consensus       259 ~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~  293 (731)
T KOG0347|consen  259 AKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIR  293 (731)
T ss_pred             hccCcceeEEecChHHHHHHHHHHHHHhccccCeE
Confidence            23445  9999999999999999999999987764

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.53  E-value=1.1e-14  Score=131.06  Aligned_cols=112  Identities=16%  Similarity=0.224  Sum_probs=84.8

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+.+|+  +++++||+|||++|.+|++...+.           +.++.|++||++||.|.++++..+.+.+|  +++.++
T Consensus        67 ~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~-----------G~~V~VvTpt~~LA~qdae~~~~l~~~LG--Lsv~~i  131 (745)
T TIGR00963        67 ALHKGK--IAEMKTGEGKTLTATLPAYLNALT-----------GKGVHVVTVNDYLAQRDAEWMGQVYRFLG--LSVGLI  131 (745)
T ss_pred             hhcCCc--eeeecCCCccHHHHHHHHHHHHHh-----------CCCEEEEcCCHHHHHHHHHHHHHHhccCC--CeEEEE
Confidence            455565  999999999999999999644443           33599999999999999999999999998  899999


Q ss_pred             eCCcccCcchhhhhhcccccCCccccccCCccc-cCCChhH------HHHHhhhhceeeccCC
Q psy7786          83 IGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCI-LSLPDQV------HDIIRRNLRILVEGDD  138 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l-~~~~~~~------~~~l~~~~~~~V~de~  138 (252)
                      +||.+..++....  .+||      +|+||+++ .++....      ...++ .+.++|.||.
T Consensus       132 ~g~~~~~~r~~~y--~~dI------vyGT~~rlgfDyLrd~~~~~~~~~~~r-~l~~aIIDEa  185 (745)
T TIGR00963       132 LSGMSPEERREAY--ACDI------TYGTNNELGFDYLRDNMAHSKEEKVQR-PFHFAIIDEV  185 (745)
T ss_pred             eCCCCHHHHHHhc--CCCE------EEECCCchhhHHHhcccccchhhhhcc-ccceeEeecH
Confidence            9997765444333  3566      34668887 5554433      22334 4889998885

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.

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.52  E-value=1.3e-13  Score=120.84  Aligned_cols=102  Identities=41%  Similarity=0.607  Sum_probs=90.9

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      +|.++++.+.+++.+...|+..|+++|..++|+.+.|+|++++++||+|||.+|++|.+..+.....    .....+++|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~----~~~~~~~~l   77 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPR----RKSGPPRIL   77 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccc----cCCCCceEE
Confidence            5889999999999999999999999999999999999999999999999999999999998875321    122356899


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         225 IICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |++|||++|.|+++.++.++...+++
T Consensus        78 il~Pt~eLa~Q~~~~~~~l~~~~~~~  103 (434)
T PRK11192         78 ILTPTRELAMQVADQARELAKHTHLD  103 (434)
T ss_pred             EECCcHHHHHHHHHHHHHHHccCCcE
Confidence            99999999999999999999887653

>KOG0345|consensus

Probab=99.52  E-value=1.3e-13  Score=115.99  Aligned_cols=100  Identities=42%  Similarity=0.618  Sum_probs=87.7

Q ss_pred             ccccCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         145 SFRLMK--LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       145 ~~~~~~--l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      +|.++.  +++++.+.+...||+..|++|..++|..+.++|+.+.++||||||++|++|++..+...+.+.+.   ...-
T Consensus         5 ~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~---~~vg   81 (567)
T KOG0345|consen    5 SFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPP---GQVG   81 (567)
T ss_pred             chhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCc---ccee
Confidence            566655  56999999999999999999999999999999999999999999999999999999776644332   1235


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      +||.+||||+|.||.+.+..|.+.+
T Consensus        82 alIIsPTRELa~QI~~V~~~F~~~l  106 (567)
T KOG0345|consen   82 ALIISPTRELARQIREVAQPFLEHL  106 (567)
T ss_pred             EEEecCcHHHHHHHHHHHHHHHHhh
Confidence            8999999999999999999998874

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.51  E-value=1.2e-13  Score=125.18  Aligned_cols=96  Identities=38%  Similarity=0.615  Sum_probs=88.0

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++.+++.+.+.|+..|+++|..++|..+.++|++++++||+|||.+|.+|++..+...        ...+++
T Consensus         6 ~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~--------~~~~~~   77 (629)
T PRK11634          6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE--------LKAPQI   77 (629)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc--------cCCCeE
Confidence            579999999999999999999999999999999999999999999999999999999999876432        235789


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ||+||||++|.|+++.++++...+
T Consensus        78 LIL~PTreLa~Qv~~~l~~~~~~~  101 (629)
T PRK11634         78 LVLAPTRELAVQVAEAMTDFSKHM  101 (629)
T ss_pred             EEEeCcHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999998765

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.51  E-value=1.2e-14  Score=132.65  Aligned_cols=107  Identities=17%  Similarity=0.173  Sum_probs=83.3

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++.++||+|||++|.+|++...+.           +..++|++||++||.|.++++..+.+.+|  +++.+++||.+...
T Consensus        99 Iaem~TGeGKTL~a~Lpa~~~al~-----------G~~V~VvTpn~yLA~qd~e~m~~l~~~lG--Ltv~~i~gg~~~~~  165 (896)
T PRK13104         99 IAEMRTGEGKTLVATLPAYLNAIS-----------GRGVHIVTVNDYLAKRDSQWMKPIYEFLG--LTVGVIYPDMSHKE  165 (896)
T ss_pred             cccccCCCCchHHHHHHHHHHHhc-----------CCCEEEEcCCHHHHHHHHHHHHHHhcccC--ceEEEEeCCCCHHH
Confidence            789999999999999999977653           33599999999999999999999999998  89999999977766


Q ss_pred             chhhhhhcccccCCccccccCCccc-cCCChhH-HH----HHhhhhceeeccCC
Q psy7786          91 SLDVIKKGIQYNDPIKTSWRAPRCI-LSLPDQV-HD----IIRRNLRILVEGDD  138 (252)
Q Consensus        91 ~~~~l~~~~~i~~~i~t~~~~p~~l-~~~~~~~-~~----~l~~~~~~~V~de~  138 (252)
                      +....  .+||      +|+||+++ .++.... ..    ...+.++++|.||+
T Consensus       166 r~~~y--~~dI------vygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEa  211 (896)
T PRK13104        166 KQEAY--KADI------VYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEV  211 (896)
T ss_pred             HHHHh--CCCE------EEECChhhhHHHHhcCCccchHhhhccccceEEeccH
Confidence            54444  4666      35669987 5554433 11    12245889998885

>KOG0328|consensus

Probab=99.51  E-value=9.8e-15  Score=115.40  Aligned_cols=102  Identities=34%  Similarity=0.478  Sum_probs=91.9

Q ss_pred             CcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCC
Q psy7786         141 PACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEG  220 (252)
Q Consensus       141 ~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~  220 (252)
                      ....+|.+||+++++++.+...||+.|+.+|..++|..+.|+|+++++.+|+|||..|.+.++..+.-.        ...
T Consensus        24 ~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~--------~r~   95 (400)
T KOG0328|consen   24 KVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDIS--------VRE   95 (400)
T ss_pred             ccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccc--------cce
Confidence            345789999999999999999999999999999999999999999999999999999999888654432        234


Q ss_pred             cEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         221 PYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       221 ~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      .|+||+.||||+|.|+.+.+..++.++++.
T Consensus        96 tQ~lilsPTRELa~Qi~~vi~alg~~mnvq  125 (400)
T KOG0328|consen   96 TQALILSPTRELAVQIQKVILALGDYMNVQ  125 (400)
T ss_pred             eeEEEecChHHHHHHHHHHHHHhcccccce
Confidence            689999999999999999999999999875

>KOG0342|consensus

Probab=99.49  E-value=1.2e-13  Score=116.69  Aligned_cols=101  Identities=35%  Similarity=0.514  Sum_probs=91.6

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      ...|.+..+++...+.+.++||...|++|...+|+.+.|+|+++.+.||+|||++|++|.++.+.+....    ..++..
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~----~r~~~~  156 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFK----PRNGTG  156 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccC----CCCCee
Confidence            3567888999999999999999999999999999999999999999999999999999999988875432    235678


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ++|+||||++|.|++.+++++..+-
T Consensus       157 vlIi~PTRELA~Q~~~eak~Ll~~h  181 (543)
T KOG0342|consen  157 VLIICPTRELAMQIFAEAKELLKYH  181 (543)
T ss_pred             EEEecccHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999998876

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.49  E-value=3e-13  Score=119.69  Aligned_cols=106  Identities=31%  Similarity=0.353  Sum_probs=92.1

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      ..+|.++++++.+.+.+.+.|+..|+++|..+++..+.|+|+++.++||+|||++|++|++..+...... .......++
T Consensus        86 ~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~-~~~~~~~~~  164 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPP-KERYMGEPR  164 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcc-cccccCCce
Confidence            3579999999999999999999999999999999999999999999999999999999999988754211 001122578


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      +||++|||++|.|+++.++.+.+.+++
T Consensus       165 aLil~PtreLa~Q~~~~~~~l~~~~~~  191 (475)
T PRK01297        165 ALIIAPTRELVVQIAKDAAALTKYTGL  191 (475)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhccCCC
Confidence            999999999999999999999887764

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.47  E-value=7.8e-14  Score=126.32  Aligned_cols=113  Identities=15%  Similarity=0.153  Sum_probs=79.9

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCc
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGV   86 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~   86 (252)
                      ++..+++++||+|||++|++|++...+.           +..++|++||++||.|..+++..+.+.+|  +++.+++++.
T Consensus        83 ~~G~Iaem~TGeGKTLta~Lpa~l~aL~-----------g~~V~VVTpn~yLA~Rdae~m~~l~~~LG--Lsv~~~~~~s  149 (762)
T TIGR03714        83 HQGNIAEMKTGEGKTLTATMPLYLNALT-----------GKGAMLVTTNDYLAKRDAEEMGPVYEWLG--LTVSLGVVDD  149 (762)
T ss_pred             cCCceeEecCCcchHHHHHHHHHHHhhc-----------CCceEEeCCCHHHHHHHHHHHHHHHhhcC--CcEEEEECCC
Confidence            3346999999999999999998766543           34699999999999999999999999998  7777777763


Q ss_pred             ccC---cchhhhhhcccccCCccccccCCcccc-CCChh-----HHHHHhhhhceeeccCC
Q psy7786          87 PMN---QSLDVIKKGIQYNDPIKTSWRAPRCIL-SLPDQ-----VHDIIRRNLRILVEGDD  138 (252)
Q Consensus        87 ~~~---~~~~~l~~~~~i~~~i~t~~~~p~~l~-~~~~~-----~~~~l~~~~~~~V~de~  138 (252)
                      ...   ...+....++||      +|+||+++. +....     .+....+.+.++|.||+
T Consensus       150 ~~~~~~~~~rr~~y~~dI------vygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEa  204 (762)
T TIGR03714       150 PDEEYDANEKRKIYNSDI------VYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEV  204 (762)
T ss_pred             CccccCHHHHHHhCCCCE------EEECchhhhhhHHHHHhhcchhhcccccCcEEEEecH
Confidence            322   222333346777      345688882 32211     11222334889998885

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.

>KOG0343|consensus

Probab=99.44  E-value=2.5e-13  Score=116.35  Aligned_cols=101  Identities=37%  Similarity=0.529  Sum_probs=91.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ..|.++.++..+.+.|...+|-.++.+|..++|..+.|+|++..+.||+|||++|++|++..++...    -....|.-+
T Consensus        69 ~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~k----Ws~~DGlGa  144 (758)
T KOG0343|consen   69 KKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLK----WSPTDGLGA  144 (758)
T ss_pred             hhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcC----CCCCCCcee
Confidence            6899999999999999999999999999999999999999999999999999999999999887642    233446679


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      ||..|||++|.|+++.|++.|++-.
T Consensus       145 lIISPTRELA~QtFevL~kvgk~h~  169 (758)
T KOG0343|consen  145 LIISPTRELALQTFEVLNKVGKHHD  169 (758)
T ss_pred             EEecchHHHHHHHHHHHHHHhhccc
Confidence            9999999999999999999998754

>KOG0344|consensus

Probab=99.44  E-value=5.4e-13  Score=114.97  Aligned_cols=117  Identities=39%  Similarity=0.548  Sum_probs=104.3

Q ss_pred             HHhhhhceeeccCCCCCccccccc----CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHH
Q psy7786         125 IIRRNLRILVEGDDVPPACCSFRL----MKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVL  200 (252)
Q Consensus       125 ~l~~~~~~~V~de~~~~~~~~~~~----~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~  200 (252)
                      ..++..++-|.|.+++.++.+|.+    ..+...+++.+...+|..|+++|.+++|..+.+++++.|++||+|||++|.+
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            456667899999999999999987    5689999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         201 PILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       201 ~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      |++.++.....   -....+.+++|+.|||++|.|++.+++++.
T Consensus       193 Pil~~L~~~~~---~~~~~gl~a~Il~ptreLa~Qi~re~~k~~  233 (593)
T KOG0344|consen  193 PILQHLKDLSQ---EKHKVGLRALILSPTRELAAQIYREMRKYS  233 (593)
T ss_pred             HHHHHHHHhhc---ccCccceEEEEecchHHHHHHHHHHHHhcC
Confidence            99998876542   122446799999999999999999999887

>KOG0326|consensus

Probab=99.42  E-value=6.1e-14  Score=112.73  Aligned_cols=99  Identities=35%  Similarity=0.519  Sum_probs=91.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ..|++..+..+++..+.+.||+.|+++|...+|..+.|+|+++.+..|+|||.+|++|+++++....        ..-|+
T Consensus        85 ~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~--------~~IQ~  156 (459)
T KOG0326|consen   85 NEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKK--------NVIQA  156 (459)
T ss_pred             ccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccc--------cceeE
Confidence            4699999999999999999999999999999999999999999999999999999999998775432        35689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      +|++||||+|-|....++++++.++++
T Consensus       157 ~ilVPtrelALQtSqvc~~lskh~~i~  183 (459)
T KOG0326|consen  157 IILVPTRELALQTSQVCKELSKHLGIK  183 (459)
T ss_pred             EEEeecchhhHHHHHHHHHHhcccCeE
Confidence            999999999999999999999999875

>PTZ00424 helicase 45; Provisional

Probab=99.42  E-value=1.5e-12  Score=112.88  Aligned_cols=98  Identities=37%  Similarity=0.532  Sum_probs=88.2

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++.+.+.+.+.++..|+++|..+++..+.++|.+++++||+|||.+|+++.+..+...        ..+.++
T Consensus        28 ~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~--------~~~~~~   99 (401)
T PTZ00424         28 DSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD--------LNACQA   99 (401)
T ss_pred             CCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC--------CCCceE
Confidence            579999999999999999999999999999999999999999999999999999999998765321        235689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      ||++|||++|.|+.+.+++++..+++
T Consensus       100 lil~Pt~~L~~Q~~~~~~~~~~~~~~  125 (401)
T PTZ00424        100 LILAPTRELAQQIQKVVLALGDYLKV  125 (401)
T ss_pred             EEECCCHHHHHHHHHHHHHHhhhcCc
Confidence            99999999999999999999877654

>KOG0337|consensus

Probab=99.41  E-value=5.6e-13  Score=110.78  Aligned_cols=100  Identities=38%  Similarity=0.606  Sum_probs=93.1

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|+.||++..+.+.+.+.|+..|+++|+.++|..+.++|++..+.+|+|||.+|++|+++++....       ..+.++
T Consensus        21 g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s-------~~g~Ra   93 (529)
T KOG0337|consen   21 GGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS-------QTGLRA   93 (529)
T ss_pred             CCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc-------ccccce
Confidence            6899999999999999999999999999999999999999999999999999999999999887754       236799


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      +|..|||++|.|..+.++.++...++.
T Consensus        94 lilsptreLa~qtlkvvkdlgrgt~lr  120 (529)
T KOG0337|consen   94 LILSPTRELALQTLKVVKDLGRGTKLR  120 (529)
T ss_pred             eeccCcHHHHHHHHHHHHHhccccchh
Confidence            999999999999999999999977654

>KOG0336|consensus

Probab=99.36  E-value=1.2e-12  Score=108.59  Aligned_cols=103  Identities=37%  Similarity=0.619  Sum_probs=90.0

Q ss_pred             CCCcccccccC-CCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCC
Q psy7786         139 VPPACCSFRLM-KLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLP  217 (252)
Q Consensus       139 ~~~~~~~~~~~-~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~  217 (252)
                      +|+|..+|.+. ..-+++++.+.+.||..|++||+++||.++.|.|++..+.||+|||++|+.|-+.++..+....  ..
T Consensus       214 IPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~--~q  291 (629)
T KOG0336|consen  214 IPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRR--EQ  291 (629)
T ss_pred             CCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhh--hc
Confidence            78888899875 6788999999999999999999999999999999999999999999999999988777654322  34


Q ss_pred             CCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         218 GEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       218 ~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ..++.+|+++|||+||.|+.-+..+.
T Consensus       292 r~~p~~lvl~ptreLalqie~e~~ky  317 (629)
T KOG0336|consen  292 RNGPGVLVLTPTRELALQIEGEVKKY  317 (629)
T ss_pred             cCCCceEEEeccHHHHHHHHhHHhHh
Confidence            56789999999999999998876543

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

Probab=99.35  E-value=2.9e-12  Score=114.87  Aligned_cols=80  Identities=23%  Similarity=0.222  Sum_probs=68.0

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH-HhCCCCcceee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC-AALPIPLRTCL   81 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~-~~~~~~~~~~~   81 (252)
                      .+.+++.+++.|+||||||+||++|++..+...         .+.++||++||++|+.|+.+.+..+. +.++.++++..
T Consensus        12 al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~---------~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i~~~~   82 (636)
T TIGR03117        12 SLRQKRIGMLEASTGVGKTLAMIMAALTMLKER---------PDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGF   82 (636)
T ss_pred             HHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc---------cCceEEEECCcHHHHHHHHHHHHHHHHhhcCCCeeEEE
Confidence            356788999999999999999999999877532         14579999999999999999999998 67766789999


Q ss_pred             eeCCcccCcc
Q psy7786          82 AIGGVPMNQS   91 (252)
Q Consensus        82 ~~g~~~~~~~   91 (252)
                      +.|+.++-..
T Consensus        83 lkGr~nYlCl   92 (636)
T TIGR03117        83 FPGSQEFVSP   92 (636)
T ss_pred             EECCcccccH
Confidence            9999887433

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.

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

Probab=99.34  E-value=8.8e-12  Score=115.15  Aligned_cols=86  Identities=28%  Similarity=0.391  Sum_probs=80.2

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCc
Q psy7786         150 KLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPS  229 (252)
Q Consensus       150 ~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~t  229 (252)
                      .+++.+.+.+.+.|+..|+++|..++|..+.|+|+++.++||+|||++|.+|++..+...         .+.++||++||
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~---------~~~~aL~l~Pt   90 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD---------PRATALYLAPT   90 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC---------CCcEEEEEcCh
Confidence            488999999999999999999999999999999999999999999999999999988653         25689999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy7786         230 RELARQTHDIIQYYC  244 (252)
Q Consensus       230 r~~a~~i~~~l~~l~  244 (252)
                      |+||.|+.+.+++++
T Consensus        91 raLa~q~~~~l~~l~  105 (742)
T TIGR03817        91 KALAADQLRAVRELT  105 (742)
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999886

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=99.33  E-value=2.5e-11  Score=95.40  Aligned_cols=98  Identities=43%  Similarity=0.656  Sum_probs=87.1

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEE
Q psy7786         146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI  225 (252)
Q Consensus       146 ~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LI  225 (252)
                      |.++++++.+.+.+.+.++..|++.|..+++....++++++.++||+|||..++++++..+....      ...+++++|
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~------~~~~~~vii   74 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP------KKDGPQALI   74 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc------ccCCceEEE
Confidence            56788999999999999999999999999999999999999999999999999999998877652      124678999


Q ss_pred             EcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         226 ICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       226 f~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      ++||++++.|+...++++....++
T Consensus        75 i~p~~~L~~q~~~~~~~~~~~~~~   98 (203)
T cd00268          75 LAPTRELALQIAEVARKLGKHTNL   98 (203)
T ss_pred             EcCCHHHHHHHHHHHHHHhccCCc
Confidence            999999999999999988765443

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.

>KOG0329|consensus

Probab=99.29  E-value=4.7e-12  Score=99.11  Aligned_cols=97  Identities=33%  Similarity=0.462  Sum_probs=87.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ..|.+..+.+++++++-..||++|+.+|..++|...-|-|+++++.+|.|||..|.+..++.+-..        .+...+
T Consensus        42 sgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv--------~g~vsv  113 (387)
T KOG0329|consen   42 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPV--------DGQVSV  113 (387)
T ss_pred             cchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCC--------CCeEEE
Confidence            468999999999999999999999999999999999999999999999999999999988754322        123568


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      +++|+||++|.||.++..+++++++
T Consensus       114 lvmchtrelafqi~~ey~rfskymP  138 (387)
T KOG0329|consen  114 LVMCHTRELAFQISKEYERFSKYMP  138 (387)
T ss_pred             EEEeccHHHHHHHHHHHHHHHhhCC
Confidence            9999999999999999999999987

>KOG0332|consensus

Probab=99.28  E-value=4e-12  Score=104.28  Aligned_cols=101  Identities=29%  Similarity=0.422  Sum_probs=91.1

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCC
Q psy7786         142 ACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGE  219 (252)
Q Consensus       142 ~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~--~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~  219 (252)
                      ...+|.++++.+++++.+..++|..|+.||..++|.++..  ++++.++.+|+|||.+|.+.++.++.-.        ..
T Consensus        88 S~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~--------~~  159 (477)
T KOG0332|consen   88 SAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPD--------VV  159 (477)
T ss_pred             ccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCcc--------cc
Confidence            4578999999999999999999999999999999998865  7999999999999999999999876543        34


Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      .|+++.++|||++|.|+.+.+.+.|++.++.
T Consensus       160 ~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~it  190 (477)
T KOG0332|consen  160 VPQCICLAPTRELAPQTGEVVEEMGKFTELT  190 (477)
T ss_pred             CCCceeeCchHHHHHHHHHHHHHhcCceeee
Confidence            6899999999999999999999999987653

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

Probab=99.28  E-value=1.1e-11  Score=115.49  Aligned_cols=74  Identities=18%  Similarity=0.201  Sum_probs=63.2

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHH-HHHHHHHHHhCCCCcceeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT-HDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~-~~~~~~l~~~~~~~~~~~~~   82 (252)
                      +.+|++++++|+||||||+||++|+++..            .+.+++|++|||+|+.|+ .+.+..+++.++  +++..+
T Consensus       261 l~~~~~~~~eA~tGtGKT~ayllp~l~~~------------~~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~~--~~~~~~  326 (820)
T PRK07246        261 FHDGPASFIEAQTGIGKTYGYLLPLLAQS------------DQRQIIVSVPTKILQDQIMAEEVKAIQEVFH--IDCHSL  326 (820)
T ss_pred             HhCCCcEEEECCCCCcHHHHHHHHHHHhc------------CCCcEEEEeCcHHHHHHHHHHHHHHHHHhcC--CcEEEE
Confidence            45788999999999999999999988643            246799999999999999 688999999887  777889


Q ss_pred             eCCcccCcc
Q psy7786          83 IGGVPMNQS   91 (252)
Q Consensus        83 ~g~~~~~~~   91 (252)
                      .|+.++-..
T Consensus       327 kg~~~ylcl  335 (820)
T PRK07246        327 KGPQNYLKL  335 (820)
T ss_pred             ECCcccccH
Confidence            999887433

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.27  E-value=5.6e-12  Score=115.23  Aligned_cols=111  Identities=17%  Similarity=0.237  Sum_probs=83.5

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      .+|+  ++.++||+|||+++.+|++-..+.           +-++-|++||.+||.|.++.+..+.+.+|  +++.+++|
T Consensus        94 ~~G~--Iaem~TGeGKTLva~lpa~l~aL~-----------G~~V~IvTpn~yLA~rd~e~~~~l~~~LG--lsv~~i~~  158 (830)
T PRK12904         94 HEGK--IAEMKTGEGKTLVATLPAYLNALT-----------GKGVHVVTVNDYLAKRDAEWMGPLYEFLG--LSVGVILS  158 (830)
T ss_pred             cCCc--hhhhhcCCCcHHHHHHHHHHHHHc-----------CCCEEEEecCHHHHHHHHHHHHHHHhhcC--CeEEEEcC
Confidence            3454  889999999999999999643332           22466999999999999999999999998  89999999


Q ss_pred             CcccCcchhhhhhcccccCCccccccCCccc-cCCChhHH-----HHHhhhhceeeccCC
Q psy7786          85 GVPMNQSLDVIKKGIQYNDPIKTSWRAPRCI-LSLPDQVH-----DIIRRNLRILVEGDD  138 (252)
Q Consensus        85 ~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l-~~~~~~~~-----~~l~~~~~~~V~de~  138 (252)
                      +.+.+++.....  +||      +|+||+++ .++.....     ....+.+.++|.||+
T Consensus       159 ~~~~~er~~~y~--~dI------~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEa  210 (830)
T PRK12904        159 GMSPEERREAYA--ADI------TYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEV  210 (830)
T ss_pred             CCCHHHHHHhcC--CCe------EEECCcchhhhhhhcccccchhhhcccccceEEEech
Confidence            988877666543  666      45668888 55554332     122344788888875

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.26  E-value=1.9e-11  Score=112.05  Aligned_cols=106  Identities=17%  Similarity=0.250  Sum_probs=73.7

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCc
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGV   86 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~   86 (252)
                      ++++++.++||||||.+|+.++.+.+..           +.++||++||++|+.|+.+.+++.   ++  .++..++|+.
T Consensus       162 ~~~~Ll~~~TGSGKT~v~l~~i~~~l~~-----------g~~vLvLvPt~~L~~Q~~~~l~~~---fg--~~v~~~~s~~  225 (679)
T PRK05580        162 FSPFLLDGVTGSGKTEVYLQAIAEVLAQ-----------GKQALVLVPEIALTPQMLARFRAR---FG--APVAVLHSGL  225 (679)
T ss_pred             CCcEEEECCCCChHHHHHHHHHHHHHHc-----------CCeEEEEeCcHHHHHHHHHHHHHH---hC--CCEEEEECCC
Confidence            5789999999999999999887766532           457999999999999999888753   35  6788899998


Q ss_pred             ccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          87 PMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        87 ~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +..++.+...+-..         +.+..++.++......+.+ +.++|.||+
T Consensus       226 s~~~r~~~~~~~~~---------g~~~IVVgTrsal~~p~~~-l~liVvDEe  267 (679)
T PRK05580        226 SDGERLDEWRKAKR---------GEAKVVIGARSALFLPFKN-LGLIIVDEE  267 (679)
T ss_pred             CHHHHHHHHHHHHc---------CCCCEEEeccHHhcccccC-CCEEEEECC
Confidence            77665544332000         1123344444333333444 788887775

>KOG0327|consensus

Probab=99.25  E-value=5.1e-12  Score=104.00  Aligned_cols=99  Identities=34%  Similarity=0.518  Sum_probs=89.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ++|.+|++.+.+++.+...||+.|+.||..++.+...|.|+..++.+|+|||.+|.++.++.+--.        ....++
T Consensus        26 dsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~--------~ke~qa   97 (397)
T KOG0327|consen   26 DSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMS--------VKETQA   97 (397)
T ss_pred             hhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcc--------hHHHHH
Confidence            589999999999999999999999999999999999999999999999999999999999876322        224679


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |+++|||++|.|+.+..+.++..++++
T Consensus        98 lilaPtreLa~qi~~v~~~lg~~~~~~  124 (397)
T KOG0327|consen   98 LILAPTRELAQQIQKVVRALGDHMDVS  124 (397)
T ss_pred             HHhcchHHHHHHHHHHHHhhhccccee
Confidence            999999999999999999999888654

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.19  E-value=3.6e-11  Score=110.06  Aligned_cols=107  Identities=19%  Similarity=0.209  Sum_probs=80.6

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++.++||+|||++|.+|++.+.+.           +..+.|++|+++||.|..+++..+.+.+|  +++.++.|+.+..+
T Consensus        99 IaEm~TGEGKTL~a~lp~~l~al~-----------g~~VhIvT~ndyLA~RD~e~m~~l~~~lG--lsv~~i~~~~~~~~  165 (908)
T PRK13107         99 IAEMRTGEGKTLTATLPAYLNALT-----------GKGVHVITVNDYLARRDAENNRPLFEFLG--LTVGINVAGLGQQE  165 (908)
T ss_pred             cccccCCCCchHHHHHHHHHHHhc-----------CCCEEEEeCCHHHHHHHHHHHHHHHHhcC--CeEEEecCCCCHHH
Confidence            789999999999999999977754           33499999999999999999999999998  89998899876532


Q ss_pred             chhhhhhcccccCCccccccCCccc-cCCChhH-----HHHHhhhhceeeccCC
Q psy7786          91 SLDVIKKGIQYNDPIKTSWRAPRCI-LSLPDQV-----HDIIRRNLRILVEGDD  138 (252)
Q Consensus        91 ~~~~l~~~~~i~~~i~t~~~~p~~l-~~~~~~~-----~~~l~~~~~~~V~de~  138 (252)
                      +...  -.+||      .|+||+.+ .++....     .....+.+.+.|.||.
T Consensus       166 r~~~--Y~~dI------~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEv  211 (908)
T PRK13107        166 KKAA--YNADI------TYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEV  211 (908)
T ss_pred             HHhc--CCCCe------EEeCCCcccchhhhccCccchhhhhccccceeeecch
Confidence            2211  14676      46678887 5554332     1222345778887775

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

Probab=99.19  E-value=1.7e-10  Score=101.87  Aligned_cols=127  Identities=16%  Similarity=0.239  Sum_probs=87.7

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |..+++|+|+++.-|||.||+++|.+|.+-.             .| -+|||+|..+|..++.+.++..    |  +++.
T Consensus        26 I~~~l~g~d~lvvmPTGgGKSlCyQiPAll~-------------~G-~TLVVSPLiSLM~DQV~~l~~~----G--i~A~   85 (590)
T COG0514          26 IDALLSGKDTLVVMPTGGGKSLCYQIPALLL-------------EG-LTLVVSPLISLMKDQVDQLEAA----G--IRAA   85 (590)
T ss_pred             HHHHHcCCcEEEEccCCCCcchHhhhHHHhc-------------CC-CEEEECchHHHHHHHHHHHHHc----C--ceee
Confidence            3467899999999999999999999998732             13 3899999999999888877654    3  7777


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCC--CCHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK--LPESL  155 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~--l~~~l  155 (252)
                      .+.+.-+.+++...+.+-..-.  +..+|-.|.++..-.-..... ...+..+|.||+     +=..+.|  |.++-
T Consensus        86 ~lnS~l~~~e~~~v~~~l~~g~--~klLyisPErl~~~~f~~~L~-~~~i~l~vIDEA-----HCiSqWGhdFRP~Y  154 (590)
T COG0514          86 YLNSTLSREERQQVLNQLKSGQ--LKLLYISPERLMSPRFLELLK-RLPISLVAIDEA-----HCISQWGHDFRPDY  154 (590)
T ss_pred             hhhcccCHHHHHHHHHHHhcCc--eeEEEECchhhcChHHHHHHH-hCCCceEEechH-----HHHhhcCCccCHhH
Confidence            7777777777766655422210  222455688887653222222 445778889987     3344554  66665

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

Probab=99.17  E-value=7.4e-11  Score=111.07  Aligned_cols=75  Identities=24%  Similarity=0.270  Sum_probs=64.1

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHH-HHHHHHHHhCCCCcceee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH-DIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~-~~~~~l~~~~~~~~~~~~   81 (252)
                      .+.+|+++++.||||+|||+||++|++.... .          +.+++|.+||++|+.|+. +.+..+.+.++.++++..
T Consensus       260 ~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~----------~~~vvi~t~t~~Lq~Ql~~~~~~~l~~~~~~~~~~~~  328 (850)
T TIGR01407       260 QLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-T----------EKPVVISTNTKVLQSQLLEKDIPLLNEILNFKINAAL  328 (850)
T ss_pred             HhccCCcEEEECCCCCchhHHHHHHHHHHhc-C----------CCeEEEEeCcHHHHHHHHHHHHHHHHHHcCCCceEEE
Confidence            4568999999999999999999999987654 1          336999999999999985 578888888877789999


Q ss_pred             eeCCccc
Q psy7786          82 AIGGVPM   88 (252)
Q Consensus        82 ~~g~~~~   88 (252)
                      +.|+.++
T Consensus       329 ~kG~~~y  335 (850)
T TIGR01407       329 IKGKSNY  335 (850)
T ss_pred             EEcchhh
Confidence            9999877

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=99.17  E-value=4.9e-11  Score=106.09  Aligned_cols=108  Identities=16%  Similarity=0.122  Sum_probs=70.4

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.++++++.++++|||||||+.+.. +...+...         ...++||++||+||+.|..+.+++++....  ..+..
T Consensus       124 ~~~l~~~~~il~apTGsGKT~i~~~-l~~~~~~~---------~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~--~~~~~  191 (501)
T PHA02558        124 YEGLKNNRRLLNLPTSAGKSLIQYL-LSRYYLEN---------YEGKVLIIVPTTSLVTQMIDDFVDYRLFPR--EAMHK  191 (501)
T ss_pred             HHHHhcCceEEEeCCCCCHHHHHHH-HHHHHHhc---------CCCeEEEEECcHHHHHHHHHHHHHhccccc--cceeE
Confidence            3456788999999999999987643 22222221         134899999999999999999998765432  34445


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +.||....       .+.+|.  |.    +|+++...+..   .+. .+.++|.||+
T Consensus       192 i~~g~~~~-------~~~~I~--Va----T~qsl~~~~~~---~~~-~~~~iIvDEa  231 (501)
T PHA02558        192 IYSGTAKD-------TDAPIV--VS----TWQSAVKQPKE---WFD-QFGMVIVDEC  231 (501)
T ss_pred             EecCcccC-------CCCCEE--Ee----eHHHHhhchhh---hcc-ccCEEEEEch
Confidence            56664322       123332  33    37777654422   233 4889999996

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

Probab=99.13  E-value=3.1e-10  Score=96.88  Aligned_cols=112  Identities=15%  Similarity=0.139  Sum_probs=79.5

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCc
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGV   86 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~   86 (252)
                      .+|.+++.|||-|||...++-+..++....         + ++|+++||+-|+.|....+++....-+  -.++.++|.+
T Consensus        29 ~~NtLvvlPTGLGKT~IA~~V~~~~l~~~~---------~-kvlfLAPTKPLV~Qh~~~~~~v~~ip~--~~i~~ltGev   96 (542)
T COG1111          29 FKNTLVVLPTGLGKTFIAAMVIANRLRWFG---------G-KVLFLAPTKPLVLQHAEFCRKVTGIPE--DEIAALTGEV   96 (542)
T ss_pred             hcCeEEEecCCccHHHHHHHHHHHHHHhcC---------C-eEEEecCCchHHHHHHHHHHHHhCCCh--hheeeecCCC
Confidence            359999999999999988888887776543         4 799999999999999999988764322  4677899999


Q ss_pred             ccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          87 PMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        87 ~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +.+++.....++--+   ++|    |..+.+=......++.. +..+|-||+
T Consensus        97 ~p~~R~~~w~~~kVf---vaT----PQvveNDl~~Grid~~d-v~~lifDEA  140 (542)
T COG1111          97 RPEEREELWAKKKVF---VAT----PQVVENDLKAGRIDLDD-VSLLIFDEA  140 (542)
T ss_pred             ChHHHHHHHhhCCEE---Eec----cHHHHhHHhcCccChHH-ceEEEechh
Confidence            988777666654322   333    55544433333333443 556666665

>KOG0951|consensus

Probab=99.09  E-value=1.1e-09  Score=101.93  Aligned_cols=82  Identities=22%  Similarity=0.130  Sum_probs=62.1

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      ....++++|||||+|||...++.+++.+-.........+-...+.+|++|.++|+..+-..+.+--...|  +++.-.+|
T Consensus       323 ~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~G--I~V~ElTg  400 (1674)
T KOG0951|consen  323 RGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPLG--ITVLELTG  400 (1674)
T ss_pred             cCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhccccC--cEEEEecc
Confidence            3455899999999999999999999998765442222333466899999999999887665554444445  89999999


Q ss_pred             Cccc
Q psy7786          85 GVPM   88 (252)
Q Consensus        85 ~~~~   88 (252)
                      +...
T Consensus       401 D~~l  404 (1674)
T KOG0951|consen  401 DSQL  404 (1674)
T ss_pred             cccc
Confidence            8554

>PRK02362 ski2-like helicase; Provisional

Probab=99.09  E-value=5.3e-10  Score=103.98  Aligned_cols=90  Identities=30%  Similarity=0.454  Sum_probs=81.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~-~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .|.++++++.+.+.+...|+..++++|..+++. ...|++++++++||+|||.++.++++..+..           +.++
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~-----------~~ka   70 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR-----------GGKA   70 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc-----------CCcE
Confidence            477889999999999999999999999999988 6789999999999999999999999987642           4579


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHh
Q psy7786         224 LIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      ++++|+|++|.|.++.++++++
T Consensus        71 l~i~P~raLa~q~~~~~~~~~~   92 (737)
T PRK02362         71 LYIVPLRALASEKFEEFERFEE   92 (737)
T ss_pred             EEEeChHHHHHHHHHHHHHhhc
Confidence            9999999999999999998753

>PRK13766 Hef nuclease; Provisional

Probab=99.06  E-value=3.8e-10  Score=105.76  Aligned_cols=111  Identities=16%  Similarity=0.213  Sum_probs=73.7

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcc
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVP   87 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~   87 (252)
                      +|+++++|||+|||..+++++...+. .         .+.++||++||++|+.|..+.++++....+  .++..++|+.+
T Consensus        30 ~n~lv~~ptG~GKT~~a~~~i~~~l~-~---------~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~--~~v~~~~g~~~   97 (773)
T PRK13766         30 KNTLVVLPTGLGKTAIALLVIAERLH-K---------KGGKVLILAPTKPLVEQHAEFFRKFLNIPE--EKIVVFTGEVS   97 (773)
T ss_pred             CCeEEEcCCCccHHHHHHHHHHHHHH-h---------CCCeEEEEeCcHHHHHHHHHHHHHHhCCCC--ceEEEEeCCCC
Confidence            39999999999999999999988762 1         245799999999999999999888754322  46777888876


Q ss_pred             cCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          88 MNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        88 ~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      ..++.+ +....++.  +    ++|..+..........+. .+.++|.||+
T Consensus        98 ~~~r~~-~~~~~~ii--v----~T~~~l~~~l~~~~~~~~-~~~liVvDEa  140 (773)
T PRK13766         98 PEKRAE-LWEKAKVI--V----ATPQVIENDLIAGRISLE-DVSLLIFDEA  140 (773)
T ss_pred             HHHHHH-HHhCCCEE--E----ECHHHHHHHHHcCCCChh-hCcEEEEECC
Confidence            654333 33333431  2    235544322111111222 3778888886

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

Probab=99.04  E-value=1.6e-09  Score=99.36  Aligned_cols=80  Identities=21%  Similarity=0.328  Sum_probs=57.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC-CCcceeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP-IPLRTCLA   82 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~-~~~~~~~~   82 (252)
                      +..|+++-+.||||.||| +|.+-+--.+..          .+-+++||+||+-|+.|+++.++++++..+ ..+++. .
T Consensus        94 ~~rg~SFaiiAPTGvGKT-Tfg~~~sl~~a~----------kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~-y  161 (1187)
T COG1110          94 LVRGKSFAIIAPTGVGKT-TFGLLMSLYLAK----------KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVV-Y  161 (1187)
T ss_pred             HHcCCceEEEcCCCCchh-HHHHHHHHHHHh----------cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeee-e
Confidence            578999999999999999 444433322222          245799999999999999999999998777 334443 5


Q ss_pred             eCCcccCcchhhh
Q psy7786          83 IGGVPMNQSLDVI   95 (252)
Q Consensus        83 ~g~~~~~~~~~~l   95 (252)
                      +|..+.++....+
T Consensus       162 h~~l~~~ekee~l  174 (1187)
T COG1110         162 HSALPTKEKEEAL  174 (1187)
T ss_pred             ccccchHHHHHHH
Confidence            5654554433333

>PRK00254 ski2-like helicase; Provisional

Probab=99.04  E-value=1.4e-09  Score=101.02  Aligned_cols=90  Identities=23%  Similarity=0.371  Sum_probs=81.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~-~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      +|.++++++.+.+.+.+.|+..|+++|..+++. ...|+|++++++||+|||.++.++++..+...          +.++
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~----------~~~~   71 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE----------GGKA   71 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc----------CCeE
Confidence            467888999999999999999999999999986 78999999999999999999999999876542          4589


Q ss_pred             EEEcCcHHHHHHHHHHHHHHH
Q psy7786         224 LIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      |+++|+|++|.|.++.++++.
T Consensus        72 l~l~P~~aLa~q~~~~~~~~~   92 (720)
T PRK00254         72 VYLVPLKALAEEKYREFKDWE   92 (720)
T ss_pred             EEEeChHHHHHHHHHHHHHHh
Confidence            999999999999999998764

>KOG0352|consensus

Probab=99.02  E-value=1.1e-09  Score=91.88  Aligned_cols=115  Identities=19%  Similarity=0.225  Sum_probs=70.5

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +...+|+.++-|||+||+++|.||.+-.             .+ ..++++|..+|..++.+.+.+|      ++++..+.
T Consensus        33 VK~k~DVyVsMPTGaGKSLCyQLPaL~~-------------~g-ITIV~SPLiALIkDQiDHL~~L------KVp~~SLN   92 (641)
T KOG0352|consen   33 VKRKCDVYVSMPTGAGKSLCYQLPALVH-------------GG-ITIVISPLIALIKDQIDHLKRL------KVPCESLN   92 (641)
T ss_pred             HhccCcEEEeccCCCchhhhhhchHHHh-------------CC-eEEEehHHHHHHHHHHHHHHhc------CCchhHhc
Confidence            4567899999999999999999998732             13 5899999999999888877765      25555556


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChh-HHH--HHhhhhceeeccCC
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQ-VHD--IIRRNLRILVEGDD  138 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~-~~~--~l~~~~~~~V~de~  138 (252)
                      ...+..++.+.+.+--...+.+...|.+|..--.-.-+ ...  .-++.+.++|.||+
T Consensus        93 SKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEA  150 (641)
T KOG0352|consen   93 SKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEA  150 (641)
T ss_pred             chhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechh
Confidence            66555555444433111111122233334332211111 111  11345688888886

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.01  E-value=3.3e-09  Score=77.52  Aligned_cols=106  Identities=28%  Similarity=0.461  Sum_probs=71.8

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcc
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVP   87 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~   87 (252)
                      +++++.++||||||..+...+.......         ...+++|++|+++++.|..+.+...... +  +.+..+.++..
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~---------~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~--~~~~~~~~~~~   68 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL---------KGGQVLVLAPTRELANQVAERLKELFGE-G--IKVGYLIGGTS   68 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc---------cCCCEEEEcCcHHHHHHHHHHHHHHhhC-C--cEEEEEecCcc
Confidence            4789999999999999988888766542         2457999999999999999988887664 3  56666666644


Q ss_pred             cCcchhhhhhcccccCCccccccCCccccCCChhHHHHHh------hhhceeeccCC
Q psy7786          88 MNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIR------RNLRILVEGDD  138 (252)
Q Consensus        88 ~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~------~~~~~~V~de~  138 (252)
                      ...+.......             ...++.+++.......      ....++|.||.
T Consensus        69 ~~~~~~~~~~~-------------~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~  112 (144)
T cd00046          69 IKQQEKLLSGK-------------TDIVVGTPGRLLDELERLKLSLKKLDLLILDEA  112 (144)
T ss_pred             hhHHHHHhcCC-------------CCEEEECcHHHHHHHHcCCcchhcCCEEEEeCH
Confidence            44333222222             3334444444333332      24778888985

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

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

Probab=99.01  E-value=3.7e-09  Score=96.91  Aligned_cols=97  Identities=29%  Similarity=0.302  Sum_probs=86.5

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCc
Q psy7786         150 KLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPS  229 (252)
Q Consensus       150 ~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~t  229 (252)
                      .+++.+.+.+.+. +..|++.|.+++|....|+++++++|||+|||.+.++|.+..+.+..   ......+-.+|..+|-
T Consensus         7 ~l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~---~~~~~~~i~~lYIsPL   82 (814)
T COG1201           7 ILDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG---KGKLEDGIYALYISPL   82 (814)
T ss_pred             hcCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhcc---CCCCCCceEEEEeCcH
Confidence            3788899999888 99999999999999999999999999999999999999999988763   1122446789999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCC
Q psy7786         230 RELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       230 r~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |.|...+.+.|+..++.+|++
T Consensus        83 kALn~Di~~rL~~~~~~~G~~  103 (814)
T COG1201          83 KALNNDIRRRLEEPLRELGIE  103 (814)
T ss_pred             HHHHHHHHHHHHHHHHHcCCc
Confidence            999999999999999999874

>KOG0350|consensus

Probab=99.00  E-value=6.5e-10  Score=94.63  Aligned_cols=92  Identities=32%  Similarity=0.415  Sum_probs=76.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhh---------cCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCc
Q psy7786         151 LPESLVRALEAKGIKKPTPIQVQGIPAAL---------SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP  221 (252)
Q Consensus       151 l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~---------~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~  221 (252)
                      |++.+...+.++++..-+++|...+|..+         .++|+.+.++||+|||++|.+|+++.+....       -...
T Consensus       144 lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~-------v~~L  216 (620)
T KOG0350|consen  144 LEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRP-------VKRL  216 (620)
T ss_pred             HHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCC-------ccce
Confidence            44455666889999999999988887764         3579999999999999999999998765432       1247


Q ss_pred             EEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         222 YGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       222 ~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      |++|++|||+++.|+++.+.++++..|+
T Consensus       217 RavVivPtr~L~~QV~~~f~~~~~~tgL  244 (620)
T KOG0350|consen  217 RAVVIVPTRELALQVYDTFKRLNSGTGL  244 (620)
T ss_pred             EEEEEeeHHHHHHHHHHHHHHhccCCce
Confidence            8999999999999999999999988775

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.99  E-value=6.5e-10  Score=86.24  Aligned_cols=117  Identities=27%  Similarity=0.357  Sum_probs=73.6

Q ss_pred             ccCC-CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           4 YRNS-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         4 ~~~g-~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      +.++ +++++.++||||||.++..+++..+....         ..++++++||++++.|..+.+..+.....  ......
T Consensus        20 ~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~---------~~~~l~~~p~~~~~~~~~~~~~~~~~~~~--~~~~~~   88 (201)
T smart00487       20 LLSGLRDVILAAPTGSGKTLAALLPALEALKRGK---------GKRVLVLVPTRELAEQWAEELKKLGPSLG--LKVVGL   88 (201)
T ss_pred             HHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC---------CCcEEEEeCCHHHHHHHHHHHHHHhccCC--eEEEEE
Confidence            4556 89999999999999999999998775532         34699999999999999988888765433  233344


Q ss_pred             eCCcccCcchhhhhhcc-cccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          83 IGGVPMNQSLDVIKKGI-QYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~-~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .++.........+..+. ++.  +    .+++.+.+.......... ...++|.||.
T Consensus        89 ~~~~~~~~~~~~~~~~~~~v~--~----~t~~~l~~~~~~~~~~~~-~~~~iIiDE~  138 (201)
T smart00487       89 YGGDSKREQLRKLESGKTDIL--V----TTPGRLLDLLENDLLELS-NVDLVILDEA  138 (201)
T ss_pred             eCCcchHHHHHHHhcCCCCEE--E----eChHHHHHHHHcCCcCHh-HCCEEEEECH
Confidence            55544333344444432 331  1    224433333222221222 3668888885

>PRK13767 ATP-dependent helicase; Provisional

Probab=98.96  E-value=5.1e-09  Score=98.79  Aligned_cols=88  Identities=25%  Similarity=0.274  Sum_probs=73.3

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcH
Q psy7786         151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSR  230 (252)
Q Consensus       151 l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr  230 (252)
                      +++.+.+.+.. ++..|+++|..++|..+.|+|++++++||+|||.++++|++..+.......  ....+.++|+++|||
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~--~~~~~~~~LyIsPtr   94 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREG--ELEDKVYCLYVSPLR   94 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhcccc--CCCCCeEEEEEcCHH
Confidence            67777777665 688999999999999999999999999999999999999999887532110  113467899999999


Q ss_pred             HHHHHHHHHHH
Q psy7786         231 ELARQTHDIIQ  241 (252)
Q Consensus       231 ~~a~~i~~~l~  241 (252)
                      ++|.|+++.+.
T Consensus        95 aLa~di~~~L~  105 (876)
T PRK13767         95 ALNNDIHRNLE  105 (876)
T ss_pred             HHHHHHHHHHH
Confidence            99999988765

>TIGR00595 priA primosomal protein N'

Probab=98.94  E-value=1.9e-09  Score=95.74  Aligned_cols=102  Identities=19%  Similarity=0.269  Sum_probs=64.8

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++.++||||||+.|+..+- ..+..          +-++||++|+++|+.|+++.+++.   .+  .++..++|+.+..+
T Consensus         1 LL~g~TGsGKT~v~l~~i~-~~l~~----------g~~vLvlvP~i~L~~Q~~~~l~~~---f~--~~v~vlhs~~~~~e   64 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIE-KVLAL----------GKSVLVLVPEIALTPQMIQRFKYR---FG--SQVAVLHSGLSDSE   64 (505)
T ss_pred             CccCCCCCCHHHHHHHHHH-HHHHc----------CCeEEEEeCcHHHHHHHHHHHHHH---hC--CcEEEEECCCCHHH
Confidence            4679999999999965543 33332          457999999999999999888753   34  56778888877665


Q ss_pred             chhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          91 SLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        91 ~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +.+...+-..         +....++.+.......+.+ +.++|.||.
T Consensus        65 r~~~~~~~~~---------g~~~IVVGTrsalf~p~~~-l~lIIVDEe  102 (505)
T TIGR00595        65 KLQAWRKVKN---------GEILVVIGTRSALFLPFKN-LGLIIVDEE  102 (505)
T ss_pred             HHHHHHHHHc---------CCCCEEECChHHHcCcccC-CCEEEEECC
Confidence            5444332100         0122233333333333444 788887774

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).

>KOG4284|consensus

Probab=98.93  E-value=4.3e-10  Score=98.50  Aligned_cols=97  Identities=28%  Similarity=0.368  Sum_probs=86.4

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      ...|.++.+...++..|.+.+|..|+++|..++|..+.+-|+++++.+|+|||+.|.+..+..+...        ...++
T Consensus        24 ~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~--------~~~~q   95 (980)
T KOG4284|consen   24 TPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSR--------SSHIQ   95 (980)
T ss_pred             CCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcc--------cCcce
Confidence            3578899999999999999999999999999999999999999999999999999888777654332        34678


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      .+|++|||++|.||.+.++++|..+
T Consensus        96 ~~Iv~PTREiaVQI~~tv~~v~~sf  120 (980)
T KOG4284|consen   96 KVIVTPTREIAVQIKETVRKVAPSF  120 (980)
T ss_pred             eEEEecchhhhhHHHHHHHHhcccc
Confidence            9999999999999999999998754

>PRK09694 helicase Cas3; Provisional

Probab=98.93  E-value=1.1e-07  Score=89.05  Aligned_cols=74  Identities=20%  Similarity=0.073  Sum_probs=53.7

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCC
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGG   85 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~   85 (252)
                      ++.-+++.||||+|||.|.+.... ++....        ..-+++|..||+++++|++++++.+.+..-....+...+|+
T Consensus       300 ~pgl~ileApTGsGKTEAAL~~A~-~l~~~~--------~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~v~L~Hg~  370 (878)
T PRK09694        300 QPGLTIIEAPTGSGKTEAALAYAW-RLIDQG--------LADSIIFALPTQATANAMLSRLEALASKLFPSPNLILAHGN  370 (878)
T ss_pred             CCCeEEEEeCCCCCHHHHHHHHHH-HHHHhC--------CCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCceEeecCc
Confidence            355689999999999999766554 443322        23578999999999999999998766543212466777777


Q ss_pred             ccc
Q psy7786          86 VPM   88 (252)
Q Consensus        86 ~~~   88 (252)
                      ...
T Consensus       371 a~l  373 (878)
T PRK09694        371 SRF  373 (878)
T ss_pred             chh
Confidence            654

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.92  E-value=3.4e-09  Score=101.35  Aligned_cols=114  Identities=18%  Similarity=0.221  Sum_probs=66.6

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEE--cC----cHHHHHHHHHHHHH-HHHhCCC
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLII--CP----SRELARQTHDIIQY-YCAALPI   75 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil--~p----treLa~q~~~~~~~-l~~~~~~   75 (252)
                      .+.++..++++|+||||||.  .+|.+..  ....        +..+.|+  -|    +++||.|+.+++.. +++..|.
T Consensus        85 ai~~~~VviI~GeTGSGKTT--qlPq~ll--e~g~--------g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY  152 (1294)
T PRK11131         85 AIRDHQVVIVAGETGSGKTT--QLPKICL--ELGR--------GVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGY  152 (1294)
T ss_pred             HHHhCCeEEEECCCCCCHHH--HHHHHHH--HcCC--------CCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceece
Confidence            34566778888999999998  5884422  2211        2122232  24    67999999887764 4444442


Q ss_pred             CcceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccc-ccccCCCCH
Q psy7786          76 PLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACC-SFRLMKLPE  153 (252)
Q Consensus        76 ~~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~-~~~~~~l~~  153 (252)
                      .+         ..+++.   .++.+|      .+.|||+++....... .+. .+.++|.||+     + ++.+++|.-
T Consensus       153 ~v---------rf~~~~---s~~t~I------~v~TpG~LL~~l~~d~-~Ls-~~~~IIIDEA-----HERsLn~DfLL  206 (1294)
T PRK11131        153 KV---------RFNDQV---SDNTMV------KLMTDGILLAEIQQDR-LLM-QYDTIIIDEA-----HERSLNIDFIL  206 (1294)
T ss_pred             ee---------cCcccc---CCCCCE------EEEChHHHHHHHhcCC-ccc-cCcEEEecCc-----cccccccchHH
Confidence            11         222222   233444      2345999988766432 244 4899999997     4 345555543

>PRK01172 ski2-like helicase; Provisional

Probab=98.90  E-value=9.8e-09  Score=94.81  Aligned_cols=88  Identities=19%  Similarity=0.204  Sum_probs=78.6

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      .|.++++++.+.+.+...++. ++++|..+++....+++++++++||+|||..+.++++..+..           +.+++
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~-----------~~k~v   69 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA-----------GLKSI   69 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh-----------CCcEE
Confidence            467889999999999999887 999999999999999999999999999999998888876542           35799


Q ss_pred             EEcCcHHHHHHHHHHHHHHH
Q psy7786         225 IICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~  244 (252)
                      +++|+|++|.|.++.++++.
T Consensus        70 ~i~P~raLa~q~~~~~~~l~   89 (674)
T PRK01172         70 YIVPLRSLAMEKYEELSRLR   89 (674)
T ss_pred             EEechHHHHHHHHHHHHHHh
Confidence            99999999999999998764

>TIGR01054 rgy reverse gyrase

Probab=98.89  E-value=1.1e-08  Score=98.55  Aligned_cols=88  Identities=26%  Similarity=0.267  Sum_probs=71.9

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHH
Q psy7786         152 PESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE  231 (252)
Q Consensus       152 ~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~  231 (252)
                      -.++.+.+.+.....|+++|..++|..+.|++++++++||+|||. |.++++..+..          .+++++|++|||+
T Consensus        64 ~~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~----------~g~~vLIL~PTre  132 (1171)
T TIGR01054        64 LKEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK----------KGKRCYIILPTTL  132 (1171)
T ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh----------cCCeEEEEeCHHH
Confidence            344555566655568999999999999999999999999999997 66666654432          2678999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCC
Q psy7786         232 LARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       232 ~a~~i~~~l~~l~~~~~i~  250 (252)
                      +|.|+++.++.+++.+++.
T Consensus       133 La~Qi~~~l~~l~~~~~i~  151 (1171)
T TIGR01054       133 LVIQVAEKISSLAEKAGVG  151 (1171)
T ss_pred             HHHHHHHHHHHHHHhcCCc
Confidence            9999999999999887653

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.

>KOG0354|consensus

Probab=98.87  E-value=2.5e-09  Score=96.17  Aligned_cols=116  Identities=15%  Similarity=0.093  Sum_probs=77.7

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      ++| |+|+++++|||+|||.....-+.+++-..+         ..++++++|||-|..|+...++.++..    -+....
T Consensus        73 ~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p---------~~KiVF~aP~~pLv~QQ~a~~~~~~~~----~~~T~~  138 (746)
T KOG0354|consen   73 PAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRP---------KGKVVFLAPTRPLVNQQIACFSIYLIP----YSVTGQ  138 (746)
T ss_pred             Hhh-cCCeEEEeecCCCccchHHHHHHHHHhcCC---------cceEEEeeCCchHHHHHHHHHhhccCc----ccceee
Confidence            456 999999999999999998888888875544         358999999999999998777766543    344445


Q ss_pred             eCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          83 IGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .||.........+-...++.  +.|    |..+.+-.......-.+.+..+|.||+
T Consensus       139 l~~~~~~~~r~~i~~s~~vf--f~T----pQil~ndL~~~~~~~ls~fs~iv~DE~  188 (746)
T KOG0354|consen  139 LGDTVPRSNRGEIVASKRVF--FRT----PQILENDLKSGLHDELSDFSLIVFDEC  188 (746)
T ss_pred             ccCccCCCchhhhhcccceE--EeC----hHhhhhhcccccccccceEEEEEEccc
Confidence            56644444444444444441  333    666655544432222234778888886

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.86  E-value=1.5e-08  Score=93.51  Aligned_cols=93  Identities=22%  Similarity=0.249  Sum_probs=79.7

Q ss_pred             ccCCCCHHHHHHHH-----HCCCCCC---hHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCC
Q psy7786         147 RLMKLPESLVRALE-----AKGIKKP---TPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPG  218 (252)
Q Consensus       147 ~~~~l~~~l~~~l~-----~~~~~~p---~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~  218 (252)
                      ..+++..++.+.+.     ..|+..|   +++|.+.+|..+.++++++.++||+|||++|++|++..++..         
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g---------  135 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG---------  135 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc---------
Confidence            45566777766665     5688888   999999999999999999999999999999999999876532         


Q ss_pred             CCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         219 EGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       219 ~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                        ..++|++|||+||.|+++++..++++++++
T Consensus       136 --~~v~IVTpTrELA~Qdae~m~~L~k~lGLs  165 (970)
T PRK12899        136 --KPVHLVTVNDYLAQRDCEWVGSVLRWLGLT  165 (970)
T ss_pred             --CCeEEEeCCHHHHHHHHHHHHHHHhhcCCe
Confidence              238999999999999999999999998864

>KOG0351|consensus

Probab=98.85  E-value=5.8e-09  Score=97.36  Aligned_cols=204  Identities=17%  Similarity=0.261  Sum_probs=114.9

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      ..+.|+|.++..|||.||.++|.||.+-   .           +.-.|+|+|..+|..++...+.    ..+  |....+
T Consensus       275 ~~l~Gkd~fvlmpTG~GKSLCYQlPA~l---~-----------~gitvVISPL~SLm~DQv~~L~----~~~--I~a~~L  334 (941)
T KOG0351|consen  275 ATLSGKDCFVLMPTGGGKSLCYQLPALL---L-----------GGVTVVISPLISLMQDQVTHLS----KKG--IPACFL  334 (941)
T ss_pred             HHHcCCceEEEeecCCceeeEeeccccc---c-----------CCceEEeccHHHHHHHHHHhhh----hcC--cceeec
Confidence            4689999999999999999999999872   1           2258999999999887755442    223  777788


Q ss_pred             eCCcccCcchhh---hhhcccccCCccccccCCccccCCChhHHHHH-hh---hhceeeccCC--CCCcccccc------
Q psy7786          83 IGGVPMNQSLDV---IKKGIQYNDPIKTSWRAPRCILSLPDQVHDII-RR---NLRILVEGDD--VPPACCSFR------  147 (252)
Q Consensus        83 ~g~~~~~~~~~~---l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l-~~---~~~~~V~de~--~~~~~~~~~------  147 (252)
                      .++....++...   +.++..+   +...|.+|..+..--.-..... ..   .+..+|.||+  +..-.+.|.      
T Consensus       335 ~s~q~~~~~~~i~q~l~~~~~~---ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l  411 (941)
T KOG0351|consen  335 SSIQTAAERLAILQKLANGNPI---IKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPSYKRL  411 (941)
T ss_pred             cccccHHHHHHHHHHHhCCCCe---EEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccHHHHHH
Confidence            888776644433   3444323   3445666877766544332221 22   2567788886  000000010      


Q ss_pred             -----------cCCCCHH-----HHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhc
Q psy7786         148 -----------LMKLPES-----LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQET  211 (252)
Q Consensus       148 -----------~~~l~~~-----l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~  211 (252)
                                 -+++.++     -.+++...++.+|...     ...+...++.+.-....++...+.+-.  .+...  
T Consensus       412 ~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~-----~~sfnR~NL~yeV~~k~~~~~~~~~~~--~~~~~--  482 (941)
T KOG0351|consen  412 GLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELF-----KSSFNRPNLKYEVSPKTDKDALLDILE--ESKLR--  482 (941)
T ss_pred             HHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCccee-----cccCCCCCceEEEEeccCccchHHHHH--Hhhhc--
Confidence                       0111111     1334444455444411     111222233222222222333322211  11111  


Q ss_pred             cCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         212 KLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       212 ~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                            ..+...||.|.+|..|+++...|++++
T Consensus       483 ------~~~~s~IIYC~sr~~ce~vs~~L~~~~  509 (941)
T KOG0351|consen  483 ------HPDQSGIIYCLSRKECEQVSAVLRSLG  509 (941)
T ss_pred             ------CCCCCeEEEeCCcchHHHHHHHHHHhc
Confidence                  223458999999999999999999877

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

Probab=98.84  E-value=8.4e-09  Score=97.92  Aligned_cols=76  Identities=25%  Similarity=0.308  Sum_probs=62.5

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHH-HHHHHHHHhCCCCcceeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH-DIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~-~~~~~l~~~~~~~~~~~~~   82 (252)
                      +-+++++++.|+||+|||+||++|.+.....+          +-+++|.++|+.|..|+. +.+..+.+.++.+++++.+
T Consensus       273 l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~----------~~~vvIsT~T~~LQ~Ql~~kDiP~L~~~~~~~~~~~~l  342 (928)
T PRK08074        273 LRDSEHALIEAGTGTGKSLAYLLPAAYFAKKK----------EEPVVISTYTIQLQQQLLEKDIPLLQKIFPFPVEAALL  342 (928)
T ss_pred             HhcCCCEEEECCCCCchhHHHHHHHHHHhhcc----------CCeEEEEcCCHHHHHHHHHhhHHHHHHHcCCCceEEEE
Confidence            45788999999999999999999998654322          446999999999999974 5677777888877899989


Q ss_pred             eCCcccC
Q psy7786          83 IGGVPMN   89 (252)
Q Consensus        83 ~g~~~~~   89 (252)
                      .|..++-
T Consensus       343 KGr~nYl  349 (928)
T PRK08074        343 KGRSHYL  349 (928)
T ss_pred             Ecccccc
Confidence            9887763

>PRK09401 reverse gyrase; Reviewed

Probab=98.82  E-value=2.7e-08  Score=95.88  Aligned_cols=84  Identities=29%  Similarity=0.379  Sum_probs=67.6

Q ss_pred             HHHHHHHC-CCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHH
Q psy7786         155 LVRALEAK-GIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA  233 (252)
Q Consensus       155 l~~~l~~~-~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a  233 (252)
                      +.+.+.+. |+ .|+++|..++|..+.|+|++++++||+|||. +.++++..+..          .+.+++|++|||+||
T Consensus        69 ~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~----------~g~~alIL~PTreLa  136 (1176)
T PRK09401         69 FEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK----------KGKKSYIIFPTRLLV  136 (1176)
T ss_pred             HHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh----------cCCeEEEEeccHHHH
Confidence            34445444 44 8999999999999999999999999999996 44555443321          267899999999999


Q ss_pred             HHHHHHHHHHHhhCCCC
Q psy7786         234 RQTHDIIQYYCAALPIG  250 (252)
Q Consensus       234 ~~i~~~l~~l~~~~~i~  250 (252)
                      .|+++.+++++...++.
T Consensus       137 ~Qi~~~l~~l~~~~~~~  153 (1176)
T PRK09401        137 EQVVEKLEKFGEKVGCG  153 (1176)
T ss_pred             HHHHHHHHHHhhhcCce
Confidence            99999999999877653

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

Probab=98.80  E-value=2.9e-08  Score=75.42  Aligned_cols=72  Identities=38%  Similarity=0.547  Sum_probs=62.9

Q ss_pred             hHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         168 TPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       168 ~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      |+.|..+++....++++++.+++|+|||.++..+++..+.+..         ..++++++|++++++++.+.++++....
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~---------~~~~lii~P~~~l~~q~~~~~~~~~~~~   71 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGK---------DARVLIIVPTRALAEQQFERLRKFFSNT   71 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTS---------SSEEEEEESSHHHHHHHHHHHHHHTTTT
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCC---------CceEEEEeeccccccccccccccccccc
Confidence            5789999999999999999999999999999999998776641         3479999999999999999999888764


Q ss_pred             C
Q psy7786         248 P  248 (252)
Q Consensus       248 ~  248 (252)
                      +
T Consensus        72 ~   72 (169)
T PF00270_consen   72 N   72 (169)
T ss_dssp             T
T ss_pred             c
Confidence            3

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 ....

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.77  E-value=2.5e-08  Score=91.99  Aligned_cols=75  Identities=20%  Similarity=0.124  Sum_probs=62.7

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHH-HHHHHHHHHhCCCCcceeeeeCC
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT-HDIIQYYCAALPIPLRTCLAIGG   85 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~-~~~~~~l~~~~~~~~~~~~~~g~   85 (252)
                      ++.+++.|+||+|||+||++|.+-.....          +-+++|-+.|+.|-.|+ .+.+-.+.+.++.+++++++-|.
T Consensus        49 ~~~lviEAgTGtGKTlaYLlPai~~A~~~----------~k~vVIST~T~~LQeQL~~kDlP~l~~~l~~~~~~~llKGr  118 (697)
T PRK11747         49 GRILVIEAGTGVGKTLSYLLAGIPIARAE----------KKKLVISTATVALQEQLVSKDLPLLLKISGLDFKFTLAKGR  118 (697)
T ss_pred             cceEEEECCCCcchhHHHHHHHHHHHHHc----------CCeEEEEcCCHHHHHHHHhhhhhHHHHHcCCCceEEEEcCc
Confidence            57899999999999999999998655433          34699999999999997 57788888888888999988888


Q ss_pred             cccCcc
Q psy7786          86 VPMNQS   91 (252)
Q Consensus        86 ~~~~~~   91 (252)
                      .++-..
T Consensus       119 ~nYlCl  124 (697)
T PRK11747        119 GRYVCP  124 (697)
T ss_pred             cccccH
Confidence            777544

>PRK14701 reverse gyrase; Provisional

Probab=98.76  E-value=5.1e-08  Score=96.25  Aligned_cols=84  Identities=26%  Similarity=0.305  Sum_probs=68.8

Q ss_pred             HHHHHHHHH-CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHH
Q psy7786         153 ESLVRALEA-KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE  231 (252)
Q Consensus       153 ~~l~~~l~~-~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~  231 (252)
                      .++.+.+.+ .|+ .|+++|..++|..+.|+|++++++||+|||..++++.+...           ..+.+++|++|||+
T Consensus        66 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~-----------~~g~~aLVl~PTre  133 (1638)
T PRK14701         66 EEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLA-----------LKGKKCYIILPTTL  133 (1638)
T ss_pred             HHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHH-----------hcCCeEEEEECHHH
Confidence            334556665 688 69999999999999999999999999999996555544321           12568999999999


Q ss_pred             HHHHHHHHHHHHHhhCC
Q psy7786         232 LARQTHDIIQYYCAALP  248 (252)
Q Consensus       232 ~a~~i~~~l~~l~~~~~  248 (252)
                      |+.|+.+.++.+++.++
T Consensus       134 La~Qi~~~l~~l~~~~~  150 (1638)
T PRK14701        134 LVKQTVEKIESFCEKAN  150 (1638)
T ss_pred             HHHHHHHHHHHHHhhcC
Confidence            99999999999998764

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=98.76  E-value=2.4e-08  Score=88.42  Aligned_cols=69  Identities=30%  Similarity=0.399  Sum_probs=61.7

Q ss_pred             HCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         161 AKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ..|+..|+++|..++++.+.|+|+++.++||+|||++|++|.+..              +..+||++|||+|+.+..+.+
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~--------------~~~~lVi~P~~~L~~dq~~~l   71 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS--------------DGITLVISPLISLMEDQVLQL   71 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc--------------CCcEEEEecHHHHHHHHHHHH
Confidence            458899999999999999999999999999999999999998741              346999999999999998888


Q ss_pred             HHH
Q psy7786         241 QYY  243 (252)
Q Consensus       241 ~~l  243 (252)
                      +.+
T Consensus        72 ~~~   74 (470)
T TIGR00614        72 KAS   74 (470)
T ss_pred             HHc
Confidence            754

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

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.73  E-value=6.8e-08  Score=87.13  Aligned_cols=75  Identities=29%  Similarity=0.284  Sum_probs=67.4

Q ss_pred             CCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         163 GIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       163 ~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .-..|+++|..++|.++.|+  +..+.||+|||+++.+|++....           .+.+++|++||++||.|.++++..
T Consensus       100 lg~~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al-----------~G~~v~VvTptreLA~qdae~~~~  166 (656)
T PRK12898        100 LGQRHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL-----------AGLPVHVITVNDYLAERDAELMRP  166 (656)
T ss_pred             hCCCCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh-----------cCCeEEEEcCcHHHHHHHHHHHHH
Confidence            34479999999999999999  89999999999999999997543           267899999999999999999999


Q ss_pred             HHhhCCCC
Q psy7786         243 YCAALPIG  250 (252)
Q Consensus       243 l~~~~~i~  250 (252)
                      +.+.+|++
T Consensus       167 l~~~lGls  174 (656)
T PRK12898        167 LYEALGLT  174 (656)
T ss_pred             HHhhcCCE
Confidence            99998875

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

Probab=98.69  E-value=9.9e-08  Score=89.32  Aligned_cols=86  Identities=33%  Similarity=0.464  Sum_probs=78.6

Q ss_pred             HHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHH
Q psy7786         154 SLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA  233 (252)
Q Consensus       154 ~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a  233 (252)
                      .+...+...+...+...|..++.....|+++++.+.||||||.+|++|++..++.+.         ..++|++.||+.||
T Consensus        58 ~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~---------~a~AL~lYPtnALa  128 (851)
T COG1205          58 SLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDP---------SARALLLYPTNALA  128 (851)
T ss_pred             HHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCc---------CccEEEEechhhhH
Confidence            346778888888899999999999999999999999999999999999999988764         34799999999999


Q ss_pred             HHHHHHHHHHHhhCC
Q psy7786         234 RQTHDIIQYYCAALP  248 (252)
Q Consensus       234 ~~i~~~l~~l~~~~~  248 (252)
                      +...+.|+++.+.++
T Consensus       129 ~DQ~~rl~~~~~~~~  143 (851)
T COG1205         129 NDQAERLRELISDLP  143 (851)
T ss_pred             hhHHHHHHHHHHhCC
Confidence            999999999999887

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=98.69  E-value=1.3e-07  Score=89.26  Aligned_cols=86  Identities=22%  Similarity=0.256  Sum_probs=70.9

Q ss_pred             CHHHHHHHHHC-CCCCChHHHHhhhhhhhcC------CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         152 PESLVRALEAK-GIKKPTPIQVQGIPAALSG------RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       152 ~~~l~~~l~~~-~~~~p~~iQ~~~~p~~~~~------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      .....+.+... ++ .||+.|..+++....+      .|.++++++|+|||.+++.+++..+..           +.+++
T Consensus       437 ~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~-----------g~qvl  504 (926)
T TIGR00580       437 DLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD-----------GKQVA  504 (926)
T ss_pred             CHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh-----------CCeEE
Confidence            33445555554 56 5999999999998875      689999999999999999998876542           46899


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         225 IICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      |++||++||.|.++.++++.+.+++
T Consensus       505 vLvPT~~LA~Q~~~~f~~~~~~~~i  529 (926)
T TIGR00580       505 VLVPTTLLAQQHFETFKERFANFPV  529 (926)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCc
Confidence            9999999999999999988777665

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.

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

Probab=98.66  E-value=7e-08  Score=89.10  Aligned_cols=76  Identities=24%  Similarity=0.276  Sum_probs=60.9

Q ss_pred             CCCCChHHHHhhhhhhhcCC-cEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEc-CcHHHHHHHHHHH
Q psy7786         163 GIKKPTPIQVQGIPAALSGR-DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC-PSRELARQTHDII  240 (252)
Q Consensus       163 ~~~~p~~iQ~~~~p~~~~~~-~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~-~tr~~a~~i~~~l  240 (252)
                      |+. |+++|...+|..+.|+ ++++.++||+|||.++.+..+..  .       .....++.|||+ |||++|.|+++.+
T Consensus        13 G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~--~-------~~~~~~~rLv~~vPtReLa~Qi~~~~   82 (844)
T TIGR02621        13 GYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV--E-------IGAKVPRRLVYVVNRRTVVDQVTEEA   82 (844)
T ss_pred             CCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc--c-------ccccccceEEEeCchHHHHHHHHHHH
Confidence            676 9999999999999998 57778999999999765444421  1       112357788866 9999999999999


Q ss_pred             HHHHhhCC
Q psy7786         241 QYYCAALP  248 (252)
Q Consensus       241 ~~l~~~~~  248 (252)
                      ++++++++
T Consensus        83 ~~~~k~l~   90 (844)
T TIGR02621        83 EKIGERLP   90 (844)
T ss_pred             HHHHHHhc
Confidence            99999874

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.

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.65  E-value=6.3e-08  Score=80.16  Aligned_cols=62  Identities=13%  Similarity=0.037  Sum_probs=49.5

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .+.+|+++++.||||||||++|++|++..+......     ....+++|.++|..+..|....++++
T Consensus        23 ~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~-----~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488       23 VLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER-----IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             HHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc-----ccccceeEEeccHHHHHHHHHHHHhc
Confidence            456899999999999999999999999876543320     02347999999999999987777765

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.65  E-value=6.3e-08  Score=80.16  Aligned_cols=62  Identities=13%  Similarity=0.037  Sum_probs=49.5

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .+.+|+++++.||||||||++|++|++..+......     ....+++|.++|..+..|....++++
T Consensus        23 ~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~-----~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489       23 VLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER-----IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             HHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc-----ccccceeEEeccHHHHHHHHHHHHhc
Confidence            456899999999999999999999999876543320     02347999999999999987777765

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=98.65  E-value=1.9e-07  Score=86.20  Aligned_cols=86  Identities=22%  Similarity=0.220  Sum_probs=70.6

Q ss_pred             HHHHHHH-HHCCCCCChHHHHhhhhhhhcC------CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEE
Q psy7786         153 ESLVRAL-EAKGIKKPTPIQVQGIPAALSG------RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI  225 (252)
Q Consensus       153 ~~l~~~l-~~~~~~~p~~iQ~~~~p~~~~~------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LI  225 (252)
                      ..+.+.+ ....+ .|++.|..+++....+      .+.++++++|+|||.+++++++..+.           .+.+++|
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~-----------~g~q~li  315 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE-----------AGYQAAL  315 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH-----------cCCeEEE
Confidence            3444444 44455 6999999999988876      37999999999999999999987653           2668999


Q ss_pred             EcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         226 ICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       226 f~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ++||+++|.|+++.++++.+.++++
T Consensus       316 laPT~~LA~Q~~~~l~~l~~~~~i~  340 (681)
T PRK10917        316 MAPTEILAEQHYENLKKLLEPLGIR  340 (681)
T ss_pred             EeccHHHHHHHHHHHHHHHhhcCcE
Confidence            9999999999999999999887653

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=98.62  E-value=1.9e-07  Score=85.49  Aligned_cols=84  Identities=27%  Similarity=0.241  Sum_probs=70.3

Q ss_pred             HHHHHHHHCCCCCChHHHHhhhhhhhcC------CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEc
Q psy7786         154 SLVRALEAKGIKKPTPIQVQGIPAALSG------RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC  227 (252)
Q Consensus       154 ~l~~~l~~~~~~~p~~iQ~~~~p~~~~~------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~  227 (252)
                      .+.+.+...+| .|++.|..+++..+.+      .+.++++++|+|||.+++++++..+..           +.+++|++
T Consensus       224 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~-----------g~qvlila  291 (630)
T TIGR00643       224 LLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA-----------GYQVALMA  291 (630)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc-----------CCcEEEEC
Confidence            34455667777 6999999999988865      257999999999999999998876532           56899999


Q ss_pred             CcHHHHHHHHHHHHHHHhhCCC
Q psy7786         228 PSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       228 ~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      ||+++|.|+++.++++.+.+++
T Consensus       292 PT~~LA~Q~~~~~~~l~~~~gi  313 (630)
T TIGR00643       292 PTEILAEQHYNSLRNLLAPLGI  313 (630)
T ss_pred             CHHHHHHHHHHHHHHHhcccCc
Confidence            9999999999999999887665

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.56  E-value=3e-07  Score=83.83  Aligned_cols=74  Identities=30%  Similarity=0.432  Sum_probs=63.7

Q ss_pred             HHHHHH-CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHH
Q psy7786         156 VRALEA-KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR  234 (252)
Q Consensus       156 ~~~l~~-~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~  234 (252)
                      .+.+++ .|+..++++|..+++..+.|+|+++.++||+|||++|.+|.+..              ...+||++|+++++.
T Consensus        14 ~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~--------------~g~tlVisPl~sL~~   79 (607)
T PRK11057         14 KQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL--------------DGLTLVVSPLISLMK   79 (607)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc--------------CCCEEEEecHHHHHH
Confidence            344433 58999999999999999999999999999999999999998842              235899999999999


Q ss_pred             HHHHHHHHH
Q psy7786         235 QTHDIIQYY  243 (252)
Q Consensus       235 ~i~~~l~~l  243 (252)
                      +..+.++.+
T Consensus        80 dqv~~l~~~   88 (607)
T PRK11057         80 DQVDQLLAN   88 (607)
T ss_pred             HHHHHHHHc
Confidence            998888764

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

Probab=98.46  E-value=3.9e-06  Score=75.03  Aligned_cols=103  Identities=22%  Similarity=0.319  Sum_probs=78.0

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++++-=|||||+..++.+++.+..           |.|+..++||--||.|=++.+.++...+|  +++...+|....+.
T Consensus       287 LlQGDVGSGKTvVA~laml~ai~~-----------G~Q~ALMAPTEILA~QH~~~~~~~l~~~~--i~V~lLtG~~kgk~  353 (677)
T COG1200         287 LLQGDVGSGKTVVALLAMLAAIEA-----------GYQAALMAPTEILAEQHYESLRKWLEPLG--IRVALLTGSLKGKA  353 (677)
T ss_pred             HhccCcCCCHHHHHHHHHHHHHHc-----------CCeeEEeccHHHHHHHHHHHHHHHhhhcC--CeEEEeecccchhH
Confidence            567788999999999999987743           66899999999999999999999999888  89999999988776


Q ss_pred             chhhhhh---c-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          91 SLDVIKK---G-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        91 ~~~~l~~---~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +.+.+.+   | .|++  |.|    .-.+     ++...|.+ +.++|.||-
T Consensus       354 r~~~l~~l~~G~~~iv--VGT----HALi-----Qd~V~F~~-LgLVIiDEQ  393 (677)
T COG1200         354 RKEILEQLASGEIDIV--VGT----HALI-----QDKVEFHN-LGLVIIDEQ  393 (677)
T ss_pred             HHHHHHHHhCCCCCEE--EEc----chhh-----hcceeecc-eeEEEEecc
Confidence            6665554   3 3331  333    2111     22344555 888888884

>PRK10689 transcription-repair coupling factor; Provisional

Probab=98.44  E-value=1.3e-06  Score=84.36  Aligned_cols=78  Identities=27%  Similarity=0.247  Sum_probs=64.0

Q ss_pred             HHCCCCCChHHHHhhhhhhhcC------CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHH
Q psy7786         160 EAKGIKKPTPIQVQGIPAALSG------RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA  233 (252)
Q Consensus       160 ~~~~~~~p~~iQ~~~~p~~~~~------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a  233 (252)
                      ....+ .||++|..+++..+.+      .|.++++++|+|||..++.+....+.           .+.+++|++||+++|
T Consensus       595 ~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~-----------~g~qvlvLvPT~eLA  662 (1147)
T PRK10689        595 DSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE-----------NHKQVAVLVPTTLLA  662 (1147)
T ss_pred             HhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH-----------cCCeEEEEeCcHHHH
Confidence            44445 7999999999998887      79999999999999988777654432           267899999999999


Q ss_pred             HHHHHHHHHHHhhCCC
Q psy7786         234 RQTHDIIQYYCAALPI  249 (252)
Q Consensus       234 ~~i~~~l~~l~~~~~i  249 (252)
                      .|+++.+++.....++
T Consensus       663 ~Q~~~~f~~~~~~~~v  678 (1147)
T PRK10689        663 QQHYDNFRDRFANWPV  678 (1147)
T ss_pred             HHHHHHHHHhhccCCc
Confidence            9999999886665543

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

Probab=98.43  E-value=9.6e-07  Score=83.56  Aligned_cols=83  Identities=25%  Similarity=0.301  Sum_probs=65.4

Q ss_pred             ccccCCC--CHHHHHHHHH-CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCc
Q psy7786         145 SFRLMKL--PESLVRALEA-KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP  221 (252)
Q Consensus       145 ~~~~~~l--~~~l~~~l~~-~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~  221 (252)
                      .|....|  ...+...+.+ .|+..+.+.|..++++++.|+|++++++||+|||++|.+|.+..              ..
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~--------------~G  501 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC--------------PG  501 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc--------------CC
Confidence            4554444  4445444443 47899999999999999999999999999999999999999842              34


Q ss_pred             EEEEEcCcHHHHHHHHHHHH
Q psy7786         222 YGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       222 ~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .+||++|+++|+++....+.
T Consensus       502 iTLVISPLiSLmqDQV~~L~  521 (1195)
T PLN03137        502 ITLVISPLVSLIQDQIMNLL  521 (1195)
T ss_pred             cEEEEeCHHHHHHHHHHHHH
Confidence            69999999999985444443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=98.40  E-value=9.3e-07  Score=80.59  Aligned_cols=70  Identities=27%  Similarity=0.413  Sum_probs=62.1

Q ss_pred             HCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         161 AKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ..|+..+.+.|..++++++.|+|++++++||+|||.+|.+|.+..              ...++|++|+++++.+..+.+
T Consensus         8 ~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~--------------~g~~lVisPl~sL~~dq~~~l   73 (591)
T TIGR01389         8 TFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL--------------KGLTVVISPLISLMKDQVDQL   73 (591)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc--------------CCcEEEEcCCHHHHHHHHHHH
Confidence            368999999999999999999999999999999999999998741              235899999999999999888


Q ss_pred             HHHH
Q psy7786         241 QYYC  244 (252)
Q Consensus       241 ~~l~  244 (252)
                      +.++
T Consensus        74 ~~~g   77 (591)
T TIGR01389        74 RAAG   77 (591)
T ss_pred             HHcC
Confidence            8753

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.39  E-value=1.8e-06  Score=83.31  Aligned_cols=109  Identities=19%  Similarity=0.155  Sum_probs=60.2

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +.++..++++|+||||||.  .+|.+.  +.....      ...+.++.-|-|--|..   ..+.+++.++  ..+...+
T Consensus        79 l~~~~vvii~g~TGSGKTT--qlPq~l--le~~~~------~~~~I~~tQPRRlAA~s---vA~RvA~elg--~~lG~~V  143 (1283)
T TIGR01967        79 IAENQVVIIAGETGSGKTT--QLPKIC--LELGRG------SHGLIGHTQPRRLAART---VAQRIAEELG--TPLGEKV  143 (1283)
T ss_pred             HHhCceEEEeCCCCCCcHH--HHHHHH--HHcCCC------CCceEecCCccHHHHHH---HHHHHHHHhC--CCcceEE
Confidence            4456678999999999997  467553  222210      11223333465544433   3445555555  3444445


Q ss_pred             CC-cccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          84 GG-VPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        84 g~-~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      |. ...+.+..   ....|.  +    .|+|+++.......  +...+.++|.||.
T Consensus       144 GY~vR~~~~~s---~~T~I~--~----~TdGiLLr~l~~d~--~L~~~~~IIIDEa  188 (1283)
T TIGR01967       144 GYKVRFHDQVS---SNTLVK--L----MTDGILLAETQQDR--FLSRYDTIIIDEA  188 (1283)
T ss_pred             eeEEcCCcccC---CCceee--e----ccccHHHHHhhhCc--ccccCcEEEEcCc
Confidence            52 33433332   223331  3    34999987765432  2344899999997

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.

>KOG0353|consensus

Probab=98.36  E-value=9.6e-07  Score=73.45  Aligned_cols=68  Identities=22%  Similarity=0.325  Sum_probs=51.9

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      -+.+.|+|+++.-|||-||+++|.||.+.   .           .-.+|+++|...|..++.-.++.++      +....
T Consensus       104 n~~ma~ed~~lil~tgggkslcyqlpal~---a-----------dg~alvi~plislmedqil~lkqlg------i~as~  163 (695)
T KOG0353|consen  104 NATMAGEDAFLILPTGGGKSLCYQLPALC---A-----------DGFALVICPLISLMEDQILQLKQLG------IDASM  163 (695)
T ss_pred             hhhhccCceEEEEeCCCccchhhhhhHHh---c-----------CCceEeechhHHHHHHHHHHHHHhC------cchhh
Confidence            45678999999999999999999999873   2           2248999999999998887777663      44444


Q ss_pred             eeCCcccC
Q psy7786          82 AIGGVPMN   89 (252)
Q Consensus        82 ~~g~~~~~   89 (252)
                      +...++.+
T Consensus       164 lnansske  171 (695)
T KOG0353|consen  164 LNANSSKE  171 (695)
T ss_pred             ccCcccHH
Confidence            44444443

>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=98.31  E-value=2e-06  Score=65.96  Aligned_cols=52  Identities=31%  Similarity=0.355  Sum_probs=41.9

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA   71 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~   71 (252)
                      +++++++.++||||||..++..+.... .             ++++++|++.|+.|..+.++.+..
T Consensus        24 ~~~~~ll~~~tGsGKT~~~~~~~~~l~-~-------------~~l~~~p~~~l~~Q~~~~~~~~~~   75 (184)
T PF04851_consen   24 EERRVLLNAPTGSGKTIIALALILELA-R-------------KVLIVAPNISLLEQWYDEFDDFGS   75 (184)
T ss_dssp             GCSEEEEEESTTSSHHHHHHHHHHHHH-C-------------EEEEEESSHHHHHHHHHHHHHHST
T ss_pred             CCCCEEEEECCCCCcChhhhhhhhccc-c-------------ceeEecCHHHHHHHHHHHHHHhhh
Confidence            368999999999999988875444332 1             699999999999999999866643

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 ....

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=98.30  E-value=3.5e-06  Score=77.92  Aligned_cols=73  Identities=26%  Similarity=0.327  Sum_probs=64.9

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|+++|....+....|+  +..+.||+|||+++.+|.+...+.           +.++.|++||++||.|.++++..+.
T Consensus        77 ~~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~-----------G~~v~VvTpt~~LA~qd~e~~~~l~  143 (790)
T PRK09200         77 MRPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE-----------GKGVHLITVNDYLAKRDAEEMGQVY  143 (790)
T ss_pred             CCCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc-----------CCCeEEEeCCHHHHHHHHHHHHHHH
Confidence            389999999999888876  899999999999999999855442           6679999999999999999999999


Q ss_pred             hhCCCC
Q psy7786         245 AALPIG  250 (252)
Q Consensus       245 ~~~~i~  250 (252)
                      +.+|++
T Consensus       144 ~~lGl~  149 (790)
T PRK09200        144 EFLGLT  149 (790)
T ss_pred             hhcCCe
Confidence            999875

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.30  E-value=1.6e-06  Score=80.32  Aligned_cols=107  Identities=20%  Similarity=0.181  Sum_probs=77.2

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++.-+||+|||++..+|++-..+.           |.++-+++||--||.|-++++..+-+.+|  +++.++.|+.+.++
T Consensus        99 iaEM~TGEGKTLvA~l~a~l~al~-----------G~~VhvvT~ndyLA~RD~e~m~~l~~~lG--l~v~~i~~~~~~~e  165 (913)
T PRK13103         99 IAEMRTGEGKTLVGTLAVYLNALS-----------GKGVHVVTVNDYLARRDANWMRPLYEFLG--LSVGIVTPFQPPEE  165 (913)
T ss_pred             cccccCCCCChHHHHHHHHHHHHc-----------CCCEEEEeCCHHHHHHHHHHHHHHhcccC--CEEEEECCCCCHHH
Confidence            678899999999999999866554           55699999999999999999999999988  89998888877666


Q ss_pred             chhhhhhcccccCCccccccCCccc-----cCCCh-hHHHHHhhhhceeeccCC
Q psy7786          91 SLDVIKKGIQYNDPIKTSWRAPRCI-----LSLPD-QVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        91 ~~~~l~~~~~i~~~i~t~~~~p~~l-----~~~~~-~~~~~l~~~~~~~V~de~  138 (252)
                      +.....  +||      .|+|...+     .+... .......+.+.+.+.||.
T Consensus       166 rr~~Y~--~dI------~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEv  211 (913)
T PRK13103        166 KRAAYA--ADI------TYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEV  211 (913)
T ss_pred             HHHHhc--CCE------EEEcccccccchhhccceechhhhcccccceeEechh
Confidence            555444  565      34444443     22222 222233345777777664

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.28  E-value=5.2e-06  Score=76.12  Aligned_cols=62  Identities=21%  Similarity=0.204  Sum_probs=44.7

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCC
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGG   85 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~   85 (252)
                      +..+++.|||+|||+..+.-+ ..+             .-++|||+|+.+|+.|-.+.+.++....+  ..+..++|+
T Consensus       274 r~GIIvLPtGaGKTlvai~aa-~~l-------------~k~tLILvps~~Lv~QW~~ef~~~~~l~~--~~I~~~tg~  335 (732)
T TIGR00603       274 RSGIIVLPCGAGKSLVGVTAA-CTV-------------KKSCLVLCTSAVSVEQWKQQFKMWSTIDD--SQICRFTSD  335 (732)
T ss_pred             CCcEEEeCCCCChHHHHHHHH-HHh-------------CCCEEEEeCcHHHHHHHHHHHHHhcCCCC--ceEEEEecC
Confidence            467999999999998765432 222             12499999999999999998888753322  445555665

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).

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

Probab=98.27  E-value=2.6e-05  Score=64.29  Aligned_cols=98  Identities=15%  Similarity=0.181  Sum_probs=66.6

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +.+.+|.++.|-||+|||.- +.+.++..+.          .|-++.|.+|-.+-+..++.+++.-  ..+  ..+.+++
T Consensus       113 i~~k~~~lv~AV~GaGKTEM-if~~i~~al~----------~G~~vciASPRvDVclEl~~Rlk~a--F~~--~~I~~Ly  177 (441)
T COG4098         113 IKQKEDTLVWAVTGAGKTEM-IFQGIEQALN----------QGGRVCIASPRVDVCLELYPRLKQA--FSN--CDIDLLY  177 (441)
T ss_pred             HHhcCcEEEEEecCCCchhh-hHHHHHHHHh----------cCCeEEEecCcccchHHHHHHHHHh--hcc--CCeeeEe
Confidence            45678999999999999953 3455666555          3567899999999998888877643  333  5677889


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccC
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGD  137 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de  137 (252)
                      |+++..-+      .              ..++.+.++.... +....+++.||
T Consensus       178 g~S~~~fr------~--------------plvVaTtHQLlrF-k~aFD~liIDE  210 (441)
T COG4098         178 GDSDSYFR------A--------------PLVVATTHQLLRF-KQAFDLLIIDE  210 (441)
T ss_pred             cCCchhcc------c--------------cEEEEehHHHHHH-HhhccEEEEec
Confidence            98653322      1              1244455554443 34477888777

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.25  E-value=4.7e-06  Score=76.12  Aligned_cols=74  Identities=26%  Similarity=0.274  Sum_probs=63.5

Q ss_pred             CCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         164 IKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       164 ~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      -..|+.+|....+.+..|+  +..+.||+|||+++.+|++...+.           +.++.|++||++||.|.++++..+
T Consensus        54 g~~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~-----------G~~V~VvTpt~~LA~qdae~~~~l  120 (745)
T TIGR00963        54 GMRPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT-----------GKGVHVVTVNDYLAQRDAEWMGQV  120 (745)
T ss_pred             CCCccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh-----------CCCEEEEcCCHHHHHHHHHHHHHH
Confidence            4479999999888887776  899999999999999999644432           346999999999999999999999


Q ss_pred             HhhCCCC
Q psy7786         244 CAALPIG  250 (252)
Q Consensus       244 ~~~~~i~  250 (252)
                      .+.+|++
T Consensus       121 ~~~LGLs  127 (745)
T TIGR00963       121 YRFLGLS  127 (745)
T ss_pred             hccCCCe
Confidence            9999875

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.

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.23  E-value=4.1e-06  Score=77.17  Aligned_cols=80  Identities=19%  Similarity=0.210  Sum_probs=65.7

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      .+|+  ++.-+||+|||+...+|++...+.           |-++-+++||--||.|=++.+..+-+.+|  +++.+..|
T Consensus        93 ~~G~--iaEm~TGEGKTLvA~l~a~l~al~-----------G~~v~vvT~neyLA~Rd~e~~~~~~~~LG--l~vg~i~~  157 (796)
T PRK12906         93 HEGN--IAEMKTGEGKTLTATLPVYLNALT-----------GKGVHVVTVNEYLSSRDATEMGELYRWLG--LTVGLNLN  157 (796)
T ss_pred             hcCC--cccccCCCCCcHHHHHHHHHHHHc-----------CCCeEEEeccHHHHHhhHHHHHHHHHhcC--CeEEEeCC
Confidence            4555  788899999999999999877765           55699999999999999999999999998  89998888


Q ss_pred             CcccCcchhhhhhcccc
Q psy7786          85 GVPMNQSLDVIKKGIQY  101 (252)
Q Consensus        85 ~~~~~~~~~~l~~~~~i  101 (252)
                      +.+.+++.+..  .+||
T Consensus       158 ~~~~~~r~~~y--~~dI  172 (796)
T PRK12906        158 SMSPDEKRAAY--NCDI  172 (796)
T ss_pred             CCCHHHHHHHh--cCCC
Confidence            86666554444  3455

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.20  E-value=9.5e-06  Score=74.56  Aligned_cols=72  Identities=25%  Similarity=0.315  Sum_probs=60.1

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .|+.+|.........|  .++.++||+|||+++++|.+...+.           +..++|++|+++||.|.++++..+.+
T Consensus        70 rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~-----------g~~V~VVTpn~yLA~Rdae~m~~l~~  136 (762)
T TIGR03714        70 FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALT-----------GKGAMLVTTNDYLAKRDAEEMGPVYE  136 (762)
T ss_pred             CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhc-----------CCceEEeCCCHHHHHHHHHHHHHHHh
Confidence            7888887766665555  6999999999999999997654432           44699999999999999999999999


Q ss_pred             hCCCC
Q psy7786         246 ALPIG  250 (252)
Q Consensus       246 ~~~i~  250 (252)
                      .+|++
T Consensus       137 ~LGLs  141 (762)
T TIGR03714       137 WLGLT  141 (762)
T ss_pred             hcCCc
Confidence            99875

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.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.18  E-value=5.9e-06  Score=76.27  Aligned_cols=110  Identities=19%  Similarity=0.205  Sum_probs=78.3

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcc
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVP   87 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~   87 (252)
                      +.-++..+||.|||+++.+|+.-..+.           |..+-|++++..||.+-.+++..+-+.+|  +++.+..++.+
T Consensus        90 ~G~IaEm~TGEGKTL~a~l~ayl~aL~-----------G~~VhVvT~NdyLA~RD~e~m~pvy~~LG--Lsvg~i~~~~~  156 (870)
T CHL00122         90 DGKIAEMKTGEGKTLVATLPAYLNALT-----------GKGVHIVTVNDYLAKRDQEWMGQIYRFLG--LTVGLIQEGMS  156 (870)
T ss_pred             CCccccccCCCCchHHHHHHHHHHHhc-----------CCceEEEeCCHHHHHHHHHHHHHHHHHcC--CceeeeCCCCC
Confidence            345889999999999999999644433           45689999999999999999999999999  88888888877


Q ss_pred             cCcchhhhhhcccccCCccccccCCc-----cccCCCh-hHHHHHhhhhceeeccCC
Q psy7786          88 MNQSLDVIKKGIQYNDPIKTSWRAPR-----CILSLPD-QVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        88 ~~~~~~~l~~~~~i~~~i~t~~~~p~-----~l~~~~~-~~~~~l~~~~~~~V~de~  138 (252)
                      ..++.+...  +||      .|++..     .|-+... .......+.+.+.+.||.
T Consensus       157 ~~err~aY~--~DI------tYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEv  205 (870)
T CHL00122        157 SEERKKNYL--KDI------TYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEV  205 (870)
T ss_pred             hHHHHHhcC--CCC------EecCCccccccchhhccCcChHHhhccccceeeeecc
Confidence            665555444  455      344443     3333332 222223345777777774

>KOG0948|consensus

Probab=98.18  E-value=8e-06  Score=73.45  Aligned_cols=155  Identities=18%  Similarity=0.216  Sum_probs=97.3

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+-++..+++.|-|-+|||...--.+-+.+..           .-|++|-+|-++|.+|-|.++..  +.-    -+...
T Consensus       140 Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~-----------kQRVIYTSPIKALSNQKYREl~~--EF~----DVGLM  202 (1041)
T KOG0948|consen  140 CIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE-----------KQRVIYTSPIKALSNQKYRELLE--EFK----DVGLM  202 (1041)
T ss_pred             hhcCCceEEEEeecCCCcchHHHHHHHHHHHh-----------cCeEEeeChhhhhcchhHHHHHH--Hhc----cccee
Confidence            46688999999999999997655555555533           23699999999999999886643  232    34557


Q ss_pred             eCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC------------------CCCcc-
Q psy7786          83 IGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD------------------VPPAC-  143 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~------------------~~~~~-  143 (252)
                      +|+.+.+....-|         +.    |-.+|-++.-+....++. +..+|-||-                  +|+.+ 
T Consensus       203 TGDVTInP~ASCL---------VM----TTEILRsMLYRGSEvmrE-VaWVIFDEIHYMRDkERGVVWEETIIllP~~vr  268 (1041)
T KOG0948|consen  203 TGDVTINPDASCL---------VM----TTEILRSMLYRGSEVMRE-VAWVIFDEIHYMRDKERGVVWEETIILLPDNVR  268 (1041)
T ss_pred             ecceeeCCCCcee---------ee----HHHHHHHHHhccchHhhe-eeeEEeeeehhccccccceeeeeeEEeccccce
Confidence            8887776554322         12    245677777777777776 677776652                  23222 


Q ss_pred             cccccCCCCH--HHHHHH---HHCC------CCCChHHHHhhhhhhhcCCcEEEEc
Q psy7786         144 CSFRLMKLPE--SLVRAL---EAKG------IKKPTPIQVQGIPAALSGRDIIGIA  188 (252)
Q Consensus       144 ~~~~~~~l~~--~l~~~l---~~~~------~~~p~~iQ~~~~p~~~~~~~~~~~~  188 (252)
                      .-|....++.  +..+++   ++.-      -..|||.|.+.+|+.-+|-..++..
T Consensus       269 ~VFLSATiPNA~qFAeWI~~ihkQPcHVVYTdyRPTPLQHyifP~ggdGlylvVDe  324 (1041)
T KOG0948|consen  269 FVFLSATIPNARQFAEWICHIHKQPCHVVYTDYRPTPLQHYIFPAGGDGLYLVVDE  324 (1041)
T ss_pred             EEEEeccCCCHHHHHHHHHHHhcCCceEEeecCCCCcceeeeecCCCCeeEEEEec
Confidence            1122222222  222333   3322      2379999999999877665555544

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

Probab=98.15  E-value=1.6e-06  Score=81.40  Aligned_cols=107  Identities=17%  Similarity=0.151  Sum_probs=69.5

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH-HHhCCCCcceee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY-CAALPIPLRTCL   81 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l-~~~~~~~~~~~~   81 (252)
                      .+.+|..++++||||||||+.--..+-..+..           +-+++|.+|.++|.+|.+..+... ++. -  =.+..
T Consensus       130 ~Ler~esVlV~ApTssGKTvVaeyAi~~al~~-----------~qrviYTsPIKALsNQKyrdl~~~fgdv-~--~~vGL  195 (1041)
T COG4581         130 ILERGESVLVCAPTSSGKTVVAEYAIALALRD-----------GQRVIYTSPIKALSNQKYRDLLAKFGDV-A--DMVGL  195 (1041)
T ss_pred             HHhCCCcEEEEccCCCCcchHHHHHHHHHHHc-----------CCceEeccchhhhhhhHHHHHHHHhhhh-h--hhccc
Confidence            35689999999999999998755554444432           445999999999999998776533 322 0  13456


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGD  137 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de  137 (252)
                      .+|+.+.+....       +     .+.|| .+|-++.-+....++. +..+|-||
T Consensus       196 ~TGDv~IN~~A~-------c-----lvMTT-EILRnMlyrg~~~~~~-i~~ViFDE  237 (1041)
T COG4581         196 MTGDVSINPDAP-------C-----LVMTT-EILRNMLYRGSESLRD-IEWVVFDE  237 (1041)
T ss_pred             eecceeeCCCCc-------e-----EEeeH-HHHHHHhccCcccccc-cceEEEEe
Confidence            788866544321       1     11233 5566666565555665 77777666

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.15  E-value=8.5e-06  Score=73.96  Aligned_cols=107  Identities=18%  Similarity=0.153  Sum_probs=76.6

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++.-.||+|||+...+|++...+.           |.++-+++||--||.|-++++..+-+.+|  +++.+..++.+.++
T Consensus        95 VaEM~TGEGKTLvA~l~a~l~AL~-----------G~~VhvvT~NdyLA~RDae~m~~ly~~LG--Lsvg~i~~~~~~~e  161 (764)
T PRK12326         95 VIEMATGEGKTLAGAIAAAGYALQ-----------GRRVHVITVNDYLARRDAEWMGPLYEALG--LTVGWITEESTPEE  161 (764)
T ss_pred             cccccCCCCHHHHHHHHHHHHHHc-----------CCCeEEEcCCHHHHHHHHHHHHHHHHhcC--CEEEEECCCCCHHH
Confidence            567889999999999999877654           55699999999999999999999999998  89998888876655


Q ss_pred             chhhhhhcccccCCccccccCCccc-----cCCCh-hHHHHHhhhhceeeccCC
Q psy7786          91 SLDVIKKGIQYNDPIKTSWRAPRCI-----LSLPD-QVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        91 ~~~~l~~~~~i~~~i~t~~~~p~~l-----~~~~~-~~~~~l~~~~~~~V~de~  138 (252)
                      +.+..  .+||      .|++...+     -+... .......+...+.+.||.
T Consensus       162 rr~aY--~~DI------tYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEv  207 (764)
T PRK12326        162 RRAAY--ACDV------TYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEA  207 (764)
T ss_pred             HHHHH--cCCC------EEcCCcccccccchhhhccChHhhcCCccceeeecch
Confidence            54444  3566      35554332     22221 122223344677777764

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

Probab=98.14  E-value=4.2e-06  Score=77.29  Aligned_cols=56  Identities=25%  Similarity=0.318  Sum_probs=47.3

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      +.+|+.+++.||||||||++|++|++.......          .+++|.++|+.|-.|+.+....+
T Consensus        31 ~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~----------~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          31 LKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG----------KKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             HcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC----------CcEEEECCCHHHHHHHHHhhcch
Confidence            456777999999999999999999998765543          46999999999999998877665

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.10  E-value=3.9e-05  Score=71.59  Aligned_cols=59  Identities=17%  Similarity=0.063  Sum_probs=49.4

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      .+++.||||.|||.+.+.+....+....       ....+.+++.|+|.+.+++++.++......+
T Consensus       216 ~~vl~aPTG~GKT~asl~~a~~~~~~~~-------~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~  274 (733)
T COG1203         216 LVVLEAPTGYGKTEASLILALALLDEKI-------KLKSRVIYVLPFRTIIEDMYRRAKEIFGLFS  274 (733)
T ss_pred             cEEEEeCCCCChHHHHHHHHHHHhhccc-------cccceEEEEccHHHHHHHHHHHHHhhhcccc
Confidence            7899999999999999999987765531       1367899999999999999999998765544

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

Probab=98.09  E-value=2.2e-05  Score=71.94  Aligned_cols=105  Identities=17%  Similarity=0.279  Sum_probs=72.2

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcc
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVP   87 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~   87 (252)
                      +-.++.+.||||||..|+ .++...+..          |-++|+++|-.+|-.|+.+.++..   .|  .++.+++++-+
T Consensus       218 ~~~Ll~GvTGSGKTEvYl-~~i~~~L~~----------GkqvLvLVPEI~Ltpq~~~rf~~r---Fg--~~v~vlHS~Ls  281 (730)
T COG1198         218 APFLLDGVTGSGKTEVYL-EAIAKVLAQ----------GKQVLVLVPEIALTPQLLARFKAR---FG--AKVAVLHSGLS  281 (730)
T ss_pred             cceeEeCCCCCcHHHHHH-HHHHHHHHc----------CCEEEEEeccccchHHHHHHHHHH---hC--CChhhhcccCC
Confidence            467899999999999995 444444443          457999999999999998877643   34  56777888888


Q ss_pred             cCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          88 MNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        88 ~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      ..++.+..++-       ..  +....++.+-.-...-|++ +..+|.||.
T Consensus       282 ~~er~~~W~~~-------~~--G~~~vVIGtRSAlF~Pf~~-LGLIIvDEE  322 (730)
T COG1198         282 PGERYRVWRRA-------RR--GEARVVIGTRSALFLPFKN-LGLIIVDEE  322 (730)
T ss_pred             hHHHHHHHHHH-------hc--CCceEEEEechhhcCchhh-ccEEEEecc
Confidence            77776666551       11  1233455554444555666 887777664

>KOG0950|consensus

Probab=98.02  E-value=1.7e-05  Score=73.04  Aligned_cols=78  Identities=19%  Similarity=0.194  Sum_probs=60.7

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      |.+++++|.+..+||+-|||++.-+=++..++.-.+          .++.+.|-..-+..-...+..+....|  +.+..
T Consensus       235 ~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr----------~~llilp~vsiv~Ek~~~l~~~~~~~G--~~ve~  302 (1008)
T KOG0950|consen  235 PRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR----------NVLLILPYVSIVQEKISALSPFSIDLG--FPVEE  302 (1008)
T ss_pred             hhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh----------ceeEecceeehhHHHHhhhhhhccccC--Ccchh
Confidence            567899999999999999999999999988887654          378888888777776677777777777  56665


Q ss_pred             eeCCcccCcc
Q psy7786          82 AIGGVPMNQS   91 (252)
Q Consensus        82 ~~g~~~~~~~   91 (252)
                      .+|+......
T Consensus       303 y~g~~~p~~~  312 (1008)
T KOG0950|consen  303 YAGRFPPEKR  312 (1008)
T ss_pred             hcccCCCCCc
Confidence            5676555444

>PHA02558 uvsW UvsW helicase; Provisional

Probab=98.01  E-value=2.2e-05  Score=70.19  Aligned_cols=71  Identities=25%  Similarity=0.227  Sum_probs=56.4

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|.+.|..+++..+.+.+.+++++||+|||..... +.......         ...++||++||+++++|+.+.+++++
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~-l~~~~~~~---------~~~~vLilvpt~eL~~Q~~~~l~~~~  182 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYL-LSRYYLEN---------YEGKVLIIVPTTSLVTQMIDDFVDYR  182 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHH-HHHHHHhc---------CCCeEEEEECcHHHHHHHHHHHHHhc
Confidence            479999999999999999999999999999986432 22222221         13489999999999999999999876


Q ss_pred             h
Q psy7786         245 A  245 (252)
Q Consensus       245 ~  245 (252)
                      .
T Consensus       183 ~  183 (501)
T PHA02558        183 L  183 (501)
T ss_pred             c
Confidence            3

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

Probab=98.01  E-value=2.9e-05  Score=70.47  Aligned_cols=64  Identities=23%  Similarity=0.188  Sum_probs=52.8

Q ss_pred             hhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH-hhCC
Q psy7786         176 PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC-AALP  248 (252)
Q Consensus       176 p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~-~~~~  248 (252)
                      .+...+..+++.++||+|||++|++|.+..+...         .+.+++|.+||+++++|+.+.+..+. +.++
T Consensus        11 ~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~---------~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~   75 (636)
T TIGR03117        11 TSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER---------PDQKIAIAVPTLALMGQLWSELERLTAEGLA   75 (636)
T ss_pred             HHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc---------cCceEEEECCcHHHHHHHHHHHHHHHHhhcC
Confidence            3445678899999999999999999999876532         14689999999999999999999888 5443

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.

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

Probab=98.00  E-value=4.7e-05  Score=72.32  Aligned_cols=85  Identities=21%  Similarity=0.256  Sum_probs=66.4

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhh----hhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEc
Q psy7786         152 PESLVRALEAKGIKKPTPIQVQGIP----AALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC  227 (252)
Q Consensus       152 ~~~l~~~l~~~~~~~p~~iQ~~~~p----~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~  227 (252)
                      ++...+.+...+++ +.+.|..++.    ....++++++.++||+|||.+|++|.+.... +          +.+++|.|
T Consensus       232 ~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~----------~~~vvi~t  299 (850)
T TIGR01407       232 SSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-T----------EKPVVIST  299 (850)
T ss_pred             cHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-C----------CCeEEEEe
Confidence            34566677777776 6688887664    5557889999999999999999999987544 1          34799999


Q ss_pred             CcHHHHHHHHH-HHHHHHhhCC
Q psy7786         228 PSRELARQTHD-IIQYYCAALP  248 (252)
Q Consensus       228 ~tr~~a~~i~~-~l~~l~~~~~  248 (252)
                      ||+++.+|+.. .+..+.+.++
T Consensus       300 ~t~~Lq~Ql~~~~~~~l~~~~~  321 (850)
T TIGR01407       300 NTKVLQSQLLEKDIPLLNEILN  321 (850)
T ss_pred             CcHHHHHHHHHHHHHHHHHHcC
Confidence            99999999865 6777777655

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.

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.96  E-value=2.1e-05  Score=73.16  Aligned_cols=60  Identities=17%  Similarity=0.166  Sum_probs=52.0

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      .+.+|+++++.||||||||++-+.|.+.......        ...+.+|.+.|..-..|+.++++++.
T Consensus        25 ~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~--------~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604        25 SLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP--------EVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             HhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc--------ccccEEEEcccchHHHHHHHHHHhhh
Confidence            4678999999999999999999999998765432        24689999999999999999999975

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).

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

Probab=97.89  E-value=4.9e-05  Score=71.62  Aligned_cols=73  Identities=22%  Similarity=0.226  Sum_probs=57.1

Q ss_pred             CChHHHHhhh----hhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHH-HHHH
Q psy7786         166 KPTPIQVQGI----PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT-HDII  240 (252)
Q Consensus       166 ~p~~iQ~~~~----p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i-~~~l  240 (252)
                      .+.+-|..+.    .+...+..+++.+.||+|||++|++|.+...            .+.+++|.||||++++|+ .+.+
T Consensus       245 e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~------------~~~~vvI~t~T~~Lq~Ql~~~~i  312 (820)
T PRK07246        245 EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS------------DQRQIIVSVPTKILQDQIMAEEV  312 (820)
T ss_pred             ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc------------CCCcEEEEeCcHHHHHHHHHHHH
Confidence            3555666644    3334568899999999999999999988632            145799999999999999 5788


Q ss_pred             HHHHhhCCCC
Q psy7786         241 QYYCAALPIG  250 (252)
Q Consensus       241 ~~l~~~~~i~  250 (252)
                      ..+++.++++
T Consensus       313 ~~l~~~~~~~  322 (820)
T PRK07246        313 KAIQEVFHID  322 (820)
T ss_pred             HHHHHhcCCc
Confidence            8888887764

>KOG0951|consensus

Probab=97.86  E-value=4.5e-05  Score=72.24  Aligned_cols=71  Identities=23%  Similarity=0.239  Sum_probs=55.2

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHH-HHHHHhCCCCcceeeeeC
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII-QYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~-~~l~~~~~~~~~~~~~~g   84 (252)
                      ...++++.||+|||||....+.++.   .         ....++++++|.-+.+..++..+ ++|++.+|  .++....|
T Consensus      1158 ~nd~v~vga~~gsgkt~~ae~a~l~---~---------~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G--~~~~~l~g 1223 (1674)
T KOG0951|consen 1158 TNDNVLVGAPNGSGKTACAELALLR---P---------DTIGRAVYIAPLEEIADEQYRDWEKKFSKLLG--LRIVKLTG 1223 (1674)
T ss_pred             ccceEEEecCCCCchhHHHHHHhcC---C---------ccceEEEEecchHHHHHHHHHHHHHhhccccC--ceEEecCC
Confidence            4678999999999999988888774   1         13568999999999998876554 67777766  78888888


Q ss_pred             CcccCc
Q psy7786          85 GVPMNQ   90 (252)
Q Consensus        85 ~~~~~~   90 (252)
                      ..+...
T Consensus      1224 e~s~~l 1229 (1674)
T KOG0951|consen 1224 ETSLDL 1229 (1674)
T ss_pred             ccccch
Confidence            766543

>PF13245 AAA_19: Part of AAA domain

Probab=97.85  E-value=0.00011  Score=47.96  Aligned_cols=53  Identities=19%  Similarity=0.281  Sum_probs=35.4

Q ss_pred             CCc-EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786           7 SRD-IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII   66 (252)
Q Consensus         7 g~d-~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~   66 (252)
                      +.+ +++.++.|||||....- .+..+......      .+-++++++||+..+.++.+.+
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~-~i~~l~~~~~~------~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAA-RIAELLAARAD------PGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHH-HHHHHHHHhcC------CCCeEEEECCCHHHHHHHHHHH
Confidence            444 45599999999955433 33333332110      1447999999999999887776

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.85  E-value=5.8e-05  Score=69.99  Aligned_cols=107  Identities=19%  Similarity=0.186  Sum_probs=76.0

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++.-+||-|||++..+|+.-..+.           |..+-|++++--||.+-.+++..+-+.+|  +++.+..++.+..+
T Consensus       102 IAEM~TGEGKTL~atlpaylnAL~-----------GkgVhVVTvNdYLA~RDae~m~~vy~~LG--Ltvg~i~~~~~~~e  168 (939)
T PRK12902        102 IAEMKTGEGKTLVATLPSYLNALT-----------GKGVHVVTVNDYLARRDAEWMGQVHRFLG--LSVGLIQQDMSPEE  168 (939)
T ss_pred             eeeecCCCChhHHHHHHHHHHhhc-----------CCCeEEEeCCHHHHHhHHHHHHHHHHHhC--CeEEEECCCCChHH
Confidence            788999999999999999865554           45689999999999999999999999999  88888877755544


Q ss_pred             chhhhhhcccccCCccccccCCccc-----cCCChh-HHHHHhhhhceeeccCC
Q psy7786          91 SLDVIKKGIQYNDPIKTSWRAPRCI-----LSLPDQ-VHDIIRRNLRILVEGDD  138 (252)
Q Consensus        91 ~~~~l~~~~~i~~~i~t~~~~p~~l-----~~~~~~-~~~~l~~~~~~~V~de~  138 (252)
                      +...  -.+||      .|+++..+     .+.... ......+.+.+.+.||.
T Consensus       169 rr~a--Y~~DI------tYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEv  214 (939)
T PRK12902        169 RKKN--YACDI------TYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEV  214 (939)
T ss_pred             HHHh--cCCCe------EEecCCcccccchhhhhcccccccccCccceEEEecc
Confidence            3332  34666      45666554     222221 11123345777777764

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.84  E-value=9.1e-05  Score=57.06  Aligned_cols=76  Identities=39%  Similarity=0.482  Sum_probs=63.4

Q ss_pred             CCCCCChHHHHhhhhhhhcC-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         162 KGIKKPTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       162 ~~~~~p~~iQ~~~~p~~~~~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      .+...+.+.|..++...... +..++.+++|+|||..+...++..+....         ..++++++|++.++.++.+.+
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~---------~~~~l~~~p~~~~~~~~~~~~   74 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK---------GKRVLVLVPTRELAEQWAEEL   74 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC---------CCcEEEEeCCHHHHHHHHHHH
Confidence            34567899999999999988 99999999999999988888877654321         346999999999999999999


Q ss_pred             HHHHhh
Q psy7786         241 QYYCAA  246 (252)
Q Consensus       241 ~~l~~~  246 (252)
                      .++...
T Consensus        75 ~~~~~~   80 (201)
T smart00487       75 KKLGPS   80 (201)
T ss_pred             HHHhcc
Confidence            887754

>PHA02653 RNA helicase NPH-II; Provisional

Probab=97.82  E-value=6.8e-05  Score=68.82  Aligned_cols=75  Identities=15%  Similarity=0.003  Sum_probs=55.7

Q ss_pred             ChHHHHhhhhhhhcCCcEEEEccCCCchhHH---------hHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHH
Q psy7786         167 PTPIQVQGIPAALSGRDIIGIAFTGSGKTLV---------FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH  237 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~---------~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~  237 (252)
                      +..+|.+.++....++++++.++||+|||.+         |+++.+..+..-.     ......+++|.+|||++|.|+.
T Consensus       165 ~~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~-----~~~~~~~ilvt~PrreLa~qi~  239 (675)
T PHA02653        165 QPDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID-----PNFIERPIVLSLPRVALVRLHS  239 (675)
T ss_pred             hHHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc-----cccCCcEEEEECcHHHHHHHHH
Confidence            4468999999999999999999999999986         3334443321100     0123468999999999999999


Q ss_pred             HHHHHHHhh
Q psy7786         238 DIIQYYCAA  246 (252)
Q Consensus       238 ~~l~~l~~~  246 (252)
                      ..+.+...+
T Consensus       240 ~~i~~~vg~  248 (675)
T PHA02653        240 ITLLKSLGF  248 (675)
T ss_pred             HHHHHHhCc
Confidence            888765544

>COG1204 Superfamily II helicase [General function prediction only]

Probab=97.81  E-value=9.9e-05  Score=68.70  Aligned_cols=88  Identities=31%  Similarity=0.335  Sum_probs=66.5

Q ss_pred             CCHHHHHHHHHCCCCCChH-HHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCc
Q psy7786         151 LPESLVRALEAKGIKKPTP-IQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPS  229 (252)
Q Consensus       151 l~~~l~~~l~~~~~~~p~~-iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~t  229 (252)
                      ..+.+.+.+...++....+ +|....+....+.|++++++||+|||.-..+.+++.+.+.          +.+++..||+
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~----------~~k~vYivPl   85 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG----------GGKVVYIVPL   85 (766)
T ss_pred             ccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc----------CCcEEEEeCh
Confidence            5566666666666644444 4444445566779999999999999999999999887763          4579999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCC
Q psy7786         230 RELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       230 r~~a~~i~~~l~~l~~~~~i  249 (252)
                      |.||++.++.+++ -+.+|+
T Consensus        86 kALa~Ek~~~~~~-~~~~Gi  104 (766)
T COG1204          86 KALAEEKYEEFSR-LEELGI  104 (766)
T ss_pred             HHHHHHHHHHhhh-HHhcCC
Confidence            9999999999983 334443

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=97.80  E-value=8.8e-05  Score=69.15  Aligned_cols=73  Identities=23%  Similarity=0.212  Sum_probs=59.0

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|..+|...--++  ...-+..+.||+|||+++.+|.+...+.           +..+.|++||++||.|.++++..+.
T Consensus        81 ~~~ydvQliGg~~L--h~G~Iaem~TGeGKTL~a~Lpa~~~al~-----------G~~V~VvTpn~yLA~qd~e~m~~l~  147 (896)
T PRK13104         81 LRHFDVQLIGGMVL--HEGNIAEMRTGEGKTLVATLPAYLNAIS-----------GRGVHIVTVNDYLAKRDSQWMKPIY  147 (896)
T ss_pred             CCcchHHHhhhhhh--ccCccccccCCCCchHHHHHHHHHHHhc-----------CCCEEEEcCCHHHHHHHHHHHHHHh
Confidence            36777777543333  4555889999999999999999976543           3459999999999999999999999


Q ss_pred             hhCCCC
Q psy7786         245 AALPIG  250 (252)
Q Consensus       245 ~~~~i~  250 (252)
                      +.+|++
T Consensus       148 ~~lGLt  153 (896)
T PRK13104        148 EFLGLT  153 (896)
T ss_pred             cccCce
Confidence            998874

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=97.79  E-value=9.2e-05  Score=63.33  Aligned_cols=63  Identities=27%  Similarity=0.378  Sum_probs=52.6

Q ss_pred             HHhhhhhhhcCCc--EEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         171 QVQGIPAALSGRD--IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       171 Q~~~~p~~~~~~~--~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      |.++++.+..+.+  +++.++||+|||.+++++.+..              ..++++++|+++++++.++.++++...+
T Consensus         2 Q~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~--------------~~~~~~~~P~~aL~~~~~~~~~~~~~~~   66 (357)
T TIGR03158         2 QVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG--------------ENDTIALYPTNALIEDQTEAIKEFVDVF   66 (357)
T ss_pred             HHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc--------------CCCEEEEeChHHHHHHHHHHHHHHHHhc
Confidence            6778888888764  7889999999999999988741              2358999999999999999999887654

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.

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

Probab=97.78  E-value=5.8e-05  Score=73.00  Aligned_cols=54  Identities=22%  Similarity=0.246  Sum_probs=42.8

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .+..+++.+||||||.+. +.++.+++...        ...++|+|+|+++|+.|..+.++.+
T Consensus       433 ~r~~Ll~maTGSGKT~ta-i~li~~L~~~~--------~~~rVLfLvDR~~L~~Qa~~~F~~~  486 (1123)
T PRK11448        433 QREILLAMATGTGKTRTA-IALMYRLLKAK--------RFRRILFLVDRSALGEQAEDAFKDT  486 (1123)
T ss_pred             cCCeEEEeCCCCCHHHHH-HHHHHHHHhcC--------ccCeEEEEecHHHHHHHHHHHHHhc
Confidence            367999999999999873 44555555432        2458999999999999999988876

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=97.75  E-value=5.9e-05  Score=64.55  Aligned_cols=52  Identities=23%  Similarity=0.080  Sum_probs=44.7

Q ss_pred             cEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         183 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       183 ~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ++++.++||+|||.+++.+.+..+...         ...++++++|+|+++.|+++.++.+
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~---------~~~~ii~v~P~~~L~~q~~~~l~~~   52 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ---------KADRVIIALPTRATINAMYRRAKEL   52 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC---------CCCeEEEEeehHHHHHHHHHHHHHH
Confidence            578999999999999999998765432         2568999999999999999999886

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=97.73  E-value=0.00013  Score=67.49  Aligned_cols=66  Identities=24%  Similarity=0.287  Sum_probs=54.6

Q ss_pred             CChHHHHhhhhhhhcC---CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSG---RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~---~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .+++.|..++.....+   .+.++.++||+|||..|+.++...+.           .+.++||++||++++.|+.+.+++
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~-----------~g~~vLvLvPt~~L~~Q~~~~l~~  212 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLA-----------QGKQALVLVPEIALTPQMLARFRA  212 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHH-----------cCCeEEEEeCcHHHHHHHHHHHHH
Confidence            4788999999888763   78999999999999999876554332           156899999999999999998875

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

Probab=97.69  E-value=0.00022  Score=62.85  Aligned_cols=96  Identities=28%  Similarity=0.376  Sum_probs=83.2

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~-~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ...++.+++++.+.+...|++...|+|..++.+ ++.|.|.++.+.|++|||+.--+.-+.+++.          .+.+.
T Consensus       195 ~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~----------~g~Km  264 (830)
T COG1202         195 PVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS----------GGKKM  264 (830)
T ss_pred             cccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh----------CCCeE
Confidence            356788999999999999999999999999966 6799999999999999999777777766654          25679


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |.++|-..+|+|=++.+++--+.++++
T Consensus       265 lfLvPLVALANQKy~dF~~rYs~Lglk  291 (830)
T COG1202         265 LFLVPLVALANQKYEDFKERYSKLGLK  291 (830)
T ss_pred             EEEehhHHhhcchHHHHHHHhhcccce
Confidence            999999999999999999887888765

>KOG0952|consensus

Probab=97.67  E-value=0.00015  Score=67.65  Aligned_cols=86  Identities=28%  Similarity=0.256  Sum_probs=66.3

Q ss_pred             CCCCChHHHHhhhhhhhc-CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         163 GIKKPTPIQVQGIPAALS-GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       163 ~~~~p~~iQ~~~~p~~~~-~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      ++.....+|+.++|.... +.++++|++||+|||..+++.+++.+.+++.. -.....+.+++..+|++.||.++.+.+.
T Consensus       107 ~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~-~~i~k~~fKiVYIaPmKALa~Em~~~~~  185 (1230)
T KOG0952|consen  107 SFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQ-GDIAKDDFKIVYIAPMKALAAEMVDKFS  185 (1230)
T ss_pred             cHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccc-cccccCCceEEEEechHHHHHHHHHHHh
Confidence            455667899999988774 57999999999999999999999988763322 2234456789999999999999887776


Q ss_pred             HHHhhCCC
Q psy7786         242 YYCAALPI  249 (252)
Q Consensus       242 ~l~~~~~i  249 (252)
                      +--..+|+
T Consensus       186 kkl~~~gi  193 (1230)
T KOG0952|consen  186 KKLAPLGI  193 (1230)
T ss_pred             hhcccccc
Confidence            54443443

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

Probab=97.66  E-value=0.00041  Score=64.89  Aligned_cols=82  Identities=23%  Similarity=0.212  Sum_probs=67.2

Q ss_pred             HHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHH
Q psy7786         156 VRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ  235 (252)
Q Consensus       156 ~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~  235 (252)
                      .+-+.+..-..|+..|+.+....+.|+.+.+.||||.|||..-++-.+...           .++.++++.+||+.|+.|
T Consensus        72 ~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a-----------~kgkr~yii~PT~~Lv~Q  140 (1187)
T COG1110          72 EEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLA-----------KKGKRVYIIVPTTTLVRQ  140 (1187)
T ss_pred             HHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHH-----------hcCCeEEEEecCHHHHHH
Confidence            444555545589999999999999999999999999999987655554321           135689999999999999


Q ss_pred             HHHHHHHHHhhCC
Q psy7786         236 THDIIQYYCAALP  248 (252)
Q Consensus       236 i~~~l~~l~~~~~  248 (252)
                      +++.++++++..+
T Consensus       141 ~~~kl~~~~e~~~  153 (1187)
T COG1110         141 VYERLKKFAEDAG  153 (1187)
T ss_pred             HHHHHHHHHhhcC
Confidence            9999999998776

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

Probab=97.60  E-value=0.00016  Score=63.69  Aligned_cols=49  Identities=27%  Similarity=0.338  Sum_probs=37.0

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      ++..++..|||+|||..++--+-. +             ...+|||+||++|+.|-.+.+...
T Consensus        55 ~~~gvivlpTGaGKT~va~~~~~~-~-------------~~~~Lvlv~~~~L~~Qw~~~~~~~  103 (442)
T COG1061          55 ERRGVIVLPTGAGKTVVAAEAIAE-L-------------KRSTLVLVPTKELLDQWAEALKKF  103 (442)
T ss_pred             CCceEEEeCCCCCHHHHHHHHHHH-h-------------cCCEEEEECcHHHHHHHHHHHHHh
Confidence            788999999999999766544321 1             223999999999999987555443

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=97.57  E-value=0.0009  Score=63.74  Aligned_cols=198  Identities=19%  Similarity=0.200  Sum_probs=118.0

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCccc
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPM   88 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~   88 (252)
                      |=++|+--|-|||...+=.++..++.           |.|+.+++||--||+|=++.++.  +..|+++++..+..=.+.
T Consensus       617 DRLiCGDVGFGKTEVAmRAAFkAV~~-----------GKQVAvLVPTTlLA~QHy~tFke--RF~~fPV~I~~LSRF~s~  683 (1139)
T COG1197         617 DRLICGDVGFGKTEVAMRAAFKAVMD-----------GKQVAVLVPTTLLAQQHYETFKE--RFAGFPVRIEVLSRFRSA  683 (1139)
T ss_pred             hheeecCcCCcHHHHHHHHHHHHhcC-----------CCeEEEEcccHHhHHHHHHHHHH--HhcCCCeeEEEecccCCH
Confidence            77999999999998777666655543           67899999999999999888874  344556898877766666


Q ss_pred             Ccchhhhhh---c-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHHCCC
Q psy7786          89 NQSLDVIKK---G-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGI  164 (252)
Q Consensus        89 ~~~~~~l~~---~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~  164 (252)
                      +++.+.++.   | +||+  |.|     |+|++-    ...|++ +..+|.||.        +..|..+.  +.+++...
T Consensus       684 kE~~~il~~la~G~vDIv--IGT-----HrLL~k----dv~Fkd-LGLlIIDEE--------qRFGVk~K--EkLK~Lr~  741 (1139)
T COG1197         684 KEQKEILKGLAEGKVDIV--IGT-----HRLLSK----DVKFKD-LGLLIIDEE--------QRFGVKHK--EKLKELRA  741 (1139)
T ss_pred             HHHHHHHHHHhcCCccEE--Eec-----hHhhCC----CcEEec-CCeEEEech--------hhcCccHH--HHHHHHhc
Confidence            666555543   3 5653  444     233321    233444 888888886        34443332  23333210


Q ss_pred             ------CCChHHHHhhhhhhhcC-CcEEEEccCCCchh--HHhH----HHHHHHHHhhhccCCCCCCCCcEEEEEcCcHH
Q psy7786         165 ------KKPTPIQVQGIPAALSG-RDIIGIAFTGSGKT--LVFV----LPILMFCLEQETKLPFLPGEGPYGLIICPSRE  231 (252)
Q Consensus       165 ------~~p~~iQ~~~~p~~~~~-~~~~~~~~~g~gKt--~~~~----~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~  231 (252)
                            ...|||=+ ++...+.| +|+.+++.+..++-  -.|+    -..+......+.      ..+.|+-.+.|..+
T Consensus       742 ~VDvLTLSATPIPR-TL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl------~RgGQvfYv~NrV~  814 (1139)
T COG1197         742 NVDVLTLSATPIPR-TLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILREL------LRGGQVFYVHNRVE  814 (1139)
T ss_pred             cCcEEEeeCCCCcc-hHHHHHhcchhhhhccCCCCCCcceEEEEecCChHHHHHHHHHHH------hcCCEEEEEecchh
Confidence                  01112111 12222333 55555554433320  0111    112222222221      34789999999999


Q ss_pred             HHHHHHHHHHHHHhhCC
Q psy7786         232 LARQTHDIIQYYCAALP  248 (252)
Q Consensus       232 ~a~~i~~~l~~l~~~~~  248 (252)
                      .-+++++.|+.+.+...
T Consensus       815 ~Ie~~~~~L~~LVPEar  831 (1139)
T COG1197         815 SIEKKAERLRELVPEAR  831 (1139)
T ss_pred             hHHHHHHHHHHhCCceE
Confidence            99999999999877654

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

Probab=97.53  E-value=0.00018  Score=66.45  Aligned_cols=55  Identities=27%  Similarity=0.248  Sum_probs=42.3

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      ++..++..+||||||++.+.-+-. +....        ...++|+|+|+++|..|..+.++.++
T Consensus       263 ~~~gli~~~TGsGKT~t~~~la~~-l~~~~--------~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       263 ERGGLIWHTQGSGKTLTMLFAARK-ALELL--------KNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             CceeEEEEecCCCccHHHHHHHHH-HHhhc--------CCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            357899999999999776544432 32222        36789999999999999999988774

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

>KOG0349|consensus

Probab=97.52  E-value=6e-05  Score=64.06  Aligned_cols=67  Identities=36%  Similarity=0.448  Sum_probs=61.3

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhh
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE  210 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~  210 (252)
                      ..|.++|.-+++-....++.+..|+.+|..++|..+.|-|++..+.+|+|||-+|.+|+++-+.+..
T Consensus         2 ~af~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv~etl   68 (725)
T KOG0349|consen    2 TAFEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWETL   68 (725)
T ss_pred             cchHhhCcchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHHHHHH
Confidence            3588999999998888999999999999999999999999999999999999999999998777543

>KOG0947|consensus

Probab=97.37  E-value=7.3e-05  Score=69.12  Aligned_cols=102  Identities=19%  Similarity=0.264  Sum_probs=72.7

Q ss_pred             cccCCCcEEEEcCCCchHHHH--hHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLV--FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a--~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      .+.+|-.+.+.|.|-+|||+.  |.+.+-|.             .+.+++|-+|-++|.+|-+..++.-   .+   -+.
T Consensus       308 ~lerg~SVFVAAHTSAGKTvVAEYAialaq~-------------h~TR~iYTSPIKALSNQKfRDFk~t---F~---Dvg  368 (1248)
T KOG0947|consen  308 HLERGDSVFVAAHTSAGKTVVAEYAIALAQK-------------HMTRTIYTSPIKALSNQKFRDFKET---FG---DVG  368 (1248)
T ss_pred             HHHcCCeEEEEecCCCCcchHHHHHHHHHHh-------------hccceEecchhhhhccchHHHHHHh---cc---ccc
Confidence            467899999999999999975  44444332             3678999999999999988777643   33   123


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGD  137 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de  137 (252)
                      .++|+.........+         |.|    -.+|-+|.-+..+..+. +.++|-||
T Consensus       369 LlTGDvqinPeAsCL---------IMT----TEILRsMLYrgadliRD-vE~VIFDE  411 (1248)
T KOG0947|consen  369 LLTGDVQINPEASCL---------IMT----TEILRSMLYRGADLIRD-VEFVIFDE  411 (1248)
T ss_pred             eeecceeeCCCcceE---------eeh----HHHHHHHHhcccchhhc-cceEEEee
Confidence            688987665553322         222    45677777777777777 88888776

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=97.31  E-value=0.00055  Score=67.70  Aligned_cols=57  Identities=28%  Similarity=0.195  Sum_probs=44.3

Q ss_pred             EEccCCCchhHHhHHHHHHHHHhhhccCC--CCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         186 GIAFTGSGKTLVFVLPILMFCLEQETKLP--FLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       186 ~~~~~g~gKt~~~~~~~l~~i~~~~~~~~--~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      ++++||||||.++.+|.+..++.+.....  .....+.++|+++|+|+|+.|+.+.++.
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~   59 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQI   59 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHH
Confidence            46899999999999999999886431100  0112357899999999999999999875

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=97.30  E-value=0.00065  Score=63.99  Aligned_cols=62  Identities=19%  Similarity=0.149  Sum_probs=48.3

Q ss_pred             hhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH-HHHhhC
Q psy7786         175 IPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ-YYCAAL  247 (252)
Q Consensus       175 ~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~-~l~~~~  247 (252)
                      +....+++++++.++||+|||..+.++++....           ...+++|..|||++|.++++.+. .++..+
T Consensus        14 ~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~-----------~~~~ilvlqPrR~aA~qia~rva~~l~~~~   76 (812)
T PRK11664         14 LTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG-----------INGKIIMLEPRRLAARNVAQRLAEQLGEKP   76 (812)
T ss_pred             HHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC-----------cCCeEEEECChHHHHHHHHHHHHHHhCccc
Confidence            344556789999999999999999888885321           13489999999999999999884 444444

>PRK13766 Hef nuclease; Provisional

Probab=97.30  E-value=0.0011  Score=62.75  Aligned_cols=68  Identities=24%  Similarity=0.265  Sum_probs=55.5

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      .|...|.......+.+ +.+++.++|.|||..+++.+...+..          .+.++||+|||+.+++|..+.++++.
T Consensus        15 ~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~----------~~~~vLvl~Pt~~L~~Q~~~~~~~~~   82 (773)
T PRK13766         15 EARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK----------KGGKVLILAPTKPLVEQHAEFFRKFL   82 (773)
T ss_pred             CccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh----------CCCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            5677888877767766 89999999999999888777765521          25689999999999999999998764

>KOG0353|consensus

Probab=97.27  E-value=0.00089  Score=56.20  Aligned_cols=84  Identities=26%  Similarity=0.402  Sum_probs=69.8

Q ss_pred             ccCCCCHHHHHHHHHCC-CCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEE
Q psy7786         147 RLMKLPESLVRALEAKG-IKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI  225 (252)
Q Consensus       147 ~~~~l~~~l~~~l~~~~-~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LI  225 (252)
                      .+.+.+.+..+++.... ++...|.|..++.+++.+.|.+++.++|.||.++|-+|.+.              ....+||
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~--------------adg~alv  139 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALC--------------ADGFALV  139 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHh--------------cCCceEe
Confidence            35667888877776653 55678899999999999999999999999999999999984              2456999


Q ss_pred             EcCcHHHHHHHHHHHHHHH
Q psy7786         226 ICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       226 f~~tr~~a~~i~~~l~~l~  244 (252)
                      +||...+.+..--.|+.++
T Consensus       140 i~plislmedqil~lkqlg  158 (695)
T KOG0353|consen  140 ICPLISLMEDQILQLKQLG  158 (695)
T ss_pred             echhHHHHHHHHHHHHHhC
Confidence            9999999988777777654

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=97.23  E-value=0.0015  Score=54.18  Aligned_cols=74  Identities=18%  Similarity=0.113  Sum_probs=56.0

Q ss_pred             CChHHHHhhh----hhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGI----PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       166 ~p~~iQ~~~~----p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .|.+.|...+    .....+.+.++.++||+|||++++.|.+.+.......     ....++++.++|..+.++....++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~-----~~~~kvi~~t~T~~~~~q~i~~l~   82 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER-----IQKIKLIYLSRTVSEIEKRLEELR   82 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc-----ccccceeEEeccHHHHHHHHHHHH
Confidence            3577787744    4455788999999999999999999999876543211     023478999999999999888787


Q ss_pred             HHH
Q psy7786         242 YYC  244 (252)
Q Consensus       242 ~l~  244 (252)
                      ++.
T Consensus        83 ~~~   85 (289)
T smart00488       83 KLM   85 (289)
T ss_pred             hcc
Confidence            653

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=97.23  E-value=0.0015  Score=54.18  Aligned_cols=74  Identities=18%  Similarity=0.113  Sum_probs=56.0

Q ss_pred             CChHHHHhhh----hhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGI----PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       166 ~p~~iQ~~~~----p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .|.+.|...+    .....+.+.++.++||+|||++++.|.+.+.......     ....++++.++|..+.++....++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~-----~~~~kvi~~t~T~~~~~q~i~~l~   82 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER-----IQKIKLIYLSRTVSEIEKRLEELR   82 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc-----ccccceeEEeccHHHHHHHHHHHH
Confidence            3577787744    4455788999999999999999999999876543211     023478999999999999888787


Q ss_pred             HHH
Q psy7786         242 YYC  244 (252)
Q Consensus       242 ~l~  244 (252)
                      ++.
T Consensus        83 ~~~   85 (289)
T smart00489       83 KLM   85 (289)
T ss_pred             hcc
Confidence            653

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=97.22  E-value=0.00053  Score=50.13  Aligned_cols=53  Identities=19%  Similarity=0.247  Sum_probs=35.8

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      .+|+=.++--.+|+|||--.+--++.....          .+.++|+|.|||.++..+++.++
T Consensus         2 ~kg~~~~~d~hpGaGKTr~vlp~~~~~~i~----------~~~rvLvL~PTRvva~em~~aL~   54 (148)
T PF07652_consen    2 RKGELTVLDLHPGAGKTRRVLPEIVREAIK----------RRLRVLVLAPTRVVAEEMYEALK   54 (148)
T ss_dssp             STTEEEEEE--TTSSTTTTHHHHHHHHHHH----------TT--EEEEESSHHHHHHHHHHTT
T ss_pred             CCCceeEEecCCCCCCcccccHHHHHHHHH----------ccCeEEEecccHHHHHHHHHHHh
Confidence            455666778889999996665445544433          25679999999999988877664

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 ....

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=97.16  E-value=0.0017  Score=60.60  Aligned_cols=74  Identities=24%  Similarity=0.226  Sum_probs=58.7

Q ss_pred             CCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         164 IKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       164 ~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      -..|..+|....=++..|  -+..+.||+|||+++.+|++-..+.           +.++-|++||+.||.|.++++..+
T Consensus        79 g~~~~dvQlig~l~L~~G--~Iaem~TGeGKTLva~lpa~l~aL~-----------G~~V~IvTpn~yLA~rd~e~~~~l  145 (830)
T PRK12904         79 GMRHFDVQLIGGMVLHEG--KIAEMKTGEGKTLVATLPAYLNALT-----------GKGVHVVTVNDYLAKRDAEWMGPL  145 (830)
T ss_pred             CCCCCccHHHhhHHhcCC--chhhhhcCCCcHHHHHHHHHHHHHc-----------CCCEEEEecCHHHHHHHHHHHHHH
Confidence            347888888655555444  5888999999999999999643332           334779999999999999999999


Q ss_pred             HhhCCCC
Q psy7786         244 CAALPIG  250 (252)
Q Consensus       244 ~~~~~i~  250 (252)
                      .+.+|++
T Consensus       146 ~~~LGls  152 (830)
T PRK12904        146 YEFLGLS  152 (830)
T ss_pred             HhhcCCe
Confidence            9999875

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=97.16  E-value=0.0014  Score=61.70  Aligned_cols=62  Identities=21%  Similarity=0.144  Sum_probs=49.0

Q ss_pred             hhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH-HHHhhC
Q psy7786         175 IPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ-YYCAAL  247 (252)
Q Consensus       175 ~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~-~l~~~~  247 (252)
                      +..+..+.+++++++||+|||..+.++++....           .+.+++|+.|+|+.|.++++.+. .++..+
T Consensus        11 ~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~-----------~~~~ilvlqPrR~aA~qiA~rva~~~~~~~   73 (819)
T TIGR01970        11 RDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG-----------IGGKIIMLEPRRLAARSAAQRLASQLGEAV   73 (819)
T ss_pred             HHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc-----------cCCeEEEEeCcHHHHHHHHHHHHHHhCCCc
Confidence            344556789999999999999999999886541           14589999999999999999884 444433

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.

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=97.15  E-value=0.0019  Score=60.51  Aligned_cols=72  Identities=24%  Similarity=0.216  Sum_probs=58.7

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .|..+|..  ..+.-...-+..+.||+|||+++.+|.+...+.           +..+.|++++++||.+.++++..+.+
T Consensus        82 ~~ydVQli--Ggl~L~~G~IaEm~TGEGKTL~a~lp~~l~al~-----------g~~VhIvT~ndyLA~RD~e~m~~l~~  148 (908)
T PRK13107         82 RHFDVQLL--GGMVLDSNRIAEMRTGEGKTLTATLPAYLNALT-----------GKGVHVITVNDYLARRDAENNRPLFE  148 (908)
T ss_pred             CcCchHHh--cchHhcCCccccccCCCCchHHHHHHHHHHHhc-----------CCCEEEEeCCHHHHHHHHHHHHHHHH
Confidence            67777774  333334566888999999999999999866553           33499999999999999999999999


Q ss_pred             hCCCC
Q psy7786         246 ALPIG  250 (252)
Q Consensus       246 ~~~i~  250 (252)
                      .+|++
T Consensus       149 ~lGls  153 (908)
T PRK13107        149 FLGLT  153 (908)
T ss_pred             hcCCe
Confidence            99875

>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=97.08  E-value=0.0018  Score=53.96  Aligned_cols=61  Identities=18%  Similarity=0.127  Sum_probs=43.9

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhC
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL   73 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~   73 (252)
                      ...+++|.|..|||||.+.+-=+...+.....       +.-+.|++++|+..|..+.+.+.......
T Consensus        12 ~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~-------~~~~Il~lTft~~aa~e~~~ri~~~l~~~   72 (315)
T PF00580_consen   12 TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGV-------PPERILVLTFTNAAAQEMRERIRELLEEE   72 (315)
T ss_dssp             -SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSS-------TGGGEEEEESSHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCEEEEeCCCCCchHHHHHHHHHhhccccC-------ChHHheecccCHHHHHHHHHHHHHhcCcc
Confidence            36789999999999998765555544433211       23459999999999999999998875543

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 ....

>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=97.04  E-value=0.0012  Score=53.85  Aligned_cols=73  Identities=19%  Similarity=0.280  Sum_probs=57.6

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      +++=.||=|||++-.+|..-..+.           |..+=|++...-||.+=++.+..+-+.+|  +++...+++.+.++
T Consensus        94 laEm~TGEGKTli~~l~a~~~AL~-----------G~~V~vvT~NdyLA~RD~~~~~~~y~~LG--lsv~~~~~~~~~~~  160 (266)
T PF07517_consen   94 LAEMKTGEGKTLIAALPAALNALQ-----------GKGVHVVTSNDYLAKRDAEEMRPFYEFLG--LSVGIITSDMSSEE  160 (266)
T ss_dssp             EEEESTTSHHHHHHHHHHHHHHTT-----------SS-EEEEESSHHHHHHHHHHHHHHHHHTT----EEEEETTTEHHH
T ss_pred             eEEecCCCCcHHHHHHHHHHHHHh-----------cCCcEEEeccHHHhhccHHHHHHHHHHhh--hccccCccccCHHH
Confidence            889999999999999988765543           45688999999999999999999999999  88888888876544


Q ss_pred             chhhhh
Q psy7786          91 SLDVIK   96 (252)
Q Consensus        91 ~~~~l~   96 (252)
                      +.+...
T Consensus       161 r~~~Y~  166 (266)
T PF07517_consen  161 RREAYA  166 (266)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            444333

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 ....

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=96.97  E-value=0.0037  Score=45.01  Aligned_cols=55  Identities=40%  Similarity=0.533  Sum_probs=43.5

Q ss_pred             CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       182 ~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      +++++..++|+|||...+..+.......         ...+++|+||++.++++..+.+....+
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~---------~~~~~lv~~p~~~l~~~~~~~~~~~~~   55 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL---------KGGQVLVLAPTRELANQVAERLKELFG   55 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc---------cCCCEEEEcCcHHHHHHHHHHHHHHhh
Confidence            3578899999999998777766544331         245799999999999999998887765

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

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.95  E-value=0.0013  Score=60.54  Aligned_cols=101  Identities=13%  Similarity=0.116  Sum_probs=64.4

Q ss_pred             EcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCcch
Q psy7786          13 IAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSL   92 (252)
Q Consensus        13 ~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~~~   92 (252)
                      .+-+|||||..|+=-+- ..+..          |-++|+++|...|..|+.+.++..   .+ .-.+..++++.+..++.
T Consensus       166 ~~~~GSGKTevyl~~i~-~~l~~----------Gk~vLvLvPEi~lt~q~~~rl~~~---f~-~~~v~~lhS~l~~~~R~  230 (665)
T PRK14873        166 QALPGEDWARRLAAAAA-ATLRA----------GRGALVVVPDQRDVDRLEAALRAL---LG-AGDVAVLSAGLGPADRY  230 (665)
T ss_pred             hcCCCCcHHHHHHHHHH-HHHHc----------CCeEEEEecchhhHHHHHHHHHHH---cC-CCcEEEECCCCCHHHHH
Confidence            34469999999965443 33332          447999999999999998888743   22 13567788887777666


Q ss_pred             hhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          93 DVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        93 ~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +...+-       ..  +...+++.+-.-...-+.+ +..+|.||+
T Consensus       231 ~~w~~~-------~~--G~~~IViGtRSAvFaP~~~-LgLIIvdEE  266 (665)
T PRK14873        231 RRWLAV-------LR--GQARVVVGTRSAVFAPVED-LGLVAIWDD  266 (665)
T ss_pred             HHHHHH-------hC--CCCcEEEEcceeEEeccCC-CCEEEEEcC
Confidence            655441       10  2234455555555555666 776665553

>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=96.90  E-value=0.0043  Score=47.29  Aligned_cols=65  Identities=28%  Similarity=0.303  Sum_probs=47.4

Q ss_pred             ChHHHHhhhhhhh-------cCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHH
Q psy7786         167 PTPIQVQGIPAAL-------SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI  239 (252)
Q Consensus       167 p~~iQ~~~~p~~~-------~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~  239 (252)
                      +.+.|..++..+.       .....++.+++|+|||...+... ..+..             +++++||++.+++|..+.
T Consensus         4 lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~-~~l~~-------------~~l~~~p~~~l~~Q~~~~   69 (184)
T PF04851_consen    4 LRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALI-LELAR-------------KVLIVAPNISLLEQWYDE   69 (184)
T ss_dssp             E-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHH-HHHHC-------------EEEEEESSHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhh-hcccc-------------ceeEecCHHHHHHHHHHH
Confidence            4566777775555       25889999999999998866322 22221             699999999999999998


Q ss_pred             HHHHHh
Q psy7786         240 IQYYCA  245 (252)
Q Consensus       240 l~~l~~  245 (252)
                      +..+..
T Consensus        70 ~~~~~~   75 (184)
T PF04851_consen   70 FDDFGS   75 (184)
T ss_dssp             HHHHST
T ss_pred             HHHhhh
Confidence            865543

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 ....

>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=96.83  E-value=0.0072  Score=50.05  Aligned_cols=73  Identities=22%  Similarity=0.201  Sum_probs=39.7

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      ...+..+++...|+|||...+.-+. .+......     ...-.+||++|. .+..|=.+++.++.....  +++....|
T Consensus        23 ~~~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~-----~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~--~~v~~~~~   93 (299)
T PF00176_consen   23 SPPRGGLLADEMGLGKTITAIALIS-YLKNEFPQ-----RGEKKTLIVVPS-SLLSQWKEEIEKWFDPDS--LRVIIYDG   93 (299)
T ss_dssp             TTT-EEEE---TTSSHHHHHHHHHH-HHHHCCTT-----SS-S-EEEEE-T-TTHHHHHHHHHHHSGT-T--S-EEEESS
T ss_pred             cCCCCEEEEECCCCCchhhhhhhhh-hhhhcccc-----ccccceeEeecc-chhhhhhhhhcccccccc--cccccccc
Confidence            3456789999999999976654433 33322210     011249999999 677777777776654323  56666666


Q ss_pred             Cc
Q psy7786          85 GV   86 (252)
Q Consensus        85 ~~   86 (252)
                      +.
T Consensus        94 ~~   95 (299)
T PF00176_consen   94 DS   95 (299)
T ss_dssp             SC
T ss_pred             cc
Confidence            54

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.

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=96.72  E-value=0.004  Score=58.49  Aligned_cols=23  Identities=13%  Similarity=0.179  Sum_probs=20.2

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      ....|||.|-.+..++..+.|++
T Consensus       259 ~GdILvFLpG~~EI~~~~~~L~~  281 (845)
T COG1643         259 SGSILVFLPGQREIERTAEWLEK  281 (845)
T ss_pred             CCCEEEECCcHHHHHHHHHHHHh
Confidence            55799999999999999998886

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

Probab=96.61  E-value=0.0059  Score=48.48  Aligned_cols=62  Identities=18%  Similarity=0.170  Sum_probs=39.0

Q ss_pred             ccCCCc-EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           4 YRNSRD-IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         4 ~~~g~d-~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      +++..+ .++++|.||||| ..+.-++..+.....  ......+.+.|+++||.+-+.++.+.+.+
T Consensus        13 ~~~~~~~~~i~GpPGTGKT-~~l~~~i~~~~~~~~--~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   13 ALSSNGITLIQGPPGTGKT-TTLASIIAQLLQRFK--SRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             HCTSSE-EEEE-STTSSHH-HHHHHHHHHH---------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             HHcCCCCEEEECCCCCChH-HHHHHHHHHhccchh--hhhhhccccceeecCCchhHHHHHHHHHh
Confidence            455666 899999999999 333445555421100  00112466799999999999998887776

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

Probab=96.61  E-value=0.012  Score=56.67  Aligned_cols=73  Identities=21%  Similarity=0.212  Sum_probs=53.3

Q ss_pred             CChHHHHhhhhh----hhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHH-H
Q psy7786         166 KPTPIQVQGIPA----ALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI-I  240 (252)
Q Consensus       166 ~p~~iQ~~~~p~----~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~-l  240 (252)
                      .+.+-|..+...    .-.+...++-++||+|||++|++|.+.....+          +.+++|-++|+.+-+|+... +
T Consensus       257 e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~----------~~~vvIsT~T~~LQ~Ql~~kDi  326 (928)
T PRK08074        257 EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKK----------EEPVVISTYTIQLQQQLLEKDI  326 (928)
T ss_pred             cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhcc----------CCeEEEEcCCHHHHHHHHHhhH
Confidence            466667765533    34567888999999999999999998654432          45799999999999998663 4


Q ss_pred             HHHHhhCC
Q psy7786         241 QYYCAALP  248 (252)
Q Consensus       241 ~~l~~~~~  248 (252)
                      -.+.+-++
T Consensus       327 P~L~~~~~  334 (928)
T PRK08074        327 PLLQKIFP  334 (928)
T ss_pred             HHHHHHcC
Confidence            44444333

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

Probab=96.59  E-value=0.0086  Score=52.82  Aligned_cols=65  Identities=25%  Similarity=0.313  Sum_probs=51.6

Q ss_pred             CChHHHHhhhhhhhc----CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALS----GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~----~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .+.+.|..++.+...    ++..+++.+||+|||...+..+.. +             ..++||+||+++++.|.++.+.
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~-~-------------~~~~Lvlv~~~~L~~Qw~~~~~  101 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAE-L-------------KRSTLVLVPTKELLDQWAEALK  101 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHH-h-------------cCCEEEEECcHHHHHHHHHHHH
Confidence            578899999988887    899999999999999876554432 1             2239999999999999987665


Q ss_pred             HHH
Q psy7786         242 YYC  244 (252)
Q Consensus       242 ~l~  244 (252)
                      +..
T Consensus       102 ~~~  104 (442)
T COG1061         102 KFL  104 (442)
T ss_pred             Hhc
Confidence            443

>PRK09694 helicase Cas3; Provisional

Probab=96.52  E-value=0.014  Score=55.55  Aligned_cols=73  Identities=21%  Similarity=0.107  Sum_probs=53.0

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|.++|..+........-+++.++||+|||.+.+.... .+...        ....++++-.||+..+++++++++++.
T Consensus       285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~-~l~~~--------~~~~gi~~aLPT~Atan~m~~Rl~~~~  355 (878)
T PRK09694        285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAW-RLIDQ--------GLADSIIFALPTQATANAMLSRLEALA  355 (878)
T ss_pred             CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHH-HHHHh--------CCCCeEEEECcHHHHHHHHHHHHHHHH
Confidence            368899997654433445688999999999998766544 33322        123568888899999999999998765


Q ss_pred             hh
Q psy7786         245 AA  246 (252)
Q Consensus       245 ~~  246 (252)
                      ..
T Consensus       356 ~~  357 (878)
T PRK09694        356 SK  357 (878)
T ss_pred             HH
Confidence            54

>KOG0354|consensus

Probab=96.51  E-value=0.0067  Score=55.67  Aligned_cols=69  Identities=23%  Similarity=0.233  Sum_probs=53.5

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      .+...|.....+.+ |++++++.|||+|||.....-+..++-..         ...++++++||+-++.|....++..+
T Consensus        62 ~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~---------p~~KiVF~aP~~pLv~QQ~a~~~~~~  130 (746)
T KOG0354|consen   62 ELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWR---------PKGKVVFLAPTRPLVNQQIACFSIYL  130 (746)
T ss_pred             cccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcC---------CcceEEEeeCCchHHHHHHHHHhhcc
Confidence            45567887777777 99999999999999997666665544322         23689999999999999887766554

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=96.42  E-value=0.041  Score=51.20  Aligned_cols=49  Identities=14%  Similarity=0.141  Sum_probs=36.8

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      .++.||.|||||.+..-++-+.+..          ..-++|+++-.|.|+.+..+.++.
T Consensus        52 ~vVRSpMGTGKTtaLi~wLk~~l~~----------~~~~VLvVShRrSL~~sL~~rf~~  100 (824)
T PF02399_consen   52 LVVRSPMGTGKTTALIRWLKDALKN----------PDKSVLVVSHRRSLTKSLAERFKK  100 (824)
T ss_pred             EEEECCCCCCcHHHHHHHHHHhccC----------CCCeEEEEEhHHHHHHHHHHHHhh
Confidence            5789999999997764443332221          245799999999999999887764

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

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=96.35  E-value=0.0075  Score=53.07  Aligned_cols=48  Identities=21%  Similarity=0.295  Sum_probs=36.0

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      ++-.+.+-||||||.+.. -++..+             +--+||++|.+-||-|.+.+++.|
T Consensus        33 ~~QtLLGvTGSGKTfT~A-nVI~~~-------------~rPtLV~AhNKTLAaQLy~Efk~f   80 (663)
T COG0556          33 KHQTLLGVTGSGKTFTMA-NVIAKV-------------QRPTLVLAHNKTLAAQLYSEFKEF   80 (663)
T ss_pred             eeeEEeeeccCCchhHHH-HHHHHh-------------CCCeEEEecchhHHHHHHHHHHHh
Confidence            356778899999996642 222222             123899999999999999999987

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=96.24  E-value=0.017  Score=54.12  Aligned_cols=76  Identities=17%  Similarity=0.188  Sum_probs=59.4

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++.-.||=|||++..+|+.-..+.           |-.+=|++..--||..=.+++..+-+.+|  +++.+...+.+..+
T Consensus        95 IAEMkTGEGKTLvAtLpayLnAL~-----------GkgVhVVTvNdYLA~RDae~mg~vy~fLG--LsvG~i~~~~~~~~  161 (925)
T PRK12903         95 VAEMKTGEGKTITSIAPVYLNALT-----------GKGVIVSTVNEYLAERDAEEMGKVFNFLG--LSVGINKANMDPNL  161 (925)
T ss_pred             eeeecCCCCccHHHHHHHHHHHhc-----------CCceEEEecchhhhhhhHHHHHHHHHHhC--CceeeeCCCCChHH
Confidence            688899999999999998755443           44578889999999999999999999999  78887777655554


Q ss_pred             chhhhhhcccc
Q psy7786          91 SLDVIKKGIQY  101 (252)
Q Consensus        91 ~~~~l~~~~~i  101 (252)
                      +.+..  .+||
T Consensus       162 rr~aY--~~DI  170 (925)
T PRK12903        162 KREAY--ACDI  170 (925)
T ss_pred             HHHhc--cCCC
Confidence            44443  3566

>KOG0949|consensus

Probab=96.07  E-value=0.006  Score=57.23  Aligned_cols=116  Identities=17%  Similarity=0.230  Sum_probs=66.3

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +-.+..+++.|||-+|||.. ....++..++...        .--+++++||++|.+|+...+..--. .....+.....
T Consensus       523 vDr~eSavIVAPTSaGKTfi-sfY~iEKVLResD--------~~VVIyvaPtKaLVnQvsa~VyaRF~-~~t~~rg~sl~  592 (1330)
T KOG0949|consen  523 VDRNESAVIVAPTSAGKTFI-SFYAIEKVLRESD--------SDVVIYVAPTKALVNQVSANVYARFD-TKTFLRGVSLL  592 (1330)
T ss_pred             hhcccceEEEeeccCCceec-cHHHHHHHHhhcC--------CCEEEEecchHHHhhhhhHHHHHhhc-cCccccchhhH
Confidence            34577899999999999953 2345666666542        23489999999999999776643221 11113444455


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChh---HHHHHhhhhceeeccCC
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQ---VHDIIRRNLRILVEGDD  138 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~---~~~~l~~~~~~~V~de~  138 (252)
                      |....+-+....  .|.+   ..|   -|+.+.++.-.   ...... .++++|-||-
T Consensus       593 g~ltqEYsinp~--nCQV---LIT---vPecleslLlspp~~q~~ce-rIRyiIfDEV  641 (1330)
T KOG0949|consen  593 GDLTQEYSINPW--NCQV---LIT---VPECLESLLLSPPHHQKFCE-RIRYIIFDEV  641 (1330)
T ss_pred             hhhhHHhcCCch--hceE---EEE---chHHHHHHhcCchhhhhhhh-cceEEEechh
Confidence            554433333211  2444   233   36555444333   222333 3788887763

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.04  E-value=0.0087  Score=50.31  Aligned_cols=47  Identities=19%  Similarity=0.178  Sum_probs=31.9

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      +..+++++++++|||||| +++=.++..+....        ..-+.+.+-.+.||.
T Consensus       141 v~~~~nilI~G~tGSGKT-Tll~aL~~~i~~~~--------~~~rivtiEd~~El~  187 (323)
T PRK13833        141 IDSRLNIVISGGTGSGKT-TLANAVIAEIVASA--------PEDRLVILEDTAEIQ  187 (323)
T ss_pred             HHcCCeEEEECCCCCCHH-HHHHHHHHHHhcCC--------CCceEEEecCCcccc
Confidence            456889999999999999 34344444443211        134678888888874

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.95  E-value=0.009  Score=50.25  Aligned_cols=47  Identities=34%  Similarity=0.350  Sum_probs=33.3

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      +..+++++++++|||||| +++-.++..+....        ..-+.+++-.+.||.
T Consensus       145 v~~~~~ilI~G~tGSGKT-Tll~aL~~~~~~~~--------~~~rivtIEd~~El~  191 (319)
T PRK13894        145 VRAHRNILVIGGTGSGKT-TLVNAIINEMVIQD--------PTERVFIIEDTGEIQ  191 (319)
T ss_pred             HHcCCeEEEECCCCCCHH-HHHHHHHHhhhhcC--------CCceEEEEcCCCccc
Confidence            567899999999999999 55555555442111        234678888888874

>PF13245 AAA_19: Part of AAA domain

Probab=95.95  E-value=0.07  Score=34.71  Aligned_cols=52  Identities=19%  Similarity=0.254  Sum_probs=35.4

Q ss_pred             CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       182 ~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      .-+++.+++|+|||...+--....+....      .. +.+++++++|+..++.+.+.+
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l~~~~~------~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAELLAARA------DP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHHhc------CC-CCeEEEECCCHHHHHHHHHHH
Confidence            33555999999998654433333332111      11 557999999999999999888

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.87  E-value=0.0057  Score=51.92  Aligned_cols=44  Identities=20%  Similarity=0.104  Sum_probs=30.6

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      +..+++++++++|||||| +++-.++..+-.           .-+.+.+-.+.||.
T Consensus       159 v~~~~nilI~G~tGSGKT-Tll~aLl~~i~~-----------~~rivtiEd~~El~  202 (344)
T PRK13851        159 VVGRLTMLLCGPTGSGKT-TMSKTLISAIPP-----------QERLITIEDTLELV  202 (344)
T ss_pred             HHcCCeEEEECCCCccHH-HHHHHHHcccCC-----------CCCEEEECCCcccc
Confidence            457899999999999999 443444443321           23567788888874

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

Probab=95.85  E-value=0.048  Score=49.58  Aligned_cols=88  Identities=25%  Similarity=0.247  Sum_probs=68.3

Q ss_pred             CCHHHHHHH-HHCCCCCChHHHHhhhhhhhcC------CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         151 LPESLVRAL-EAKGIKKPTPIQVQGIPAALSG------RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       151 l~~~l~~~l-~~~~~~~p~~iQ~~~~p~~~~~------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ...++.+.+ +...| .+|..|..++.....+      -+-+++.+.|||||...++.++.-+.           .|.|+
T Consensus       247 ~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~-----------~G~Q~  314 (677)
T COG1200         247 ANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIE-----------AGYQA  314 (677)
T ss_pred             ccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHH-----------cCCee
Confidence            444444444 44444 6888999888666543      35678889999999999998887554           37789


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ...+||--+|+|-++.++++.+.++++
T Consensus       315 ALMAPTEILA~QH~~~~~~~l~~~~i~  341 (677)
T COG1200         315 ALMAPTEILAEQHYESLRKWLEPLGIR  341 (677)
T ss_pred             EEeccHHHHHHHHHHHHHHHhhhcCCe
Confidence            999999999999999999999988764

>KOG0352|consensus

Probab=95.82  E-value=0.024  Score=48.65  Aligned_cols=63  Identities=27%  Similarity=0.409  Sum_probs=52.0

Q ss_pred             ChHHHHhhhhhhhcC-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         167 PTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      -++.|..++-....+ .|+.++.+||+||.++|-+|.|..              +.-+|||.|-..+.....+.|.++
T Consensus        21 Ks~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~--------------~gITIV~SPLiALIkDQiDHL~~L   84 (641)
T KOG0352|consen   21 KSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH--------------GGITIVISPLIALIKDQIDHLKRL   84 (641)
T ss_pred             cChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh--------------CCeEEEehHHHHHHHHHHHHHHhc
Confidence            467888888776654 799999999999999999999852              336999999999998888887654

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=95.79  E-value=0.038  Score=51.62  Aligned_cols=57  Identities=21%  Similarity=0.118  Sum_probs=44.2

Q ss_pred             CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHH-HHHHHHhhCC
Q psy7786         182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD-IIQYYCAALP  248 (252)
Q Consensus       182 ~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~-~l~~l~~~~~  248 (252)
                      ...++-|+||+|||++|++|.+......          +.+++|=++|+.|-+|+.. -+-.+.+.++
T Consensus        50 ~~lviEAgTGtGKTlaYLlPai~~A~~~----------~k~vVIST~T~~LQeQL~~kDlP~l~~~l~  107 (697)
T PRK11747         50 RILVIEAGTGVGKTLSYLLAGIPIARAE----------KKKLVISTATVALQEQLVSKDLPLLLKISG  107 (697)
T ss_pred             ceEEEECCCCcchhHHHHHHHHHHHHHc----------CCeEEEEcCCHHHHHHHHhhhhhHHHHHcC
Confidence            5678889999999999999998765532          4569999999999999864 3444444443

>KOG4150|consensus

Probab=95.79  E-value=0.012  Score=52.36  Aligned_cols=52  Identities=15%  Similarity=-0.033  Sum_probs=42.6

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD   64 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~   64 (252)
                      +-+|+++++...|-+||.+.|.+..+..+....         ....+++.||+|++....+
T Consensus       298 ~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~---------~s~~~~~~~~~~~~~~~~~  349 (1034)
T KOG4150|consen  298 ASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH---------ATNSLLPSEMVEHLRNGSK  349 (1034)
T ss_pred             hhhcccccccchhhcCCccCcccchhhhhhcCc---------ccceecchhHHHHhhccCC
Confidence            457999999999999999999999887766544         3357999999999987654

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.78  E-value=0.016  Score=48.37  Aligned_cols=47  Identities=28%  Similarity=0.305  Sum_probs=32.0

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      +..+++++++++|||||| +++-.++..+....        ..-+.+++--+.||.
T Consensus       129 v~~~~~ilI~G~tGSGKT-Tll~al~~~i~~~~--------~~~ri~tiEd~~El~  175 (299)
T TIGR02782       129 VLARKNILVVGGTGSGKT-TLANALLAEIAKND--------PTDRVVIIEDTRELQ  175 (299)
T ss_pred             HHcCCeEEEECCCCCCHH-HHHHHHHHHhhccC--------CCceEEEECCchhhc
Confidence            456789999999999999 44344444443211        134688888888874

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.

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=95.71  E-value=0.032  Score=53.14  Aligned_cols=52  Identities=23%  Similarity=0.215  Sum_probs=40.9

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      ..++.+.-+||||||.+|+-.++......         +..+.||++|+.+.-..+.+.+.
T Consensus        59 ~~n~~~~M~TGtGKT~~~~~~i~~l~~~~---------~~~~fii~vp~~aI~egv~~~l~  110 (986)
T PRK15483         59 KANIDIKMETGTGKTYVYTRLMYELHQKY---------GLFKFIIVVPTPAIKEGTRNFIQ  110 (986)
T ss_pred             cceEEEEeCCCCCHHHHHHHHHHHHHHHc---------CCcEEEEEeCCHHHHHHHHHHhh
Confidence            35789999999999999988776543221         35679999999999888876664

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

Probab=95.67  E-value=0.051  Score=42.41  Aligned_cols=46  Identities=15%  Similarity=0.161  Sum_probs=30.9

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI   65 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~   65 (252)
                      =.+++++.|||||.+ +-.+...+..          .+.++++++||...+..+.+.
T Consensus        20 ~~~l~G~aGtGKT~~-l~~~~~~~~~----------~g~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen   20 VSVLQGPAGTGKTTL-LKALAEALEA----------AGKRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             EEEEEESTTSTHHHH-HHHHHHHHHH----------TT--EEEEESSHHHHHHHHHH
T ss_pred             EEEEEECCCCCHHHH-HHHHHHHHHh----------CCCeEEEECCcHHHHHHHHHh
Confidence            367889999999954 2334444333          246799999999988776554

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.65  E-value=0.0089  Score=50.58  Aligned_cols=44  Identities=23%  Similarity=0.133  Sum_probs=30.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      +..+++++++++|||||| +++-.++..+-.           .-+.+.+--+.||.
T Consensus       157 v~~~~nili~G~tgSGKT-Tll~aL~~~ip~-----------~~ri~tiEd~~El~  200 (332)
T PRK13900        157 VISKKNIIISGGTSTGKT-TFTNAALREIPA-----------IERLITVEDAREIV  200 (332)
T ss_pred             HHcCCcEEEECCCCCCHH-HHHHHHHhhCCC-----------CCeEEEecCCCccc
Confidence            346899999999999999 444444544422           23567776777764

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

Probab=95.59  E-value=0.065  Score=49.80  Aligned_cols=71  Identities=28%  Similarity=0.308  Sum_probs=55.1

Q ss_pred             CCCChHHHHhhhh----hhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHH
Q psy7786         164 IKKPTPIQVQGIP----AALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI  239 (252)
Q Consensus       164 ~~~p~~iQ~~~~p----~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~  239 (252)
                      ...|.+.|..++.    +...+...++-++||+|||++|+.|.+......          +.+++|-++|+.+-+|+.+.
T Consensus        13 ~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~----------~~~viist~t~~lq~q~~~~   82 (654)
T COG1199          13 GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE----------GKKVIISTRTKALQEQLLEE   82 (654)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHc----------CCcEEEECCCHHHHHHHHHh
Confidence            3456777777663    333456699999999999999999999876543          35699999999999999888


Q ss_pred             HHHHH
Q psy7786         240 IQYYC  244 (252)
Q Consensus       240 l~~l~  244 (252)
                      ...+.
T Consensus        83 ~~~~~   87 (654)
T COG1199          83 DLPIH   87 (654)
T ss_pred             hcchh
Confidence            76653

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

Probab=95.55  E-value=0.032  Score=50.37  Aligned_cols=68  Identities=29%  Similarity=0.432  Sum_probs=59.4

Q ss_pred             CCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         163 GIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       163 ~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      |+....+-|...+...++++|.++..+||.||+++|-+|.+..              ..-+||+.|-..|-+...+.+++
T Consensus        14 Gy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~--------------~G~TLVVSPLiSLM~DQV~~l~~   79 (590)
T COG0514          14 GYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL--------------EGLTLVVSPLISLMKDQVDQLEA   79 (590)
T ss_pred             CccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc--------------CCCEEEECchHHHHHHHHHHHHH
Confidence            6777888899999999999999999999999999999999853              12489999999999988888877


Q ss_pred             HH
Q psy7786         243 YC  244 (252)
Q Consensus       243 l~  244 (252)
                      .|
T Consensus        80 ~G   81 (590)
T COG0514          80 AG   81 (590)
T ss_pred             cC
Confidence            65

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=95.54  E-value=0.027  Score=41.35  Aligned_cols=50  Identities=18%  Similarity=0.200  Sum_probs=37.8

Q ss_pred             cEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         183 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       183 ~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      -.++..-+|+|||-..+..++....+.          +.++||+.|||-.++.+.+.|+.
T Consensus         6 ~~~~d~hpGaGKTr~vlp~~~~~~i~~----------~~rvLvL~PTRvva~em~~aL~~   55 (148)
T PF07652_consen    6 LTVLDLHPGAGKTRRVLPEIVREAIKR----------RLRVLVLAPTRVVAEEMYEALKG   55 (148)
T ss_dssp             EEEEE--TTSSTTTTHHHHHHHHHHHT----------T--EEEEESSHHHHHHHHHHTTT
T ss_pred             eeEEecCCCCCCcccccHHHHHHHHHc----------cCeEEEecccHHHHHHHHHHHhc
Confidence            345667789999998888887766654          45799999999999999999864

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 ....

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

Probab=95.42  E-value=0.064  Score=52.59  Aligned_cols=70  Identities=21%  Similarity=0.164  Sum_probs=51.6

Q ss_pred             CChHHHHhhhhhhh----c-CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAAL----S-GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~----~-~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      .+.+.|..++..+.    . .+..+++.+||+|||... +.++..++...        ...++|+++++++|+.|..+.+
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~~--------~~~rVLfLvDR~~L~~Qa~~~F  483 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKAK--------RFRRILFLVDRSALGEQAEDAF  483 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhcC--------ccCeEEEEecHHHHHHHHHHHH
Confidence            46778888886654    2 367899999999999763 33444444321        2458999999999999999998


Q ss_pred             HHHH
Q psy7786         241 QYYC  244 (252)
Q Consensus       241 ~~l~  244 (252)
                      +.++
T Consensus       484 ~~~~  487 (1123)
T PRK11448        484 KDTK  487 (1123)
T ss_pred             Hhcc
Confidence            8653

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=95.39  E-value=0.073  Score=49.92  Aligned_cols=72  Identities=19%  Similarity=0.156  Sum_probs=56.5

Q ss_pred             CCChHHHHhhh----hhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGI----PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       165 ~~p~~iQ~~~~----p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ..+.+.|...+    .++-.+.+.++-+|||+|||++.+.+.+.+.....        ..++.++.+.|...-.|+.++|
T Consensus         9 ~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~--------~~~kIiy~sRThsQl~q~i~El   80 (705)
T TIGR00604         9 EKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP--------EVRKIIYASRTHSQLEQATEEL   80 (705)
T ss_pred             CCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc--------ccccEEEEcccchHHHHHHHHH
Confidence            33466777665    44457789999999999999999999998765421        2357888889999999999999


Q ss_pred             HHHH
Q psy7786         241 QYYC  244 (252)
Q Consensus       241 ~~l~  244 (252)
                      +++.
T Consensus        81 k~~~   84 (705)
T TIGR00604        81 RKLM   84 (705)
T ss_pred             Hhhh
Confidence            9865

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).

>KOG1803|consensus

Probab=95.24  E-value=0.029  Score=50.15  Aligned_cols=45  Identities=22%  Similarity=0.169  Sum_probs=35.0

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI   65 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~   65 (252)
                      .++++|+|||||.+...-+.|.+..           +-++|+.+||++-..-+.+.
T Consensus       204 ~~I~GPPGTGKT~TlvEiI~qlvk~-----------~k~VLVcaPSn~AVdNiver  248 (649)
T KOG1803|consen  204 LIIHGPPGTGKTRTLVEIISQLVKQ-----------KKRVLVCAPSNVAVDNIVER  248 (649)
T ss_pred             eEeeCCCCCCceeeHHHHHHHHHHc-----------CCeEEEEcCchHHHHHHHHH
Confidence            6789999999998877666665543           34699999999877666664

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=95.15  E-value=0.17  Score=46.91  Aligned_cols=77  Identities=25%  Similarity=0.244  Sum_probs=62.7

Q ss_pred             HCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         161 AKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      +..-..|..+|....-.++.|+  +....||+|||+...+|.....+.           |.++-|++++-.||.+=++++
T Consensus        73 R~lg~r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~-----------G~~VhvvT~NdyLA~RDae~m  139 (764)
T PRK12326         73 RTLGLRPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ-----------GRRVHVITVNDYLARRDAEWM  139 (764)
T ss_pred             HHcCCCcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc-----------CCCeEEEcCCHHHHHHHHHHH
Confidence            3334478999998887777764  567889999999988888765443           567999999999999999999


Q ss_pred             HHHHhhCCCC
Q psy7786         241 QYYCAALPIG  250 (252)
Q Consensus       241 ~~l~~~~~i~  250 (252)
                      ..+-+.+|++
T Consensus       140 ~~ly~~LGLs  149 (764)
T PRK12326        140 GPLYEALGLT  149 (764)
T ss_pred             HHHHHhcCCE
Confidence            9999998875

>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=95.10  E-value=0.12  Score=43.05  Aligned_cols=71  Identities=20%  Similarity=0.098  Sum_probs=49.4

Q ss_pred             hHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         168 TPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       168 ~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ++-|..++..  ....+++.+..|+|||...+.-++..+....       ....+.|+++.|+..|..+.+.+.......
T Consensus         2 ~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~-------~~~~~Il~lTft~~aa~e~~~ri~~~l~~~   72 (315)
T PF00580_consen    2 TDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG-------VPPERILVLTFTNAAAQEMRERIRELLEEE   72 (315)
T ss_dssp             -HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS-------STGGGEEEEESSHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhcccc-------CChHHheecccCHHHHHHHHHHHHHhcCcc
Confidence            3456655554  5678999999999999987665555444321       123469999999999999999998876544

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 ....

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

Probab=95.08  E-value=0.021  Score=50.79  Aligned_cols=48  Identities=33%  Similarity=0.432  Sum_probs=36.6

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      ++++.|+||||||.+|++|.+-   ...         + -++|.-|-.||........++.
T Consensus        46 h~lvig~tgSGKt~~~viP~ll---~~~---------~-s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   46 HVLVIGPTGSGKTTSFVIPNLL---NYP---------G-SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             EEEEEeCCCCCccceeeHhHHH---hcc---------C-CEEEEECCCcHHHHHHHHHHHC
Confidence            6999999999999999999762   211         2 4788889999987766555443

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

>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=95.08  E-value=0.018  Score=47.25  Aligned_cols=44  Identities=27%  Similarity=0.214  Sum_probs=30.1

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      ..+.+++++++|||||| +++-.++..+...          .-+.+++-.+.|+-
T Consensus       125 ~~~~~ili~G~tGSGKT-T~l~all~~i~~~----------~~~iv~iEd~~E~~  168 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKT-TLLNALLEEIPPE----------DERIVTIEDPPELR  168 (270)
T ss_dssp             HTTEEEEEEESTTSSHH-HHHHHHHHHCHTT----------TSEEEEEESSS-S-
T ss_pred             ccceEEEEECCCccccc-hHHHHHhhhcccc----------ccceEEecccccee
Confidence            45789999999999999 4445556555443          23578887777763

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 ....

>TIGR00376 DNA helicase, putative

Probab=95.06  E-value=0.066  Score=49.46  Aligned_cols=50  Identities=18%  Similarity=0.192  Sum_probs=36.2

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      ..+++++|+|||||.+-. -++..+..          .+.++|+++||..-+.++.+.+..
T Consensus       174 ~~~lI~GpPGTGKT~t~~-~ii~~~~~----------~g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRTLV-ELIRQLVK----------RGLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CeEEEEcCCCCCHHHHHH-HHHHHHHH----------cCCCEEEEcCcHHHHHHHHHHHHh
Confidence            568899999999995443 33333332          245799999999988888776654

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.

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=95.02  E-value=0.14  Score=48.06  Aligned_cols=79  Identities=22%  Similarity=0.192  Sum_probs=62.2

Q ss_pred             HHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786         159 LEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD  238 (252)
Q Consensus       159 l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~  238 (252)
                      ..+..-..|..+|...-=++..|+  +....||+|||+...+|.+...+.           |.++-|+++|-.||.+=++
T Consensus        73 ~~R~~g~~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~-----------G~~v~vvT~neyLA~Rd~e  139 (796)
T PRK12906         73 AKRVLGLRPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT-----------GKGVHVVTVNEYLSSRDAT  139 (796)
T ss_pred             HHHHhCCCCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc-----------CCCeEEEeccHHHHHhhHH
Confidence            333334478888886655555554  888899999999988888765543           5679999999999999999


Q ss_pred             HHHHHHhhCCCC
Q psy7786         239 IIQYYCAALPIG  250 (252)
Q Consensus       239 ~l~~l~~~~~i~  250 (252)
                      ++..+-+.+|++
T Consensus       140 ~~~~~~~~LGl~  151 (796)
T PRK12906        140 EMGELYRWLGLT  151 (796)
T ss_pred             HHHHHHHhcCCe
Confidence            999999999875

>TIGR00603 rad25 DNA repair helicase rad25

Probab=95.00  E-value=0.086  Score=49.09  Aligned_cols=65  Identities=23%  Similarity=0.295  Sum_probs=49.5

Q ss_pred             CChHHHHhhhhhhhc-C--CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALS-G--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~-~--~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .+.+.|..++...+. +  +.-+++.++|+|||...+..+.. +             ..++||+||+..+++|..+.+.+
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l-------------~k~tLILvps~~Lv~QW~~ef~~  320 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-V-------------KKSCLVLCTSAVSVEQWKQQFKM  320 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-h-------------CCCEEEEeCcHHHHHHHHHHHHH
Confidence            456788888877663 3  36788999999999986543321 1             23499999999999999999987


Q ss_pred             HH
Q psy7786         243 YC  244 (252)
Q Consensus       243 l~  244 (252)
                      +.
T Consensus       321 ~~  322 (732)
T TIGR00603       321 WS  322 (732)
T ss_pred             hc
Confidence            74

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).

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.95  E-value=0.011  Score=51.09  Aligned_cols=47  Identities=26%  Similarity=0.248  Sum_probs=36.1

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      ++++.|+||||||.+|++|-+-..             .-.++|.-|--|+........+.
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-------------~~s~vv~D~Kge~~~~t~~~r~~   47 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-------------PGSVVVLDPKGENFELTSEHRRA   47 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-------------CCCEEEEccchhHHHHHHHHHHH
Confidence            578999999999999999976321             12488888999998776655443

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.

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=94.90  E-value=0.085  Score=51.04  Aligned_cols=60  Identities=25%  Similarity=0.243  Sum_probs=44.7

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      .|+.-+|.--+|||||++-+-..-. +....        ..+.+++|+-.++|-.|+.+.+..++....
T Consensus       272 ~~~~G~IWHtqGSGKTlTm~~~A~~-l~~~~--------~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~  331 (962)
T COG0610         272 DGKGGYIWHTQGSGKTLTMFKLARL-LLELP--------KNPKVLFVVDRKDLDDQTSDEFQSFGKVAF  331 (962)
T ss_pred             cCCceEEEeecCCchHHHHHHHHHH-HHhcc--------CCCeEEEEechHHHHHHHHHHHHHHHHhhh
Confidence            4556788889999999774332221 11211        478899999999999999999999987654

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.81  E-value=0.098  Score=44.93  Aligned_cols=22  Identities=23%  Similarity=0.138  Sum_probs=18.3

Q ss_pred             ccCCCcEEEEcCCCchHHHHhH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFV   25 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~   25 (252)
                      +-+|+.+++.+|||+|||.+..
T Consensus       134 ~~~g~ii~lvGptGvGKTTtia  155 (374)
T PRK14722        134 MERGGVFALMGPTGVGKTTTTA  155 (374)
T ss_pred             ccCCcEEEEECCCCCCHHHHHH
Confidence            4568899999999999996654

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

Probab=94.80  E-value=0.068  Score=41.02  Aligned_cols=47  Identities=23%  Similarity=0.292  Sum_probs=27.3

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT   62 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~   62 (252)
                      +.+++++++.+++|+|||... ..+...+...          +..++++ .+.+|..++
T Consensus        44 ~~~~~~l~l~G~~G~GKThLa-~ai~~~~~~~----------g~~v~f~-~~~~L~~~l   90 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTHLA-VAIANEAIRK----------GYSVLFI-TASDLLDEL   90 (178)
T ss_dssp             -SC--EEEEEESTTSSHHHHH-HHHHHHHHHT----------T--EEEE-EHHHHHHHH
T ss_pred             cccCeEEEEEhhHhHHHHHHH-HHHHHHhccC----------CcceeEe-ecCceeccc
Confidence            457889999999999999543 3334444442          3346665 566666544

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.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=94.76  E-value=0.11  Score=49.70  Aligned_cols=107  Identities=15%  Similarity=0.181  Sum_probs=70.8

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      |+.-+||-|||++..+|+.-..+.           |-.+=|++-.==||..=.+++..+-+.+|  +++.+...+.+..+
T Consensus       155 IAEM~TGEGKTLvatlp~yLnAL~-----------G~gVHvVTvNDYLA~RDaewm~p~y~flG--LtVg~i~~~~~~~~  221 (1025)
T PRK12900        155 ISEMATGEGKTLVSTLPTFLNALT-----------GRGVHVVTVNDYLAQRDKEWMNPVFEFHG--LSVGVILNTMRPEE  221 (1025)
T ss_pred             ccccCCCCCcchHhHHHHHHHHHc-----------CCCcEEEeechHhhhhhHHHHHHHHHHhC--CeeeeeCCCCCHHH
Confidence            567789999999999999866655           33466777788899999999999999999  78887766544443


Q ss_pred             chhhhhhcccccCCccccccCCcc-----ccCCC-hhHHHHHhhhhceeeccCC
Q psy7786          91 SLDVIKKGIQYNDPIKTSWRAPRC-----ILSLP-DQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        91 ~~~~l~~~~~i~~~i~t~~~~p~~-----l~~~~-~~~~~~l~~~~~~~V~de~  138 (252)
                      +++  .-.+||      .|+|...     |-+.. ........+...|.+.||.
T Consensus       222 Rr~--aY~~DI------tYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEv  267 (1025)
T PRK12900        222 RRE--QYLCDI------TYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEV  267 (1025)
T ss_pred             HHH--hCCCcc------eecCCCccccccchhccccchhhhhccCCceEEEech
Confidence            332  334666      3444432     22222 2223333445777776664

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.64  E-value=0.025  Score=51.69  Aligned_cols=50  Identities=26%  Similarity=0.182  Sum_probs=39.2

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .+++++.||||||||..|++|-+-..             +-.++|+=|--|+........++.
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnLL~~-------------~~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNLLFW-------------EDSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhHHhC-------------CCCEEEEeCcHHHHHHHHHHHHHC
Confidence            34799999999999999999987542             113888889999997777655543

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=94.58  E-value=0.12  Score=48.01  Aligned_cols=48  Identities=23%  Similarity=0.306  Sum_probs=37.0

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      +.++.+-||||||+... -+++.+             +-.+|||+|++.+|.|+++.++.|.
T Consensus        31 ~~~l~Gvtgs~kt~~~a-~~~~~~-------------~~p~Lvi~~n~~~A~ql~~el~~f~   78 (655)
T TIGR00631        31 HQTLLGVTGSGKTFTMA-NVIAQV-------------NRPTLVIAHNKTLAAQLYNEFKEFF   78 (655)
T ss_pred             cEEEECCCCcHHHHHHH-HHHHHh-------------CCCEEEEECCHHHHHHHHHHHHHhC
Confidence            66789999999997643 233321             1238999999999999999998874

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

>KOG0922|consensus

Probab=94.43  E-value=0.33  Score=44.16  Aligned_cols=51  Identities=14%  Similarity=0.143  Sum_probs=34.1

Q ss_pred             chhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         193 GKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       193 gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      ..+..|+-..+..+++=...     +...-.|||-+..+..+.+.+.|++..+.++
T Consensus       236 ~p~~dYv~a~~~tv~~Ih~~-----E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~  286 (674)
T KOG0922|consen  236 EPTADYVDAALITVIQIHLT-----EPPGDILVFLTGQEEIEAACELLRERAKSLP  286 (674)
T ss_pred             CCchhhHHHHHHHHHHHHcc-----CCCCCEEEEeCCHHHHHHHHHHHHHHhhhcc
Confidence            34455666665555443221     2233699999999999999999988766654

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=94.43  E-value=0.23  Score=46.87  Aligned_cols=72  Identities=25%  Similarity=0.277  Sum_probs=57.6

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .|..+|...  .+.-....+....||.|||+...+|..-..+.           |..+-|++.+..||.+-++++..+-+
T Consensus        76 r~ydvQlig--~l~L~~G~IaEm~TGEGKTL~a~l~ayl~aL~-----------G~~VhVvT~NdyLA~RD~e~m~pvy~  142 (870)
T CHL00122         76 RHFDVQLIG--GLVLNDGKIAEMKTGEGKTLVATLPAYLNALT-----------GKGVHIVTVNDYLAKRDQEWMGQIYR  142 (870)
T ss_pred             CCCchHhhh--hHhhcCCccccccCCCCchHHHHHHHHHHHhc-----------CCceEEEeCCHHHHHHHHHHHHHHHH
Confidence            577887754  44445667888999999999988888643332           45699999999999999999999999


Q ss_pred             hCCCC
Q psy7786         246 ALPIG  250 (252)
Q Consensus       246 ~~~i~  250 (252)
                      .+|+.
T Consensus       143 ~LGLs  147 (870)
T CHL00122        143 FLGLT  147 (870)
T ss_pred             HcCCc
Confidence            99875

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=94.39  E-value=0.13  Score=44.31  Aligned_cols=82  Identities=13%  Similarity=0.259  Sum_probs=49.0

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      ..++-+.+.+|||.|||.+-.==.-...+....        .--++|-+-|-=.+  -.+.++.+++-+++++  .+++.
T Consensus       201 ~~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~--------~kVaiITtDtYRIG--A~EQLk~Ya~im~vp~--~vv~~  268 (407)
T COG1419         201 EQKRVIALVGPTGVGKTTTLAKLAARYVMLKKK--------KKVAIITTDTYRIG--AVEQLKTYADIMGVPL--EVVYS  268 (407)
T ss_pred             ccCcEEEEECCCCCcHHHHHHHHHHHHHhhccC--------cceEEEEeccchhh--HHHHHHHHHHHhCCce--EEecC
Confidence            458899999999999997644222222222211        22366666554333  2355788888888544  44566


Q ss_pred             CcccCcchhhhhhc
Q psy7786          85 GVPMNQSLDVIKKG   98 (252)
Q Consensus        85 ~~~~~~~~~~l~~~   98 (252)
                      .....+.+..+++.
T Consensus       269 ~~el~~ai~~l~~~  282 (407)
T COG1419         269 PKELAEAIEALRDC  282 (407)
T ss_pred             HHHHHHHHHHhhcC
Confidence            65566666666653

>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=94.37  E-value=0.54  Score=38.49  Aligned_cols=76  Identities=25%  Similarity=0.330  Sum_probs=56.2

Q ss_pred             CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         162 KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       162 ~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      ..-..|..+|....=.+..|+  ++...||.|||+...++.....+.           |..+=|+|.+..||.+=++++.
T Consensus        73 ~~g~~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~-----------G~~V~vvT~NdyLA~RD~~~~~  139 (266)
T PF07517_consen   73 TLGLRPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ-----------GKGVHVVTSNDYLAKRDAEEMR  139 (266)
T ss_dssp             HTS----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT-----------SS-EEEEESSHHHHHHHHHHHH
T ss_pred             HcCCcccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh-----------cCCcEEEeccHHHhhccHHHHH
Confidence            334478899988776665555  888999999999877777655443           5569999999999999999999


Q ss_pred             HHHhhCCCC
Q psy7786         242 YYCAALPIG  250 (252)
Q Consensus       242 ~l~~~~~i~  250 (252)
                      .+-+.+|++
T Consensus       140 ~~y~~LGls  148 (266)
T PF07517_consen  140 PFYEFLGLS  148 (266)
T ss_dssp             HHHHHTT--
T ss_pred             HHHHHhhhc
Confidence            999999875

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 ....

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=94.29  E-value=0.12  Score=48.58  Aligned_cols=58  Identities=21%  Similarity=0.200  Sum_probs=40.3

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA   71 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~   71 (252)
                      ...++|.|..|||||.+-+-=+. ++.....-      ..-+.|+++-|+..|..+.+.+.++..
T Consensus        22 ~g~~lV~AgaGSGKT~vl~~Ria-~Li~~~~v------~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773         22 LGNMLVLAGAGSGKTRVLVHRIA-WLMQVENA------SPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHH-HHHHcCCC------ChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            45789999999999966433333 22221110      123589999999999999998887653

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=94.28  E-value=0.055  Score=50.23  Aligned_cols=57  Identities=16%  Similarity=0.197  Sum_probs=42.6

Q ss_pred             ccCCC-cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           4 YRNSR-DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         4 ~~~g~-d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      +.+|+ -+++.-.||||||-+. +.++.+|+....        --++|+|+-.+.|..|.+..+..+
T Consensus       181 f~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~--------~KRVLFLaDR~~Lv~QA~~af~~~  238 (875)
T COG4096         181 FSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGW--------VKRVLFLADRNALVDQAYGAFEDF  238 (875)
T ss_pred             HhcCCceEEEEEecCCCcceeH-HHHHHHHHhcch--------hheeeEEechHHHHHHHHHHHHHh
Confidence            33444 3888889999999654 455667766542        347999999999999999876655

>PRK11054 helD DNA helicase IV; Provisional

Probab=94.22  E-value=0.1  Score=48.53  Aligned_cols=58  Identities=22%  Similarity=0.237  Sum_probs=39.1

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      ...+++|.|..|||||...+-=+ .+++.....      ..-+.|+++.||..|..+.+.+....
T Consensus       208 ~~~~~lV~agaGSGKT~vl~~r~-ayLl~~~~~------~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        208 GEDSLLVLAGAGSGKTSVLVARA-GWLLARGQA------QPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCCeEEEEeCCCCHHHHHHHHH-HHHHHhCCC------CHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            34568999999999996543332 223322111      23369999999999999988776543

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

Probab=94.10  E-value=0.25  Score=43.47  Aligned_cols=67  Identities=22%  Similarity=0.219  Sum_probs=47.1

Q ss_pred             ChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         167 PTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      |...|....-..+. ++.+++.|||-|||+-.+.-+...+...         .+ ++|+++||+-|+.|-++.+++..
T Consensus        16 ~R~YQ~~i~a~al~-~NtLvvlPTGLGKT~IA~~V~~~~l~~~---------~~-kvlfLAPTKPLV~Qh~~~~~~v~   82 (542)
T COG1111          16 PRLYQLNIAAKALF-KNTLVVLPTGLGKTFIAAMVIANRLRWF---------GG-KVLFLAPTKPLVLQHAEFCRKVT   82 (542)
T ss_pred             HHHHHHHHHHHHhh-cCeEEEecCCccHHHHHHHHHHHHHHhc---------CC-eEEEecCCchHHHHHHHHHHHHh
Confidence            44455543333333 4899999999999987655554443332         23 89999999999999999887654

>TIGR01075 uvrD DNA helicase II

Probab=94.07  E-value=0.12  Score=48.49  Aligned_cols=58  Identities=21%  Similarity=0.188  Sum_probs=40.4

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA   71 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~   71 (252)
                      +.+++|.|..|||||.+-+-=+. ++.....-      ..-+.|+++-|+..|..+.+.+..+..
T Consensus        17 ~g~~lV~AgaGSGKT~~L~~Ria-~Li~~~~v------~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075        17 PGNLLVLAGAGSGKTRVLTHRIA-WLLSVENA------SPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHH-HHHHcCCC------CHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            45799999999999966433332 33322110      123589999999999999998887754

Designed to identify uvrD members of the uvrD/rep subfamily.

>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=94.06  E-value=0.082  Score=41.45  Aligned_cols=45  Identities=27%  Similarity=0.207  Sum_probs=28.7

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSREL   58 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreL   58 (252)
                      ++..-+++.+|.|||||+..+...++.+....         .-+.+|.-|+.+.
T Consensus        17 ~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~---------~~kiii~Rp~v~~   61 (205)
T PF02562_consen   17 LNNDLVIVNGPAGTGKTFLALAAALELVKEGE---------YDKIIITRPPVEA   61 (205)
T ss_dssp             HH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS----------SEEEEEE-S--T
T ss_pred             HhCCeEEEECCCCCcHHHHHHHHHHHHHHhCC---------CcEEEEEecCCCC
Confidence            34456889999999999888888888876633         3467777787764

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

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

Probab=93.96  E-value=0.22  Score=47.97  Aligned_cols=70  Identities=23%  Similarity=0.232  Sum_probs=53.8

Q ss_pred             HCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         161 AKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ..+| .+-++|..++-.+-.+..++++++|++|||...-..+-..+.           .+.+++.-+|.+.+.+|.++.+
T Consensus       115 ~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~-----------~~qrviYTsPIKALsNQKyrdl  182 (1041)
T COG4581         115 EYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALR-----------DGQRVIYTSPIKALSNQKYRDL  182 (1041)
T ss_pred             hCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHH-----------cCCceEeccchhhhhhhHHHHH
Confidence            3344 466789999999999999999999999999864433332222           1446999999999999999887


Q ss_pred             HH
Q psy7786         241 QY  242 (252)
Q Consensus       241 ~~  242 (252)
                      ..
T Consensus       183 ~~  184 (1041)
T COG4581         183 LA  184 (1041)
T ss_pred             HH
Confidence            64

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=93.93  E-value=0.15  Score=47.49  Aligned_cols=57  Identities=18%  Similarity=0.078  Sum_probs=40.0

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      +..++|.|..|||||.+-+-=+...+.....       ..-+.|+++-|+.-|..+.+.+..+.
T Consensus        15 ~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v-------~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919         15 TGPCLVLAGAGSGKTRVITNKIAHLIRGCGY-------QARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHhcCC-------CHHHeeeEechHHHHHHHHHHHHHHh
Confidence            4578899999999997654444333322111       12358999999999999988887653

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=93.90  E-value=0.21  Score=40.08  Aligned_cols=49  Identities=24%  Similarity=0.226  Sum_probs=33.0

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc---CcHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC---PSRELARQT   62 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~---ptreLa~q~   62 (252)
                      +..|.=+++.|++|+||| +|++-++.......         +..+++++   |..++..+.
T Consensus        10 l~~G~l~lI~G~~G~GKT-~~~~~~~~~~~~~~---------g~~vly~s~E~~~~~~~~r~   61 (242)
T cd00984          10 LQPGDLIIIAARPSMGKT-AFALNIAENIAKKQ---------GKPVLFFSLEMSKEQLLQRL   61 (242)
T ss_pred             CCCCeEEEEEeCCCCCHH-HHHHHHHHHHHHhC---------CCceEEEeCCCCHHHHHHHH
Confidence            456778899999999999 66665554444431         34578887   556665544

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.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=93.81  E-value=0.17  Score=47.09  Aligned_cols=57  Identities=18%  Similarity=0.097  Sum_probs=40.2

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      +.+++|.|..|||||.+-+-=+...+.....       ..-+.|+++.|+.-|.++.+.+....
T Consensus        14 ~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~-------~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074        14 TGPCLVLAGAGSGKTRVITNKIAYLIQNCGY-------KARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHhcCC-------CHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            5689999999999996654444333322111       12358999999999999988887654

Designed to identify rep members of the uvrD/rep subfamily.

>PF12846 AAA_10: AAA-like domain

Probab=93.71  E-value=0.14  Score=42.25  Aligned_cols=42  Identities=26%  Similarity=0.385  Sum_probs=30.0

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR   60 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~   60 (252)
                      +++++.++||||||.+.. .++..+...          +..++++=|..+...
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~~----------g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIRR----------GPRVVIFDPKGDYSP   43 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHHc----------CCCEEEEcCCchHHH
Confidence            689999999999996555 555555442          456788877766554

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=93.69  E-value=0.33  Score=46.16  Aligned_cols=73  Identities=23%  Similarity=0.235  Sum_probs=57.9

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|..+|...  ...-...-+.-..||+|||+...+|.+...+.           |.++-|+++|-.||.+=++++..+-
T Consensus        81 m~~ydVQliG--g~~Lh~G~iaEM~TGEGKTLvA~l~a~l~al~-----------G~~VhvvT~ndyLA~RD~e~m~~l~  147 (913)
T PRK13103         81 MRHFDVQLIG--GMTLHEGKIAEMRTGEGKTLVGTLAVYLNALS-----------GKGVHVVTVNDYLARRDANWMRPLY  147 (913)
T ss_pred             CCcchhHHHh--hhHhccCccccccCCCCChHHHHHHHHHHHHc-----------CCCEEEEeCCHHHHHHHHHHHHHHh
Confidence            4678887744  33334556778899999999988888755443           5679999999999999999999999


Q ss_pred             hhCCCC
Q psy7786         245 AALPIG  250 (252)
Q Consensus       245 ~~~~i~  250 (252)
                      +.+|++
T Consensus       148 ~~lGl~  153 (913)
T PRK13103        148 EFLGLS  153 (913)
T ss_pred             cccCCE
Confidence            998874

>PRK08181 transposase; Validated

Probab=93.66  E-value=0.16  Score=41.71  Aligned_cols=47  Identities=17%  Similarity=0.244  Sum_probs=28.7

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH   63 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~   63 (252)
                      -+++++++.+|+|+|||.... .+.+.+...          +..++++ +..+|..++.
T Consensus       104 ~~~~nlll~Gp~GtGKTHLa~-Aia~~a~~~----------g~~v~f~-~~~~L~~~l~  150 (269)
T PRK08181        104 AKGANLLLFGPPGGGKSHLAA-AIGLALIEN----------GWRVLFT-RTTDLVQKLQ  150 (269)
T ss_pred             hcCceEEEEecCCCcHHHHHH-HHHHHHHHc----------CCceeee-eHHHHHHHHH
Confidence            367899999999999993322 222233222          3345544 5677776664

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=93.61  E-value=0.051  Score=50.25  Aligned_cols=48  Identities=21%  Similarity=0.134  Sum_probs=37.1

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      .++++.||||||||..|++|-+-..             .-.++|+=|--|+........++
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~-------------~gS~VV~DpKGE~~~~Ta~~R~~  187 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF-------------KGSVIALDVKGELFELTSRARKA  187 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC-------------CCCEEEEeCCchHHHHHHHHHHh
Confidence            3899999999999999999976432             11488888999998777655543

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=93.59  E-value=0.11  Score=45.44  Aligned_cols=49  Identities=20%  Similarity=0.240  Sum_probs=33.7

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ   61 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q   61 (252)
                      |.-...+++++.++||||||.. +-.++..+...          +-+++|+=|..|+...
T Consensus        37 ~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~~----------~~~~vi~D~kg~~~~~   85 (410)
T cd01127          37 PKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRAR----------GDRAIIYDPNGGFVSK   85 (410)
T ss_pred             CcchhhccEEEEcCCCCCHHHH-HHHHHHHHHhc----------CCCEEEEeCCcchhHh
Confidence            4455678999999999999964 44445444332          3358888888886543

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.

>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=93.57  E-value=0.067  Score=44.93  Aligned_cols=45  Identities=27%  Similarity=0.208  Sum_probs=30.9

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      .+..+++++++++|||||| +++.+++..+-.           ..+.+.+--|.|+-
T Consensus       139 ~ie~~~siii~G~t~sGKT-t~lnall~~Ip~-----------~~rivtIEdt~E~~  183 (312)
T COG0630         139 AIEARKSIIICGGTASGKT-TLLNALLDFIPP-----------EERIVTIEDTPELK  183 (312)
T ss_pred             HHHcCCcEEEECCCCCCHH-HHHHHHHHhCCc-----------hhcEEEEecccccc
Confidence            3567899999999999999 555555544432           23466666666653

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

Probab=93.52  E-value=0.043  Score=45.56  Aligned_cols=18  Identities=50%  Similarity=0.584  Sum_probs=15.3

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ++.-|+++.+|||||||+
T Consensus        95 L~KSNILLiGPTGsGKTl  112 (408)
T COG1219          95 LSKSNILLIGPTGSGKTL  112 (408)
T ss_pred             eeeccEEEECCCCCcHHH
Confidence            345589999999999995

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=93.35  E-value=0.29  Score=47.03  Aligned_cols=61  Identities=23%  Similarity=0.176  Sum_probs=50.2

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      |+.-.||-|||++..+|+.-..+..           -.+=|++..==||..=.+++..+-+.+|  +++.+...
T Consensus       186 IAEM~TGEGKTLvAtlp~yLnAL~G-----------kgVHvVTVNDYLA~RDaewmgply~fLG--Lsvg~i~~  246 (1112)
T PRK12901        186 IAEMATGEGKTLVATLPVYLNALTG-----------NGVHVVTVNDYLAKRDSEWMGPLYEFHG--LSVDCIDK  246 (1112)
T ss_pred             eeeecCCCCchhHHHHHHHHHHHcC-----------CCcEEEEechhhhhccHHHHHHHHHHhC--CceeecCC
Confidence            6677899999999999998766653           3467778888899999999999999999  77776654

>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=93.35  E-value=0.14  Score=44.34  Aligned_cols=53  Identities=26%  Similarity=0.291  Sum_probs=35.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD   64 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~   64 (252)
                      ||.-...+++++.+.||||||. ++-+++..+...          +-+++|.=|.-|.....++
T Consensus         9 l~~~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~----------g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen    9 LPKDSENRHILIIGATGSGKTQ-AIRHLLDQIRAR----------GDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             E-GGGGGG-EEEEE-TTSSHHH-HHHHHHHHHHHT----------T-EEEEEEETTHHHHHH--
T ss_pred             cccchhhCcEEEECCCCCCHHH-HHHHHHHHHHHc----------CCEEEEEECCchHHHHhcC
Confidence            3556678899999999999996 446677666553          4468888899887654443

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.

>KOG0953|consensus

Probab=93.31  E-value=0.13  Score=45.74  Aligned_cols=55  Identities=27%  Similarity=0.254  Sum_probs=42.5

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCC
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGG   85 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~   85 (252)
                      ++-++||.||||.-    .++++....           .+++--|.|-||..|++.+...    |  +.|...+|.
T Consensus       194 i~H~GPTNSGKTy~----ALqrl~~ak-----------sGvycGPLrLLA~EV~~r~na~----g--ipCdL~TGe  248 (700)
T KOG0953|consen  194 IMHVGPTNSGKTYR----ALQRLKSAK-----------SGVYCGPLRLLAHEVYDRLNAL----G--IPCDLLTGE  248 (700)
T ss_pred             EEEeCCCCCchhHH----HHHHHhhhc-----------cceecchHHHHHHHHHHHhhhc----C--CCccccccc
Confidence            55678999999943    467776544           4789999999999999988755    3  677777776

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=93.29  E-value=0.28  Score=43.58  Aligned_cols=51  Identities=20%  Similarity=0.256  Sum_probs=37.5

Q ss_pred             CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         181 GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       181 ~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .+...+...||+|||+.... ++    .+.         +.-+||++|.+-+|-|++.+++.|=+
T Consensus        32 ~~~QtLLGvTGSGKTfT~An-VI----~~~---------~rPtLV~AhNKTLAaQLy~Efk~fFP   82 (663)
T COG0556          32 LKHQTLLGVTGSGKTFTMAN-VI----AKV---------QRPTLVLAHNKTLAAQLYSEFKEFFP   82 (663)
T ss_pred             ceeeEEeeeccCCchhHHHH-HH----HHh---------CCCeEEEecchhHHHHHHHHHHHhCc
Confidence            36778888999999875321 11    111         22389999999999999999998744

>cd01131 PilT Pilus retraction ATPase PilT

Probab=93.22  E-value=0.12  Score=40.27  Aligned_cols=22  Identities=23%  Similarity=0.416  Sum_probs=15.6

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +++++|||||||... -.++..+
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~   25 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYI   25 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHh
Confidence            688999999999543 3344444

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.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=93.15  E-value=0.066  Score=49.50  Aligned_cols=48  Identities=21%  Similarity=0.153  Sum_probs=37.5

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      .++++.||||||||..|++|-+-..   .          -.++|.=|--|+.......-++
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~---~----------~S~VV~D~KGEl~~~Ta~~R~~  192 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTW---P----------GSAIVHDIKGENWQLTAGFRAR  192 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhC---C----------CCEEEEeCcchHHHHHHHHHHh
Confidence            5899999999999999999976432   1          1388888999998776655443

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=93.11  E-value=0.074  Score=44.61  Aligned_cols=20  Identities=40%  Similarity=0.396  Sum_probs=17.1

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..|+++++.++||||||..
T Consensus       141 v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH
Confidence            44689999999999999943

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.

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

Probab=93.09  E-value=0.095  Score=43.27  Aligned_cols=26  Identities=23%  Similarity=0.369  Sum_probs=20.2

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhh
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQE   36 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~   36 (252)
                      +++.+|||||||.+ +..+++++..+.
T Consensus       128 ILVTGpTGSGKSTT-lAamId~iN~~~  153 (353)
T COG2805         128 ILVTGPTGSGKSTT-LAAMIDYINKHK  153 (353)
T ss_pred             EEEeCCCCCcHHHH-HHHHHHHHhccC
Confidence            78999999999954 466778776543

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=93.06  E-value=0.26  Score=44.53  Aligned_cols=61  Identities=16%  Similarity=0.187  Sum_probs=40.0

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHh
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA   72 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~   72 (252)
                      ++=+++++..|||||.+.+== +..++.....  ..  ..-.+||+.|.|-++.-+.+++-.|++.
T Consensus       226 ~~ilVVQGaAGSGKTtiALHR-vAyLlY~~R~--~l--~~k~vlvl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         226 NKILVVQGAAGSGKTTIALHR-VAYLLYGYRG--PL--QAKPVLVLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             CCeEEEecCCCCCchhHHHHH-HHHHHhcccc--cc--ccCceEEEcCcHHHHHHHHHhchhhccC
Confidence            455899999999999654211 1122222111  11  1223999999999999999999888754

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

Probab=93.04  E-value=0.088  Score=48.32  Aligned_cols=49  Identities=24%  Similarity=0.194  Sum_probs=37.2

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .++++.||||||||..+++|-+-   .-.         + .++++=|..|++..+...-++.
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL---~~~---------g-S~VV~DpKgE~~~~Ta~~R~~~  260 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTAL---KYG---------G-PLVCLDPSTEVAPMVCEHRRQA  260 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhh---cCC---------C-CEEEEEChHHHHHHHHHHHHHc
Confidence            58999999999999999999642   211         1 3788889999987776544443

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.

>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=92.98  E-value=0.12  Score=41.57  Aligned_cols=22  Identities=32%  Similarity=0.602  Sum_probs=17.8

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMF   31 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~   31 (252)
                      .+++.+++||||| +|++-++..
T Consensus        15 r~viIG~sGSGKT-~li~~lL~~   36 (241)
T PF04665_consen   15 RMVIIGKSGSGKT-TLIKSLLYY   36 (241)
T ss_pred             eEEEECCCCCCHH-HHHHHHHHh
Confidence            6889999999999 666666644

This is thought to be an ATPase involved in viral DNA packaging [].

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=92.91  E-value=0.37  Score=39.20  Aligned_cols=50  Identities=18%  Similarity=0.205  Sum_probs=33.9

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      +++++++.+++|+|||.-.. .+-+.+..          .+.+++ .+++.||+.++.....
T Consensus       104 ~~~nl~l~G~~G~GKThLa~-Ai~~~l~~----------~g~sv~-f~~~~el~~~Lk~~~~  153 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAI-AIGNELLK----------AGISVL-FITAPDLLSKLKAAFD  153 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHH-HHHHHHHH----------cCCeEE-EEEHHHHHHHHHHHHh
Confidence            68899999999999994432 23344432          144555 5578889888766544

>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=92.90  E-value=0.21  Score=38.20  Aligned_cols=48  Identities=25%  Similarity=0.275  Sum_probs=29.2

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      +++.+++|||||. +.+-++.....          .+..++|++ +-|-..++.+.++.+
T Consensus         2 ~li~G~~G~GKT~-l~~~~~~~~~~----------~g~~v~~~s-~e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTT-FALQFLYAGLA----------RGEPGLYVT-LEESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHH-HHHHHHHHHHH----------CCCcEEEEE-CCCCHHHHHHHHHHc
Confidence            6889999999993 33333322222          244577775 445666666655544

A related protein is found in archaea.

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

Probab=92.87  E-value=0.29  Score=45.70  Aligned_cols=69  Identities=28%  Similarity=0.313  Sum_probs=49.3

Q ss_pred             hHHHHhhhhhhhcC----CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH-H
Q psy7786         168 TPIQVQGIPAALSG----RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ-Y  242 (252)
Q Consensus       168 ~~iQ~~~~p~~~~~----~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~-~  242 (252)
                      ..-|..+...+...    ...++...||||||..|+ ..+...+.+          |.++||++|-..+..|+.+.++ +
T Consensus       200 n~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl-~~i~~~L~~----------GkqvLvLVPEI~Ltpq~~~rf~~r  268 (730)
T COG1198         200 NQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYL-EAIAKVLAQ----------GKQVLVLVPEIALTPQLLARFKAR  268 (730)
T ss_pred             CHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHH-HHHHHHHHc----------CCEEEEEeccccchHHHHHHHHHH
Confidence            34555555554433    678899999999998774 444444443          6789999999999999998886 4


Q ss_pred             HHhhC
Q psy7786         243 YCAAL  247 (252)
Q Consensus       243 l~~~~  247 (252)
                      |+..+
T Consensus       269 Fg~~v  273 (730)
T COG1198         269 FGAKV  273 (730)
T ss_pred             hCCCh
Confidence            55443

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=92.81  E-value=0.42  Score=46.18  Aligned_cols=49  Identities=22%  Similarity=0.137  Sum_probs=33.2

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII   66 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~   66 (252)
                      .-++++-..|.|||.-..+-+-+.+....         .-++|||||+ .|..|=..++
T Consensus       170 ~R~LLADEvGLGKTIeAglil~~l~~~g~---------~~rvLIVvP~-sL~~QW~~El  218 (956)
T PRK04914        170 PRVLLADEVGLGKTIEAGMIIHQQLLTGR---------AERVLILVPE-TLQHQWLVEM  218 (956)
T ss_pred             CCEEEEeCCcCcHHHHHHHHHHHHHHcCC---------CCcEEEEcCH-HHHHHHHHHH
Confidence            35889999999999776555444333221         2369999998 6876654444

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=92.75  E-value=0.083  Score=37.74  Aligned_cols=17  Identities=35%  Similarity=0.427  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCchHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a   23 (252)
                      +..+++.+|+|||||..
T Consensus         2 ~~~~~l~G~~G~GKTtl   18 (148)
T smart00382        2 GEVILIVGPPGSGKTTL   18 (148)
T ss_pred             CCEEEEECCCCCcHHHH
Confidence            67899999999999944

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.

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

Probab=92.68  E-value=0.61  Score=36.73  Aligned_cols=72  Identities=21%  Similarity=0.233  Sum_probs=46.8

Q ss_pred             hHHHHhhhhhhhcCCc-EEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         168 TPIQVQGIPAALSGRD-IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       168 ~~iQ~~~~p~~~~~~~-~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .+-|..++...+.... .++.+++|+|||.... .++..+.....  ......+.++|+.++|..-++.+.+.+.+
T Consensus         3 n~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~--~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    3 NESQREAIQSALSSNGITLIQGPPGTGKTTTLA-SIIAQLLQRFK--SRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             -HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHH-HHHHHH---------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHcCCCCEEEECCCCCChHHHHH-HHHHHhccchh--hhhhhccccceeecCCchhHHHHHHHHHh
Confidence            3567888888888887 8899999999985422 33333321000  00113466899999999999999988876

>PRK06921 hypothetical protein; Provisional

Probab=92.67  E-value=0.51  Score=38.70  Aligned_cols=49  Identities=20%  Similarity=0.076  Sum_probs=29.6

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI   65 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~   65 (252)
                      .+..+++.+++|+|||... ..+.+.+....         +..++++. ..++..++...
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~~---------g~~v~y~~-~~~l~~~l~~~  164 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRKK---------GVPVLYFP-FVEGFGDLKDD  164 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhhc---------CceEEEEE-HHHHHHHHHHH
Confidence            4678999999999999322 23344443321         34566654 55666665443

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=92.50  E-value=0.084  Score=48.75  Aligned_cols=45  Identities=29%  Similarity=0.270  Sum_probs=35.2

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI   65 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~   65 (252)
                      +++++.|+||||||..|++|.+-..             +-.++|+=|-.|+.......
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~~-------------~~S~VV~D~KGE~~~~Tag~  220 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLSW-------------GHSSVITDLKGELWALTAGW  220 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhhC-------------CCCEEEEeCcHHHHHHHHHH
Confidence            5799999999999999999987421             22488899999997655443

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=92.49  E-value=0.31  Score=48.66  Aligned_cols=56  Identities=27%  Similarity=0.249  Sum_probs=42.2

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .|++++|.|..|||||...+-=++..+....        .--+.|+++=|+.-|..+.+.+..-
T Consensus        13 ~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~--------~~~~il~~tFt~~aa~e~~~ri~~~   68 (1232)
T TIGR02785        13 RGQNILVSASAGSGKTAVLVERIIKKILRGV--------DIDRLLVVTFTNAAAREMKERIEEA   68 (1232)
T ss_pred             CCCCEEEEecCCCcHHHHHHHHHHHHHhcCC--------CHhhEEEEeccHHHHHHHHHHHHHH
Confidence            5889999999999999877666666554321        1125899999999998877777553

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.

>PRK13764 ATPase; Provisional

Probab=92.47  E-value=0.18  Score=46.08  Aligned_cols=27  Identities=22%  Similarity=0.389  Sum_probs=20.7

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      .+++++++++|||||| +++-.+++.+.
T Consensus       256 ~~~~ILIsG~TGSGKT-Tll~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKS-TFAQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHH-HHHHHHHHHHh
Confidence            4678999999999999 45455666554

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

Probab=92.39  E-value=0.36  Score=45.06  Aligned_cols=55  Identities=27%  Similarity=0.223  Sum_probs=41.0

Q ss_pred             CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       182 ~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      +..++..++|+|||...+.-.. .+...        ...+++||++++++|.+|+.+.+++++.
T Consensus       264 ~~gli~~~TGsGKT~t~~~la~-~l~~~--------~~~~~vl~lvdR~~L~~Q~~~~f~~~~~  318 (667)
T TIGR00348       264 RGGLIWHTQGSGKTLTMLFAAR-KALEL--------LKNPKVFFVVDRRELDYQLMKEFQSLQK  318 (667)
T ss_pred             ceeEEEEecCCCccHHHHHHHH-HHHhh--------cCCCeEEEEECcHHHHHHHHHHHHhhCC
Confidence            5688889999999976443322 22221        2357899999999999999999988764

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

>PRK10536 hypothetical protein; Provisional

Probab=92.26  E-value=0.23  Score=40.36  Aligned_cols=45  Identities=13%  Similarity=0.118  Sum_probs=29.7

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE   57 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptre   57 (252)
                      +.++.-+++.+++|||||+.-..-.++.+....         .-+.+|.-|+-+
T Consensus        71 l~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~---------~~kIiI~RP~v~  115 (262)
T PRK10536         71 IESKQLIFATGEAGCGKTWISAAKAAEALIHKD---------VDRIIVTRPVLQ  115 (262)
T ss_pred             HhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCC---------eeEEEEeCCCCC
Confidence            455667889999999999776666665554321         234555557654

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

Probab=92.22  E-value=0.1  Score=40.33  Aligned_cols=21  Identities=33%  Similarity=0.407  Sum_probs=17.8

Q ss_pred             ccCCCcEEEEcCCCchHHHHh
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~   24 (252)
                      +..|+.+++.++||||||...
T Consensus        22 v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130          22 VEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             HhCCCEEEEECCCCCCHHHHH
Confidence            457899999999999999543

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=92.20  E-value=0.24  Score=42.21  Aligned_cols=44  Identities=18%  Similarity=0.135  Sum_probs=26.6

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      .+..+++++|||||||... -.++..+...         .+.+.+.+--..|+.
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~~~---------~~~~i~tiEdp~E~~  164 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYINKN---------AAGHIITIEDPIEYV  164 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhCcC---------CCCEEEEEcCChhhh
Confidence            4667999999999999543 3344444221         123466665555543

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.

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=92.15  E-value=0.11  Score=47.85  Aligned_cols=49  Identities=24%  Similarity=0.198  Sum_probs=36.7

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      ..++++.|+||||||..+++|-+-   .-          +-.++|+=|-.|++..+...-++
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL---~~----------~gS~VV~DpKgEl~~~Ta~~R~~  272 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTAL---KW----------GGPLVVLDPSTEVAPMVSEHRRD  272 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhh---cC----------CCCEEEEeCcHHHHHHHHHHHHH
Confidence            358899999999999999999652   11          11377777999998776664443

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.12  E-value=0.79  Score=39.72  Aligned_cols=62  Identities=26%  Similarity=0.289  Sum_probs=33.0

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc--CcHHHHHHHHHHHHHHHHhCCCCc
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC--PSRELARQTHDIIQYYCAALPIPL   77 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~--ptreLa~q~~~~~~~l~~~~~~~~   77 (252)
                      .++.+++.+|||+|||.+..-=..........       .+-++.+++  +.|.-|..+   ++.+++.+|.++
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~-------~g~~V~lit~Dt~R~aa~eQ---L~~~a~~lgvpv  236 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDD-------KSLNIKIITIDNYRIGAKKQ---IQTYGDIMGIPV  236 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhcc-------CCCeEEEEeccCccHHHHHH---HHHHhhcCCcce
Confidence            35678999999999996543211111111100       133444444  444444333   667777777444

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=92.11  E-value=0.43  Score=44.13  Aligned_cols=54  Identities=20%  Similarity=0.258  Sum_probs=35.7

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHH--HHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE--LARQTHDIIQYYC   70 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptre--La~q~~~~~~~l~   70 (252)
                      ..+++++.++||+|||..+.+ ++......          +..++++=|-.+  |...++..++..+
T Consensus       175 ~~~H~lv~G~TGsGKT~l~~~-l~~q~i~~----------g~~viv~DpKgD~~l~~~~~~~~~~~G  230 (634)
T TIGR03743       175 RVGHTLVLGTTGVGKTRLAEL-LITQDIRR----------GDVVIVIDPKGDADLKRRMRAEAKRAG  230 (634)
T ss_pred             CCCcEEEECCCCCCHHHHHHH-HHHHHHHc----------CCeEEEEeCCCchHHHHHHHHHHHHhC
Confidence            457899999999999977644 44333331          345677777765  6666666665553

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.

>KOG0351|consensus

Probab=92.07  E-value=0.22  Score=47.86  Aligned_cols=72  Identities=32%  Similarity=0.426  Sum_probs=59.1

Q ss_pred             HHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHH
Q psy7786         155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR  234 (252)
Q Consensus       155 l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~  234 (252)
                      +.......|.+...+-|..++.+++.|+|.++..+||.||.++|-+|.+.              .++-+||+.|-..|.+
T Consensus       253 ~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l--------------~~gitvVISPL~SLm~  318 (941)
T KOG0351|consen  253 ELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALL--------------LGGVTVVISPLISLMQ  318 (941)
T ss_pred             HHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeeccccc--------------cCCceEEeccHHHHHH
Confidence            33344555788888999999999999999999999999999999888873              1336899999999888


Q ss_pred             HHHHHH
Q psy7786         235 QTHDII  240 (252)
Q Consensus       235 ~i~~~l  240 (252)
                      .....|
T Consensus       319 DQv~~L  324 (941)
T KOG0351|consen  319 DQVTHL  324 (941)
T ss_pred             HHHHhh
Confidence            777666

>PRK12377 putative replication protein; Provisional

Probab=91.98  E-value=0.49  Score=38.34  Aligned_cols=46  Identities=15%  Similarity=0.214  Sum_probs=27.8

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD   64 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~   64 (252)
                      ..++++.+++|+|||.. +..+.+.+...          +..+++ ++..+|..++..
T Consensus       101 ~~~l~l~G~~GtGKThL-a~AIa~~l~~~----------g~~v~~-i~~~~l~~~l~~  146 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHL-AAAIGNRLLAK----------GRSVIV-VTVPDVMSRLHE  146 (248)
T ss_pred             CCeEEEECCCCCCHHHH-HHHHHHHHHHc----------CCCeEE-EEHHHHHHHHHH
Confidence            35799999999999932 22333444332          333444 456677776654

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=91.97  E-value=0.35  Score=38.87  Aligned_cols=53  Identities=13%  Similarity=0.111  Sum_probs=32.9

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      -.|.-+++.+++|||||.-..--+.+.+ .          ++-.++|++ +-|-..|+.+.+..+
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~~~-~----------~ge~~lyvs-~ee~~~~i~~~~~~~   71 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWNGL-Q----------MGEPGIYVA-LEEHPVQVRRNMAQF   71 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHHH-H----------cCCcEEEEE-eeCCHHHHHHHHHHh
Confidence            3577899999999999942211122222 1          244588887 556666666665544

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.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=91.81  E-value=0.35  Score=41.68  Aligned_cols=28  Identities=29%  Similarity=0.255  Sum_probs=19.9

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      .+..+++++|||||||. ++-.+++.+..
T Consensus       148 ~~GlilI~G~TGSGKTT-~l~al~~~i~~  175 (372)
T TIGR02525       148 AAGLGLICGETGSGKST-LAASIYQHCGE  175 (372)
T ss_pred             cCCEEEEECCCCCCHHH-HHHHHHHHHHh
Confidence            34468999999999994 44456666543

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).

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

Probab=91.78  E-value=0.14  Score=43.14  Aligned_cols=46  Identities=24%  Similarity=0.112  Sum_probs=29.6

Q ss_pred             CCCcEEEEcCCCchHHHH-hHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV-FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD   64 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a-~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~   64 (252)
                      ...++++++.||||||.. +.+..+  +..          .. +++.+--|.||-.+.-.
T Consensus       172 ~r~NILisGGTGSGKTTlLNal~~~--i~~----------~e-RvItiEDtaELql~~ph  218 (355)
T COG4962         172 IRCNILISGGTGSGKTTLLNALSGF--IDS----------DE-RVITIEDTAELQLAHPH  218 (355)
T ss_pred             hceeEEEeCCCCCCHHHHHHHHHhc--CCC----------cc-cEEEEeehhhhccCCCc
Confidence            345999999999999942 222211  111          12 78999889888655433

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=91.76  E-value=0.68  Score=45.11  Aligned_cols=69  Identities=23%  Similarity=0.228  Sum_probs=41.8

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      .+|.+.|++-..|.|||+.- +.++..+.....       ..-..|||+|..-| .|=.+.++++   .+ .+++..++|
T Consensus       186 ~~g~gGILADEMGLGKTlQa-IalL~~L~~~~~-------~~gp~LIVvP~SlL-~nW~~Ei~kw---~p-~l~v~~~~G  252 (1033)
T PLN03142        186 ENGINGILADEMGLGKTLQT-ISLLGYLHEYRG-------ITGPHMVVAPKSTL-GNWMNEIRRF---CP-VLRAVKFHG  252 (1033)
T ss_pred             hcCCCEEEEeCCCccHHHHH-HHHHHHHHHhcC-------CCCCEEEEeChHHH-HHHHHHHHHH---CC-CCceEEEeC
Confidence            46788999999999999753 333333332211       12247999997644 4444444444   34 367777777


Q ss_pred             Cc
Q psy7786          85 GV   86 (252)
Q Consensus        85 ~~   86 (252)
                      ..
T Consensus       253 ~~  254 (1033)
T PLN03142        253 NP  254 (1033)
T ss_pred             CH
Confidence            63

>PRK06526 transposase; Provisional

Probab=91.73  E-value=0.26  Score=40.08  Aligned_cols=20  Identities=20%  Similarity=0.380  Sum_probs=16.9

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..++++++.+|+|+|||..
T Consensus        95 i~~~~nlll~Gp~GtGKThL  114 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHL  114 (254)
T ss_pred             hhcCceEEEEeCCCCchHHH
Confidence            34678999999999999943

>PRK05973 replicative DNA helicase; Provisional

Probab=91.72  E-value=0.35  Score=38.89  Aligned_cols=54  Identities=17%  Similarity=0.226  Sum_probs=30.9

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      +..|.-+++.+++|+||| +|.+=.+.....          ++-+++|++ .=|=..|+.+.+..+
T Consensus        61 l~~Gsl~LIaG~PG~GKT-~lalqfa~~~a~----------~Ge~vlyfS-lEes~~~i~~R~~s~  114 (237)
T PRK05973         61 LKPGDLVLLGARPGHGKT-LLGLELAVEAMK----------SGRTGVFFT-LEYTEQDVRDRLRAL  114 (237)
T ss_pred             CCCCCEEEEEeCCCCCHH-HHHHHHHHHHHh----------cCCeEEEEE-EeCCHHHHHHHHHHc
Confidence            345777899999999999 444443333222          134577775 222234555555443

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=91.70  E-value=0.75  Score=35.37  Aligned_cols=63  Identities=19%  Similarity=0.079  Sum_probs=32.5

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      .|.=+++.|++|+||| +|++-+...+.....-.........+++++..--. ..++.+.+..+.
T Consensus        31 ~g~l~~i~g~~g~GKT-~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~   93 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKT-TLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALL   93 (193)
T ss_dssp             TTSEEEEEECSTSSHH-HHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHH-HHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHh
Confidence            5666899999999999 55555555554321110101113556888764333 445666666554

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=91.68  E-value=0.38  Score=45.10  Aligned_cols=55  Identities=16%  Similarity=0.117  Sum_probs=37.9

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHh
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA   72 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~   72 (252)
                      ++=|.-+||||||.+|+=-|+.. .. ..       +-.+-+|++||.+.-.-+....+...++
T Consensus        76 NiDI~METGTGKTy~YlrtmfeL-hk-~Y-------G~~KFIivVPs~AIkeGv~~~s~~~~eh  130 (985)
T COG3587          76 NIDILMETGTGKTYTYLRTMFEL-HK-KY-------GLFKFIIVVPSLAIKEGVFLTSKETTEH  130 (985)
T ss_pred             eeeEEEecCCCceeeHHHHHHHH-HH-Hh-------CceeEEEEeccHHHHhhhHHHHHHHHHH
Confidence            45567889999999998666642 22 21       4567999999998876655555544443

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=91.65  E-value=0.45  Score=44.89  Aligned_cols=58  Identities=22%  Similarity=0.183  Sum_probs=39.9

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA   71 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~   71 (252)
                      ..+++|.|..|||||.+..-=+...+.....       ..-+.|+++-|+.-|..+.+.+..+..
T Consensus        17 ~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i-------~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073        17 EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNV-------APWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCC-------CHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            4579999999999996654443333321111       112589999999999999888877643

Designed to identify pcrA members of the uvrD/rep subfamily.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=91.65  E-value=0.32  Score=39.62  Aligned_cols=53  Identities=19%  Similarity=0.260  Sum_probs=34.7

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      -.|+-+++.+++||||| .|.+=.+......          +-.+++++ +.|...++.+.+..+
T Consensus        21 p~g~~~lI~G~pGsGKT-~f~~qfl~~~~~~----------ge~vlyvs-~~e~~~~l~~~~~~~   73 (260)
T COG0467          21 PRGSVVLITGPPGTGKT-IFALQFLYEGARE----------GEPVLYVS-TEESPEELLENARSF   73 (260)
T ss_pred             cCCcEEEEEcCCCCcHH-HHHHHHHHHHHhc----------CCcEEEEE-ecCCHHHHHHHHHHc
Confidence            46788999999999999 3433333222221          33466664 777777777777655

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=91.40  E-value=0.15  Score=43.39  Aligned_cols=44  Identities=20%  Similarity=0.179  Sum_probs=29.2

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      +..++++++.++||||||.. +-.++..+..           ..+.+++--+.||.
T Consensus       175 v~~~~~ili~G~tGsGKTTl-l~al~~~i~~-----------~~riv~iEd~~El~  218 (340)
T TIGR03819       175 VAARLAFLISGGTGSGKTTL-LSALLALVAP-----------DERIVLVEDAAELR  218 (340)
T ss_pred             HhCCCeEEEECCCCCCHHHH-HHHHHccCCC-----------CCcEEEECCcceec
Confidence            45678999999999999943 3333333211           23567777888874

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.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=91.35  E-value=0.51  Score=40.38  Aligned_cols=51  Identities=22%  Similarity=0.268  Sum_probs=34.8

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      ++|.+..|||||+.. +-++..+...        ..+..++++++..+|...+++.+..-
T Consensus         4 ~~I~G~aGTGKTvla-~~l~~~l~~~--------~~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    4 ILITGGAGTGKTVLA-LNLAKELQNS--------EEGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             EEEEecCCcCHHHHH-HHHHHHhhcc--------ccCCceEEEEecchHHHHHHHHHhhh
Confidence            688999999999543 2222222111        13567999999999999887777543

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=91.33  E-value=1.6  Score=42.62  Aligned_cols=87  Identities=22%  Similarity=0.218  Sum_probs=64.5

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhcC------CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEE
Q psy7786         152 PESLVRALEAKGIKKPTPIQVQGIPAALSG------RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI  225 (252)
Q Consensus       152 ~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LI  225 (252)
                      ..+..+.+....--.-|+-|..++......      -|-++|...|-|||...+-....-++.           |.|+.|
T Consensus       580 d~~~q~~F~~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~-----------GKQVAv  648 (1139)
T COG1197         580 DTEWQEEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMD-----------GKQVAV  648 (1139)
T ss_pred             ChHHHHHHHhcCCCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcC-----------CCeEEE
Confidence            333455555554445677888888665532      489999999999998877766655443           679999


Q ss_pred             EcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         226 ICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       226 f~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      ++||--||+|=++.+++.=+.+||
T Consensus       649 LVPTTlLA~QHy~tFkeRF~~fPV  672 (1139)
T COG1197         649 LVPTTLLAQQHYETFKERFAGFPV  672 (1139)
T ss_pred             EcccHHhHHHHHHHHHHHhcCCCe
Confidence            999999999999888876666665

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=91.32  E-value=0.18  Score=31.32  Aligned_cols=18  Identities=22%  Similarity=0.231  Sum_probs=14.9

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .|...++.+++|||||..
T Consensus        22 ~g~~tli~G~nGsGKSTl   39 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTL   39 (62)
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            356799999999999953

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

Probab=91.27  E-value=0.34  Score=38.55  Aligned_cols=43  Identities=35%  Similarity=0.380  Sum_probs=29.8

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      ++++.|.+.||||||.+ +--+++.+...         .+...+|+=|.-|=+
T Consensus        23 ~~H~~I~G~TGsGKS~~-~~~ll~~l~~~---------~~~~~ii~D~~GEY~   65 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNT-VKVLLEELLKK---------KGAKVIIFDPHGEYA   65 (229)
T ss_pred             cceEEEECCCCCCHHHH-HHHHHHHHHhc---------CCCCEEEEcCCCcch
Confidence            57899999999999944 34455555531         255678887776644

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

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=91.23  E-value=0.47  Score=37.79  Aligned_cols=18  Identities=22%  Similarity=0.194  Sum_probs=15.4

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      -.|.-+++.+++|+|||.
T Consensus        18 ~~G~~~~i~G~~G~GKT~   35 (229)
T TIGR03881        18 PRGFFVAVTGEPGTGKTI   35 (229)
T ss_pred             cCCeEEEEECCCCCChHH
Confidence            357789999999999983

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=91.21  E-value=0.62  Score=37.29  Aligned_cols=19  Identities=16%  Similarity=0.148  Sum_probs=15.9

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      -.|.-+++.+++|+|||..
T Consensus        22 ~~g~~~~i~G~~G~GKTtl   40 (230)
T PRK08533         22 PAGSLILIEGDESTGKSIL   40 (230)
T ss_pred             CCCcEEEEECCCCCCHHHH
Confidence            4577899999999999943

>PRK06835 DNA replication protein DnaC; Validated

Probab=91.16  E-value=0.63  Score=39.40  Aligned_cols=46  Identities=24%  Similarity=0.249  Sum_probs=28.5

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH   63 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~   63 (252)
                      .++++++.++||+|||.. +..+.+.+...          +..++++ +..+|..++.
T Consensus       182 ~~~~Lll~G~~GtGKThL-a~aIa~~l~~~----------g~~V~y~-t~~~l~~~l~  227 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFL-SNCIAKELLDR----------GKSVIYR-TADELIEILR  227 (329)
T ss_pred             cCCcEEEECCCCCcHHHH-HHHHHHHHHHC----------CCeEEEE-EHHHHHHHHH
Confidence            457899999999999952 22344444432          3456655 4566655543

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=91.15  E-value=1.5  Score=41.84  Aligned_cols=72  Identities=24%  Similarity=0.230  Sum_probs=57.2

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .|..+|..  ....-...-+....||.|||+...+|..-..+.           |..+-|++.+..||.+=++++..+-+
T Consensus        85 r~ydVQli--Ggl~Lh~G~IAEM~TGEGKTL~atlpaylnAL~-----------GkgVhVVTvNdYLA~RDae~m~~vy~  151 (939)
T PRK12902         85 RHFDVQLI--GGMVLHEGQIAEMKTGEGKTLVATLPSYLNALT-----------GKGVHVVTVNDYLARRDAEWMGQVHR  151 (939)
T ss_pred             CcchhHHH--hhhhhcCCceeeecCCCChhHHHHHHHHHHhhc-----------CCCeEEEeCCHHHHHhHHHHHHHHHH
Confidence            67777774  343445566888899999999988888754433           45699999999999999999999999


Q ss_pred             hCCCC
Q psy7786         246 ALPIG  250 (252)
Q Consensus       246 ~~~i~  250 (252)
                      .+|+.
T Consensus       152 ~LGLt  156 (939)
T PRK12902        152 FLGLS  156 (939)
T ss_pred             HhCCe
Confidence            99875

>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=91.09  E-value=0.11  Score=42.79  Aligned_cols=19  Identities=32%  Similarity=0.511  Sum_probs=17.0

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +.+|+.+++++|+|||||.
T Consensus        30 ~~~~~pvLl~G~~GtGKT~   48 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTS   48 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHH
T ss_pred             HHcCCcEEEECCCCCchhH
Confidence            4578999999999999995

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=91.07  E-value=0.44  Score=37.86  Aligned_cols=51  Identities=18%  Similarity=0.122  Sum_probs=28.2

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHH-HHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLP-ILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp-~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      -.|.-+++.+++|||||. |.+= +.+.+...          +-++++++ +-|=..++.+.++
T Consensus        17 p~gs~~li~G~~GsGKT~-l~~q~l~~~~~~~----------ge~vlyvs-~ee~~~~l~~~~~   68 (226)
T PF06745_consen   17 PKGSVVLISGPPGSGKTT-LALQFLYNGLKNF----------GEKVLYVS-FEEPPEELIENMK   68 (226)
T ss_dssp             ETTSEEEEEESTTSSHHH-HHHHHHHHHHHHH----------T--EEEEE-SSS-HHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCcHH-HHHHHHHHhhhhc----------CCcEEEEE-ecCCHHHHHHHHH
Confidence            357789999999999993 3332 22333220          22477777 3333444444444

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 ....

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=91.04  E-value=0.49  Score=39.17  Aligned_cols=19  Identities=32%  Similarity=0.298  Sum_probs=15.9

Q ss_pred             CCCcEEEEcCCCchHHHHh
Q psy7786           6 NSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~   24 (252)
                      .++-+++.+|||+|||.+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~  211 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTL  211 (282)
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            5678999999999999543

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=91.03  E-value=0.49  Score=46.91  Aligned_cols=55  Identities=22%  Similarity=0.280  Sum_probs=41.6

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhh-cCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQE-TKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~-~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      .+.++++.|..|||||.+-..=++..++... .       +--+.|+++-|+.=|.....++.
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~-------~v~~ILvvTFT~aAa~Emk~RI~   70 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPL-------DVDEILVVTFTKAAAAEMKERIR   70 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCC-------ChhHeeeeeccHHHHHHHHHHHH
Confidence            4679999999999999887777777776632 1       22358999999988877666553

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

Probab=91.03  E-value=0.45  Score=38.95  Aligned_cols=40  Identities=33%  Similarity=0.239  Sum_probs=25.7

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC   53 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~   53 (252)
                      +..|.-+++.+++|+||| +|++-+...+...         .+-.+++++
T Consensus        27 ~~~g~~~~i~g~~G~GKT-~l~~~~~~~~~~~---------~g~~vl~iS   66 (271)
T cd01122          27 LRKGELIILTAGTGVGKT-TFLREYALDLITQ---------HGVRVGTIS   66 (271)
T ss_pred             EcCCcEEEEEcCCCCCHH-HHHHHHHHHHHHh---------cCceEEEEE
Confidence            356778899999999999 4444433333222         144577776

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

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.00  E-value=1.1  Score=39.05  Aligned_cols=19  Identities=37%  Similarity=0.373  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCchHHHHhH
Q psy7786           7 SRDIIGIAFTGSGKTLVFV   25 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~   25 (252)
                      ++.+.+.+|||+|||.+..
T Consensus       241 ~~vI~LVGptGvGKTTTia  259 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLA  259 (436)
T ss_pred             CcEEEEECCCCCcHHHHHH
Confidence            4678999999999996543

>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=90.87  E-value=1.4  Score=35.17  Aligned_cols=73  Identities=18%  Similarity=0.285  Sum_probs=49.7

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHH-HHHHHhCCCCcceeeee
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII-QYYCAALPIPLRTCLAI   83 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~-~~l~~~~~~~~~~~~~~   83 (252)
                      -+|+|.+.+--.|.||| +-++|++..++.+..         --+.+++| ++|..|..+.+ .+++.-.+.++...-+.
T Consensus        39 ~~~~n~v~QlnMGeGKT-sVI~Pmla~~LAdg~---------~LvrviVp-k~Ll~q~~~~L~~~lg~l~~r~i~~lpFs  107 (229)
T PF12340_consen   39 PSGKNSVMQLNMGEGKT-SVIVPMLALALADGS---------RLVRVIVP-KALLEQMRQMLRSRLGGLLNRRIYHLPFS  107 (229)
T ss_pred             CCCCCeEeeecccCCcc-chHHHHHHHHHcCCC---------cEEEEEcC-HHHHHHHHHHHHHHHHHHhCCeeEEeccc
Confidence            36899999999999999 778999998887653         23445554 55888887777 45555555334444444


Q ss_pred             CCccc
Q psy7786          84 GGVPM   88 (252)
Q Consensus        84 g~~~~   88 (252)
                      .++..
T Consensus       108 R~~~~  112 (229)
T PF12340_consen  108 RSTPL  112 (229)
T ss_pred             CCCCC
Confidence            44443

There are two conserved sequence motifs: LLE and NMG.

>PRK09183 transposase/IS protein; Provisional

Probab=90.84  E-value=0.65  Score=37.92  Aligned_cols=19  Identities=26%  Similarity=0.408  Sum_probs=16.9

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +.+|.++++.+|+|+|||.
T Consensus        99 i~~~~~v~l~Gp~GtGKTh  117 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTH  117 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHH
Confidence            5678899999999999994

>PRK04328 hypothetical protein; Provisional

Probab=90.76  E-value=0.58  Score=37.93  Aligned_cols=51  Identities=16%  Similarity=0.194  Sum_probs=30.4

Q ss_pred             CCCcEEEEcCCCchHHHHhHHH-HHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLP-ILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp-~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .|.-+++.+++|||||. |.+= +.+.+.           ++-.++|++ +-|-..++.+.++.+
T Consensus        22 ~gs~ili~G~pGsGKT~-l~~~fl~~~~~-----------~ge~~lyis-~ee~~~~i~~~~~~~   73 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSI-FSQQFLWNGLQ-----------MGEPGVYVA-LEEHPVQVRRNMRQF   73 (249)
T ss_pred             CCcEEEEEcCCCCCHHH-HHHHHHHHHHh-----------cCCcEEEEE-eeCCHHHHHHHHHHc
Confidence            57789999999999983 2222 222221           234577776 555555555555544

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=90.75  E-value=0.16  Score=36.39  Aligned_cols=19  Identities=32%  Similarity=0.378  Sum_probs=11.8

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      .+++-+++.+++|+|||..
T Consensus         2 ~~~~~~~i~G~~G~GKT~~   20 (131)
T PF13401_consen    2 QSQRILVISGPPGSGKTTL   20 (131)
T ss_dssp             -----EEEEE-TTSSHHHH
T ss_pred             CCCcccEEEcCCCCCHHHH
Confidence            3567899999999999954

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

Probab=90.72  E-value=0.15  Score=44.99  Aligned_cols=23  Identities=35%  Similarity=0.257  Sum_probs=16.0

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      +++.+|||||||.+. -.+++.+.
T Consensus       261 iLvTGPTGSGKTTTL-Y~~L~~ln  283 (500)
T COG2804         261 ILVTGPTGSGKTTTL-YAALSELN  283 (500)
T ss_pred             EEEeCCCCCCHHHHH-HHHHHHhc
Confidence            789999999999552 23344443

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=90.44  E-value=0.74  Score=42.42  Aligned_cols=54  Identities=17%  Similarity=0.079  Sum_probs=38.0

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcH--HHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSR--ELARQTHDIIQYYCA   71 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptr--eLa~q~~~~~~~l~~   71 (252)
                      ..+.++.++||+|||..+.+=+.|.+..           +..++++=|-.  |+...++..++..++
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~~-----------g~~vi~fDpkgD~el~~~~~~~~~~~GR  235 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIRR-----------GDVVIVFDPKGDADLLKRMYAEAKRAGR  235 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHHc-----------CCeEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            4578999999999998776655555532           44577777877  566666666666554

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=90.38  E-value=1.3  Score=40.78  Aligned_cols=58  Identities=17%  Similarity=0.119  Sum_probs=37.7

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      .++++-.++.+++|||||.+- .-++..+.....      ....++++.+||.--|..+.+.+..
T Consensus       164 a~~~~~~vItGgpGTGKTt~v-~~ll~~l~~~~~------~~~~~i~l~APTgkAA~rL~e~~~~  221 (615)
T PRK10875        164 ALTRRISVISGGPGTGKTTTV-AKLLAALIQLAD------GERCRIRLAAPTGKAAARLTESLGK  221 (615)
T ss_pred             HhcCCeEEEEeCCCCCHHHHH-HHHHHHHHHhcC------CCCcEEEEECCcHHHHHHHHHHHHh
Confidence            355677899999999999542 222222222111      0245788899999988888776654

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=90.27  E-value=1.2  Score=39.09  Aligned_cols=20  Identities=25%  Similarity=0.313  Sum_probs=16.4

Q ss_pred             cCCCcEEEEcCCCchHHHHh
Q psy7786           5 RNSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~   24 (252)
                      ..|+-+++.+|||+|||.+-
T Consensus       219 ~~~~~i~~vGptGvGKTTt~  238 (424)
T PRK05703        219 KQGGVVALVGPTGVGKTTTL  238 (424)
T ss_pred             cCCcEEEEECCCCCCHHHHH
Confidence            35778999999999999543

>PRK08116 hypothetical protein; Validated

Probab=89.96  E-value=1  Score=36.98  Aligned_cols=44  Identities=18%  Similarity=0.160  Sum_probs=26.7

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH   63 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~   63 (252)
                      .-+++.+++|||||... ..+.+.+...          +..++++ +..+|..++.
T Consensus       115 ~gl~l~G~~GtGKThLa-~aia~~l~~~----------~~~v~~~-~~~~ll~~i~  158 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLA-ACIANELIEK----------GVPVIFV-NFPQLLNRIK  158 (268)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHHc----------CCeEEEE-EHHHHHHHHH
Confidence            44999999999999433 2455555442          2335444 4566655443

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=89.95  E-value=1.1  Score=36.67  Aligned_cols=17  Identities=24%  Similarity=0.194  Sum_probs=14.7

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .|.=+++.+++|+|||.
T Consensus        35 ~gs~~lI~G~pGtGKT~   51 (259)
T TIGR03878        35 AYSVINITGVSDTGKSL   51 (259)
T ss_pred             CCcEEEEEcCCCCCHHH
Confidence            56678999999999993

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.91  E-value=1.2  Score=39.02  Aligned_cols=62  Identities=18%  Similarity=0.163  Sum_probs=35.2

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIP   76 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~   76 (252)
                      ..|+-+.+.++||+|||.+...=.-..+....        ...-+++...+.-.+  ..+.+..+++.+|++
T Consensus       189 ~~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~--------~~~v~~i~~d~~rig--alEQL~~~a~ilGvp  250 (420)
T PRK14721        189 EQGGVYALIGPTGVGKTTTTAKLAARAVIRHG--------ADKVALLTTDSYRIG--GHEQLRIYGKLLGVS  250 (420)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHhcC--------CCeEEEEecCCcchh--HHHHHHHHHHHcCCc
Confidence            45777899999999999765432222222211        012356666664332  234466777777743

>PRK08727 hypothetical protein; Validated

Probab=89.88  E-value=0.92  Score=36.37  Aligned_cols=49  Identities=14%  Similarity=0.100  Sum_probs=28.8

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .+++.+++|||||..-. .+.+.+..          .+.+++++. ..++.....+.++.+
T Consensus        43 ~l~l~G~~G~GKThL~~-a~~~~~~~----------~~~~~~y~~-~~~~~~~~~~~~~~l   91 (233)
T PRK08727         43 WLYLSGPAGTGKTHLAL-ALCAAAEQ----------AGRSSAYLP-LQAAAGRLRDALEAL   91 (233)
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHHH----------cCCcEEEEe-HHHhhhhHHHHHHHH
Confidence            48999999999993322 22223222          134577764 555665555555544

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=89.86  E-value=0.21  Score=36.31  Aligned_cols=44  Identities=23%  Similarity=0.212  Sum_probs=29.4

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT   62 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~   62 (252)
                      ..|.-+++.++.|+||| +|+-.+...+             +...-|-+||-.|++..
T Consensus        20 ~~~~~i~l~G~lGaGKT-tl~~~l~~~l-------------g~~~~v~SPTf~lv~~Y   63 (133)
T TIGR00150        20 DFGTVVLLKGDLGAGKT-TLVQGLLQGL-------------GIQGNVTSPTFTLVNEY   63 (133)
T ss_pred             CCCCEEEEEcCCCCCHH-HHHHHHHHHc-------------CCCCcccCCCeeeeeec
Confidence            45667889999999999 5555555433             12234678888777554

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>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=89.67  E-value=0.26  Score=35.42  Aligned_cols=17  Identities=24%  Similarity=0.409  Sum_probs=15.0

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .++.+++.+++|+|||.
T Consensus        18 ~~~~v~i~G~~G~GKT~   34 (151)
T cd00009          18 PPKNLLLYGPPGTGKTT   34 (151)
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            37789999999999993

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.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=89.49  E-value=0.4  Score=40.63  Aligned_cols=27  Identities=26%  Similarity=0.309  Sum_probs=21.0

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +.||-+++.+|+||||| |..+.+-+.+
T Consensus        63 ~aGrgiLi~GppgTGKT-AlA~gIa~eL   89 (450)
T COG1224          63 MAGRGILIVGPPGTGKT-ALAMGIAREL   89 (450)
T ss_pred             ccccEEEEECCCCCcHH-HHHHHHHHHh
Confidence            46889999999999999 4455555555

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=89.47  E-value=0.23  Score=40.58  Aligned_cols=20  Identities=20%  Similarity=0.232  Sum_probs=17.5

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..|+++++.+++|||||..
T Consensus        18 l~~g~~vLL~G~~GtGKT~l   37 (262)
T TIGR02640        18 LKSGYPVHLRGPAGTGKTTL   37 (262)
T ss_pred             HhcCCeEEEEcCCCCCHHHH
Confidence            56789999999999999943

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).

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=89.33  E-value=1.4  Score=43.90  Aligned_cols=55  Identities=18%  Similarity=0.111  Sum_probs=40.5

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .+++++.|..|||||...+-=++..+....        ..-+.++|+-|+.=|..+.+++...
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~--------~~~~i~~~t~t~~aa~em~~Ri~~~   64 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGV--------PPSKILCLTYTKAAAAEMQNRVFDR   64 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCC--------CCCeEEEEecCHHHHHHHHHHHHHH
Confidence            468999999999999877666665554321        1236899999999998877666543

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 alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>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=89.30  E-value=0.32  Score=41.52  Aligned_cols=26  Identities=27%  Similarity=0.316  Sum_probs=18.9

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      .||-+++.+|+||||| |..+.+-+.+
T Consensus        49 aGr~iLiaGppGtGKT-AlA~~ia~eL   74 (398)
T PF06068_consen   49 AGRAILIAGPPGTGKT-ALAMAIAKEL   74 (398)
T ss_dssp             TT-EEEEEE-TTSSHH-HHHHHHHHHC
T ss_pred             cCcEEEEeCCCCCCch-HHHHHHHHHh
Confidence            6889999999999999 5555665554

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.

>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=89.23  E-value=0.3  Score=37.51  Aligned_cols=20  Identities=30%  Similarity=0.464  Sum_probs=14.4

Q ss_pred             CCcEEEEcCCCchHHHHhHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVL   26 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~l   26 (252)
                      ...+++.+|.|||||.-|..
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            46799999999999976643

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=89.20  E-value=1.4  Score=40.46  Aligned_cols=59  Identities=19%  Similarity=0.134  Sum_probs=37.8

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      +++++-.++.++.|||||.. +.-++..+......     ....+.++.+||.--|..+.+.+..
T Consensus       157 al~~~~~vitGgpGTGKTt~-v~~ll~~l~~~~~~-----~~~~~I~l~APTGkAA~rL~e~~~~  215 (586)
T TIGR01447       157 ALKSNFSLITGGPGTGKTTT-VARLLLALVKQSPK-----QGKLRIALAAPTGKAAARLAESLRK  215 (586)
T ss_pred             HhhCCeEEEEcCCCCCHHHH-HHHHHHHHHHhccc-----cCCCcEEEECCcHHHHHHHHHHHHh
Confidence            45677889999999999953 22333333222110     0135789999999888777665544

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.

>TIGR00376 DNA helicase, putative

Probab=89.11  E-value=2.1  Score=39.78  Aligned_cols=66  Identities=18%  Similarity=0.189  Sum_probs=48.1

Q ss_pred             CChHHHHhhhhhhhcC-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .....|..++...+.. ...++..++|+|||... ..++..+..          .+.++|+.+||..-++.+.+.+..
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~-~~ii~~~~~----------~g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTL-VELIRQLVK----------RGLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHH-HHHHHHHHH----------cCCCEEEEcCcHHHHHHHHHHHHh
Confidence            4467888888777765 56778999999998643 233333322          145799999999999999988865

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.

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

Probab=89.06  E-value=0.46  Score=38.89  Aligned_cols=25  Identities=32%  Similarity=0.209  Sum_probs=17.5

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +.-+++.++||||||.. +-.+++.+
T Consensus        80 ~GlilisG~tGSGKTT~-l~all~~i  104 (264)
T cd01129          80 HGIILVTGPTGSGKTTT-LYSALSEL  104 (264)
T ss_pred             CCEEEEECCCCCcHHHH-HHHHHhhh
Confidence            34689999999999943 34455444

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.

>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=89.01  E-value=1.7  Score=35.32  Aligned_cols=48  Identities=29%  Similarity=0.259  Sum_probs=30.6

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc---CcHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC---PSRELARQT   62 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~---ptreLa~q~   62 (252)
                      ..|.=+++.|.||.||| +|++-+...+....         +..+++++   +-.+++..+
T Consensus        17 ~~g~L~vi~a~pg~GKT-~~~l~ia~~~a~~~---------~~~vly~SlEm~~~~l~~R~   67 (259)
T PF03796_consen   17 RPGELTVIAARPGVGKT-AFALQIALNAALNG---------GYPVLYFSLEMSEEELAARL   67 (259)
T ss_dssp             -TT-EEEEEESTTSSHH-HHHHHHHHHHHHTT---------SSEEEEEESSS-HHHHHHHH
T ss_pred             CcCcEEEEEecccCCch-HHHHHHHHHHHHhc---------CCeEEEEcCCCCHHHHHHHH
Confidence            34555789999999999 77777776665532         35688887   334444433

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 ....

>KOG1802|consensus

Probab=89.01  E-value=0.78  Score=42.03  Aligned_cols=56  Identities=16%  Similarity=0.072  Sum_probs=39.2

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      +|+..=.++++|.|||||.+-.--+++.+-..          .-.+|+.+|+.--+.|+.+.+.+.
T Consensus       422 VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~----------~~~VLvcApSNiAVDqLaeKIh~t  477 (935)
T KOG1802|consen  422 VLQRPLSLIQGPPGTGKTVTSATIVYHLARQH----------AGPVLVCAPSNIAVDQLAEKIHKT  477 (935)
T ss_pred             HHcCCceeeecCCCCCceehhHHHHHHHHHhc----------CCceEEEcccchhHHHHHHHHHhc
Confidence            34444568999999999977655555544332          345899999998777777666543

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=88.99  E-value=1.4  Score=41.04  Aligned_cols=48  Identities=21%  Similarity=0.261  Sum_probs=36.6

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      ..++.+.+|||||+... .+++..             +..+|||+|+.+.|.|+++.++.+.
T Consensus        34 ~~ll~Gl~gs~ka~lia-~l~~~~-------------~r~vLIVt~~~~~A~~l~~dL~~~~   81 (652)
T PRK05298         34 HQTLLGVTGSGKTFTMA-NVIARL-------------QRPTLVLAHNKTLAAQLYSEFKEFF   81 (652)
T ss_pred             cEEEEcCCCcHHHHHHH-HHHHHh-------------CCCEEEEECCHHHHHHHHHHHHHhc
Confidence            56789999999997743 233221             2248999999999999999998774

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

Probab=88.91  E-value=2.8  Score=32.58  Aligned_cols=62  Identities=24%  Similarity=0.285  Sum_probs=41.5

Q ss_pred             hHHHHhhhhhhhcC--CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         168 TPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       168 ~~iQ~~~~p~~~~~--~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ++-|..++...+..  +-.++..+.|+|||..  +..+...+...         +.++++++||..-+..+.+..
T Consensus         3 ~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~--l~~~~~~~~~~---------g~~v~~~apT~~Aa~~L~~~~   66 (196)
T PF13604_consen    3 NEEQREAVRAILTSGDRVSVLQGPAGTGKTTL--LKALAEALEAA---------GKRVIGLAPTNKAAKELREKT   66 (196)
T ss_dssp             -HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH--HHHHHHHHHHT---------T--EEEEESSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH--HHHHHHHHHhC---------CCeEEEECCcHHHHHHHHHhh
Confidence            45577777666543  3466778999999875  33344444432         467999999999999988764

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=88.70  E-value=1.2  Score=40.53  Aligned_cols=61  Identities=13%  Similarity=0.145  Sum_probs=45.7

Q ss_pred             CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhh
Q psy7786         181 GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA  246 (252)
Q Consensus       181 ~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~  246 (252)
                      +.-++++...|||||...+.-+...++.....     .+...+|||.|.|-..+.+.+.|-.||+.
T Consensus       226 ~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~-----l~~k~vlvl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         226 NKILVVQGAAGSGKTTIALHRVAYLLYGYRGP-----LQAKPVLVLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             CCeEEEecCCCCCchhHHHHHHHHHHhccccc-----cccCceEEEcCcHHHHHHHHHhchhhccC
Confidence            35678888899999998777666655553311     22334999999999999999999877753

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=88.66  E-value=2  Score=37.36  Aligned_cols=58  Identities=16%  Similarity=0.075  Sum_probs=43.0

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHH-HHHHHHHHHHHHHHhCC
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE-LARQTHDIIQYYCAALP   74 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptre-La~q~~~~~~~l~~~~~   74 (252)
                      -.++.+..|||||.+..+-++..++...        .+.+++++.+|.. |..-++..+++....+|
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~--------~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g   61 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINK--------KQQNILAARKVQNSIRDSVFKDIENLLSIEG   61 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcC--------CCcEEEEEehhhhHHHHHHHHHHHHHHHHcC
Confidence            3578899999999999988888777651        2467999999887 55556777766555444

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=88.56  E-value=0.68  Score=42.28  Aligned_cols=19  Identities=32%  Similarity=0.403  Sum_probs=16.5

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      -.+.+++++.++||||||.
T Consensus       173 ~~e~~h~li~G~tGsGKs~  191 (566)
T TIGR02759       173 GSETQHILIHGTTGSGKSV  191 (566)
T ss_pred             cccccceEEEcCCCCCHHH
Confidence            4567799999999999994

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).

>KOG1133|consensus

Probab=88.34  E-value=0.45  Score=43.61  Aligned_cols=32  Identities=22%  Similarity=0.219  Sum_probs=27.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHh
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQ   35 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~   35 (252)
                      +-+|+=-|..+|||||||++.+...++.+...
T Consensus        31 Le~GkIgIfESPTGTGKSLSLiCaaltWL~~~   62 (821)
T KOG1133|consen   31 LEEGKIGIFESPTGTGKSLSLICAALTWLRDF   62 (821)
T ss_pred             HhcCCeeeeeCCCCCCchHHHHHHHHHHHHHh
Confidence            45677778899999999999999999888654

>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=88.30  E-value=1  Score=35.18  Aligned_cols=27  Identities=22%  Similarity=0.317  Sum_probs=16.4

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      +..++++.+.||||||.+... ++..+.
T Consensus        37 ~~~h~li~G~tgsGKS~~l~~-ll~~l~   63 (205)
T PF01580_consen   37 KNPHLLIAGATGSGKSTLLRT-LLLSLA   63 (205)
T ss_dssp             GS-SEEEE--TTSSHHHHHHH-HHHHHH
T ss_pred             CCceEEEEcCCCCCccHHHHH-HHHHHH
Confidence            345899999999999955443 443333

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.

>KOG1942|consensus

Probab=88.24  E-value=0.53  Score=38.92  Aligned_cols=27  Identities=26%  Similarity=0.282  Sum_probs=22.1

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +.||-+++.+|.||||| |..+.+-|.+
T Consensus        62 maGravLlaGppgtGKT-AlAlaisqEL   88 (456)
T KOG1942|consen   62 MAGRAVLLAGPPGTGKT-ALALAISQEL   88 (456)
T ss_pred             ccCcEEEEecCCCCchh-HHHHHHHHHh
Confidence            57999999999999999 5556666655

>PTZ00301 uridine kinase; Provisional

Probab=88.24  E-value=0.97  Score=35.67  Aligned_cols=22  Identities=27%  Similarity=0.150  Sum_probs=15.0

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +-+.+++||||| ++.-.+.+.+
T Consensus         6 IgIaG~SgSGKT-Tla~~l~~~l   27 (210)
T PTZ00301          6 IGISGASGSGKS-SLSTNIVSEL   27 (210)
T ss_pred             EEEECCCcCCHH-HHHHHHHHHH
Confidence            457899999999 4444444444

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=88.24  E-value=1.2  Score=35.35  Aligned_cols=52  Identities=25%  Similarity=0.273  Sum_probs=29.8

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .|.-+++.+++|+|||. |++-++.....          ++-.++|++- -+-..|+.+.+..+
T Consensus        15 ~g~~~li~G~~G~GKt~-~~~~~~~~~~~----------~g~~~~y~s~-e~~~~~l~~~~~~~   66 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTT-FSLQFLYQGLK----------NGEKAMYISL-EEREERILGYAKSK   66 (224)
T ss_pred             CCeEEEEECCCCCCHHH-HHHHHHHHHHh----------CCCeEEEEEC-CCCHHHHHHHHHHc
Confidence            47778999999999983 33322222211          1335777653 44455555555443

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PF02500 DNA_pack_N: Probable DNA packing protein, N-terminus ; InterPro: IPR003499 This family includes proteins that are probably involved in DNA packing in Herpesviridae

Probab=88.19  E-value=0.64  Score=38.00  Aligned_cols=48  Identities=23%  Similarity=0.229  Sum_probs=40.8

Q ss_pred             cCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786          14 AFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus        14 a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      =|---||| +|++|+|..++..-        ++++.-|++..|-.++-|.+++..-.
T Consensus       195 VPRRHGKT-WfvVpiIsllL~s~--------~gI~IGYvAHqKhvs~~VF~EI~~~l  242 (284)
T PF02500_consen  195 VPRRHGKT-WFVVPIISLLLASF--------EGIKIGYVAHQKHVSEPVFEEIINRL  242 (284)
T ss_pred             eeccCCCc-chHHHHHHHHHHHh--------cCceeeehHHHHHhhHHHHHHHHHHH
Confidence            45567999 89999999999887        48999999999999999988775443

This domain is normally found at the N terminus of the protein.; GO: 0006323 DNA packaging

>PRK07952 DNA replication protein DnaC; Validated

Probab=88.14  E-value=1.7  Score=35.13  Aligned_cols=44  Identities=23%  Similarity=0.181  Sum_probs=26.4

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH   63 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~   63 (252)
                      ..+++.+++|+|||... ..+.+.+...          +..++++ +..+|...+.
T Consensus       100 ~~~~l~G~~GtGKThLa-~aia~~l~~~----------g~~v~~i-t~~~l~~~l~  143 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLA-AAICNELLLR----------GKSVLII-TVADIMSAMK  143 (244)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHhc----------CCeEEEE-EHHHHHHHHH
Confidence            47899999999999433 2334444332          3446555 4555554443

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=87.87  E-value=0.64  Score=35.30  Aligned_cols=29  Identities=28%  Similarity=0.327  Sum_probs=14.8

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      .+++.+++.+++|+|||. ++--++.++..
T Consensus        22 ~~~~~~ll~G~~G~GKT~-ll~~~~~~~~~   50 (185)
T PF13191_consen   22 GSPRNLLLTGESGSGKTS-LLRALLDRLAE   50 (185)
T ss_dssp             -----EEE-B-TTSSHHH-HHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHH-HHHHHHHHHHh
Confidence            356789999999999993 33334444443

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=87.83  E-value=1.6  Score=39.38  Aligned_cols=22  Identities=27%  Similarity=0.276  Sum_probs=18.2

Q ss_pred             cccCCCcEEEEcCCCchHHHHh
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~   24 (252)
                      .+..|+-+.+.++||+|||...
T Consensus       346 ~l~~G~vIaLVGPtGvGKTTta  367 (559)
T PRK12727        346 PLERGGVIALVGPTGAGKTTTI  367 (559)
T ss_pred             cccCCCEEEEECCCCCCHHHHH
Confidence            3567888999999999999654

>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

Probab=87.56  E-value=0.45  Score=39.65  Aligned_cols=12  Identities=50%  Similarity=0.445  Sum_probs=11.4

Q ss_pred             EEEEcCCCchHH
Q psy7786          10 IIGIAFTGSGKT   21 (252)
Q Consensus        10 ~~~~a~tgsGKT   21 (252)
                      +++.+||+||||
T Consensus         6 i~I~GPTAsGKT   17 (308)
T COG0324           6 IVIAGPTASGKT   17 (308)
T ss_pred             EEEECCCCcCHH
Confidence            789999999999

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=87.51  E-value=0.4  Score=41.14  Aligned_cols=27  Identities=22%  Similarity=0.199  Sum_probs=19.2

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      .+.-+++++|||||||... -.++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            5667999999999999543 33444443

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.

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=87.45  E-value=0.37  Score=41.42  Aligned_cols=29  Identities=24%  Similarity=0.335  Sum_probs=23.8

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      ..|+.++|.+.+||||| .|.+-+++.+..
T Consensus         8 ~~G~TLLIKG~PGTGKT-tfaLelL~~l~~   36 (484)
T PF07088_consen    8 EPGQTLLIKGEPGTGKT-TFALELLNSLKD   36 (484)
T ss_pred             CCCcEEEEecCCCCCce-eeehhhHHHHhc
Confidence            46889999999999999 677777776654

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

>TIGR00665 DnaB replicative DNA helicase

Probab=87.38  E-value=1.9  Score=38.08  Aligned_cols=28  Identities=36%  Similarity=0.230  Sum_probs=20.9

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      ..|.=+++.|++|+||| +|.+-+..++.
T Consensus       193 ~~G~l~vi~g~pg~GKT-~~~l~~a~~~a  220 (434)
T TIGR00665       193 QPSDLIILAARPSMGKT-AFALNIAENAA  220 (434)
T ss_pred             CCCeEEEEEeCCCCChH-HHHHHHHHHHH
Confidence            34556789999999999 77776665544

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

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=87.33  E-value=0.53  Score=42.99  Aligned_cols=24  Identities=29%  Similarity=0.303  Sum_probs=17.4

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      .-+++++|||||||.+. -.++..+
T Consensus       317 Glilv~G~tGSGKTTtl-~a~l~~~  340 (564)
T TIGR02538       317 GMVLVTGPTGSGKTVSL-YTALNIL  340 (564)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHhh
Confidence            35789999999999653 3455544

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.

>KOG0745|consensus

Probab=87.15  E-value=0.37  Score=41.89  Aligned_cols=19  Identities=37%  Similarity=0.469  Sum_probs=16.1

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      -|+.-|+++.+|||||||+
T Consensus       223 ~LeKSNvLllGPtGsGKTl  241 (564)
T KOG0745|consen  223 ELEKSNVLLLGPTGSGKTL  241 (564)
T ss_pred             eeecccEEEECCCCCchhH
Confidence            3556689999999999995

>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=87.06  E-value=0.44  Score=33.57  Aligned_cols=13  Identities=46%  Similarity=0.445  Sum_probs=11.5

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      +++.+++|||||.
T Consensus         2 I~I~G~~gsGKST   14 (121)
T PF13207_consen    2 IIISGPPGSGKST   14 (121)
T ss_dssp             EEEEESTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            6789999999993

...

>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=86.97  E-value=0.46  Score=33.81  Aligned_cols=13  Identities=38%  Similarity=0.414  Sum_probs=11.6

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      +++.+|+|+|||.
T Consensus         1 ill~G~~G~GKT~   13 (132)
T PF00004_consen    1 ILLHGPPGTGKTT   13 (132)
T ss_dssp             EEEESSTTSSHHH
T ss_pred             CEEECcCCCCeeH
Confidence            5889999999994

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 ....

>KOG2340|consensus

Probab=86.90  E-value=2.9  Score=37.45  Aligned_cols=80  Identities=19%  Similarity=0.180  Sum_probs=56.1

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCC-Cch--hHHhHHHHHHHHHhhhccC-------CC-------------CCCCCcE
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTG-SGK--TLVFVLPILMFCLEQETKL-------PF-------------LPGEGPY  222 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g-~gK--t~~~~~~~l~~i~~~~~~~-------~~-------------~~~~~~~  222 (252)
                      ..++.|...+-.+.+-+|++....+. .|+  ...|++..+.++++.....       ..             .....|+
T Consensus       216 pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRpk  295 (698)
T KOG2340|consen  216 PLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRPK  295 (698)
T ss_pred             cchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCce
Confidence            34778888888888888988776653 344  3467788888777543210       00             1122479


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         223 GLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      +||+||+|+-|..+.+.|..+.+
T Consensus       296 VLivvpfRe~A~riVn~lis~l~  318 (698)
T KOG2340|consen  296 VLIVVPFRESAYRIVNLLISLLS  318 (698)
T ss_pred             EEEEecchHHHHHHHHHHHHHhc
Confidence            99999999999999999887743

>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=86.84  E-value=0.44  Score=34.60  Aligned_cols=14  Identities=29%  Similarity=0.472  Sum_probs=12.5

Q ss_pred             cEEEEcCCCchHHH
Q psy7786           9 DIIGIAFTGSGKTL   22 (252)
Q Consensus         9 d~~~~a~tgsGKT~   22 (252)
                      ++++.+|+|+|||.
T Consensus         1 ~vlL~G~~G~GKt~   14 (139)
T PF07728_consen    1 PVLLVGPPGTGKTT   14 (139)
T ss_dssp             EEEEEESSSSSHHH
T ss_pred             CEEEECCCCCCHHH
Confidence            58999999999994

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.

>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=86.81  E-value=0.44  Score=37.18  Aligned_cols=15  Identities=40%  Similarity=0.417  Sum_probs=12.7

Q ss_pred             EEEEcCCCchHHHHh
Q psy7786          10 IIGIAFTGSGKTLVF   24 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~   24 (252)
                      +++.+|||+|||.+-
T Consensus         4 i~lvGptGvGKTTt~   18 (196)
T PF00448_consen    4 IALVGPTGVGKTTTI   18 (196)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCchHhHH
Confidence            678999999999654

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 ....

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=86.80  E-value=0.55  Score=38.89  Aligned_cols=19  Identities=26%  Similarity=0.202  Sum_probs=15.7

Q ss_pred             CCCcEEEEcCCCchHHHHh
Q psy7786           6 NSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~   24 (252)
                      .+.++++.+|+|||||...
T Consensus        57 ~~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        57 PTLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CCceEEEEcCCCCCHHHHH
Confidence            4568999999999999543

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.

>KOG1132|consensus

Probab=86.75  E-value=0.72  Score=43.40  Aligned_cols=69  Identities=13%  Similarity=0.031  Sum_probs=44.6

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhh---c----CCCC--------C------------C----CCCcEEEEE
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQE---T----KLPF--------L------------P----GEGPYGLII   52 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~---~----~~~~--------~------------~----~~~~~~lil   52 (252)
                      +.++.|.+..+|||||||++.+...+...-...   .    +...        +            +    ..-|+..|-
T Consensus        37 L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~~e~~~~~~~ipkIyya  116 (945)
T KOG1132|consen   37 LDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEAGEPIACYTGIPKIYYA  116 (945)
T ss_pred             HHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhhcCccccccCCceEEEe
Confidence            345667899999999999998876664332111   0    0000        0            0    124677888


Q ss_pred             cCcHHHHHHHHHHHHHHHHh
Q psy7786          53 CPSRELARQTHDIIQYYCAA   72 (252)
Q Consensus        53 ~ptreLa~q~~~~~~~l~~~   72 (252)
                      +-|+....|+.+++++.+-.
T Consensus       117 SRTHsQltQvvrElrrT~Y~  136 (945)
T KOG1132|consen  117 SRTHSQLTQVVRELRRTGYR  136 (945)
T ss_pred             cchHHHHHHHHHHHhhcCCC
Confidence            88998888888888776533

>PRK10436 hypothetical protein; Provisional

Probab=86.61  E-value=0.42  Score=42.41  Aligned_cols=25  Identities=32%  Similarity=0.283  Sum_probs=17.7

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +.-+++++|||||||.+. -.++..+
T Consensus       218 ~GliLvtGpTGSGKTTtL-~a~l~~~  242 (462)
T PRK10436        218 QGLILVTGPTGSGKTVTL-YSALQTL  242 (462)
T ss_pred             CCeEEEECCCCCChHHHH-HHHHHhh
Confidence            345899999999999653 2345544

>cd01394 radB RadB

Probab=86.55  E-value=1.2  Score=35.01  Aligned_cols=23  Identities=17%  Similarity=0.167  Sum_probs=16.8

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPIL   29 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~   29 (252)
                      .|.=+.+.+++||||| +|++-+.
T Consensus        18 ~g~i~~i~G~~GsGKT-~l~~~~a   40 (218)
T cd01394          18 RGTVTQVYGPPGTGKT-NIAIQLA   40 (218)
T ss_pred             CCeEEEEECCCCCCHH-HHHHHHH
Confidence            4566889999999999 4444433

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=86.53  E-value=2.1  Score=37.09  Aligned_cols=21  Identities=48%  Similarity=0.453  Sum_probs=17.0

Q ss_pred             cCCCcEEEEcCCCchHHHHhH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFV   25 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~   25 (252)
                      ..|+-+++.+|+|+|||....
T Consensus       204 ~~~~ii~lvGptGvGKTTt~a  224 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLV  224 (407)
T ss_pred             cCCeEEEEECCCCCCHHHHHH
Confidence            457788999999999995543

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=86.47  E-value=2.2  Score=37.41  Aligned_cols=28  Identities=25%  Similarity=0.080  Sum_probs=21.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +..|.=+++.|++|+||| +|++-+...+
T Consensus       191 ~~~g~liviag~pg~GKT-~~al~ia~~~  218 (421)
T TIGR03600       191 LVKGDLIVIGARPSMGKT-TLALNIAENV  218 (421)
T ss_pred             CCCCceEEEEeCCCCCHH-HHHHHHHHHH
Confidence            345666889999999999 7777666544

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.

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=86.32  E-value=2.4  Score=40.08  Aligned_cols=74  Identities=16%  Similarity=0.078  Sum_probs=53.6

Q ss_pred             hHHHHhhhhhhhc---CC-cEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         168 TPIQVQGIPAALS---GR-DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       168 ~~iQ~~~~p~~~~---~~-~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      .+.|...+.....   .. .+++.++||.|||.+.+.+.........       ....+.+...|+|...+++++.++..
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~-------~~~~r~i~vlP~~t~ie~~~~r~~~~  269 (733)
T COG1203         197 YELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKI-------KLKSRVIYVLPFRTIIEDMYRRAKEI  269 (733)
T ss_pred             hHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccc-------cccceEEEEccHHHHHHHHHHHHHhh
Confidence            4555555533332   23 7889999999999999988887554420       13578899999999999999999876


Q ss_pred             HhhCC
Q psy7786         244 CAALP  248 (252)
Q Consensus       244 ~~~~~  248 (252)
                      ....+
T Consensus       270 ~~~~~  274 (733)
T COG1203         270 FGLFS  274 (733)
T ss_pred             hcccc
Confidence            65544

>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=86.23  E-value=0.44  Score=37.34  Aligned_cols=20  Identities=25%  Similarity=0.434  Sum_probs=14.2

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..|+++++.++.|||||+.
T Consensus        19 AaG~h~lLl~GppGtGKTml   38 (206)
T PF01078_consen   19 AAGGHHLLLIGPPGTGKTML   38 (206)
T ss_dssp             HHCC--EEEES-CCCTHHHH
T ss_pred             HcCCCCeEEECCCCCCHHHH
Confidence            34688999999999999953

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.

>KOG0060|consensus

Probab=86.16  E-value=0.54  Score=42.34  Aligned_cols=21  Identities=19%  Similarity=0.357  Sum_probs=18.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHh
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~   24 (252)
                      +-+|++++|++|+|+|||--+
T Consensus       458 V~~g~~LLItG~sG~GKtSLl  478 (659)
T KOG0060|consen  458 VPSGQNLLITGPSGCGKTSLL  478 (659)
T ss_pred             ecCCCeEEEECCCCCchhHHH
Confidence            568999999999999999543

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=86.14  E-value=0.22  Score=40.28  Aligned_cols=85  Identities=13%  Similarity=0.166  Sum_probs=58.7

Q ss_pred             CCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee-eeeCCcccCcchhhhhhc-ccccCCccccccCCccccCCCh
Q psy7786          43 PGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC-LAIGGVPMNQSLDVIKKG-IQYNDPIKTSWRAPRCILSLPD  120 (252)
Q Consensus        43 ~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~-~~~g~~~~~~~~~~l~~~-~~i~~~i~t~~~~p~~l~~~~~  120 (252)
                      ..+.|.+|||+..---|.++...++.|... +  ..++ .+.--...++|...++++ ++|.  +    +||+|+..+.+
T Consensus       123 ~~gsP~~lvvs~SalRa~dl~R~l~~~~~k-~--~~v~KLFaKH~Kl~eqv~~L~~~~~~i~--v----GTP~Rl~kLle  193 (252)
T PF14617_consen  123 EKGSPHVLVVSSSALRAADLIRALRSFKGK-D--CKVAKLFAKHIKLEEQVKLLKKTRVHIA--V----GTPGRLSKLLE  193 (252)
T ss_pred             CCCCCEEEEEcchHHHHHHHHHHHHhhccC-C--chHHHHHHhhccHHHHHHHHHhCCceEE--E----eChHHHHHHHH
Confidence            346799999999988888888888776311 1  1222 222234567888888864 4442  3    55999999998


Q ss_pred             hHHHHHhhhhceeeccC
Q psy7786         121 QVHDIIRRNLRILVEGD  137 (252)
Q Consensus       121 ~~~~~l~~~~~~~V~de  137 (252)
                      .....+.+ +.++|.|.
T Consensus       194 ~~~L~l~~-l~~ivlD~  209 (252)
T PF14617_consen  194 NGALSLSN-LKRIVLDW  209 (252)
T ss_pred             cCCCCccc-CeEEEEcC
Confidence            87777766 78888776

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=86.12  E-value=2.4  Score=41.13  Aligned_cols=41  Identities=20%  Similarity=0.314  Sum_probs=28.1

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE   57 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptre   57 (252)
                      ..|.+|.++||||||..... ++..++..         .+++++|+=|-++
T Consensus       475 n~n~~I~G~TGSGKS~l~~~-li~q~~~~---------~~~~v~IiD~g~s  515 (893)
T TIGR03744       475 NAHLLILGPTGAGKSATLTN-LLMQVMAV---------HRPRLFIVEAGNS  515 (893)
T ss_pred             cccEEEECCCCCCHHHHHHH-HHHHHHHh---------cCCEEEEEcCCCC
Confidence            56899999999999955433 33333321         1567888888876

Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=86.07  E-value=0.44  Score=41.59  Aligned_cols=24  Identities=17%  Similarity=0.384  Sum_probs=20.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhH
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFV   25 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~   25 (252)
                      |.+.++.|++..+|+|+|||..|.
T Consensus       204 ~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       204 PLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHH
Confidence            556788999999999999996554

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.

>KOG0389|consensus

Probab=85.81  E-value=3.4  Score=38.75  Aligned_cols=113  Identities=19%  Similarity=0.308  Sum_probs=66.8

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCc
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGV   86 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~   86 (252)
                      +-+-|++-.-|-|||.- ++.-+..+.....       .|| -|||+|..-|    .++++.|.+..+ .+++...+|..
T Consensus       418 ~l~gILADEMGLGKTiQ-vIaFlayLkq~g~-------~gp-HLVVvPsSTl----eNWlrEf~kwCP-sl~Ve~YyGSq  483 (941)
T KOG0389|consen  418 KLNGILADEMGLGKTIQ-VIAFLAYLKQIGN-------PGP-HLVVVPSSTL----ENWLREFAKWCP-SLKVEPYYGSQ  483 (941)
T ss_pred             cccceehhhccCcchhH-HHHHHHHHHHcCC-------CCC-cEEEecchhH----HHHHHHHHHhCC-ceEEEeccCcH
Confidence            44558888999999942 2222333333322       345 4888897764    577888888887 59999999886


Q ss_pred             ccCcchhhh-hhc-ccccCCccccccCCccccCCChhHHHHHh-hhhceeeccCC
Q psy7786          87 PMNQSLDVI-KKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIR-RNLRILVEGDD  138 (252)
Q Consensus        87 ~~~~~~~~l-~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~-~~~~~~V~de~  138 (252)
                      ....+++.. .++ .+++ ++.|-|    .+......+...|+ ..+.++|-||.
T Consensus       484 ~ER~~lR~~i~~~~~~yd-VllTTY----~la~~~kdDRsflk~~~~n~viyDEg  533 (941)
T KOG0389|consen  484 DERRELRERIKKNKDDYD-VLLTTY----NLAASSKDDRSFLKNQKFNYVIYDEG  533 (941)
T ss_pred             HHHHHHHHHHhccCCCcc-EEEEEe----ecccCChHHHHHHHhccccEEEecch
Confidence            544433332 222 3432 244422    24444444444444 45778998885

>KOG1533|consensus

Probab=85.75  E-value=0.96  Score=36.15  Aligned_cols=26  Identities=23%  Similarity=0.250  Sum_probs=20.7

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhh
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQE   36 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~   36 (252)
                      -++++|+||||| +|+..+.+.+....
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls~~g   30 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLSAIG   30 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHHHhC
Confidence            368999999999 89988877765543

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=85.58  E-value=0.59  Score=37.22  Aligned_cols=58  Identities=28%  Similarity=0.228  Sum_probs=32.4

Q ss_pred             HHHhhhh-hhhcCCcEEEEcc-CCC--chhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHH
Q psy7786         170 IQVQGIP-AALSGRDIIGIAF-TGS--GKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT  236 (252)
Q Consensus       170 iQ~~~~p-~~~~~~~~~~~~~-~g~--gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i  236 (252)
                      -|+.++- ++.....+++... ||.  .++...++.++..+.++.         +.-+++.++..++|...
T Consensus       148 qQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~---------g~tii~VTHd~~lA~~~  209 (226)
T COG1136         148 QQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKER---------GKTIIMVTHDPELAKYA  209 (226)
T ss_pred             HHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhc---------CCEEEEEcCCHHHHHhC
Confidence            4555553 3444555555543 442  355556666666554432         33477778888887653

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=85.36  E-value=0.56  Score=39.13  Aligned_cols=16  Identities=19%  Similarity=0.237  Sum_probs=13.4

Q ss_pred             CCCcEEEEcCCCchHH
Q psy7786           6 NSRDIIGIAFTGSGKT   21 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT   21 (252)
                      .++=+++.+|||||||
T Consensus         3 ~~~ii~I~GpTasGKS   18 (300)
T PRK14729          3 ENKIVFIFGPTAVGKS   18 (300)
T ss_pred             CCcEEEEECCCccCHH
Confidence            3445899999999999

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=85.36  E-value=0.61  Score=36.80  Aligned_cols=19  Identities=26%  Similarity=0.364  Sum_probs=15.6

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +..|.=+++++|+|||||.
T Consensus        25 v~~Gevv~iiGpSGSGKST   43 (240)
T COG1126          25 VEKGEVVVIIGPSGSGKST   43 (240)
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            3466778999999999993

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=85.32  E-value=1.6  Score=34.08  Aligned_cols=17  Identities=29%  Similarity=0.079  Sum_probs=14.3

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .|.=+.+.+++|||||.
T Consensus        11 ~g~i~~i~G~~GsGKT~   27 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTN   27 (209)
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            45668899999999994

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>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=85.28  E-value=0.75  Score=36.58  Aligned_cols=14  Identities=29%  Similarity=0.290  Sum_probs=12.7

Q ss_pred             cEEEEcCCCchHHH
Q psy7786           9 DIIGIAFTGSGKTL   22 (252)
Q Consensus         9 d~~~~a~tgsGKT~   22 (252)
                      +++..+|+|+|||.
T Consensus        52 h~lf~GPPG~GKTT   65 (233)
T PF05496_consen   52 HMLFYGPPGLGKTT   65 (233)
T ss_dssp             EEEEESSTTSSHHH
T ss_pred             eEEEECCCccchhH
Confidence            68999999999993

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.

>PRK04296 thymidine kinase; Provisional

Probab=85.18  E-value=2.2  Score=33.01  Aligned_cols=35  Identities=23%  Similarity=0.083  Sum_probs=22.0

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcC
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICP   54 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~p   54 (252)
                      =.++.++.|+|||.+ ++-.+.++..          .+-+++++-|
T Consensus         4 i~litG~~GsGKTT~-~l~~~~~~~~----------~g~~v~i~k~   38 (190)
T PRK04296          4 LEFIYGAMNSGKSTE-LLQRAYNYEE----------RGMKVLVFKP   38 (190)
T ss_pred             EEEEECCCCCHHHHH-HHHHHHHHHH----------cCCeEEEEec
Confidence            357889999999943 3444444432          2446777755

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=85.18  E-value=1.2  Score=41.47  Aligned_cols=51  Identities=16%  Similarity=0.201  Sum_probs=33.3

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHH
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT   62 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~   62 (252)
                      ||.-.+.+++++.+-||||||.++ --++..+..          ++=+++|.=|+-+....-
T Consensus       179 ip~~~E~~H~li~GttGSGKS~~i-~~LL~~ir~----------RGdrAIIyD~~GeFv~~F  229 (732)
T PRK13700        179 IIRDSEIQNFCLHGTVGAGKSEVI-RRLANYARQ----------RGDMVVIYDRSGEFVKSY  229 (732)
T ss_pred             CCcchhhcceEEeCCCCCCHHHHH-HHHHHHHHH----------cCCeEEEEeCCCchHHHh
Confidence            355567889999999999999743 334433332          234577776776665433

>PRK05595 replicative DNA helicase; Provisional

Probab=85.17  E-value=3  Score=36.98  Aligned_cols=26  Identities=31%  Similarity=0.342  Sum_probs=19.3

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      .|.=+++.|.||+||| +|.+-+..++
T Consensus       200 ~g~liviaarpg~GKT-~~al~ia~~~  225 (444)
T PRK05595        200 KGDMILIAARPSMGKT-TFALNIAEYA  225 (444)
T ss_pred             CCcEEEEEecCCCChH-HHHHHHHHHH
Confidence            3445678999999999 7777666554

>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=85.13  E-value=3.1  Score=32.97  Aligned_cols=46  Identities=22%  Similarity=0.230  Sum_probs=26.8

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD   64 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~   64 (252)
                      -+++.+++|+|||- .+-.+.+.+....        .+.+++|+.. .+....+.+
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~~~--------~~~~v~y~~~-~~f~~~~~~   81 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQKQH--------PGKRVVYLSA-EEFIREFAD   81 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHHC--------TTS-EEEEEH-HHHHHHHHH
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHhcc--------ccccceeecH-HHHHHHHHH
Confidence            37999999999996 3334444444332        2556777753 345444433

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.

>PHA00729 NTP-binding motif containing protein

Probab=85.11  E-value=0.7  Score=36.81  Aligned_cols=18  Identities=28%  Similarity=0.368  Sum_probs=14.5

Q ss_pred             cEEEEcCCCchHH-HHhHH
Q psy7786           9 DIIGIAFTGSGKT-LVFVL   26 (252)
Q Consensus         9 d~~~~a~tgsGKT-~a~~l   26 (252)
                      ++++.+++|+||| +|..+
T Consensus        19 nIlItG~pGvGKT~LA~aL   37 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALKV   37 (226)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            7999999999999 34433

>KOG0385|consensus

Probab=84.99  E-value=5.4  Score=37.46  Aligned_cols=70  Identities=26%  Similarity=0.325  Sum_probs=47.9

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      ..+|-+.|..-+-|-|||+-- +..+-++..-..      -.|| -||++|..-|.    ++...+.+.++ .+++.+.+
T Consensus       183 ~engingILaDEMGLGKTlQt-Is~l~yl~~~~~------~~GP-fLVi~P~StL~----NW~~Ef~rf~P-~l~~~~~~  249 (971)
T KOG0385|consen  183 YENGINGILADEMGLGKTLQT-ISLLGYLKGRKG------IPGP-FLVIAPKSTLD----NWMNEFKRFTP-SLNVVVYH  249 (971)
T ss_pred             HhcCcccEeehhcccchHHHH-HHHHHHHHHhcC------CCCC-eEEEeeHhhHH----HHHHHHHHhCC-CcceEEEe
Confidence            356788999999999999632 233333322111      1345 69999998876    56677777777 58999999


Q ss_pred             CCc
Q psy7786          84 GGV   86 (252)
Q Consensus        84 g~~   86 (252)
                      |+.
T Consensus       250 Gdk  252 (971)
T KOG0385|consen  250 GDK  252 (971)
T ss_pred             CCH
Confidence            984

>PRK07004 replicative DNA helicase; Provisional

Probab=84.90  E-value=2.5  Score=37.69  Aligned_cols=28  Identities=25%  Similarity=0.239  Sum_probs=20.7

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      ..|.=+++.|.+|+||| +|.+-+..++.
T Consensus       211 ~~g~liviaarpg~GKT-~~al~ia~~~a  238 (460)
T PRK07004        211 HGGELIIVAGRPSMGKT-AFSMNIGEYVA  238 (460)
T ss_pred             CCCceEEEEeCCCCCcc-HHHHHHHHHHH
Confidence            34566788999999999 67776665543

>PRK05748 replicative DNA helicase; Provisional

Probab=84.87  E-value=1.8  Score=38.41  Aligned_cols=28  Identities=32%  Similarity=0.239  Sum_probs=21.4

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      ..|.=+++.|.||+||| +|.+-++..+.
T Consensus       201 ~~G~livIaarpg~GKT-~~al~ia~~~a  228 (448)
T PRK05748        201 QPNDLIIVAARPSVGKT-AFALNIAQNVA  228 (448)
T ss_pred             CCCceEEEEeCCCCCch-HHHHHHHHHHH
Confidence            45566889999999999 77777765543

>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=84.85  E-value=0.6  Score=33.91  Aligned_cols=13  Identities=46%  Similarity=0.465  Sum_probs=11.6

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      +++++++|||||.
T Consensus         2 ii~~G~pgsGKSt   14 (143)
T PF13671_consen    2 IILCGPPGSGKST   14 (143)
T ss_dssp             EEEEESTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            6889999999994

...

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=84.73  E-value=1.6  Score=33.37  Aligned_cols=17  Identities=35%  Similarity=0.538  Sum_probs=14.9

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      ++|-+++.+|+||||+.
T Consensus         1 ~~r~ivl~Gpsg~GK~~   17 (183)
T PF00625_consen    1 KRRPIVLVGPSGSGKST   17 (183)
T ss_dssp             SSSEEEEESSTTSSHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            46789999999999993

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=84.55  E-value=0.37  Score=34.48  Aligned_cols=41  Identities=24%  Similarity=0.205  Sum_probs=24.2

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR   60 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~   60 (252)
                      .|.=++..++-|+||| +|+=.++..+             +...-+-+||-.|++
T Consensus        14 ~g~vi~L~GdLGaGKT-tf~r~l~~~l-------------g~~~~V~SPTF~l~~   54 (123)
T PF02367_consen   14 PGDVILLSGDLGAGKT-TFVRGLARAL-------------GIDEEVTSPTFSLVN   54 (123)
T ss_dssp             S-EEEEEEESTTSSHH-HHHHHHHHHT-------------T--S----TTTTSEE
T ss_pred             CCCEEEEECCCCCCHH-HHHHHHHHHc-------------CCCCCcCCCCeEEEE
Confidence            3444678899999999 6666655544             233477889888763

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=84.55  E-value=2.8  Score=35.18  Aligned_cols=18  Identities=17%  Similarity=0.226  Sum_probs=15.3

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .++.+++.+++|+|||..
T Consensus       155 ~~~gl~L~G~~G~GKThL  172 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYL  172 (306)
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            467899999999999943

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=84.53  E-value=2.3  Score=31.14  Aligned_cols=24  Identities=17%  Similarity=0.159  Sum_probs=17.8

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      +.++++.+|||| +++--+++.+..
T Consensus         3 v~VvG~~~sGKT-Tl~~~Li~~l~~   26 (140)
T PF03205_consen    3 VQVVGPKNSGKT-TLIRKLINELKR   26 (140)
T ss_dssp             EEEEESTTSSHH-HHHHHHHHHHHH
T ss_pred             EEEECCCCCCHH-HHHHHHHHHHhH
Confidence            578999999999 555556666554

>PRK11823 DNA repair protein RadA; Provisional

Probab=84.45  E-value=2.1  Score=37.95  Aligned_cols=53  Identities=17%  Similarity=0.080  Sum_probs=32.2

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      .|.=+++.+++|+||| ++++-+...+..          .+-+++|++ +-|-..|+....+.++
T Consensus        79 ~Gs~~lI~G~pG~GKT-tL~lq~a~~~a~----------~g~~vlYvs-~Ees~~qi~~ra~rlg  131 (446)
T PRK11823         79 PGSVVLIGGDPGIGKS-TLLLQVAARLAA----------AGGKVLYVS-GEESASQIKLRAERLG  131 (446)
T ss_pred             CCEEEEEECCCCCCHH-HHHHHHHHHHHh----------cCCeEEEEE-ccccHHHHHHHHHHcC
Confidence            4667889999999999 343333333321          134577776 4455566666555543

>PRK08506 replicative DNA helicase; Provisional

Probab=84.44  E-value=3  Score=37.30  Aligned_cols=28  Identities=29%  Similarity=0.250  Sum_probs=21.2

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      ..|.=+++.|.||.||| +|.+-+...+.
T Consensus       190 ~~G~LivIaarpg~GKT-~fal~ia~~~~  217 (472)
T PRK08506        190 NKGDLIIIAARPSMGKT-TLCLNMALKAL  217 (472)
T ss_pred             CCCceEEEEcCCCCChH-HHHHHHHHHHH
Confidence            34556788999999999 77777766554

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=84.29  E-value=2.5  Score=31.59  Aligned_cols=22  Identities=18%  Similarity=0.164  Sum_probs=14.2

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +.+.+++|||||. ++--++..+
T Consensus         2 i~i~G~~gsGKTt-l~~~l~~~l   23 (155)
T TIGR00176         2 LQIVGPKNSGKTT-LIERLVKAL   23 (155)
T ss_pred             EEEECCCCCCHHH-HHHHHHHHH
Confidence            4678999999993 333333333

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PF05729 NACHT: NACHT domain

Probab=84.14  E-value=1.3  Score=32.83  Aligned_cols=24  Identities=21%  Similarity=0.142  Sum_probs=16.5

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      +++.++.|+|||. ++--+...+..
T Consensus         3 l~I~G~~G~GKSt-ll~~~~~~~~~   26 (166)
T PF05729_consen    3 LWISGEPGSGKST-LLRKLAQQLAE   26 (166)
T ss_pred             EEEECCCCCChHH-HHHHHHHHHHh
Confidence            6899999999994 33444444433

>COG4889 Predicted helicase [General function prediction only]

Probab=84.12  E-value=2.4  Score=40.44  Aligned_cols=61  Identities=23%  Similarity=0.208  Sum_probs=41.0

Q ss_pred             CchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCcchh
Q psy7786          17 GSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLD   93 (252)
Q Consensus        17 gsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~~~~   93 (252)
                      |+|||.+-+ -+.+.+.            ..+.|+++|+..|..|..+.+   ......+++...++.+.......+
T Consensus       190 GTGKTfTsL-kisEala------------~~~iL~LvPSIsLLsQTlrew---~~~~~l~~~a~aVcSD~kvsrs~e  250 (1518)
T COG4889         190 GTGKTFTSL-KISEALA------------AARILFLVPSISLLSQTLREW---TAQKELDFRASAVCSDDKVSRSAE  250 (1518)
T ss_pred             CCCccchHH-HHHHHHh------------hhheEeecchHHHHHHHHHHH---hhccCccceeEEEecCcccccccc
Confidence            899997643 3333332            346999999999999976544   444444588888887765544433

>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=84.09  E-value=0.74  Score=32.55  Aligned_cols=13  Identities=46%  Similarity=0.376  Sum_probs=11.5

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      |++.+.+|||||.
T Consensus         1 I~i~G~~GsGKtT   13 (129)
T PF13238_consen    1 IGISGIPGSGKTT   13 (129)
T ss_dssp             EEEEESTTSSHHH
T ss_pred             CEEECCCCCCHHH
Confidence            5789999999994

...

>PLN02165 adenylate isopentenyltransferase

Probab=84.06  E-value=0.89  Score=38.42  Aligned_cols=19  Identities=26%  Similarity=0.403  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCchHHHHh
Q psy7786           6 NSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~   24 (252)
                      .|+-+++.+|||||||...
T Consensus        42 ~g~iivIiGPTGSGKStLA   60 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLS   60 (334)
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            4566899999999999443

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=84.01  E-value=0.95  Score=31.53  Aligned_cols=21  Identities=19%  Similarity=0.172  Sum_probs=16.5

Q ss_pred             cCCCcEEEEcCCCchHHHHhH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFV   25 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~   25 (252)
                      ..|+-+.+.+|+|||||....
T Consensus        13 ~~ge~v~I~GpSGsGKSTLl~   33 (107)
T cd00820          13 YGKVGVLITGDSGIGKTELAL   33 (107)
T ss_pred             cCCEEEEEEcCCCCCHHHHHH
Confidence            456678999999999996443

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>KOG1802|consensus

Probab=83.99  E-value=3.5  Score=38.02  Aligned_cols=76  Identities=18%  Similarity=0.133  Sum_probs=56.1

Q ss_pred             HHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786         159 LEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD  238 (252)
Q Consensus       159 l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~  238 (252)
                      +...++.....-|..+....+...=-+++.++|+|||.... .++.++.++         ....+||.+|+.--++++++
T Consensus       403 ~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa-~IVyhl~~~---------~~~~VLvcApSNiAVDqLae  472 (935)
T KOG1802|consen  403 FSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ---------HAGPVLVCAPSNIAVDQLAE  472 (935)
T ss_pred             hcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhH-HHHHHHHHh---------cCCceEEEcccchhHHHHHH
Confidence            34445555667889999999988889999999999987532 222333332         24579999999999999999


Q ss_pred             HHHHHH
Q psy7786         239 IIQYYC  244 (252)
Q Consensus       239 ~l~~l~  244 (252)
                      .+.+.+
T Consensus       473 KIh~tg  478 (935)
T KOG1802|consen  473 KIHKTG  478 (935)
T ss_pred             HHHhcC
Confidence            987654

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=83.95  E-value=2.2  Score=36.75  Aligned_cols=47  Identities=17%  Similarity=0.272  Sum_probs=33.6

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT   62 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~   62 (252)
                      .+|..+.+.++-|||||.  ++=.+......         .+..+++++||---|..+
T Consensus        20 ~~~~~~fv~G~~GtGKs~--l~~~i~~~~~~---------~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen   20 EEGLNFFVTGPAGTGKSF--LIKAIIDYLRS---------RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             cCCcEEEEEcCCCCChhH--HHHHHHHHhcc---------ccceEEEecchHHHHHhc
Confidence            578899999999999994  44333333322         245689999999877666

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=83.95  E-value=0.68  Score=40.74  Aligned_cols=20  Identities=20%  Similarity=0.449  Sum_probs=17.6

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      ...|+++++.+|.|||||+.
T Consensus       195 AAGgHnLl~~GpPGtGKTml  214 (490)
T COG0606         195 AAGGHNLLLVGPPGTGKTML  214 (490)
T ss_pred             HhcCCcEEEecCCCCchHHh
Confidence            45689999999999999964

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=83.92  E-value=2  Score=33.97  Aligned_cols=18  Identities=28%  Similarity=0.082  Sum_probs=14.9

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..|.=+.+.+++|||||.
T Consensus        21 ~~g~i~~i~G~~GsGKT~   38 (225)
T PRK09361         21 ERGTITQIYGPPGSGKTN   38 (225)
T ss_pred             CCCeEEEEECCCCCCHHH
Confidence            346678999999999993

>cd01918 HprK_C HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria

Probab=83.75  E-value=0.9  Score=33.71  Aligned_cols=18  Identities=17%  Similarity=0.165  Sum_probs=15.5

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..|+-+++.+++|+|||.
T Consensus        12 ~~g~gvLi~G~sG~GKSt   29 (149)
T cd01918          12 VGGIGVLITGPSGIGKSE   29 (149)
T ss_pred             ECCEEEEEEcCCCCCHHH
Confidence            357889999999999993

It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.

>PRK11054 helD DNA helicase IV; Provisional

Probab=83.69  E-value=5.8  Score=37.26  Aligned_cols=70  Identities=20%  Similarity=0.188  Sum_probs=47.7

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..++-|..++-  .....+++.+..|+|||...+--....+....       ....++|+++-||..|..+.+.+.+..
T Consensus       196 ~L~~~Q~~av~--~~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~-------~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        196 PLNPSQARAVV--NGEDSLLVLAGAGSGKTSVLVARAGWLLARGQ-------AQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCHHHHHHHh--CCCCCeEEEEeCCCCHHHHHHHHHHHHHHhCC-------CCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            45667766553  23356789999999999876554443332211       123479999999999999998887544

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=83.66  E-value=3.9  Score=31.04  Aligned_cols=45  Identities=20%  Similarity=0.158  Sum_probs=26.6

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      +++.+++||||| +|..-...   .          .+.+++|++-.+.+-....+.+.+
T Consensus         2 ~li~G~~~sGKS-~~a~~~~~---~----------~~~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKS-RFAERLAA---E----------LGGPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHH-HHHHHHHH---h----------cCCCeEEEEccCcCCHHHHHHHHH
Confidence            578999999999 44332221   1          133578886666554444444443

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=83.63  E-value=0.96  Score=36.90  Aligned_cols=18  Identities=33%  Similarity=0.318  Sum_probs=14.8

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      ...++++.+|+|||||..
T Consensus        41 ~~~~vll~GppGtGKTtl   58 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTV   58 (261)
T ss_pred             CcceEEEEcCCCCCHHHH
Confidence            345799999999999943

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.

>KOG0924|consensus

Probab=83.46  E-value=2.9  Score=38.66  Aligned_cols=58  Identities=21%  Similarity=0.196  Sum_probs=34.8

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      +.++.=+++.++||||||.-    +-|+++.+.+..     +| -.-+--|-|.-|.-+.+.+   ++.++
T Consensus       368 ir~n~vvvivgETGSGKTTQ----l~QyL~edGY~~-----~G-mIGcTQPRRvAAiSVAkrV---a~EM~  425 (1042)
T KOG0924|consen  368 IRENQVVVIVGETGSGKTTQ----LAQYLYEDGYAD-----NG-MIGCTQPRRVAAISVAKRV---AEEMG  425 (1042)
T ss_pred             HhhCcEEEEEecCCCCchhh----hHHHHHhccccc-----CC-eeeecCchHHHHHHHHHHH---HHHhC
Confidence            44566689999999999954    345566665420     11 1222338888777665444   44554

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=83.44  E-value=2.7  Score=37.74  Aligned_cols=53  Identities=21%  Similarity=0.175  Sum_probs=32.8

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      -.|.-+++.+++|+|||. +.+=.+.....          ++-+++|++ .-|=..|+...++.+
T Consensus       261 ~~gs~~li~G~~G~GKt~-l~~~f~~~~~~----------~ge~~~y~s-~eEs~~~i~~~~~~l  313 (484)
T TIGR02655       261 FKDSIILATGATGTGKTL-LVSKFLENACA----------NKERAILFA-YEESRAQLLRNAYSW  313 (484)
T ss_pred             cCCcEEEEECCCCCCHHH-HHHHHHHHHHH----------CCCeEEEEE-eeCCHHHHHHHHHHc
Confidence            356678999999999994 32222222212          244688876 556666666665544

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=83.44  E-value=5.2  Score=35.21  Aligned_cols=15  Identities=40%  Similarity=0.530  Sum_probs=12.6

Q ss_pred             cEEEEcCCCchHHHH
Q psy7786           9 DIIGIAFTGSGKTLV   23 (252)
Q Consensus         9 d~~~~a~tgsGKT~a   23 (252)
                      =+++++++|+|||.+
T Consensus       102 vi~lvG~~GvGKTTt  116 (429)
T TIGR01425       102 VIMFVGLQGSGKTTT  116 (429)
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999844

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=83.41  E-value=2.5  Score=33.73  Aligned_cols=16  Identities=25%  Similarity=0.164  Sum_probs=14.1

Q ss_pred             CCCcEEEEcCCCchHH
Q psy7786           6 NSRDIIGIAFTGSGKT   21 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT   21 (252)
                      .|.-+++.+++|||||
T Consensus        24 ~g~~~~i~G~~GsGKt   39 (234)
T PRK06067         24 FPSLILIEGDHGTGKS   39 (234)
T ss_pred             CCcEEEEECCCCCChH
Confidence            4667899999999999

>TIGR02012 tigrfam_recA protein RecA

Probab=83.34  E-value=3.5  Score=34.77  Aligned_cols=40  Identities=23%  Similarity=0.142  Sum_probs=26.1

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSR   56 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptr   56 (252)
                      .|+=+.+.+|+||||| ++++.++......          +-.++++..-.
T Consensus        54 ~G~iteI~G~~GsGKT-tLaL~~~~~~~~~----------g~~v~yId~E~   93 (321)
T TIGR02012        54 RGRIIEIYGPESSGKT-TLALHAIAEAQKA----------GGTAAFIDAEH   93 (321)
T ss_pred             CCeEEEEECCCCCCHH-HHHHHHHHHHHHc----------CCcEEEEcccc
Confidence            5677889999999999 5555555444321          34577775443

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.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=83.19  E-value=5.3  Score=35.78  Aligned_cols=20  Identities=25%  Similarity=0.149  Sum_probs=16.4

Q ss_pred             CCCcEEEEcCCCchHHHHhH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFV   25 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~   25 (252)
                      .|+=+.+.+|||+|||.+..
T Consensus       255 ~g~Vi~LvGpnGvGKTTTia  274 (484)
T PRK06995        255 RGGVFALMGPTGVGKTTTTA  274 (484)
T ss_pred             CCcEEEEECCCCccHHHHHH
Confidence            46678899999999997654

>PRK05642 DNA replication initiation factor; Validated

Probab=83.08  E-value=4  Score=32.70  Aligned_cols=50  Identities=12%  Similarity=0.119  Sum_probs=28.4

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      ..+++.+++|+|||.- +-.+.+.+..          .+.+++|+. ..++.....+..+.+
T Consensus        46 ~~l~l~G~~G~GKTHL-l~a~~~~~~~----------~~~~v~y~~-~~~~~~~~~~~~~~~   95 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL-LQAACLRFEQ----------RGEPAVYLP-LAELLDRGPELLDNL   95 (234)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHh----------CCCcEEEee-HHHHHhhhHHHHHhh
Confidence            4588999999999943 2222333322          134577765 466765543333333

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=83.03  E-value=2.8  Score=41.86  Aligned_cols=60  Identities=30%  Similarity=0.350  Sum_probs=36.7

Q ss_pred             hhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEc--C----cHHHHHHHHHHHHH-HHhhCC
Q psy7786         177 AALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC--P----SRELARQTHDIIQY-YCAALP  248 (252)
Q Consensus       177 ~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~--~----tr~~a~~i~~~l~~-l~~~~~  248 (252)
                      ....++.+++++.||+|||..  +|.+..-..          .+....|.|  |    ++++|.++++++.. +++.+|
T Consensus        85 ai~~~~VviI~GeTGSGKTTq--lPq~lle~g----------~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VG  151 (1294)
T PRK11131         85 AIRDHQVVIVAGETGSGKTTQ--LPKICLELG----------RGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVG  151 (1294)
T ss_pred             HHHhCCeEEEECCCCCCHHHH--HHHHHHHcC----------CCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceec
Confidence            333455677778999999994  664422111          122223333  3    67999999998874 666555

>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=83.01  E-value=0.83  Score=34.76  Aligned_cols=14  Identities=29%  Similarity=0.337  Sum_probs=12.6

Q ss_pred             cEEEEcCCCchHHH
Q psy7786           9 DIIGIAFTGSGKTL   22 (252)
Q Consensus         9 d~~~~a~tgsGKT~   22 (252)
                      +++..+|||+|||.
T Consensus         5 ~~ll~GpsGvGKT~   18 (171)
T PF07724_consen    5 NFLLAGPSGVGKTE   18 (171)
T ss_dssp             EEEEESSTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            67899999999994

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 ....

>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=82.80  E-value=1.5  Score=35.38  Aligned_cols=22  Identities=32%  Similarity=0.314  Sum_probs=16.8

Q ss_pred             EEcCCCchHHHHhHHHHHHHHHH
Q psy7786          12 GIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus        12 ~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      |.+|.||||| +|+-.+-+.+..
T Consensus         1 ViGpaGSGKT-T~~~~~~~~~~~   22 (238)
T PF03029_consen    1 VIGPAGSGKT-TFCKGLSEWLES   22 (238)
T ss_dssp             -EESTTSSHH-HHHHHHHHHHTT
T ss_pred             CCCCCCCCHH-HHHHHHHHHHHh
Confidence            4689999999 888777776644

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=82.74  E-value=0.97  Score=34.76  Aligned_cols=17  Identities=29%  Similarity=0.313  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCchHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a   23 (252)
                      |.-+++.+|+|||||..
T Consensus         2 g~~i~l~G~sGsGKsTl   18 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSL   18 (186)
T ss_pred             CcEEEEECCCCCCHHHH
Confidence            66789999999999943

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=82.72  E-value=0.96  Score=35.76  Aligned_cols=17  Identities=29%  Similarity=0.262  Sum_probs=14.8

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .++.+++.+++|||||.
T Consensus        37 ~~~~lll~G~~G~GKT~   53 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSH   53 (226)
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            45689999999999994

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.

>CHL00181 cbbX CbbX; Provisional

Probab=82.44  E-value=1.1  Score=37.10  Aligned_cols=18  Identities=28%  Similarity=0.241  Sum_probs=15.3

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .|.++++.+|+|||||..
T Consensus        58 ~~~~ill~G~pGtGKT~l   75 (287)
T CHL00181         58 PGLHMSFTGSPGTGKTTV   75 (287)
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            466799999999999954

>PHA02244 ATPase-like protein

Probab=82.43  E-value=0.9  Score=39.00  Aligned_cols=18  Identities=22%  Similarity=0.174  Sum_probs=16.2

Q ss_pred             ccCCCcEEEEcCCCchHH
Q psy7786           4 YRNSRDIIGIAFTGSGKT   21 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT   21 (252)
                      +..+.++++.+|||+|||
T Consensus       116 l~~~~PVLL~GppGtGKT  133 (383)
T PHA02244        116 VNANIPVFLKGGAGSGKN  133 (383)
T ss_pred             HhcCCCEEEECCCCCCHH
Confidence            456889999999999999

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=82.41  E-value=0.83  Score=40.90  Aligned_cols=22  Identities=36%  Similarity=0.324  Sum_probs=15.5

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +++++|||||||.+. -.+++.+
T Consensus       245 ilitGptGSGKTTtL-~a~L~~l  266 (486)
T TIGR02533       245 ILVTGPTGSGKTTTL-YAALSRL  266 (486)
T ss_pred             EEEEcCCCCCHHHHH-HHHHhcc
Confidence            789999999999543 2234444

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.

>PHA02542 41 41 helicase; Provisional

Probab=82.40  E-value=4.5  Score=36.16  Aligned_cols=26  Identities=15%  Similarity=-0.001  Sum_probs=19.4

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      |.=+++.|.+|.||| +|.+-+.....
T Consensus       190 G~LiiIaarPgmGKT-tfalniA~~~a  215 (473)
T PHA02542        190 KTLNVLLAGVNVGKS-LGLCSLAADYL  215 (473)
T ss_pred             CcEEEEEcCCCccHH-HHHHHHHHHHH
Confidence            444778999999999 77776665553

>PRK06904 replicative DNA helicase; Validated

Probab=82.38  E-value=4.9  Score=35.92  Aligned_cols=27  Identities=30%  Similarity=0.199  Sum_probs=20.0

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      .|.=+++.|.+|.||| +|.+-+..++.
T Consensus       220 ~G~LiiIaarPg~GKT-afalnia~~~a  246 (472)
T PRK06904        220 PSDLIIVAARPSMGKT-TFAMNLCENAA  246 (472)
T ss_pred             CCcEEEEEeCCCCChH-HHHHHHHHHHH
Confidence            4455778999999999 57777666554

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=82.10  E-value=6.1  Score=31.64  Aligned_cols=13  Identities=31%  Similarity=0.281  Sum_probs=11.3

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      .++.++.|+|||.
T Consensus         4 ~ll~g~~G~GKS~   16 (239)
T cd01125           4 SALVAPGGTGKSS   16 (239)
T ss_pred             eEEEcCCCCCHHH
Confidence            4789999999994

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=81.99  E-value=1.1  Score=39.26  Aligned_cols=18  Identities=50%  Similarity=0.654  Sum_probs=15.3

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      ...++++.+|||||||..
T Consensus       107 ~~~~iLl~Gp~GtGKT~l  124 (412)
T PRK05342        107 QKSNILLIGPTGSGKTLL  124 (412)
T ss_pred             CCceEEEEcCCCCCHHHH
Confidence            457899999999999953

>PRK14530 adenylate kinase; Provisional

Probab=81.93  E-value=1  Score=35.51  Aligned_cols=17  Identities=24%  Similarity=0.364  Sum_probs=15.0

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .|..+++.+++|||||.
T Consensus         2 ~~~~I~i~G~pGsGKsT   18 (215)
T PRK14530          2 SQPRILLLGAPGAGKGT   18 (215)
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57789999999999994

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=81.79  E-value=1.1  Score=34.03  Aligned_cols=18  Identities=28%  Similarity=0.246  Sum_probs=15.3

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .|+-+++.+++|||||..
T Consensus         1 ~~~~i~l~G~~gsGKst~   18 (175)
T cd00227           1 TGRIIILNGGSSAGKSSI   18 (175)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            377899999999999943

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=81.76  E-value=6.2  Score=37.03  Aligned_cols=69  Identities=19%  Similarity=0.066  Sum_probs=46.8

Q ss_pred             ChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         167 PTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      .++-|..++..  .+..+++.+..|+|||.....-+...+....       -...+.|+++-||.-|..+.+.+.++.
T Consensus         3 Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~-------v~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          3 LNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCG-------YQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcC-------CCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            44556665533  2356888999999999876555444332211       012369999999999999999887664

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=81.70  E-value=0.91  Score=33.09  Aligned_cols=13  Identities=31%  Similarity=0.378  Sum_probs=11.4

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      +++.+|||||||.
T Consensus         2 i~i~GpsGsGKst   14 (137)
T cd00071           2 IVLSGPSGVGKST   14 (137)
T ss_pred             EEEECCCCCCHHH
Confidence            5789999999994

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.

>PRK08840 replicative DNA helicase; Provisional

Probab=81.68  E-value=5.2  Score=35.67  Aligned_cols=28  Identities=29%  Similarity=0.226  Sum_probs=20.4

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      ..|.=+++.|.+|.||| +|.+-+...+.
T Consensus       215 ~~g~LiviaarPg~GKT-afalnia~~~a  242 (464)
T PRK08840        215 QGSDLIIVAARPSMGKT-TFAMNLCENAA  242 (464)
T ss_pred             CCCceEEEEeCCCCchH-HHHHHHHHHHH
Confidence            34555788999999999 66666665553

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=81.68  E-value=4.3  Score=36.62  Aligned_cols=16  Identities=31%  Similarity=0.451  Sum_probs=14.6

Q ss_pred             CCCcEEEEcCCCchHH
Q psy7786           6 NSRDIIGIAFTGSGKT   21 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT   21 (252)
                      .|.-+++.+++|||||
T Consensus        30 ~Gs~~li~G~pGsGKT   45 (509)
T PRK09302         30 KGRPTLVSGTAGTGKT   45 (509)
T ss_pred             CCcEEEEEeCCCCCHH
Confidence            5778999999999999

>PRK13531 regulatory ATPase RavA; Provisional

Probab=81.50  E-value=1  Score=40.13  Aligned_cols=21  Identities=14%  Similarity=0.237  Sum_probs=18.4

Q ss_pred             cccCCCcEEEEcCCCchHHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a   23 (252)
                      .++.|.++++.+|+|+|||..
T Consensus        35 aalag~hVLL~GpPGTGKT~L   55 (498)
T PRK13531         35 AALSGESVFLLGPPGIAKSLI   55 (498)
T ss_pred             HHccCCCEEEECCCChhHHHH
Confidence            367899999999999999954

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=81.46  E-value=6.7  Score=34.70  Aligned_cols=18  Identities=33%  Similarity=0.503  Sum_probs=14.3

Q ss_pred             CCcEEEEcCCCchHHHHh
Q psy7786           7 SRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~   24 (252)
                      ..-+++++++|+|||.+-
T Consensus        95 p~vI~lvG~~GsGKTTta  112 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTA  112 (437)
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            346889999999999543

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=81.44  E-value=6  Score=35.11  Aligned_cols=47  Identities=17%  Similarity=0.187  Sum_probs=27.1

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD   64 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~   64 (252)
                      ..+++.+++|+|||... -.+.+.+....        .+.+++++. ..++..+...
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~~~--------~~~~v~yi~-~~~~~~~~~~  195 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILEKN--------PNAKVVYVT-SEKFTNDFVN  195 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhC--------CCCeEEEEE-HHHHHHHHHH
Confidence            45899999999999432 22334443321        245677664 4455554433

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=81.42  E-value=0.99  Score=39.78  Aligned_cols=22  Identities=32%  Similarity=0.324  Sum_probs=18.4

Q ss_pred             cccCCCcEEEEcCCCchHHHHh
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~   24 (252)
                      .+..++++++.+++|+|||...
T Consensus       190 ~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        190 RLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             HHhcCCCEEEECCCCCCHHHHH
Confidence            3557899999999999999543

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=81.42  E-value=6.1  Score=36.91  Aligned_cols=66  Identities=24%  Similarity=0.341  Sum_probs=45.5

Q ss_pred             CChHHHHhhhhhhhcC-----CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSG-----RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~-----~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      .|+.-|...+..+..+     +...+...+|+|||+.... ++    .+.         +..+||+++++.+|.|+++.|
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~-~~----~~~---------~~p~Lvi~~n~~~A~ql~~el   74 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN-VI----AQV---------NRPTLVIAHNKTLAAQLYNEF   74 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH-HH----HHh---------CCCEEEEECCHHHHHHHHHHH
Confidence            4666666666554332     2556888999999776332 22    211         234899999999999999999


Q ss_pred             HHHHh
Q psy7786         241 QYYCA  245 (252)
Q Consensus       241 ~~l~~  245 (252)
                      +.+.+
T Consensus        75 ~~f~p   79 (655)
T TIGR00631        75 KEFFP   79 (655)
T ss_pred             HHhCC
Confidence            98753

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

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=81.41  E-value=6  Score=35.18  Aligned_cols=48  Identities=19%  Similarity=0.133  Sum_probs=28.5

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI   65 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~   65 (252)
                      ..+++.+++|+|||.. +-.+.+.+....        .+.+++++.. .++..++.+.
T Consensus       142 npl~i~G~~G~GKTHL-l~Ai~~~l~~~~--------~~~~v~yv~~-~~f~~~~~~~  189 (450)
T PRK14087        142 NPLFIYGESGMGKTHL-LKAAKNYIESNF--------SDLKVSYMSG-DEFARKAVDI  189 (450)
T ss_pred             CceEEECCCCCcHHHH-HHHHHHHHHHhC--------CCCeEEEEEH-HHHHHHHHHH
Confidence            3588999999999922 233344443322        2456777654 5666665443

>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=81.34  E-value=1.4  Score=31.78  Aligned_cols=19  Identities=21%  Similarity=0.265  Sum_probs=16.5

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +..|.-+.+.+++|||||.
T Consensus         8 i~~g~~~~i~G~nGsGKSt   26 (137)
T PF00005_consen    8 IKPGEIVAIVGPNGSGKST   26 (137)
T ss_dssp             EETTSEEEEEESTTSSHHH
T ss_pred             EcCCCEEEEEccCCCcccc
Confidence            4568889999999999994

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 ....

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=81.32  E-value=1.8  Score=33.54  Aligned_cols=12  Identities=50%  Similarity=0.376  Sum_probs=10.6

Q ss_pred             EEEEcCCCchHH
Q psy7786          10 IIGIAFTGSGKT   21 (252)
Q Consensus        10 ~~~~a~tgsGKT   21 (252)
                      |-+++++|||||
T Consensus         2 IgI~G~sgSGKT   13 (194)
T PF00485_consen    2 IGIAGPSGSGKT   13 (194)
T ss_dssp             EEEEESTTSSHH
T ss_pred             EEEECCCCCCHH
Confidence            458899999999

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=81.28  E-value=1.1  Score=37.75  Aligned_cols=19  Identities=21%  Similarity=0.559  Sum_probs=16.4

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +..++++++.+++|+|||.
T Consensus        61 l~~~~~ilL~G~pGtGKTt   79 (327)
T TIGR01650        61 FAYDRRVMVQGYHGTGKST   79 (327)
T ss_pred             HhcCCcEEEEeCCCChHHH
Confidence            3458899999999999994

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=81.28  E-value=1  Score=35.79  Aligned_cols=16  Identities=25%  Similarity=0.237  Sum_probs=14.1

Q ss_pred             CCCcEEEEcCCCchHH
Q psy7786           6 NSRDIIGIAFTGSGKT   21 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT   21 (252)
                      .++.+++.+++|||||
T Consensus        41 ~~~~~~l~G~~G~GKT   56 (227)
T PRK08903         41 ADRFFYLWGEAGSGRS   56 (227)
T ss_pred             CCCeEEEECCCCCCHH
Confidence            3567999999999999

>KOG1002|consensus

Probab=81.19  E-value=5.2  Score=35.64  Aligned_cols=61  Identities=21%  Similarity=0.259  Sum_probs=38.3

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVP   87 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~   87 (252)
                      +++.+-|.|||.-    .+..++.+.        ++...|+++|+.+|. |=.+++..+..  | .+++...+|...
T Consensus       208 iLADEMGMGKTIQ----tIaLllae~--------~ra~tLVvaP~VAlm-QW~nEI~~~T~--g-slkv~~YhG~~R  268 (791)
T KOG1002|consen  208 ILADEMGMGKTIQ----TIALLLAEV--------DRAPTLVVAPTVALM-QWKNEIERHTS--G-SLKVYIYHGAKR  268 (791)
T ss_pred             eehhhhccchHHH----HHHHHHhcc--------ccCCeeEEccHHHHH-HHHHHHHHhcc--C-ceEEEEEecccc
Confidence            5667889999943    333344443        244489999999986 34444555444  3 377777776633

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=81.11  E-value=1.1  Score=39.06  Aligned_cols=18  Identities=50%  Similarity=0.658  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .+.++++.+|||+|||..
T Consensus       115 ~~~~iLL~GP~GsGKT~l  132 (413)
T TIGR00382       115 SKSNILLIGPTGSGKTLL  132 (413)
T ss_pred             CCceEEEECCCCcCHHHH
Confidence            356899999999999954

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.

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=81.03  E-value=2.6  Score=40.24  Aligned_cols=15  Identities=40%  Similarity=0.492  Sum_probs=13.5

Q ss_pred             CcEEEEcCCCchHHH
Q psy7786           8 RDIIGIAFTGSGKTL   22 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~   22 (252)
                      .+.+|+++||+|||.
T Consensus       437 ghT~I~G~tGaGKTv  451 (796)
T COG3451         437 GHTLIIGPTGAGKTV  451 (796)
T ss_pred             CCeEEECCCCCCHHH
Confidence            489999999999993

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=80.99  E-value=3.5  Score=37.02  Aligned_cols=54  Identities=15%  Similarity=0.133  Sum_probs=30.4

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      -.|+-+++.+++|||||.-..-=+.+.+...          +-.++|++- -|=..++.+.+..+
T Consensus        19 p~g~~~Li~G~pGsGKT~la~qfl~~g~~~~----------ge~~lyvs~-eE~~~~l~~~~~~~   72 (484)
T TIGR02655        19 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIHF----------DEPGVFVTF-EESPQDIIKNARSF   72 (484)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHHHhC----------CCCEEEEEE-ecCHHHHHHHHHHc
Confidence            4678899999999999933221222222221          234777763 34444554444444

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR01075 uvrD DNA helicase II

Probab=80.88  E-value=5.9  Score=37.46  Aligned_cols=71  Identities=18%  Similarity=0.134  Sum_probs=48.8

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      ..++-|..++..  .+..+++.+..|+|||.....-+...+ .+..      -...+.|+++-|+.-|..+.+.+.++..
T Consensus         4 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li-~~~~------v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         4 GLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLL-SVEN------ASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             ccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHH-HcCC------CCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            456677766643  245689999999999987554444333 2210      1123689999999999999999887654

Designed to identify uvrD members of the uvrD/rep subfamily.

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=80.87  E-value=0.52  Score=36.33  Aligned_cols=21  Identities=33%  Similarity=0.420  Sum_probs=16.3

Q ss_pred             cccCCCc--EEEEcCCCchHHHH
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLV   23 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a   23 (252)
                      .+++|.|  +++-++||||||.+
T Consensus        18 ~~~~G~n~~i~~yG~tGsGKT~T   40 (186)
T cd01363          18 SALDGYNVCIFAYGQTGSGKTYT   40 (186)
T ss_pred             HHhCCcceeEEEECCCCCcceEe
Confidence            4567776  57788999999955

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

>PRK08006 replicative DNA helicase; Provisional

Probab=80.87  E-value=6.1  Score=35.32  Aligned_cols=27  Identities=30%  Similarity=0.199  Sum_probs=20.3

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      .|.=+++.|.+|.||| +|.+-+..++.
T Consensus       223 ~G~LiiIaarPgmGKT-afalnia~~~a  249 (471)
T PRK08006        223 PSDLIIVAARPSMGKT-TFAMNLCENAA  249 (471)
T ss_pred             CCcEEEEEeCCCCCHH-HHHHHHHHHHH
Confidence            4455788999999999 77777665553

>PRK00300 gmk guanylate kinase; Provisional

Probab=80.78  E-value=1.1  Score=34.93  Aligned_cols=18  Identities=28%  Similarity=0.298  Sum_probs=15.7

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..|+=+++.+++|||||.
T Consensus         3 ~~g~~i~i~G~sGsGKst   20 (205)
T PRK00300          3 RRGLLIVLSGPSGAGKST   20 (205)
T ss_pred             CCCCEEEEECCCCCCHHH
Confidence            467889999999999994

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=80.69  E-value=6.3  Score=34.38  Aligned_cols=46  Identities=15%  Similarity=0.096  Sum_probs=27.0

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH   63 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~   63 (252)
                      ..+++.+++|+|||... -.+.+.+....        .+.+++++.. .++..++.
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~--------~~~~v~yi~~-~~~~~~~~  182 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENN--------PNAKVVYVSS-EKFTNDFV  182 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhC--------CCCcEEEEEH-HHHHHHHH
Confidence            35789999999999432 33444443321        2456777753 45554443

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).

>PRK00131 aroK shikimate kinase; Reviewed

Probab=80.62  E-value=1.4  Score=33.09  Aligned_cols=18  Identities=33%  Similarity=0.586  Sum_probs=15.7

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..++.+++.+++|||||.
T Consensus         2 ~~~~~i~l~G~~GsGKst   19 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKST   19 (175)
T ss_pred             CCCCeEEEEcCCCCCHHH
Confidence            467889999999999994

>KOG1131|consensus

Probab=80.62  E-value=8.2  Score=34.72  Aligned_cols=57  Identities=12%  Similarity=0.095  Sum_probs=33.0

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .+-+.++.-|+|||||.+.+--++.+.+.-+.       ...+.++-+-|-.=......+++.+
T Consensus        34 akGh~llEMPSGTGKTvsLLSli~aYq~~~p~-------~~~KliYCSRTvpEieK~l~El~~l   90 (755)
T KOG1131|consen   34 AKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPD-------EHRKLIYCSRTVPEIEKALEELKRL   90 (755)
T ss_pred             cCCcEEEECCCCCCcchHHHHHHHHHHHhCCc-------ccceEEEecCcchHHHHHHHHHHHH
Confidence            45578899999999998876555555444331       1334555555544333333444443

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=80.39  E-value=1.1  Score=38.57  Aligned_cols=15  Identities=47%  Similarity=0.521  Sum_probs=13.5

Q ss_pred             cEEEEcCCCchHHHH
Q psy7786           9 DIIGIAFTGSGKTLV   23 (252)
Q Consensus         9 d~~~~a~tgsGKT~a   23 (252)
                      |+++-++||||||.+
T Consensus        44 n~~iyG~~GTGKT~~   58 (366)
T COG1474          44 NIIIYGPTGTGKTAT   58 (366)
T ss_pred             cEEEECCCCCCHhHH
Confidence            699999999999965

>PRK08084 DNA replication initiation factor; Provisional

Probab=80.21  E-value=1.2  Score=35.82  Aligned_cols=17  Identities=24%  Similarity=0.219  Sum_probs=14.5

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .+..+++.+|+|+|||.
T Consensus        44 ~~~~l~l~Gp~G~GKTh   60 (235)
T PRK08084         44 HSGYIYLWSREGAGRSH   60 (235)
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            34679999999999993

>KOG1803|consensus

Probab=80.17  E-value=6.4  Score=35.87  Aligned_cols=64  Identities=22%  Similarity=0.239  Sum_probs=44.9

Q ss_pred             ChHHHHhhhhhhhcCCc-EEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         167 PTPIQVQGIPAALSGRD-IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~~-~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      ...-|..++......++ ..++.++|+|||..... ++..+..+          +.|+||-+||+.-++.+.+++-
T Consensus       186 ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvE-iI~qlvk~----------~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  186 LNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVE-IISQLVKQ----------KKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             ccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHH-HHHHHHHc----------CCeEEEEcCchHHHHHHHHHhc
Confidence            34577777877777744 56677899999876433 23223322          4579999999999999888653

>PRK07261 topology modulation protein; Provisional

Probab=80.07  E-value=1.2  Score=33.90  Aligned_cols=15  Identities=40%  Similarity=0.687  Sum_probs=12.6

Q ss_pred             cEEEEcCCCchHHHH
Q psy7786           9 DIIGIAFTGSGKTLV   23 (252)
Q Consensus         9 d~~~~a~tgsGKT~a   23 (252)
                      -+++.+++|||||..
T Consensus         2 ri~i~G~~GsGKSTl   16 (171)
T PRK07261          2 KIAIIGYSGSGKSTL   16 (171)
T ss_pred             EEEEEcCCCCCHHHH
Confidence            378999999999943

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=80.06  E-value=1.3  Score=36.91  Aligned_cols=51  Identities=18%  Similarity=0.122  Sum_probs=29.5

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      .+|-+||||||+-     ++..++....-.|    ..=.+++|+|++.-.--.+..+.+.
T Consensus        90 ~~VYGPTG~GKSq-----LlRNLis~~lI~P----~PETVfFItP~~~mIpp~E~~aW~~  140 (369)
T PF02456_consen   90 GVVYGPTGSGKSQ-----LLRNLISCQLIQP----PPETVFFITPQKDMIPPQEITAWET  140 (369)
T ss_pred             EEEECCCCCCHHH-----HHHHhhhcCcccC----CCCceEEECCCCCCCCHHHHHHHHH
Confidence            4678999999982     1222332221111    1124899999998766555544433

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PF00735 Septin: Septin; InterPro: IPR000038 Septins constitute a eukaryotic family of guanine nucleotide-binding proteins, most of which polymerise to form filaments []

Probab=80.02  E-value=1.2  Score=36.91  Aligned_cols=21  Identities=29%  Similarity=0.528  Sum_probs=16.3

Q ss_pred             cEEEEcCCCchHHHHhHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILM   30 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~   30 (252)
                      ++++++++|+||| +|+=.+++
T Consensus         6 nImVvG~sG~GKT-TFIntL~~   26 (281)
T PF00735_consen    6 NIMVVGESGLGKT-TFINTLFN   26 (281)
T ss_dssp             EEEEEECTTSSHH-HHHHHHHT
T ss_pred             EEEEECCCCCCHH-HHHHHHHh
Confidence            5899999999999 66544443

Members of the family were first identified by genetic screening for Saccharomyces cerevisiae (Baker's yeast) mutants defective in cytokinesis []. Temperature-sensitive mutations in four genes, CDC3, CDC10, CDC11 and CDC12, were found to cause cell-cycle arrest and defects in bud growth and cytokinesis. The protein products of these genes localise at the division plane between mother and daughter cells, indicating a role in mother-daughter separation during cytokinesis []. Members of the family were therefore termed septins to reflect their role in septation and cell division. The identification of septin homologues in higher eukaryotes, which localise to the cleavage furrow in dividing cells, supports an orthologous function in cytokinesis. Septins have since been identified in most eukaryotes, except plants []. Septins are approximately 40-50 kDa in molecular mass, and typically comprise a conserved central core domain (more than 35% sequence identity between mammalian and yeast homologues) flanked by more divergent N- and C-termini. Most septins possess a P-loop motif in their N-terminal domain (which is characteristic of GTP-binding proteins), and a predicted C-terminal coiled-coil domain []. A number of septin interaction partners have been identified in yeast, many of which are components of the budding site selection machinery, kinase cascades or of the ubiquitination pathway. It has been proposed that septins may act as a scaffold that provides an interaction matrix for other proteins [, ]. In mammals, septins have been shown to regulate vesicle dynamics []. Mammalian septins have also been implicated in a variety of other cellular processes, including apoptosis, carcinogenesis and neurodegeneration []. This entry represents a variety of septins and homologous sequences involved in the cell division process.; GO: 0005525 GTP binding, 0007049 cell cycle; PDB: 2QAG_B 3FTQ_D 2QA5_A 2QNR_B 3TW4_A 3T5D_C.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	252
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		6e-19
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		6e-19
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		1e-15
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		1e-13
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		3e-12
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		3e-12
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		7e-12
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		5e-11
3ly5_A	262	Ddx18 Dead-Domain Length = 262		7e-11
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		2e-10
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		3e-10
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-10
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		4e-10
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		8e-10
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		9e-10
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-09
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-09
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-09
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-09
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-09
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-09
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		6e-09
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-08
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		1e-08
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-08
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		4e-07
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		9e-07
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		1e-06
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		1e-06
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-06
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-06
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-06
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		2e-06
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		3e-06
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		4e-06
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		4e-06
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		5e-06
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-05
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		4e-05
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		3e-04
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		3e-04
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		3e-04
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		3e-04
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		3e-04
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		3e-04
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-04
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		4e-04
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		4e-04
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		6e-04
2va8_A	715	Dna Repair Helicase Hel308 Length = 715		7e-04

>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 = 90.9 bits (224), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 49/129 (37%), Positives = 73/129 (56%), Gaps = 5/129 (3%)
Query: 124 DIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRD 183
           +  RR+  I V G + P    +F     P +++  +  +   +PT IQ QG P ALSG D
Sbjct: 23  ETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLD 82
Query: 184 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLP-GEGPYGLIICPSRELARQTHDIIQY 242
           ++G+A TGSGKTL ++LP ++    Q    PFL  G+GP  L++ P+RELA+Q   +   
Sbjct: 83  MVGVAQTGSGKTLSYLLPAIVHINHQ----PFLERGDGPICLVLAPTRELAQQVQQVAAE 138
Query: 243 YCAALPIGS 251
           YC A  + S
Sbjct: 139 YCRACRLKS 147

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

Iteration: 1
 Score = 90.9 bits (224), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 50/132 (37%), Positives = 74/132 (56%), Gaps = 5/132 (3%)
Query: 121 QVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALS 180
           Q  +  RR+  I V G + P    +F     P +++  +  +   +PT IQ QG P ALS
Sbjct: 6   QEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALS 65
Query: 181 GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLP-GEGPYGLIICPSRELARQTHDI 239
           G D++G+A TGSGKTL ++LP ++    Q    PFL  G+GP  L++ P+RELA+Q   +
Sbjct: 66  GLDMVGVAQTGSGKTLSYLLPAIVHINHQ----PFLERGDGPICLVLAPTRELAQQVQQV 121
Query: 240 IQYYCAALPIGS 251
              YC A  + S
Sbjct: 122 AAEYCRACRLKS 133

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 47/118 (39%), Positives = 68/118 (57%), Gaps = 11/118 (9%)
Query: 124 DIIRRNLRILVEGDDVPPACCSFRLM----KLPESLVRALEAKGIKKPTPIQVQGIPAAL 179
           + +R   +I V+G D+P    +F+ +    K+   L++ +   G + PTPIQ+Q IP  L
Sbjct: 5   NFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVML 64
Query: 180 SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH 237
            GR+++  A TGSGKTL F +PILM     + K P    +G   LII P+RELA Q H
Sbjct: 65  HGRELLASAPTGSGKTLAFSIPILM-----QLKQP--ANKGFRALIISPTRELASQIH 115

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

Iteration: 1
 Score = 73.2 bits (178), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 42/107 (39%), Positives = 62/107 (57%), Gaps = 8/107 (7%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F+ + + + L  A +  G  KPT IQ++ IP AL GRDIIG+A TGSGKT  F LPIL 
Sbjct: 44  TFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILN 103
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGS 251
             LE   +L        + L++ P+RELA Q  +  +   +++ + S
Sbjct: 104 ALLETPQRL--------FALVLTPTRELAFQISEQFEALGSSIGVQS 142

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 37/92 (40%), Positives = 51/92 (55%), Gaps = 5/92 (5%)
Query: 144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL 203
             F+   L   ++ AL  +G+  PTPIQ   +P AL G+D+IG A TG+GKTL F LPI 
Sbjct: 1   MEFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIA 60
Query: 204 MFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
                 + +     G  P  L++ P+RELA Q
Sbjct: 61  ERLAPSQER-----GRKPRALVLTPTRELALQ 87

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 45/114 (39%), Positives = 59/114 (51%), Gaps = 3/114 (2%)
Query: 122 VHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG 181
           +H     N+ + V G DVP     F    L + ++  +   G K PTPIQ   IP   SG
Sbjct: 34  IHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSG 93
Query: 182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
           RD++  A TGSGKT  F+LPIL   LE   +L       P  +I+ P+RELA Q
Sbjct: 94  RDLMACAQTGSGKTAAFLLPILSKLLEDPHELEL---GRPQVVIVSPTRELAIQ 144

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 51/92 (55%), Gaps = 5/92 (5%)
Query: 144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL 203
             F+   L   ++ AL  +G+  PTPI+   +P AL G+D+IG A TG+GKTL F LPI 
Sbjct: 1   MEFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIA 60
Query: 204 MFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
                 + +     G  P  L++ P+RELA Q
Sbjct: 61  ERLAPSQER-----GRKPRALVLTPTRELALQ 87

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 40/106 (37%), Positives = 60/106 (56%), Gaps = 10/106 (9%)
Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           L +  ++ L+    +  T IQ Q I  AL G+D++G A TGSGKTL F++P+    LE  
Sbjct: 32  LSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPV----LEAL 87
Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQY------YCAALPIG 250
            +L +   +G   LII P+RELA QT ++++       + A L IG
Sbjct: 88  YRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIG 133

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 36/89 (40%), Positives = 53/89 (59%), Gaps = 4/89 (4%)
Query: 153 ESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETK 212
           E+ ++A++  G    T IQ + I   L GRD++  A TGSGKTL F++P     +E   K
Sbjct: 63  ENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIP----AVELIVK 118
Query: 213 LPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L F+P  G   LI+ P+RELA QT  +++
Sbjct: 119 LRFMPRNGTGVLILSPTRELAMQTFGVLK 147

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/108 (35%), Positives = 57/108 (52%), Gaps = 9/108 (8%)
Query: 135 EGDDV-PPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSG 193
           + DDV      +F    L   L+  +   G +KP+PIQ + IP A++GRDI+  A  G+G
Sbjct: 11  QTDDVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTG 70
Query: 194 KTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           KT  FV+P L     +  K+          LI+ P+RELA QT  +++
Sbjct: 71  KTAAFVIPTLEKVKPKLNKIQ--------ALIMVPTRELALQTSQVVR 110

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 54/96 (56%), Gaps = 8/96 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           SF  M L ESL+R + A G +KP+ IQ + I   + G D+I  A +G+GKT  F + IL 
Sbjct: 15  SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISIL- 73
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
               Q+ +L     +    L++ P+RELA+Q   ++
Sbjct: 74  ----QQIELDL---KATQALVLAPTRELAQQIQKVV 102

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 61.6 bits (148), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 54/96 (56%), Gaps = 8/96 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           SF  M L ESL+R + A G +KP+ IQ + I   + G D+I  A +G+GKT  F + IL 
Sbjct: 41  SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISIL- 99
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
               Q+ +L     +    L++ P+RELA+Q   ++
Sbjct: 100 ----QQIELDL---KATQALVLAPTRELAQQIQKVV 128

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 55/96 (57%), Gaps = 8/96 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F  M L ESL+R + A G +KP+ IQ + I   + G D+I  A +G+GKT  F + IL 
Sbjct: 31  NFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISIL- 89
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
               Q+ ++ F   +    L++ P+RELA+Q   +I
Sbjct: 90  ----QQLEIEFKETQ---ALVLAPTRELAQQIQKVI 118

>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 = 60.5 bits (145), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 38/108 (35%), Positives = 57/108 (52%), Gaps = 1/108 (0%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F  +KL  ++   +     ++PTPIQ   IPA L  RDI+  A TGSGKT  F++PI+ 
Sbjct: 24  NFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83
Query: 205 FCLEQE-TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGS 251
             + Q+  +  +     P  LI+ P+RELA Q     Q +    P+ S
Sbjct: 84  HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRS 131

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 59/113 (52%), Gaps = 10/113 (8%)
Query: 136 GDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKT 195
           G++ PP   SF  +++ E ++  +E     +PTP+Q   IP     RD++  A TGSGKT
Sbjct: 7   GNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKT 66
Query: 196 LVFVLPIL--MFCLEQETKLPFLPGEGPYG--------LIICPSRELARQTHD 238
             F+LPIL  ++       L  +   G YG        L++ P+RELA Q ++
Sbjct: 67  AAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYE 119

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 36/98 (36%), Positives = 54/98 (55%), Gaps = 11/98 (11%)
Query: 138 DVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLV 197
           DV P   +F  M L E L+R + A G +KP+ IQ + I   + GRD+I  + +G+GKT  
Sbjct: 35  DVTP---TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTAT 91
Query: 198 FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
           F + +L  CL+ + +           LI+ P+RELA Q
Sbjct: 92  FSISVLQ-CLDIQVR-------ETQALILAPTRELAVQ 121

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 36/98 (36%), Positives = 54/98 (55%), Gaps = 11/98 (11%)
Query: 138 DVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLV 197
           DV P   +F  M L E L+R + A G +KP+ IQ + I   + GRD+I  + +G+GKT  
Sbjct: 35  DVTP---TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTAT 91
Query: 198 FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
           F + +L  CL+ + +           LI+ P+RELA Q
Sbjct: 92  FSISVLQ-CLDIQVR-------ETQALILAPTRELAVQ 121

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 36/98 (36%), Positives = 54/98 (55%), Gaps = 11/98 (11%)
Query: 138 DVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLV 197
           DV P   +F  M L E L+R + A G +KP+ IQ + I   + GRD+I  + +G+GKT  
Sbjct: 34  DVTP---TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTAT 90
Query: 198 FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
           F + +L  CL+ + +           LI+ P+RELA Q
Sbjct: 91  FSISVLQ-CLDIQVR-------ETQALILAPTRELAVQ 120

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/98 (36%), Positives = 54/98 (55%), Gaps = 11/98 (11%)
Query: 138 DVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLV 197
           DV P   +F  M L E L+R + A G +KP+ IQ + I   + GRD+I  + +G+GKT  
Sbjct: 13  DVTP---TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTAT 69
Query: 198 FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
           F + +L  CL+ + +           LI+ P+RELA Q
Sbjct: 70  FSISVLQ-CLDIQVR-------ETQALILAPTRELAVQ 99

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/93 (35%), Positives = 51/93 (54%), Gaps = 8/93 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F  M L E L+R + A G +KP+ IQ + I   + GRD+I  + +G+GKT  F + +L 
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTH 237
            CL+ + +           LI+ P+RELA Q  
Sbjct: 62  -CLDIQVR-------ETQALILAPTRELAVQVQ 86

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/93 (35%), Positives = 51/93 (54%), Gaps = 8/93 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F  M L E L+R + A G +KP+ IQ + I   + GRD+I  + +G+GKT  F + +L 
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTH 237
            CL+ + +           LI+ P+RELA Q  
Sbjct: 62  -CLDIQVR-------ETQALILAPTRELAVQVQ 86

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 34/98 (34%), Positives = 53/98 (54%), Gaps = 10/98 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGR-DIIGIAFTGSGKTLVFVLPIL 203
           +F  + L ++++ A+  KG +KPT IQ + IP  L+   +I+  A TGSGKT  F +P++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 204 MFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
               E           G   +I+ P+RELA Q  D I+
Sbjct: 67  ELVNEN---------NGIEAIILTPTRELAIQVADEIE 95

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/96 (34%), Positives = 52/96 (54%), Gaps = 8/96 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           SF  M L ESL+R + A G + P+ IQ + I   + G D+I  A +G+G T  F + IL 
Sbjct: 16  SFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISIL- 74
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
               Q+ +L     +    L++ P+RELA+Q   ++
Sbjct: 75  ----QQIELDLXATQ---ALVLAPTRELAQQIQXVV 103

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 55/97 (56%), Gaps = 5/97 (5%)
Query: 139 VPPACCSFR--LMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTL 196
           +P   C F+    + P+ L++++   GI KPTPIQ Q  P  L G D+I +A TG+GKTL
Sbjct: 14  IPKPTCRFKDAFQQYPD-LLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTL 72
Query: 197 VFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA 233
            +++P  +    Q   +      GP  L++ P+RELA
Sbjct: 73  SYLMPGFIHLDSQP--ISREQRNGPGMLVLTPTRELA 107

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 50/89 (56%), Gaps = 8/89 (8%)
Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           L   L+  +   G +KP+PIQ + IP ALSGRDI+  A  G+GK+  +++P+L       
Sbjct: 10  LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL------- 62
Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDI 239
            +L  L  +    ++I P+RELA Q   I
Sbjct: 63  ERLD-LKKDNIQAMVIVPTRELALQVSQI 90

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 14/85 (16%)
Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           + E + +A+   G K  T +Q + IP  L G++++  A TGSGKT  + +PIL       
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 211 TKLPFLPGEGPYGLIICPSRELARQ 235
                    G   L++ P+REL RQ
Sbjct: 56  ---------GMKSLVVTPTRELTRQ 71

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 37/115 (32%), Positives = 57/115 (49%), Gaps = 8/115 (6%)
Query: 134 VEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSG 193
           V+G  V      FR   L   L+RA+   G + P+ +Q + IP A+ G D++  A +G G
Sbjct: 4   VKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMG 63
Query: 194 KTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
           KT VFVL  L        +L  + G+    L++C +RELA Q     + +   +P
Sbjct: 64  KTAVFVLATL-------QQLEPVTGQVSV-LVMCHTRELAFQISKEYERFSKYMP 110

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/102 (30%), Positives = 53/102 (51%), Gaps = 10/102 (9%)
Query: 142 ACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFV 199
           +  SF  + L   L++ + A   +KP+ IQ + +P  L    R++I  + +G+GKT  F 
Sbjct: 20  SAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 79
Query: 200 LPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L +L     ++          P  + + PSRELARQT +++Q
Sbjct: 80  LTMLTRVNPEDA--------SPQAICLAPSRELARQTLEVVQ 113

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 55/107 (51%), Gaps = 12/107 (11%)
Query: 136 GDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKT 195
           GD +      F  + L   ++  L A G ++P+P+Q++ IP    G D+I  A +G+GKT
Sbjct: 16  GDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKT 75
Query: 196 LVF-VLPILMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDII 240
            VF  + +    LE   T++          LI+ P+RE+A Q H +I
Sbjct: 76  CVFSTIALDSLVLENLSTQI----------LILAPTREIAVQIHSVI 112

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  + L   L++ + A   +KP+ IQ + +P  L    R++I  + +G+GKT  F L +
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L     ++          P  + + PSRELARQT +++Q
Sbjct: 66  LTRVNPEDA--------SPQAICLAPSRELARQTLEVVQ 96

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  + L   L++ + A   +KP+ IQ + +P  L    R++I  + +G+GKT  F L +
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L     ++          P  + + PSRELARQT +++Q
Sbjct: 66  LTRVNPEDA--------SPQAICLAPSRELARQTLEVVQ 96

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 51/95 (53%), Gaps = 8/95 (8%)
Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
           F  M+L E+L+R +   G ++P+ IQ + I   + G D++  A +G+GKT  F +  L  
Sbjct: 24  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 83
Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
               +T +     + P  L++ P+RELA Q   ++
Sbjct: 84  I---DTSV-----KAPQALMLAPTRELALQIQKVV 110

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/109 (32%), Positives = 54/109 (49%), Gaps = 8/109 (7%)
Query: 140 PPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFV 199
           P     FR   L   L+RA+   G + P+ +Q + IP A+ G D++  A +G GKT VFV
Sbjct: 3   PGHMSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV 62
Query: 200 LPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
           L  L        +L  + G+    L++C +RELA Q     + +   +P
Sbjct: 63  LATL-------QQLEPVTGQVSV-LVMCHTRELAFQISKEYERFSKYMP 103

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 51/96 (53%), Gaps = 8/96 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F  M+L E+L+R +   G ++P+ IQ + I   + G D++  A +G+GKT  F +  L 
Sbjct: 15  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 74
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
                +T +     + P  L++ P+RELA Q   ++
Sbjct: 75  RI---DTSV-----KAPQALMLAPTRELALQIQKVV 102

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 50/95 (52%), Gaps = 8/95 (8%)
Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
           F  M+L E L+R +   G ++P+ IQ + I   + G D++  A +G+GKT  F +  L  
Sbjct: 23  FDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
               +T +     + P  L++ P+RELA Q   ++
Sbjct: 83  I---DTSV-----KAPQALMLAPTRELALQIQKVV 109

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 34/103 (33%), Positives = 53/103 (51%), Gaps = 8/103 (7%)
Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
           FR   L   L+RA+   G + P+ +Q + IP A+ G D++  A +G GKT VFVL  L  
Sbjct: 10  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL-- 67
Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
                 +L  + G+    L++C +RELA Q     + +   +P
Sbjct: 68  -----QQLEPVTGQVSV-LVMCHTRELAFQISKEYERFSKYMP 104

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 34/103 (33%), Positives = 53/103 (51%), Gaps = 8/103 (7%)
Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
           FR   L   L+RA+   G + P+ +Q + IP A+ G D++  A +G GKT VFVL  L  
Sbjct: 10  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL-- 67
Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
                 +L  + G+    L++C +RELA Q     + +   +P
Sbjct: 68  -----QQLEPVTGQVSV-LVMCHTRELAFQISKEYERFSKYMP 104

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 49/95 (51%), Gaps = 8/95 (8%)
Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
           F   +L E+L+R +   G ++P+ IQ + I   + G D++  A +G+GKT  F +  L  
Sbjct: 23  FDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
               +T +     + P  L + P+RELA Q   ++
Sbjct: 83  I---DTSV-----KAPQALXLAPTRELALQIQKVV 109

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 46/98 (46%), Gaps = 14/98 (14%)
Query: 155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP 214
           ++ A++     KPT IQ + IP AL G   +G + TG+GKT  ++LPI      +  ++ 
Sbjct: 15  IIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKIKPERAEV- 73
Query: 215 FLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIGSF 252
                    +I  P+RELA       Q Y   L I  F
Sbjct: 74  -------QAVITAPTRELA------TQIYHETLKITKF 98

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85
Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L   +E   K        P  L + P+ ELA QT  +I+
Sbjct: 86  LS-QVEPANKY-------PQCLCLSPTYELALQTGKVIE 116

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 48/97 (49%), Gaps = 17/97 (17%)
Query: 168 TPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI 225
           TP+Q + I   LS    D+I  A TG+GKT  F++PI    +  +    ++       +I
Sbjct: 45  TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVK----AVI 100
Query: 226 ICPSRELA-------RQTHD----IIQYYCAALPIGS 251
           + P+R+LA       ++ HD    + +Y C +L  G+
Sbjct: 101 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGT 137

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152
Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L   +E   K        P  L + P+ ELA QT  +I+
Sbjct: 153 LS-QVEPANKY-------PQCLCLSPTYELALQTGKVIE 183

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85
Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L   +E   K        P  L + P+ ELA QT  +I+
Sbjct: 86  LS-QVEPANKY-------PQCLCLSPTYELALQTGKVIE 116

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 63  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 122
Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L   +E   K        P  L + P+ ELA QT  +I+
Sbjct: 123 LS-QVEPANKY-------PQCLCLSPTYELALQTGKVIE 153

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 42  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 101
Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L   +E   K        P  L + P+ ELA QT  +I+
Sbjct: 102 LS-QVEPANKY-------PQCLCLSPTYELALQTGKVIE 132

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152
Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           L   +E   K        P  L + P+ ELA QT  +I+
Sbjct: 153 LS-QVEPANKY-------PQCLCLSPTYELALQTGKVIE 183

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 48/97 (49%), Gaps = 17/97 (17%)
Query: 168 TPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI 225
           TP+Q + I   LS    D+I  A TG+GKT  F++PI    +  +    ++       +I
Sbjct: 96  TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVK----AVI 151
Query: 226 ICPSRELA-------RQTHD----IIQYYCAALPIGS 251
           + P+R+LA       ++ HD    + +Y C +L  G+
Sbjct: 152 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGT 188

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 48/97 (49%), Gaps = 17/97 (17%)
Query: 168 TPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI 225
           TP+Q + I   LS    D+I  A TG+GKT  F++PI    +  +    ++       +I
Sbjct: 45  TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVK----AVI 100
Query: 226 ICPSRELA-------RQTHD----IIQYYCAALPIGS 251
           + P+R+LA       ++ HD    + +Y C +L  G+
Sbjct: 101 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGT 137

>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308 Length = 715

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 45/90 (50%), Gaps = 11/90 (12%)
Query: 149 MKLPESLVRALEAKGIKKPTPIQVQGIPAA-LSGRDIIGIAFTGSGKTLVFVLPILMFCL 207
           +KLP +++  ++ +GIKK  P Q + +    L G  ++  + TGSGKTL+  + I+ F L
Sbjct: 13  LKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLL 72
Query: 208 EQETKLPFLPGEGPYGLIICPSRELARQTH 237
           +           G   + + P R L  + +
Sbjct: 73  KN----------GGKAIYVTPLRALTNEKY 92

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	252
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	2e-47
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	8e-26
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-44
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	2e-26
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	3e-43
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-25
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	2e-39
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	6e-20
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	2e-36
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	9e-22
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	4e-35
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	8e-21
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	2e-31
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-20
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	7e-31
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	1e-20
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-30
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-18
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-26
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	4e-15
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	5e-26
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	6e-17
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	6e-26
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	7e-17
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-25
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-12
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-25
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	3e-10
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	2e-25
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-12
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	2e-25
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	4e-13
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	4e-25
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-10
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	5e-25
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-10
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	8e-25
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	3e-10
3bor_A	237	Human initiation factor 4A-II; translation initiat	8e-25
3bor_A	237	Human initiation factor 4A-II; translation initiat	6e-11
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	8e-25
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	9e-11
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	4e-24
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	3e-14
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	5e-24
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	3e-11
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-23
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-13
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-23
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	2e-10
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	3e-23
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	4e-11
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	6e-23
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-12
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-22
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-12
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-22
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-11
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-22
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-12
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	4e-16
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	5e-13
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	7e-07
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	5e-06
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	7e-06
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	3e-05
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	4e-05
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	6e-05
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-05
3b6e_A	216	Interferon-induced helicase C domain-containing P;	5e-04

>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 =  156 bits (397), Expect = 2e-47
 Identities = 46/133 (34%), Positives = 70/133 (52%), Gaps = 3/133 (2%)

Query: 117 SLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIP 176
               Q  +  RR+  I V G + P    +F     P +++  +  +   +PT IQ QG P
Sbjct: 2   MRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWP 61

Query: 177 AALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT 236
            ALSG D++G+A TGSGKTL ++LP ++    Q        G+GP  L++ P+RELA+Q 
Sbjct: 62  VALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQP---FLERGDGPICLVLAPTRELAQQV 118

Query: 237 HDIIQYYCAALPI 249
             +   YC A  +
Sbjct: 119 QQVAAEYCRACRL 131

>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 =  100 bits (251), Expect = 8e-26
 Identities = 30/93 (32%), Positives = 52/93 (55%), Gaps = 5/93 (5%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D++G+A TGSGKTL ++LP ++    Q        G+GP  L++ P+RELA+Q   +  
Sbjct: 67  LDMVGVAQTGSGKTLSYLLPAIVHINHQP---FLERGDGPICLVLAPTRELAQQVQQVAA 123

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
            YC A  +  ++    GG P    +  +++G++
Sbjct: 124 EYCRACRL--KSTCIYGGAPKGPQIRDLERGVE 154

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  153 bits (390), Expect = 1e-44
 Identities = 35/128 (27%), Positives = 58/128 (45%), Gaps = 10/128 (7%)

Query: 132 ILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTG 191
           +   G++ PP   SF  +++ E ++  +E     +PTP+Q   IP     RD++  A TG
Sbjct: 3   VEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTG 62

Query: 192 SGKTLVFVLPILMFCLEQETKLPFLP----------GEGPYGLIICPSRELARQTHDIIQ 241
           SGKT  F+LPIL                         + P  L++ P+RELA Q ++  +
Sbjct: 63  SGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEAR 122

Query: 242 YYCAALPI 249
            +     +
Sbjct: 123 KFSYRSRV 130

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  104 bits (263), Expect = 2e-26
 Identities = 28/101 (27%), Positives = 46/101 (45%), Gaps = 12/101 (11%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLP----------GEGPYGLIICPSRE 57
           RD++  A TGSGKT  F+LPIL                         + P  L++ P+RE
Sbjct: 53  RDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRE 112

Query: 58  LARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKG 98
           LA Q ++  + +     +  R C+  GG  + Q +  +++G
Sbjct: 113 LAVQIYEEARKFSYRSRV--RPCVVYGGADIGQQIRDLERG 151

>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 =  150 bits (382), Expect = 3e-43
 Identities = 44/123 (35%), Positives = 60/123 (48%), Gaps = 3/123 (2%)

Query: 127 RRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIG 186
             N+ + V G DVP     F    L + ++  +   G K PTPIQ   IP   SGRD++ 
Sbjct: 39  YNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMA 98

Query: 187 IAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA 246
            A TGSGKT  F+LPIL   LE       L    P  +I+ P+RELA Q  +  + +   
Sbjct: 99  CAQTGSGKTAAFLLPILSKLLEDP---HELELGRPQVVIVSPTRELAIQIFNEARKFAFE 155

Query: 247 LPI 249
             +
Sbjct: 156 SYL 158

>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 =  103 bits (259), Expect = 1e-25
 Identities = 29/91 (31%), Positives = 43/91 (47%), Gaps = 5/91 (5%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           RD++  A TGSGKT  F+LPIL   LE       L    P  +I+ P+RELA Q  +  +
Sbjct: 94  RDLMACAQTGSGKTAAFLLPILSKLLEDP---HELELGRPQVVIVSPTRELAIQIFNEAR 150

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKG 98
            +     +  +  +  GG       + I +G
Sbjct: 151 KFAFESYL--KIGIVYGGTSFRHQNECITRG 179

>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 =  136 bits (344), Expect = 2e-39
 Identities = 45/128 (35%), Positives = 65/128 (50%), Gaps = 11/128 (8%)

Query: 126 IRRNLRILVEGDDVPPACCSF----RLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG 181
           +R   +I V+G D+P    +F    +  K+   L++ +   G + PTPIQ+Q IP  L G
Sbjct: 7   LRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHG 66

Query: 182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           R+++  A TGSGKTL F +PILM   +          +G   LII P+RELA Q H  + 
Sbjct: 67  RELLASAPTGSGKTLAFSIPILMQLKQP-------ANKGFRALIISPTRELASQIHRELI 119

Query: 242 YYCAALPI 249
                   
Sbjct: 120 KISEGTGF 127

>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 = 84.9 bits (211), Expect = 6e-20
 Identities = 27/92 (29%), Positives = 37/92 (40%), Gaps = 10/92 (10%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           R+++  A TGSGKTL F +PILM   +          +G   LII P+RELA Q H  + 
Sbjct: 67  RELLASAPTGSGKTLAFSIPILMQLKQP-------ANKGFRALIISPTRELASQIHRELI 119

Query: 68  YYCAALPIPLRTCLAIGGVP-MNQSLDVIKKG 98
                     R  +         +      K 
Sbjct: 120 KISEGT--GFRIHMIHKAAVAAKKFGPKSSKK 149

>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 =  128 bits (323), Expect = 2e-36
 Identities = 37/114 (32%), Positives = 54/114 (47%), Gaps = 3/114 (2%)

Query: 134 VEGDDVPPACCSFR-LMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGS 192
            E   +P   C F+   +    L++++   GI KPTPIQ Q  P  L G D+I +A TG+
Sbjct: 9   GEKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGT 68

Query: 193 GKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA 246
           GKTL +++P  +    Q          GP  L++ P+RELA         Y   
Sbjct: 69  GKTLSYLMPGFIHLDSQPISRE--QRNGPGMLVLTPTRELALHVEAECSKYSYK 120

>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 = 89.2 bits (222), Expect = 9e-22
 Identities = 27/93 (29%), Positives = 42/93 (45%), Gaps = 5/93 (5%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D+I +A TG+GKTL +++P  +    Q          GP  L++ P+RELA        
Sbjct: 58  IDLIVVAQTGTGKTLSYLMPGFIHLDSQPISRE--QRNGPGMLVLTPTRELALHVEAECS 115

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
            Y       L++    GG   N  ++ I KG+ 
Sbjct: 116 KYSYK---GLKSICIYGGRNRNGQIEDISKGVD 145

>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 =  124 bits (315), Expect = 4e-35
 Identities = 40/124 (32%), Positives = 60/124 (48%), Gaps = 3/124 (2%)

Query: 129 NLRILVEGDD--VPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIG 186
           ++ + V G D        +F  +KL  ++   +     ++PTPIQ   IPA L  RDI+ 
Sbjct: 6   SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMA 65

Query: 187 IAFTGSGKTLVFVLPILMFCLEQETKLPFL-PGEGPYGLIICPSRELARQTHDIIQYYCA 245
            A TGSGKT  F++PI+   + Q+           P  LI+ P+RELA Q     Q +  
Sbjct: 66  CAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSL 125

Query: 246 ALPI 249
             P+
Sbjct: 126 NTPL 129

>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 = 87.2 bits (217), Expect = 8e-21
 Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 3/92 (3%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL-PGEGPYGLIICPSRELARQTHDII 66
           RDI+  A TGSGKT  F++PI+   + Q+           P  LI+ P+RELA Q     
Sbjct: 61  RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSES 120

Query: 67  QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKG 98
           Q +    P+  R+C+  GG   +  +  ++ G
Sbjct: 121 QKFSLNTPL--RSCVVYGGADTHSQIREVQMG 150

>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 =  115 bits (289), Expect = 2e-31
 Identities = 37/105 (35%), Positives = 56/105 (53%), Gaps = 4/105 (3%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F    L +  ++ L+    +  T IQ Q I  AL G+D++G A TGSGKTL F++P+  
Sbjct: 26  RFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPV-- 83

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI 249
             LE   +L +   +G   LII P+RELA QT ++++        
Sbjct: 84  --LEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDF 126

>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 = 85.4 bits (212), Expect = 3e-20
 Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 6/90 (6%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           +D++G A TGSGKTL F++P+    LE   +L +   +G   LII P+RELA QT ++++
Sbjct: 63  KDVLGAAKTGSGKTLAFLVPV----LEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLR 118

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKK 97
                        L IGG  +    + I  
Sbjct: 119 KVGKN--HDFSAGLIIGGKDLKHEAERINN 146

>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 =  114 bits (287), Expect = 7e-31
 Identities = 36/100 (36%), Positives = 54/100 (54%), Gaps = 4/100 (4%)

Query: 150 KLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQ 209
            + E+ ++A++  G    T IQ + I   L GRD++  A TGSGKTL F++P     +E 
Sbjct: 60  LVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPA----VEL 115

Query: 210 ETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI 249
             KL F+P  G   LI+ P+RELA QT  +++        
Sbjct: 116 IVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVH 155

>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 = 87.0 bits (216), Expect = 1e-20
 Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 6/92 (6%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           RD++  A TGSGKTL F++P     +E   KL F+P  G   LI+ P+RELA QT  +++
Sbjct: 92  RDLLAAAKTGSGKTLAFLIPA----VELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLK 147

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGI 99
                        L +GG   +     +  GI
Sbjct: 148 ELMTH--HVHTYGLIMGGSNRSAEAQKLGNGI 177

>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 =  112 bits (282), Expect = 3e-30
 Identities = 40/105 (38%), Positives = 60/105 (57%), Gaps = 8/105 (7%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F+ + + + L  A +  G  KPT IQ++ IP AL GRDIIG+A TGSGKT  F LPIL 
Sbjct: 44  TFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPIL- 102

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI 249
                   L   P +  + L++ P+RELA Q  +  +   +++ +
Sbjct: 103 ------NALLETP-QRLFALVLTPTRELAFQISEQFEALGSSIGV 140

>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 = 80.0 bits (198), Expect = 3e-18
 Identities = 30/91 (32%), Positives = 46/91 (50%), Gaps = 10/91 (10%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           RDIIG+A TGSGKT  F LPIL         L   P +  + L++ P+RELA Q  +  +
Sbjct: 81  RDIIGLAETGSGKTGAFALPIL-------NALLETP-QRLFALVLTPTRELAFQISEQFE 132

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKG 98
              +   I +++ + +GG+        + K 
Sbjct: 133 ALGS--SIGVQSAVIVGGIDSMSQSLALAKK 161

>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 =  101 bits (253), Expect = 2e-26
 Identities = 37/99 (37%), Positives = 51/99 (51%), Gaps = 5/99 (5%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F+   L   ++ AL  +G+  PTPIQ   +P AL G+D+IG A TG+GKTL F LPI  
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIA- 60

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
               +        G  P  L++ P+RELA Q    +   
Sbjct: 61  ----ERLAPSQERGRKPRALVLTPTRELALQVASELTAV 95

>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 = 70.6 bits (174), Expect = 4e-15
 Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 9/93 (9%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           +D+IG A TG+GKTL F LPI      +        G  P  L++ P+RELA Q    + 
Sbjct: 39  KDLIGQARTGTGKTLAFALPIA-----ERLAPSQERGRKPRALVLTPTRELALQVASELT 93

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
                    L+     GG    +  + + +G  
Sbjct: 94  AVAPH----LKVVAVYGGTGYGKQKEALLRGAD 122

>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 =  105 bits (263), Expect = 5e-26
 Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 6/99 (6%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
                 L + + +A+        TP+Q + I   LS    D+I  A TG+GKT  F++PI
Sbjct: 73  LLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPI 132

Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
                +      F        +I+ P+R+LA Q    ++
Sbjct: 133 ----FQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVK 167

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score = 78.7 bits (194), Expect = 6e-17
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 6/93 (6%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D+I  A TG+GKT  F++PI     +      F        +I+ P+R+LA Q    ++
Sbjct: 112 HDVIARAKTGTGKTFAFLIPI----FQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVK 167

Query: 68  YYCAALP--IPLRTCLAIGGVPMNQSLDVIKKG 98
                            +GG     +++ + K 
Sbjct: 168 KIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKL 200

>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 =  104 bits (262), Expect = 6e-26
 Identities = 26/102 (25%), Positives = 43/102 (42%), Gaps = 6/102 (5%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
                 L + + +A+        TP+Q + I   LS    D+I  A TG+GKT  F++PI
Sbjct: 22  LLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPI 81

Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC 244
                +      F        +I+ P+R+LA Q    ++   
Sbjct: 82  ----FQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIH 119

>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 = 78.7 bits (194), Expect = 7e-17
 Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 7/96 (7%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D+I  A TG+GKT  F++PI     +      F        +I+ P+R+LA Q    ++
Sbjct: 61  HDVIARAKTGTGKTFAFLIPI----FQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVK 116

Query: 68  YYCAALP--IPLRTCLAIGGVPMNQSLDVIKK-GIQ 100
                            +GG     +++ + K    
Sbjct: 117 KIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPN 152

>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 =  103 bits (258), Expect = 1e-25
 Identities = 33/99 (33%), Positives = 52/99 (52%), Gaps = 8/99 (8%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F  M L E L+R + A G +KP+ IQ + I   + GRD+I  + +G+GKT  F + +L 
Sbjct: 38  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 97

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
            CL+ + +           LI+ P+RELA Q    +   
Sbjct: 98  -CLDIQVR-------ETQALILAPTRELAVQIQKGLLAL 128

>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 = 65.7 bits (161), Expect = 1e-12
 Identities = 34/139 (24%), Positives = 58/139 (41%), Gaps = 33/139 (23%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           RD+I  + +G+GKT  F + +L  CL+ + +           LI+ P+RELA Q    + 
Sbjct: 75  RDVIAQSQSGTGKTATFSISVLQ-CLDIQVR-------ETQALILAPTRELAVQIQKGLL 126

Query: 68  YYCAALPIPLRTCLAI-GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDII 126
                + +    C A  GG  + + +  +  G                +   P +V D+I
Sbjct: 127 ALGDYMNV---QCHACIGGTNVGEDIRKLDYGQH-------------VVAGTPGRVFDMI 170

Query: 127 RR------NLRILV--EGD 137
           RR       +++LV  E D
Sbjct: 171 RRRSLRTRAIKMLVLDEAD 189

>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 = 99.2 bits (248), Expect = 1e-25
 Identities = 32/114 (28%), Positives = 52/114 (45%), Gaps = 10/114 (8%)

Query: 136 GDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKT 195
           GD +      F  + L   ++  L A G ++P+P+Q++ IP    G D+I  A +G+GKT
Sbjct: 16  GDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKT 75

Query: 196 LVFVLPILMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
            VF        L+    +           LI+ P+RE+A Q H +I      + 
Sbjct: 76  CVFSTIA----LDSLVLENL-----STQILILAPTREIAVQIHSVITAIGIKME 120

>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 = 57.6 bits (140), Expect = 3e-10
 Identities = 27/92 (29%), Positives = 41/92 (44%), Gaps = 11/92 (11%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDII 66
            D+I  A +G+GKT VF        L+    +           LI+ P+RE+A Q H +I
Sbjct: 62  LDLIVQAKSGTGKTCVFSTIA----LDSLVLENL-----STQILILAPTREIAVQIHSVI 112

Query: 67  QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKG 98
                 +   L   + IGG P++Q    +KK 
Sbjct: 113 TAIGIKME-GLECHVFIGGTPLSQDKTRLKKC 143

>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 =  102 bits (257), Expect = 2e-25
 Identities = 34/99 (34%), Positives = 53/99 (53%), Gaps = 8/99 (8%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F    L   L+  +   G +KP+PIQ + IP A++GRDI+  A  G+GKT  FV+P L 
Sbjct: 22  TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 81

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
             ++ +             LI+ P+RELA QT  +++  
Sbjct: 82  -KVKPKLN-------KIQALIMVPTRELALQTSQVVRTL 112

>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 = 65.7 bits (161), Expect = 1e-12
 Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 12/94 (12%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           RDI+  A  G+GKT  FV+P L   ++ +             LI+ P+RELA QT  +++
Sbjct: 59  RDILARAKNGTGKTAAFVIPTLE-KVKPKLN-------KIQALIMVPTRELALQTSQVVR 110

Query: 68  YYCAALPIPLRTCLAI-GGVPMNQSLDVIKKGIQ 100
                  I   +C+   GG  +   +  + + + 
Sbjct: 111 TLGKHCGI---SCMVTTGGTNLRDDILRLNETVH 141

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 98.8 bits (247), Expect = 2e-25
 Identities = 30/104 (28%), Positives = 47/104 (45%), Gaps = 8/104 (7%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F        ++ A++     KPT IQ + IP AL G  ++G + TG+GKT  ++LPI+ 
Sbjct: 5   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 64

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
             ++ E             +I  P+RELA Q +          P
Sbjct: 65  -KIKPERA-------EVQAVITAPTRELATQIYHETLKITKFCP 100

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 65.7 bits (161), Expect = 4e-13
 Identities = 21/95 (22%), Positives = 38/95 (40%), Gaps = 10/95 (10%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
             ++G + TG+GKT  ++LPI+   ++ E             +I  P+RELA Q +    
Sbjct: 42  ESMVGQSQTGTGKTHAYLLPIME-KIKPERA-------EVQAVITAPTRELATQIYHETL 93

Query: 68  YYCAALPIPLR-TCLAI-GGVPMNQSLDVIKKGIQ 100
                 P         + GG    ++L+ +     
Sbjct: 94  KITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPH 128

>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 =  101 bits (253), Expect = 4e-25
 Identities = 29/99 (29%), Positives = 50/99 (50%), Gaps = 8/99 (8%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F  M+L E+L+R +   G ++P+ IQ + I   + G D++  A +G+GKT  F +  L 
Sbjct: 22  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 81

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
             ++   K        P  L++ P+RELA Q   ++   
Sbjct: 82  -RIDTSVK-------APQALMLAPTRELALQIQKVVMAL 112

>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 = 59.5 bits (145), Expect = 1e-10
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 12/92 (13%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D++  A +G+GKT  F +  L   ++   K        P  L++ P+RELA Q   ++ 
Sbjct: 59  HDVLAQAQSGTGKTGTFSIAALQ-RIDTSVK-------APQALMLAPTRELALQIQKVVM 110

Query: 68  YYCAALPIPLRTCLAI-GGVPMNQSLDVIKKG 98
                + I      A  GG    +  + ++  
Sbjct: 111 ALAFHMDI---KVHACIGGTSFVEDAEGLRDA 139

>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 =  101 bits (253), Expect = 5e-25
 Identities = 35/99 (35%), Positives = 53/99 (53%), Gaps = 8/99 (8%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           SF  M L ESL+R + A G +KP+ IQ + I   + G D+I  A +G+GKT  F + IL 
Sbjct: 41  SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ 100

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
             +E + K           L++ P+RELA+Q   ++   
Sbjct: 101 -QIELDLK-------ATQALVLAPTRELAQQIQKVVMAL 131

>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 = 59.1 bits (144), Expect = 2e-10
 Identities = 33/139 (23%), Positives = 58/139 (41%), Gaps = 32/139 (23%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D+I  A +G+GKT  F + IL   +E + K           L++ P+RELA+Q   ++ 
Sbjct: 78  YDVIAQAQSGTGKTATFAISILQ-QIELDLK-------ATQALVLAPTRELAQQIQKVVM 129

Query: 68  YYCAALPIPLRTCLAI-GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDII 126
                +     +C A  GG  +   +  ++              AP  I+  P +V D++
Sbjct: 130 ALGDYMGA---SCHACIGGTNVRAEVQKLQM------------EAPHIIVGTPGRVFDML 174

Query: 127 RR------NLRILV--EGD 137
            R       +++ V  E D
Sbjct: 175 NRRYLSPKYIKMFVLDEAD 193

>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 = 97.2 bits (243), Expect = 8e-25
 Identities = 29/99 (29%), Positives = 50/99 (50%), Gaps = 8/99 (8%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F  M+L E+L+R +   G ++P+ IQ + I   + G D++  A +G+GKT  F +  L 
Sbjct: 15  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 74

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
             ++   K        P  L++ P+RELA Q   ++   
Sbjct: 75  -RIDTSVK-------APQALMLAPTRELALQIQKVVMAL 105

>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 = 57.6 bits (140), Expect = 3e-10
 Identities = 29/138 (21%), Positives = 54/138 (39%), Gaps = 32/138 (23%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D++  A +G+GKT  F +  L   ++   K        P  L++ P+RELA Q   ++ 
Sbjct: 52  HDVLAQAQSGTGKTGTFSIAALQ-RIDTSVK-------APQALMLAPTRELALQIQKVVM 103

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIR 127
                + I      A  G            G  + +  +   R  + ++  P +V D I+
Sbjct: 104 ALAFHMDI---KVHACIG------------GTSFVEDAE-GLRDAQIVVGTPGRVFDNIQ 147

Query: 128 R------NLRILV--EGD 137
           R       +++ +  E D
Sbjct: 148 RRRFRTDKIKMFILDEAD 165

>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 = 97.7 bits (244), Expect = 8e-25
 Identities = 37/99 (37%), Positives = 53/99 (53%), Gaps = 8/99 (8%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F  M L ESL+R + A G +KP+ IQ + I   + G D+I  A +G+GKT  F + IL 
Sbjct: 31  NFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQ 90

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
             LE E K           L++ P+RELA+Q   +I   
Sbjct: 91  -QLEIEFK-------ETQALVLAPTRELAQQIQKVILAL 121

>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 = 59.5 bits (145), Expect = 6e-11
 Identities = 35/138 (25%), Positives = 57/138 (41%), Gaps = 30/138 (21%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D+I  A +G+GKT  F + IL   LE E K           L++ P+RELA+Q   +I 
Sbjct: 68  YDVIAQAQSGTGKTATFAISILQ-QLEIEFK-------ETQALVLAPTRELAQQIQKVIL 119

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIR 127
                +      C  IGG  +   +  ++              AP  ++  P +V D++ 
Sbjct: 120 ALGDYMGATCHAC--IGGTNVRNEMQKLQA------------EAPHIVVGTPGRVFDMLN 165

Query: 128 R------NLRILV--EGD 137
           R       +++ V  E D
Sbjct: 166 RRYLSPKWIKMFVLDEAD 183

>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 = 96.8 bits (242), Expect = 8e-25
 Identities = 34/100 (34%), Positives = 51/100 (51%), Gaps = 10/100 (10%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F    L   L+  +   G +KP+PIQ + IP ALSGRDI+  A  G+GK+  +++P+  
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPL-- 61

Query: 205 FCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
             LE+ + K           ++I P+RELA Q   I    
Sbjct: 62  --LERLDLKKD-----NIQAMVIVPTRELALQVSQICIQV 94

>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 = 58.7 bits (143), Expect = 9e-11
 Identities = 21/94 (22%), Positives = 39/94 (41%), Gaps = 11/94 (11%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDII 66
           RDI+  A  G+GK+  +++P+    LE+ + K           ++I P+RELA Q   I 
Sbjct: 41  RDILARAKNGTGKSGAYLIPL----LERLDLKKD-----NIQAMVIVPTRELALQVSQIC 91

Query: 67  QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
                 +    +     GG  +   +  +   + 
Sbjct: 92  IQVSKHMG-GAKVMATTGGTNLRDDIMRLDDTVH 124

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 99.0 bits (247), Expect = 4e-24
 Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 11/98 (11%)

Query: 147 RLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFC 206
                 E      + K  K  T  Q       + G+    +A TG GKT   ++  L   
Sbjct: 2   EFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTAL--- 58

Query: 207 LEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC 244
                   +L  +G    ++ P+  L +QT + +Q   
Sbjct: 59  --------WLARKGKKSALVFPTVTLVKQTLERLQKLA 88

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 70.5 bits (173), Expect = 3e-14
 Identities = 16/98 (16%), Positives = 34/98 (34%), Gaps = 14/98 (14%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           +    +A TG GKT   ++  L           +L  +G    ++ P+  L +QT + +Q
Sbjct: 37  KSFTMVAPTGVGKTTFGMMTAL-----------WLARKGKKSALVFPTVTLVKQTLERLQ 85

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPI 105
                    ++       +   +     K   + +  I
Sbjct: 86  KLADE---KVKIFGFYSSMKKEEKEKFEKSFEEDDYHI 120

>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 = 97.6 bits (244), Expect = 5e-24
 Identities = 29/99 (29%), Positives = 46/99 (46%), Gaps = 14/99 (14%)

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
           + E + +A+   G K  T +Q + IP  L G++++  A TGSGKT  + +PIL       
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54

Query: 211 TKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI 249
                    G   L++ P+REL RQ    I+     +  
Sbjct: 55  --------LGMKSLVVTPTRELTRQVASHIRDIGRYMDT 85

>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 = 61.4 bits (150), Expect = 3e-11
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 18/92 (19%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           ++++  A TGSGKT  + +PIL                G   L++ P+REL RQ    I+
Sbjct: 32  KNVVVRAKTGSGKTAAYAIPILE--------------LGMKSLVVTPTRELTRQVASHIR 77

Query: 68  YYCAALPIPLRTCLAI-GGVPMNQSLDVIKKG 98
                +         + GG+P    ++ ++  
Sbjct: 78  DIGRYMDT---KVAEVYGGMPYKAQINRVRNA 106

>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 = 94.2 bits (235), Expect = 1e-23
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 8/104 (7%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            FR   L   L+RA+   G + P+ +Q + IP A+ G D++  A +G GKT VFVL  L 
Sbjct: 15  GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL- 73

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
                  +L  + G+    L++C +RELA Q     + +   +P
Sbjct: 74  ------QQLEPVTGQ-VSVLVMCHTRELAFQISKEYERFSKYMP 110

>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 = 66.5 bits (163), Expect = 2e-13
 Identities = 31/138 (22%), Positives = 60/138 (43%), Gaps = 29/138 (21%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            D++  A +G GKT VFVL  L        +L  + G+    L++C +RELA Q     +
Sbjct: 52  MDVLCQAKSGMGKTAVFVLATL-------QQLEPVTGQ-VSVLVMCHTRELAFQISKEYE 103

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIR 127
            +   +P  ++  +  GG+ + +  +V+KK              P  ++  P ++  + R
Sbjct: 104 RFSKYMP-NVKVAVFFGGLSIKKDEEVLKKN------------CPHIVVGTPGRILALAR 150

Query: 128 R------NLRILV--EGD 137
                  +++  +  E D
Sbjct: 151 NKSLNLKHIKHFILDECD 168

>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 = 96.8 bits (242), Expect = 1e-23
 Identities = 33/100 (33%), Positives = 54/100 (54%), Gaps = 10/100 (10%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGR-DIIGIAFTGSGKTLVFVLPIL 203
           +F  + L ++++ A+  KG +KPT IQ++ IP  L+   +I+  A TGSGKT  F +P++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

Query: 204 MFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
                    +      G   +I+ P+RELA Q  D I+  
Sbjct: 67  -------ELVN--ENNGIEAIILTPTRELAIQVADEIESL 97

>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 = 59.5 bits (145), Expect = 2e-10
 Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 13/92 (14%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
            +I+  A TGSGKT  F +P++         +      G   +I+ P+RELA Q  D I+
Sbjct: 45  YNIVAQARTGSGKTASFAIPLI-------ELVN--ENNGIEAIILTPTRELAIQVADEIE 95

Query: 68  YYCAALPIPLRTCLAI-GGVPMNQSLDVIKKG 98
                  +       I GG  +   +  +K  
Sbjct: 96  SLKGNKNL---KIAKIYGGKAIYPQIKALKNA 124

>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 = 96.1 bits (240), Expect = 3e-23
 Identities = 32/101 (31%), Positives = 52/101 (51%), Gaps = 10/101 (9%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  + L   L++ + A   +KP+ IQ + +P  L    R++I  + +G+GKT  F L +
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65

Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
           L   +  E          P  + + PSRELARQT +++Q  
Sbjct: 66  LT-RVNPEDA-------SPQAICLAPSRELARQTLEVVQEM 98

>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 = 61.0 bits (149), Expect = 4e-11
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 10/78 (12%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           R++I  + +G+GKT  F L +L   +  E          P  + + PSRELARQT +++Q
Sbjct: 45  RNMIAQSQSGTGKTAAFSLTMLT-RVNPEDA-------SPQAICLAPSRELARQTLEVVQ 96

Query: 68  YYCAALPIPLRTCLAIGG 85
                  I   + L +  
Sbjct: 97  EMGKFTKI--TSQLIVPD 112

>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 = 95.0 bits (237), Expect = 6e-23
 Identities = 34/105 (32%), Positives = 51/105 (48%), Gaps = 10/105 (9%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            FR   L   L+RA+   G + P+ +Q + IP A+ G D++  A +G GKT VFVL    
Sbjct: 9   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT-- 66

Query: 205 FCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
             L+Q E             L++C +RELA Q     + +   +P
Sbjct: 67  --LQQLEPVTG-----QVSVLVMCHTRELAFQISKEYERFSKYMP 104

>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 = 64.9 bits (159), Expect = 2e-12
 Identities = 31/139 (22%), Positives = 58/139 (41%), Gaps = 31/139 (22%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDII 66
            D++  A +G GKT VFVL      L+Q E             L++C +RELA Q     
Sbjct: 46  MDVLCQAKSGMGKTAVFVLAT----LQQLEPVTG-----QVSVLVMCHTRELAFQISKEY 96

Query: 67  QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDII 126
           + +   +P  ++  +  GG+ + +  +V+KK              P  ++  P ++  + 
Sbjct: 97  ERFSKYMP-NVKVAVFFGGLSIKKDEEVLKKN------------CPHIVVGTPGRILALA 143

Query: 127 RR------NLRILV--EGD 137
           R       +++  +  E D
Sbjct: 144 RNKSLNLKHIKHFILDECD 162

>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 = 95.1 bits (237), Expect = 1e-22
 Identities = 31/102 (30%), Positives = 52/102 (50%), Gaps = 12/102 (11%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152

Query: 203 LMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
               L Q E    +     P  L + P+ ELA QT  +I+  
Sbjct: 153 ----LSQVEPANKY-----PQCLCLSPTYELALQTGKVIEQM 185

>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 = 64.6 bits (158), Expect = 4e-12
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 14/94 (14%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDII 66
           +++I  + +G+GKT  FVL +    L Q E    +     P  L + P+ ELA QT  +I
Sbjct: 132 QNLIAQSQSGTGKTAAFVLAM----LSQVEPANKY-----PQCLCLSPTYELALQTGKVI 182

Query: 67  QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
           +      P  L+   A+ G  + +     K   Q
Sbjct: 183 EQMGKFYPE-LKLAYAVRGNKLERGQ---KISEQ 212

>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 = 94.5 bits (236), Expect = 1e-22
 Identities = 31/102 (30%), Positives = 52/102 (50%), Gaps = 12/102 (11%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85

Query: 203 LMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
               L Q E    +     P  L + P+ ELA QT  +I+  
Sbjct: 86  ----LSQVEPANKY-----PQCLCLSPTYELALQTGKVIEQM 118

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score = 63.0 bits (154), Expect = 1e-11
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 14/94 (14%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQ-ETKLPFLPGEGPYGLIICPSRELARQTHDII 66
           +++I  + +G+GKT  FVL +    L Q E    +     P  L + P+ ELA QT  +I
Sbjct: 65  QNLIAQSQSGTGKTAAFVLAM----LSQVEPANKY-----PQCLCLSPTYELALQTGKVI 115

Query: 67  QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
           +      P  L+   A+ G  + +     K   Q
Sbjct: 116 EQMGKFYPE-LKLAYAVRGNKLERGQ---KISEQ 145

>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 = 92.5 bits (230), Expect = 2e-22
 Identities = 31/101 (30%), Positives = 52/101 (51%), Gaps = 10/101 (9%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPI 202
           SF  ++L   L++ + A G  +P+ IQ   +P  L+   +++I  + +G+GKT  FVL +
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152

Query: 203 LMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY 243
           L   +E   K        P  L + P+ ELA QT  +I+  
Sbjct: 153 LS-QVEPANK-------YPQCLCLSPTYELALQTGKVIEQM 185

>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 = 64.0 bits (156), Expect = 4e-12
 Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 12/93 (12%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
           +++I  + +G+GKT  FVL +L   +E   K        P  L + P+ ELA QT  +I+
Sbjct: 132 QNLIAQSQSGTGKTAAFVLAMLS-QVEPANK-------YPQCLCLSPTYELALQTGKVIE 183

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
                 P  L+   A+ G  + +     K   Q
Sbjct: 184 QMGKFYPE-LKLAYAVRGNKLERGQ---KISEQ 212

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 48.6 bits (116), Expect = 7e-07
 Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 149 MKLPESLVRALEAKGIKKPTPIQVQGIPAAL-SGRDIIGIAFTGSGKTLVFVLPILMFCL 207
           +KLP +++  ++ +GIKK  P Q + +   L  G  ++  + TGSGKTL+  + I+ F L
Sbjct: 13  LKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLL 72

Query: 208 EQETK 212
           +   K
Sbjct: 73  KNGGK 77

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 46.3 bits (110), Expect = 5e-06
 Identities = 13/53 (24%), Positives = 29/53 (54%)

Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL 203
           +    V  L+ +GI++  P Q + +    SG++++    T +GKTL+  + ++
Sbjct: 10  ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMV 62

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 45.6 bits (108), Expect = 7e-06
 Identities = 16/66 (24%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 148 LMKLPESLVRALEAKGIKKPTPIQVQGIPAAL-SGRDIIGIAFTGSGKTLVFVLPILMFC 206
            +++ E +   L+ +GI+   P Q + + + +  G++ +    T SGKTL+  + ++   
Sbjct: 5   ELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRI 64

Query: 207 LEQETK 212
           L Q  K
Sbjct: 65  LTQGGK 70

>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 Length = 494

 Score = 44.8 bits (105), Expect = 1e-05
 Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 11/79 (13%)

Query: 166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI 225
           +P   Q           + + +  TG GKTL+ ++       +   K+          L+
Sbjct: 9   QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKV----------LM 57

Query: 226 ICPSRELARQTHDIIQYYC 244
           + P++ L  Q  +  +   
Sbjct: 58  LAPTKPLVLQHAESFRRLF 76

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

 Score = 44.1 bits (103), Expect = 3e-05
 Identities = 41/217 (18%), Positives = 72/217 (33%), Gaps = 65/217 (29%)

Query: 5   RNSRDII--GIAFTGSGKTLVFVLPILMFCL--EQETKLPFLPGEGPY----GLIICPSR 56
           R +++++  G+   GSGKT    +  L  CL  + + K+ F      +         P  
Sbjct: 148 RPAKNVLIDGVL--GSGKT---WV-ALDVCLSYKVQCKMDF----KIFWLNLKNCNSPET 197

Query: 57  ELARQT---HDIIQYYCA----ALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSW 109
            L       + I   + +    +  I LR          +     +++ ++       S 
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRI---------HSIQAELRRLLK-------SK 241

Query: 110 RAPRCILSLPDQVHD--IIRR-NL--RILV------EGDDVPPAC-CSFRLMKLPESL-- 155
               C+L L   V +       NL  +IL+        D +  A      L     +L  
Sbjct: 242 PYENCLLVL-LNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300

Query: 156 --VRALEAK--GIKKPT-PIQVQGI-PAALSGRDIIG 186
             V++L  K    +    P +V    P  LS   II 
Sbjct: 301 DEVKSLLLKYLDCRPQDLPREVLTTNPRRLS---IIA 334

>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* Length = 556

 Score = 43.8 bits (102), Expect = 3e-05
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 164 IKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG 223
            KK    Q++    A++G++ +  A TGSGKT V +L                 G     
Sbjct: 5   TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA------GRKAKV 58

Query: 224 LIICPSRELARQTHDIIQYYC 244
           + +     +  Q  ++ +++ 
Sbjct: 59  VFLATKVPVYEQQKNVFKHHF 79

>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} Length = 797

 Score = 43.4 bits (101), Expect = 4e-05
 Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 6/108 (5%)

Query: 137 DDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTL 196
           +  P    S  L    E + +       KK    Q++    A++G++ +  A TGSGKT 
Sbjct: 219 EAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTF 278

Query: 197 VFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC 244
           V +L       +         G     + +     +  Q  ++ +++ 
Sbjct: 279 VSILICEHH-FQN-----MPAGRKAKVVFLATKVPVYEQQKNVFKHHF 320

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 43.0 bits (100), Expect = 6e-05
 Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI 225
           KP   Q++    A+ G++ I  A TG GKT V +L       +      F  G+    + 
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKK------FPQGQKGKVVF 66

Query: 226 ICPSRELARQTHDIIQYYC 244
                 +  Q   +   Y 
Sbjct: 67  FANQIPVYEQNKSVFSKYF 85

>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} Length = 936

 Score = 42.6 bits (99), Expect = 8e-05
 Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 6/108 (5%)

Query: 137 DDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTL 196
           +  P    S  L    E + +       KK    Q++    A++G++ +  A TGSGKT 
Sbjct: 219 EAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTF 278

Query: 197 VFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC 244
           V +L       +         G     + +     +  Q  ++ +++ 
Sbjct: 279 VSILICEHH-FQN-----MPAGRKAKVVFLATKVPVYEQQKNVFKHHF 320

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 39.4 bits (92), Expect = 5e-04
 Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 5/90 (5%)

Query: 152 PESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQET 211
            E++      +   +  P Q++    AL G++II    TGSGKT V V       L+++ 
Sbjct: 19  EENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDH-LDKKK 77

Query: 212 KLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
           K      E    +++     L  Q      
Sbjct: 78  K----ASEPGKVIVLVNKVLLVEQLFRKEF 103

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	252
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.94
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.9
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.88
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.88
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.88
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.87
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.87
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.86
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.86
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.85
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.85
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.85
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.84
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.84
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.83
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.83
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.83
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.83
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.83
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.82
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.82
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.82
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.82
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.82
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.81
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.81
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.8
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.8
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.8
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.8
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.79
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.78
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.77
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.77
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.76
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.76
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.76
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.75
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.75
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.74
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.73
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.73
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.73
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.73
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.73
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.73
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.73
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.72
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.72
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.71
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.71
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.7
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.67
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.67
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.67
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.67
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.66
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.65
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.65
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.65
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.64
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.64
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.63
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.63
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.61
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.56
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.55
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.55
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.54
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.53
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.53
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.53
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.52
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.52
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.52
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.51
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.5
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.49
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.48
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.47
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.46
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.45
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.42
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.42
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.41
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.38
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.37
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.37
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.36
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.35
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.34
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.34
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.32
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.3
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.29
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.25
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.24
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.22
3h1t_A	590	Type I site-specific restriction-modification syst	99.21
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.2
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.15
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.15
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.13
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.02
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.02
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	98.99
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	98.96
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	98.95
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	98.94
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	98.94
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	98.93
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.83
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	98.81
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	98.8
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	98.79
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	98.77
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	98.76
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	98.76
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.74
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	98.69
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.68
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	98.65
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	98.61
3b6e_A	216	Interferon-induced helicase C domain-containing P;	98.6
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	98.52
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	98.51
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.49
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.47
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	98.39
4gl2_A	699	Interferon-induced helicase C domain-containing P;	98.33
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.31
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	98.28
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.28
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	98.28
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	98.26
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	98.18
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.14
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.14
1yks_A	440	Genome polyprotein [contains: flavivirin protease	98.13
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.12
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.11
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.1
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.08
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	98.07
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.0
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	97.97
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.97
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	97.94
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	97.87
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	97.7
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	97.47
3jux_A	822	Protein translocase subunit SECA; protein transloc	97.33
3h1t_A	590	Type I site-specific restriction-modification syst	97.32
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	97.21
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	97.16
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	97.11
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.02
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	96.28
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.18
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	95.55
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	95.31
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.22
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	95.16
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	95.12
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	94.98
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	94.72
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	94.6
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	94.49
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	94.22
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.04
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	93.69
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	93.34
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	93.34
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	93.31
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	91.97
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	91.61
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.59
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	91.21
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	91.09
3co5_A	143	Putative two-component system transcriptional RES	90.7
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	90.49
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	90.3
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	90.15
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	89.97
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	89.96
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	89.64
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	89.53
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	89.5
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	89.25
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	88.75
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	88.74
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	88.55
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	88.16
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	88.08
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	88.05
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	88.0
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	87.93
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	87.82
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	87.47
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	87.31
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	87.26
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	87.13
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	87.06
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	86.84
2eyu_A	261	Twitching motility protein PILT; pilus retraction	86.83
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	86.82
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	86.5
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	86.15
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	86.15
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	85.95
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	85.92
3bos_A	242	Putative DNA replication factor; P-loop containing	85.92
2r6a_A	454	DNAB helicase, replicative helicase; replication,	85.86
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	85.8
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	85.75
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	85.54
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	85.26
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	85.2
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	85.16
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	85.12
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	85.08
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	84.81
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	84.76
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	84.74
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	84.63
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	84.57
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	84.45
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	84.34
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	84.26
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	84.2
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	84.09
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	84.02
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	83.84
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	83.83
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	83.81
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	83.72
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	83.55
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	83.47
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	83.37
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	83.33
1xp8_A	366	RECA protein, recombinase A; recombination, radior	83.33
1tue_A	212	Replication protein E1; helicase, replication, E1E	83.18
2ewv_A	372	Twitching motility protein PILT; pilus retraction	83.12
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	82.99
2qgz_A	308	Helicase loader, putative primosome component; str	82.97
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	82.88
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	82.87
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	82.69
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	82.58
1u94_A	356	RECA protein, recombinase A; homologous recombinat	82.55
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	82.49
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	82.47
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	82.47
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	82.35
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	82.31
2r44_A	331	Uncharacterized protein; putative ATPase, structur	82.23
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	82.23
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	82.07
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	82.04
2chg_A	226	Replication factor C small subunit; DNA-binding pr	82.01
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	81.99
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	81.96
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	81.93
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	81.88
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	81.84
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	81.84
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	81.8
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	81.79
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	81.79
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	81.73
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	81.7
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	81.7
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	81.61
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	81.55
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	81.48
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	81.45
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	81.28
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	81.25
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	81.23
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	81.01
3u06_A	412	Protein claret segregational; motor domain, stalk	80.82
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	80.81
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	80.75
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	80.59
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	80.55
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	80.45
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	80.37
2z43_A	324	DNA repair and recombination protein RADA; archaea	80.24
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	80.24
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	80.2
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	80.18
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	80.15
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	80.1

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.94  E-value=2.3e-27  Score=206.12  Aligned_cols=145  Identities=27%  Similarity=0.381  Sum_probs=118.4

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|++++++.....   ....++++||++||||||.|+++.+++++...+  +++.
T Consensus        87 i~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~---~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~--~~~~  161 (434)
T 2db3_A           87 IPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHE---LELGRPQVVIVSPTRELAIQIFNEARKFAFESY--LKIG  161 (434)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCC---CCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSS--CCCC
T ss_pred             HHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccc---cccCCccEEEEecCHHHHHHHHHHHHHHhccCC--cEEE
Confidence            46788999999999999999999999999999875421   223478999999999999999999999988776  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+...+.+.+.++++|.  |.    ||+++.++..+....+.+ ++++|.||+     +.+.+++|.+++.+.+.
T Consensus       162 ~~~gg~~~~~~~~~l~~~~~Iv--v~----Tp~~l~~~l~~~~~~l~~-~~~lVlDEa-----h~~~~~gf~~~~~~i~~  229 (434)
T 2db3_A          162 IVYGGTSFRHQNECITRGCHVV--IA----TPGRLLDFVDRTFITFED-TRFVVLDEA-----DRMLDMGFSEDMRRIMT  229 (434)
T ss_dssp             EECTTSCHHHHHHHHTTCCSEE--EE----CHHHHHHHHHTTSCCCTT-CCEEEEETH-----HHHTSTTTHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHhhcCCCEE--EE----ChHHHHHHHHhCCccccc-CCeEEEccH-----hhhhccCcHHHHHHHHH
Confidence            9999998888888888888773  33    488887665544433444 889999997     88899999999877776


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       230 ~~  231 (434)
T 2db3_A          230 HV  231 (434)
T ss_dssp             CT
T ss_pred             hc
Confidence            54

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

Probab=99.90  E-value=1e-24  Score=188.12  Aligned_cols=147  Identities=23%  Similarity=0.341  Sum_probs=110.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcC----------CCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETK----------LPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~----------~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      ||.+++|+|++++||||||||++|++|+++.+......          .......++++||++||||||.|+++.+++++
T Consensus        46 i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  125 (417)
T 2i4i_A           46 IPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFS  125 (417)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHH
T ss_pred             HHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHh
Confidence            46688999999999999999999999999998764311          00111235789999999999999999999998


Q ss_pred             HhCCCCcceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCC
Q psy7786          71 AALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK  150 (252)
Q Consensus        71 ~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~  150 (252)
                      ...+  +++..++||.+..++.+.+.++++|.  +    +||+++..+.......+. .+.++|.||+     +.+.+.+
T Consensus       126 ~~~~--~~~~~~~g~~~~~~~~~~~~~~~~I~--v----~Tp~~l~~~l~~~~~~~~-~~~~iViDEa-----h~~~~~~  191 (417)
T 2i4i_A          126 YRSR--VRPCVVYGGADIGQQIRDLERGCHLL--V----ATPGRLVDMMERGKIGLD-FCKYLVLDEA-----DRMLDMG  191 (417)
T ss_dssp             TTSS--CCEEEECSSSCHHHHHHHHTTCCSEE--E----ECHHHHHHHHHTTSBCCT-TCCEEEESSH-----HHHHHTT
T ss_pred             CcCC--ceEEEEECCCCHHHHHHHhhCCCCEE--E----EChHHHHHHHHcCCcChh-hCcEEEEECh-----hHhhccC
Confidence            8776  88889999988887777777776662  2    347776654443322233 3788999997     6777777


Q ss_pred             CCHHHHHHHHH
Q psy7786         151 LPESLVRALEA  161 (252)
Q Consensus       151 l~~~l~~~l~~  161 (252)
                      +...+...+..
T Consensus       192 ~~~~~~~i~~~  202 (417)
T 2i4i_A          192 FEPQIRRIVEQ  202 (417)
T ss_dssp             CHHHHHHHHTS
T ss_pred             cHHHHHHHHHh
Confidence            77777665553

>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=99.88  E-value=1.3e-24  Score=174.50  Aligned_cols=144  Identities=26%  Similarity=0.472  Sum_probs=114.7

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+.....   .....++++||++||||||.|+++.++++....+  +++.
T Consensus        60 i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~---~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~--~~~~  134 (242)
T 3fe2_A           60 WPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPF---LERGDGPICLVLAPTRELAQQVQQVAAEYCRACR--LKST  134 (242)
T ss_dssp             HHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCC---CCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTT--CCEE
T ss_pred             HHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccc---cccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcC--ceEE
Confidence            3567899999999999999999999999998865331   1223578899999999999999999999999887  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+...+.+.+.++++|.  |    ++|+++.++..+....+.+ ++++|.||+     +.+.+.++...+...+.
T Consensus       135 ~~~g~~~~~~~~~~~~~~~~I~--v----~Tp~~l~~~l~~~~~~~~~-~~~lViDEa-----h~l~~~~~~~~~~~i~~  202 (242)
T 3fe2_A          135 CIYGGAPKGPQIRDLERGVEIC--I----ATPGRLIDFLECGKTNLRR-TTYLVLDEA-----DRMLDMGFEPQIRKIVD  202 (242)
T ss_dssp             EECTTSCHHHHHHHHHHCCSEE--E----ECHHHHHHHHHHTSCCCTT-CCEEEETTH-----HHHHHTTCHHHHHHHHT
T ss_pred             EEECCCChHHHHHHhcCCCCEE--E----ECHHHHHHHHHcCCCCccc-ccEEEEeCH-----HHHhhhCcHHHHHHHHH
Confidence            9999998888888888887772  2    3488876665544333444 889999997     77888888888766654


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       203 ~  203 (242)
T 3fe2_A          203 Q  203 (242)
T ss_dssp             T
T ss_pred             h
Confidence            4

>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=99.88  E-value=8.5e-23  Score=182.84  Aligned_cols=144  Identities=17%  Similarity=0.250  Sum_probs=109.1

Q ss_pred             Cccc--CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhC-CC-Cc
Q psy7786           2 VTYR--NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL-PI-PL   77 (252)
Q Consensus         2 ~~~~--~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~-~~-~~   77 (252)
                      |.++  +|+|++++||||||||++|++|+++.+......    ...++++||++||||||.|+++.++.+.... +. .+
T Consensus       104 ~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~----~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~  179 (563)
T 3i5x_A          104 KPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD----SQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKY  179 (563)
T ss_dssp             HHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS----STTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTS
T ss_pred             HHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcccc----ccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCce
Confidence            4556  689999999999999999999999999775431    1236789999999999999999999986542 11 25


Q ss_pred             ceeeeeCCcccCcchhhhhh-cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHH
Q psy7786          78 RTCLAIGGVPMNQSLDVIKK-GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLV  156 (252)
Q Consensus        78 ~~~~~~g~~~~~~~~~~l~~-~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~  156 (252)
                      .+...+||.+...+.+.+.+ +++|.  |    +||+++.++..+......+.+.++|.||+     +.+.+.+|.+.+.
T Consensus       180 ~~~~~~g~~~~~~~~~~~~~~~~~Ii--v----~Tp~~l~~~l~~~~~~~~~~~~~lViDEa-----h~l~~~~f~~~~~  248 (563)
T 3i5x_A          180 ACVSLVGGTDFRAAMNKMNKLRPNIV--I----ATPGRLIDVLEKYSNKFFRFVDYKVLDEA-----DRLLEIGFRDDLE  248 (563)
T ss_dssp             CEEEECTTSCHHHHHHHHHHHCCSEE--E----ECHHHHHHHHHHHHHHHCTTCCEEEEETH-----HHHTSTTTHHHHH
T ss_pred             eEEEEECCcCHHHHHHHHhcCCCCEE--E----ECcHHHHHHHHhccccccccceEEEEeCH-----HHHhccchHHHHH
Confidence            67788999887777666644 56662  3    34888877776654444455899999997     7788888888775


Q ss_pred             HHHH
Q psy7786         157 RALE  160 (252)
Q Consensus       157 ~~l~  160 (252)
                      ..+.
T Consensus       249 ~i~~  252 (563)
T 3i5x_A          249 TISG  252 (563)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.88  E-value=1e-22  Score=182.91  Aligned_cols=144  Identities=17%  Similarity=0.239  Sum_probs=110.4

Q ss_pred             Cccc--CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhC-C-CCc
Q psy7786           2 VTYR--NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL-P-IPL   77 (252)
Q Consensus         2 ~~~~--~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~-~-~~~   77 (252)
                      |.++  +|+|++++||||||||++|++|+++.+......    ...++++||++||||||.|+.+.++.+.... + ..+
T Consensus        53 ~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~----~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~  128 (579)
T 3sqw_A           53 KPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD----SQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKY  128 (579)
T ss_dssp             HHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS----STTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTS
T ss_pred             HHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcccc----ccCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccce
Confidence            4566  789999999999999999999999998775421    1236789999999999999999999987542 1 126


Q ss_pred             ceeeeeCCcccCcchhhhhh-cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHH
Q psy7786          78 RTCLAIGGVPMNQSLDVIKK-GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLV  156 (252)
Q Consensus        78 ~~~~~~g~~~~~~~~~~l~~-~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~  156 (252)
                      .+...+||.....+.+.+.+ +++|.  |    +||+++.++..+........+.++|.||+     +.+.+++|.+++.
T Consensus       129 ~~~~~~gg~~~~~~~~~l~~~~~~Il--V----~Tp~~l~~~l~~~~~~~~~~~~~lViDEa-----h~l~~~gf~~~~~  197 (579)
T 3sqw_A          129 ACVSLVGGTDFRAAMNKMNKLRPNIV--I----ATPGRLIDVLEKYSNKFFRFVDYKVLDEA-----DRLLEIGFRDDLE  197 (579)
T ss_dssp             CEEEECTTSCHHHHHHHHHHHCCSEE--E----ECHHHHHHHHHHHHHHHCTTCCEEEEETH-----HHHTSTTTHHHHH
T ss_pred             EEEEEECCccHHHHHHHHhcCCCCEE--E----ECHHHHHHHHHhccccccccCCEEEEECh-----HHhhcCCCHHHHH
Confidence            67788999887777777654 56662  3    34888887776654444455899999997     7888888888875


Q ss_pred             HHHH
Q psy7786         157 RALE  160 (252)
Q Consensus       157 ~~l~  160 (252)
                      ..+.
T Consensus       198 ~i~~  201 (579)
T 3sqw_A          198 TISG  201 (579)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5543

>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=99.87  E-value=3.1e-23  Score=178.54  Aligned_cols=139  Identities=19%  Similarity=0.265  Sum_probs=106.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++++|||||||++|++|+++.+....        .+.++||++|||+|+.|+++.+++++...+  +++.
T Consensus        68 i~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~--------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~--~~~~  137 (410)
T 2j0s_A           68 IKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV--------RETQALILAPTRELAVQIQKGLLALGDYMN--VQCH  137 (410)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHTTTTT--CCEE
T ss_pred             HHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhcc--------CCceEEEEcCcHHHHHHHHHHHHHHhccCC--eEEE
Confidence            356789999999999999999999999998764322        367899999999999999999999988877  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+...+...+..+++|.  +    ++|+++.++..+....+. .+.++|.||+     +.+.+.++...+...+.
T Consensus       138 ~~~g~~~~~~~~~~~~~~~~iv--v----~Tp~~l~~~l~~~~~~~~-~~~~vViDEa-----h~~~~~~~~~~~~~i~~  205 (410)
T 2j0s_A          138 ACIGGTNVGEDIRKLDYGQHVV--A----GTPGRVFDMIRRRSLRTR-AIKMLVLDEA-----DEMLNKGFKEQIYDVYR  205 (410)
T ss_dssp             EECTTSCHHHHHHHHHHCCSEE--E----ECHHHHHHHHHTTSSCCT-TCCEEEEETH-----HHHTSTTTHHHHHHHHT
T ss_pred             EEECCCCHHHHHHHhhcCCCEE--E----cCHHHHHHHHHhCCccHh-heeEEEEccH-----HHHHhhhhHHHHHHHHH
Confidence            8999988888877777777662  2    347776655444322233 3789999997     66777777776655554


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       206 ~  206 (410)
T 2j0s_A          206 Y  206 (410)
T ss_dssp             T
T ss_pred             h
Confidence            3

>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=99.87  E-value=9.6e-24  Score=170.56  Aligned_cols=148  Identities=24%  Similarity=0.374  Sum_probs=111.7

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcC-CCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcce
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETK-LPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRT   79 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~-~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~   79 (252)
                      |+.+++|+|++++||||||||++|++|+++.+...... .......++++||++||||||.|+++.+++++...+  +++
T Consensus        54 i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~--~~~  131 (253)
T 1wrb_A           54 IPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP--LRS  131 (253)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSS--CCE
T ss_pred             HHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCC--ceE
Confidence            35678999999999999999999999999988754321 111123467899999999999999999999988776  788


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      ..++||.+...+.+.+..+++|.  |    ++|+++.....+....+. .+.++|.||+     +.+.+.++...+...+
T Consensus       132 ~~~~g~~~~~~~~~~~~~~~~Iv--v----~Tp~~l~~~l~~~~~~~~-~~~~lViDEa-----h~~~~~~~~~~~~~i~  199 (253)
T 1wrb_A          132 CVVYGGADTHSQIREVQMGCHLL--V----ATPGRLVDFIEKNKISLE-FCKYIVLDEA-----DRMLDMGFEPQIRKII  199 (253)
T ss_dssp             EEECSSSCSHHHHHHHSSCCSEE--E----ECHHHHHHHHHTTSBCCT-TCCEEEEETH-----HHHHHTTCHHHHHHHH
T ss_pred             EEEECCCCHHHHHHHhCCCCCEE--E----ECHHHHHHHHHcCCCChh-hCCEEEEeCH-----HHHHhCchHHHHHHHH
Confidence            88999988877777777776762  2    347776654443332333 3789999997     7788888888887777


Q ss_pred             HHC
Q psy7786         160 EAK  162 (252)
Q Consensus       160 ~~~  162 (252)
                      ...
T Consensus       200 ~~~  202 (253)
T 1wrb_A          200 EES  202 (253)
T ss_dssp             HSS
T ss_pred             hhc
Confidence            643

>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=99.86  E-value=9.5e-24  Score=174.68  Aligned_cols=135  Identities=21%  Similarity=0.280  Sum_probs=99.4

Q ss_pred             CCcccCC--CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcc
Q psy7786           1 MVTYRNS--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLR   78 (252)
Q Consensus         1 i~~~~~g--~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~   78 (252)
                      ||.+++|  +|++++||||||||++|++|+++++....        .++++||++||||||.|+++.++.+++..+ +++
T Consensus       123 i~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~--------~~~~~lil~PtreLa~Q~~~~~~~l~~~~~-~~~  193 (300)
T 3fmo_B          123 LPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN--------KYPQCLCLSPTYELALQTGKVIEQMGKFYP-ELK  193 (300)
T ss_dssp             HHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHTTTST-TCC
T ss_pred             HHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccC--------CCceEEEEcCcHHHHHHHHHHHHHHHhhCC-CcE
Confidence            4667887  99999999999999999999999875433        477899999999999999999999988764 378


Q ss_pred             eeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhH-HHHHhhhhceeeccCCCCCccccccc-CCCCHHHH
Q psy7786          79 TCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQV-HDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLV  156 (252)
Q Consensus        79 ~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~-~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~  156 (252)
                      +...+|+.......   ..+++|.  |    +||+++.++..+. ...+. .++++|.||+     +.+.+ .++...+.
T Consensus       194 ~~~~~~~~~~~~~~---~~~~~Il--V----~TP~~l~~~l~~~~~~~l~-~l~~lVlDEa-----d~l~~~~~~~~~~~  258 (300)
T 3fmo_B          194 LAYAVRGNKLERGQ---KISEQIV--I----GTPGTVLDWCSKLKFIDPK-KIKVFVLDEA-----DVMIATQGHQDQSI  258 (300)
T ss_dssp             EEEESTTCCCCTTC---CCCCSEE--E----ECHHHHHHHHTTTCCCCGG-GCSEEEETTH-----HHHHHSTTHHHHHH
T ss_pred             EEEEeCCccHhhhh---cCCCCEE--E----ECHHHHHHHHHhcCCCChh-hceEEEEeCH-----HHHhhccCcHHHHH
Confidence            88888887654433   3345552  2    3477776555432 22233 4899999997     67666 56666654


Q ss_pred             HHH
Q psy7786         157 RAL  159 (252)
Q Consensus       157 ~~l  159 (252)
                      ..+
T Consensus       259 ~i~  261 (300)
T 3fmo_B          259 RIQ  261 (300)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=99.86  E-value=1.4e-23  Score=170.52  Aligned_cols=145  Identities=25%  Similarity=0.364  Sum_probs=112.2

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+.....    ....+.++||++||||||.|+++.++++....+  +++.
T Consensus        85 i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~----~~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~~--~~~~  158 (262)
T 3ly5_A           85 IRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRF----MPRNGTGVLILSPTRELAMQTFGVLKELMTHHV--HTYG  158 (262)
T ss_dssp             HHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTC----CGGGCCCEEEECSSHHHHHHHHHHHHHHTTTCC--SCEE
T ss_pred             HHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccc----cccCCceEEEEeCCHHHHHHHHHHHHHHHhhcC--ceEE
Confidence            3567889999999999999999999999998876331    112367899999999999999999999988776  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.....+...+.++++|.  |    +||+++..+...........+.++|.||+     +.+.+.++...+...+.
T Consensus       159 ~~~g~~~~~~~~~~~~~~~~Ii--v----~Tp~~l~~~~~~~~~~~~~~l~~lViDEa-----h~l~~~~~~~~l~~i~~  227 (262)
T 3ly5_A          159 LIMGGSNRSAEAQKLGNGINII--V----ATPGRLLDHMQNTPGFMYKNLQCLVIDEA-----DRILDVGFEEELKQIIK  227 (262)
T ss_dssp             EECSSSCHHHHHHHHHHCCSEE--E----ECHHHHHHHHHHCTTCCCTTCCEEEECSH-----HHHHHTTCHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHhcCCCCEE--E----EcHHHHHHHHHccCCcccccCCEEEEcCh-----HHHhhhhHHHHHHHHHH
Confidence            8999988877777777777762  2    34777765544432222234889999997     77888888888776665


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       228 ~~  229 (262)
T 3ly5_A          228 LL  229 (262)
T ss_dssp             HS
T ss_pred             hC
Confidence            53

>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=99.85  E-value=3.4e-23  Score=164.76  Aligned_cols=145  Identities=24%  Similarity=0.287  Sum_probs=102.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+......  .....++++||++||||||.|+++.++++. ..+  +++.
T Consensus        51 i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~--~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~--~~~~  125 (228)
T 3iuy_A           51 WPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPIS--REQRNGPGMLVLTPTRELALHVEAECSKYS-YKG--LKSI  125 (228)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-----------CCCSEEEECSSHHHHHHHHHHHHHHC-CTT--CCEE
T ss_pred             HHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccch--hhccCCCcEEEEeCCHHHHHHHHHHHHHhc-ccC--ceEE
Confidence            35678999999999999999999999999887643221  112357889999999999999999999885 233  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+...+.+.+.++++|.  |    ++|+++..+..+....+.+ +.++|.||+     +.+.+.++...+...+.
T Consensus       126 ~~~~~~~~~~~~~~~~~~~~ii--v----~Tp~~l~~~~~~~~~~~~~-~~~lViDEa-----h~~~~~~~~~~~~~i~~  193 (228)
T 3iuy_A          126 CIYGGRNRNGQIEDISKGVDII--I----ATPGRLNDLQMNNSVNLRS-ITYLVIDEA-----DKMLDMEFEPQIRKILL  193 (228)
T ss_dssp             EECC------CHHHHHSCCSEE--E----ECHHHHHHHHHTTCCCCTT-CCEEEECCH-----HHHHHTTCHHHHHHHHH
T ss_pred             EEECCCChHHHHHHhcCCCCEE--E----ECHHHHHHHHHcCCcCccc-ceEEEEECH-----HHHhccchHHHHHHHHH
Confidence            9999999888888888877762  2    3477776544333333333 789999997     77778888888877665


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       194 ~~  195 (228)
T 3iuy_A          194 DV  195 (228)
T ss_dssp             HS
T ss_pred             hC
Confidence            53

>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=99.85  E-value=4.9e-23  Score=166.08  Aligned_cols=140  Identities=26%  Similarity=0.373  Sum_probs=108.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|++++||||||||++|++|+++.+....        .++++||++|||||+.|+++.+++++...+  +++.
T Consensus        74 i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~--------~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~--~~~~  143 (249)
T 3ber_A           74 IPLALQGRDIIGLAETGSGKTGAFALPILNALLETP--------QRLFALVLTPTRELAFQISEQFEALGSSIG--VQSA  143 (249)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC--------CSSCEEEECSSHHHHHHHHHHHHHHHGGGT--CCEE
T ss_pred             HHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC--------CCceEEEEeCCHHHHHHHHHHHHHHhccCC--eeEE
Confidence            356789999999999999999999999999887643        367899999999999999999999998877  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+...+...+.++++|.  +    ++|+++.....+........+.++|.||+     +.+.+.++...+...+.
T Consensus       144 ~~~g~~~~~~~~~~~~~~~~I~--v----~Tp~~l~~~l~~~~~~~l~~~~~lViDEa-----h~l~~~~~~~~l~~i~~  212 (249)
T 3ber_A          144 VIVGGIDSMSQSLALAKKPHII--I----ATPGRLIDHLENTKGFNLRALKYLVMDEA-----DRILNMDFETEVDKILK  212 (249)
T ss_dssp             EECTTSCHHHHHHHHHTCCSEE--E----ECHHHHHHHHHHSTTCCCTTCCEEEECSH-----HHHHHTTCHHHHHHHHH
T ss_pred             EEECCCChHHHHHHhcCCCCEE--E----ECHHHHHHHHHcCCCcCccccCEEEEcCh-----hhhhccChHHHHHHHHH
Confidence            8999988776666666776662  2    34777655443321111234789999997     77777788887766554


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       213 ~  213 (249)
T 3ber_A          213 V  213 (249)
T ss_dssp             S
T ss_pred             h
Confidence            3

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.85  E-value=5.4e-22  Score=171.19  Aligned_cols=137  Identities=12%  Similarity=0.167  Sum_probs=100.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|++..+.           .+.++||++||||||.|+++.++.++. .+  +++.
T Consensus        30 i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~-----------~~~~~lil~Pt~~L~~q~~~~~~~~~~-~~--~~v~   95 (414)
T 3oiy_A           30 AKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR-----------KGKKSALVFPTVTLVKQTLERLQKLAD-EK--VKIF   95 (414)
T ss_dssp             HHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT-----------TTCCEEEEESSHHHHHHHHHHHHHHCC-SS--CCEE
T ss_pred             HHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc-----------CCCEEEEEECCHHHHHHHHHHHHHHcc-CC--ceEE
Confidence            356889999999999999999999999887651           367899999999999999999999877 55  8999


Q ss_pred             eeeCCccc---Ccchhhhhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCC--C---Cccccccc-CC
Q psy7786          81 LAIGGVPM---NQSLDVIKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDV--P---PACCSFRL-MK  150 (252)
Q Consensus        81 ~~~g~~~~---~~~~~~l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~--~---~~~~~~~~-~~  150 (252)
                      .++||.+.   ..+.+.+.++ ++|.  +.    ||+++.++...   .....+.++|.||+-  .   +..+.+.+ ++
T Consensus        96 ~~~g~~~~~~~~~~~~~l~~~~~~Ii--v~----Tp~~l~~~l~~---~~~~~~~~iViDEaH~~~~~~~~~d~~l~~~~  166 (414)
T 3oiy_A           96 GFYSSMKKEEKEKFEKSFEEDDYHIL--VF----STQFVSKNREK---LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVG  166 (414)
T ss_dssp             ECCTTSCHHHHHHHHHHHHHTCCSEE--EE----EHHHHHHCHHH---HTTCCCSEEEESCHHHHHHCHHHHHHHHHHTT
T ss_pred             EEECCCChhhHHHHHHHhhcCCCCEE--EE----CHHHHHHHHHH---hccccccEEEEeChHhhhhccchhhhHHhhcC
Confidence            99999887   4555666665 6662  33    48888766542   222358999999960  0   00023444 78


Q ss_pred             CCHH-HHHHHH
Q psy7786         151 LPES-LVRALE  160 (252)
Q Consensus       151 l~~~-l~~~l~  160 (252)
                      |.++ +...+.
T Consensus       167 ~~~~~~~~i~~  177 (414)
T 3oiy_A          167 IPEEIIRKAFS  177 (414)
T ss_dssp             CCHHHHHHHHH
T ss_pred             CcHHHHHHHHH
Confidence            8888 444443

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.84  E-value=5.4e-23  Score=162.64  Aligned_cols=140  Identities=20%  Similarity=0.198  Sum_probs=104.0

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCC--Ccce
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI--PLRT   79 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~--~~~~   79 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .+.++||++|||||+.|+++.++++....+.  ++++
T Consensus        36 ~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~--------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  107 (219)
T 1q0u_A           36 PGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER--------AEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVA  107 (219)
T ss_dssp             HHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCE
T ss_pred             HHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCc--------CCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEE
Confidence            56788999999999999999999999998875432        3678999999999999999999999887621  2778


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      ..++||.+...+.+.+..+++|.  +    ++|+++.....+....+. .+.++|.||+     +.+.+.++...+...+
T Consensus       108 ~~~~g~~~~~~~~~~~~~~~~Ii--v----~Tp~~l~~~l~~~~~~~~-~~~~lViDEa-----h~~~~~~~~~~l~~i~  175 (219)
T 1q0u_A          108 RCLIGGTDKQKALEKLNVQPHIV--I----GTPGRINDFIREQALDVH-TAHILVVDEA-----DLMLDMGFITDVDQIA  175 (219)
T ss_dssp             EEECCCSHHHHTTCCCSSCCSEE--E----ECHHHHHHHHHTTCCCGG-GCCEEEECSH-----HHHHHTTCHHHHHHHH
T ss_pred             EEEeCCCCHHHHHHHcCCCCCEE--E----eCHHHHHHHHHcCCCCcC-cceEEEEcCc-----hHHhhhChHHHHHHHH
Confidence            88899987766666555555552  2    347666654433222333 4789999997     6777777777665555


Q ss_pred             HH
Q psy7786         160 EA  161 (252)
Q Consensus       160 ~~  161 (252)
                      ..
T Consensus       176 ~~  177 (219)
T 1q0u_A          176 AR  177 (219)
T ss_dssp             HT
T ss_pred             Hh
Confidence            43

>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=99.84  E-value=8.1e-23  Score=163.61  Aligned_cols=139  Identities=17%  Similarity=0.266  Sum_probs=95.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++++|||||||++|++|+++.+....        .+.++||++|||||+.|+++.++.++...+  +++.
T Consensus        61 i~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~--------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~--~~~~  130 (237)
T 3bor_A           61 IIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEF--------KETQALVLAPTRELAQQIQKVILALGDYMG--ATCH  130 (237)
T ss_dssp             HHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHTTTTT--CCEE
T ss_pred             HHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcC--------CCceEEEEECcHHHHHHHHHHHHHHhhhcC--ceEE
Confidence            356789999999999999999999999998875432        367899999999999999999999988776  7788


Q ss_pred             eeeCCcccCcchhhhhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      .++||.+...+.+.+.++ ++|.  +    ++|+++.++..+....+. .+.++|.||+     +.+.+.++...+...+
T Consensus       131 ~~~g~~~~~~~~~~l~~~~~~Il--v----~Tp~~l~~~l~~~~~~~~-~~~~lViDEa-----h~~~~~~~~~~l~~i~  198 (237)
T 3bor_A          131 ACIGGTNVRNEMQKLQAEAPHIV--V----GTPGRVFDMLNRRYLSPK-WIKMFVLDEA-----DEMLSRGFKDQIYEIF  198 (237)
T ss_dssp             EECC-------------CCCSEE--E----ECHHHHHHHHHTTSSCST-TCCEEEEESH-----HHHHHTTCHHHHHHHH
T ss_pred             EEECCCchHHHHHHHhcCCCCEE--E----ECHHHHHHHHHhCCcCcc-cCcEEEECCc-----hHhhccCcHHHHHHHH
Confidence            889998877777766655 5552  2    336666554433332333 3789999997     6777777777776655


Q ss_pred             HH
Q psy7786         160 EA  161 (252)
Q Consensus       160 ~~  161 (252)
                      ..
T Consensus       199 ~~  200 (237)
T 3bor_A          199 QK  200 (237)
T ss_dssp             HH
T ss_pred             Hh
Confidence            54

>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=99.83  E-value=6.6e-22  Score=170.26  Aligned_cols=139  Identities=16%  Similarity=0.259  Sum_probs=103.2

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .+.++||++|||+|+.|+.+.++.++...+  +.+..
T Consensus        72 ~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~--------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~--~~~~~  141 (414)
T 3eiq_A           72 LPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL--------KATQALVLAPTRELAQQIQKVVMALGDYMG--ASCHA  141 (414)
T ss_dssp             HHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHGGGSC--CCEEE
T ss_pred             HHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcC--------CceeEEEEeChHHHHHHHHHHHHHHhcccC--ceEEE
Confidence            56789999999999999999999999998875432        366899999999999999999999998877  78888


Q ss_pred             eeCCcccCcchhhhh-hcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIK-KGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~-~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ++||.+...+.+.+. .+++|.  +    ++|+++.+...+....+.. +.++|.||+     +.+.+.++...+...+.
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~ii--v----~T~~~l~~~l~~~~~~~~~-~~~vViDEa-----h~~~~~~~~~~~~~~~~  209 (414)
T 3eiq_A          142 CIGGTNVRAEVQKLQMEAPHII--V----GTPGRVFDMLNRRYLSPKY-IKMFVLDEA-----DEMLSRGFKDQIYDIFQ  209 (414)
T ss_dssp             CCCCTTHHHHHHHHTTTCCSEE--E----ECHHHHHHHHHHTSSCSTT-CCEEEECSH-----HHHHHTTTHHHHHHHHT
T ss_pred             EECCcchHHHHHHHhcCCCCEE--E----ECHHHHHHHHHcCCccccc-CcEEEEECH-----HHhhccCcHHHHHHHHH
Confidence            899987776666655 344541  2    3366665544433323333 789999997     56666666666665554


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       210 ~~  211 (414)
T 3eiq_A          210 KL  211 (414)
T ss_dssp             TS
T ss_pred             hC
Confidence            43

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.83  E-value=3e-22  Score=160.11  Aligned_cols=142  Identities=27%  Similarity=0.373  Sum_probs=103.1

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+.....    ....++++||++|||+|+.|+++.++.++...+  +++..
T Consensus        57 ~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~----~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~--~~~~~  130 (236)
T 2pl3_A           57 GLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQW----TSTDGLGVLIISPTRELAYQTFEVLRKVGKNHD--FSAGL  130 (236)
T ss_dssp             HHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTC----CGGGCCCEEEECSSHHHHHHHHHHHHHHTTTSS--CCEEE
T ss_pred             HHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcc----cccCCceEEEEeCCHHHHHHHHHHHHHHhCCCC--eeEEE
Confidence            567899999999999999999999999998875321    112467899999999999999999999987766  78888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEA  161 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~  161 (252)
                      ++||.+...+...+. +++|.  |    ++|+++.....+........+.++|.||+     +.+.+.++...+...+..
T Consensus       131 ~~g~~~~~~~~~~~~-~~~ii--v----~Tp~~l~~~l~~~~~~~~~~~~~lViDEa-----h~~~~~~~~~~~~~i~~~  198 (236)
T 2pl3_A          131 IIGGKDLKHEAERIN-NINIL--V----CTPGRLLQHMDETVSFHATDLQMLVLDEA-----DRILDMGFADTMNAVIEN  198 (236)
T ss_dssp             ECCC--CHHHHHHHT-TCSEE--E----ECHHHHHHHHHHCSSCCCTTCCEEEETTH-----HHHHHTTTHHHHHHHHHT
T ss_pred             EECCCCHHHHHHhCC-CCCEE--E----ECHHHHHHHHHhcCCcccccccEEEEeCh-----HHHhcCCcHHHHHHHHHh
Confidence            999987766655553 44541  2    34777655433322122234789999997     777777887777655544

>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=99.83  E-value=5.2e-22  Score=170.30  Aligned_cols=120  Identities=22%  Similarity=0.340  Sum_probs=89.8

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .+.++||++||++|+.|+.+.++++....+  +++..
T Consensus        53 ~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~--------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~--~~~~~  122 (400)
T 1s2m_A           53 PVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL--------NKIQALIMVPTRELALQTSQVVRTLGKHCG--ISCMV  122 (400)
T ss_dssp             HHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHTTTTT--CCEEE
T ss_pred             HHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhcc--------CCccEEEEcCCHHHHHHHHHHHHHHhcccC--ceEEE
Confidence            45778999999999999999999999998764332        356899999999999999999999988776  78888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .+|+.....+...+..+.+|.  +    ++|+++.....+....+. .+.++|.||+
T Consensus       123 ~~g~~~~~~~~~~~~~~~~Iv--v----~T~~~l~~~~~~~~~~~~-~~~~vIiDEa  172 (400)
T 1s2m_A          123 TTGGTNLRDDILRLNETVHIL--V----GTPGRVLDLASRKVADLS-DCSLFIMDEA  172 (400)
T ss_dssp             ECSSSCHHHHHHHTTSCCSEE--E----ECHHHHHHHHHTTCSCCT-TCCEEEEESH
T ss_pred             EeCCcchHHHHHHhcCCCCEE--E----EchHHHHHHHHhCCcccc-cCCEEEEeCc
Confidence            899877666555555555551  2    346666443333222233 3788999986

>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=99.83  E-value=2.4e-22  Score=157.20  Aligned_cols=139  Identities=18%  Similarity=0.261  Sum_probs=103.5

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .++++||++|||+|+.|+++.++.+.+..+ ++++..
T Consensus        35 ~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~--------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~  105 (206)
T 1vec_A           35 PIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK--------DNIQAMVIVPTRELALQVSQICIQVSKHMG-GAKVMA  105 (206)
T ss_dssp             HHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTS--------CSCCEEEECSCHHHHHHHHHHHHHHTTTSS-SCCEEE
T ss_pred             HHHccCCCEEEECCCCCchHHHHHHHHHHHhcccC--------CCeeEEEEeCcHHHHHHHHHHHHHHHhhcC-CceEEE
Confidence            56789999999999999999999999998774432        367899999999999999999999988763 378888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEA  161 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~  161 (252)
                      .+|+.+..++...+..+++|.  +    ++|+++.....+....+. .+.++|.||+     +.+.+.++...+...+..
T Consensus       106 ~~g~~~~~~~~~~~~~~~~i~--v----~T~~~l~~~~~~~~~~~~-~~~~lViDEa-----h~~~~~~~~~~l~~i~~~  173 (206)
T 1vec_A          106 TTGGTNLRDDIMRLDDTVHVV--I----ATPGRILDLIKKGVAKVD-HVQMIVLDEA-----DKLLSQDFVQIMEDIILT  173 (206)
T ss_dssp             ECSSSCHHHHHHHTTSCCSEE--E----ECHHHHHHHHHTTCSCCT-TCCEEEEETH-----HHHTSTTTHHHHHHHHHH
T ss_pred             EeCCccHHHHHHhcCCCCCEE--E----eCHHHHHHHHHcCCcCcc-cCCEEEEECh-----HHhHhhCcHHHHHHHHHh
Confidence            999988776666666666652  2    336665444333222233 4789999997     667776776666555543

>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=99.83  E-value=2.5e-22  Score=176.43  Aligned_cols=135  Identities=22%  Similarity=0.287  Sum_probs=92.5

Q ss_pred             CcccCC--CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcce
Q psy7786           2 VTYRNS--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRT   79 (252)
Q Consensus         2 ~~~~~g--~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~   79 (252)
                      |.+++|  +|++++||||||||++|++|+++.+....        .++++||++|||+||.|+++.++.+.+..+ .+.+
T Consensus       124 ~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~--------~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~-~~~~  194 (479)
T 3fmp_B          124 PLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN--------KYPQCLCLSPTYELALQTGKVIEQMGKFYP-ELKL  194 (479)
T ss_dssp             HHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHHTTST-TCCE
T ss_pred             HHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcC--------CCCcEEEEeChHHHHHHHHHHHHHHHhhCC-CceE
Confidence            456666  99999999999999999999998764432        366899999999999999999999988765 3777


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-CCCCHHHHHH
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLVRA  158 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~~~  158 (252)
                      ....|+.......   +.+.+|.  |    ++|+++.++..+........+.++|.||+     +.+.+ .++...+...
T Consensus       195 ~~~~~~~~~~~~~---~~~~~Iv--v----~Tp~~l~~~l~~~~~~~~~~~~~iViDEa-----h~~~~~~~~~~~~~~i  260 (479)
T 3fmp_B          195 AYAVRGNKLERGQ---KISEQIV--I----GTPGTVLDWCSKLKFIDPKKIKVFVLDEA-----DVMIATQGHQDQSIRI  260 (479)
T ss_dssp             EEESTTCCCCTTC---CCCCSEE--E----ECHHHHHHHHTTSCCCCGGGCCEEEECCH-----HHHHTSTTHHHHHHHH
T ss_pred             EEEeCCccccccc---cCCCCEE--E----ECchHHHHHHHhcCCcCcccCCEEEEECH-----HHHhhcCCcHHHHHHH
Confidence            7777776554332   2233441  2    34666654443321111235889999996     55544 4555555433


Q ss_pred             H
Q psy7786         159 L  159 (252)
Q Consensus       159 l  159 (252)
                      +
T Consensus       261 ~  261 (479)
T 3fmp_B          261 Q  261 (479)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.82  E-value=2.3e-21  Score=165.67  Aligned_cols=138  Identities=20%  Similarity=0.292  Sum_probs=98.5

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .+.++||++||++|+.|+.+.++++.+..+ ++++..
T Consensus        40 ~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~--------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~-~~~~~~  110 (391)
T 1xti_A           40 PQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT--------GQVSVLVMCHTRELAFQISKEYERFSKYMP-NVKVAV  110 (391)
T ss_dssp             HHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCT--------TCCCEEEECSCHHHHHHHHHHHHHHTTTCT-TCCEEE
T ss_pred             HHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccC--------CCeeEEEECCCHHHHHHHHHHHHHHHhhCC-CeEEEE
Confidence            56788999999999999999999999998764322        356899999999999999999999988763 388899


Q ss_pred             eeCCcccCcchhhhhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-CCCCHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLVRAL  159 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~~~l  159 (252)
                      ++|+.+...+.+.+.++ ++|.  +    ++|+++..........+. .+.++|.||+     +.+.+ .++...+...+
T Consensus       111 ~~g~~~~~~~~~~~~~~~~~ii--v----~T~~~l~~~~~~~~~~~~-~~~~vViDEa-----H~~~~~~~~~~~~~~~~  178 (391)
T 1xti_A          111 FFGGLSIKKDEEVLKKNCPHIV--V----GTPGRILALARNKSLNLK-HIKHFILDEC-----DKMLEQLDMRRDVQEIF  178 (391)
T ss_dssp             ECTTSCHHHHHHHHHHSCCSEE--E----ECHHHHHHHHHTTSSCCT-TCSEEEECSH-----HHHTSSHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHhcCCCCEE--E----ECHHHHHHHHHcCCcccc-ccCEEEEeCH-----HHHhhccchHHHHHHHH
Confidence            99998877766666654 3441  2    336666543333222223 4788999996     44443 34445554444


Q ss_pred             H
Q psy7786         160 E  160 (252)
Q Consensus       160 ~  160 (252)
                      .
T Consensus       179 ~  179 (391)
T 1xti_A          179 R  179 (391)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.82  E-value=1.1e-21  Score=156.19  Aligned_cols=138  Identities=23%  Similarity=0.240  Sum_probs=102.4

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .+.++||++|||||+.|+++.++.++.... ++++..
T Consensus        56 ~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~--------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~  126 (230)
T 2oxc_A           56 PLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLEN--------LSTQILILAPTREIAVQIHSVITAIGIKME-GLECHV  126 (230)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHTTTST-TCCEEE
T ss_pred             HHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcC--------CCceEEEEeCCHHHHHHHHHHHHHHhcccC-CceEEE
Confidence            56789999999999999999999999998875432        367899999999999999999999987652 378888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCC-CCHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK-LPESLVRALE  160 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~-l~~~l~~~l~  160 (252)
                      ++||.+...+.+.++ +++|.  +    ++|+++..........+. .++++|.||+     +.+.+.+ +...+...+.
T Consensus       127 ~~g~~~~~~~~~~~~-~~~Ii--v----~Tp~~l~~~~~~~~~~~~-~~~~lViDEa-----h~~~~~~~~~~~~~~i~~  193 (230)
T 2oxc_A          127 FIGGTPLSQDKTRLK-KCHIA--V----GSPGRIKQLIELDYLNPG-SIRLFILDEA-----DKLLEEGSFQEQINWIYS  193 (230)
T ss_dssp             ECTTSCHHHHHHHTT-SCSEE--E----ECHHHHHHHHHTTSSCGG-GCCEEEESSH-----HHHHSTTSSHHHHHHHHH
T ss_pred             EeCCCCHHHHHHhcc-CCCEE--E----ECHHHHHHHHhcCCcccc-cCCEEEeCCc-----hHhhcCcchHHHHHHHHH
Confidence            999977766555543 45541  2    347776654433332333 4789999997     7777776 7776655554


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       194 ~  194 (230)
T 2oxc_A          194 S  194 (230)
T ss_dssp             H
T ss_pred             h
Confidence            4

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.82  E-value=2.9e-21  Score=183.42  Aligned_cols=137  Identities=14%  Similarity=0.164  Sum_probs=103.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+.           .+.++||++||||||.|+++.++.++ ..+  +++.
T Consensus        87 i~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~-----------~~~~~Lil~PtreLa~Q~~~~l~~l~-~~~--i~v~  152 (1104)
T 4ddu_A           87 AKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR-----------KGKKSALVFPTVTLVKQTLERLQKLA-DEK--VKIF  152 (1104)
T ss_dssp             HHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT-----------TTCCEEEEESSHHHHHHHHHHHHTTS-CTT--SCEE
T ss_pred             HHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh-----------cCCeEEEEechHHHHHHHHHHHHHhh-CCC--CeEE
Confidence            467899999999999999999988888887661           36789999999999999999999987 444  8999


Q ss_pred             eeeCCccc---Ccchhhhhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC--CCCc---cccccc-CC
Q psy7786          81 LAIGGVPM---NQSLDVIKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD--VPPA---CCSFRL-MK  150 (252)
Q Consensus        81 ~~~g~~~~---~~~~~~l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~--~~~~---~~~~~~-~~  150 (252)
                      .++||.+.   ..+.+.+.++ ++|.  |.    ||+++.++...  ..+ ..+.++|.||+  +...   .+++.+ +|
T Consensus       153 ~l~Gg~~~~er~~~~~~l~~g~~~Il--V~----Tp~rL~~~l~~--l~~-~~l~~lViDEaH~l~~~~r~~Dr~L~~~g  223 (1104)
T 4ddu_A          153 GFYSSMKKEEKEKFEKSFEEDDYHIL--VF----STQFVSKNREK--LSQ-KRFDFVFVDDVDAVLKASRNIDTLLMMVG  223 (1104)
T ss_dssp             EECTTCCTTHHHHHHHHHHTSCCSEE--EE----EHHHHHHSHHH--HHT-SCCSEEEESCHHHHTTSSHHHHHHHHTSS
T ss_pred             EEeCCCCHHHHHHHHHHHhCCCCCEE--EE----CHHHHHHHHHh--hcc-cCcCEEEEeCCCccccccccchhhhHhcC
Confidence            99999888   5556666665 6763  33    48888776653  223 35899999996  1111   144556 88


Q ss_pred             CCHH-HHHHHH
Q psy7786         151 LPES-LVRALE  160 (252)
Q Consensus       151 l~~~-l~~~l~  160 (252)
                      |.++ +...+.
T Consensus       224 f~~~~i~~il~  234 (1104)
T 4ddu_A          224 IPEEIIRKAFS  234 (1104)
T ss_dssp             CCHHHHHHHHH
T ss_pred             CCHHHHHHHHH
Confidence            9988 544444

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

Probab=99.82  E-value=2e-20  Score=166.64  Aligned_cols=123  Identities=15%  Similarity=0.105  Sum_probs=97.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+.....      ..+.++||++||++|+.|+.+.++++....+  +++..
T Consensus        14 ~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~--~~~~~   85 (555)
T 3tbk_A           14 LPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPC------GQKGKVVFFANQIPVYEQQATVFSRYFERLG--YNIAS   85 (555)
T ss_dssp             HHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS------SCCCCEEEECSSHHHHHHHHHHHHHHHHTTT--CCEEE
T ss_pred             HHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhccc------CCCCEEEEEeCCHHHHHHHHHHHHHHhccCC--cEEEE
Confidence            567899999999999999999999999998865431      1366899999999999999999999998877  88999


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      ++|+.+...+.+.+.++++|.  |    ++|+++..............+.++|.||+
T Consensus        86 ~~g~~~~~~~~~~~~~~~~i~--v----~T~~~l~~~~~~~~~~~~~~~~~vViDEa  136 (555)
T 3tbk_A           86 ISGATSDSVSVQHIIEDNDII--I----LTPQILVNNLNNGAIPSLSVFTLMIFDEC  136 (555)
T ss_dssp             ECTTTGGGSCHHHHHHHCSEE--E----ECHHHHHHHHHTSSSCCGGGCSEEEETTG
T ss_pred             EcCCCcchhhHHHHhcCCCEE--E----ECHHHHHHHHhcCcccccccCCEEEEECc
Confidence            999998888877777777762  2    34777766554433312234789999996

>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=99.82  E-value=2.5e-20  Score=169.17  Aligned_cols=114  Identities=18%  Similarity=0.159  Sum_probs=88.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+  +++++||||||+||.+|++...+.           +.+++||+||||||.|+.+++..+.+++|  +++.
T Consensus        92 ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~-----------g~~vlVltptreLA~qd~e~~~~l~~~lg--l~v~  156 (844)
T 1tf5_A           92 GVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT-----------GKGVHVVTVNEYLASRDAEQMGKIFEFLG--LTVG  156 (844)
T ss_dssp             HHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT-----------SSCEEEEESSHHHHHHHHHHHHHHHHHTT--CCEE
T ss_pred             hHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc-----------CCCEEEEeCCHHHHHHHHHHHHHHHhhcC--CeEE
Confidence            46788999  999999999999999999854322           55799999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccc-----cCCCh--hHHHHHhhhhceeeccCC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCI-----LSLPD--QVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l-----~~~~~--~~~~~l~~~~~~~V~de~  138 (252)
                      +++||.+..  .+....++||      +|+||+++     .+...  .....+ +.++++|.||+
T Consensus       157 ~i~gg~~~~--~r~~~~~~dI------v~gTpgrlgfD~L~D~m~~~~~~l~l-r~~~~lVlDEa  212 (844)
T 1tf5_A          157 LNLNSMSKD--EKREAYAADI------TYSTNNELGFDYLRDNMVLYKEQMVQ-RPLHFAVIDEV  212 (844)
T ss_dssp             ECCTTSCHH--HHHHHHHSSE------EEEEHHHHHHHHHHHTTCSSGGGCCC-CCCCEEEEETH
T ss_pred             EEeCCCCHH--HHHHhcCCCE------EEECchhhhHHHHHHhhhcchhhhcc-cCCCEEEECch
Confidence            999997654  3444557887      34458888     43322  111223 34889999986

>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=99.81  E-value=9e-22  Score=156.01  Aligned_cols=137  Identities=16%  Similarity=0.279  Sum_probs=95.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .+.++||++|||+|+.|+++.++.+....+  +++..
T Consensus        46 ~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~--------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~--~~~~~  115 (224)
T 1qde_A           46 MPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV--------KAPQALMLAPTRELALQIQKVVMALAFHMD--IKVHA  115 (224)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTC--------CSCCEEEECSSHHHHHHHHHHHHHHTTTSC--CCEEE
T ss_pred             HHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccC--------CCceEEEEECCHHHHHHHHHHHHHHhcccC--ceEEE
Confidence            56789999999999999999999999998875432        367899999999999999999999988776  78888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEA  161 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~  161 (252)
                      ++|+.+..++.+.+.+ ++|.  +    ++|+++.....+....+. .+.++|.||+     +.+.+.++...+...+..
T Consensus       116 ~~g~~~~~~~~~~~~~-~~ii--v----~Tp~~l~~~~~~~~~~~~-~~~~iViDEa-----h~~~~~~~~~~l~~i~~~  182 (224)
T 1qde_A          116 CIGGTSFVEDAEGLRD-AQIV--V----GTPGRVFDNIQRRRFRTD-KIKMFILDEA-----DEMLSSGFKEQIYQIFTL  182 (224)
T ss_dssp             ECC----------CTT-CSEE--E----ECHHHHHHHHHTTSSCCT-TCCEEEEETH-----HHHHHTTCHHHHHHHHHH
T ss_pred             EeCCcchHHHHhcCCC-CCEE--E----ECHHHHHHHHHhCCcchh-hCcEEEEcCh-----hHHhhhhhHHHHHHHHHh
Confidence            9999887766665554 4441  2    236665543333222223 3789999997     667777777776655544

>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=99.81  E-value=3.4e-21  Score=182.76  Aligned_cols=132  Identities=17%  Similarity=0.227  Sum_probs=104.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCc---
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPL---   77 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~---   77 (252)
                      ||.+++|+|++++||||||||+ |.+|++..+..          .++++||++||||||.|+++.++.++..++  +   
T Consensus        65 i~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~----------~~~~~lil~PtreLa~Q~~~~l~~l~~~~~--i~~~  131 (1054)
T 1gku_B           65 AKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL----------KGKRCYVIFPTSLLVIQAAETIRKYAEKAG--VGTE  131 (1054)
T ss_dssp             HHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT----------TSCCEEEEESCHHHHHHHHHHHHHHHTTTC--CSGG
T ss_pred             HHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh----------cCCeEEEEeccHHHHHHHHHHHHHHHhhcC--CCcc
Confidence            4678899999999999999998 99999988754          257899999999999999999999998877  6   


Q ss_pred             -ceeeeeCCcccCcc---hhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCH
Q psy7786          78 -RTCLAIGGVPMNQS---LDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPE  153 (252)
Q Consensus        78 -~~~~~~g~~~~~~~---~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~  153 (252)
                       ++..++||.+...+   .+.+++ ++|.  |.    ||+++.++..+    +. .+.++|.||+     +.+.+  +..
T Consensus       132 ~~v~~~~Gg~~~~~~~~~~~~l~~-~~Il--V~----TP~~L~~~l~~----L~-~l~~lViDEa-----h~~l~--~~~  192 (1054)
T 1gku_B          132 NLIGYYHGRIPKREKENFMQNLRN-FKIV--IT----TTQFLSKHYRE----LG-HFDFIFVDDV-----DAILK--ASK  192 (1054)
T ss_dssp             GSEEECCSSCCSHHHHHHHHSGGG-CSEE--EE----EHHHHHHCSTT----SC-CCSEEEESCH-----HHHHT--STH
T ss_pred             ceEEEEeCCCChhhHHHHHhhccC-CCEE--EE----cHHHHHHHHHH----hc-cCCEEEEeCh-----hhhhh--ccc
Confidence             88899999887664   334444 6652  33    48888887766    33 4889999997     66666  466


Q ss_pred             HHHHHHHHCCC
Q psy7786         154 SLVRALEAKGI  164 (252)
Q Consensus       154 ~l~~~l~~~~~  164 (252)
                      .+...+...++
T Consensus       193 ~~~~i~~~lgf  203 (1054)
T 1gku_B          193 NVDKLLHLLGF  203 (1054)
T ss_dssp             HHHHHHHHTTE
T ss_pred             cHHHHHHHhCc
Confidence            77666666653

>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=99.80  E-value=1.5e-20  Score=161.53  Aligned_cols=136  Identities=22%  Similarity=0.286  Sum_probs=92.0

Q ss_pred             CcccCC--CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcce
Q psy7786           2 VTYRNS--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRT   79 (252)
Q Consensus         2 ~~~~~g--~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~   79 (252)
                      |.+++|  +|++++||||||||++|++|+++.+....        .+.++||++|||+|+.|+++.++++.+..+ ++++
T Consensus        57 ~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~--------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~-~~~~  127 (412)
T 3fht_A           57 PLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN--------KYPQCLCLSPTYELALQTGKVIEQMGKFYP-ELKL  127 (412)
T ss_dssp             HHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHTTTST-TCCE
T ss_pred             HHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcC--------CCCCEEEECCCHHHHHHHHHHHHHHHhhcc-cceE
Confidence            456666  99999999999999999999998875433        366899999999999999999999987764 3777


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-CCCCHHHHHH
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLVRA  158 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~~~  158 (252)
                      ....|+.......   ..+.+|.  +    ++|+++..+..+........+.++|.||+     +.+.+ .++...+...
T Consensus       128 ~~~~~~~~~~~~~---~~~~~iv--v----~T~~~l~~~~~~~~~~~~~~~~~iViDEa-----h~~~~~~~~~~~~~~~  193 (412)
T 3fht_A          128 AYAVRGNKLERGQ---KISEQIV--I----GTPGTVLDWCSKLKFIDPKKIKVFVLDEA-----DVMIATQGHQDQSIRI  193 (412)
T ss_dssp             EEECTTCCCCTTC---CCCCSEE--E----ECHHHHHHHHTTSCSSCGGGCCEEEEETH-----HHHHSTTTTHHHHHHH
T ss_pred             EEeecCcchhhhh---cCCCCEE--E----ECchHHHHHHHhcCCcChhhCcEEEEeCH-----HHHhhcCCcHHHHHHH
Confidence            7778876554332   2233431  2    23666544332211111134889999996     55544 4555554433


Q ss_pred             HH
Q psy7786         159 LE  160 (252)
Q Consensus       159 l~  160 (252)
                      +.
T Consensus       194 ~~  195 (412)
T 3fht_A          194 QR  195 (412)
T ss_dssp             HH
T ss_pred             Hh
Confidence            33

>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=99.80  E-value=2.6e-20  Score=166.07  Aligned_cols=124  Identities=13%  Similarity=0.069  Sum_probs=92.2

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++++|||||||++|++|+++.+.....      ..+.++||++||++|+.|+.+.++++....+  +++.
T Consensus        16 i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~--~~~~   87 (556)
T 4a2p_A           16 AQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA------GRKAKVVFLATKVPVYEQQKNVFKHHFERQG--YSVQ   87 (556)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS------SCCCCEEEECSSHHHHHHHHHHHHHHHGGGT--CCEE
T ss_pred             HHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcc------cCCCeEEEEeCCHHHHHHHHHHHHHHhcccC--ceEE
Confidence            3567899999999999999999999999988865432      1366899999999999999999999998877  8889


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .++|+.+...+.+.+..+++|.  |    ++|+++..............+.++|.||+
T Consensus        88 ~~~g~~~~~~~~~~~~~~~~i~--v----~T~~~l~~~~~~~~~~~~~~~~~vViDEa  139 (556)
T 4a2p_A           88 GISGENFSNVSVEKVIEDSDII--V----VTPQILVNSFEDGTLTSLSIFTLMIFDEC  139 (556)
T ss_dssp             ECCCC-----CHHHHHHHCSEE--E----ECHHHHHHHHHSSSCCCSTTCSEEEEETG
T ss_pred             EEeCCCCcchhHHHhhCCCCEE--E----ECHHHHHHHHHhCcccccccCCEEEEECC
Confidence            9999988887777777777762  2    34777665443332211233789999996

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

Probab=99.80  E-value=6.2e-21  Score=153.27  Aligned_cols=140  Identities=24%  Similarity=0.290  Sum_probs=96.5

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+....       ..++++||++||||||.|+++.++++....+  +++.
T Consensus        60 i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~-------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~--~~~~  130 (245)
T 3dkp_A           60 IPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA-------NKGFRALIISPTRELASQIHRELIKISEGTG--FRIH  130 (245)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCC-------SSSCCEEEECSSHHHHHHHHHHHHHHTTTSC--CCEE
T ss_pred             HHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcc-------cCCceEEEEeCCHHHHHHHHHHHHHHhcccC--ceEE
Confidence            356789999999999999999999999998875322       2467899999999999999999999988777  7777


Q ss_pred             eeeCCcccCcch-hhhhhcccccCCccccccCCccccCCChhHH--HHHhhhhceeeccCCCCCccccccc---CCCCHH
Q psy7786          81 LAIGGVPMNQSL-DVIKKGIQYNDPIKTSWRAPRCILSLPDQVH--DIIRRNLRILVEGDDVPPACCSFRL---MKLPES  154 (252)
Q Consensus        81 ~~~g~~~~~~~~-~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~--~~l~~~~~~~V~de~~~~~~~~~~~---~~l~~~  154 (252)
                      .+.|+.....+. .....+++|.  |    ++|+++.++..+..  ..+. .+.++|.||+     +.+.+   .++...
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~I~--v----~Tp~~l~~~l~~~~~~~~~~-~~~~lViDEa-----h~~~~~~~~~~~~~  198 (245)
T 3dkp_A          131 MIHKAAVAAKKFGPKSSKKFDIL--V----TTPNRLIYLLKQDPPGIDLA-SVEWLVVDES-----DKLFEDGKTGFRDQ  198 (245)
T ss_dssp             CCCHHHHHHTTTSTTSCCCCCEE--E----ECHHHHHHHHHSSSCSCCCT-TCCEEEESSH-----HHHHHHC--CHHHH
T ss_pred             EEecCccHHHHhhhhhcCCCCEE--E----ECHHHHHHHHHhCCCCcccc-cCcEEEEeCh-----HHhcccccccHHHH
Confidence            777765433322 2223344441  2    23666544433321  1222 3788999996     66655   567677


Q ss_pred             HHHHHHH
Q psy7786         155 LVRALEA  161 (252)
Q Consensus       155 l~~~l~~  161 (252)
                      +...+..
T Consensus       199 ~~~i~~~  205 (245)
T 3dkp_A          199 LASIFLA  205 (245)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            7666544

>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=99.80  E-value=1.2e-20  Score=161.25  Aligned_cols=138  Identities=16%  Similarity=0.271  Sum_probs=99.6

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .+.++||++||++|+.|+++.++++....+  +++..
T Consensus        53 ~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~--------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~--~~~~~  122 (394)
T 1fuu_A           53 MPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV--------KAPQALMLAPTRELALQIQKVVMALAFHMD--IKVHA  122 (394)
T ss_dssp             HHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTC--------CSCCEEEECSSHHHHHHHHHHHHHHTTTSC--CCEEE
T ss_pred             HHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccC--------CCCCEEEEcCCHHHHHHHHHHHHHHhccCC--eeEEE
Confidence            45778999999999999999999999998875432        367899999999999999999999987776  78888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEA  161 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~  161 (252)
                      ++|+.+..++...+. +.+|.  +    ++|+++.....+....+ ..+.++|.||+     +.+.+.++...+...+..
T Consensus       123 ~~g~~~~~~~~~~~~-~~~i~--v----~T~~~l~~~~~~~~~~~-~~~~~vIiDEa-----h~~~~~~~~~~~~~~~~~  189 (394)
T 1fuu_A          123 CIGGTSFVEDAEGLR-DAQIV--V----GTPGRVFDNIQRRRFRT-DKIKMFILDEA-----DEMLSSGFKEQIYQIFTL  189 (394)
T ss_dssp             ECSSCCHHHHHHHHH-HCSEE--E----ECHHHHHHHHHTTSSCC-TTCCEEEEETH-----HHHHHTTCHHHHHHHHHH
T ss_pred             EeCCCchHHHHhhcC-CCCEE--E----ECHHHHHHHHHhCCcch-hhCcEEEEECh-----HHhhCCCcHHHHHHHHHh
Confidence            999977665555544 33431  2    23555543332222112 24789999996     566666676766665554


Q ss_pred             C
Q psy7786         162 K  162 (252)
Q Consensus       162 ~  162 (252)
                      .
T Consensus       190 ~  190 (394)
T 1fuu_A          190 L  190 (394)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.79  E-value=4.6e-21  Score=149.95  Aligned_cols=138  Identities=25%  Similarity=0.317  Sum_probs=102.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....     ....++++||++|||+|+.|+++.++.+...    +++..
T Consensus        33 ~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~-----~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~----~~~~~  103 (207)
T 2gxq_A           33 PLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ-----ERGRKPRALVLTPTRELALQVASELTAVAPH----LKVVA  103 (207)
T ss_dssp             HHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCC-----CTTCCCSEEEECSSHHHHHHHHHHHHHHCTT----SCEEE
T ss_pred             HHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhcc-----ccCCCCcEEEEECCHHHHHHHHHHHHHHhhc----ceEEE
Confidence            56789999999999999999999999998875421     1224678999999999999999999887543    57778


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ++|+.+...+.+.+.+++++.  +    ++|+++.....+....+. .+.++|.||+     +.+.+.++...+...+.
T Consensus       104 ~~~~~~~~~~~~~~~~~~~i~--v----~T~~~l~~~~~~~~~~~~-~~~~iViDEa-----h~~~~~~~~~~~~~i~~  170 (207)
T 2gxq_A          104 VYGGTGYGKQKEALLRGADAV--V----ATPGRALDYLRQGVLDLS-RVEVAVLDEA-----DEMLSMGFEEEVEALLS  170 (207)
T ss_dssp             ECSSSCSHHHHHHHHHCCSEE--E----ECHHHHHHHHHHTSSCCT-TCSEEEEESH-----HHHHHTTCHHHHHHHHH
T ss_pred             EECCCChHHHHHHhhCCCCEE--E----ECHHHHHHHHHcCCcchh-hceEEEEECh-----hHhhccchHHHHHHHHH
Confidence            899988777777777776662  2    347666554443322333 3789999997     66767777776655543

>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=99.78  E-value=3.2e-21  Score=152.45  Aligned_cols=136  Identities=21%  Similarity=0.291  Sum_probs=98.0

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+....        .++++||++|||+|+.|+++.++++.+..+ ++++..
T Consensus        46 ~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~--------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~v~~  116 (220)
T 1t6n_A           46 PQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT--------GQVSVLVMCHTRELAFQISKEYERFSKYMP-NVKVAV  116 (220)
T ss_dssp             HHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCT--------TCCCEEEECSCHHHHHHHHHHHHHHTTTST-TCCEEE
T ss_pred             HHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccC--------CCEEEEEEeCCHHHHHHHHHHHHHHHhhCC-CceEEE
Confidence            46788999999999999999999999998764321        356899999999999999999999987763 388888


Q ss_pred             eeCCcccCcchhhhhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-CCCCHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLVRA  158 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~~~  158 (252)
                      ++||.+...+.+.+.++ +++.  +    ++|+++..........+. .+.++|.||+     +.+.+ .++...+...
T Consensus       117 ~~g~~~~~~~~~~~~~~~~~i~--v----~T~~~l~~~~~~~~~~~~-~~~~lViDEa-----h~~~~~~~~~~~~~~i  183 (220)
T 1t6n_A          117 FFGGLSIKKDEEVLKKNCPHIV--V----GTPGRILALARNKSLNLK-HIKHFILDEC-----DKMLEQLDMRRDVQEI  183 (220)
T ss_dssp             ESCCSCHHHHHHHHHHSCCSEE--E----ECHHHHHHHHHTTSSCCT-TCCEEEEESH-----HHHHSSHHHHHHHHHH
T ss_pred             EeCCCChHHHHHHHhcCCCCEE--E----eCHHHHHHHHHhCCCCcc-cCCEEEEcCH-----HHHhcccCcHHHHHHH
Confidence            99998877776666653 3541  2    336666544333222233 4789999996     55543 3444444333

>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=99.77  E-value=1.9e-19  Score=153.71  Aligned_cols=132  Identities=22%  Similarity=0.300  Sum_probs=88.6

Q ss_pred             CcccCC--CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcce
Q psy7786           2 VTYRNS--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRT   79 (252)
Q Consensus         2 ~~~~~g--~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~   79 (252)
                      +.+++|  +|+++++|||||||++|++|+++.+....        .+.++||++||++|+.|+++.+++++...+  +.+
T Consensus        37 ~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~--------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~--~~~  106 (395)
T 3pey_A           37 PLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPED--------ASPQAICLAPSRELARQTLEVVQEMGKFTK--ITS  106 (395)
T ss_dssp             HHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTC--------CSCCEEEECSSHHHHHHHHHHHHHHTTTSC--CCE
T ss_pred             HHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCC--------CCccEEEECCCHHHHHHHHHHHHHHhcccC--eeE
Confidence            445666  99999999999999999999998775432        366899999999999999999999987776  677


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-CCCCHHHHHH
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLVRA  158 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~~~  158 (252)
                      ...+|+......    ..+.+|.  +    ++|+++.....+....+. .+.++|.||+     +.+.+ .++...+...
T Consensus       107 ~~~~~~~~~~~~----~~~~~ii--v----~T~~~l~~~~~~~~~~~~-~~~~iIiDEa-----h~~~~~~~~~~~~~~~  170 (395)
T 3pey_A          107 QLIVPDSFEKNK----QINAQVI--V----GTPGTVLDLMRRKLMQLQ-KIKIFVLDEA-----DNMLDQQGLGDQCIRV  170 (395)
T ss_dssp             EEESTTSSCTTS----CBCCSEE--E----ECHHHHHHHHHTTCBCCT-TCCEEEEETH-----HHHHHSTTHHHHHHHH
T ss_pred             EEEecCchhhhc----cCCCCEE--E----EcHHHHHHHHHcCCcccc-cCCEEEEECh-----hhhcCccccHHHHHHH
Confidence            777776443222    1233431  1    236555443322222223 3788999996     44443 4444444433


Q ss_pred             H
Q psy7786         159 L  159 (252)
Q Consensus       159 l  159 (252)
                      .
T Consensus       171 ~  171 (395)
T 3pey_A          171 K  171 (395)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.77  E-value=4.6e-19  Score=149.83  Aligned_cols=136  Identities=24%  Similarity=0.350  Sum_probs=96.7

Q ss_pred             CcccCC-CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           2 VTYRNS-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         2 ~~~~~g-~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      +.+++| +|+++.+|||||||++|++|+++.+...         .+.++||++||++|+.|+.+.++++....+  +++.
T Consensus        38 ~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~---------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~--~~v~  106 (367)
T 1hv8_A           38 PLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN---------NGIEAIILTPTRELAIQVADEIESLKGNKN--LKIA  106 (367)
T ss_dssp             HHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS---------SSCCEEEECSCHHHHHHHHHHHHHHHCSSC--CCEE
T ss_pred             HHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc---------CCCcEEEEcCCHHHHHHHHHHHHHHhCCCC--ceEE
Confidence            345667 7999999999999999999999776432         367899999999999999999999987665  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ..+|+.....+...+. ..++.  +    ++|+++..........+. .+.++|.||+     +.+.+.++...+...+.
T Consensus       107 ~~~~~~~~~~~~~~~~-~~~ii--v----~T~~~l~~~~~~~~~~~~-~~~~iIiDEa-----h~~~~~~~~~~~~~~~~  173 (367)
T 1hv8_A          107 KIYGGKAIYPQIKALK-NANIV--V----GTPGRILDHINRGTLNLK-NVKYFILDEA-----DEMLNMGFIKDVEKILN  173 (367)
T ss_dssp             EECTTSCHHHHHHHHH-TCSEE--E----ECHHHHHHHHHTTCSCTT-SCCEEEEETH-----HHHHTTTTHHHHHHHHH
T ss_pred             EEECCcchHHHHhhcC-CCCEE--E----ecHHHHHHHHHcCCcccc-cCCEEEEeCc-----hHhhhhchHHHHHHHHH
Confidence            8899877665555554 33441  2    236655443322222223 3788999996     66666667666655554


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       174 ~  174 (367)
T 1hv8_A          174 A  174 (367)
T ss_dssp             T
T ss_pred             h
Confidence            4

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

Probab=99.76  E-value=1.7e-18  Score=158.52  Aligned_cols=122  Identities=15%  Similarity=0.121  Sum_probs=95.8

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|.+|+++.+.....      ..+.++||++||++|+.|+.+.++++....+  +++..
T Consensus        23 ~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~------~~~~~~lvl~Pt~~L~~Q~~~~~~~~~~~~~--~~v~~   94 (696)
T 2ykg_A           23 LPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQ------GQKGKVVFFANQIPVYEQNKSVFSKYFERHG--YRVTG   94 (696)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCT------TCCCCEEEECSSHHHHHHHHHHHHHHTTTTT--CCEEE
T ss_pred             HHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCcc------CCCCeEEEEECCHHHHHHHHHHHHHHhccCC--ceEEE
Confidence            567899999999999999999999999998765431      1236799999999999999999999987666  78889


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHH-HHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHD-IIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~-~l~~~~~~~V~de~  138 (252)
                      ++|+.+...+.+.+..+.+|.  +    +||+++......... .+. .+.++|.||+
T Consensus        95 ~~g~~~~~~~~~~~~~~~~Ii--v----~Tp~~L~~~l~~~~~~~l~-~~~~vViDEa  145 (696)
T 2ykg_A           95 ISGATAENVPVEQIVENNDII--I----LTPQILVNNLKKGTIPSLS-IFTLMIFDEC  145 (696)
T ss_dssp             ECSSSCSSSCHHHHHHTCSEE--E----ECHHHHHHHHHTTSSCCGG-GCSEEEEETG
T ss_pred             EeCCccccccHHHhccCCCEE--E----ECHHHHHHHHhcCcccccc-cccEEEEeCC
Confidence            999988888777777777762  2    348877665444322 233 3789999996

>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=99.76  E-value=5.8e-19  Score=163.88  Aligned_cols=122  Identities=13%  Similarity=0.088  Sum_probs=92.1

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||++|++|+++.+.....      ..+.++||++||++|+.|+.+.++++....+  +++..
T Consensus       258 ~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~------~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~--~~v~~  329 (797)
T 4a2q_A          258 QPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA------GRKAKVVFLATKVPVYEQQKNVFKHHFERQG--YSVQG  329 (797)
T ss_dssp             HHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS------SCCCCEEEECSSHHHHHHHHHHHHHHHGGGT--CCEEE
T ss_pred             HHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccc------cCCCeEEEEeCCHHHHHHHHHHHHHhcccCC--ceEEE
Confidence            567899999999999999999999999998865421      1366899999999999999999999988777  88999


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHH-HHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHD-IIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~-~l~~~~~~~V~de~  138 (252)
                      ++|+.+...+.+.+..+++|.  |    ++|+++......... .+. .+.++|.||+
T Consensus       330 ~~g~~~~~~~~~~~~~~~~Iv--v----~Tp~~l~~~l~~~~~~~~~-~~~~iViDEa  380 (797)
T 4a2q_A          330 ISGENFSNVSVEKVIEDSDII--V----VTPQILVNSFEDGTLTSLS-IFTLMIFDEC  380 (797)
T ss_dssp             ECCC-----CHHHHHHTCSEE--E----ECHHHHHHHHHSSSCCCGG-GCSEEEETTG
T ss_pred             EeCCcchhhhHHHhhCCCCEE--E----EchHHHHHHHHhccccccc-cCCEEEEECc
Confidence            999998888777777777762  2    347776654443322 233 3789999996

>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=99.76  E-value=9.1e-19  Score=172.00  Aligned_cols=123  Identities=15%  Similarity=0.084  Sum_probs=90.8

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +.+++|++++||||||||++|.+|+++.+............++.++||++|+|+||+|+++.+++..+..|  +++..++
T Consensus        92 l~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~~~~~~~g--i~V~~~t  169 (1724)
T 4f92_B           92 LETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYG--ITVAELT  169 (1724)
T ss_dssp             HTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHHHHHTTTT--CCEEECC
T ss_pred             HcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHHHHHhhCC--CEEEEEE
Confidence            34689999999999999999999999999875443333445688999999999999999999988777777  8999999


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhH--HHHHhhhhceeeccCC
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQV--HDIIRRNLRILVEGDD  138 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~--~~~l~~~~~~~V~de~  138 (252)
                      |+++...+.   .++++|   +.   +||+++..+..+.  ...+ +.++++|.||.
T Consensus       170 Gd~~~~~~~---~~~~~I---lV---tTpEkld~llr~~~~~~~l-~~v~~vIiDEv  216 (1724)
T 4f92_B          170 GDHQLCKEE---ISATQI---IV---CTPEKWDIITRKGGERTYT-QLVRLIILDEI  216 (1724)
T ss_dssp             SSCSSCCTT---GGGCSE---EE---ECHHHHHHHTTSSTTHHHH-TTEEEEEETTG
T ss_pred             CCCCCCccc---cCCCCE---EE---ECHHHHHHHHcCCccchhh-cCcCEEEEecc
Confidence            998765432   234555   22   3466654333221  2233 34899999995

>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=99.75  E-value=3.6e-19  Score=148.90  Aligned_cols=132  Identities=21%  Similarity=0.325  Sum_probs=95.6

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++.+|||||||++|++|+++.              +.++||++||++|+.|+++.+++++...+  +++..
T Consensus        26 ~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~--------------~~~~liv~P~~~L~~q~~~~~~~~~~~~~--~~~~~   89 (337)
T 2z0m_A           26 PLMLQGKNVVVRAKTGSGKTAAYAIPILEL--------------GMKSLVVTPTRELTRQVASHIRDIGRYMD--TKVAE   89 (337)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHHHHHHHHHH--------------TCCEEEECSSHHHHHHHHHHHHHHTTTSC--CCEEE
T ss_pred             HHHhcCCCEEEEcCCCCcHHHHHHHHHHhh--------------cCCEEEEeCCHHHHHHHHHHHHHHhhhcC--CcEEE
Confidence            457789999999999999999999998863              34699999999999999999999988777  78888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEA  161 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~  161 (252)
                      ++|+.+...+...+.+ .+|.  +    ++|+++..........+. .+.++|.||+     +.+.+.++...+...+..
T Consensus        90 ~~~~~~~~~~~~~~~~-~~i~--v----~T~~~l~~~~~~~~~~~~-~~~~iViDEa-----h~~~~~~~~~~~~~~~~~  156 (337)
T 2z0m_A           90 VYGGMPYKAQINRVRN-ADIV--V----ATPGRLLDLWSKGVIDLS-SFEIVIIDEA-----DLMFEMGFIDDIKIILAQ  156 (337)
T ss_dssp             ECTTSCHHHHHHHHTT-CSEE--E----ECHHHHHHHHHTTSCCGG-GCSEEEEESH-----HHHHHTTCHHHHHHHHHH
T ss_pred             EECCcchHHHHhhcCC-CCEE--E----ECHHHHHHHHHcCCcchh-hCcEEEEECh-----HHhhccccHHHHHHHHhh
Confidence            8998776665555543 4441  2    336666543322222233 3788999996     566666666666555554


Q ss_pred             C
Q psy7786         162 K  162 (252)
Q Consensus       162 ~  162 (252)
                      .
T Consensus       157 ~  157 (337)
T 2z0m_A          157 T  157 (337)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.75  E-value=3.5e-18  Score=162.49  Aligned_cols=125  Identities=13%  Similarity=0.098  Sum_probs=93.1

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|++++|+||||||++|.+|+++.+..           +.+++|++|||+||+|+++.++.+..      .+.
T Consensus       193 I~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~-----------g~rvlvl~PtraLa~Q~~~~l~~~~~------~Vg  255 (1108)
T 3l9o_A          193 ISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN-----------KQRVIYTSPIKALSNQKYRELLAEFG------DVG  255 (1108)
T ss_dssp             HHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT-----------TCEEEEEESSHHHHHHHHHHHHHHTS------SEE
T ss_pred             HHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc-----------CCeEEEEcCcHHHHHHHHHHHHHHhC------Ccc
Confidence            3567899999999999999999999999988732           56899999999999999998887643      455


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++|+.+...       ..+|.  |.    ||+++.++..+....+++ +.++|.||+     +.+.+.++...+...+.
T Consensus       256 lltGd~~~~~-------~~~Il--V~----Tpe~L~~~L~~~~~~l~~-l~lVVIDEa-----H~l~d~~rg~~~e~ii~  316 (1108)
T 3l9o_A          256 LMTGDITINP-------DAGCL--VM----TTEILRSMLYRGSEVMRE-VAWVIFDEV-----HYMRDKERGVVWEETII  316 (1108)
T ss_dssp             EECSSCBCCC-------SCSEE--EE----EHHHHHHHHHHCSSHHHH-EEEEEEETG-----GGTTSHHHHHHHHHHHH
T ss_pred             EEeCccccCC-------CCCEE--Ee----ChHHHHHHHHcCcccccc-CCEEEEhhh-----hhccccchHHHHHHHHH
Confidence            6788866432       24442  33    488887766665555555 899999997     66666555555555444


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       317 ~  317 (1108)
T 3l9o_A          317 L  317 (1108)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.74  E-value=2.1e-18  Score=156.80  Aligned_cols=115  Identities=16%  Similarity=0.188  Sum_probs=86.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      +|.+++|+  +++++||+|||++|.+|++...+.           +.+++|++||++||.|+.+++..+.+++|  +++.
T Consensus       120 ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~-----------g~~v~VvTpTreLA~Qdae~m~~l~~~lG--Lsv~  184 (922)
T 1nkt_A          120 AAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA-----------GNGVHIVTVNDYLAKRDSEWMGRVHRFLG--LQVG  184 (922)
T ss_dssp             HHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT-----------TSCEEEEESSHHHHHHHHHHHHHHHHHTT--CCEE
T ss_pred             HHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh-----------CCCeEEEeCCHHHHHHHHHHHHHHHhhcC--CeEE
Confidence            36778898  999999999999999999765432           44699999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccc-cCCChhH-----HHHHhhhhceeeccCC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCI-LSLPDQV-----HDIIRRNLRILVEGDD  138 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l-~~~~~~~-----~~~l~~~~~~~V~de~  138 (252)
                      +++||.+.  +.+....++||      +|+||+++ .++....     .....+.++++|.||+
T Consensus       185 ~i~gg~~~--~~r~~~y~~DI------vygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEa  240 (922)
T 1nkt_A          185 VILATMTP--DERRVAYNADI------TYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEV  240 (922)
T ss_dssp             ECCTTCCH--HHHHHHHHSSE------EEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTH
T ss_pred             EEeCCCCH--HHHHHhcCCCE------EEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeCh
Confidence            99999764  33444556777      34558887 2322211     1112234889999986

>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=99.73  E-value=5.5e-19  Score=160.17  Aligned_cols=115  Identities=17%  Similarity=0.175  Sum_probs=88.3

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      +|.+++|+  ++.++||||||++|++|++...+.           +.+++|++||||||.|++++++.+.+++|  +++.
T Consensus        83 i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~-----------g~~vlVltPTreLA~Q~~e~~~~l~~~lg--l~v~  147 (853)
T 2fsf_A           83 GMVLNERC--IAEMRTGEGKTLTATLPAYLNALT-----------GKGVHVVTVNDYLAQRDAENNRPLFEFLG--LTVG  147 (853)
T ss_dssp             HHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT-----------SSCCEEEESSHHHHHHHHHHHHHHHHHTT--CCEE
T ss_pred             cccccCCe--eeeecCCchHHHHHHHHHHHHHHc-----------CCcEEEEcCCHHHHHHHHHHHHHHHHhcC--CeEE
Confidence            36778898  999999999999999999965432           55799999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccc-cCCChhH-----HHHHhhhhceeeccCC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCI-LSLPDQV-----HDIIRRNLRILVEGDD  138 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l-~~~~~~~-----~~~l~~~~~~~V~de~  138 (252)
                      +++||.+.  +.+.+..++||.      ++||+++ .++....     .....+.++++|.||+
T Consensus       148 ~i~GG~~~--~~r~~~~~~dIv------vgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEa  203 (853)
T 2fsf_A          148 INLPGMPA--PAKREAYAADIT------YGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEV  203 (853)
T ss_dssp             ECCTTCCH--HHHHHHHHSSEE------EEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCH
T ss_pred             EEeCCCCH--HHHHHhcCCCEE------EECCchhhHHHHHhhhhccHhHhcccCCcEEEECch
Confidence            99999765  345555677773      3448887 3333221     1112245889999996

>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=99.73  E-value=3.4e-17  Score=145.15  Aligned_cols=123  Identities=19%  Similarity=0.244  Sum_probs=85.6

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++.+|||||||++|.+|++..              ...+||++|+++|+.|+.+.++.+    +  +.+.
T Consensus        34 i~~il~g~d~lv~apTGsGKTl~~~lp~l~~--------------~g~~lvi~P~~aL~~q~~~~l~~~----g--i~~~   93 (523)
T 1oyw_A           34 IDTVLSGRDCLVVMPTGGGKSLCYQIPALLL--------------NGLTVVVSPLISLMKDQVDQLQAN----G--VAAA   93 (523)
T ss_dssp             HHHHHTTCCEEEECSCHHHHHHHHHHHHHHS--------------SSEEEEECSCHHHHHHHHHHHHHT----T--CCEE
T ss_pred             HHHHHcCCCEEEECCCCcHHHHHHHHHHHHh--------------CCCEEEECChHHHHHHHHHHHHHc----C--CcEE
Confidence            3567899999999999999999999998832              235899999999999999888764    4  6777


Q ss_pred             eeeCCcccCcchhhh---hh-cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCC--CCHH
Q psy7786          81 LAIGGVPMNQSLDVI---KK-GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMK--LPES  154 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l---~~-~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~--l~~~  154 (252)
                      .+.|+.+..++....   .. ..++      ++++|+++.......... ...+.++|.||+     +.+.+.|  |.+.
T Consensus        94 ~l~~~~~~~~~~~~~~~~~~~~~~i------lv~Tpe~l~~~~~~~~l~-~~~~~~vViDEa-----H~i~~~g~~fr~~  161 (523)
T 1oyw_A           94 CLNSTQTREQQLEVMTGCRTGQIRL------LYIAPERLMLDNFLEHLA-HWNPVLLAVDEA-----HCISQWGHDFRPE  161 (523)
T ss_dssp             EECTTSCHHHHHHHHHHHHHTCCSE------EEECHHHHTSTTHHHHHT-TSCEEEEEESSG-----GGGCTTSSCCCHH
T ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCE------EEECHHHHhChHHHHHHh-hCCCCEEEEeCc-----cccCcCCCccHHH
Confidence            788876655443322   22 2444      234588886543222222 245889999997     5565554  5554


Q ss_pred             H
Q psy7786         155 L  155 (252)
Q Consensus       155 l  155 (252)
                      .
T Consensus       162 ~  162 (523)
T 1oyw_A          162 Y  162 (523)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.73  E-value=3.1e-17  Score=147.08  Aligned_cols=124  Identities=14%  Similarity=0.205  Sum_probs=85.4

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++.+|||+|||++|.+|++..              ..++||++||++|+.|+.+.++.+    |  +++.
T Consensus        53 i~~il~g~d~lv~~pTGsGKTl~~~lpal~~--------------~g~~lVisP~~~L~~q~~~~l~~~----g--i~~~  112 (591)
T 2v1x_A           53 INVTMAGKEVFLVMPTGGGKSLCYQLPALCS--------------DGFTLVICPLISLMEDQLMVLKQL----G--ISAT  112 (591)
T ss_dssp             HHHHHTTCCEEEECCTTSCTTHHHHHHHHTS--------------SSEEEEECSCHHHHHHHHHHHHHH----T--CCEE
T ss_pred             HHHHHcCCCEEEEECCCChHHHHHHHHHHHc--------------CCcEEEEeCHHHHHHHHHHHHHhc----C--CcEE
Confidence            3567899999999999999999999999741              237999999999999999988876    4  7788


Q ss_pred             eeeCCcccCcchhhhh------hcccccCCccccccCCccccCC---ChhHH-HHHhhhhceeeccCCCCCcccccccCC
Q psy7786          81 LAIGGVPMNQSLDVIK------KGIQYNDPIKTSWRAPRCILSL---PDQVH-DIIRRNLRILVEGDDVPPACCSFRLMK  150 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~------~~~~i~~~i~t~~~~p~~l~~~---~~~~~-~~l~~~~~~~V~de~~~~~~~~~~~~~  150 (252)
                      .+.|+.+..++.....      ...++      ++.+|+++...   ..... ......+.++|.||+     +.+.+.|
T Consensus       113 ~l~~~~~~~~~~~~~~~l~~~~~~~~I------lv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEA-----H~is~~g  181 (591)
T 2v1x_A          113 MLNASSSKEHVKWVHAEMVNKNSELKL------IYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEV-----HCCSQWG  181 (591)
T ss_dssp             ECCSSCCHHHHHHHHHHHHCTTCCCCE------EEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETG-----GGGSTTC
T ss_pred             EEeCCCCHHHHHHHHHHhhcccCCCCE------EEEChhHhhccHHHHHHHHhhhhccCCcEEEEECc-----ccccccc
Confidence            8888877655443332      12333      23457776542   11111 111235788999997     5555554


Q ss_pred             --CCHHH
Q psy7786         151 --LPESL  155 (252)
Q Consensus       151 --l~~~l  155 (252)
                        |.+..
T Consensus       182 ~dfr~~~  188 (591)
T 2v1x_A          182 HDFRPDY  188 (591)
T ss_dssp             TTCCGGG
T ss_pred             cccHHHH
Confidence              54443

>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=2.6e-18  Score=161.67  Aligned_cols=122  Identities=13%  Similarity=0.088  Sum_probs=91.0

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|++++++||||||++|++|+++.+.....      ..+.++||++||++|+.|+++.++++....+  +++..
T Consensus       258 ~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~------~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~--~~v~~  329 (936)
T 4a2w_A          258 QPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA------GRKAKVVFLATKVPVYEQQKNVFKHHFERQG--YSVQG  329 (936)
T ss_dssp             HHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCS------SCCCCEEEECSSHHHHHHHHHHHHHHHHTTT--CCEEE
T ss_pred             HHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccc------cCCCeEEEEeCCHHHHHHHHHHHHHHhcccC--ceEEE
Confidence            457899999999999999999999999877654321      1256799999999999999999999988776  88999


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHH-HHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHD-IIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~-~l~~~~~~~V~de~  138 (252)
                      ++|+.+...+.+.+..+.+|.  |    ++|+++......... .+. .+.++|.||+
T Consensus       330 ~~G~~~~~~~~~~~~~~~~Iv--I----~Tp~~L~~~l~~~~~~~l~-~~~liViDEa  380 (936)
T 4a2w_A          330 ISGENFSNVSVEKVIEDSDII--V----VTPQILVNSFEDGTLTSLS-IFTLMIFDEC  380 (936)
T ss_dssp             ECCC-----CCHHHHHHCSEE--E----ECHHHHHHHHHSSSCCCGG-GCSEEEEETG
T ss_pred             EECCcchhhHHHHhccCCCEE--E----ecHHHHHHHHHcCcccccc-CCCEEEEECc
Confidence            999988887777777777762  2    347777655443322 233 3789999996

>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=99.73  E-value=9.8e-19  Score=157.39  Aligned_cols=182  Identities=14%  Similarity=0.016  Sum_probs=108.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|+++.+..          .+.++||++||||||.|+++.++      +  ..+.
T Consensus       180 i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~----------~~~~vLvl~PtreLa~Qi~~~l~------~--~~v~  241 (618)
T 2whx_A          180 EDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK----------RRLRTLILAPTRVVAAEMEEALR------G--LPIR  241 (618)
T ss_dssp             GGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH----------TTCCEEEEESSHHHHHHHHHHTT------T--SCEE
T ss_pred             HHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh----------CCCeEEEEcChHHHHHHHHHHhc------C--Ccee
Confidence            5779999999999999999999999999998865          25689999999999999998765      2  2222


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHH--H-----hhhhceeeccCCCCCcccccccCCCCH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDI--I-----RRNLRILVEGDDVPPACCSFRLMKLPE  153 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~--l-----~~~~~~~V~de~~~~~~~~~~~~~l~~  153 (252)
                       ..++        .+..       +    .+|++++++.......  +     ...+.++|.||+     +.+ ++++..
T Consensus       242 -~~~~--------~l~~-------~----~tp~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEa-----h~~-~~~~~~  295 (618)
T 2whx_A          242 -YQTP--------AVKS-------D----HTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEA-----HFT-DPCSVA  295 (618)
T ss_dssp             -ECCT--------TSSC-------C----CCSSSCEEEEEHHHHHHHHHHCSSCCCCSEEEEEST-----TCC-SHHHHH
T ss_pred             -Eecc--------ccee-------c----cCCCceEEEEChHHHHHHHhccccccCCeEEEEECC-----CCC-CccHHH
Confidence             1111        0100       2    2378887766544322  0     244899999997     554 444444


Q ss_pred             HHHHHHHHCCCCCChHHHHhhhhhhhcCC---------cEE-EEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         154 SLVRALEAKGIKKPTPIQVQGIPAALSGR---------DII-GIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       154 ~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~---------~~~-~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+...+....   ....|...+++++.+.         ..+ +.......+ ...++..   +.+          ...++
T Consensus       296 ~~~~i~~~l~---~~~~q~il~SAT~~~~~~~~~~~~~~~~~v~~~~~~~~-~~~ll~~---l~~----------~~~~~  358 (618)
T 2whx_A          296 ARGYISTRVE---MGEAAAIFMTATPPGSTDPFPQSNSPIEDIEREIPERS-WNTGFDW---ITD----------YQGKT  358 (618)
T ss_dssp             HHHHHHHHHH---HTSCEEEEECSSCTTCCCSSCCCSSCEEEEECCCCSSC-CSSSCHH---HHH----------CCSCE
T ss_pred             HHHHHHHHhc---ccCccEEEEECCCchhhhhhhccCCceeeecccCCHHH-HHHHHHH---HHh----------CCCCE
Confidence            4433332210   0112333334443221         111 111000011 0111111   111          13479


Q ss_pred             EEEcCcHHHHHHHHHHHHHH
Q psy7786         224 LIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ||||+|++.|+.+++.|++.
T Consensus       359 LVF~~s~~~a~~l~~~L~~~  378 (618)
T 2whx_A          359 VWFVPSIKAGNDIANCLRKS  378 (618)
T ss_dssp             EEECSSHHHHHHHHHHHHHT
T ss_pred             EEEECChhHHHHHHHHHHHc
Confidence            99999999999999999865

>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=99.73  E-value=2.1e-18  Score=158.53  Aligned_cols=130  Identities=20%  Similarity=0.189  Sum_probs=93.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +++|+|++++||||||||++|.+|+++.+...          +.+++|++|+|+||.|+++.++++.+. |  +++...+
T Consensus        36 ~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~----------~~~~l~i~P~raLa~q~~~~~~~l~~~-g--~~v~~~~  102 (720)
T 2zj8_A           36 ILEGKNALISIPTASGKTLIAEIAMVHRILTQ----------GGKAVYIVPLKALAEEKFQEFQDWEKI-G--LRVAMAT  102 (720)
T ss_dssp             GGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH----------CSEEEEECSSGGGHHHHHHHTGGGGGG-T--CCEEEEC
T ss_pred             hcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC----------CCEEEEEcCcHHHHHHHHHHHHHHHhc-C--CEEEEec
Confidence            78899999999999999999999999888643          457999999999999999999766543 5  7888899


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHH
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEA  161 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~  161 (252)
                      |+.+...+.  + ...+|      +++||+++..+..+....+. .+.++|.||.     +.+.+......+...+..
T Consensus       103 G~~~~~~~~--~-~~~~I------iv~Tpe~l~~~~~~~~~~l~-~~~~vIiDE~-----H~l~~~~r~~~~~~ll~~  165 (720)
T 2zj8_A          103 GDYDSKDEW--L-GKYDI------IIATAEKFDSLLRHGSSWIK-DVKILVADEI-----HLIGSRDRGATLEVILAH  165 (720)
T ss_dssp             SCSSCCCGG--G-GGCSE------EEECHHHHHHHHHHTCTTGG-GEEEEEEETG-----GGGGCTTTHHHHHHHHHH
T ss_pred             CCCCccccc--c-CCCCE------EEECHHHHHHHHHcChhhhh-cCCEEEEECC-----cccCCCcccHHHHHHHHH
Confidence            987655432  2 23444      12347766554443322233 4789999996     555555555555444443

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

Probab=99.72  E-value=1.1e-17  Score=153.81  Aligned_cols=128  Identities=15%  Similarity=0.165  Sum_probs=92.0

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +.+|+|++++||||||||++|.+|+++.+...          +.+++|++|+|+||.|+.+.++.+.. .|  +++...+
T Consensus        43 ~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~----------~~~il~i~P~r~La~q~~~~~~~~~~-~g--~~v~~~~  109 (715)
T 2va8_A           43 LLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN----------GGKAIYVTPLRALTNEKYLTFKDWEL-IG--FKVAMTS  109 (715)
T ss_dssp             TTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS----------CSEEEEECSCHHHHHHHHHHHGGGGG-GT--CCEEECC
T ss_pred             hcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC----------CCeEEEEeCcHHHHHHHHHHHHHhhc-CC--CEEEEEe
Confidence            68899999999999999999999999887642          45899999999999999999976643 35  7888889


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      |+....++  .+. ..+|      .++||+++..+.......+.+ +.++|.||.     +.+.+..+...+...+
T Consensus       110 G~~~~~~~--~~~-~~~I------iv~Tpe~l~~~~~~~~~~l~~-~~~vIiDE~-----H~l~~~~~~~~l~~i~  170 (715)
T 2va8_A          110 GDYDTDDA--WLK-NYDI------IITTYEKLDSLWRHRPEWLNE-VNYFVLDEL-----HYLNDPERGPVVESVT  170 (715)
T ss_dssp             SCSSSCCG--GGG-GCSE------EEECHHHHHHHHHHCCGGGGG-EEEEEECSG-----GGGGCTTTHHHHHHHH
T ss_pred             CCCCCchh--hcC-CCCE------EEEcHHHHHHHHhCChhHhhc-cCEEEEech-----hhcCCcccchHHHHHH
Confidence            98765543  222 4444      123477776654443333444 889999996     5555555555554444

>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=99.72  E-value=1.3e-16  Score=127.72  Aligned_cols=127  Identities=36%  Similarity=0.639  Sum_probs=111.8

Q ss_pred             hHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHH
Q psy7786         121 QVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVL  200 (252)
Q Consensus       121 ~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~  200 (252)
                      +....+++..++.+.+++.|++..+|.++++++.+.+.+.+.++..|+++|..+++..+.|+++++.++||+|||.+|++
T Consensus         6 ~~~~~~~~~~~i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l   85 (242)
T 3fe2_A            6 QEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLL   85 (242)
T ss_dssp             CHHHHHHHHHTEEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHH
T ss_pred             HHHHHHHhcCceEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHH
Confidence            34556667789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         201 PILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       201 ~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      |++..+..+..   .....++++||++|||+++.|+++.+++++...++.
T Consensus        86 ~~l~~l~~~~~---~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~  132 (242)
T 3fe2_A           86 PAIVHINHQPF---LERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLK  132 (242)
T ss_dssp             HHHHHHHTSCC---CCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHhccc---cccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCce
Confidence            99988765321   122346789999999999999999999999887654

>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=99.71  E-value=2.9e-18  Score=148.93  Aligned_cols=99  Identities=13%  Similarity=0.176  Sum_probs=72.6

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      ..+++|+|++++||||||||++|++|+++.+..          ++.+++|++||||||.|+++.++.+    +  +.  .
T Consensus         3 ~~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~----------~~~~~lil~Ptr~La~Q~~~~l~~~----~--v~--~   64 (440)
T 1yks_A            3 HMLKKGMTTVLDFHPGAGKTRRFLPQILAECAR----------RRLRTLVLAPTRVVLSEMKEAFHGL----D--VK--F   64 (440)
T ss_dssp             CTTSTTCEEEECCCTTSSTTTTHHHHHHHHHHH----------TTCCEEEEESSHHHHHHHHHHTTTS----C--EE--E
T ss_pred             hHhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh----------cCCeEEEEcchHHHHHHHHHHHhcC----C--eE--E
Confidence            357899999999999999999999999998765          2568999999999999999877622    2  22  1


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHH-------hhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDII-------RRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l-------~~~~~~~V~de~  138 (252)
                      ..+.         +.    .   +    ++|+++++.........       ..++.++|.||+
T Consensus        65 ~~~~---------~~----~---v----~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEa  108 (440)
T 1yks_A           65 HTQA---------FS----A---H----GSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEA  108 (440)
T ss_dssp             ESSC---------CC----C---C----CCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTT
T ss_pred             eccc---------ce----e---c----cCCccceeeecccchhHhhhCcccccCccEEEEECc
Confidence            1111         00    0   2    34888888776654331       234899999997

>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=99.71  E-value=3.4e-18  Score=156.76  Aligned_cols=127  Identities=17%  Similarity=0.164  Sum_probs=90.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|++++||||||||++|.+|+++.+..           +.+++|++|+|+||.|+.+.++++.. .|  +++..
T Consensus        35 ~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~-----------~~~~l~i~P~r~La~q~~~~~~~~~~-~g--~~v~~  100 (702)
T 2p6r_A           35 EKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-----------GGKSLYVVPLRALAGEKYESFKKWEK-IG--LRIGI  100 (702)
T ss_dssp             HHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-----------TCCEEEEESSHHHHHHHHHHHTTTTT-TT--CCEEE
T ss_pred             HHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh-----------CCcEEEEeCcHHHHHHHHHHHHHHHh-cC--CEEEE
Confidence            456889999999999999999999999988653           34799999999999999999975543 34  78888


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVR  157 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~  157 (252)
                      .+|+....++.  + ...+|.  +    +||+++..+..+....+. .+.++|.||.     +.+.+......+..
T Consensus       101 ~~G~~~~~~~~--~-~~~~Ii--v----~Tpe~l~~~l~~~~~~l~-~~~~vIiDE~-----H~l~~~~r~~~~~~  161 (702)
T 2p6r_A          101 STGDYESRDEH--L-GDCDII--V----TTSEKADSLIRNRASWIK-AVSCLVVDEI-----HLLDSEKRGATLEI  161 (702)
T ss_dssp             ECSSCBCCSSC--S-TTCSEE--E----EEHHHHHHHHHTTCSGGG-GCCEEEETTG-----GGGGCTTTHHHHHH
T ss_pred             EeCCCCcchhh--c-cCCCEE--E----ECHHHHHHHHHcChhHHh-hcCEEEEeee-----eecCCCCcccHHHH
Confidence            99986655431  2 234441  2    347776554444322344 4889999996     55555555555433

>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=99.70  E-value=3.8e-18  Score=153.13  Aligned_cols=187  Identities=16%  Similarity=0.099  Sum_probs=109.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+.+|+|++++||||||||++|.+|+++              .+.++||++||||||.|+++.+.   +.++  ..+..
T Consensus       227 ~~L~~~~~vlv~ApTGSGKT~a~~l~ll~--------------~g~~vLVl~PTReLA~Qia~~l~---~~~g--~~vg~  287 (666)
T 3o8b_A          227 AVPQSFQVAHLHAPTGSGKSTKVPAAYAA--------------QGYKVLVLNPSVAATLGFGAYMS---KAHG--IDPNI  287 (666)
T ss_dssp             CCCSSCEEEEEECCTTSCTTTHHHHHHHH--------------TTCCEEEEESCHHHHHHHHHHHH---HHHS--CCCEE
T ss_pred             HHHHcCCeEEEEeCCchhHHHHHHHHHHH--------------CCCeEEEEcchHHHHHHHHHHHH---HHhC--CCeeE
Confidence            45668899999999999999999999875              14579999999999999987554   4444  45566


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEA  161 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~  161 (252)
                      .+|+..       +..+.+|.  +.    +|++++..   .... .++++++|.||+      ++.++++...+...+..
T Consensus       288 ~vG~~~-------~~~~~~Il--V~----TPGrLl~~---~~l~-l~~l~~lVlDEA------H~l~~~~~~~l~~Il~~  344 (666)
T 3o8b_A          288 RTGVRT-------ITTGAPVT--YS----TYGKFLAD---GGCS-GGAYDIIICDEC------HSTDSTTILGIGTVLDQ  344 (666)
T ss_dssp             ECSSCE-------ECCCCSEE--EE----EHHHHHHT---TSCC-TTSCSEEEETTT------TCCSHHHHHHHHHHHHH
T ss_pred             EECcEe-------ccCCCCEE--EE----CcHHHHhC---CCcc-cCcccEEEEccc------hhcCccHHHHHHHHHHh
Confidence            677743       23445552  33    48887321   1112 234899999996      44555565555555544


Q ss_pred             CCCCCChHHHHhhhhhhhcCC------cEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHH
Q psy7786         162 KGIKKPTPIQVQGIPAALSGR------DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ  235 (252)
Q Consensus       162 ~~~~~p~~iQ~~~~p~~~~~~------~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~  235 (252)
                      ........  ...+++++...      +.........+. ..+    .      ..........+.++||||||++.|++
T Consensus       345 l~~~~~~l--lil~SAT~~~~i~~~~p~i~~v~~~~~~~-i~~----~------~~~~~l~~~~~~~vLVFv~Tr~~ae~  411 (666)
T 3o8b_A          345 AETAGARL--VVLATATPPGSVTVPHPNIEEVALSNTGE-IPF----Y------GKAIPIEAIRGGRHLIFCHSKKKCDE  411 (666)
T ss_dssp             TTTTTCSE--EEEEESSCTTCCCCCCTTEEEEECBSCSS-EEE----T------TEEECGGGSSSSEEEEECSCHHHHHH
T ss_pred             hhhcCCce--EEEECCCCCcccccCCcceEEEeecccch-hHH----H------HhhhhhhhccCCcEEEEeCCHHHHHH
Confidence            32211100  01113333221      111000000000 000    0      00000112245689999999999999


Q ss_pred             HHHHHHHH
Q psy7786         236 THDIIQYY  243 (252)
Q Consensus       236 i~~~l~~l  243 (252)
                      +++.|++.
T Consensus       412 la~~L~~~  419 (666)
T 3o8b_A          412 LAAKLSGL  419 (666)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHHhC
Confidence            99999864

>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=99.67  E-value=3.1e-17  Score=150.32  Aligned_cols=122  Identities=15%  Similarity=0.077  Sum_probs=90.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHH-HHHHHHHHHhCCCCccee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT-HDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~-~~~~~~l~~~~~~~~~~~   80 (252)
                      +.+++|+|+++++|||||||++|.+|+++.+......     ..+.++||++||++|+.|+ .+.++.+... +  +++.
T Consensus        17 ~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~-----~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~-~--~~v~   88 (699)
T 4gl2_A           17 QPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKA-----SEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-W--YRVI   88 (699)
T ss_dssp             HHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHH-----TCCCCBCCEESCSHHHHHHHHHTHHHHHTT-T--SCEE
T ss_pred             HHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccc-----CCCCeEEEEECCHHHHHHHHHHHHHHHcCc-C--ceEE
Confidence            4578899999999999999999999999988765320     1235799999999999999 9999998765 2  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHH------HHHhhhhceeeccCC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVH------DIIRRNLRILVEGDD  138 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~------~~l~~~~~~~V~de~  138 (252)
                      .++|+.+...+.+.+....+|.  |    ++|+++.......+      ..+ ..+.++|.||+
T Consensus        89 ~~~g~~~~~~~~~~~~~~~~Il--v----~Tp~~L~~~l~~~~~~~~~~~~~-~~~~lvViDEa  145 (699)
T 4gl2_A           89 GLSGDTQLKISFPEVVKSCDII--I----STAQILENSLLNLENGEDAGVQL-SDFSLIIIDEC  145 (699)
T ss_dssp             EEC----CCCCHHHHHHSCSEE--E----EEHHHHHHHTC--------CCCG-GGCSEEEEESG
T ss_pred             EEeCCcchhhHHHhhhcCCCEE--E----ECHHHHHHHHhccccccccceec-ccCcEEEEECc
Confidence            9999998888877777777762  3    34888876553221      223 34889999996

>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=99.67  E-value=1.7e-17  Score=144.85  Aligned_cols=55  Identities=18%  Similarity=0.259  Sum_probs=49.4

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      .+.+|+|++++||||||||++|++|+++.+..          .+.++||++||||||.|+++.++
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~----------~~~~~lvl~Ptr~La~Q~~~~l~   71 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ----------QRLRTAVLAPTRVVAAEMAEALR   71 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH----------TTCCEEEEECSHHHHHHHHHHTT
T ss_pred             HHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh----------CCCcEEEECchHHHHHHHHHHhc
Confidence            47789999999999999999999999998764          25689999999999999998876

>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=99.67  E-value=1.9e-16  Score=155.70  Aligned_cols=113  Identities=20%  Similarity=0.183  Sum_probs=81.9

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH-HHHhCCCCcceeeee
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY-YCAALPIPLRTCLAI   83 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~-l~~~~~~~~~~~~~~   83 (252)
                      .+++|++++||||||||++|.+|+++.+....         +.+++|++|||+||+|+++.+++ |++.+|  +++..++
T Consensus       940 ~~~~nvlv~APTGSGKTliaelail~~l~~~~---------~~kavyi~P~raLa~q~~~~~~~~f~~~~g--~~V~~lt 1008 (1724)
T 4f92_B          940 NSDDNVFVGAPTGSGKTICAEFAILRMLLQSS---------EGRCVYITPMEALAEQVYMDWYEKFQDRLN--KKVVLLT 1008 (1724)
T ss_dssp             SCCSCEEEECCTTSCCHHHHHHHHHHHHHHCT---------TCCEEEECSCHHHHHHHHHHHHHHHTTTSC--CCEEECC
T ss_pred             cCCCcEEEEeCCCCCchHHHHHHHHHHHHhCC---------CCEEEEEcChHHHHHHHHHHHHHHhchhcC--CEEEEEE
Confidence            35678999999999999999999999987643         45799999999999999988854 666666  8889999


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChh--HHHHHhhhhceeeccCC
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQ--VHDIIRRNLRILVEGDD  138 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~--~~~~l~~~~~~~V~de~  138 (252)
                      |+.+.+.  +. .++.+|.  |    +||+++..+..+  ....+. .++++|.||.
T Consensus      1009 Gd~~~~~--~~-~~~~~Ii--V----~TPEkld~llr~~~~~~~l~-~v~lvViDE~ 1055 (1724)
T 4f92_B         1009 GETSTDL--KL-LGKGNII--I----STPEKWDILSRRWKQRKNVQ-NINLFVVDEV 1055 (1724)
T ss_dssp             SCHHHHH--HH-HHHCSEE--E----ECHHHHHHHHTTTTTCHHHH-SCSEEEECCG
T ss_pred             CCCCcch--hh-cCCCCEE--E----ECHHHHHHHHhCcccccccc-eeeEEEeech
Confidence            9865432  22 2344552  2    247765443322  122344 4899999996

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.67  E-value=8.9e-16  Score=133.15  Aligned_cols=118  Identities=36%  Similarity=0.522  Sum_probs=105.3

Q ss_pred             hceeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhh
Q psy7786         130 LRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQ  209 (252)
Q Consensus       130 ~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~  209 (252)
                      +.+-+.+++.|.++.+|.++++++.+++.+.+.++..|+++|..++|..+.|+|++++++||+|||.+|++|++..+...
T Consensus        42 ~~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~  121 (434)
T 2db3_A           42 IPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLED  121 (434)
T ss_dssp             SCEEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHS
T ss_pred             ceeEecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhc
Confidence            56777888999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             hccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         210 ETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       210 ~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ...   ....++++||++|||++|.|+++.+++++...+++
T Consensus       122 ~~~---~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~  159 (434)
T 2db3_A          122 PHE---LELGRPQVVIVSPTRELAIQIFNEARKFAFESYLK  159 (434)
T ss_dssp             CCC---CCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCC
T ss_pred             ccc---cccCCccEEEEecCHHHHHHHHHHHHHHhccCCcE
Confidence            321   22346789999999999999999999998776543

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.66  E-value=2.9e-17  Score=148.91  Aligned_cols=100  Identities=13%  Similarity=0.156  Sum_probs=70.8

Q ss_pred             CCccc------CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           1 MVTYR------NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         1 i~~~~------~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      ||.++      +|+|++++|+||||||++|++|+++.+..          .+.++||++||||||.|+++.++.+    +
T Consensus       229 Ip~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~----------~~~~~lilaPTr~La~Q~~~~l~~~----~  294 (673)
T 2wv9_A          229 VPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ----------KRLRTAVLAPTRVVAAEMAEALRGL----P  294 (673)
T ss_dssp             -CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH----------TTCCEEEEESSHHHHHHHHHHTTTS----C
T ss_pred             hHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh----------CCCcEEEEccHHHHHHHHHHHHhcC----C
Confidence            45566      99999999999999999999999988764          2568999999999999999877632    2


Q ss_pred             CCcceeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHH-------HhhhhceeeccCC
Q psy7786          75 IPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDI-------IRRNLRILVEGDD  138 (252)
Q Consensus        75 ~~~~~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~-------l~~~~~~~V~de~  138 (252)
                        +.  ...+         .+..       +    .+|+++++........       ....+.++|.||+
T Consensus       295 --i~--~~~~---------~l~~-------v----~tp~~ll~~l~~~~l~~~l~~~~~l~~l~lvViDEa  341 (673)
T 2wv9_A          295 --VR--YLTP---------AVQR-------E----HSGNEIVDVMCHATLTHRLMSPLRVPNYNLFVMDEA  341 (673)
T ss_dssp             --CE--ECCC------------C-------C----CCSCCCEEEEEHHHHHHHHHSSSCCCCCSEEEEEST
T ss_pred             --ee--eecc---------cccc-------c----CCHHHHHHHHHhhhhHHHHhcccccccceEEEEeCC
Confidence              22  1011         1111       2    3488887776654431       1234899999997

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

Probab=99.65  E-value=2.5e-16  Score=148.63  Aligned_cols=123  Identities=13%  Similarity=0.095  Sum_probs=88.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|++++||||||||++|.+|+++.+.           .+.++||++|||+|++|+++.++.+..      ++..
T Consensus        96 ~~l~~g~~vLV~apTGSGKTlva~lai~~~l~-----------~g~rvL~l~PtkaLa~Q~~~~l~~~~~------~vgl  158 (1010)
T 2xgj_A           96 SCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK-----------NKQRVIYTSPIKALSNQKYRELLAEFG------DVGL  158 (1010)
T ss_dssp             HHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH-----------TTCEEEEEESSHHHHHHHHHHHHHHHS------CEEE
T ss_pred             HHHHcCCCEEEECCCCCChHHHHHHHHHHHhc-----------cCCeEEEECChHHHHHHHHHHHHHHhC------CEEE
Confidence            45678999999999999999999999988763           256899999999999999999987653      4566


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ++|+.+...       ..++.  |    +||+++.++..+....+++ +.++|.||.     +.+.+..........+.
T Consensus       159 ltGd~~~~~-------~~~Iv--V----~Tpe~L~~~L~~~~~~l~~-l~lVViDEa-----H~l~d~~rg~~~e~il~  218 (1010)
T 2xgj_A          159 MTGDITINP-------DAGCL--V----MTTEILRSMLYRGSEVMRE-VAWVIFDEV-----HYMRDKERGVVWEETII  218 (1010)
T ss_dssp             ECSSCEECT-------TCSEE--E----EEHHHHHHHHHHTCTTGGG-EEEEEEETG-----GGGGCTTTHHHHHHHHH
T ss_pred             EeCCCccCC-------CCCEE--E----EcHHHHHHHHHcCcchhhc-CCEEEEech-----hhhcccchhHHHHHHHH
Confidence            788866542       23331  3    3477776554443334444 899999997     66666655554444443

>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=99.65  E-value=1.1e-15  Score=122.54  Aligned_cols=119  Identities=38%  Similarity=0.625  Sum_probs=105.8

Q ss_pred             HHHhhhhceeeccCCCCCcccccccC----CCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhH
Q psy7786         124 DIIRRNLRILVEGDDVPPACCSFRLM----KLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFV  199 (252)
Q Consensus       124 ~~l~~~~~~~V~de~~~~~~~~~~~~----~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~  199 (252)
                      ..+++..++.+.+.+.|++..+|.++    ++++.+.+.+.+.|+..|+++|..+++..+.++++++.++||+|||.+|+
T Consensus         5 ~~~~~~~~i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~   84 (245)
T 3dkp_A            5 NFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFS   84 (245)
T ss_dssp             HHHHHHTTEEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH
T ss_pred             HHHHHhCceEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHH
Confidence            45666678899999999999999987    89999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         200 LPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       200 ~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      +|++..+....       ..++++||++|||++|.|+++.+++++...++
T Consensus        85 l~~l~~l~~~~-------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  127 (245)
T 3dkp_A           85 IPILMQLKQPA-------NKGFRALIISPTRELASQIHRELIKISEGTGF  127 (245)
T ss_dssp             HHHHHHHCSCC-------SSSCCEEEECSSHHHHHHHHHHHHHHTTTSCC
T ss_pred             HHHHHHHhhcc-------cCCceEEEEeCCHHHHHHHHHHHHHHhcccCc
Confidence            99998775321       24668999999999999999999999876654

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

Probab=99.65  E-value=6.7e-17  Score=152.43  Aligned_cols=127  Identities=16%  Similarity=0.123  Sum_probs=91.0

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      |+.+++|+|+++++|||||||++|.+|+...+.           .+.+++|++|||+|+.|+++.++.+..  +  +++.
T Consensus        48 I~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~-----------~g~~vlvl~PtraLa~Q~~~~l~~~~~--~--~~v~  112 (997)
T 4a4z_A           48 VYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR-----------NMTKTIYTSPIKALSNQKFRDFKETFD--D--VNIG  112 (997)
T ss_dssp             HHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH-----------TTCEEEEEESCGGGHHHHHHHHHTTC------CCEE
T ss_pred             HHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh-----------cCCeEEEEeCCHHHHHHHHHHHHHHcC--C--CeEE
Confidence            356789999999999999999999999887542           256899999999999999998876532  3  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++|+.+...+       .++.  +    .||+++.++..+....+.+ +.++|.||+     +.+.+.++.....+.+.
T Consensus       113 ~l~G~~~~~~~-------~~Il--V----~Tpe~L~~~l~~~~~~l~~-l~lvViDEa-----H~l~d~~~g~~~e~ii~  173 (997)
T 4a4z_A          113 LITGDVQINPD-------ANCL--I----MTTEILRSMLYRGADLIRD-VEFVIFDEV-----HYVNDQDRGVVWEEVII  173 (997)
T ss_dssp             EECSSCEECTT-------SSEE--E----EEHHHHHHHHHHTCSGGGG-EEEEEECCT-----TCCCTTCTTCCHHHHHH
T ss_pred             EEeCCCccCCC-------CCEE--E----ECHHHHHHHHHhCchhhcC-CCEEEEECc-----ccccccchHHHHHHHHH
Confidence            88998654322       3331  2    3488886655544444444 899999997     56666655555544444


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       174 ~  174 (997)
T 4a4z_A          174 M  174 (997)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.64  E-value=9.8e-17  Score=125.88  Aligned_cols=135  Identities=14%  Similarity=0.070  Sum_probs=89.4

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHH-HHHHHHHHHHhCCCCccee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ-THDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q-~~~~~~~l~~~~~~~~~~~   80 (252)
                      +.+++|+|+++.+|||||||++|++|+.+.+......     ..+.++||++||++|+.| +.+.++.+... +  +++.
T Consensus        43 ~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~-----~~~~~~lil~p~~~L~~q~~~~~~~~~~~~-~--~~v~  114 (216)
T 3b6e_A           43 QPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKA-----SEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-W--YRVI  114 (216)
T ss_dssp             HHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHT-----TCCCCEEEEESSHHHHHHHHHHTHHHHHTT-T--SCEE
T ss_pred             HHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccc-----cCCCcEEEEECHHHHHHHHHHHHHHHHhcc-C--ceEE
Confidence            3467899999999999999999999999887654321     135679999999999999 77888888654 3  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHH-----HHhhhhceeeccCCCCCcccccccCCCCHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHD-----IIRRNLRILVEGDDVPPACCSFRLMKLPESL  155 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~-----~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l  155 (252)
                      .++|+.....+...+..+++|.  +    ++|+.+.........     .....+.++|.||+     +.+.+.++-..+
T Consensus       115 ~~~g~~~~~~~~~~~~~~~~i~--v----~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEa-----h~~~~~~~~~~~  183 (216)
T 3b6e_A          115 GLSGDTQLKISFPEVVKSCDII--I----STAQILENSLLNLENGEDAGVQLSDFSLIIIDEC-----HHTNKEAVYNNI  183 (216)
T ss_dssp             ECCC---CCCCHHHHHHHCSEE--E----EEHHHHHHHHHC-------CCCGGGCSEEEETTC------------CHHHH
T ss_pred             EEeCCcccchhHHhhccCCCEE--E----ECHHHHHHHHhccCcccccccchhcccEEEEECc-----hhhccCCcHHHH
Confidence            8899988877776766666662  2    337776554443321     12234789999997     555444444444

>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=99.64  E-value=1.2e-16  Score=139.27  Aligned_cols=57  Identities=21%  Similarity=0.234  Sum_probs=50.7

Q ss_pred             CCcccCCCcE-EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           1 MVTYRNSRDI-IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         1 i~~~~~g~d~-~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      ||.+++|+|+ +++||||||||++|++|+++.+..          .+.++||++||||||.|+++.++
T Consensus        12 i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~----------~~~~~lvl~Ptr~La~Q~~~~l~   69 (451)
T 2jlq_A           12 DEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL----------RRLRTLILAPTRVVAAEMEEALR   69 (451)
T ss_dssp             CGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH----------TTCCEEEEESSHHHHHHHHHHTT
T ss_pred             HHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh----------cCCcEEEECCCHHHHHHHHHHhc
Confidence            6888999998 999999999999999999987764          25689999999999999998774

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.63  E-value=2.9e-17  Score=149.18  Aligned_cols=115  Identities=16%  Similarity=0.114  Sum_probs=87.3

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||++++|+  +++++||||||++|.+|++...+.           +.+++|++||++||.|.++++..+.+++|  +++.
T Consensus        88 ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~-----------G~qv~VvTPTreLA~Qdae~m~~l~~~lG--Lsv~  152 (997)
T 2ipc_A           88 GAVLHEGK--IAEMKTGEGKTLVATLAVALNALT-----------GKGVHVVTVNDYLARRDAEWMGPVYRGLG--LSVG  152 (997)
T ss_dssp             HHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT-----------CSCCEEEESSHHHHHHHHHHHHHHHHTTT--CCEE
T ss_pred             cccccCCc--eeeccCCCchHHHHHHHHHHHHHh-----------CCCEEEEeCCHHHHHHHHHHHHHHHHhcC--CeEE
Confidence            46788998  999999999999999999754432           45799999999999999999999999998  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccc-cCCChhHH------HHHh--hhhceeeccCC
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCI-LSLPDQVH------DIIR--RNLRILVEGDD  138 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l-~~~~~~~~------~~l~--~~~~~~V~de~  138 (252)
                      +++||.+.  +.+....++||      +|+||+++ .++.....      ..++  ..++++|.||.
T Consensus       153 ~i~Gg~~~--~~r~~ay~~DI------vyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEa  211 (997)
T 2ipc_A          153 VIQHASTP--AERRKAYLADV------TYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEV  211 (997)
T ss_dssp             ECCTTCCH--HHHHHHHTSSE------EEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTH
T ss_pred             EEeCCCCH--HHHHHHcCCCE------EEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEech
Confidence            99999763  34444556777      34458887 34333221      1233  14889998885

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.63  E-value=1.4e-16  Score=138.04  Aligned_cols=52  Identities=15%  Similarity=0.213  Sum_probs=45.4

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      +|+|+++++|||||||++|++|+++.+..          .+.+++|++|||+||.|+++.++
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~----------~g~~~lvl~Pt~~La~Q~~~~~~   52 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK----------KRLRTVILAPTRVVASEMYEALR   52 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH----------TTCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh----------CCCCEEEECcHHHHHHHHHHHhC
Confidence            48999999999999999999999977754          25689999999999999987765

>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=99.61  E-value=5e-15  Score=122.25  Aligned_cols=109  Identities=28%  Similarity=0.412  Sum_probs=93.3

Q ss_pred             ceeeccCCCCC---cccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--CcEEEEccCCCchhHHhHHHHHHH
Q psy7786         131 RILVEGDDVPP---ACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMF  205 (252)
Q Consensus       131 ~~~V~de~~~~---~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~--~~~~~~~~~g~gKt~~~~~~~l~~  205 (252)
                      .+.|.+.+.+.   ...+|.++++++.+++.+...++..|+++|..++|..+.+  +|++++++||+|||.+|++|++..
T Consensus        76 ~v~v~~~~~~~p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~  155 (300)
T 3fmo_B           76 QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQ  155 (300)
T ss_dssp             CEEEECSSTTCCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cceeccCCCCCCcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHh
Confidence            34444444333   3568999999999999999999999999999999999987  999999999999999999999987


Q ss_pred             HHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         206 CLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       206 i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      +...        ..++++||++|||++|.|+++.+++++...
T Consensus       156 l~~~--------~~~~~~lil~PtreLa~Q~~~~~~~l~~~~  189 (300)
T 3fmo_B          156 VEPA--------NKYPQCLCLSPTYELALQTGKVIEQMGKFY  189 (300)
T ss_dssp             CCTT--------SCSCCEEEECSSHHHHHHHHHHHHHHTTTS
T ss_pred             hhcc--------CCCceEEEEcCcHHHHHHHHHHHHHHHhhC
Confidence            6432        246789999999999999999999998764

>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=99.56  E-value=7.3e-15  Score=118.27  Aligned_cols=121  Identities=33%  Similarity=0.479  Sum_probs=100.4

Q ss_pred             hceeeccCCCCC--cccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHH
Q psy7786         130 LRILVEGDDVPP--ACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCL  207 (252)
Q Consensus       130 ~~~~V~de~~~~--~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~  207 (252)
                      +.+.+.+...+.  +..+|.++++++.+.+.+...++..|+++|..+++..+.+++++++++||+|||.+|++|++..+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~   86 (253)
T 1wrb_A            7 IPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLV   86 (253)
T ss_dssp             CCCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CceeeeCCCCCCCCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHH
Confidence            455666666665  778899999999999999999999999999999999999999999999999999999999998876


Q ss_pred             hhhccC-CCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         208 EQETKL-PFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       208 ~~~~~~-~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ...... ......++++||++|||++|.|+++.+++++...++.
T Consensus        87 ~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  130 (253)
T 1wrb_A           87 CQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLR  130 (253)
T ss_dssp             TTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCC
T ss_pred             hhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCce
Confidence            543110 0112335789999999999999999999998876543

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

Probab=99.55  E-value=4.5e-14  Score=121.40  Aligned_cols=119  Identities=29%  Similarity=0.432  Sum_probs=101.0

Q ss_pred             eeeccCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhc
Q psy7786         132 ILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQET  211 (252)
Q Consensus       132 ~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~  211 (252)
                      +-+.++++|++..+|.++++++.+.+.+...++..|+++|..++|..+.++++++.++||+|||.+|++|++..+.....
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            34567788999999999999999999999999999999999999999999999999999999999999999998775431


Q ss_pred             c----------CCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         212 K----------LPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       212 ~----------~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      .          .......++++||++|||++|.|+++.+++++...+++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  131 (417)
T 2i4i_A           83 GEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVR  131 (417)
T ss_dssp             CHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCC
T ss_pred             cchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCce
Confidence            0          00011234689999999999999999999998776653

>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=99.55  E-value=1.7e-14  Score=115.06  Aligned_cols=103  Identities=32%  Similarity=0.431  Sum_probs=90.6

Q ss_pred             CCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCC
Q psy7786         139 VPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPG  218 (252)
Q Consensus       139 ~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~  218 (252)
                      .+++..+|.++++++.+.+.+...++..|+++|..+++..+.++++++.++||+|||.+|+++.+..+...        .
T Consensus        25 ~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~--------~   96 (237)
T 3bor_A           25 WNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE--------F   96 (237)
T ss_dssp             --CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTT--------S
T ss_pred             CCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc--------C
Confidence            45556789999999999999999999999999999999999999999999999999999999999865432        2


Q ss_pred             CCcEEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         219 EGPYGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       219 ~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      .+.++||++|||+++.|+++.+++++...++
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  127 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGA  127 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTC
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCc
Confidence            3568999999999999999999999876554

>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=99.54  E-value=5e-14  Score=113.22  Aligned_cols=100  Identities=40%  Similarity=0.604  Sum_probs=90.9

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      ..+|.++++++.+.+.+.+.++..|+++|..+++..+.++++++.++||+|||.+|+++++..+....        .+++
T Consensus        42 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~--------~~~~  113 (249)
T 3ber_A           42 TKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETP--------QRLF  113 (249)
T ss_dssp             HCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC--------CSSC
T ss_pred             cCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC--------CCce
Confidence            45799999999999999999999999999999999999999999999999999999999998876532        3567


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      +||++|||+++.|+++.+++++...++.
T Consensus       114 ~lil~Ptr~L~~q~~~~~~~~~~~~~~~  141 (249)
T 3ber_A          114 ALVLTPTRELAFQISEQFEALGSSIGVQ  141 (249)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHGGGTCC
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhccCCee
Confidence            9999999999999999999998876653

>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=99.53  E-value=2.9e-14  Score=124.27  Aligned_cols=115  Identities=14%  Similarity=0.141  Sum_probs=78.2

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+++| +++++++||+|||++|++++...+..          .+.++||++||++|+.|..+.++++....  ..++..+
T Consensus        20 ~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~----------~~~~~liv~P~~~L~~q~~~~~~~~~~~~--~~~v~~~   86 (494)
T 1wp9_A           20 KCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK----------YGGKVLMLAPTKPLVLQHAESFRRLFNLP--PEKIVAL   86 (494)
T ss_dssp             HGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH----------SCSCEEEECSSHHHHHHHHHHHHHHBCSC--GGGEEEE
T ss_pred             HHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc----------CCCeEEEEECCHHHHHHHHHHHHHHhCcc--hhheEEe
Confidence            45677 99999999999999999999987751          25579999999999999999998775221  2578888


Q ss_pred             eCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          83 IGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +|+....++.... ...++.  |    ++|+.+..........+ ....++|.||+
T Consensus        87 ~g~~~~~~~~~~~-~~~~iv--v----~T~~~l~~~~~~~~~~~-~~~~~vIiDEa  134 (494)
T 1wp9_A           87 TGEKSPEERSKAW-ARAKVI--V----ATPQTIENDLLAGRISL-EDVSLIVFDEA  134 (494)
T ss_dssp             CSCSCHHHHHHHH-HHCSEE--E----ECHHHHHHHHHTTSCCT-TSCSEEEEETG
T ss_pred             eCCcchhhhhhhc-cCCCEE--E----ecHHHHHHHHhcCCcch-hhceEEEEECC
Confidence            8887655433322 233441  1    23555543322211112 24678999996

>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=99.53  E-value=4.5e-14  Score=112.09  Aligned_cols=101  Identities=30%  Similarity=0.446  Sum_probs=87.5

Q ss_pred             CCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCC
Q psy7786         139 VPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPG  218 (252)
Q Consensus       139 ~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~  218 (252)
                      .+.+..+|.++++++.+.+.+.+.++..|+++|..+++..+.++++++.++||+|||.+|+++++..+...        .
T Consensus        19 ~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~--------~   90 (230)
T 2oxc_A           19 LLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLE--------N   90 (230)
T ss_dssp             -----CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT--------S
T ss_pred             CCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc--------C
Confidence            34445689999999999999999999999999999999999999999999999999999999999876532        2


Q ss_pred             CCcEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         219 EGPYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       219 ~~~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      .++++||++|||+++.|+++.+++++...
T Consensus        91 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  119 (230)
T 2oxc_A           91 LSTQILILAPTREIAVQIHSVITAIGIKM  119 (230)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTS
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            35689999999999999999999987654

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.53  E-value=8.7e-14  Score=110.75  Aligned_cols=104  Identities=34%  Similarity=0.446  Sum_probs=91.3

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCc
Q psy7786         142 ACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP  221 (252)
Q Consensus       142 ~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~  221 (252)
                      ...+|.++++++.+.+.+.+.++..|+++|..+++..+.++++++.++||+|||.+|++|++..+.....    ....++
T Consensus        23 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~----~~~~~~   98 (236)
T 2pl3_A           23 EITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQW----TSTDGL   98 (236)
T ss_dssp             GCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTC----CGGGCC
T ss_pred             ccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcc----cccCCc
Confidence            3467999999999999999999999999999999999999999999999999999999999988765321    112357


Q ss_pred             EEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         222 YGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       222 ~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      ++||++|||+++.|+++.+++++...++
T Consensus        99 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~  126 (236)
T 2pl3_A           99 GVLIISPTRELAYQTFEVLRKVGKNHDF  126 (236)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSSC
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhCCCCe
Confidence            8999999999999999999999876554

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.52  E-value=6.2e-14  Score=110.38  Aligned_cols=96  Identities=29%  Similarity=0.396  Sum_probs=87.7

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++.+.+.+.+.++..|+++|..+++..+.++++++.++||+|||.+|+++++..+...        ..+.++
T Consensus         4 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~--------~~~~~~   75 (219)
T 1q0u_A            4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE--------RAEVQA   75 (219)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT--------SCSCCE
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhC--------cCCceE
Confidence            579999999999999999999999999999999999999999999999999999999999876432        235689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ||++|||+++.|+++.+++++...
T Consensus        76 lil~Pt~~L~~q~~~~~~~~~~~~   99 (219)
T 1q0u_A           76 VITAPTRELATQIYHETLKITKFC   99 (219)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHTTS
T ss_pred             EEEcCcHHHHHHHHHHHHHHhhhc
Confidence            999999999999999999998765

>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=99.52  E-value=6.8e-14  Score=110.43  Aligned_cols=103  Identities=28%  Similarity=0.437  Sum_probs=92.0

Q ss_pred             CCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCC
Q psy7786         139 VPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPG  218 (252)
Q Consensus       139 ~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~  218 (252)
                      .+++..+|.++++++.+.+.+.+.++..|+++|..+++..+.++++++.++||+|||.+|+++++..+...        .
T Consensus         9 ~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~--------~   80 (224)
T 1qde_A            9 YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS--------V   80 (224)
T ss_dssp             CCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT--------C
T ss_pred             cCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhcc--------C
Confidence            45666789999999999999999999999999999999999999999999999999999999999876432        2


Q ss_pred             CCcEEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         219 EGPYGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       219 ~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      .++++||++|||+++.|+++.+++++...++
T Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (224)
T 1qde_A           81 KAPQALMLAPTRELALQIQKVVMALAFHMDI  111 (224)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCC
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHHhcccCc
Confidence            3568999999999999999999998876654

>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=99.52  E-value=6e-14  Score=111.13  Aligned_cols=106  Identities=34%  Similarity=0.519  Sum_probs=90.0

Q ss_pred             CCCCCccccccc-CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCC
Q psy7786         137 DDVPPACCSFRL-MKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPF  215 (252)
Q Consensus       137 e~~~~~~~~~~~-~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~  215 (252)
                      ..+|++..+|.+ +++++++.+.+.+.|+..|+++|..+++..+.++++++.++||+|||.+|++|.+..+..+...  .
T Consensus        12 ~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~--~   89 (228)
T 3iuy_A           12 RLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPIS--R   89 (228)
T ss_dssp             CCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC--------
T ss_pred             CcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccch--h
Confidence            357888889999 7999999999999999999999999999999999999999999999999999999877643211  1


Q ss_pred             CCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         216 LPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       216 ~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ....++++||++|||++|.|+++.+++++
T Consensus        90 ~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  118 (228)
T 3iuy_A           90 EQRNGPGMLVLTPTRELALHVEAECSKYS  118 (228)
T ss_dssp             ---CCCSEEEECSSHHHHHHHHHHHHHHC
T ss_pred             hccCCCcEEEEeCCHHHHHHHHHHHHHhc
Confidence            12346789999999999999999999875

>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=99.51  E-value=1.2e-13  Score=132.06  Aligned_cols=107  Identities=19%  Similarity=0.191  Sum_probs=76.7

Q ss_pred             CC--cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           7 SR--DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         7 g~--d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      |+  |++++++||||||++|+++++..+.           .+.+++|++||++||.|.++.+++.....+  +++..+.|
T Consensus       622 g~p~d~ll~~~TGsGKT~val~aa~~~~~-----------~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~--i~v~~l~~  688 (1151)
T 2eyq_A          622 PLAMDRLVCGDVGFGKTEVAMRAAFLAVD-----------NHKQVAVLVPTTLLAQQHYDNFRDRFANWP--VRIEMISR  688 (1151)
T ss_dssp             SSCCEEEEECCCCTTTHHHHHHHHHHHHT-----------TTCEEEEECSSHHHHHHHHHHHHHHSTTTT--CCEEEEST
T ss_pred             CCcCcEEEECCCCCCHHHHHHHHHHHHHH-----------hCCeEEEEechHHHHHHHHHHHHHHhhcCC--CeEEEEeC
Confidence            66  9999999999999999999987653           256899999999999999999987765555  78888877


Q ss_pred             CcccCcchhh---hhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          85 GVPMNQSLDV---IKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        85 ~~~~~~~~~~---l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      ..+..++.+.   +..+ ++|.  |.    ||..+....     .+ .++.++|.||+
T Consensus       689 ~~~~~~~~~~~~~l~~g~~dIv--V~----T~~ll~~~~-----~~-~~l~lvIiDEa  734 (1151)
T 2eyq_A          689 FRSAKEQTQILAEVAEGKIDIL--IG----THKLLQSDV-----KF-KDLGLLIVDEE  734 (1151)
T ss_dssp             TSCHHHHHHHHHHHHTTCCSEE--EE----CTHHHHSCC-----CC-SSEEEEEEESG
T ss_pred             CCCHHHHHHHHHHHhcCCCCEE--EE----CHHHHhCCc-----cc-cccceEEEech
Confidence            7655544333   3333 5552  22    365443211     12 34789999996

>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=99.50  E-value=1.2e-13  Score=107.50  Aligned_cols=96  Identities=33%  Similarity=0.479  Sum_probs=87.1

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++++.+.+.+.|+..|+++|..+++..+.++++++.++||+|||.++++|.+..+...        ..++++
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~--------~~~~~~   74 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK--------KDNIQA   74 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT--------SCSCCE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhccc--------CCCeeE
Confidence            479999999999999999999999999999999999999999999999999999999999765432        235689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ||++|||+++.|+++.++++....
T Consensus        75 lil~Pt~~L~~q~~~~~~~~~~~~   98 (206)
T 1vec_A           75 MVIVPTRELALQVSQICIQVSKHM   98 (206)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTS
T ss_pred             EEEeCcHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999988765

>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=99.49  E-value=1.2e-14  Score=133.47  Aligned_cols=106  Identities=22%  Similarity=0.212  Sum_probs=80.6

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcc
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVP   87 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~   87 (252)
                      +|++++++||||||++|++|+++.+..           +.+++|++||++||.|+++.++++....+  +++..++|+.+
T Consensus       390 ~~~Ll~a~TGSGKTlvall~il~~l~~-----------g~qvlvlaPtr~La~Q~~~~l~~~~~~~g--i~v~~l~G~~~  456 (780)
T 1gm5_A          390 MNRLLQGDVGSGKTVVAQLAILDNYEA-----------GFQTAFMVPTSILAIQHYRRTVESFSKFN--IHVALLIGATT  456 (780)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHHHH-----------TSCEEEECSCHHHHHHHHHHHHHHHTCSS--CCEEECCSSSC
T ss_pred             CcEEEEcCCCCCHHHHHHHHHHHHHHc-----------CCeEEEEeCcHHHHHHHHHHHHHHhhhcC--ceEEEEeCCCC
Confidence            599999999999999999999988753           45799999999999999999999987776  88999999987


Q ss_pred             cCcchhh---hhhc-ccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          88 MNQSLDV---IKKG-IQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        88 ~~~~~~~---l~~~-~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      ..++.+.   +.++ ++|.  |    +||+++.+.     ..+ .++.++|.||.
T Consensus       457 ~~~r~~~~~~l~~g~~~Iv--V----gT~~ll~~~-----~~~-~~l~lVVIDEa  499 (780)
T 1gm5_A          457 PSEKEKIKSGLRNGQIDVV--I----GTHALIQED-----VHF-KNLGLVIIDEQ  499 (780)
T ss_dssp             HHHHHHHHHHHHSSCCCEE--E----ECTTHHHHC-----CCC-SCCCEEEEESC
T ss_pred             HHHHHHHHHHHhcCCCCEE--E----ECHHHHhhh-----hhc-cCCceEEeccc
Confidence            7654433   3333 4552  2    236554221     123 34789998886

>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=99.48  E-value=2.5e-13  Score=106.90  Aligned_cols=96  Identities=32%  Similarity=0.435  Sum_probs=86.4

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++.+.+.+.+.++..|+++|..+++..+.++++++.++||+|||.+++++.+..+...        ..+.++
T Consensus        14 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~--------~~~~~~   85 (220)
T 1t6n_A           14 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV--------TGQVSV   85 (220)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC--------TTCCCE
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc--------CCCEEE
Confidence            569999999999999999999999999999999999999999999999999999999998765321        234589


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ||++|||+++.|+++.++++.+..
T Consensus        86 lil~Pt~~L~~q~~~~~~~~~~~~  109 (220)
T 1t6n_A           86 LVMCHTRELAFQISKEYERFSKYM  109 (220)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTS
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhC
Confidence            999999999999999999997765

>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=99.47  E-value=2.6e-13  Score=105.70  Aligned_cols=98  Identities=39%  Similarity=0.628  Sum_probs=86.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      +|.++++++.+.+.+.+.++..|+++|..+++..+.++++++.++||+|||.+++++++..+....     ....++++|
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~-----~~~~~~~~l   76 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ-----ERGRKPRAL   76 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCC-----CTTCCCSEE
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhcc-----ccCCCCcEE
Confidence            588999999999999999999999999999999999999999999999999999999998765321     123467899


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         225 IICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      |++|||+++.|+++.++++...+
T Consensus        77 il~P~~~L~~q~~~~~~~~~~~~   99 (207)
T 2gxq_A           77 VLTPTRELALQVASELTAVAPHL   99 (207)
T ss_dssp             EECSSHHHHHHHHHHHHHHCTTS
T ss_pred             EEECCHHHHHHHHHHHHHHhhcc
Confidence            99999999999999999886553

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.46  E-value=1.6e-13  Score=124.34  Aligned_cols=114  Identities=16%  Similarity=0.027  Sum_probs=80.2

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      .++|+|++++||||||||+    ++++.+....           +++|++||||||.|+++.++.+    |  +++...+
T Consensus       152 ~l~rk~vlv~apTGSGKT~----~al~~l~~~~-----------~gl~l~PtR~LA~Qi~~~l~~~----g--~~v~llt  210 (677)
T 3rc3_A          152 AMQRKIIFHSGPTNSGKTY----HAIQKYFSAK-----------SGVYCGPLKLLAHEIFEKSNAA----G--VPCDLVT  210 (677)
T ss_dssp             TSCCEEEEEECCTTSSHHH----HHHHHHHHSS-----------SEEEEESSHHHHHHHHHHHHHT----T--CCEEEEC
T ss_pred             hcCCCEEEEEcCCCCCHHH----HHHHHHHhcC-----------CeEEEeCHHHHHHHHHHHHHhc----C--CcEEEEE
Confidence            4689999999999999997    6666665532           3699999999999999988764    4  6788888


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHH--HHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHH
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVH--DIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEA  161 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~--~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~  161 (252)
                      |+...            +   +.    +|++..++.....  ..+...+.++|.||+     +.+.+.++...+...+..
T Consensus       211 G~~~~------------i---v~----TpGr~~~il~~T~e~~~l~~~v~lvVIDEa-----H~l~d~~~g~~~~~~l~~  266 (677)
T 3rc3_A          211 GEERV------------T---VQ----PNGKQASHVSCTVEMCSVTTPYEVAVIDEI-----QMIRDPARGWAWTRALLG  266 (677)
T ss_dssp             SSCEE------------C---CS----TTCCCCSEEEEEGGGCCSSSCEEEEEECSG-----GGGGCTTTHHHHHHHHHH
T ss_pred             CCeeE------------E---ec----CCCcccceeEecHhHhhhcccCCEEEEecc-----eecCCccchHHHHHHHHc
Confidence            88543            0   11    2444333322211  113345799999997     778788888877777766


Q ss_pred             C
Q psy7786         162 K  162 (252)
Q Consensus       162 ~  162 (252)
                      .
T Consensus       267 l  267 (677)
T 3rc3_A          267 L  267 (677)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.45  E-value=3.8e-13  Score=108.88  Aligned_cols=101  Identities=34%  Similarity=0.508  Sum_probs=85.3

Q ss_pred             ccccCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         145 SFRLMK--LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       145 ~~~~~~--l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      +|.+++  +++.+++.+...|+..|+++|..+++..+.+++++++++||+|||.+|++|++..+.....    ....+.+
T Consensus        53 ~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~----~~~~~~~  128 (262)
T 3ly5_A           53 SFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRF----MPRNGTG  128 (262)
T ss_dssp             CC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTC----CGGGCCC
T ss_pred             ChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccc----cccCCce
Confidence            456665  8999999999999999999999999999999999999999999999999999988775321    1123668


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      +||++|||++|.|+++.+++++...++
T Consensus       129 ~lil~Pt~~La~q~~~~~~~~~~~~~~  155 (262)
T 3ly5_A          129 VLILSPTRELAMQTFGVLKELMTHHVH  155 (262)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTCCS
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHhhcCc
Confidence            999999999999999999999876654

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.42  E-value=1.9e-14  Score=128.36  Aligned_cols=69  Identities=22%  Similarity=0.109  Sum_probs=59.5

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+.+|+|++++||||||||++|++|++.     .         +.+++|++||++|+.|+.+.++.+.+..+  +++..+
T Consensus        18 ~l~~~~~~~~~a~TGtGKT~~~l~p~l~-----~---------~~~v~i~~pt~~l~~q~~~~~~~l~~~~~--~~~~~l   81 (551)
T 3crv_A           18 GLRNNFLVALNAPTGSGKTLFSLLVSLE-----V---------KPKVLFVVRTHNEFYPIYRDLTKIREKRN--ITFSFL   81 (551)
T ss_dssp             HHHTTCEEEEECCTTSSHHHHHHHHHHH-----H---------CSEEEEEESSGGGHHHHHHHHTTCCCSSC--CCEEEC
T ss_pred             HHHcCCcEEEECCCCccHHHHHHHHHHh-----C---------CCeEEEEcCCHHHHHHHHHHHHHHhhhcC--ccEEEE
Confidence            3568999999999999999999999997     1         46899999999999999999999877765  777777


Q ss_pred             eCCcc
Q psy7786          83 IGGVP   87 (252)
Q Consensus        83 ~g~~~   87 (252)
                      .|+.+
T Consensus        82 ~gr~~   86 (551)
T 3crv_A           82 VGKPS   86 (551)
T ss_dssp             CCHHH
T ss_pred             ccccc
Confidence            77543

>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=99.42  E-value=1.9e-14  Score=114.72  Aligned_cols=115  Identities=13%  Similarity=0.022  Sum_probs=73.2

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+.+|++++++|+||||||.+|.+++++.......      ..+++++++.|||+|+.|+.+.+...   .+..+  ..
T Consensus        71 ~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~------~~~~~~l~~~p~~~la~q~~~~~~~~---~~~~~--~~  139 (235)
T 3llm_A           71 EAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR------AAECNIVVTQPRRISAVSVAERVAFE---RGEEP--GK  139 (235)
T ss_dssp             HHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC------GGGCEEEEEESSHHHHHHHHHHHHHT---TTCCT--TS
T ss_pred             HHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC------CCceEEEEeccchHHHHHHHHHHHHH---hcccc--Cc
Confidence            456789999999999999999999999987765432      13568999999999999997766543   22111  11


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .+|. .........+.+.+|.  +    .+|+++.++...   .+ ++++++|.||+
T Consensus       140 ~~g~-~~~~~~~~~~~~~~Iv--v----~Tpg~l~~~l~~---~l-~~~~~lVlDEa  185 (235)
T 3llm_A          140 SCGY-SVRFESILPRPHASIM--F----CTVGVLLRKLEA---GI-RGISHVIVDEI  185 (235)
T ss_dssp             SEEE-EETTEEECCCSSSEEE--E----EEHHHHHHHHHH---CC-TTCCEEEECCT
T ss_pred             eEEE-eechhhccCCCCCeEE--E----ECHHHHHHHHHh---hh-cCCcEEEEECC
Confidence            1221 1111111111233442  2    337777665433   23 34899999997

>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=99.41  E-value=7.5e-13  Score=113.60  Aligned_cols=101  Identities=32%  Similarity=0.447  Sum_probs=89.9

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCc
Q psy7786         142 ACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP  221 (252)
Q Consensus       142 ~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~  221 (252)
                      ...+|.++++++.+.+.+...++..|+++|..+++..+.++++++.++||+|||.+++++++..+...        ..+.
T Consensus        35 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~--------~~~~  106 (410)
T 2j0s_A           35 VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ--------VRET  106 (410)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT--------SCSC
T ss_pred             CCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc--------cCCc
Confidence            34689999999999999999999999999999999999999999999999999999999998755321        2356


Q ss_pred             EEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         222 YGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       222 ~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ++||++|||+++.|+++.+++++...++.
T Consensus       107 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  135 (410)
T 2j0s_A          107 QALILAPTRELAVQIQKGLLALGDYMNVQ  135 (410)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTTTCC
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHhccCCeE
Confidence            89999999999999999999998877653

>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=99.38  E-value=2.7e-13  Score=110.84  Aligned_cols=110  Identities=16%  Similarity=0.089  Sum_probs=77.0

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      ++++++.+++++||||||+++++++...+...          ..++||++||++|+.|..+.++++....+  ..+..++
T Consensus       125 ~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~----------~~~~lil~Pt~~L~~q~~~~l~~~~~~~~--~~~~~~~  192 (282)
T 1rif_A          125 GLVNRRRILNLPTSAGRSLIQALLARYYLENY----------EGKILIIVPTTALTTQMADDFVDYRLFSH--AMIKKIG  192 (282)
T ss_dssp             HHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC----------SSEEEEECSSHHHHHHHHHHHHHHTSCCG--GGEEECS
T ss_pred             HHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC----------CCeEEEEECCHHHHHHHHHHHHHhccccc--ceEEEEe
Confidence            45667889999999999999998887765421          33799999999999999999998854433  6777777


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      ||.....   ....+.+|.  |    ++|+.+.....    .....+.++|.||+
T Consensus       193 ~~~~~~~---~~~~~~~I~--v----~T~~~l~~~~~----~~~~~~~~vIiDEa  234 (282)
T 1rif_A          193 GGASKDD---KYKNDAPVV--V----GTWQTVVKQPK----EWFSQFGMMMNDEC  234 (282)
T ss_dssp             TTCSSTT---CCCTTCSEE--E----ECHHHHTTSCG----GGGGGEEEEEEETG
T ss_pred             CCCcchh---hhccCCcEE--E----EchHHHHhhHH----HHHhhCCEEEEECC
Confidence            7754432   111233441  2    34777765533    22344789999996

>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=99.37  E-value=2.9e-12  Score=109.04  Aligned_cols=99  Identities=32%  Similarity=0.487  Sum_probs=88.8

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCC
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEG  220 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~--~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~  220 (252)
                      ..+|.++++++.+.+.+.+.++..|+++|..+++..+.+  +++++.++||+|||.+++++++..+...        ..+
T Consensus         4 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~--------~~~   75 (395)
T 3pey_A            4 AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPE--------DAS   75 (395)
T ss_dssp             CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT--------CCS
T ss_pred             ccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccC--------CCC
Confidence            468999999999999999999999999999999999988  9999999999999999999998765432        235


Q ss_pred             cEEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         221 PYGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       221 ~~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      .++||++||++++.|+++.+++++...++
T Consensus        76 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~  104 (395)
T 3pey_A           76 PQAICLAPSRELARQTLEVVQEMGKFTKI  104 (395)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTSCC
T ss_pred             ccEEEECCCHHHHHHHHHHHHHHhcccCe
Confidence            68999999999999999999998876654

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

Probab=99.37  E-value=3.4e-13  Score=119.18  Aligned_cols=111  Identities=16%  Similarity=0.122  Sum_probs=81.4

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+++++|++++++||||||++|++|+...+...          ..++||++||++|+.|.++.+++++...+  +++..+
T Consensus       124 ~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~----------~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~--~~v~~~  191 (510)
T 2oca_A          124 EGLVNRRRILNLPTSAGRSLIQALLARYYLENY----------EGKILIIVPTTALTTQMADDFVDYRLFSH--AMIKKI  191 (510)
T ss_dssp             HHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC----------SSEEEEEESSHHHHHHHHHHHHHTTSSCG--GGEEEC
T ss_pred             HHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC----------CCeEEEEECcHHHHHHHHHHHHHhhcCCc--cceEEE
Confidence            456789999999999999999999988776431          34899999999999999999988755443  678888


Q ss_pred             eCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          83 IGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        83 ~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .|+.+..++   +..+.+|.  |.    +|+.+.....   ..+. .+.++|.||+
T Consensus       192 ~~~~~~~~~---~~~~~~I~--i~----T~~~l~~~~~---~~~~-~~~liIiDE~  234 (510)
T 2oca_A          192 GGGASKDDK---YKNDAPVV--VG----TWQTVVKQPK---EWFS-QFGMMMNDEC  234 (510)
T ss_dssp             GGGCCTTGG---GCTTCSEE--EE----EHHHHTTSCG---GGGG-GEEEEEEETG
T ss_pred             ecCCccccc---cccCCcEE--EE----eHHHHhhchh---hhhh-cCCEEEEECC
Confidence            888665544   33445552  33    3776655422   2233 4889999996

>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=99.36  E-value=3.7e-12  Score=109.12  Aligned_cols=97  Identities=30%  Similarity=0.447  Sum_probs=87.3

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCC
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEG  220 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~--~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~  220 (252)
                      ..+|.++++++.+.+.+.+.++..|+++|..+++..+.+  +++++.++||+|||.+++++++..+...        ..+
T Consensus        24 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~--------~~~   95 (412)
T 3fht_A           24 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA--------NKY   95 (412)
T ss_dssp             SSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT--------SCS
T ss_pred             cCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhc--------CCC
Confidence            467999999999999999999999999999999999987  9999999999999999999999766432        235


Q ss_pred             cEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         221 PYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       221 ~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      +++||++|||+++.|+++.+++++...
T Consensus        96 ~~~lil~P~~~L~~q~~~~~~~~~~~~  122 (412)
T 3fht_A           96 PQCLCLSPTYELALQTGKVIEQMGKFY  122 (412)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTS
T ss_pred             CCEEEECCCHHHHHHHHHHHHHHHhhc
Confidence            689999999999999999999988754

>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=99.35  E-value=2.5e-12  Score=112.76  Aligned_cols=97  Identities=30%  Similarity=0.447  Sum_probs=86.8

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCC
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEG  220 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~--~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~  220 (252)
                      ..+|.++++++.+.+.+...++..|+++|..+++..+.+  ++++++++||+|||.+|++|++..+...        ..+
T Consensus        91 ~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~--------~~~  162 (479)
T 3fmp_B           91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA--------NKY  162 (479)
T ss_dssp             CCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTT--------SCS
T ss_pred             cCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhc--------CCC
Confidence            467899999999999999999999999999999999987  9999999999999999999998755332        235


Q ss_pred             cEEEEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         221 PYGLIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       221 ~~~LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      +++||++|||++|.|+++.+++++...
T Consensus       163 ~~~lil~Pt~~La~Q~~~~~~~~~~~~  189 (479)
T 3fmp_B          163 PQCLCLSPTYELALQTGKVIEQMGKFY  189 (479)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHHTTS
T ss_pred             CcEEEEeChHHHHHHHHHHHHHHHhhC
Confidence            689999999999999999999998764

>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=99.34  E-value=4.5e-12  Score=108.31  Aligned_cols=99  Identities=35%  Similarity=0.522  Sum_probs=88.9

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++.+.+.+.+.|+..|+++|..+++..+.++++++.++||+|||.+++++++..+...        ..+.++
T Consensus        21 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~--------~~~~~~   92 (400)
T 1s2m_A           21 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK--------LNKIQA   92 (400)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT--------SCSCCE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhc--------cCCccE
Confidence            579999999999999999999999999999999999999999999999999999999998765432        235689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ||++||++++.|+++.+++++...++.
T Consensus        93 lil~P~~~L~~q~~~~~~~~~~~~~~~  119 (400)
T 1s2m_A           93 LIMVPTRELALQTSQVVRTLGKHCGIS  119 (400)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTTTCC
T ss_pred             EEEcCCHHHHHHHHHHHHHHhcccCce
Confidence            999999999999999999998876653

>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=99.34  E-value=7.5e-12  Score=107.31  Aligned_cols=103  Identities=32%  Similarity=0.444  Sum_probs=91.2

Q ss_pred             CCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCC
Q psy7786         139 VPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPG  218 (252)
Q Consensus       139 ~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~  218 (252)
                      ......+|.++++++.+.+.+.+.++..|+++|..+++..+.++++++.++||+|||.+++++++..+...        .
T Consensus        35 ~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~--------~  106 (414)
T 3eiq_A           35 WNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD--------L  106 (414)
T ss_dssp             CCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTT--------S
T ss_pred             ccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhc--------C
Confidence            34445789999999999999999999999999999999999999999999999999999999999765432        2


Q ss_pred             CCcEEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         219 EGPYGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       219 ~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      .+.++||++|||+++.|+++.+++++...++
T Consensus       107 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  137 (414)
T 3eiq_A          107 KATQALVLAPTRELAQQIQKVVMALGDYMGA  137 (414)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHGGGSCC
T ss_pred             CceeEEEEeChHHHHHHHHHHHHHHhcccCc
Confidence            3567999999999999999999999877664

>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=99.32  E-value=4.4e-12  Score=107.99  Aligned_cols=100  Identities=29%  Similarity=0.458  Sum_probs=89.5

Q ss_pred             cccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCc
Q psy7786         142 ACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP  221 (252)
Q Consensus       142 ~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~  221 (252)
                      ...+|.++++++.+.+.+...++..|+++|..+++..+.++++++.++||+|||.+++++++..+...        ..++
T Consensus        19 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~--------~~~~   90 (394)
T 1fuu_A           19 VVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS--------VKAP   90 (394)
T ss_dssp             CCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTT--------CCSC
T ss_pred             ccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhcc--------CCCC
Confidence            34679999999999999999999999999999999999999999999999999999999999765432        2356


Q ss_pred             EEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         222 YGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       222 ~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      ++||++||++++.|+++.++++....++
T Consensus        91 ~~lil~P~~~L~~q~~~~~~~~~~~~~~  118 (394)
T 1fuu_A           91 QALMLAPTRELALQIQKVVMALAFHMDI  118 (394)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSCC
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccCCe
Confidence            8999999999999999999998877654

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.30  E-value=2.4e-12  Score=116.04  Aligned_cols=73  Identities=19%  Similarity=0.208  Sum_probs=64.0

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+.+|+|++++||||||||++|++|++..+...          +.+++|++||++|+.|+.+.++.+.+..+  +++..+
T Consensus        18 ~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~----------~~kvli~t~T~~l~~Qi~~el~~l~~~~~--~~~~~l   85 (620)
T 4a15_A           18 SLQKSYGVALESPTGSGKTIMALKSALQYSSER----------KLKVLYLVRTNSQEEQVIKELRSLSSTMK--IRAIPM   85 (620)
T ss_dssp             HHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH----------TCEEEEEESSHHHHHHHHHHHHHHHHHSC--CCEEEC
T ss_pred             HHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc----------CCeEEEECCCHHHHHHHHHHHHHHhhccC--eEEEEE
Confidence            457899999999999999999999999987642          45899999999999999999999998875  788887


Q ss_pred             eCCcc
Q psy7786          83 IGGVP   87 (252)
Q Consensus        83 ~g~~~   87 (252)
                      .|+.+
T Consensus        86 ~gr~~   90 (620)
T 4a15_A           86 QGRVN   90 (620)
T ss_dssp             CCHHH
T ss_pred             ECCCc
Confidence            77654

>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=99.29  E-value=1e-11  Score=105.59  Aligned_cols=96  Identities=32%  Similarity=0.435  Sum_probs=85.7

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++.+.+.+...++..|+++|..+++..+.++++++.++||+|||.+++++++..+...        ..+.++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~--------~~~~~~   79 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV--------TGQVSV   79 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCC--------TTCCCE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhccc--------CCCeeE
Confidence            468999999999999999999999999999999999999999999999999999999998765321        235689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      ||+|||++++.|+++.++++.+..
T Consensus        80 lil~P~~~L~~q~~~~~~~~~~~~  103 (391)
T 1xti_A           80 LVMCHTRELAFQISKEYERFSKYM  103 (391)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTC
T ss_pred             EEECCCHHHHHHHHHHHHHHHhhC
Confidence            999999999999999999997765

>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=99.25  E-value=2.2e-11  Score=102.48  Aligned_cols=96  Identities=35%  Similarity=0.544  Sum_probs=85.7

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      .+|.++++++.+.+.+.+.++..|+++|..+++..+.+ +++++.++||+|||..++.+++..+..         ..+.+
T Consensus         6 ~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~---------~~~~~   76 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE---------NNGIE   76 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS---------SSSCC
T ss_pred             CchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcc---------cCCCc
Confidence            57999999999999999999999999999999999988 799999999999999999998875532         23568


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      +||++|+++++.|+++.++++....+
T Consensus        77 ~lil~P~~~L~~q~~~~~~~~~~~~~  102 (367)
T 1hv8_A           77 AIILTPTRELAIQVADEIESLKGNKN  102 (367)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHCSSC
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhCCCC
Confidence            99999999999999999999876554

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.24  E-value=3.4e-11  Score=108.02  Aligned_cols=92  Identities=26%  Similarity=0.379  Sum_probs=81.9

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhh--cCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcC
Q psy7786         151 LPESLVRALEAKGIKKPTPIQVQGIPAAL--SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICP  228 (252)
Q Consensus       151 l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~--~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~  228 (252)
                      +++++++.+...++..|+++|..+++.++  .++++++.++||+|||.+|++|++..+.....    ....++++||++|
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~----~~~~~~~~lvl~P  103 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF----DSQYMVKAVIVAP  103 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT----SSTTSCCEEEECS
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccc----cccCCCeEEEEcc
Confidence            99999999999999999999999999999  78899999999999999999999998876431    1233578999999


Q ss_pred             cHHHHHHHHHHHHHHHhh
Q psy7786         229 SRELARQTHDIIQYYCAA  246 (252)
Q Consensus       229 tr~~a~~i~~~l~~l~~~  246 (252)
                      ||++|.|+++.++++...
T Consensus       104 tr~La~Q~~~~~~~~~~~  121 (579)
T 3sqw_A          104 TRDLALQIEAEVKKIHDM  121 (579)
T ss_dssp             SHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhh
Confidence            999999999999998753

>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=99.22  E-value=3.8e-12  Score=117.39  Aligned_cols=112  Identities=15%  Similarity=0.107  Sum_probs=64.8

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeee
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAI   83 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~   83 (252)
                      +.+|++++++||||||||+  ++|++-  ......    ...+.++++++|+|+||.|+.+.+   ++.++  ..+...+
T Consensus       106 l~~~~~vii~gpTGSGKTt--llp~ll--~~~~~~----~~~g~~ilvl~P~r~La~q~~~~l---~~~~~--~~v~~~v  172 (773)
T 2xau_A          106 YQNNQIMVFVGETGSGKTT--QIPQFV--LFDEMP----HLENTQVACTQPRRVAAMSVAQRV---AEEMD--VKLGEEV  172 (773)
T ss_dssp             HHHCSEEEEECCTTSSHHH--HHHHHH--HHHHCG----GGGTCEEEEEESCHHHHHHHHHHH---HHHTT--CCBTTTE
T ss_pred             HhCCCeEEEECCCCCCHHH--HHHHHH--HHhccc----cCCCceEEecCchHHHHHHHHHHH---HHHhC--Cchhhee
Confidence            3467789999999999998  677772  222110    012567999999999999998654   44455  3444444


Q ss_pred             CCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          84 GGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        84 g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      |+....+..  .....+|.  +    .+||++.......  .+...+.++|.||.
T Consensus       173 G~~i~~~~~--~~~~~~I~--v----~T~G~l~r~l~~~--~~l~~~~~lIlDEa  217 (773)
T 2xau_A          173 GYSIRFENK--TSNKTILK--Y----MTDGMLLREAMED--HDLSRYSCIILDEA  217 (773)
T ss_dssp             EEEETTEEE--CCTTCSEE--E----EEHHHHHHHHHHS--TTCTTEEEEEECSG
T ss_pred             cceeccccc--cCCCCCEE--E----ECHHHHHHHHhhC--ccccCCCEEEecCc
Confidence            432111110  11223331  2    2366665432221  12334889999996

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.21  E-value=2.9e-11  Score=108.71  Aligned_cols=110  Identities=14%  Similarity=0.059  Sum_probs=52.5

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHH-HHHHHHHHhCCCCcceeeeeCC
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH-DIIQYYCAALPIPLRTCLAIGG   85 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~-~~~~~l~~~~~~~~~~~~~~g~   85 (252)
                      +++++++++||||||+++ ++++..+...... ......+.++||++||++|+.|.. +.++.++      ..+..+.++
T Consensus       198 ~~~~ll~~~TGsGKT~~~-~~~~~~l~~~~~~-~~~~~~~~~vlil~P~~~L~~Q~~~~~~~~~~------~~~~~~~~~  269 (590)
T 3h1t_A          198 KKRSLITMATGTGKTVVA-FQISWKLWSARWN-RTGDYRKPRILFLADRNVLVDDPKDKTFTPFG------DARHKIEGG  269 (590)
T ss_dssp             CSEEEEEECTTSCHHHHH-HHHHHHHHHTTCC-SSCSSSCCCEEEEEC-----------CCTTTC------SSEEECCC-
T ss_pred             CCceEEEecCCCChHHHH-HHHHHHHHhcccc-cccccCCCeEEEEeCCHHHHHHHHHHHHHhcc------hhhhhhhcc
Confidence            356999999999999995 4555555543210 001124678999999999999998 6666542      222223322


Q ss_pred             cccCcchhhhhhcccccCCccccccCCccccCCChhH--HHHH-hhhhceeeccCC
Q psy7786          86 VPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQV--HDII-RRNLRILVEGDD  138 (252)
Q Consensus        86 ~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~--~~~l-~~~~~~~V~de~  138 (252)
                      .        ...+.+|.  |    ++|+++.......  ...+ .....++|.||+
T Consensus       270 ~--------~~~~~~I~--v----~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEa  311 (590)
T 3h1t_A          270 K--------VVKSREIY--F----AIYQSIASDERRPGLYKEFPQDFFDLIIIDEC  311 (590)
T ss_dssp             ---------CCSSCSEE--E----EEGGGC------CCGGGGSCTTSCSEEEESCC
T ss_pred             C--------CCCCCcEE--E----EEhhhhccccccccccccCCCCccCEEEEECC
Confidence            1        12233441  2    3478777654311  1111 233678898997

>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=99.20  E-value=6.2e-11  Score=105.88  Aligned_cols=92  Identities=26%  Similarity=0.395  Sum_probs=81.6

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhh--cCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcC
Q psy7786         151 LPESLVRALEAKGIKKPTPIQVQGIPAAL--SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICP  228 (252)
Q Consensus       151 l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~--~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~  228 (252)
                      +++.+.+.+.+.++..|+++|..+++..+  .++++++.++||+|||.+|++|++..+......    ...++++||++|
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~----~~~~~~~lil~P  154 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD----SQYMVKAVIVAP  154 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS----STTSCCEEEECS
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcccc----ccCCeeEEEEcC
Confidence            99999999999999999999999999999  678999999999999999999999988765321    223568999999


Q ss_pred             cHHHHHHHHHHHHHHHhh
Q psy7786         229 SRELARQTHDIIQYYCAA  246 (252)
Q Consensus       229 tr~~a~~i~~~l~~l~~~  246 (252)
                      ||++|.|+++.++++...
T Consensus       155 tr~La~Q~~~~~~~~~~~  172 (563)
T 3i5x_A          155 TRDLALQIEAEVKKIHDM  172 (563)
T ss_dssp             SHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHhh
Confidence            999999999999998653

>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=99.15  E-value=2.1e-11  Score=106.65  Aligned_cols=97  Identities=16%  Similarity=0.121  Sum_probs=70.6

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcc-eee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLR-TCL   81 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~-~~~   81 (252)
                      .++++++++++++||||||++|+.++...              +.++||++||++|+.|..+.++++    +  ++ +..
T Consensus       104 ~i~~~~~~ll~~~TGsGKT~~~l~~i~~~--------------~~~~Lvl~P~~~L~~Q~~~~~~~~----~--~~~v~~  163 (472)
T 2fwr_A          104 RWLVDKRGCIVLPTGSGKTHVAMAAINEL--------------STPTLIVVPTLALAEQWKERLGIF----G--EEYVGE  163 (472)
T ss_dssp             HHTTTTEEEEECCTTSCHHHHHHHHHHHH--------------CSCEEEEESSHHHHHHHHHHGGGG----C--GGGEEE
T ss_pred             HHHhcCCEEEEeCCCCCHHHHHHHHHHHc--------------CCCEEEEECCHHHHHHHHHHHHhC----C--CcceEE
Confidence            46778899999999999999999998753              346999999999999999988874    4  67 777


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +.|+.+.         ..+|.  |.    +|+.+....    ..+.+.+.++|.||+
T Consensus       164 ~~g~~~~---------~~~Iv--v~----T~~~l~~~~----~~~~~~~~liIvDEa  201 (472)
T 2fwr_A          164 FSGRIKE---------LKPLT--VS----TYDSAYVNA----EKLGNRFMLLIFDEV  201 (472)
T ss_dssp             BSSSCBC---------CCSEE--EE----EHHHHHHTH----HHHTTTCSEEEEETG
T ss_pred             ECCCcCC---------cCCEE--EE----EcHHHHHHH----HHhcCCCCEEEEECC
Confidence            7777542         22331  22    365554332    223345889999996

>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=99.15  E-value=2.3e-10  Score=95.14  Aligned_cols=85  Identities=34%  Similarity=0.534  Sum_probs=77.3

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcH
Q psy7786         151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSR  230 (252)
Q Consensus       151 l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr  230 (252)
                      +++++.+.+.+.|+..|++.|..+++..+.++++++.++||+|||.+++.+++..              +.++||++|++
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~--------------~~~~liv~P~~   66 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL--------------GMKSLVVTPTR   66 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH--------------TCCEEEECSSH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh--------------cCCEEEEeCCH
Confidence            4678999999999999999999999999999999999999999999999988752              45699999999


Q ss_pred             HHHHHHHHHHHHHHhhCCC
Q psy7786         231 ELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       231 ~~a~~i~~~l~~l~~~~~i  249 (252)
                      +++.|+++.+++++...++
T Consensus        67 ~L~~q~~~~~~~~~~~~~~   85 (337)
T 2z0m_A           67 ELTRQVASHIRDIGRYMDT   85 (337)
T ss_dssp             HHHHHHHHHHHHHTTTSCC
T ss_pred             HHHHHHHHHHHHHhhhcCC
Confidence            9999999999999877654

>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=99.13  E-value=1e-10  Score=110.43  Aligned_cols=108  Identities=14%  Similarity=0.048  Sum_probs=67.9

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCc
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGV   86 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~   86 (252)
                      +++.+++++||||||+++ ++++..+....        ...++|||+|+++|+.|+.+.++.++..        .+.|+.
T Consensus       300 ~~~gli~~~TGSGKT~t~-~~l~~ll~~~~--------~~~rvLvlvpr~eL~~Q~~~~f~~f~~~--------~v~~~~  362 (1038)
T 2w00_A          300 ESGGYIWHTTGSGKTLTS-FKAARLATELD--------FIDKVFFVVDRKDLDYQTMKEYQRFSPD--------SVNGSE  362 (1038)
T ss_dssp             GGSEEEEECTTSSHHHHH-HHHHHHHTTCT--------TCCEEEEEECGGGCCHHHHHHHHTTSTT--------CSSSSC
T ss_pred             CCCEEEEecCCCCHHHHH-HHHHHHHHhcC--------CCceEEEEeCcHHHHHHHHHHHHHhccc--------cccccc
Confidence            579999999999999997 77775442211        2468999999999999999988876432        123555


Q ss_pred             ccCcchhhhhh-cccccCCccccccCCccccCCChhHH--HHHhhhhceeeccCC
Q psy7786          87 PMNQSLDVIKK-GIQYNDPIKTSWRAPRCILSLPDQVH--DIIRRNLRILVEGDD  138 (252)
Q Consensus        87 ~~~~~~~~l~~-~~~i~~~i~t~~~~p~~l~~~~~~~~--~~l~~~~~~~V~de~  138 (252)
                      +.....+.+.+ +.+|.  |    ++|+++........  ..+. ...++|.||+
T Consensus       363 s~~~l~~~L~~~~~~Ii--V----tTiqkl~~~l~~~~~~~~~~-~~~lvIiDEA  410 (1038)
T 2w00_A          363 NTAGLKRNLDKDDNKII--V----TTIQKLNNLMKAESDLPVYN-QQVVFIFDEC  410 (1038)
T ss_dssp             CCHHHHHHHHCSSCCEE--E----EEHHHHHHHHHHCCCCGGGG-SCEEEEEESC
T ss_pred             CHHHHHHHhcCCCCCEE--E----EEHHHHHHHHhcccchhccc-cccEEEEEcc
Confidence            55455555532 34441  2    23555543322110  1122 3568888887

>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=99.02  E-value=7.3e-10  Score=101.14  Aligned_cols=76  Identities=26%  Similarity=0.311  Sum_probs=68.3

Q ss_pred             HCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         161 AKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ..|+ .|+++|..++|.++.|+  +..+.||+|||++|.+|++...+.           +.+++|+||||+||.|+++++
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~-----------g~~vlVltptreLA~qd~e~~  144 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT-----------GKGVHVVTVNEYLASRDAEQM  144 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT-----------SSCEEEEESSHHHHHHHHHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc-----------CCCEEEEeCCHHHHHHHHHHH
Confidence            4688 99999999999999998  899999999999999999854321           457999999999999999999


Q ss_pred             HHHHhhCCCC
Q psy7786         241 QYYCAALPIG  250 (252)
Q Consensus       241 ~~l~~~~~i~  250 (252)
                      ..+++.+|++
T Consensus       145 ~~l~~~lgl~  154 (844)
T 1tf5_A          145 GKIFEFLGLT  154 (844)
T ss_dssp             HHHHHHTTCC
T ss_pred             HHHHhhcCCe
Confidence            9999999875

>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=99.02  E-value=1.7e-10  Score=91.87  Aligned_cols=97  Identities=16%  Similarity=0.121  Sum_probs=67.3

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcc-eee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLR-TCL   81 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~-~~~   81 (252)
                      .++++++++++++||+|||.+++.++...              +.+++|++||++|+.|..+.++++    +  ++ +..
T Consensus       104 ~~~~~~~~ll~~~tG~GKT~~a~~~~~~~--------------~~~~liv~P~~~L~~q~~~~~~~~----~--~~~v~~  163 (237)
T 2fz4_A          104 RWLVDKRGCIVLPTGSGKTHVAMAAINEL--------------STPTLIVVPTLALAEQWKERLGIF----G--EEYVGE  163 (237)
T ss_dssp             HHTTTSEEEEEESSSTTHHHHHHHHHHHS--------------CSCEEEEESSHHHHHHHHHHHGGG----C--GGGEEE
T ss_pred             HHHhCCCEEEEeCCCCCHHHHHHHHHHHc--------------CCCEEEEeCCHHHHHHHHHHHHhC----C--CCeEEE
Confidence            35678899999999999999998887642              346999999999999998888763    4  66 666


Q ss_pred             eeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          82 AIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        82 ~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +.|+...         ..++.  +.    +++.+....    ..+.....++|.||+
T Consensus       164 ~~g~~~~---------~~~i~--v~----T~~~l~~~~----~~~~~~~~llIiDEa  201 (237)
T 2fz4_A          164 FSGRIKE---------LKPLT--VS----TYDSAYVNA----EKLGNRFMLLIFDEV  201 (237)
T ss_dssp             ESSSCBC---------CCSEE--EE----EHHHHHHTH----HHHTTTCSEEEEECS
T ss_pred             EeCCCCC---------cCCEE--EE----eHHHHHhhH----HHhcccCCEEEEECC
Confidence            7776432         22331  22    255443322    223345789999996

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.00  E-value=3.5e-10  Score=100.56  Aligned_cols=63  Identities=17%  Similarity=0.173  Sum_probs=49.8

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeee
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLA   82 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~   82 (252)
                      .+.+|+|++++||||||||++|++|+++.              +.+++|++||++|+.|+.+.++.+    +  +++..+
T Consensus        22 ~~~~~~~~~~~a~TGtGKT~~~l~~~~~~--------------~~~~~~~~~t~~l~~q~~~~~~~l----~--~~~~~l   81 (540)
T 2vl7_A           22 ALKHGKTLLLNAKPGLGKTVFVEVLGMQL--------------KKKVLIFTRTHSQLDSIYKNAKLL----G--LKTGFL   81 (540)
T ss_dssp             HHHTTCEEEEECCTTSCHHHHHHHHHHHH--------------TCEEEEEESCHHHHHHHHHHHGGG----T--CCEEEC
T ss_pred             HHHcCCCEEEEcCCCCcHHHHHHHHHHhC--------------CCcEEEEcCCHHHHHHHHHHHHhc----C--CcEEEe
Confidence            45689999999999999999999998742              457999999999999999877764    3  555555


Q ss_pred             eCC
Q psy7786          83 IGG   85 (252)
Q Consensus        83 ~g~   85 (252)
                      .|.
T Consensus        82 ~gr   84 (540)
T 2vl7_A           82 IGK   84 (540)
T ss_dssp             ---
T ss_pred             cCC
Confidence            543

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=98.99  E-value=7.7e-10  Score=95.02  Aligned_cols=80  Identities=23%  Similarity=0.213  Sum_probs=67.4

Q ss_pred             HHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHH
Q psy7786         155 LVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR  234 (252)
Q Consensus       155 l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~  234 (252)
                      +.+.+.+.....|+++|..+++..+.++++++.++||+|||.+++++.+...           ..++++||++|||++|.
T Consensus        10 ~~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~-----------~~~~~~lil~Pt~~L~~   78 (414)
T 3oiy_A           10 FRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA-----------RKGKKSALVFPTVTLVK   78 (414)
T ss_dssp             HHHHHHHHHSSCCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH-----------TTTCCEEEEESSHHHHH
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh-----------cCCCEEEEEECCHHHHH
Confidence            3444554333379999999999999999999999999999999988887654           13568999999999999


Q ss_pred             HHHHHHHHHHh
Q psy7786         235 QTHDIIQYYCA  245 (252)
Q Consensus       235 ~i~~~l~~l~~  245 (252)
                      |+++.++++++
T Consensus        79 q~~~~~~~~~~   89 (414)
T 3oiy_A           79 QTLERLQKLAD   89 (414)
T ss_dssp             HHHHHHHHHCC
T ss_pred             HHHHHHHHHcc
Confidence            99999999876

>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=98.95  E-value=2e-09  Score=98.94  Aligned_cols=91  Identities=24%  Similarity=0.351  Sum_probs=82.6

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~-~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      +|.++++++.+.+.+...++..|+++|..+++. ...+++++++++||+|||..+.++++..+...          +.++
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~----------~~~~   71 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ----------GGKA   71 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH----------CSEE
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC----------CCEE
Confidence            588999999999999999999999999999998 78899999999999999999999999877643          4689


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHh
Q psy7786         224 LIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      ++++|+|++|.|+++.++++.+
T Consensus        72 l~i~P~raLa~q~~~~~~~l~~   93 (720)
T 2zj8_A           72 VYIVPLKALAEEKFQEFQDWEK   93 (720)
T ss_dssp             EEECSSGGGHHHHHHHTGGGGG
T ss_pred             EEEcCcHHHHHHHHHHHHHHHh
Confidence            9999999999999999976554

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

Probab=98.94  E-value=4e-09  Score=96.87  Aligned_cols=92  Identities=27%  Similarity=0.448  Sum_probs=82.4

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~-~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      .+|.++++++.+.+.+.+.++..|+++|..+++. ...+++++++++||+|||..+.++++..+...          +.+
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~----------~~~   77 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN----------GGK   77 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS----------CSE
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC----------CCe
Confidence            4689999999999999999999999999999998 77899999999999999999999999876532          468


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         223 GLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      +++++|+|++|.|+++.++++.+
T Consensus        78 il~i~P~r~La~q~~~~~~~~~~  100 (715)
T 2va8_A           78 AIYVTPLRALTNEKYLTFKDWEL  100 (715)
T ss_dssp             EEEECSCHHHHHHHHHHHGGGGG
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhc
Confidence            99999999999999999965543

>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=98.94  E-value=1.6e-09  Score=95.94  Aligned_cols=86  Identities=26%  Similarity=0.405  Sum_probs=78.5

Q ss_pred             cccccCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         144 CSFRLMKLPESLVRALEA-KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~-~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      ..|.++++++++.+.+.+ .|+..|++.|..+++..+.|+|+++.++||+|||.+|.+|.+..              ...
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~--------------~g~   67 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL--------------NGL   67 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS--------------SSE
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh--------------CCC
Confidence            468899999999999998 79999999999999999999999999999999999999998741              346


Q ss_pred             EEEEcCcHHHHHHHHHHHHHH
Q psy7786         223 GLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      +||++|+++++.+..+.++++
T Consensus        68 ~lvi~P~~aL~~q~~~~l~~~   88 (523)
T 1oyw_A           68 TVVVSPLISLMKDQVDQLQAN   88 (523)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT
T ss_pred             EEEECChHHHHHHHHHHHHHc
Confidence            999999999999999998865

>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=98.93  E-value=3.9e-09  Score=94.64  Aligned_cols=83  Identities=23%  Similarity=0.428  Sum_probs=75.8

Q ss_pred             ccCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEE
Q psy7786         147 RLMKLPESLVRALEA-KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI  225 (252)
Q Consensus       147 ~~~~l~~~l~~~l~~-~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LI  225 (252)
                      .++++++.+.+.+.+ .|+..|+++|..+++.++.|+|+++.++||+|||++|.+|.+..              ..++||
T Consensus        24 ~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~--------------~g~~lV   89 (591)
T 2v1x_A           24 EDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS--------------DGFTLV   89 (591)
T ss_dssp             SCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS--------------SSEEEE
T ss_pred             ccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc--------------CCcEEE
Confidence            457889999999998 59999999999999999999999999999999999999999741              357999


Q ss_pred             EcCcHHHHHHHHHHHHHH
Q psy7786         226 ICPSRELARQTHDIIQYY  243 (252)
Q Consensus       226 f~~tr~~a~~i~~~l~~l  243 (252)
                      ++|++++++|..+.++++
T Consensus        90 isP~~~L~~q~~~~l~~~  107 (591)
T 2v1x_A           90 ICPLISLMEDQLMVLKQL  107 (591)
T ss_dssp             ECSCHHHHHHHHHHHHHH
T ss_pred             EeCHHHHHHHHHHHHHhc
Confidence            999999999999999887

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=98.83  E-value=8.2e-09  Score=94.19  Aligned_cols=73  Identities=22%  Similarity=0.165  Sum_probs=65.7

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|+++|..++|.++.|+  +..+.||+|||++|.+|++...+.           +.+++|+||||+||.|++++++.++
T Consensus        73 ~~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~-----------g~~vlVltPTreLA~Q~~e~~~~l~  139 (853)
T 2fsf_A           73 MRHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT-----------GKGVHVVTVNDYLAQRDAENNRPLF  139 (853)
T ss_dssp             CCCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT-----------SSCCEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc-----------CCcEEEEcCCHHHHHHHHHHHHHHH
Confidence            389999999999999998  899999999999999999864321           4579999999999999999999999


Q ss_pred             hhCCCC
Q psy7786         245 AALPIG  250 (252)
Q Consensus       245 ~~~~i~  250 (252)
                      ++++++
T Consensus       140 ~~lgl~  145 (853)
T 2fsf_A          140 EFLGLT  145 (853)
T ss_dssp             HHTTCC
T ss_pred             HhcCCe
Confidence            999875

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=98.81  E-value=1.1e-08  Score=97.35  Aligned_cols=76  Identities=26%  Similarity=0.290  Sum_probs=68.5

Q ss_pred             HCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         161 AKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ..|+. | ++|..++|..+.|+|++++++||+|||. +.+|.+..+..          .++++||++|||++|.|+++.+
T Consensus        53 ~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~----------~~~~~lil~PtreLa~Q~~~~l  119 (1054)
T 1gku_B           53 CVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL----------KGKRCYVIFPTSLLVIQAAETI  119 (1054)
T ss_dssp             TTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT----------TSCCEEEEESCHHHHHHHHHHH
T ss_pred             hcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh----------cCCeEEEEeccHHHHHHHHHHH
Confidence            46888 9 9999999999999999999999999998 88898877653          2568999999999999999999


Q ss_pred             HHHHhhCCC
Q psy7786         241 QYYCAALPI  249 (252)
Q Consensus       241 ~~l~~~~~i  249 (252)
                      ++++..+++
T Consensus       120 ~~l~~~~~i  128 (1054)
T 1gku_B          120 RKYAEKAGV  128 (1054)
T ss_dssp             HHHHTTTCC
T ss_pred             HHHHhhcCC
Confidence            999988766

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=98.80  E-value=1.8e-08  Score=92.30  Aligned_cols=75  Identities=28%  Similarity=0.317  Sum_probs=67.2

Q ss_pred             CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         162 KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       162 ~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .|+ .|+++|..++|.++.|+  +..+.||+|||+++.+|++...+.           +.+++|+||||+||.|.++++.
T Consensus       108 lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~-----------g~~v~VvTpTreLA~Qdae~m~  173 (922)
T 1nkt_A          108 LDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA-----------GNGVHIVTVNDYLAKRDSEWMG  173 (922)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT-----------TSCEEEEESSHHHHHHHHHHHH
T ss_pred             cCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh-----------CCCeEEEeCCHHHHHHHHHHHH
Confidence            466 99999999999999998  999999999999999999754432           4469999999999999999999


Q ss_pred             HHHhhCCCC
Q psy7786         242 YYCAALPIG  250 (252)
Q Consensus       242 ~l~~~~~i~  250 (252)
                      .+...+|++
T Consensus       174 ~l~~~lGLs  182 (922)
T 1nkt_A          174 RVHRFLGLQ  182 (922)
T ss_dssp             HHHHHTTCC
T ss_pred             HHHhhcCCe
Confidence            999999876

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

Probab=98.79  E-value=2.3e-08  Score=88.65  Aligned_cols=79  Identities=23%  Similarity=0.185  Sum_probs=68.8

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .|+++|..+++..+.++++++.++||+|||.+++++++..+....      ...+.++||++||++++.|+.+.++++.+
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~------~~~~~~~lil~P~~~L~~q~~~~~~~~~~   77 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFP------CGQKGKVVFFANQIPVYEQQATVFSRYFE   77 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC------SSCCCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcc------cCCCCEEEEEeCCHHHHHHHHHHHHHHhc
Confidence            689999999999999999999999999999999999998776532      12356899999999999999999999988


Q ss_pred             hCCCC
Q psy7786         246 ALPIG  250 (252)
Q Consensus       246 ~~~i~  250 (252)
                      ..++.
T Consensus        78 ~~~~~   82 (555)
T 3tbk_A           78 RLGYN   82 (555)
T ss_dssp             TTTCC
T ss_pred             cCCcE
Confidence            76543

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

Probab=98.77  E-value=1.9e-08  Score=91.91  Aligned_cols=87  Identities=20%  Similarity=0.145  Sum_probs=70.9

Q ss_pred             HHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHH
Q psy7786         157 RALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT  236 (252)
Q Consensus       157 ~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i  236 (252)
                      ..+...++..|+++|..+++..+.+++++++++||+|||.+++++++..+....      ...+.++||++||++++.|.
T Consensus         4 ~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~------~~~~~~~lvl~Pt~~L~~Q~   77 (696)
T 2ykg_A            4 SDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFP------QGQKGKVVFFANQIPVYEQN   77 (696)
T ss_dssp             ---CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSC------TTCCCCEEEECSSHHHHHHH
T ss_pred             CcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCc------cCCCCeEEEEECCHHHHHHH
Confidence            456677889999999999999999999999999999999999999998765432      12236799999999999999


Q ss_pred             HHHHHHHHhhCCC
Q psy7786         237 HDIIQYYCAALPI  249 (252)
Q Consensus       237 ~~~l~~l~~~~~i  249 (252)
                      .+.++++++..++
T Consensus        78 ~~~~~~~~~~~~~   90 (696)
T 2ykg_A           78 KSVFSKYFERHGY   90 (696)
T ss_dssp             HHHHHHHTTTTTC
T ss_pred             HHHHHHHhccCCc
Confidence            9999999875554

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

Probab=98.76  E-value=2.7e-08  Score=88.33  Aligned_cols=79  Identities=20%  Similarity=0.212  Sum_probs=67.4

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|+++|..+++..+.++++++.++||+|||.++++|++..+....      ...+.++||++||++++.|+.+.++++.
T Consensus         6 ~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~------~~~~~~~lil~P~~~L~~q~~~~~~~~~   79 (556)
T 4a2p_A            6 KKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP------AGRKAKVVFLATKVPVYEQQKNVFKHHF   79 (556)
T ss_dssp             --CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC------SSCCCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCc------ccCCCeEEEEeCCHHHHHHHHHHHHHHh
Confidence            4799999999999999999999999999999999999988775432      1225689999999999999999999998


Q ss_pred             hhCCC
Q psy7786         245 AALPI  249 (252)
Q Consensus       245 ~~~~i  249 (252)
                      ...++
T Consensus        80 ~~~~~   84 (556)
T 4a2p_A           80 ERQGY   84 (556)
T ss_dssp             GGGTC
T ss_pred             cccCc
Confidence            86554

>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=98.76  E-value=2.1e-09  Score=98.48  Aligned_cols=89  Identities=21%  Similarity=0.348  Sum_probs=76.4

Q ss_pred             ccccCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         145 SFRLMK--LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       145 ~~~~~~--l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      +|.+++  +++.+.+.+.+.++..|+++|..+++....+++++++++||+|||..+.++++..+..           +.+
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~-----------~~~   70 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-----------GGK   70 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-----------TCC
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh-----------CCc
Confidence            466777  8999999999999999999999999999999999999999999999999999877542           457


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHH
Q psy7786         223 GLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +++++|+|++|.|+++.++++.
T Consensus        71 ~l~i~P~r~La~q~~~~~~~~~   92 (702)
T 2p6r_A           71 SLYVVPLRALAGEKYESFKKWE   92 (702)
T ss_dssp             EEEEESSHHHHHHHHHHHTTTT
T ss_pred             EEEEeCcHHHHHHHHHHHHHHH
Confidence            9999999999999999986554

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.74  E-value=2.1e-08  Score=91.86  Aligned_cols=75  Identities=25%  Similarity=0.307  Sum_probs=67.0

Q ss_pred             CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         162 KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       162 ~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .|+ .|+++|..++|.++.|+  +..+.||+|||+++.+|++...+.           +.+++|++||++||.|.++++.
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~-----------G~qv~VvTPTreLA~Qdae~m~  141 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT-----------GKGVHVVTVNDYLARRDAEWMG  141 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT-----------CSCCEEEESSHHHHHHHHHHHH
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh-----------CCCEEEEeCCHHHHHHHHHHHH
Confidence            477 99999999999999998  899999999999999999754432           4479999999999999999999


Q ss_pred             HHHhhCCCC
Q psy7786         242 YYCAALPIG  250 (252)
Q Consensus       242 ~l~~~~~i~  250 (252)
                      .+.+.+|++
T Consensus       142 ~l~~~lGLs  150 (997)
T 2ipc_A          142 PVYRGLGLS  150 (997)
T ss_dssp             HHHHTTTCC
T ss_pred             HHHHhcCCe
Confidence            999999875

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

Probab=98.69  E-value=5.7e-08  Score=90.23  Aligned_cols=83  Identities=19%  Similarity=0.189  Sum_probs=68.5

Q ss_pred             HCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         161 AKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       161 ~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ..++..|+++|..+++..+.+++++++++||+|||.+++++++..+....      ...+.++||+|||++++.|+.+.+
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~------~~~~~~~Lvl~Pt~~L~~Q~~~~~  316 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP------AGRKAKVVFLATKVPVYEQQKNVF  316 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC------SSCCCCEEEECSSHHHHHHHHHHH
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhcc------ccCCCeEEEEeCCHHHHHHHHHHH
Confidence            34577899999999999999999999999999999999999988776531      123568999999999999999999


Q ss_pred             HHHHhhCCC
Q psy7786         241 QYYCAALPI  249 (252)
Q Consensus       241 ~~l~~~~~i  249 (252)
                      +++....++
T Consensus       317 ~~~~~~~~~  325 (797)
T 4a2q_A          317 KHHFERQGY  325 (797)
T ss_dssp             HHHHGGGTC
T ss_pred             HHhcccCCc
Confidence            999886554

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=98.68  E-value=3.4e-08  Score=94.33  Aligned_cols=71  Identities=24%  Similarity=0.255  Sum_probs=62.9

Q ss_pred             CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         162 KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       162 ~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .++ .|+++|..++|..+.|+|++++++||+|||.+++.+++..+.           .++++||++|||++|.|+++.++
T Consensus        75 ~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~-----------~~~~~Lil~PtreLa~Q~~~~l~  142 (1104)
T 4ddu_A           75 FGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR-----------KGKKSALVFPTVTLVKQTLERLQ  142 (1104)
T ss_dssp             SSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT-----------TTCCEEEEESSHHHHHHHHHHHH
T ss_pred             cCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh-----------cCCeEEEEechHHHHHHHHHHHH
Confidence            466 699999999999999999999999999999988887776541           36789999999999999999999


Q ss_pred             HHH
Q psy7786         242 YYC  244 (252)
Q Consensus       242 ~l~  244 (252)
                      +++
T Consensus       143 ~l~  145 (1104)
T 4ddu_A          143 KLA  145 (1104)
T ss_dssp             TTS
T ss_pred             Hhh
Confidence            876

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=98.65  E-value=9.6e-08  Score=87.96  Aligned_cols=86  Identities=21%  Similarity=0.079  Sum_probs=72.8

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhhhhcC------CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEE
Q psy7786         153 ESLVRALEAKGIKKPTPIQVQGIPAALSG------RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLII  226 (252)
Q Consensus       153 ~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~------~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf  226 (252)
                      +.+.+.+...++ .|++.|..+++....+      .+.+++++||+|||.+++++++..+..           +.+++|+
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~-----------g~qvlvl  423 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA-----------GFQTAFM  423 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH-----------TSCEEEE
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc-----------CCeEEEE
Confidence            444555677888 8999999999988765      589999999999999999999987643           4689999


Q ss_pred             cCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         227 CPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       227 ~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      +||+++|.|+++.++++.+.++++
T Consensus       424 aPtr~La~Q~~~~l~~~~~~~gi~  447 (780)
T 1gm5_A          424 VPTSILAIQHYRRTVESFSKFNIH  447 (780)
T ss_dssp             CSCHHHHHHHHHHHHHHHTCSSCC
T ss_pred             eCcHHHHHHHHHHHHHHhhhcCce
Confidence            999999999999999998866653

>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=98.61  E-value=2e-08  Score=95.86  Aligned_cols=92  Identities=16%  Similarity=0.099  Sum_probs=76.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      .|....++..+...+...+...|+++|..+++.+..+++++++++||+|||.++.++++..+..           +.+++
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~-----------g~rvl  231 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN-----------KQRVI  231 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT-----------TCEEE
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc-----------CCeEE
Confidence            4555666666655556666678999999999999999999999999999999999999876632           56899


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhhC
Q psy7786         225 IICPSRELARQTHDIIQYYCAAL  247 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~~~~  247 (252)
                      |.+|||++|.|+++.++++...+
T Consensus       232 vl~PtraLa~Q~~~~l~~~~~~V  254 (1108)
T 3l9o_A          232 YTSPIKALSNQKYRELLAEFGDV  254 (1108)
T ss_dssp             EEESSHHHHHHHHHHHHHHTSSE
T ss_pred             EEcCcHHHHHHHHHHHHHHhCCc
Confidence            99999999999999998876533

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=98.60  E-value=1e-07  Score=74.05  Aligned_cols=79  Identities=24%  Similarity=0.161  Sum_probs=65.3

Q ss_pred             CCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHH-HHHHHH
Q psy7786         163 GIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ-THDIIQ  241 (252)
Q Consensus       163 ~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~-i~~~l~  241 (252)
                      ....|++.|..+++..+.++++++.++||+|||..++.+++..+......     ..+.++||+||++++++| +.+.++
T Consensus        30 ~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~-----~~~~~~lil~p~~~L~~q~~~~~~~  104 (216)
T 3b6e_A           30 PELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKA-----SEPGKVIVLVNKVLLVEQLFRKEFQ  104 (216)
T ss_dssp             CCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHT-----TCCCCEEEEESSHHHHHHHHHHTHH
T ss_pred             CCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccc-----cCCCcEEEEECHHHHHHHHHHHHHH
Confidence            34578999999999999999999999999999999999888766543211     235679999999999999 788888


Q ss_pred             HHHhh
Q psy7786         242 YYCAA  246 (252)
Q Consensus       242 ~l~~~  246 (252)
                      ++...
T Consensus       105 ~~~~~  109 (216)
T 3b6e_A          105 PFLKK  109 (216)
T ss_dssp             HHHTT
T ss_pred             HHhcc
Confidence            87654

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

Probab=98.52  E-value=2.2e-07  Score=87.70  Aligned_cols=82  Identities=20%  Similarity=0.201  Sum_probs=67.5

Q ss_pred             CCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         163 GIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       163 ~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      +...|+++|..+++..+.|+++++.++||+|||.+++++++..+....      ...+.++||++||++++.|+.+.+++
T Consensus       245 ~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~------~~~~~~vLvl~Pt~~L~~Q~~~~~~~  318 (936)
T 4a2w_A          245 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP------AGRKAKVVFLATKVPVYEQQKNVFKH  318 (936)
T ss_dssp             ---CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCC------SSCCCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhcc------ccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            466899999999999999999999999999999999999886544321      12256799999999999999999999


Q ss_pred             HHhhCCCC
Q psy7786         243 YCAALPIG  250 (252)
Q Consensus       243 l~~~~~i~  250 (252)
                      +.+..+++
T Consensus       319 ~~~~~~~~  326 (936)
T 4a2w_A          319 HFERQGYS  326 (936)
T ss_dssp             HHHTTTCC
T ss_pred             HhcccCce
Confidence            98866543

>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=98.51  E-value=5.6e-08  Score=84.50  Aligned_cols=68  Identities=21%  Similarity=0.211  Sum_probs=58.5

Q ss_pred             CCCCChHHHHhhhhhhhcCCcE-EEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         163 GIKKPTPIQVQGIPAALSGRDI-IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       163 ~~~~p~~iQ~~~~p~~~~~~~~-~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      |+..|+++|. .+|..+.+++. +++++||+|||.+|++|++......          +.++||++|||++|.|+++.++
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~----------~~~~lvl~Ptr~La~Q~~~~l~   69 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLR----------RLRTLILAPTRVVAAEMEEALR   69 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT----------TCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc----------CCcEEEECCCHHHHHHHHHHhc
Confidence            4567888886 68999999888 8888999999999999999876542          4679999999999999999875

>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=98.49  E-value=2.7e-07  Score=83.17  Aligned_cols=65  Identities=25%  Similarity=0.238  Sum_probs=55.8

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      .+|+  |+.-+||+|||+++.+|++-..+.           |.++.|++||++||.|-.+++..+.+.+|  +++.+.+.
T Consensus        88 ~~G~--iaEM~TGEGKTLva~lp~~lnAL~-----------G~~vhVvT~ndyLA~rdae~m~~l~~~Lg--lsvg~i~~  152 (822)
T 3jux_A           88 HEGK--VAEMKTGEGKTLAATMPIYLNALI-----------GKGVHLVTVNDYLARRDALWMGPVYLFLG--LRVGVINS  152 (822)
T ss_dssp             HTTC--EEECCTTSCHHHHTHHHHHHHHTT-----------SSCEEEEESSHHHHHHHHHHHHHHHHHTT--CCEEEEET
T ss_pred             hCCC--hhhccCCCCccHHHHHHHHHHHhc-----------CCceEEEeccHHHHHhHHHHHHHHHHHhC--CEEEEEcC
Confidence            3555  788999999999999999855443           55699999999999999999999999999  77777776

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=98.47  E-value=6.4e-08  Score=87.18  Aligned_cols=82  Identities=20%  Similarity=0.168  Sum_probs=63.3

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcC
Q psy7786         149 MKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICP  228 (252)
Q Consensus       149 ~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~  228 (252)
                      +++++...+.+... ...|+++|...+|..+.++++++.++||+|||.+|++|++..+...          +.++||++|
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~----------~~~vLvl~P  223 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR----------RLRTLILAP  223 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT----------TCCEEEEES
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC----------CCeEEEEcC
Confidence            34555554444332 3678888888899999999999999999999999999999887652          468999999


Q ss_pred             cHHHHHHHHHHHH
Q psy7786         229 SRELARQTHDIIQ  241 (252)
Q Consensus       229 tr~~a~~i~~~l~  241 (252)
                      ||++|.|+++.++
T Consensus       224 treLa~Qi~~~l~  236 (618)
T 2whx_A          224 TRVVAAEMEEALR  236 (618)
T ss_dssp             SHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHhc
Confidence            9999999998875

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=98.39  E-value=8e-08  Score=87.24  Aligned_cols=68  Identities=16%  Similarity=0.209  Sum_probs=57.6

Q ss_pred             CChHHHH-----hhhhhhh------cCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHH
Q psy7786         166 KPTPIQV-----QGIPAAL------SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR  234 (252)
Q Consensus       166 ~p~~iQ~-----~~~p~~~------~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~  234 (252)
                      .|+++|.     .++|..+      .+++++++++||+|||.+|+++++..+...          +.+++|++|||++|.
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~----------~~~~lilaPTr~La~  284 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQK----------RLRTAVLAPTRVVAA  284 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHT----------TCCEEEEESSHHHHH
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC----------CCcEEEEccHHHHHH
Confidence            7999999     8898888      899999999999999999999999876542          468999999999999


Q ss_pred             HHHHHHHHH
Q psy7786         235 QTHDIIQYY  243 (252)
Q Consensus       235 ~i~~~l~~l  243 (252)
                      |+++.++.+
T Consensus       285 Q~~~~l~~~  293 (673)
T 2wv9_A          285 EMAEALRGL  293 (673)
T ss_dssp             HHHHHTTTS
T ss_pred             HHHHHHhcC
Confidence            999988643

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

Probab=98.33  E-value=4.2e-07  Score=83.08  Aligned_cols=76  Identities=24%  Similarity=0.190  Sum_probs=66.0

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHH-HHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT-HDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i-~~~l~~l~  244 (252)
                      .|++.|..+++.++.++++++.++||+|||.+++++++..+......     ..+.++||++|+++++.|+ .+.+++++
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~-----~~~~~vlvl~P~~~L~~Q~~~~~l~~~~   81 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKA-----SEPGKVIVLVNKVLLVEQLFRKEFQPFL   81 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHH-----TCCCCBCCEESCSHHHHHHHHHTHHHHH
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccc-----CCCCeEEEEECCHHHHHHHHHHHHHHHc
Confidence            68999999999999999999999999999999999999877654311     1235799999999999999 99999988


Q ss_pred             hh
Q psy7786         245 AA  246 (252)
Q Consensus       245 ~~  246 (252)
                      ..
T Consensus        82 ~~   83 (699)
T 4gl2_A           82 KK   83 (699)
T ss_dssp             TT
T ss_pred             Cc
Confidence            65

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.31  E-value=2.1e-06  Score=77.43  Aligned_cols=75  Identities=19%  Similarity=0.191  Sum_probs=62.1

Q ss_pred             CChHHHHhhh----hhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGI----PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       166 ~p~~iQ~~~~----p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .|.+-|...+    .+...|+++++.++||+|||.+|++|.+..+...          +.+++|.+||++++.|+.+.++
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~----------~~kvli~t~T~~l~~Qi~~el~   72 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER----------KLKVLYLVRTNSQEEQVIKELR   72 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH----------TCEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc----------CCeEEEECCCHHHHHHHHHHHH
Confidence            4566677666    4556899999999999999999999999887642          4689999999999999999999


Q ss_pred             HHHhhCCCC
Q psy7786         242 YYCAALPIG  250 (252)
Q Consensus       242 ~l~~~~~i~  250 (252)
                      .+....+++
T Consensus        73 ~l~~~~~~~   81 (620)
T 4a15_A           73 SLSSTMKIR   81 (620)
T ss_dssp             HHHHHSCCC
T ss_pred             HHhhccCeE
Confidence            998876554

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=98.28  E-value=3.8e-06  Score=80.70  Aligned_cols=75  Identities=28%  Similarity=0.239  Sum_probs=61.9

Q ss_pred             CCCCChHHHHhhhhhhhc----CC--cEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHH
Q psy7786         163 GIKKPTPIQVQGIPAALS----GR--DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT  236 (252)
Q Consensus       163 ~~~~p~~iQ~~~~p~~~~----~~--~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i  236 (252)
                      ++ .|++.|..+++..+.    ++  +.+++++||+|||..++.+.+..+.           .+.+++|++||+++|.|.
T Consensus       601 ~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~-----------~g~~vlvlvPt~~La~Q~  668 (1151)
T 2eyq_A          601 PF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD-----------NHKQVAVLVPTTLLAQQH  668 (1151)
T ss_dssp             CS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT-----------TTCEEEEECSSHHHHHHH
T ss_pred             CC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHH-----------hCCeEEEEechHHHHHHH
Confidence            44 479999999998876    55  8999999999999998888766432           256899999999999999


Q ss_pred             HHHHHHHHhhCCC
Q psy7786         237 HDIIQYYCAALPI  249 (252)
Q Consensus       237 ~~~l~~l~~~~~i  249 (252)
                      ++.+++....+++
T Consensus       669 ~~~~~~~~~~~~i  681 (1151)
T 2eyq_A          669 YDNFRDRFANWPV  681 (1151)
T ss_dssp             HHHHHHHSTTTTC
T ss_pred             HHHHHHHhhcCCC
Confidence            9999877665543

>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=98.28  E-value=9.5e-07  Score=77.57  Aligned_cols=105  Identities=15%  Similarity=0.165  Sum_probs=65.7

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      ..|++.+++.+||+|||+..+ .++..+....        ...++|||+|+ +|+.|..++++++..    .+++..+.|
T Consensus        54 ~~~~~~ilad~~GlGKT~~ai-~~i~~~~~~~--------~~~~~LIv~P~-~l~~qw~~e~~~~~~----~~~v~~~~g  119 (500)
T 1z63_A           54 KLGFGICLADDMGLGKTLQTI-AVFSDAKKEN--------ELTPSLVICPL-SVLKNWEEELSKFAP----HLRFAVFHE  119 (500)
T ss_dssp             HTTCCEEECCCTTSCHHHHHH-HHHHHHHHTT--------CCSSEEEEECS-TTHHHHHHHHHHHCT----TSCEEECSS
T ss_pred             hCCCCEEEEeCCCCcHHHHHH-HHHHHHHhcC--------CCCCEEEEccH-HHHHHHHHHHHHHCC----CceEEEEec
Confidence            468899999999999999864 4444444322        23469999995 588998888887643    256666666


Q ss_pred             CcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          85 GVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        85 ~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      +...     ......++   +.   ++++.+.....    .......++|.||+
T Consensus       120 ~~~~-----~~~~~~~i---vi---~t~~~l~~~~~----l~~~~~~~vIvDEa  158 (500)
T 1z63_A          120 DRSK-----IKLEDYDI---IL---TTYAVLLRDTR----LKEVEWKYIVIDEA  158 (500)
T ss_dssp             STTS-----CCGGGSSE---EE---EEHHHHTTCHH----HHTCCEEEEEEETG
T ss_pred             Cchh-----ccccCCcE---EE---eeHHHHhccch----hcCCCcCEEEEeCc
Confidence            6421     11122344   22   23666554322    22234678888986

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

Probab=98.28  E-value=2.1e-06  Score=81.35  Aligned_cols=72  Identities=19%  Similarity=0.146  Sum_probs=62.8

Q ss_pred             CCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         162 KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       162 ~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .++ .|+++|..+++.+..+++++++++||+|||..+.++++..+.           .+.++||++|||+++.|+++.++
T Consensus        83 ~~f-~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~-----------~g~rvL~l~PtkaLa~Q~~~~l~  150 (1010)
T 2xgj_A           83 YPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK-----------NKQRVIYTSPIKALSNQKYRELL  150 (1010)
T ss_dssp             CSS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH-----------TTCEEEEEESSHHHHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc-----------cCCeEEEECChHHHHHHHHHHHH
Confidence            344 499999999999999999999999999999999888876552           25689999999999999999998


Q ss_pred             HHHh
Q psy7786         242 YYCA  245 (252)
Q Consensus       242 ~l~~  245 (252)
                      ++..
T Consensus       151 ~~~~  154 (1010)
T 2xgj_A          151 AEFG  154 (1010)
T ss_dssp             HHHS
T ss_pred             HHhC
Confidence            8765

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=98.26  E-value=2.2e-06  Score=69.65  Aligned_cols=70  Identities=24%  Similarity=0.186  Sum_probs=59.2

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .|++.|..+++..+.+.+.++++++|+|||..++......+..          ...++||++||+++++|..+.+++++.
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~----------~~~~~lil~Pt~~L~~q~~~~l~~~~~  182 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN----------YEGKILIIVPTTALTTQMADDFVDYRL  182 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH----------CSSEEEEECSSHHHHHHHHHHHHHHTS
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc----------CCCeEEEEECCHHHHHHHHHHHHHhcc
Confidence            7899999999998888888999999999999987766654432          134799999999999999999998754

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

Probab=98.18  E-value=2.9e-06  Score=74.70  Aligned_cols=70  Identities=24%  Similarity=0.186  Sum_probs=61.0

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .|++.|..+++..+.+.+.+++++||+|||..++.++...+..          ...++||++||++++.|..+.+++++.
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~----------~~~~vlvl~P~~~L~~Q~~~~~~~~~~  182 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN----------YEGKILIIVPTTALTTQMADDFVDYRL  182 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH----------CSSEEEEEESSHHHHHHHHHHHHHTTS
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC----------CCCeEEEEECcHHHHHHHHHHHHHhhc
Confidence            7899999999999999999999999999999998877765542          134899999999999999999988744

>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=98.14  E-value=1.1e-06  Score=83.08  Aligned_cols=110  Identities=15%  Similarity=0.055  Sum_probs=65.5

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCc
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGV   86 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~   86 (252)
                      +.+++++.+||+|||..++..+...+....         .-++|||+|+ .|+.|..+.+.+.   .+  +.+..+.|+.
T Consensus       170 ~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~---------~~rvLIVvP~-sLl~Qw~~E~~~~---f~--l~v~v~~~~~  234 (968)
T 3dmq_A          170 APRVLLADEVGLGKTIEAGMILHQQLLSGA---------AERVLIIVPE-TLQHQWLVEMLRR---FN--LRFALFDDER  234 (968)
T ss_dssp             SCEEEECCCTTSCHHHHHHHHHHHHHHTSS---------CCCEEEECCT-TTHHHHHHHHHHH---SC--CCCEECCHHH
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHHhCC---------CCeEEEEeCH-HHHHHHHHHHHHH---hC--CCEEEEccch
Confidence            557899999999999998777766553322         2369999999 9998887777432   24  4555554442


Q ss_pred             ccCcchhhhh---hcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          87 PMNQSLDVIK---KGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        87 ~~~~~~~~l~---~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      ... ....-.   ...++   +.   +++..+................++|.||+
T Consensus       235 ~~~-~~~~~~~~~~~~dI---vI---~T~~~L~~~~~~~~~l~~~~~dlVIvDEA  282 (968)
T 3dmq_A          235 YAE-AQHDAYNPFDTEQL---VI---CSLDFARRSKQRLEHLCEAEWDLLVVDEA  282 (968)
T ss_dssp             HHH-HHHTTCSSSTTCSE---EE---ECHHHHHTSTTTTHHHHTSCCCEEEECCS
T ss_pred             hhh-hhhhcccccccCCE---EE---EcHHHHhhCHHHHHHhhhcCCCEEEehhh
Confidence            111 100000   11222   11   23555554444434444455788999996

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.14  E-value=1.8e-06  Score=76.90  Aligned_cols=70  Identities=21%  Similarity=0.007  Sum_probs=58.6

Q ss_pred             CChHHHHhhhh----hhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIP----AALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       166 ~p~~iQ~~~~p----~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .|.+.|..++.    +...++++++.++||+|||.+|++|.+.              .+.+++|.+||+++++|+.+.++
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~--------------~~~~v~i~~pt~~l~~q~~~~~~   68 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE--------------VKPKVLFVVRTHNEFYPIYRDLT   68 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH--------------HCSEEEEEESSGGGHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh--------------CCCeEEEEcCCHHHHHHHHHHHH
Confidence            46777877664    4557899999999999999999999996              15689999999999999999998


Q ss_pred             HHHhhCCC
Q psy7786         242 YYCAALPI  249 (252)
Q Consensus       242 ~l~~~~~i  249 (252)
                      ++.+..++
T Consensus        69 ~l~~~~~~   76 (551)
T 3crv_A           69 KIREKRNI   76 (551)
T ss_dssp             TCCCSSCC
T ss_pred             HHhhhcCc
Confidence            87665544

>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=98.13  E-value=1.8e-06  Score=74.72  Aligned_cols=56  Identities=21%  Similarity=0.293  Sum_probs=48.9

Q ss_pred             hhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         177 AALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       177 ~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      ..+.|++++++++||+|||.+|++|++..+...          +.+++|++|||++|.|+++.++.
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~----------~~~~lil~Ptr~La~Q~~~~l~~   59 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR----------RLRTLVLAPTRVVLSEMKEAFHG   59 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT----------TCCEEEEESSHHHHHHHHHHTTT
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc----------CCeEEEEcchHHHHHHHHHHHhc
Confidence            356789999999999999999999999876642          46899999999999999998864

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

Probab=98.12  E-value=2.9e-06  Score=80.38  Aligned_cols=68  Identities=19%  Similarity=0.159  Sum_probs=59.3

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      .|+++|..+++.++.++++++.++||+|||.++.+++.....           .+.++||++|+|+++.|+++.++++.
T Consensus        39 ~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~-----------~g~~vlvl~PtraLa~Q~~~~l~~~~  106 (997)
T 4a4z_A           39 ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR-----------NMTKTIYTSPIKALSNQKFRDFKETF  106 (997)
T ss_dssp             CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH-----------TTCEEEEEESCGGGHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh-----------cCCeEEEEeCCHHHHHHHHHHHHHHc
Confidence            479999999999999999999999999999998887765432           25689999999999999999998753

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=98.11  E-value=9.8e-06  Score=63.95  Aligned_cols=71  Identities=17%  Similarity=0.066  Sum_probs=58.5

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      ...+++|...++....|+++++.++||+|||..+..+++........      ....++++.+|+|+++.++++.+.
T Consensus        60 ~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~------~~~~~~l~~~p~~~la~q~~~~~~  130 (235)
T 3llm_A           60 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR------AAECNIVVTQPRRISAVSVAERVA  130 (235)
T ss_dssp             SGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC------GGGCEEEEEESSHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC------CCceEEEEeccchHHHHHHHHHHH
Confidence            34688999999999999999999999999999888888776554321      124589999999999999987765

>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=98.10  E-value=2e-06  Score=77.34  Aligned_cols=63  Identities=21%  Similarity=0.180  Sum_probs=51.9

Q ss_pred             cccCCCcEEEEcCCCchHH--HHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           3 TYRNSRDIIGIAFTGSGKT--LVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT--~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      .+++++++++++++|||||  ++++++.+..+..         ..+.++++++||+++|.++.+.+...+..++
T Consensus       160 ~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~---------~~~~~vll~APTg~AA~~L~e~~~~~~~~l~  224 (608)
T 1w36_D          160 VALTRRISVISGGPGTGKTTTVAKLLAALIQMAD---------GERCRIRLAAPTGKAAARLTESLGKALRQLP  224 (608)
T ss_dssp             HHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS---------SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSS
T ss_pred             HHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh---------cCCCeEEEEeCChhHHHHHHHHHHHHHhcCC
Confidence            4567899999999999999  7788888865421         1356899999999999999998888777765

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

Probab=98.08  E-value=1.2e-05  Score=69.58  Aligned_cols=68  Identities=19%  Similarity=0.170  Sum_probs=60.0

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      .|.+.|..+++..+.+ +.++.+++|+|||..++.+++..+..          .+.++||+||+++++.|..+.++++.
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~----------~~~~~liv~P~~~L~~q~~~~~~~~~   76 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK----------YGGKVLMLAPTKPLVLQHAESFRRLF   76 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH----------SCSCEEEECSSHHHHHHHHHHHHHHB
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc----------CCCeEEEEECCHHHHHHHHHHHHHHh
Confidence            5889999999999998 99999999999999999988876552          25579999999999999999998775

>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=98.07  E-value=2.9e-06  Score=73.83  Aligned_cols=56  Identities=18%  Similarity=0.197  Sum_probs=48.4

Q ss_pred             hhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         176 PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       176 p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .....+++++++++||+|||.+|++|++..+...          +.++||++|||++|.|+++.++
T Consensus        16 ~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~----------~~~~lvl~Ptr~La~Q~~~~l~   71 (459)
T 2z83_A           16 NMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ----------RLRTAVLAPTRVVAAEMAEALR   71 (459)
T ss_dssp             GGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHT----------TCCEEEEECSHHHHHHHHHHTT
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhC----------CCcEEEECchHHHHHHHHHHhc
Confidence            3455678999999999999999999999877642          4679999999999999999875

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

Probab=98.00  E-value=8.6e-06  Score=70.90  Aligned_cols=64  Identities=25%  Similarity=0.223  Sum_probs=57.1

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      .|++.|..+++..+.+.+.+++++||+|||..++.++...              +.++||+||+++++.|..+.++++
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~--------------~~~~Lvl~P~~~L~~Q~~~~~~~~  156 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL--------------STPTLIVVPTLALAEQWKERLGIF  156 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH--------------CSCEEEEESSHHHHHHHHHHGGGG
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc--------------CCCEEEEECCHHHHHHHHHHHHhC
Confidence            6899999999999999999999999999999988877642              346999999999999999998875

>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=97.97  E-value=2.5e-05  Score=72.11  Aligned_cols=90  Identities=19%  Similarity=0.156  Sum_probs=69.9

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCc
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP  221 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~  221 (252)
                      ...|.++++++.+.+.+...+ ..|+.+|...++..+.+ ++++++++||+|||.  ++|.+.......      ...+.
T Consensus        71 ~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~------~~~g~  141 (773)
T 2xau_A           71 INPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMP------HLENT  141 (773)
T ss_dssp             BCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCG------GGGTC
T ss_pred             CCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccc------cCCCc
Confidence            457999999999999998887 78999999999887754 679999999999999  466552211110      11256


Q ss_pred             EEEEEcCcHHHHHHHHHHHH
Q psy7786         222 YGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       222 ~~LIf~~tr~~a~~i~~~l~  241 (252)
                      ++++.+|+|++|.++++.+.
T Consensus       142 ~ilvl~P~r~La~q~~~~l~  161 (773)
T 2xau_A          142 QVACTQPRRVAAMSVAQRVA  161 (773)
T ss_dssp             EEEEEESCHHHHHHHHHHHH
T ss_pred             eEEecCchHHHHHHHHHHHH
Confidence            79999999999999987653

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.97  E-value=1.1e-05  Score=71.59  Aligned_cols=64  Identities=16%  Similarity=0.099  Sum_probs=52.9

Q ss_pred             CChHHHHhhhh----hhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIP----AALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       166 ~p~~iQ~~~~p----~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .|.+.|..++.    +...++++++.++||+|||.+|++|.+..              +.+++|.+||+++++|+.+.++
T Consensus         7 ~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~--------------~~~~~~~~~t~~l~~q~~~~~~   72 (540)
T 2vl7_A            7 QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL--------------KKKVLIFTRTHSQLDSIYKNAK   72 (540)
T ss_dssp             --CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH--------------TCEEEEEESCHHHHHHHHHHHG
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC--------------CCcEEEEcCCHHHHHHHHHHHH
Confidence            67888888754    45678999999999999999999998742              4579999999999999998887


Q ss_pred             HH
Q psy7786         242 YY  243 (252)
Q Consensus       242 ~l  243 (252)
                      ++
T Consensus        73 ~l   74 (540)
T 2vl7_A           73 LL   74 (540)
T ss_dssp             GG
T ss_pred             hc
Confidence            64

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=97.94  E-value=7.2e-06  Score=70.74  Aligned_cols=51  Identities=16%  Similarity=0.208  Sum_probs=44.7

Q ss_pred             CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         181 GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       181 ~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      +++++++++||+|||.+++++++..+...          +.+++|++|||++|+|+++.++
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~----------g~~~lvl~Pt~~La~Q~~~~~~   52 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKK----------RLRTVILAPTRVVASEMYEALR   52 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHT----------TCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhC----------CCCEEEECcHHHHHHHHHHHhC
Confidence            68899999999999999999999766542          4689999999999999998774

>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=97.87  E-value=3e-05  Score=61.28  Aligned_cols=65  Identities=25%  Similarity=0.209  Sum_probs=55.4

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ..|++.|..++...+.+.+.++++++|+|||..++......              +.+++|++|+++++.|+.+.++++
T Consensus        92 ~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~--------------~~~~liv~P~~~L~~q~~~~~~~~  156 (237)
T 2fz4_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL--------------STPTLIVVPTLALAEQWKERLGIF  156 (237)
T ss_dssp             CCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS--------------CSCEEEEESSHHHHHHHHHHHGGG
T ss_pred             CCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc--------------CCCEEEEeCCHHHHHHHHHHHHhC
Confidence            37899999999999988899999999999999877665431              346999999999999999988764

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=97.70  E-value=1.7e-05  Score=71.47  Aligned_cols=59  Identities=19%  Similarity=-0.009  Sum_probs=46.9

Q ss_pred             HHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         170 IQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       170 iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .|...++....+++++++++||+|||.++.++++.              .+.+++|++|||++|.|+++.+.+
T Consensus       221 ~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~--------------~g~~vLVl~PTReLA~Qia~~l~~  279 (666)
T 3o8b_A          221 DNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA--------------QGYKVLVLNPSVAATLGFGAYMSK  279 (666)
T ss_dssp             CCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH--------------TTCCEEEEESCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH--------------CCCeEEEEcchHHHHHHHHHHHHH
Confidence            34444444557789999999999999999988774              145799999999999999987654

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

Probab=97.47  E-value=0.0002  Score=66.47  Aligned_cols=71  Identities=18%  Similarity=0.169  Sum_probs=49.2

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      .+|++.+++.++|+|||+..+..+...+....        ..-.+|||+| ..|..|-.+.++++.   + ++++.+..|
T Consensus       253 ~~~~~~ILademGlGKT~~ai~~i~~l~~~~~--------~~~~~LIV~P-~sll~qW~~E~~~~~---p-~~~v~~~~g  319 (800)
T 3mwy_W          253 SKGDNGILADEMGLGKTVQTVAFISWLIFARR--------QNGPHIIVVP-LSTMPAWLDTFEKWA---P-DLNCICYMG  319 (800)
T ss_dssp             TTTCCEEECCCTTSSTTHHHHHHHHHHHHHHS--------CCSCEEEECC-TTTHHHHHHHHHHHS---T-TCCEEECCC
T ss_pred             hcCCCEEEEeCCCcchHHHHHHHHHHHHHhcC--------CCCCEEEEEC-chHHHHHHHHHHHHC---C-CceEEEEeC
Confidence            47889999999999999887655544333322        1334899999 667778777776664   2 367777777


Q ss_pred             Cccc
Q psy7786          85 GVPM   88 (252)
Q Consensus        85 ~~~~   88 (252)
                      +...
T Consensus       320 ~~~~  323 (800)
T 3mwy_W          320 NQKS  323 (800)
T ss_dssp             SSHH
T ss_pred             CHHH
Confidence            6443

>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=97.33  E-value=0.0013  Score=59.58  Aligned_cols=73  Identities=27%  Similarity=0.278  Sum_probs=62.7

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|..+|....-++..|+  +....||+|||+.+.+|.+-..+.           +..+.|+++|+.||.+-++++..+.
T Consensus        74 ~r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~-----------G~~vhVvT~ndyLA~rdae~m~~l~  140 (822)
T 3jux_A           74 MRPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI-----------GKGVHLVTVNDYLARRDALWMGPVY  140 (822)
T ss_dssp             CCCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT-----------SSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc-----------CCceEEEeccHHHHHhHHHHHHHHH
Confidence            368999998877777776  788899999999999998754432           5569999999999999999999999


Q ss_pred             hhCCCC
Q psy7786         245 AALPIG  250 (252)
Q Consensus       245 ~~~~i~  250 (252)
                      +.+|++
T Consensus       141 ~~Lgls  146 (822)
T 3jux_A          141 LFLGLR  146 (822)
T ss_dssp             HHTTCC
T ss_pred             HHhCCE
Confidence            999975

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=97.32  E-value=7.8e-05  Score=66.79  Aligned_cols=77  Identities=19%  Similarity=0.147  Sum_probs=45.4

Q ss_pred             CChHHHHhhhhhhhc----C-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHH-HH
Q psy7786         166 KPTPIQVQGIPAALS----G-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH-DI  239 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~----~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~-~~  239 (252)
                      .|.+.|..+++.++.    + ++++++++||+|||... +.++..+...... ......+.++||+|||++++.|.. +.
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~-~~~~~~l~~~~~~-~~~~~~~~~vlil~P~~~L~~Q~~~~~  255 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVA-FQISWKLWSARWN-RTGDYRKPRILFLADRNVLVDDPKDKT  255 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHHHHTTCC-SSCSSSCCCEEEEEC-----------C
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHH-HHHHHHHHhcccc-cccccCCCeEEEEeCCHHHHHHHHHHH
Confidence            688999999988775    4 66899999999999984 4555555442100 000113578999999999999998 76


Q ss_pred             HHHHH
Q psy7786         240 IQYYC  244 (252)
Q Consensus       240 l~~l~  244 (252)
                      ++.++
T Consensus       256 ~~~~~  260 (590)
T 3h1t_A          256 FTPFG  260 (590)
T ss_dssp             CTTTC
T ss_pred             HHhcc
Confidence            66554

>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=97.21  E-value=0.00092  Score=60.52  Aligned_cols=74  Identities=22%  Similarity=0.191  Sum_probs=50.1

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      ..++..+++.++|+|||+..+..+...+......    .....++|||+|+ +|+.|-.++++++... .  +.+..++|
T Consensus        77 ~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~----~p~~~~~LiV~P~-sll~qW~~E~~~~~~~-~--~~~~~~~~  148 (644)
T 1z3i_X           77 ENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDC----KPEIDKVIVVSPS-SLVRNWYNEVGKWLGG-R--VQPVAIDG  148 (644)
T ss_dssp             TTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTS----SCSCSCEEEEECH-HHHHHHHHHHHHHHGG-G--CCEEEECS
T ss_pred             cCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccc----cCCCCcEEEEecH-HHHHHHHHHHHHHcCC-C--eeEEEEeC
Confidence            4567899999999999998776665544322111    0113358999997 7888888888877654 2  55666666


Q ss_pred             Cc
Q psy7786          85 GV   86 (252)
Q Consensus        85 ~~   86 (252)
                      |.
T Consensus       149 g~  150 (644)
T 1z3i_X          149 GS  150 (644)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=97.16  E-value=0.00024  Score=67.41  Aligned_cols=71  Identities=21%  Similarity=0.103  Sum_probs=56.0

Q ss_pred             CChHHHHhhhhhhhc--------------CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHH
Q psy7786         166 KPTPIQVQGIPAALS--------------GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE  231 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~--------------~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~  231 (252)
                      .|.+.|..+++.++.              +++.++.+++|+|||... ++++..+.. .       ....++||+||+++
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~-~-------~~~~rvLvlvpr~e  341 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATE-L-------DFIDKVFFVVDRKD  341 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTT-C-------TTCCEEEEEECGGG
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHh-c-------CCCceEEEEeCcHH
Confidence            489999999988764              368999999999999986 555543321 1       22468999999999


Q ss_pred             HHHHHHHHHHHHHh
Q psy7786         232 LARQTHDIIQYYCA  245 (252)
Q Consensus       232 ~a~~i~~~l~~l~~  245 (252)
                      |+.|+.+.+++++.
T Consensus       342 L~~Q~~~~f~~f~~  355 (1038)
T 2w00_A          342 LDYQTMKEYQRFSP  355 (1038)
T ss_dssp             CCHHHHHHHHTTST
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999887764

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=97.11  E-value=0.00048  Score=62.55  Aligned_cols=57  Identities=19%  Similarity=0.110  Sum_probs=43.1

Q ss_pred             hhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         173 QGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       173 ~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ......+.+++++++++||+|||.    +.+..+...           .++++.+|||++|.|+++.+++++
T Consensus       147 ~p~ar~l~rk~vlv~apTGSGKT~----~al~~l~~~-----------~~gl~l~PtR~LA~Qi~~~l~~~g  203 (677)
T 3rc3_A          147 YPDARAMQRKIIFHSGPTNSGKTY----HAIQKYFSA-----------KSGVYCGPLKLLAHEIFEKSNAAG  203 (677)
T ss_dssp             CHHHHTSCCEEEEEECCTTSSHHH----HHHHHHHHS-----------SSEEEEESSHHHHHHHHHHHHHTT
T ss_pred             CHHHHhcCCCEEEEEcCCCCCHHH----HHHHHHHhc-----------CCeEEEeCHHHHHHHHHHHHHhcC
Confidence            334456789999999999999998    333333332           235889999999999999988753

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=97.02  E-value=0.0013  Score=59.18  Aligned_cols=73  Identities=22%  Similarity=0.201  Sum_probs=59.6

Q ss_pred             hHHHHhhhhhhhcCCcEEEEccCCCchh--HHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         168 TPIQVQGIPAALSGRDIIGIAFTGSGKT--LVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       168 ~~iQ~~~~p~~~~~~~~~~~~~~g~gKt--~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      ++.|..+++..+.++.+++.+++|+|||  ..++++.+..+..         ..+.++++.+||++.|.++.+.+...+.
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~---------~~~~~vll~APTg~AA~~L~e~~~~~~~  221 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD---------GERCRIRLAAPTGKAAARLTESLGKALR  221 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS---------SCCCCEEEEBSSHHHHHHHHHHHTHHHH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh---------cCCCeEEEEeCChhHHHHHHHHHHHHHh
Confidence            6789999999999999999999999999  5677777654311         1245799999999999999999988777


Q ss_pred             hCCC
Q psy7786         246 ALPI  249 (252)
Q Consensus       246 ~~~i  249 (252)
                      .+++
T Consensus       222 ~l~l  225 (608)
T 1w36_D          222 QLPL  225 (608)
T ss_dssp             HSSC
T ss_pred             cCCC
Confidence            6653

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

Probab=96.28  E-value=0.0059  Score=53.30  Aligned_cols=73  Identities=22%  Similarity=0.294  Sum_probs=53.0

Q ss_pred             CChHHHHhhhhhh----hcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAA----LSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       166 ~p~~iQ~~~~p~~----~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .+.+.|..++..+    ..+.+.++..++|.|||...+ ..+..+...        ....++||+||+ .++.|..++++
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai-~~i~~~~~~--------~~~~~~LIv~P~-~l~~qw~~e~~  106 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKE--------NELTPSLVICPL-SVLKNWEEELS  106 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHT--------TCCSSEEEEECS-TTHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHH-HHHHHHHhc--------CCCCCEEEEccH-HHHHHHHHHHH
Confidence            4778888887655    357889999999999999854 344444322        123569999995 58899999999


Q ss_pred             HHHhhCC
Q psy7786         242 YYCAALP  248 (252)
Q Consensus       242 ~l~~~~~  248 (252)
                      ++...+.
T Consensus       107 ~~~~~~~  113 (500)
T 1z63_A          107 KFAPHLR  113 (500)
T ss_dssp             HHCTTSC
T ss_pred             HHCCCce
Confidence            8875443

>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=96.18  E-value=0.0092  Score=53.83  Aligned_cols=57  Identities=21%  Similarity=0.156  Sum_probs=40.4

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      +..++|.|+.|||||.+-+-=+.. +......      ..-+.|++++|+..|.++.+.+..+.
T Consensus        22 ~~~~lV~a~aGsGKT~~l~~ri~~-l~~~~~~------~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A           22 RSNLLVLAGAGSGKTRVLVHRIAW-LMSVENC------SPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHH-HHHTSCC------CGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHH-HHHhCCC------ChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            567899999999999654433333 3332110      12369999999999999999887764

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=95.55  E-value=0.023  Score=51.34  Aligned_cols=52  Identities=23%  Similarity=0.275  Sum_probs=36.3

Q ss_pred             CCCc-EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           6 NSRD-IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         6 ~g~d-~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      +.+| .+|++|.|||||.+-+ -++..+...          +.++|+.+||..-+.++.+.+..
T Consensus       203 ~~~~~~lI~GPPGTGKT~ti~-~~I~~l~~~----------~~~ILv~a~TN~AvD~i~erL~~  255 (646)
T 4b3f_X          203 SQKELAIIHGPPGTGKTTTVV-EIILQAVKQ----------GLKVLCCAPSNIAVDNLVERLAL  255 (646)
T ss_dssp             HCSSEEEEECCTTSCHHHHHH-HHHHHHHHT----------TCCEEEEESSHHHHHHHHHHHHH
T ss_pred             cCCCceEEECCCCCCHHHHHH-HHHHHHHhC----------CCeEEEEcCchHHHHHHHHHHHh
Confidence            3454 5899999999997643 333333332          45799999999988887766543

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=95.31  E-value=0.035  Score=51.49  Aligned_cols=55  Identities=15%  Similarity=0.051  Sum_probs=39.6

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      +++.-.++++|.|||||.+. .-++..+....         +.++|+++||..-+.++.+.+...
T Consensus       373 l~~~~~lI~GppGTGKT~~i-~~~i~~l~~~~---------~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          373 LQRPLSLIQGPPGTGKTVTS-ATIVYHLSKIH---------KDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             TTCSEEEEECSTTSSHHHHH-HHHHHHHHHHH---------CCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             hcCCCEEEECCCCCCHHHHH-HHHHHHHHhCC---------CCeEEEEcCcHHHHHHHHHHHHhh
Confidence            34555899999999999654 33444443322         346999999999999998877654

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=95.22  E-value=0.029  Score=50.51  Aligned_cols=54  Identities=20%  Similarity=0.115  Sum_probs=38.6

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      +++.-.++++|+|||||.+. .-++..+...         .+.++|+++||..-+.++.+.+..
T Consensus       193 l~~~~~li~GppGTGKT~~~-~~~i~~l~~~---------~~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          193 LQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ---------GNGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             HTCSEEEEECCTTSCHHHHH-HHHHHHHHTS---------SSCCEEEEESSHHHHHHHHHHHHT
T ss_pred             hcCCCeEEECCCCCCHHHHH-HHHHHHHHHc---------CCCeEEEEeCcHHHHHHHHHHHHh
Confidence            34556899999999999653 3344444321         245799999999999888777654

>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=95.16  E-value=0.034  Score=52.72  Aligned_cols=67  Identities=21%  Similarity=0.107  Sum_probs=49.7

Q ss_pred             CChHHHHhhhhhhhc--CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALS--GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~--~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .|.+.|..++...+.  +...+++.++|.|||...+..+...+..         +...++||+||+ .++.|..+.+.+
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~---------g~~~rvLIVvP~-sLl~Qw~~E~~~  221 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLS---------GAAERVLIIVPE-TLQHQWLVEMLR  221 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHT---------SSCCCEEEECCT-TTHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHh---------CCCCeEEEEeCH-HHHHHHHHHHHH
Confidence            578899998877665  3578888999999999875554433322         123479999999 999888877743

>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=95.12  E-value=0.043  Score=50.29  Aligned_cols=57  Identities=25%  Similarity=0.195  Sum_probs=40.2

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      +..++|.|..|||||.+-+-=+...+.....       ..-+.|+++.|+..|.++.+.+..+.
T Consensus        24 ~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~-------~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           24 EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV-------APWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTTCC-------CGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCHHHHHHHHHHHHHHhcCC-------CHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            4678999999999996654333333322111       12368999999999999988887764

>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=94.98  E-value=0.044  Score=49.72  Aligned_cols=57  Identities=18%  Similarity=0.073  Sum_probs=40.8

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      +..++|.|..|||||.+-+-=+...+.....       ..-+.|+++.|+..|.++.+.+....
T Consensus        15 ~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~-------~~~~IL~lTfT~~Aa~em~~Rl~~~l   71 (673)
T 1uaa_A           15 TGPCLVLAGAGSGKTRVITNKIAHLIRGCGY-------QARHIAAVTFTNKAAREMKERVGQTL   71 (673)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHHHHHHCC-------CGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEeCCCCChHHHHHHHHHHHHHhcCC-------CHHHeEEEeccHHHHHHHHHHHHHHc
Confidence            5678999999999996554434333332221       12369999999999999998887653

>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=94.72  E-value=0.047  Score=53.09  Aligned_cols=58  Identities=26%  Similarity=0.249  Sum_probs=41.5

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      .+++++|.|..|||||.+.+-=++..+.....     ..+.-+.|++++|+..|..+.+.+..
T Consensus        22 ~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~-----~~~~~~il~~Tft~~aa~e~~~ri~~   79 (1232)
T 3u4q_A           22 TGQDILVAAAAGSGKTAVLVERMIRKITAEEN-----PIDVDRLLVVTFTNASAAEMKHRIAE   79 (1232)
T ss_dssp             CSSCEEEEECTTCCHHHHHHHHHHHHHSCSSS-----CCCGGGEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCC-----CCCccceEEEeccHHHHHHHHHHHHH
Confidence            47899999999999997665445544433110     01233699999999999999888766

>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=94.60  E-value=0.054  Score=50.18  Aligned_cols=54  Identities=20%  Similarity=0.115  Sum_probs=38.5

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      +++.-.++++|+|||||.+. .-++..+...         .+.++|+++||..-|.++.+.+..
T Consensus       369 l~~~~~lI~GppGTGKT~ti-~~~i~~l~~~---------~~~~ilv~a~tn~A~~~l~~~l~~  422 (800)
T 2wjy_A          369 LQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ---------GNGPVLVCAPSNIAVDQLTEKIHQ  422 (800)
T ss_dssp             HTSSEEEEECCTTSCHHHHH-HHHHHHHHTT---------CSSCEEEEESSHHHHHHHHHHHHT
T ss_pred             ccCCeEEEEcCCCCCHHHHH-HHHHHHHHHc---------CCCcEEEEcCcHHHHHHHHHHHHH
Confidence            34556799999999999653 3344444331         245799999999999888776654

>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=94.49  E-value=0.074  Score=48.23  Aligned_cols=48  Identities=21%  Similarity=0.251  Sum_probs=37.0

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      +.++.+.||||||+++.- ++...   .         . .+|||+|+..+|.|.++.++.|.
T Consensus        30 ~~~l~g~tgs~kt~~~a~-~~~~~---~---------~-~~lvv~~~~~~A~ql~~el~~~~   77 (664)
T 1c4o_A           30 FVTLLGATGTGKTVTMAK-VIEAL---G---------R-PALVLAPNKILAAQLAAEFRELF   77 (664)
T ss_dssp             EEEEEECTTSCHHHHHHH-HHHHH---T---------C-CEEEEESSHHHHHHHHHHHHHHC
T ss_pred             cEEEEcCCCcHHHHHHHH-HHHHh---C---------C-CEEEEecCHHHHHHHHHHHHHHC
Confidence            567889999999976642 22222   1         1 38999999999999999999884

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=94.22  E-value=0.087  Score=45.49  Aligned_cols=48  Identities=10%  Similarity=0.090  Sum_probs=33.7

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII   66 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~   66 (252)
                      .+++.++.|||||. .+.-++..+....         ...+++++||...|..+.+.+
T Consensus        47 ~~li~G~aGTGKT~-ll~~~~~~l~~~~---------~~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           47 HVTINGPAGTGATT-LTKFIIEALISTG---------ETGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             EEEEECCTTSCHHH-HHHHHHHHHHHTT---------CCCEEEEESSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHH-HHHHHHHHHHhcC---------CceEEEecCcHHHHHHHHhhh
Confidence            89999999999994 3344455554432         135899999998887665543

>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=94.04  E-value=0.1  Score=46.40  Aligned_cols=50  Identities=16%  Similarity=0.149  Sum_probs=35.7

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD   64 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~   64 (252)
                      +++++.+++.++.|||||.. +..++..+..          .+.++++++||...|.++.+
T Consensus       201 ~~~~~~~~I~G~pGTGKTt~-i~~l~~~l~~----------~g~~Vl~~ApT~~Aa~~L~e  250 (574)
T 3e1s_A          201 LAGHRLVVLTGGPGTGKSTT-TKAVADLAES----------LGLEVGLCAPTGKAARRLGE  250 (574)
T ss_dssp             HTTCSEEEEECCTTSCHHHH-HHHHHHHHHH----------TTCCEEEEESSHHHHHHHHH
T ss_pred             HHhCCEEEEEcCCCCCHHHH-HHHHHHHHHh----------cCCeEEEecCcHHHHHHhHh
Confidence            45678899999999999954 2233333322          24568999999998877655

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=93.69  E-value=0.057  Score=46.29  Aligned_cols=42  Identities=21%  Similarity=0.247  Sum_probs=30.3

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      .++.++.|||||....    +.+ ..           -..+|++||++++.++.+.+.
T Consensus       164 ~~I~G~aGsGKTt~I~----~~~-~~-----------~~~lVlTpT~~aa~~l~~kl~  205 (446)
T 3vkw_A          164 VLVDGVPGCGKTKEIL----SRV-NF-----------EEDLILVPGRQAAEMIRRRAN  205 (446)
T ss_dssp             EEEEECTTSCHHHHHH----HHC-CT-----------TTCEEEESCHHHHHHHHHHHT
T ss_pred             EEEEcCCCCCHHHHHH----HHh-cc-----------CCeEEEeCCHHHHHHHHHHhh
Confidence            5789999999996542    211 11           135999999999988877664

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

Probab=93.34  E-value=0.14  Score=47.40  Aligned_cols=74  Identities=20%  Similarity=0.146  Sum_probs=51.3

Q ss_pred             CChHHHHhhhhhhh----cCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAAL----SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ  241 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~----~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~  241 (252)
                      .+.+.|..++..+.    .+.+.++..++|.|||...+..+.. +....       .....+||+|| ..++.|..++++
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~-l~~~~-------~~~~~~LIV~P-~sll~qW~~E~~  306 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISW-LIFAR-------RQNGPHIIVVP-LSTMPAWLDTFE  306 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHH-HHHHH-------SCCSCEEEECC-TTTHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHH-HHHhc-------CCCCCEEEEEC-chHHHHHHHHHH
Confidence            45667888876554    7789999999999999875443332 22221       12345899999 667888888888


Q ss_pred             HHHhhCC
Q psy7786         242 YYCAALP  248 (252)
Q Consensus       242 ~l~~~~~  248 (252)
                      ++++.+.
T Consensus       307 ~~~p~~~  313 (800)
T 3mwy_W          307 KWAPDLN  313 (800)
T ss_dssp             HHSTTCC
T ss_pred             HHCCCce
Confidence            8875543

>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=93.34  E-value=0.1  Score=44.59  Aligned_cols=45  Identities=20%  Similarity=0.343  Sum_probs=33.1

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR   60 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~   60 (252)
                      ....++++.++||||||.+. -+++..+...          +..++|+=|..|+..
T Consensus        51 ~~~~h~~i~G~tGsGKs~~~-~~li~~~~~~----------g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           51 AEPRHLLVNGATGTGKSVLL-RELAYTGLLR----------GDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHHHT----------TCEEEEEEETTHHHH
T ss_pred             cCcceEEEECCCCCCHHHHH-HHHHHHHHHC----------CCcEEEEeCCCchhH
Confidence            45679999999999999863 4455544432          456888889999864

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

Probab=93.31  E-value=0.16  Score=38.19  Aligned_cols=24  Identities=17%  Similarity=0.189  Sum_probs=21.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      +.++||||++++.++.+++.|++.
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~   77 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLK   77 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc
Confidence            347999999999999999999865

>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=91.97  E-value=0.2  Score=36.99  Aligned_cols=19  Identities=21%  Similarity=0.356  Sum_probs=16.2

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      -.|+.+++.+|+|+|||..
T Consensus        36 ~~g~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           36 EEGKGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             GGCCEEEECCSSSSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3588999999999999943

>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=91.61  E-value=0.67  Score=41.79  Aligned_cols=76  Identities=22%  Similarity=0.178  Sum_probs=50.2

Q ss_pred             CChHHHHhhhhhhh---------cCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHH
Q psy7786         166 KPTPIQVQGIPAAL---------SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT  236 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~---------~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i  236 (252)
                      .+.+.|...+..+.         .+...++..++|.|||...+..+.. +.....   .......++||+||+ .++.|.
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~-l~~~~~---~~~p~~~~~LiV~P~-sll~qW  129 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWT-LLKQSP---DCKPEIDKVIVVSPS-SLVRNW  129 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHH-HHHCCT---TSSCSCSCEEEEECH-HHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHH-HHHhCc---cccCCCCcEEEEecH-HHHHHH
Confidence            46677777776542         4567889999999999875444433 332211   111123469999997 778888


Q ss_pred             HHHHHHHHhh
Q psy7786         237 HDIIQYYCAA  246 (252)
Q Consensus       237 ~~~l~~l~~~  246 (252)
                      .++++++...
T Consensus       130 ~~E~~~~~~~  139 (644)
T 1z3i_X          130 YNEVGKWLGG  139 (644)
T ss_dssp             HHHHHHHHGG
T ss_pred             HHHHHHHcCC
Confidence            8888888653

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.59  E-value=0.2  Score=38.74  Aligned_cols=19  Identities=21%  Similarity=0.261  Sum_probs=16.0

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +..|.-+++.+++|+|||.
T Consensus        20 l~~G~~~~i~G~~GsGKTt   38 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTI   38 (247)
T ss_dssp             EETTCEEEEEECTTSSHHH
T ss_pred             CCCCcEEEEECCCCCCHHH
Confidence            3467788999999999994

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=91.21  E-value=0.12  Score=36.89  Aligned_cols=19  Identities=11%  Similarity=0.097  Sum_probs=16.4

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..+.++++.+++|||||..
T Consensus        22 ~~~~~vll~G~~GtGKt~l   40 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTG   40 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHH
T ss_pred             CCCCCEEEECCCCCCHHHH
Confidence            4678999999999999954

>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=91.09  E-value=0.47  Score=42.93  Aligned_cols=48  Identities=21%  Similarity=0.223  Sum_probs=36.4

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      ...+.+-||||||++..- ++...   .         . .+|||+|+.++|.|.++.++.|.
T Consensus        34 ~~~l~g~~gs~k~~~~a~-~~~~~---~---------~-~~lvv~~~~~~A~~l~~el~~~~   81 (661)
T 2d7d_A           34 HQTLLGATGTGKTFTVSN-LIKEV---N---------K-PTLVIAHNKTLAGQLYSEFKEFF   81 (661)
T ss_dssp             EEEEEECTTSCHHHHHHH-HHHHH---C---------C-CEEEECSSHHHHHHHHHHHHHHC
T ss_pred             cEEEECcCCcHHHHHHHH-HHHHh---C---------C-CEEEEECCHHHHHHHHHHHHHHc
Confidence            467889999999966532 22222   1         1 38999999999999999999883

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=90.70  E-value=0.11  Score=37.05  Aligned_cols=18  Identities=11%  Similarity=0.047  Sum_probs=15.7

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..+.++++.+++|||||.
T Consensus        25 ~~~~~vll~G~~GtGKt~   42 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFET   42 (143)
T ss_dssp             TCSSCEEEEEETTCCHHH
T ss_pred             CCCCcEEEECCCCccHHH
Confidence            457789999999999994

>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=90.49  E-value=0.85  Score=40.88  Aligned_cols=70  Identities=19%  Similarity=0.128  Sum_probs=49.7

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..++-|..++..  .+..+++.+..|+|||...+.-+...+....       ....+.|+++.|+..|.++.+.+.++.
T Consensus         9 ~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~-------~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            9 SLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVEN-------CSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSC-------CCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCC-------CChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            567778877752  3556899999999999876554444332211       112469999999999999999988764

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=90.30  E-value=1.2  Score=41.32  Aligned_cols=68  Identities=15%  Similarity=0.092  Sum_probs=50.3

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ....-|..++...+.+.-.++.+++|+|||.... ..+..+....         +.++++.++|..-++++.+.+.+.
T Consensus       360 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~-~~i~~l~~~~---------~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          360 QLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSA-TIVYHLSKIH---------KDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHH-HHHHHHHHHH---------CCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH-HHHHHHHhCC---------CCeEEEEcCcHHHHHHHHHHHHhh
Confidence            4567788888777777778999999999987532 2333333221         456999999999999999988764

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=90.15  E-value=0.37  Score=37.27  Aligned_cols=23  Identities=26%  Similarity=0.432  Sum_probs=17.5

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPIL   29 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~   29 (252)
                      .|.=+++.+++|+||| +|++-++
T Consensus        29 ~G~l~~i~G~pG~GKT-~l~l~~~   51 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKT-TFAAQFI   51 (251)
T ss_dssp             TTCEEEEECCTTSSHH-HHHHHHH
T ss_pred             CCeEEEEEeCCCCCHH-HHHHHHH
Confidence            4667899999999999 4554433

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=89.97  E-value=0.88  Score=40.58  Aligned_cols=59  Identities=17%  Similarity=0.095  Sum_probs=45.1

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      .+-+++..+-|+|||.....-++-.+...         .+..+++++||++.|..+.+.++.+.+..+
T Consensus       178 ~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~---------~~~~i~~va~t~~qA~~~~~~i~~~i~~~p  236 (592)
T 3cpe_A          178 KRMTVCNLSRQLGKTTVVAIFLAHFVCFN---------KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (592)
T ss_dssp             CSEEEEEECSSSCHHHHHHHHHHHHHHTS---------SSCEEEEEESSHHHHHHHHHHHHHHHTTSC
T ss_pred             ccEEEEEEcCccChHHHHHHHHHHHHHhC---------CCCeEEEEECCHHHHHHHHHHHHHHHHhCh
Confidence            45688899999999987665444444332         245799999999999999998888877654

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

Probab=89.96  E-value=0.76  Score=33.67  Aligned_cols=24  Identities=8%  Similarity=-0.119  Sum_probs=21.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ..++||||++++.++.+++.|++.
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~   54 (172)
T 1t5i_A           31 FNQVVIFVKSVQRCIALAQLLVEQ   54 (172)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc
Confidence            457999999999999999999764

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

Probab=89.64  E-value=0.7  Score=33.46  Aligned_cols=24  Identities=21%  Similarity=0.314  Sum_probs=21.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ..++||||+|++.++.+++.|++.
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~~   58 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDDL   58 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHc
Confidence            457999999999999999999765

>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=89.53  E-value=1.1  Score=40.23  Aligned_cols=68  Identities=21%  Similarity=0.132  Sum_probs=49.9

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ....-|..++...+.+.-.++.+++|+|||.... ..+..+...         .+.++++.++|..-++++.+.+.+.
T Consensus       180 ~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~-~~i~~l~~~---------~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          180 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ---------GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHH-HHHHHHHTS---------SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHH-HHHHHHHHc---------CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            4567888888777777778899999999987532 233333221         2457999999999999999887653

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=89.50  E-value=1.8  Score=36.41  Aligned_cols=74  Identities=16%  Similarity=0.054  Sum_probs=53.9

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .+.+.|...+......+..++....+.|||.....-.+..+..         ..+..++++.+|++.|..+.+.++.+.+
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~---------~~g~~v~~vA~t~~qA~~vf~~i~~mi~  233 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF---------NKDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS---------SSSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh---------CCCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            4577777766544344567777788999998766555544332         1256799999999999999999998887


Q ss_pred             hCC
Q psy7786         246 ALP  248 (252)
Q Consensus       246 ~~~  248 (252)
                      ..+
T Consensus       234 ~~P  236 (385)
T 2o0j_A          234 LLP  236 (385)
T ss_dssp             HSC
T ss_pred             hCh
Confidence            665

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=89.25  E-value=1.3  Score=37.27  Aligned_cols=58  Identities=17%  Similarity=0.096  Sum_probs=44.6

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      |-+++..+-+.|||.....-++-.+...         .+..+++++||++.|..+.+.++.+.+..+
T Consensus       179 R~~vi~~sRq~GKT~l~a~~~l~~a~~~---------~g~~v~~vA~t~~qA~~vf~~i~~mi~~~P  236 (385)
T 2o0j_A          179 RMTVCNLSRQLGKTTVVAIFLAHFVCFN---------KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (385)
T ss_dssp             SEEEEEECSSSCHHHHHHHHHHHHHHSS---------SSCEEEEEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             cEEEEEEcCcCChhHHHHHHHHHHHHhC---------CCCeEEEEeCCHHHHHHHHHHHHHHHHhCh
Confidence            4578888999999987666555433321         256799999999999999999998887765

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=88.75  E-value=1.4  Score=39.74  Aligned_cols=66  Identities=24%  Similarity=0.202  Sum_probs=46.9

Q ss_pred             ChHHHHhhhhhhhcCC-cEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         167 PTPIQVQGIPAALSGR-DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~-~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ..+-|..++...+..+ -.++.+++|+|||.... ..+..+..+          +.++|+.++|..-++.+.+.|...
T Consensus       190 LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~-~~I~~l~~~----------~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVV-EIILQAVKQ----------GLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             CCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHH-HHHHHHHHT----------TCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHH-HHHHHHHhC----------CCeEEEEcCchHHHHHHHHHHHhc
Confidence            3567787787777655 46778889999987633 333333332          457999999999999998887643

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=88.74  E-value=1.2  Score=36.16  Aligned_cols=39  Identities=18%  Similarity=0.119  Sum_probs=26.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC   53 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~   53 (252)
                      +..|.=+++.+++|+||| +|++-+...+...          +-.+++++
T Consensus        65 l~~G~l~li~G~pG~GKT-tl~l~ia~~~a~~----------g~~vl~~s  103 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKT-AFALKQAKNMSDN----------DDVVNLHS  103 (315)
T ss_dssp             BCTTCEEEEECCTTSSHH-HHHHHHHHHHHTT----------TCEEEEEE
T ss_pred             CCCCcEEEEEeCCCCCHH-HHHHHHHHHHHHc----------CCeEEEEE
Confidence            345667899999999999 5655555443321          23577776

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=88.55  E-value=0.68  Score=34.63  Aligned_cols=16  Identities=25%  Similarity=0.283  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCchHHHH
Q psy7786           8 RDIIGIAFTGSGKTLV   23 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a   23 (252)
                      +.+++.+++|+|||..
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            7899999999999953

>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=88.16  E-value=1.4  Score=42.96  Aligned_cols=70  Identities=27%  Similarity=0.226  Sum_probs=51.2

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      ..++-|..++...  +.++++.+..|||||...+--++..+.....     .....+.++++.|+.-|..+.+.+.+
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~-----~~~~~~il~~Tft~~aa~e~~~ri~~   79 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEEN-----PIDVDRLLVVTFTNASAAEMKHRIAE   79 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSS-----CCCGGGEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCC-----CCCccceEEEeccHHHHHHHHHHHHH
Confidence            3567777766543  7799999999999998876666655543210     01234799999999999999988875

>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=88.08  E-value=0.31  Score=35.84  Aligned_cols=20  Identities=25%  Similarity=0.273  Sum_probs=17.3

Q ss_pred             cccCCCcEEEEcCCCchHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~   22 (252)
                      .+..++.+++.+++|||||.
T Consensus         7 ~~~~~~~i~i~G~~GsGKst   26 (180)
T 3iij_A            7 EFMLLPNILLTGTPGVGKTT   26 (180)
T ss_dssp             TTCCCCCEEEECSTTSSHHH
T ss_pred             ccccCCeEEEEeCCCCCHHH
Confidence            45677889999999999995

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=88.05  E-value=0.21  Score=40.86  Aligned_cols=27  Identities=7%  Similarity=-0.096  Sum_probs=19.0

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      .+.++++.+|+|||||... --++..+.
T Consensus        44 ~~~~lli~GpPGTGKT~~v-~~v~~~L~   70 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLV-NDVMDELI   70 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHH-HHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            4668999999999999543 33344443

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

Probab=88.00  E-value=1.1  Score=32.44  Aligned_cols=24  Identities=13%  Similarity=0.225  Sum_probs=21.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ..++||||+|++.++.+++.|++.
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~~   53 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRND   53 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc
Confidence            457999999999999999999764

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

Probab=87.93  E-value=0.74  Score=33.74  Aligned_cols=24  Identities=17%  Similarity=0.095  Sum_probs=21.4

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ..++||||++++.|+.+++.|++.
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~~   57 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQD   57 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHTT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc
Confidence            468999999999999999999764

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=87.82  E-value=0.22  Score=43.68  Aligned_cols=20  Identities=30%  Similarity=0.237  Sum_probs=17.0

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..|..+++.+|||||||..
T Consensus       257 v~~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          257 IEHKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHTTCCEEEEESTTSSHHHH
T ss_pred             HhCCCEEEEECCCCCCHHHH
Confidence            35788999999999999954

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=87.47  E-value=0.8  Score=34.83  Aligned_cols=19  Identities=26%  Similarity=0.176  Sum_probs=16.0

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +..|.-+++.+++|+|||.
T Consensus        20 i~~G~~~~i~G~~GsGKTt   38 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTI   38 (235)
T ss_dssp             EETTCEEEEECSTTSSHHH
T ss_pred             CcCCCEEEEEcCCCCCHHH
Confidence            4467788999999999993

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

Probab=87.31  E-value=1.1  Score=33.25  Aligned_cols=24  Identities=13%  Similarity=0.159  Sum_probs=21.4

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      +.++||||++++.|+.+++.|++.
T Consensus        46 ~~k~lVF~~~~~~~~~l~~~L~~~   69 (185)
T 2jgn_A           46 DSLTLVFVETKKGADSLEDFLYHE   69 (185)
T ss_dssp             CSCEEEEESCHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHc
Confidence            567999999999999999999764

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=87.26  E-value=0.28  Score=35.93  Aligned_cols=17  Identities=29%  Similarity=0.378  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCchHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a   23 (252)
                      ++.+++.+++|+|||..
T Consensus        43 ~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            46799999999999943

>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=87.13  E-value=1.7  Score=39.28  Aligned_cols=69  Identities=19%  Similarity=0.062  Sum_probs=48.3

Q ss_pred             ChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         167 PTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      .++-|..++..  .+..+++.+..|+|||....--+...+....       ....+.|+++-|+..|.++.+.+.+..
T Consensus         3 L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~-------~~~~~IL~lTfT~~Aa~em~~Rl~~~l   71 (673)
T 1uaa_A            3 LNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCG-------YQARHIAAVTFTNKAAREMKERVGQTL   71 (673)
T ss_dssp             CCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHC-------CCGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcC-------CCHHHeEEEeccHHHHHHHHHHHHHHc
Confidence            45666666643  2567889999999999876555544443311       012469999999999999999887653

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

Probab=87.06  E-value=1.4  Score=33.41  Aligned_cols=25  Identities=0%  Similarity=-0.019  Sum_probs=21.9

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +.++||||+|++.++.+++.|++.+
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~~   55 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRLG   55 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHcC
Confidence            4579999999999999999998754

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=86.84  E-value=2.7  Score=37.42  Aligned_cols=73  Identities=16%  Similarity=0.049  Sum_probs=54.1

Q ss_pred             ChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhh
Q psy7786         167 PTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA  246 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~  246 (252)
                      +.+.|...+......+..++....+.|||.....-.+..+...         .+.+++++.+|++.|..+.+.++.+.+.
T Consensus       164 l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~---------~~~~i~~va~t~~qA~~~~~~i~~~i~~  234 (592)
T 3cpe_A          164 LRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN---------KDKAVGILAHKGSMSAEVLDRTKQAIEL  234 (592)
T ss_dssp             CCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS---------SSCEEEEEESSHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC---------CCCeEEEEECCHHHHHHHHHHHHHHHHh
Confidence            5677877665544456788888889999987665444444321         2457999999999999999999988877


Q ss_pred             CC
Q psy7786         247 LP  248 (252)
Q Consensus       247 ~~  248 (252)
                      .+
T Consensus       235 ~p  236 (592)
T 3cpe_A          235 LP  236 (592)
T ss_dssp             SC
T ss_pred             Ch
Confidence            65

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=86.83  E-value=0.32  Score=38.59  Aligned_cols=20  Identities=35%  Similarity=0.298  Sum_probs=16.4

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..|.-+.+.+|||||||..
T Consensus        22 i~~g~~v~i~Gp~GsGKSTl   41 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTT   41 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHH
T ss_pred             hCCCCEEEEECCCCccHHHH
Confidence            34677789999999999954

>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=86.82  E-value=2  Score=39.78  Aligned_cols=68  Identities=21%  Similarity=0.126  Sum_probs=49.3

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY  243 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l  243 (252)
                      ....-|..++...+.+.-.++.+++|+|||... ...+..+...         .+.++++.+||..-|+++.+.+.+.
T Consensus       356 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti-~~~i~~l~~~---------~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          356 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ---------GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHH-HHHHHHHHTT---------CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHH-HHHHHHHHHc---------CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            346678888877777777889999999998753 2333333321         2457999999999999999887653

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=86.50  E-value=1.7  Score=35.86  Aligned_cols=38  Identities=16%  Similarity=0.142  Sum_probs=26.2

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC   53 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~   53 (252)
                      ..|.=+++.|++|+||| +|++-+...+...          +..++|++
T Consensus        44 ~~G~LiiIaG~pG~GKT-t~al~ia~~~a~~----------g~~Vl~fS   81 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKT-SLMMNMVLSALND----------DRGVAVFS   81 (338)
T ss_dssp             CTTCEEEEEECTTSCHH-HHHHHHHHHHHHT----------TCEEEEEE
T ss_pred             CCCcEEEEEeCCCCCHH-HHHHHHHHHHHHc----------CCeEEEEe
Confidence            45666899999999999 5666655554432          34577776

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=86.15  E-value=0.4  Score=35.45  Aligned_cols=19  Identities=11%  Similarity=0.335  Sum_probs=16.0

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..|+=+++.+|+|||||..
T Consensus         3 ~~g~~i~i~GpsGsGKSTL   21 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHI   21 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            4678899999999999953

>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=86.15  E-value=1.5  Score=39.67  Aligned_cols=66  Identities=24%  Similarity=0.336  Sum_probs=46.0

Q ss_pred             CChHHHHhhhhhhh----cC-CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAAL----SG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~----~~-~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      .|+..|...+....    .| +...+...+|+|||+.... ++...             +..+||++|+..+|.|+++.|
T Consensus         8 ~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~-------------~~~~lvv~~~~~~A~ql~~el   73 (664)
T 1c4o_A            8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEAL-------------GRPALVLAPNKILAAQLAAEF   73 (664)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH-------------TCCEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHh-------------CCCEEEEecCHHHHHHHHHHH
Confidence            67777776665433    23 2466788999999776432 22211             123899999999999999999


Q ss_pred             HHHHh
Q psy7786         241 QYYCA  245 (252)
Q Consensus       241 ~~l~~  245 (252)
                      +.+..
T Consensus        74 ~~~~~   78 (664)
T 1c4o_A           74 RELFP   78 (664)
T ss_dssp             HHHCT
T ss_pred             HHHCC
Confidence            98853

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=85.95  E-value=0.28  Score=35.92  Aligned_cols=16  Identities=31%  Similarity=0.318  Sum_probs=14.2

Q ss_pred             CCcEEEEcCCCchHHH
Q psy7786           7 SRDIIGIAFTGSGKTL   22 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~   22 (252)
                      ++.+++.+++|+|||.
T Consensus        43 ~~~vll~G~~G~GKT~   58 (187)
T 2p65_A           43 KNNPILLGDPGVGKTA   58 (187)
T ss_dssp             SCEEEEESCGGGCHHH
T ss_pred             CCceEEECCCCCCHHH
Confidence            5689999999999994

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=85.92  E-value=1.1  Score=38.41  Aligned_cols=39  Identities=18%  Similarity=0.119  Sum_probs=27.2

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC   53 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~   53 (252)
                      +..|.=+++.|++|+||| +|++-+...+...          +-.+++++
T Consensus       194 l~~G~liiIaG~pG~GKT-tlal~ia~~~a~~----------g~~vl~fS  232 (444)
T 3bgw_A          194 YKRRNFVLIAARPSMGKT-AFALKQAKNMSDN----------DDVVNLHS  232 (444)
T ss_dssp             BCSSCEEEEEECSSSSHH-HHHHHHHHHHHHT----------TCEEEEEC
T ss_pred             CCCCcEEEEEeCCCCChH-HHHHHHHHHHHHc----------CCEEEEEE
Confidence            345667899999999999 6666666555432          33577776

>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=85.92  E-value=0.36  Score=36.96  Aligned_cols=17  Identities=24%  Similarity=0.108  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .++.+++.+|+|+|||.
T Consensus        51 ~~~~~ll~G~~G~GKT~   67 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTH   67 (242)
T ss_dssp             SCSEEEEECSTTSSHHH
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            47789999999999994

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=85.86  E-value=0.96  Score=38.85  Aligned_cols=30  Identities=33%  Similarity=0.306  Sum_probs=22.2

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      +..|.=+++.+++|+||| +|++-+...+..
T Consensus       200 l~~G~liiI~G~pG~GKT-tl~l~ia~~~~~  229 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKT-AFALNIAQNVAT  229 (454)
T ss_dssp             BCTTCEEEEECCTTSCHH-HHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHH-HHHHHHHHHHHH
Confidence            346777899999999999 566666555543

>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=85.80  E-value=2.5  Score=38.57  Aligned_cols=70  Identities=21%  Similarity=0.154  Sum_probs=49.8

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..++-|..++..  .+..+++.+..|+|||.....-+...+....       ....+.|+++-|+..|.++.+.+.++.
T Consensus        11 ~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~-------~~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKH-------VAPWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTC-------CCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcC-------CCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            567778876654  3457899999999999876555544433211       112469999999999999999887764

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=85.75  E-value=0.95  Score=38.76  Aligned_cols=30  Identities=27%  Similarity=0.084  Sum_probs=22.0

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      +..|.=+++.|++|+||| +|++-+...+..
T Consensus       197 l~~G~l~ii~G~pg~GKT-~lal~ia~~~a~  226 (444)
T 2q6t_A          197 LGPGSLNIIAARPAMGKT-AFALTIAQNAAL  226 (444)
T ss_dssp             CCTTCEEEEEECTTSCHH-HHHHHHHHHHHH
T ss_pred             cCCCcEEEEEeCCCCCHH-HHHHHHHHHHHH
Confidence            345667899999999999 666666655543

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=85.54  E-value=0.38  Score=40.06  Aligned_cols=20  Identities=40%  Similarity=0.386  Sum_probs=17.0

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..|..+++.++||||||..
T Consensus       172 i~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHH
Confidence            34788999999999999953

>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=85.26  E-value=0.39  Score=39.83  Aligned_cols=23  Identities=30%  Similarity=0.419  Sum_probs=18.1

Q ss_pred             CcccCCCc--EEEEcCCCchHHHHh
Q psy7786           2 VTYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         2 ~~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      ..+++|.|  +++-++||||||.+.
T Consensus        78 ~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           78 QSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             GGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHhcCCceeEEEEECCCCCCCcEec
Confidence            34678888  566789999999775

>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=85.20  E-value=0.46  Score=37.37  Aligned_cols=18  Identities=28%  Similarity=0.412  Sum_probs=15.7

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..+..+++.+++|||||.
T Consensus        27 ~~~~~vll~G~~GtGKt~   44 (265)
T 2bjv_A           27 PLDKPVLIIGERGTGKEL   44 (265)
T ss_dssp             TSCSCEEEECCTTSCHHH
T ss_pred             CCCCCEEEECCCCCcHHH
Confidence            456789999999999994

>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=85.16  E-value=3  Score=36.97  Aligned_cols=64  Identities=16%  Similarity=0.086  Sum_probs=46.1

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII  240 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l  240 (252)
                      ..++-|..++...+.+..+++..++|+|||..  +..+...+..         .+.++++.+||..-|..+.+.+
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~--i~~l~~~l~~---------~g~~Vl~~ApT~~Aa~~L~e~~  252 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTT--TKAVADLAES---------LGLEVGLCAPTGKAARRLGEVT  252 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHH--HHHHHHHHHH---------TTCCEEEEESSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHH--HHHHHHHHHh---------cCCeEEEecCcHHHHHHhHhhh
Confidence            35677888888778888899999999999864  2222222222         2456899999999998887643

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=85.12  E-value=0.48  Score=38.09  Aligned_cols=18  Identities=28%  Similarity=0.255  Sum_probs=15.1

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .+.++++.+|+|+|||..
T Consensus        66 ~~~~vll~G~~GtGKT~l   83 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTV   83 (309)
T ss_dssp             CCCEEEEEECTTSSHHHH
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            455799999999999953

>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=85.08  E-value=0.86  Score=38.23  Aligned_cols=42  Identities=26%  Similarity=0.374  Sum_probs=28.3

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSREL   58 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreL   58 (252)
                      .+.++++.++||||||...-. ++..+..          .+.+++++=|.+|.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~-~~~~~~~----------~~~~~~~~D~~~~~   75 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKM-LLLREYM----------QGSRVIIIDPEREY   75 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHH-HHHHHHT----------TTCCEEEEESSCCS
T ss_pred             ccCceEEEcCCCCCHHHHHHH-HHHHHHH----------CCCEEEEEeCCcCH
Confidence            577999999999999954332 3322222          24567888888763

>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=84.81  E-value=2.7  Score=35.99  Aligned_cols=71  Identities=10%  Similarity=0.042  Sum_probs=46.3

Q ss_pred             HHCCCCCChHHHHhhhhhhhc-----CCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHH
Q psy7786         160 EAKGIKKPTPIQVQGIPAALS-----GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR  234 (252)
Q Consensus       160 ~~~~~~~p~~iQ~~~~p~~~~-----~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~  234 (252)
                      .-..+..+++-|..++...+.     ...+++.++.|+|||... ...+..+....         ..++++.++|..-|.
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~---------~~~il~~a~T~~Aa~   88 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTG---------ETGIILAAPTHAAKK   88 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTT---------CCCEEEEESSHHHHH
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcC---------CceEEEecCcHHHHH
Confidence            334566777788877765432     238999999999999542 33333333321         135899999999888


Q ss_pred             HHHHHH
Q psy7786         235 QTHDII  240 (252)
Q Consensus       235 ~i~~~l  240 (252)
                      .+.+.+
T Consensus        89 ~l~~~~   94 (459)
T 3upu_A           89 ILSKLS   94 (459)
T ss_dssp             HHHHHH
T ss_pred             HHHhhh
Confidence            877654

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=84.76  E-value=1.2  Score=35.56  Aligned_cols=26  Identities=27%  Similarity=0.305  Sum_probs=18.7

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILM   30 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~   30 (252)
                      +..|.=+++.+++|+|||. ++.-+..
T Consensus        32 l~~G~~~~i~G~~G~GKTT-l~~~ia~   57 (296)
T 1cr0_A           32 ARGGEVIMVTSGSGMGKST-FVRQQAL   57 (296)
T ss_dssp             BCTTCEEEEEESTTSSHHH-HHHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHH-HHHHHHH
Confidence            4567778999999999994 4333333

>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=84.74  E-value=0.44  Score=36.21  Aligned_cols=16  Identities=19%  Similarity=0.254  Sum_probs=14.2

Q ss_pred             CCCcEEEEcCCCchHH
Q psy7786           6 NSRDIIGIAFTGSGKT   21 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT   21 (252)
                      .|+-+++.++||+|||
T Consensus        33 ~g~~ilI~GpsGsGKS   48 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKS   48 (205)
T ss_dssp             TTEEEEEECCCTTTTH
T ss_pred             CCEEEEEECCCCCCHH
Confidence            5667899999999998

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=84.63  E-value=0.49  Score=35.64  Aligned_cols=19  Identities=21%  Similarity=0.431  Sum_probs=14.8

Q ss_pred             CCCcEEEEcCCCchHHHHh
Q psy7786           6 NSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~   24 (252)
                      .|+-+.+.+|+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5788999999999999543

>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=84.57  E-value=0.41  Score=35.87  Aligned_cols=15  Identities=33%  Similarity=0.470  Sum_probs=13.4

Q ss_pred             CcEEEEcCCCchHHH
Q psy7786           8 RDIIGIAFTGSGKTL   22 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~   22 (252)
                      |-+++.+|+|+|||.
T Consensus         2 RpIVi~GPSG~GK~T   16 (186)
T 1ex7_A            2 RPIVISGPSGTGKST   16 (186)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CEEEEECCCCCCHHH
Confidence            568999999999994

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=84.45  E-value=1.5  Score=38.38  Aligned_cols=19  Identities=21%  Similarity=0.275  Sum_probs=16.1

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..+-++++.+.||||||..
T Consensus       165 ~~~pHlLIaG~TGSGKSt~  183 (512)
T 2ius_A          165 AKMPHLLVAGTTGSGASVG  183 (512)
T ss_dssp             GGSCSEEEECCTTSSHHHH
T ss_pred             ccCceEEEECCCCCCHHHH
Confidence            3567999999999999954

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=84.34  E-value=0.45  Score=35.72  Aligned_cols=19  Identities=26%  Similarity=0.384  Sum_probs=15.7

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..|+.+++.+++|||||..
T Consensus        23 ~~~~~i~l~G~~GsGKsTl   41 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTL   41 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHH
Confidence            4678899999999999943

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=84.26  E-value=0.54  Score=35.46  Aligned_cols=19  Identities=16%  Similarity=0.156  Sum_probs=16.8

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +..|+-+++.+++|||||.
T Consensus         9 ~~~~~~i~l~G~sGsGKsT   27 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGT   27 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHH
T ss_pred             cccCCEEEEECCCCCCHHH
Confidence            5678889999999999994

>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=84.20  E-value=0.42  Score=39.32  Aligned_cols=18  Identities=39%  Similarity=0.412  Sum_probs=16.2

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..|+.+.+.++||||||.
T Consensus       169 ~~g~~v~i~G~~GsGKTT  186 (330)
T 2pt7_A          169 AIGKNVIVCGGTGSGKTT  186 (330)
T ss_dssp             HHTCCEEEEESTTSCHHH
T ss_pred             cCCCEEEEECCCCCCHHH
Confidence            468899999999999995

>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=84.09  E-value=0.49  Score=35.84  Aligned_cols=19  Identities=16%  Similarity=0.513  Sum_probs=16.5

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      ...|+=+++.+|+|+|||.
T Consensus        16 ~~~g~~ivl~GPSGaGKsT   34 (197)
T 3ney_A           16 FQGRKTLVLIGASGVGRSH   34 (197)
T ss_dssp             CCSCCEEEEECCTTSSHHH
T ss_pred             CCCCCEEEEECcCCCCHHH
Confidence            3578889999999999995

>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=84.02  E-value=0.51  Score=38.11  Aligned_cols=19  Identities=32%  Similarity=0.448  Sum_probs=16.0

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..++.+++.+|+|||||..
T Consensus        47 ~~~~~vLL~Gp~GtGKT~l   65 (301)
T 3cf0_A           47 TPSKGVLFYGPPGCGKTLL   65 (301)
T ss_dssp             CCCSEEEEECSSSSSHHHH
T ss_pred             CCCceEEEECCCCcCHHHH
Confidence            4567899999999999953

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=83.84  E-value=0.44  Score=39.65  Aligned_cols=22  Identities=27%  Similarity=0.371  Sum_probs=17.0

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        99 ~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           99 QALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHhCCCCEEEEEeCCCCCCccEEe
Confidence            3577887  566789999999764

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=83.83  E-value=3.1  Score=32.86  Aligned_cols=19  Identities=16%  Similarity=0.111  Sum_probs=16.0

Q ss_pred             ccCCCcEEEEcCCCchHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~   22 (252)
                      +..|.=+++.+++|||||.
T Consensus        27 l~~G~i~~i~G~~GsGKTt   45 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSM   45 (279)
T ss_dssp             EETTSEEEEEESTTSSHHH
T ss_pred             ccCCCEEEEEcCCCCCHHH
Confidence            3467788999999999994

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=83.81  E-value=0.53  Score=37.40  Aligned_cols=19  Identities=32%  Similarity=0.482  Sum_probs=15.9

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..++.+++.+|+|+|||..
T Consensus        49 ~~~~~~ll~G~~GtGKT~l   67 (285)
T 3h4m_A           49 EPPKGILLYGPPGTGKTLL   67 (285)
T ss_dssp             CCCSEEEEESSSSSSHHHH
T ss_pred             CCCCeEEEECCCCCcHHHH
Confidence            4567899999999999943

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=83.72  E-value=0.41  Score=39.72  Aligned_cols=22  Identities=27%  Similarity=0.416  Sum_probs=17.5

Q ss_pred             cccCCCcE--EEEcCCCchHHHHh
Q psy7786           3 TYRNSRDI--IGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d~--~~~a~tgsGKT~a~   24 (252)
                      .+++|.|.  ++-++||||||.+.
T Consensus        80 ~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           80 SSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             GGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHCCcceeEEEeCCCCCCCceEe
Confidence            46788884  56789999999776

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=83.55  E-value=1.9  Score=41.76  Aligned_cols=63  Identities=16%  Similarity=0.060  Sum_probs=40.2

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCC-CCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP-FLPGEGPYGLIICPSRELARQTHDIIQY   68 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~-~~~~~~~~~lil~ptreLa~q~~~~~~~   68 (252)
                      ++|.. +|.|..|||||.+-+-=++..+........ .....--+.|+|+=|+.=|....+++..
T Consensus        15 l~g~~-lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~   78 (1180)
T 1w36_B           15 LQGER-LIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (1180)
T ss_dssp             CSSCE-EEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCCE-EEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHH
Confidence            34555 899999999998777666666653210000 0001123699999999888887766654

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=83.47  E-value=3.1  Score=36.07  Aligned_cols=52  Identities=19%  Similarity=0.223  Sum_probs=38.1

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      ..|....+.+-||||||++..- ++    ...         +-..|||+|+...|.|.++.++.|.
T Consensus        12 ~~~~~~~l~g~~gs~ka~~~a~-l~----~~~---------~~p~lvv~~~~~~A~~l~~~l~~~~   63 (483)
T 3hjh_A           12 KAGEQRLLGELTGAACATLVAE-IA----ERH---------AGPVVLIAPDMQNALRLHDEISQFT   63 (483)
T ss_dssp             STTCEEEEECCCTTHHHHHHHH-HH----HHS---------SSCEEEEESSHHHHHHHHHHHHHTC
T ss_pred             CCCCeEEEeCCCchHHHHHHHH-HH----HHh---------CCCEEEEeCCHHHHHHHHHHHHhhC
Confidence            4566788999999999965321 11    211         1138999999999999999998873

>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=83.37  E-value=0.59  Score=36.49  Aligned_cols=18  Identities=28%  Similarity=0.427  Sum_probs=15.0

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      ..+.+++.+|+|+|||..
T Consensus        38 ~~~~vll~G~~GtGKT~l   55 (262)
T 2qz4_A           38 VPKGALLLGPPGCGKTLL   55 (262)
T ss_dssp             CCCEEEEESCTTSSHHHH
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            456799999999999953

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=83.33  E-value=0.55  Score=35.18  Aligned_cols=20  Identities=25%  Similarity=0.160  Sum_probs=16.3

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..|+-+.+.+++|||||..
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            45688899999999999953

>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=83.33  E-value=1.4  Score=36.80  Aligned_cols=28  Identities=21%  Similarity=0.118  Sum_probs=21.6

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      -.|+-+++.+++|+||| +|++.+...+.
T Consensus        72 ~~G~li~I~G~pGsGKT-tlal~la~~~~   99 (366)
T 1xp8_A           72 PRGRITEIYGPESGGKT-TLALAIVAQAQ   99 (366)
T ss_dssp             ETTSEEEEEESTTSSHH-HHHHHHHHHHH
T ss_pred             cCCcEEEEEcCCCCChH-HHHHHHHHHHH
Confidence            45778999999999999 66666665554

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=83.18  E-value=0.74  Score=35.14  Aligned_cols=24  Identities=17%  Similarity=0.314  Sum_probs=17.6

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      +.+++.+|.|||||. |...+.+.+
T Consensus        59 n~ili~GPPGtGKTt-~a~ala~~l   82 (212)
T 1tue_A           59 NCLVFCGPANTGKSY-FGMSFIHFI   82 (212)
T ss_dssp             SEEEEESCGGGCHHH-HHHHHHHHH
T ss_pred             cEEEEECCCCCCHHH-HHHHHHHHh
Confidence            359999999999994 335555554

>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=83.12  E-value=0.56  Score=39.23  Aligned_cols=19  Identities=37%  Similarity=0.352  Sum_probs=16.0

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..|.-+++.+|||||||..
T Consensus       134 ~~g~~i~ivG~~GsGKTTl  152 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTT  152 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4577899999999999954

>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=82.99  E-value=0.53  Score=38.64  Aligned_cols=22  Identities=27%  Similarity=0.277  Sum_probs=17.3

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        72 ~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           72 DVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCeEEEEEECCCCCCCceEe
Confidence            3567887  667889999999764

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=82.97  E-value=0.55  Score=38.17  Aligned_cols=17  Identities=18%  Similarity=0.262  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCchHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a   23 (252)
                      ++++++.+|+|+|||..
T Consensus       152 ~~~lll~G~~GtGKT~L  168 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYL  168 (308)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CceEEEECCCCCCHHHH
Confidence            68999999999999943

>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=82.88  E-value=0.63  Score=37.26  Aligned_cols=18  Identities=39%  Similarity=0.565  Sum_probs=15.3

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .++.+++.+|+|+|||..
T Consensus        49 ~~~~vll~G~~GtGKT~l   66 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEI   66 (310)
T ss_dssp             CCCCEEEECCTTSSHHHH
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            367899999999999943

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=82.87  E-value=2  Score=31.87  Aligned_cols=40  Identities=13%  Similarity=-0.007  Sum_probs=25.3

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSR   56 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptr   56 (252)
                      .|+=.++.++.|+|||.+.+ -++.+...          .+-+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll-~~~~~~~~----------~g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELL-SFVEIYKL----------GKKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHH-HHHHHHHH----------TTCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHH-HHHHHHHH----------CCCeEEEEeecc
Confidence            35667889999999996543 33333322          134688888774

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=82.69  E-value=0.62  Score=38.74  Aligned_cols=22  Identities=23%  Similarity=0.404  Sum_probs=17.0

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        75 ~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           75 DILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCcceEEEECCCCCCcceEe
Confidence            3567887  566789999999764

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=82.58  E-value=0.46  Score=39.19  Aligned_cols=20  Identities=20%  Similarity=0.034  Sum_probs=16.0

Q ss_pred             EEcCcHHHHHHHHHHHHHHH
Q psy7786         225 IICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~  244 (252)
                      +-.+||..|.+...+++++.
T Consensus       271 ik~~TR~yAKRQ~tWfr~~~  290 (339)
T 3a8t_A          271 IKENTCHLAKRQIGKILRLK  290 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHccCC
Confidence            45688999999888888764

>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=82.55  E-value=1.6  Score=36.24  Aligned_cols=27  Identities=22%  Similarity=0.176  Sum_probs=19.8

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      -.|+-+++.+++|+||| ++++-+...+
T Consensus        61 ~~G~ii~I~G~pGsGKT-tLal~la~~~   87 (356)
T 1u94_A           61 PMGRIVEIYGPESSGKT-TLTLQVIAAA   87 (356)
T ss_dssp             ETTSEEEEECSTTSSHH-HHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHH-HHHHHHHHHH
Confidence            36778999999999999 4445544444

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=82.49  E-value=0.68  Score=38.39  Aligned_cols=18  Identities=50%  Similarity=0.648  Sum_probs=15.7

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .++.+++.+|+|||||..
T Consensus        50 ~~~~vll~GppGtGKT~l   67 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLL   67 (363)
T ss_dssp             CCCCEEEECCTTSSHHHH
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            567899999999999953

>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=82.47  E-value=0.56  Score=34.71  Aligned_cols=20  Identities=20%  Similarity=0.185  Sum_probs=16.7

Q ss_pred             cccCCCcEEEEcCCCchHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~   22 (252)
                      .+..|+-+++.+++|||||.
T Consensus         5 ~i~~g~~i~l~G~~GsGKST   24 (191)
T 1zp6_A            5 DDLGGNILLLSGHPGSGKST   24 (191)
T ss_dssp             -CCTTEEEEEEECTTSCHHH
T ss_pred             CCCCCeEEEEECCCCCCHHH
Confidence            35678889999999999995

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=82.47  E-value=0.56  Score=38.77  Aligned_cols=17  Identities=29%  Similarity=0.505  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCchHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a   23 (252)
                      |+.+++.+|+|+|||..
T Consensus        70 ~~~vLl~GppGtGKT~l   86 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAI   86 (368)
T ss_dssp             TCEEEEEESTTSSHHHH
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            56899999999999953

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=82.35  E-value=0.57  Score=37.46  Aligned_cols=18  Identities=28%  Similarity=0.512  Sum_probs=15.4

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .++.+++.+|+|||||..
T Consensus        53 ~~~~vll~Gp~GtGKT~l   70 (297)
T 3b9p_A           53 PAKGLLLFGPPGNGKTLL   70 (297)
T ss_dssp             CCSEEEEESSSSSCHHHH
T ss_pred             CCCeEEEECcCCCCHHHH
Confidence            367899999999999953

>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=82.31  E-value=0.64  Score=38.63  Aligned_cols=22  Identities=27%  Similarity=0.533  Sum_probs=17.0

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus       100 ~~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A          100 SFLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HHTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HHhCCCceEEEEeCCCCCCceeee
Confidence            3567887  566789999999764

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=82.23  E-value=0.46  Score=38.78  Aligned_cols=18  Identities=28%  Similarity=0.246  Sum_probs=16.0

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..|+++++.+|+|+|||.
T Consensus        44 ~~~~~vll~G~pGtGKT~   61 (331)
T 2r44_A           44 CTGGHILLEGVPGLAKTL   61 (331)
T ss_dssp             HHTCCEEEESCCCHHHHH
T ss_pred             HcCCeEEEECCCCCcHHH
Confidence            457899999999999994

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=82.23  E-value=0.59  Score=38.45  Aligned_cols=21  Identities=29%  Similarity=0.406  Sum_probs=16.8

Q ss_pred             ccCCCc--EEEEcCCCchHHHHh
Q psy7786           4 YRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         4 ~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      +++|.|  +++-++||||||.+.
T Consensus        76 ~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           76 CIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             HHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HhCCCEEEEEeECCCCCCCcEEE
Confidence            567887  567889999999765

>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=82.07  E-value=0.37  Score=39.94  Aligned_cols=22  Identities=27%  Similarity=0.453  Sum_probs=16.9

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        78 ~~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           78 AFFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             HHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHhhcCeeEEEecccCCCceEee
Confidence            3567887  466789999999764

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=82.04  E-value=0.6  Score=38.73  Aligned_cols=21  Identities=29%  Similarity=0.368  Sum_probs=16.6

Q ss_pred             ccCCCc--EEEEcCCCchHHHHh
Q psy7786           4 YRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         4 ~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      +++|.|  +++-++||||||.+.
T Consensus        85 ~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           85 VLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HhCCCceeEEeecCCCCCCCEEe
Confidence            567777  566789999999775

>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=82.01  E-value=0.75  Score=34.46  Aligned_cols=15  Identities=27%  Similarity=0.315  Sum_probs=13.3

Q ss_pred             CcEEEEcCCCchHHH
Q psy7786           8 RDIIGIAFTGSGKTL   22 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~   22 (252)
                      ..+++.+++|+|||.
T Consensus        39 ~~~ll~G~~G~GKT~   53 (226)
T 2chg_A           39 PHLLFSGPPGTGKTA   53 (226)
T ss_dssp             CCEEEECSTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            359999999999994

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=81.99  E-value=0.79  Score=35.04  Aligned_cols=20  Identities=20%  Similarity=0.217  Sum_probs=15.8

Q ss_pred             ccCCCcEEEEcCCCchHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a   23 (252)
                      +..|+=+.+.+|+|+|||..
T Consensus        20 i~~G~~~~lvGpsGsGKSTL   39 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTL   39 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHH
Confidence            45688899999999999954

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=81.96  E-value=0.88  Score=37.55  Aligned_cols=14  Identities=43%  Similarity=0.313  Sum_probs=12.2

Q ss_pred             cEEEEcCCCchHHH
Q psy7786           9 DIIGIAFTGSGKTL   22 (252)
Q Consensus         9 d~~~~a~tgsGKT~   22 (252)
                      -+++.+|||||||.
T Consensus         9 lI~I~GptgSGKTt   22 (340)
T 3d3q_A            9 LIVIVGPTASGKTE   22 (340)
T ss_dssp             EEEEECSTTSSHHH
T ss_pred             eEEEECCCcCcHHH
Confidence            47899999999993

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=81.93  E-value=0.66  Score=33.22  Aligned_cols=17  Identities=24%  Similarity=0.206  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .|+.+++.+++|+|||.
T Consensus        35 ~g~~~~l~G~~G~GKTt   51 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSH   51 (149)
T ss_dssp             CCSEEEEESSSTTTTCH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57889999999999994

>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=81.88  E-value=0.5  Score=39.61  Aligned_cols=22  Identities=32%  Similarity=0.412  Sum_probs=17.1

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus       110 ~~l~G~N~tifAYGqTGSGKTyTM  133 (376)
T 2rep_A          110 SALDGYPVCIFAYGQTGSGKTFTM  133 (376)
T ss_dssp             GGGGTCCEEEEEECSTTSSHHHHH
T ss_pred             HhcCCCceEEEEeCCCCCCCceEe
Confidence            4678887  556689999999664

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=81.84  E-value=0.57  Score=34.32  Aligned_cols=22  Identities=23%  Similarity=0.176  Sum_probs=17.3

Q ss_pred             cCCCcEEEEcCCCchHHHHhHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVL   26 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~l   26 (252)
                      -.|.=+.+.+++|||||..+-.
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHH
Confidence            4566788999999999965543

>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=81.84  E-value=1.7  Score=33.45  Aligned_cols=40  Identities=15%  Similarity=-0.135  Sum_probs=25.0

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSR   56 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptr   56 (252)
                      .|.=+++.+++|+|||.+. +-.+.++..          .+-+++++.|..
T Consensus        11 ~G~i~litG~mGsGKTT~l-l~~~~r~~~----------~g~kVli~~~~~   50 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAEL-IRRLHRLEY----------ADVKYLVFKPKI   50 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHH-HHHHHHHHH----------TTCCEEEEEECC
T ss_pred             CcEEEEEECCCCCcHHHHH-HHHHHHHHh----------cCCEEEEEEecc
Confidence            3555778899999999554 333433332          244578886654

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=81.80  E-value=0.62  Score=38.89  Aligned_cols=22  Identities=27%  Similarity=0.259  Sum_probs=17.1

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        79 ~~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           79 DVLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCceEEEeecCCCCCCceEE
Confidence            3567887  566789999999774

>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=81.79  E-value=2  Score=38.03  Aligned_cols=27  Identities=30%  Similarity=0.370  Sum_probs=18.8

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      ++-++++.+.||||||.+ +-.++..++
T Consensus       213 k~pHlLIaG~TGSGKS~~-L~tlI~sLl  239 (574)
T 2iut_A          213 KMPHLLVAGTTGSGKSVG-VNAMLLSIL  239 (574)
T ss_dssp             GSCCEEEECCTTSSHHHH-HHHHHHHHH
T ss_pred             hCCeeEEECCCCCCHHHH-HHHHHHHHH
Confidence            356899999999999954 334444343

>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=81.79  E-value=0.69  Score=38.90  Aligned_cols=22  Identities=23%  Similarity=0.412  Sum_probs=17.3

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        93 ~~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           93 HLLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             HHTTTCCEEEEEESCTTSSHHHHH
T ss_pred             HhhcCceeeEeeecCCCCCCCeEe
Confidence            3578887  556789999999775

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=81.73  E-value=0.65  Score=34.17  Aligned_cols=16  Identities=38%  Similarity=0.472  Sum_probs=14.4

Q ss_pred             CCcEEEEcCCCchHHH
Q psy7786           7 SRDIIGIAFTGSGKTL   22 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~   22 (252)
                      ++.+++.+++|||||.
T Consensus         5 ~~~i~l~G~~GsGKst   20 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTS   20 (185)
T ss_dssp             CCEEEEECSTTSSHHH
T ss_pred             CCEEEEECCCCCCHHH
Confidence            6789999999999994

>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=81.70  E-value=0.6  Score=39.04  Aligned_cols=22  Identities=27%  Similarity=0.388  Sum_probs=16.6

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        96 ~~l~G~n~tifAYGqTGSGKTyTM  119 (372)
T 3b6u_A           96 SVLQGFNGTIFAYGQTGTGKTYTM  119 (372)
T ss_dssp             HHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHhCCCeeeEEeecCCCCCCCEeE
Confidence            3567887  456789999999764

>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=81.70  E-value=0.55  Score=39.06  Aligned_cols=18  Identities=28%  Similarity=0.259  Sum_probs=14.8

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .|.-+++.+|||||||..
T Consensus       122 ~~g~i~I~GptGSGKTTl  139 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTT  139 (356)
T ss_dssp             SSEEEEEECSTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            455789999999999944

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=81.61  E-value=0.69  Score=39.15  Aligned_cols=22  Identities=27%  Similarity=0.446  Sum_probs=17.2

Q ss_pred             cccCCCcE--EEEcCCCchHHHHh
Q psy7786           3 TYRNSRDI--IGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d~--~~~a~tgsGKT~a~   24 (252)
                      .+++|.|.  ++-++||||||.+.
T Consensus       135 ~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          135 SSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             HHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHhCCcceEEEEECCCCCCCceEe
Confidence            35688874  66789999999775

>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=81.55  E-value=0.77  Score=33.47  Aligned_cols=17  Identities=29%  Similarity=0.192  Sum_probs=14.4

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .++-+++.+++|||||.
T Consensus         2 ~~~~i~l~G~~GsGKST   18 (178)
T 1qhx_A            2 TTRMIILNGGSSAGKSG   18 (178)
T ss_dssp             CCCEEEEECCTTSSHHH
T ss_pred             CceEEEEECCCCCCHHH
Confidence            35678999999999994

>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=81.48  E-value=0.64  Score=38.81  Aligned_cols=21  Identities=24%  Similarity=0.352  Sum_probs=16.3

Q ss_pred             ccCCCc--EEEEcCCCchHHHHh
Q psy7786           4 YRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         4 ~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      +++|.|  +++-++||||||.+.
T Consensus        85 ~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           85 AFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HhcCCeeEEEEeCCCCCCCceEe
Confidence            567887  566789999999664

>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=81.45  E-value=0.77  Score=34.77  Aligned_cols=18  Identities=28%  Similarity=0.187  Sum_probs=15.3

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .|+=+++.+|+|||||..
T Consensus         7 ~g~~i~l~GpsGsGKsTl   24 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTV   24 (208)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCcEEEEECcCCCCHHHH
Confidence            577789999999999953

>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=81.28  E-value=1.8  Score=35.76  Aligned_cols=27  Identities=26%  Similarity=0.126  Sum_probs=19.3

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      -.|+-+++.+++||||| ++++-+...+
T Consensus        59 ~~G~iv~I~G~pGsGKT-tLal~la~~~   85 (349)
T 2zr9_A           59 PRGRVIEIYGPESSGKT-TVALHAVANA   85 (349)
T ss_dssp             ETTSEEEEEESTTSSHH-HHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHH-HHHHHHHHHH
Confidence            35778999999999999 4444444333

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=81.25  E-value=2  Score=32.16  Aligned_cols=40  Identities=10%  Similarity=-0.086  Sum_probs=26.0

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSR   56 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptr   56 (252)
                      .|+=.++.++.|||||.+. +-.+.+...          .+-+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~l-l~~a~r~~~----------~g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEEL-IRRIRRAKI----------AKQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHH-HHHHHHHHH----------TTCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHH-HHHHHHHHH----------CCCEEEEEEecc
Confidence            4555678888999999554 344444432          245689988874

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=81.23  E-value=0.76  Score=37.20  Aligned_cols=19  Identities=26%  Similarity=0.384  Sum_probs=16.0

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..+..+++.+++|||||..
T Consensus        23 ~~~~~vLi~Ge~GtGKt~l   41 (304)
T 1ojl_A           23 PSDATVLIHGDSGTGKELV   41 (304)
T ss_dssp             STTSCEEEESCTTSCHHHH
T ss_pred             CCCCcEEEECCCCchHHHH
Confidence            3567899999999999953

>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=81.01  E-value=0.59  Score=38.18  Aligned_cols=15  Identities=27%  Similarity=0.191  Sum_probs=12.6

Q ss_pred             CcEEEEcCCCchHHH
Q psy7786           8 RDIIGIAFTGSGKTL   22 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~   22 (252)
                      +=+++.+|||||||.
T Consensus         4 ~~i~i~GptgsGKt~   18 (322)
T 3exa_A            4 KLVAIVGPTAVGKTK   18 (322)
T ss_dssp             EEEEEECCTTSCHHH
T ss_pred             cEEEEECCCcCCHHH
Confidence            347889999999993

>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=80.82  E-value=0.69  Score=39.25  Aligned_cols=22  Identities=32%  Similarity=0.425  Sum_probs=16.9

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus       133 ~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          133 SALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             HHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHCCCceEEEEecCCCCCCeeEe
Confidence            3567887  466679999999775

>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=80.81  E-value=0.71  Score=38.27  Aligned_cols=21  Identities=29%  Similarity=0.298  Sum_probs=16.7

Q ss_pred             ccCCCc--EEEEcCCCchHHHHh
Q psy7786           4 YRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         4 ~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      +++|.|  +++-++||||||.+.
T Consensus        73 ~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           73 AIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHcCCccceeeecCCCCCCCeEE
Confidence            567877  566789999999875

>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=80.75  E-value=0.61  Score=38.01  Aligned_cols=13  Identities=46%  Similarity=0.414  Sum_probs=11.7

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      +++.+|||||||.
T Consensus        13 i~i~GptgsGKt~   25 (316)
T 3foz_A           13 IFLMGPTASGKTA   25 (316)
T ss_dssp             EEEECCTTSCHHH
T ss_pred             EEEECCCccCHHH
Confidence            7889999999993

>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=80.59  E-value=0.84  Score=33.75  Aligned_cols=18  Identities=28%  Similarity=0.344  Sum_probs=15.6

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..++.+++.+++|||||.
T Consensus         8 ~~~~~I~l~G~~GsGKST   25 (184)
T 1y63_A            8 PKGINILITGTPGTGKTS   25 (184)
T ss_dssp             CSSCEEEEECSTTSSHHH
T ss_pred             CCCCEEEEECCCCCCHHH
Confidence            357789999999999995

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

Probab=80.55  E-value=3.1  Score=33.57  Aligned_cols=25  Identities=0%  Similarity=-0.019  Sum_probs=21.5

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +.++||||+|++.++.+++.|++.+
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~g   52 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRLG   52 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTTT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhCC
Confidence            4579999999999999999987654

>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=80.45  E-value=0.7  Score=38.39  Aligned_cols=22  Identities=23%  Similarity=0.308  Sum_probs=17.1

Q ss_pred             cccCCCcE--EEEcCCCchHHHHh
Q psy7786           3 TYRNSRDI--IGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d~--~~~a~tgsGKT~a~   24 (252)
                      .+++|.|.  ++-++||||||.+.
T Consensus        87 ~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           87 NAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHhCCceeEEEeeCCCCCCCceEE
Confidence            35678874  66789999999775

>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=80.37  E-value=0.61  Score=36.85  Aligned_cols=17  Identities=24%  Similarity=0.114  Sum_probs=14.4

Q ss_pred             CCcEEEEcCCCchHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a   23 (252)
                      .+.+++.+|+|+|||..
T Consensus        64 ~~~vLl~G~~GtGKT~l   80 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTAL   80 (272)
T ss_dssp             EEEEEEECSTTSSHHHH
T ss_pred             CeEEEEECCCCCcHHHH
Confidence            35799999999999954

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=80.24  E-value=2.1  Score=34.86  Aligned_cols=18  Identities=28%  Similarity=0.074  Sum_probs=15.4

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      ..|.-+++.+++|||||.
T Consensus       105 ~~G~i~~i~G~~GsGKT~  122 (324)
T 2z43_A          105 ETRTMTEFFGEFGSGKTQ  122 (324)
T ss_dssp             ETTSEEEEEESTTSSHHH
T ss_pred             CCCcEEEEECCCCCCHhH
Confidence            457789999999999993

>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=80.24  E-value=0.91  Score=34.26  Aligned_cols=21  Identities=19%  Similarity=0.135  Sum_probs=16.0

Q ss_pred             ccCCCcEEEEcCCCchHHHHh
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~   24 (252)
                      +..|+=+.+.+|+|||||..+
T Consensus        17 i~~Gei~~l~GpnGsGKSTLl   37 (207)
T 1znw_A           17 AAVGRVVVLSGPSAVGKSTVV   37 (207)
T ss_dssp             --CCCEEEEECSTTSSHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHH
Confidence            456777899999999999543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=80.20  E-value=0.86  Score=33.05  Aligned_cols=16  Identities=31%  Similarity=0.511  Sum_probs=14.3

Q ss_pred             CCcEEEEcCCCchHHH
Q psy7786           7 SRDIIGIAFTGSGKTL   22 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~   22 (252)
                      |+-+.+.+++|||||.
T Consensus         4 ~~~i~l~G~~GsGKST   19 (173)
T 1kag_A            4 KRNIFLVGPMGAGKST   19 (173)
T ss_dssp             CCCEEEECCTTSCHHH
T ss_pred             CCeEEEECCCCCCHHH
Confidence            5779999999999994

>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=80.15  E-value=0.88  Score=36.96  Aligned_cols=18  Identities=28%  Similarity=0.233  Sum_probs=15.1

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      .+..+++.+|+|+|||..
T Consensus        36 ~~~~lll~G~~GtGKT~l   53 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHL   53 (324)
T ss_dssp             SCSSEEEECSSSSSHHHH
T ss_pred             CCCeEEEECCCCCcHHHH
Confidence            356899999999999943

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=80.10  E-value=0.94  Score=33.82  Aligned_cols=19  Identities=32%  Similarity=0.300  Sum_probs=15.8

Q ss_pred             cCCCcEEEEcCCCchHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a   23 (252)
                      ..|+=+.+.+|+|||||..
T Consensus         5 ~~g~ii~l~Gp~GsGKSTl   23 (205)
T 3tr0_A            5 NKANLFIISAPSGAGKTSL   23 (205)
T ss_dssp             CCCCEEEEECCTTSCHHHH
T ss_pred             CCCcEEEEECcCCCCHHHH
Confidence            3577788999999999953

---

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	252
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	2e-19
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-16
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	3e-16
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	4e-16
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	5e-16
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	7e-16
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	8e-15
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	3e-05
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-14
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	6e-14
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	1e-12
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	3e-11
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	5e-11
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-09
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	7e-09
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	3e-05

>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 = 82.3 bits (202), Expect = 2e-19
 Identities = 40/124 (32%), Positives = 61/124 (49%), Gaps = 3/124 (2%)

Query: 129 NLRILVEGDDV--PPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIG 186
           ++ + V G D        +F  +KL  ++   +     ++PTPIQ   IPA L  RDI+ 
Sbjct: 4   SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMA 63

Query: 187 IAFTGSGKTLVFVLPILMFCLEQETKL-PFLPGEGPYGLIICPSRELARQTHDIIQYYCA 245
            A TGSGKT  F++PI+   + Q+     +     P  LI+ P+RELA Q     Q +  
Sbjct: 64  CAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSL 123

Query: 246 ALPI 249
             P+
Sbjct: 124 NTPL 127

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.3 bits (179), Expect = 2e-16
 Identities = 33/107 (30%), Positives = 50/107 (46%), Gaps = 8/107 (7%)

Query: 138 DVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLV 197
           +      SF  M L ESL+R + A G +KP+ IQ + I   + G D+I  A +G+GKT  
Sbjct: 6   NWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTAT 65

Query: 198 FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC 244
           F + IL                    L++ P+RELA+Q   ++    
Sbjct: 66  FAISILQQIELDLK--------ATQALVLAPTRELAQQIQKVVMALG 104

>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 = 72.7 bits (177), Expect = 3e-16
 Identities = 32/101 (31%), Positives = 49/101 (48%), Gaps = 8/101 (7%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F    L   L+  +   G +KP+PIQ + IP ALSGRDI+  A  G+GK+  +++P+L 
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA 245
               ++             ++I P+RELA Q   I      
Sbjct: 64  RLDLKKD--------NIQAMVIVPTRELALQVSQICIQVSK 96

>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 = 72.3 bits (176), Expect = 4e-16
 Identities = 18/95 (18%), Positives = 42/95 (44%), Gaps = 11/95 (11%)

Query: 150 KLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQ 209
            +    V  L+ +GI++  P Q + +    SG++++    T +GKTL+  + ++   ++ 
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 210 ETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC 244
                         L + P R LA + ++  + + 
Sbjct: 69  -----------GKSLYVVPLRALAGEKYESFKKWE 92

>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 = 72.6 bits (177), Expect = 5e-16
 Identities = 35/115 (30%), Positives = 54/115 (46%), Gaps = 11/115 (9%)

Query: 135 EGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGK 194
           E  DV P   +F  M L E L+R + A G +KP+ IQ + I   + GRD+I  + +G+GK
Sbjct: 11  EEVDVTP---TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGK 67

Query: 195 TLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI 249
           T  F + +L            +       LI+ P+RELA Q    +      + +
Sbjct: 68  TATFSISVLQCL--------DIQVRETQALILAPTRELAVQIQKGLLALGDYMNV 114

>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 = 71.8 bits (175), Expect = 7e-16
 Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 8/104 (7%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            FR   L   L+RA+   G + P+ +Q + IP A+ G D++  A +G GKT VFVL  L 
Sbjct: 2   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
                  +           L++C +RELA Q     + +   +P
Sbjct: 62  QLEPVTGQ--------VSVLVMCHTRELAFQISKEYERFSKYMP 97

>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 = 69.5 bits (169), Expect = 8e-15
 Identities = 23/106 (21%), Positives = 33/106 (31%), Gaps = 12/106 (11%)

Query: 144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL 203
           C F    L +  V     K + +P  IQ       L        A TG GKT   +   L
Sbjct: 22  CLFPEDFLLKEFVEFFR-KCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSL 80

Query: 204 MFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI 249
              L+                +I P+  L  Q  + I+ Y     +
Sbjct: 81  FLALKG-----------KRCYVIFPTSLLVIQAAETIRKYAEKAGV 115

>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 = 41.8 bits (97), Expect = 3e-05
 Identities = 16/129 (12%), Positives = 34/129 (26%), Gaps = 22/129 (17%)

Query: 8   RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
                 A TG GKT   +   L   L+                +I P+  L  Q  + I+
Sbjct: 59  ESFAATAPTGVGKTSFGLAMSLFLALKG-----------KRCYVIFPTSLLVIQAAETIR 107

Query: 68  YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIR 127
            Y     +                    +   +  +    + R  + +++    +    R
Sbjct: 108 KYAEKAGVG---------TENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYR 158

Query: 128 --RNLRILV 134
              +   + 
Sbjct: 159 ELGHFDFIF 167

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 67.5 bits (164), Expect = 3e-14
 Identities = 28/101 (27%), Positives = 48/101 (47%), Gaps = 8/101 (7%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F  M+L E+L+R +   G ++P+ IQ + I   + G D++  A +G+GKT  F +  L 
Sbjct: 11  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 70

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA 245
                         + P  L++ P+RELA Q   ++     
Sbjct: 71  RIDTSV--------KAPQALMLAPTRELALQIQKVVMALAF 103

>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 = 66.5 bits (161), Expect = 6e-14
 Identities = 26/68 (38%), Positives = 38/68 (55%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
           +F    L   L+  +   G +KP+PIQ + IP A++GRDI+  A  G+GKT  FV+P L 
Sbjct: 2   TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 61

Query: 205 FCLEQETK 212
               +  K
Sbjct: 62  KVKPKLNK 69

>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 = 62.8 bits (151), Expect = 1e-12
 Identities = 24/100 (24%), Positives = 42/100 (42%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
            F        ++ A++     KPT IQ + IP AL G  ++G + TG+GKT  ++LPI+ 
Sbjct: 2   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 61

Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC 244
               +  ++  +       L      E  + T    +   
Sbjct: 62  KIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRM 101

>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 = 58.9 bits (141), Expect = 3e-11
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 145 SFRLMKLPESLVRAL-EAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL 203
              ++ L     + L E  G ++  P Q + I   LSGRD + +  TG GK+L + +P L
Sbjct: 3   QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPAL 62

Query: 204 MFCLEQETKLP 214
           +         P
Sbjct: 63  LLNGLTVVVSP 73

>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 = 58.1 bits (140), Expect = 5e-11
 Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGR-DIIGIAFTGSGKTLVFVLPIL 203
           +F  + L ++++ A+  KG +KPT IQ++ IP  L+   +I+  A TGSGKT  F +P++
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 204 MFC 206
              
Sbjct: 65  ELV 67

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 53.8 bits (128), Expect = 4e-09
 Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 10/66 (15%)

Query: 5  RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD 64
          R  R  I     G+GKT  ++  I+   +++          G   LI+ P+R +A +  +
Sbjct: 7  RKKRLTIMDLHPGAGKTKRYLPAIVREAIKR----------GLRTLILAPTRVVAAEMEE 56

Query: 65 IIQYYC 70
           ++   
Sbjct: 57 ALRGLP 62

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 53.0 bits (126), Expect = 7e-09
 Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 10/65 (15%)

Query: 180 SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI 239
             R  I     G+GKT  ++  I+   +++          G   LI+ P+R +A +  + 
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAIKR----------GLRTLILAPTRVVAAEMEEA 57

Query: 240 IQYYC 244
           ++   
Sbjct: 58  LRGLP 62

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 41.3 bits (95), Expect = 3e-05
 Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 11/87 (12%)

Query: 162 KGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP 221
           + + +P   Q           + + +  TG GKTL+ ++       +           G 
Sbjct: 5   RDLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY----------GG 53

Query: 222 YGLIICPSRELARQTHDIIQYYCAALP 248
             L++ P++ L  Q  +  +      P
Sbjct: 54  KVLMLAPTKPLVLQHAESFRRLFNLPP 80

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	252
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.96
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.95
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.94
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.93
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.93
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.91
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.88
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.87
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.82
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.79
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.78
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.77
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.76
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.75
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.74
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.71
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.64
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.59
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.54
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.54
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.53
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.5
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.48
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.3
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.13
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.09
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.06
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.02
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.87
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.73
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.61
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.39
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.33
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	98.23
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.93
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.64
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.6
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	97.5
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.4
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.15
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.08
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.06
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.3
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	95.94
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	95.7
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.51
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.49
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	95.27
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.59
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.57
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	94.5
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	94.25
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.18
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	93.99
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	93.96
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	93.93
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.64
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	93.64
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.35
d2qy9a2	211	GTPase domain of the signal recognition particle r	93.22
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	92.87
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	92.56
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	92.09
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	91.75
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.12
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	91.08
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	90.95
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	90.74
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	90.66
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	90.4
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	90.3
d1ls1a2	207	GTPase domain of the signal sequence recognition p	90.25
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	90.02
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	89.52
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	89.4
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	89.2
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	89.16
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	89.13
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	89.07
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	88.85
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	88.7
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	88.55
d1vmaa2	213	GTPase domain of the signal recognition particle r	88.46
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	88.27
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	88.19
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	88.06
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	87.72
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	86.87
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	86.68
d1okkd2	207	GTPase domain of the signal recognition particle r	86.65
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	86.57
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	86.43
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	86.14
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	85.94
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	85.87
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	85.81
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	85.8
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	85.7
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	85.55
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	85.35
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	85.33
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	85.16
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	84.9
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	84.8
d1j8yf2	211	GTPase domain of the signal sequence recognition p	84.6
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	84.38
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	83.8
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	83.58
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	83.43
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	83.37
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	83.21
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	82.7
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	82.65
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	82.53
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	82.48
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	82.24
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	81.73
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	81.65
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	81.65
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	81.25
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	81.23
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	80.92
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	80.72
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	80.53
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	80.17

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.7e-31  Score=209.20  Aligned_cols=139  Identities=19%  Similarity=0.264  Sum_probs=120.7

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||+||++|+++++....        ..++++|++||||||.|+++.+++++++.+  +++.
T Consensus        48 Ip~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~--------~~~~~lil~PtreLa~Qi~~~~~~l~~~~~--i~~~  117 (222)
T d2j0sa1          48 IKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV--------RETQALILAPTRELAVQIQKGLLALGDYMN--VQCH  117 (222)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHTTTTT--CCEE
T ss_pred             HHHHHCCCCeEEEcCcchhhhhhhcccccccccccc--------cCceeEEecchHHHHHHHHHHHHHHhCccc--eeEE
Confidence            588999999999999999999999999999886543        478999999999999999999999999877  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      .++||.+..++.+.++.+++|.  |.    +||++.++..+....+++ ++++|.||+     +.+.+.+|.+++...+.
T Consensus       118 ~~~g~~~~~~~~~~l~~~~~Il--v~----TPgrl~~~~~~~~~~~~~-l~~lVlDEa-----D~ll~~~f~~~i~~I~~  185 (222)
T d2j0sa1         118 ACIGGTNVGEDIRKLDYGQHVV--AG----TPGRVFDMIRRRSLRTRA-IKMLVLDEA-----DEMLNKGFKEQIYDVYR  185 (222)
T ss_dssp             EECTTSCHHHHHHHHHHCCSEE--EE----CHHHHHHHHHTTSSCCTT-CCEEEEETH-----HHHTSTTTHHHHHHHHT
T ss_pred             EEeecccchhhHHHhccCCeEE--eC----CCCcHHhccccccccccc-ceeeeecch-----hHhhhcCcHHHHHHHHH
Confidence            9999999999999999988873  34    488888776666555555 999999998     89999999999877765


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       186 ~  186 (222)
T d2j0sa1         186 Y  186 (222)
T ss_dssp             T
T ss_pred             h
Confidence            4

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.95  E-value=1.1e-29  Score=201.26  Aligned_cols=149  Identities=23%  Similarity=0.373  Sum_probs=122.5

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcC-CCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcce
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETK-LPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRT   79 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~-~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~   79 (252)
                      ||.+++|+|++++||||||||+||++|++++++..... .......++++||++||||||.|++++++.++...+  +++
T Consensus        52 ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~--~~~  129 (238)
T d1wrba1          52 IPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP--LRS  129 (238)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSS--CCE
T ss_pred             hhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhhhcchheeeeecccCCC--cEE
Confidence            57899999999999999999999999999999765432 223344689999999999999999999999998877  899


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      ..++|+.....+.+...+++||.  |.    ||+++..+.......+++ ++++|.||+     +.+.+.+|.+++.+.+
T Consensus       130 ~~~~g~~~~~~~~~~~~~~~~iv--V~----TP~~l~~~~~~~~~~l~~-v~~lViDEa-----D~ll~~~f~~~i~~Il  197 (238)
T d1wrba1         130 CVVYGGADTHSQIREVQMGCHLL--VA----TPGRLVDFIEKNKISLEF-CKYIVLDEA-----DRMLDMGFEPQIRKII  197 (238)
T ss_dssp             EEECSSSCSHHHHHHHSSCCSEE--EE----CHHHHHHHHHTTSBCCTT-CCEEEEETH-----HHHHHTTCHHHHHHHH
T ss_pred             EEEeccchhhHHHhhcccCCcee--ec----CHHHHHhHHccCceeccc-cceeeeehh-----hhhhhhccHHHHHHHH
Confidence            99999998888888888888873  33    488888776666555665 899999997     8889999999998887


Q ss_pred             HHCC
Q psy7786         160 EAKG  163 (252)
Q Consensus       160 ~~~~  163 (252)
                      .+..
T Consensus       198 ~~~~  201 (238)
T d1wrba1         198 EESN  201 (238)
T ss_dssp             HSSC
T ss_pred             HHhc
Confidence            7644

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=2.9e-29  Score=194.82  Aligned_cols=141  Identities=18%  Similarity=0.258  Sum_probs=118.6

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||+||++|+++++....        ++++++|++||||||.|+++.++.+.+... .+.+.
T Consensus        34 ip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~--------~~~~~lil~pt~el~~q~~~~~~~~~~~~~-~~~~~  104 (206)
T d1veca_          34 IPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK--------DNIQAMVIVPTRELALQVSQICIQVSKHMG-GAKVM  104 (206)
T ss_dssp             HHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTS--------CSCCEEEECSCHHHHHHHHHHHHHHTTTSS-SCCEE
T ss_pred             HHHHHcCCCEEeeccCccccccccccchhhcccccc--------cCcceEEEeecchhhHHHHHHHHHHhhccc-Ccccc
Confidence            578999999999999999999999999999876543        578999999999999999999999987765 47788


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ...|+.....+...+++++++.  |.    ||+++.++..+....+.+ ++++|.||+     +.+.+.+|.+++.+.+.
T Consensus       105 ~~~g~~~~~~~~~~l~~~~~iv--v~----TPgrl~~~~~~~~~~~~~-l~~lVlDEa-----D~ll~~~f~~~i~~I~~  172 (206)
T d1veca_         105 ATTGGTNLRDDIMRLDDTVHVV--IA----TPGRILDLIKKGVAKVDH-VQMIVLDEA-----DKLLSQDFVQIMEDIIL  172 (206)
T ss_dssp             EECSSSCHHHHHHHTTSCCSEE--EE----CHHHHHHHHHTTCSCCTT-CCEEEEETH-----HHHTSTTTHHHHHHHHH
T ss_pred             cccCCccHHHHHHHHHhccCeE--Ee----CCccccccccchhccccc-cceEEEecc-----ccccccchHHHHHHHHH
Confidence            8889988888888888888873  33    488888776665555555 999999998     88999999999877776


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       173 ~~  174 (206)
T d1veca_         173 TL  174 (206)
T ss_dssp             HS
T ss_pred             hC
Confidence            63

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=7.8e-29  Score=192.49  Aligned_cols=140  Identities=20%  Similarity=0.285  Sum_probs=110.8

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||+||++|+++++....        .+++++|++||||||.|+++.++.++.+++ .+++.
T Consensus        32 ip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~--------~~~~~lil~PtreL~~qi~~~~~~~~~~~~-~~~~~  102 (207)
T d1t6na_          32 IPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT--------GQVSVLVMCHTRELAFQISKEYERFSKYMP-NVKVA  102 (207)
T ss_dssp             HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCT--------TCCCEEEECSCHHHHHHHHHHHHHHTTTST-TCCEE
T ss_pred             HHHHHcCCCeEEEeccccccccccccceeeeecccC--------CCceEEEEeccchhhHHHHHHHHHHHhhCC-CceeE
Confidence            588999999999999999999999999999865433        478999999999999999999999998877 37788


Q ss_pred             eeeCCcccCcchhhhhh-cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCccccccc-CCCCHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKK-GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRL-MKLPESLVRA  158 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~-~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~-~~l~~~l~~~  158 (252)
                      .++|+.+...+...+.+ ++|+.  |    +||+++..+..+....+++ ++++|.||+     +.+.+ .++.+++.+.
T Consensus       103 ~~~g~~~~~~~~~~l~~~~~~il--I----~TP~rl~~~~~~~~~~l~~-l~~lVlDEa-----D~ll~~~~~~~~i~~I  170 (207)
T d1t6na_         103 VFFGGLSIKKDEEVLKKNCPHIV--V----GTPGRILALARNKSLNLKH-IKHFILDEC-----DKMLEQLDMRRDVQEI  170 (207)
T ss_dssp             EESCCSCHHHHHHHHHHSCCSEE--E----ECHHHHHHHHHTTSSCCTT-CCEEEEESH-----HHHHSSHHHHHHHHHH
T ss_pred             EEeccccHHHHHHHHHhcCCCEE--E----eCcchhhhhccCCceeccc-cceeehhhh-----hhhhhcCCcHHHHHHH
Confidence            88999888877777654 46662  2    3477777766655444555 899999997     66665 4677766555


Q ss_pred             HHH
Q psy7786         159 LEA  161 (252)
Q Consensus       159 l~~  161 (252)
                      +..
T Consensus       171 ~~~  173 (207)
T d1t6na_         171 FRM  173 (207)
T ss_dssp             HHT
T ss_pred             HHh
Confidence            544

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=3.5e-28  Score=190.02  Aligned_cols=140  Identities=16%  Similarity=0.263  Sum_probs=110.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++|+||||||+||++|+++++..+.        .++++||++||||||.|+++.++.+++..+  +++.
T Consensus        43 ip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~--------~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~--~~~~  112 (218)
T d2g9na1          43 ILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL--------KATQALVLAPTRELAQQIQKVVMALGDYMG--ASCH  112 (218)
T ss_dssp             HHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTC--------CSCCEEEECSSHHHHHHHHHHHHHHHTTTT--CCEE
T ss_pred             HHHHHcCCCEEEEcccchhhhhhhhhhhhheecccc--------cCccEEEEcccchhhhhHHHHHhhhccccc--eeEE
Confidence            578999999999999999999999999999985433        588999999999999999999999999887  6777


Q ss_pred             eeeCCcccCcchhhhh-hcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIK-KGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~-~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      .+.|+....++..... ++++|.  |.    ||+++.++..+....+++ ++++|.||+     +.+.+.+|.+++.+.+
T Consensus       113 ~~~~~~~~~~~~~~~~~~~~~Iv--V~----TP~rl~~~l~~~~~~~~~-l~~lVlDEa-----D~ll~~~f~~~~~~Il  180 (218)
T d2g9na1         113 ACIGGTNVRAEVQKLQMEAPHII--VG----TPGRVFDMLNRRYLSPKY-IKMFVLDEA-----DEMLSRGFKDQIYDIF  180 (218)
T ss_dssp             EECC--CCCSTTTSSSSCCCSEE--EE----CHHHHHHHHHTTSSCSTT-CCEEEEESH-----HHHHHTTCHHHHHHHH
T ss_pred             eeecccchhHHHHHHhcCCCEEE--Ee----CChhHHHHHhcCCccccc-ceEEEeeec-----chhhcCchHHHHHHHH
Confidence            7788776666554443 345552  23    377777666655555544 899999997     8899999999888777


Q ss_pred             HHC
Q psy7786         160 EAK  162 (252)
Q Consensus       160 ~~~  162 (252)
                      ...
T Consensus       181 ~~~  183 (218)
T d2g9na1         181 QKL  183 (218)
T ss_dssp             HHS
T ss_pred             HhC
Confidence            664

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=6.1e-27  Score=182.23  Aligned_cols=139  Identities=16%  Similarity=0.279  Sum_probs=106.5

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||+||++|+++++....        ++++++|++|||||+.|++..+..+.....  ++..
T Consensus        41 ip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~--------~~~~~lil~pt~el~~q~~~~~~~~~~~~~--~~~~  110 (212)
T d1qdea_          41 IMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV--------KAPQALMLAPTRELALQIQKVVMALAFHMD--IKVH  110 (212)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTC--------CSCCEEEECSSHHHHHHHHHHHHHHTTTSC--CCEE
T ss_pred             HHHHHcCCCEEeecccccchhhhhHhhhHhhhhccC--------CCcceEEEcccHHHhhhhhhhhcccccccc--ccee
Confidence            578999999999999999999999999999985443        589999999999999999999999988776  7888


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ...|+.+..++...++ +++|.  |    +||+++..+..+....+++ ++++|.||+     +.+.+.+|.+++.+.+.
T Consensus       111 ~~~~~~~~~~~~~~~~-~~~Iv--I----~TP~~l~~~~~~~~~~l~~-l~~lVlDEa-----d~lld~~f~~~v~~I~~  177 (212)
T d1qdea_         111 ACIGGTSFVEDAEGLR-DAQIV--V----GTPGRVFDNIQRRRFRTDK-IKMFILDEA-----DEMLSSGFKEQIYQIFT  177 (212)
T ss_dssp             EECC----------CT-TCSEE--E----ECHHHHHHHHHTTSSCCTT-CCEEEEETH-----HHHHHTTCHHHHHHHHH
T ss_pred             eEeeccchhHHHHHhc-CCcEE--E----ECCCccccccccCceecCc-ceEEeehhh-----hhhcccchHHHHHHHHH
Confidence            8888888877776665 45552  2    3377777766665555555 999999997     88999999999888776


Q ss_pred             HC
Q psy7786         161 AK  162 (252)
Q Consensus       161 ~~  162 (252)
                      ..
T Consensus       178 ~~  179 (212)
T d1qdea_         178 LL  179 (212)
T ss_dssp             HS
T ss_pred             hC
Confidence            63

>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=99.88  E-value=3.1e-25  Score=172.24  Aligned_cols=137  Identities=23%  Similarity=0.350  Sum_probs=109.9

Q ss_pred             CCcccCCC-cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcce
Q psy7786           1 MVTYRNSR-DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRT   79 (252)
Q Consensus         1 i~~~~~g~-d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~   79 (252)
                      ||.+++|+ |++++||||||||++|.+|+++.....         .++++||++||+|||.|+++.++.+....+  .++
T Consensus        35 ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~---------~~~~~lil~pt~~l~~q~~~~~~~~~~~~~--~~v  103 (208)
T d1hv8a1          35 IPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN---------NGIEAIILTPTRELAIQVADEIESLKGNKN--LKI  103 (208)
T ss_dssp             HHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS---------SSCCEEEECSCHHHHHHHHHHHHHHHCSSC--CCE
T ss_pred             HHHHHcCCCCeeeechhcccccceeecccccccccc---------cCcceEEEeeccccchhhhhhhhhhcccCC--eEE
Confidence            46778885 999999999999999999999865432         478999999999999999999999998877  788


Q ss_pred             eeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHH
Q psy7786          80 CLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL  159 (252)
Q Consensus        80 ~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l  159 (252)
                      ..++|+.+..++.+.++ ++||.  |.    ||+++.++..+....+++ ++++|.||+     +.+.+.++.+++.+.+
T Consensus       104 ~~~~g~~~~~~~~~~l~-~~~Il--V~----TP~~l~~~l~~~~~~~~~-l~~lViDEa-----d~l~~~~~~~~i~~I~  170 (208)
T d1hv8a1         104 AKIYGGKAIYPQIKALK-NANIV--VG----TPGRILDHINRGTLNLKN-VKYFILDEA-----DEMLNMGFIKDVEKIL  170 (208)
T ss_dssp             EEECTTSCHHHHHHHHH-TCSEE--EE----CHHHHHHHHHTTCSCTTS-CCEEEEETH-----HHHHTTTTHHHHHHHH
T ss_pred             EEeeCCCChHHHHHhcC-CCCEE--EE----ChHHHHHHHHcCCCCccc-CcEEEEECh-----HHhhcCCChHHHHHHH
Confidence            89999988877766654 56662  33    488877766655555555 899999997     7788888888777666


Q ss_pred             HH
Q psy7786         160 EA  161 (252)
Q Consensus       160 ~~  161 (252)
                      ..
T Consensus       171 ~~  172 (208)
T d1hv8a1         171 NA  172 (208)
T ss_dssp             HT
T ss_pred             Hh
Confidence            54

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.87  E-value=4.1e-25  Score=171.35  Aligned_cols=139  Identities=19%  Similarity=0.284  Sum_probs=116.6

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||+||++|+++.+..+.        .+.++++++|+++++.|.......++...+  +++.
T Consensus        32 ip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~  101 (206)
T d1s2ma1          32 IPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL--------NKIQALIMVPTRELALQTSQVVRTLGKHCG--ISCM  101 (206)
T ss_dssp             HHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHTTTTT--CCEE
T ss_pred             HHHHHcCCCEEEecCCcchhhhhhcccccccccccc--------ccccceeeccchhhhhhhhhhhhhcccccC--eeEE
Confidence            578999999999999999999999999999875543        477899999999999999999999988877  8999


Q ss_pred             eeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHHHH
Q psy7786          81 LAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALE  160 (252)
Q Consensus        81 ~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~  160 (252)
                      ..+|+.....+...+.+++||.  |.    ||+++..+.......+.+ ++++|.||+     +.+.+.+|.+++...+.
T Consensus       102 ~~~g~~~~~~~~~~l~~~~~Il--i~----TP~~l~~~l~~~~~~l~~-l~~lV~DEa-----D~l~~~~f~~~v~~I~~  169 (206)
T d1s2ma1         102 VTTGGTNLRDDILRLNETVHIL--VG----TPGRVLDLASRKVADLSD-CSLFIMDEA-----DKMLSRDFKTIIEQILS  169 (206)
T ss_dssp             EECSSSCHHHHHHHTTSCCSEE--EE----CHHHHHHHHHTTCSCCTT-CCEEEEESH-----HHHSSHHHHHHHHHHHT
T ss_pred             eecCccchhhHHHHhcccceEE--EE----CCcccccccccceeeccc-ceEEEeech-----hhhhhhhhHHHHHHHHH
Confidence            9999999888888888888873  33    488877777665555555 899999997     88888888888866664


Q ss_pred             H
Q psy7786         161 A  161 (252)
Q Consensus       161 ~  161 (252)
                      .
T Consensus       170 ~  170 (206)
T d1s2ma1         170 F  170 (206)
T ss_dssp             T
T ss_pred             h
Confidence            4

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.82  E-value=1.4e-22  Score=157.26  Aligned_cols=141  Identities=20%  Similarity=0.201  Sum_probs=109.6

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCC--Ccc
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPI--PLR   78 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~--~~~   78 (252)
                      ||.+++|+|++++||||||||+||++|+++.+....        ..+..++++|+++++.+.+..+....+....  ...
T Consensus        32 ip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (209)
T d1q0ua_          32 IPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER--------AEVQAVITAPTRELATQIYHETLKITKFCPKDRMIV  103 (209)
T ss_dssp             HHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS--------CSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCC
T ss_pred             HHHHHCCCCeEeecccccccceeeeeeecccccccc--------ccccccccccccchhHHHHHHHHhhhcccccccccc
Confidence            578899999999999999999999999999876543        4678999999999999999999888776542  245


Q ss_pred             eeeeeCCcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHHHH
Q psy7786          79 TCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRA  158 (252)
Q Consensus        79 ~~~~~g~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~  158 (252)
                      +....|+.+...+....+++++|.  +    ++|+++..+..+....+.+ ++++|.||+     +.+.+.++.+++...
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~Il--v----~TP~~l~~~~~~~~~~~~~-l~~lViDEa-----d~ll~~~f~~~v~~I  171 (209)
T d1q0ua_         104 ARCLIGGTDKQKALEKLNVQPHIV--I----GTPGRINDFIREQALDVHT-AHILVVDEA-----DLMLDMGFITDVDQI  171 (209)
T ss_dssp             EEEECCCSHHHHTTCCCSSCCSEE--E----ECHHHHHHHHHTTCCCGGG-CCEEEECSH-----HHHHHTTCHHHHHHH
T ss_pred             ccccccchhhHHHHHHhccCceEE--E----ecCchhhhhhhhhcccccc-ceEEEEeec-----ccccccccHHHHHHH
Confidence            556677777666666667777762  2    3477777765555555544 999999997     888888998888776


Q ss_pred             HHH
Q psy7786         159 LEA  161 (252)
Q Consensus       159 l~~  161 (252)
                      +..
T Consensus       172 ~~~  174 (209)
T d1q0ua_         172 AAR  174 (209)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            654

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.3e-19  Score=139.51  Aligned_cols=107  Identities=31%  Similarity=0.434  Sum_probs=97.5

Q ss_pred             cCCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCC
Q psy7786         136 GDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPF  215 (252)
Q Consensus       136 de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~  215 (252)
                      +.+.++++.+|.++++++.+++.+.+.|+..|+++|..++|..+.|+|++++++||+|||.+|++|.++.+..+      
T Consensus         4 ~~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~------   77 (218)
T d2g9na1           4 ESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD------   77 (218)
T ss_dssp             CCCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTT------
T ss_pred             CCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccc------
Confidence            34457788999999999999999999999999999999999999999999999999999999999999887442      


Q ss_pred             CCCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         216 LPGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       216 ~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                        ..++++||++|||++|.|+++.+++++...++.
T Consensus        78 --~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~  110 (218)
T d2g9na1          78 --LKATQALVLAPTRELAQQIQKVVMALGDYMGAS  110 (218)
T ss_dssp             --CCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCC
T ss_pred             --ccCccEEEEcccchhhhhHHHHHhhhcccccee
Confidence              357899999999999999999999999887754

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.4e-19  Score=139.65  Aligned_cols=100  Identities=32%  Similarity=0.451  Sum_probs=92.1

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         143 CCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       143 ~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      ..+|.++++++.+++.+.+.|+..|+++|..++|..+.|+|+++.++||+|||++|++|.++.+...        ...++
T Consensus        16 ~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~--------~~~~~   87 (222)
T d2j0sa1          16 TPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ--------VRETQ   87 (222)
T ss_dssp             CCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT--------SCSCC
T ss_pred             CCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccccccccccc--------ccCce
Confidence            4689999999999999999999999999999999999999999999999999999999999876543        24678


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ++|++|||++|.|+++.+++++++.+++
T Consensus        88 ~lil~PtreLa~Qi~~~~~~l~~~~~i~  115 (222)
T d2j0sa1          88 ALILAPTRELAVQIQKGLLALGDYMNVQ  115 (222)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTTTCC
T ss_pred             eEEecchHHHHHHHHHHHHHHhCcccee
Confidence            9999999999999999999999887764

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.77  E-value=3.9e-19  Score=140.08  Aligned_cols=113  Identities=33%  Similarity=0.466  Sum_probs=99.0

Q ss_pred             CCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCC-CC
Q psy7786         138 DVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLP-FL  216 (252)
Q Consensus       138 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~-~~  216 (252)
                      ..++++.+|.++++++++++.+.+.|+..|+++|..++|..+.|+|++++++||+|||.+|++|.+.++........ ..
T Consensus        15 ~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~   94 (238)
T d1wrba1          15 SATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYS   94 (238)
T ss_dssp             SCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------
T ss_pred             CCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhccccccccc
Confidence            35667789999999999999999999999999999999999999999999999999999999999999876532211 23


Q ss_pred             CCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         217 PGEGPYGLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       217 ~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ...+++++|++|||++|.|+.+.++.++.+.+++
T Consensus        95 ~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~  128 (238)
T d1wrba1          95 KTAYPKCLILAPTRELAIQILSESQKFSLNTPLR  128 (238)
T ss_dssp             CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCC
T ss_pred             CCCCceEEEeccchhhhcchheeeeecccCCCcE
Confidence            3556899999999999999999999999998875

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.1e-18  Score=133.10  Aligned_cols=97  Identities=33%  Similarity=0.457  Sum_probs=89.2

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ++|.++++++++++.+.+.|+..|+++|..++|..+.|+|+++.++||+|||.+|++|.++.+...        ..++++
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~--------~~~~~~   72 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV--------TGQVSV   72 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC--------TTCCCE
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeeccc--------CCCceE
Confidence            369999999999999999999999999999999999999999999999999999999999865432        346789


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      +|++|||++|.|+.+.++.++.+.+
T Consensus        73 lil~PtreL~~qi~~~~~~~~~~~~   97 (207)
T d1t6na_          73 LVMCHTRELAFQISKEYERFSKYMP   97 (207)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTST
T ss_pred             EEEeccchhhHHHHHHHHHHHhhCC
Confidence            9999999999999999999998775

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.75  E-value=3e-18  Score=132.58  Aligned_cols=105  Identities=28%  Similarity=0.435  Sum_probs=95.3

Q ss_pred             CCCCCcccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCC
Q psy7786         137 DDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL  216 (252)
Q Consensus       137 e~~~~~~~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~  216 (252)
                      .+.++++.+|.++++++++++.+.+.|+..|+++|..++|..+.|+|++++++||+|||.+|++|.+.++...       
T Consensus         3 ~~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~-------   75 (212)
T d1qdea_           3 TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-------   75 (212)
T ss_dssp             BSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-------
T ss_pred             CCCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhcc-------
Confidence            3456778999999999999999999999999999999999999999999999999999999999999987432       


Q ss_pred             CCCCcEEEEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         217 PGEGPYGLIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       217 ~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                       ..+++++|++|||++|.|+...+..++....+
T Consensus        76 -~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~  107 (212)
T d1qdea_          76 -VKAPQALMLAPTRELALQIQKVVMALAFHMDI  107 (212)
T ss_dssp             -CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCC
T ss_pred             -CCCcceEEEcccHHHhhhhhhhhccccccccc
Confidence             35789999999999999999999988877654

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.7e-18  Score=131.01  Aligned_cols=97  Identities=33%  Similarity=0.469  Sum_probs=88.9

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      .+|.++++++++++.+.+.|+..|+++|..++|..+.|+|++++++||+|||.+|++|.+.++...        ..++++
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~--------~~~~~~   74 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK--------KDNIQA   74 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT--------SCSCCE
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccccc--------ccCcce
Confidence            589999999999999999999999999999999999999999999999999999999999876543        346789


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      +|++|||++|.|+++.++++.+...
T Consensus        75 lil~pt~el~~q~~~~~~~~~~~~~   99 (206)
T d1veca_          75 MVIVPTRELALQVSQICIQVSKHMG   99 (206)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTSS
T ss_pred             EEEeecchhhHHHHHHHHHHhhccc
Confidence            9999999999999999998876543

>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=99.71  E-value=1.1e-18  Score=137.68  Aligned_cols=135  Identities=16%  Similarity=0.188  Sum_probs=85.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCccee
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTC   80 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~   80 (252)
                      ||.+++|+|++++||||||||++|++|++.....           +.++||++||++|+.|++++++++.+..+.++.+.
T Consensus        52 i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~-----------~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~  120 (237)
T d1gkub1          52 AKRILRKESFAATAPTGVGKTSFGLAMSLFLALK-----------GKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENL  120 (237)
T ss_dssp             HHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT-----------SCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGS
T ss_pred             HHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh-----------cCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEE
Confidence            4678999999999999999999999999865532           45799999999999999999999998887433322


Q ss_pred             --eeeCCcccCcchhhhhh--cccccCCccccccCCccccCCChhHHHHHhhhhceeeccCCCCCcccccccCCCCHHHH
Q psy7786          81 --LAIGGVPMNQSLDVIKK--GIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLV  156 (252)
Q Consensus        81 --~~~g~~~~~~~~~~l~~--~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~  156 (252)
                        ...++.....+.+.+..  ..+|.  +    ++|+++.....    .+ +.++++|.||.     +.+.+.  +..+.
T Consensus       121 ~~~~~~~~~~~~~~~~l~~~~~~~Il--v----~Tp~~l~~~~~----~~-~~~~~vVvDE~-----d~~l~~--~~~~~  182 (237)
T d1gkub1         121 IGYYHGRIPKREKENFMQNLRNFKIV--I----TTTQFLSKHYR----EL-GHFDFIFVDDV-----DAILKA--SKNVD  182 (237)
T ss_dssp             EEECCSSCCSHHHHHHHHSGGGCSEE--E----EEHHHHHHCST----TS-CCCSEEEESCH-----HHHHTS--THHHH
T ss_pred             Eeeeecccchhhhhhhhcccccccee--c----cChHHHHHhhh----hc-CCCCEEEEECh-----hhhhhc--ccchh
Confidence              22233332333333322  22331  1    23555433221    12 24789999995     555332  34444


Q ss_pred             HHHHHCCC
Q psy7786         157 RALEAKGI  164 (252)
Q Consensus       157 ~~l~~~~~  164 (252)
                      ..+...++
T Consensus       183 ~~~~~~g~  190 (237)
T d1gkub1         183 KLLHLLGF  190 (237)
T ss_dssp             HHHHHTTE
T ss_pred             HHHHhcCC
Confidence            44444443

>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=99.64  E-value=3.1e-16  Score=120.83  Aligned_cols=98  Identities=35%  Similarity=0.547  Sum_probs=88.9

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCC-cEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGR-DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY  222 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~-~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~  222 (252)
                      .+|.++++++++++.+.+.|+..|+++|..++|..+.|+ |++++++||+|||.+|++|.+.....         ..+++
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~---------~~~~~   74 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE---------NNGIE   74 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS---------SSSCC
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc---------ccCcc
Confidence            489999999999999999999999999999999999874 99999999999999999999976443         34789


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         223 GLIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       223 ~LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ++|+|||+++|.|+.+.++++..+.++.
T Consensus        75 ~lil~pt~~l~~q~~~~~~~~~~~~~~~  102 (208)
T d1hv8a1          75 AIILTPTRELAIQVADEIESLKGNKNLK  102 (208)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHCSSCCC
T ss_pred             eEEEeeccccchhhhhhhhhhcccCCeE
Confidence            9999999999999999999999877653

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.59  E-value=3.1e-15  Score=114.97  Aligned_cols=99  Identities=35%  Similarity=0.522  Sum_probs=90.5

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         144 CSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       144 ~~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ++|.++++++.+++.+.+.|+..|+++|..++|..+.|+|+++.+++|+|||.+|++|.+..+..+        ....++
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~--------~~~~~~   72 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK--------LNKIQA   72 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT--------SCSCCE
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccc--------cccccc
Confidence            479999999999999999999999999999999999999999999999999999999999876543        245779


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ++++++++++.+....+..++...+++
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (206)
T d1s2ma1          73 LIMVPTRELALQTSQVVRTLGKHCGIS   99 (206)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTTTCC
T ss_pred             eeeccchhhhhhhhhhhhhcccccCee
Confidence            999999999999999999988887764

>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=99.54  E-value=8.3e-16  Score=117.90  Aligned_cols=72  Identities=19%  Similarity=0.263  Sum_probs=58.0

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceee
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCL   81 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~   81 (252)
                      +.+++|+|+++++|||||||.++.++++..+..           +.++|+++||++|+.|..+.++++....   .++..
T Consensus        35 ~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~-----------~~~vl~l~P~~~L~~q~~~~~~~~~~~~---~~v~~  100 (202)
T d2p6ra3          35 EKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-----------GGKSLYVVPLRALAGEKYESFKKWEKIG---LRIGI  100 (202)
T ss_dssp             HHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-----------TCCEEEEESSHHHHHHHHHHHTTTTTTT---CCEEE
T ss_pred             HHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc-----------cCcceeecccHHHHHHHHHHHHHHhhcc---cccee
Confidence            457899999999999999999999999887643           3469999999999999999998775432   45555


Q ss_pred             eeCCcc
Q psy7786          82 AIGGVP   87 (252)
Q Consensus        82 ~~g~~~   87 (252)
                      ..|+..
T Consensus       101 ~~~~~~  106 (202)
T d2p6ra3         101 STGDYE  106 (202)
T ss_dssp             ECSSCB
T ss_pred             eccCcc
Confidence            566543

>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=99.54  E-value=5e-16  Score=126.32  Aligned_cols=58  Identities=24%  Similarity=0.356  Sum_probs=49.0

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHH
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYY   69 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l   69 (252)
                      ..+++|+++++.||||||||++|++|++......          +.++||++||||||.|+++.++.+
T Consensus         4 ~~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~----------~~~~lvi~Ptr~La~q~~~~l~~~   61 (305)
T d2bmfa2           4 DIFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR----------GLRTLILAPTRVVAAEMEEALRGL   61 (305)
T ss_dssp             SSSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH----------TCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HHhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc----------CCEEEEEccHHHHHHHHHHHHhcC
Confidence            3578999999999999999999988888766543          457999999999999998776543

>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=99.53  E-value=5.9e-16  Score=119.07  Aligned_cols=56  Identities=25%  Similarity=0.418  Sum_probs=48.9

Q ss_pred             CCcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         1 i~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      |+.+++|+|+++++|||||||++|.+|++..              ..++++++|+++|++|..+.++.+.
T Consensus        34 i~~~l~g~~vlv~apTGsGKT~~~~~~~~~~--------------~~~~~~v~P~~~L~~q~~~~l~~~~   89 (206)
T d1oywa2          34 IDTVLSGRDCLVVMPTGGGKSLCYQIPALLL--------------NGLTVVVSPLISLMKDQVDQLQANG   89 (206)
T ss_dssp             HHHHHTTCCEEEECSCHHHHHHHHHHHHHHS--------------SSEEEEECSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHcCCCEEEEcCCCCCCcchhhhhhhhc--------------cCceEEeccchhhhhhHHHHHHhhc
Confidence            3567899999999999999999999998742              3469999999999999999887764

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.50  E-value=5e-14  Score=108.33  Aligned_cols=96  Identities=30%  Similarity=0.428  Sum_probs=86.4

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEE
Q psy7786         145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGL  224 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~L  224 (252)
                      +|.++++++.+++.+.+.|+..|+++|..++|..+.|+|++++++||+|||++|++|.++.+....        .....+
T Consensus         2 ~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~--------~~~~~~   73 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER--------AEVQAV   73 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS--------CSCCEE
T ss_pred             ccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeecccccccc--------cccccc
Confidence            689999999999999999999999999999999999999999999999999999999998765432        346789


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhhCC
Q psy7786         225 IICPSRELARQTHDIIQYYCAALP  248 (252)
Q Consensus       225 If~~tr~~a~~i~~~l~~l~~~~~  248 (252)
                      +.++++..+.+.+..+........
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~   97 (209)
T d1q0ua_          74 ITAPTRELATQIYHETLKITKFCP   97 (209)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTSC
T ss_pred             ccccccchhHHHHHHHHhhhcccc
Confidence            999999999999999887766653

>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=99.48  E-value=4.2e-15  Score=113.56  Aligned_cols=113  Identities=14%  Similarity=0.146  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCC
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGG   85 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~   85 (252)
                      .++|+++++|||||||+++++++...+...          +-+++|++|+++|+.|..+.++++....+  .++....++
T Consensus        22 ~~~n~lv~~pTGsGKT~i~~~~~~~~~~~~----------~~~il~i~P~~~L~~q~~~~~~~~~~~~~--~~v~~~~~~   89 (200)
T d1wp9a1          22 KETNCLIVLPTGLGKTLIAMMIAEYRLTKY----------GGKVLMLAPTKPLVLQHAESFRRLFNLPP--EKIVALTGE   89 (200)
T ss_dssp             GGSCEEEECCTTSCHHHHHHHHHHHHHHHS----------CSCEEEECSSHHHHHHHHHHHHHHBCSCG--GGEEEECSC
T ss_pred             hcCCeEEEeCCCCcHHHHHHHHHHHHHHhc----------CCcEEEEcCchHHHHHHHHHHHHhhcccc--cceeeeecc
Confidence            467899999999999999999887765432          33699999999999999999998866555  677666666


Q ss_pred             cccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          86 VPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        86 ~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      .....+...+.+ .++.  +    ++|..+..........+ +.+.++|.||+
T Consensus        90 ~~~~~~~~~~~~-~~i~--i----~t~~~~~~~~~~~~~~~-~~~~~vIiDE~  134 (200)
T d1wp9a1          90 KSPEERSKAWAR-AKVI--V----ATPQTIENDLLAGRISL-EDVSLIVFDEA  134 (200)
T ss_dssp             SCHHHHHHHHHH-CSEE--E----ECHHHHHHHHHTTSCCT-TSCSEEEEETG
T ss_pred             cchhHHHHhhhc-cccc--c----cccchhHHHHhhhhhhc-cccceEEEEeh
Confidence            555444333333 2220  1    23444433222222222 24778888886

>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=99.30  E-value=2.5e-12  Score=100.54  Aligned_cols=87  Identities=24%  Similarity=0.271  Sum_probs=73.8

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHH
Q psy7786         152 PESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRE  231 (252)
Q Consensus       152 ~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~  231 (252)
                      ..++ +.+.+.++..|+++|..+++..+.|++++++++||+|||..++++.+.....           +.++||++|||+
T Consensus        30 ~~~~-~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~-----------~~rvliv~Pt~~   97 (237)
T d1gkub1          30 LKEF-VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK-----------GKRCYVIFPTSL   97 (237)
T ss_dssp             HHHH-HHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT-----------SCCEEEEESCHH
T ss_pred             HHHH-HHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh-----------cCeEEEEeccHH
Confidence            3344 4455667889999999999999999999999999999999998888754322           457999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCC
Q psy7786         232 LARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       232 ~a~~i~~~l~~l~~~~~i~  250 (252)
                      +++|++++++++++.+++.
T Consensus        98 La~Q~~~~l~~~~~~~~~~  116 (237)
T d1gkub1          98 LVIQAAETIRKYAEKAGVG  116 (237)
T ss_dssp             HHHHHHHHHHHHHTTTCCS
T ss_pred             HHHHHHHHHHHHHHHcCCc
Confidence            9999999999999988764

>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=99.13  E-value=3.6e-11  Score=92.82  Aligned_cols=141  Identities=16%  Similarity=0.181  Sum_probs=94.7

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCccc
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPM   88 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~   88 (252)
                      +.++++.||||||..|+..+...+..           +-++++++||..|+.|.++.++++....+  +.+..++|+.+.
T Consensus        78 ~~LL~GdvGsGKT~V~~~a~~~~~~~-----------g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~--~~v~~l~~~~~~  144 (233)
T d2eyqa3          78 DRLVCGDVGFGKTEVAMRAAFLAVDN-----------HKQVAVLVPTTLLAQQHYDNFRDRFANWP--VRIEMISRFRSA  144 (233)
T ss_dssp             EEEEECCCCTTTHHHHHHHHHHHHTT-----------TCEEEEECSSHHHHHHHHHHHHHHSTTTT--CCEEEESTTSCH
T ss_pred             CeEEEcCCCCCcHHHHHHHHHHHHHc-----------CCceEEEccHHHhHHHHHHHHHHHHhhCC--CEEEeccCcccc
Confidence            78999999999999999998877643           56899999999999999999998877666  788888998877


Q ss_pred             CcchhhhhhcccccCCccccccCCccccCCChhHHH--HHhhhhceeeccCCCCCcccccccCCCCHHHHHHHHHCCCCC
Q psy7786          89 NQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHD--IIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKK  166 (252)
Q Consensus        89 ~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~--~l~~~~~~~V~de~~~~~~~~~~~~~l~~~l~~~l~~~~~~~  166 (252)
                      .++.+.+..       +..  +.+..++.+-.-...  .++ ++.++|.||.        .+.+..+             
T Consensus       145 ~~~~~~~~~-------~~~--g~~~iviGths~l~~~~~f~-~LgLiIiDEe--------H~fg~kQ-------------  193 (233)
T d2eyqa3         145 KEQTQILAE-------VAE--GKIDILIGTHKLLQSDVKFK-DLGLLIVDEE--------HRFGVRH-------------  193 (233)
T ss_dssp             HHHHHHHHH-------HHT--TCCSEEEECTHHHHSCCCCS-SEEEEEEESG--------GGSCHHH-------------
T ss_pred             hhHHHHHHH-------HhC--CCCCEEEeehhhhccCCccc-cccceeeech--------hhhhhHH-------------
Confidence            665554433       110  123345544443322  233 4888888875        2333322             


Q ss_pred             ChHHHHhhhhhhhcCCcEEEEccCCCchhHHh
Q psy7786         167 PTPIQVQGIPAALSGRDIIGIAFTGSGKTLVF  198 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~  198 (252)
                           ...+.....+-+++..+.|..-+|++.
T Consensus       194 -----~~~l~~~~~~~~~l~~SATPiprtl~~  220 (233)
T d2eyqa3         194 -----KERIKAMRANVDILTLTATPIPRTLNM  220 (233)
T ss_dssp             -----HHHHHHHHTTSEEEEEESSCCCHHHHH
T ss_pred             -----HHHHHhhCCCCCEEEEecchhHHHHHH
Confidence                 222222334456777777777776654

>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=99.09  E-value=1.4e-10  Score=91.15  Aligned_cols=107  Identities=18%  Similarity=0.184  Sum_probs=78.6

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCccc
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPM   88 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~   88 (252)
                      +-++++-||||||..|+..+...+..           +-++++++||..||.|.++.++++-...|  +.+..++|+.+.
T Consensus       106 ~rLL~GdvGSGKT~Va~~a~~~~~~~-----------g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~--~~v~~l~~~~~~  172 (264)
T d1gm5a3         106 NRLLQGDVGSGKTVVAQLAILDNYEA-----------GFQTAFMVPTSILAIQHYRRTVESFSKFN--IHVALLIGATTP  172 (264)
T ss_dssp             CCEEECCSSSSHHHHHHHHHHHHHHH-----------TSCEEEECSCHHHHHHHHHHHHHHHTCSS--CCEEECCSSSCH
T ss_pred             eeeeeccccccccHHHHHHHHHHHhc-----------ccceeEEeehHhhhHHHHHHHHHhhhhcc--ccceeeccccch
Confidence            67999999999999999999887755           44799999999999999999998887777  788899999887


Q ss_pred             CcchhhhhhcccccCCccccccCCccccCCChhHHH--HHhhhhceeeccCC
Q psy7786          89 NQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHD--IIRRNLRILVEGDD  138 (252)
Q Consensus        89 ~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~--~l~~~~~~~V~de~  138 (252)
                      +++.+.+.+-       ..  +.+..++++-.-...  .++ ++.++|.||-
T Consensus       173 ~~r~~~~~~~-------~~--g~~~iiIGThsl~~~~~~f~-~LglviiDEq  214 (264)
T d1gm5a3         173 SEKEKIKSGL-------RN--GQIDVVIGTHALIQEDVHFK-NLGLVIIDEQ  214 (264)
T ss_dssp             HHHHHHHHHH-------HS--SCCCEEEECTTHHHHCCCCS-CCCEEEEESC
T ss_pred             HHHHHHHHHH-------HC--CCCCEEEeehHHhcCCCCcc-ccceeeeccc
Confidence            6655554431       10  123344444333332  233 4888888885

>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=99.06  E-value=4.3e-11  Score=91.08  Aligned_cols=84  Identities=23%  Similarity=0.366  Sum_probs=71.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcH
Q psy7786         151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSR  230 (252)
Q Consensus       151 l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr  230 (252)
                      +++.+...+.+.|+..+++.|..+++..+++++++++++||+|||.++.++++..+..           +.++|+++|++
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~-----------~~~vl~l~P~~   78 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-----------GGKSLYVVPLR   78 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-----------TCCEEEEESSH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc-----------cCcceeecccH
Confidence            5677888999999999999999999999999999999999999999988888776543           34799999999


Q ss_pred             HHHHHHHHHHHHHHh
Q psy7786         231 ELARQTHDIIQYYCA  245 (252)
Q Consensus       231 ~~a~~i~~~l~~l~~  245 (252)
                      +++.|..+.++++..
T Consensus        79 ~L~~q~~~~~~~~~~   93 (202)
T d2p6ra3          79 ALAGEKYESFKKWEK   93 (202)
T ss_dssp             HHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999986654

>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=99.02  E-value=2.8e-10  Score=86.63  Aligned_cols=88  Identities=26%  Similarity=0.408  Sum_probs=76.2

Q ss_pred             ccccCCCCHHHHHHHHHC-CCCCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         145 SFRLMKLPESLVRALEAK-GIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       145 ~~~~~~l~~~l~~~l~~~-~~~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ..+.+++++...+.+... |+..+.+.|..++++.+.|+|++++++||+|||.+|.+|.+..              ..++
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~--------------~~~~   68 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL--------------NGLT   68 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS--------------SSEE
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc--------------cCce
Confidence            345677888888888877 8889999999999999999999999999999999999988741              4579


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhh
Q psy7786         224 LIICPSRELARQTHDIIQYYCAA  246 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~  246 (252)
                      ++++|++.++.|..+.++..+..
T Consensus        69 ~~v~P~~~L~~q~~~~l~~~~~~   91 (206)
T d1oywa2          69 VVVSPLISLMKDQVDQLQANGVA   91 (206)
T ss_dssp             EEECSCHHHHHHHHHHHHHTTCC
T ss_pred             EEeccchhhhhhHHHHHHhhccc
Confidence            99999999999999999876543

>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=98.87  E-value=8.8e-10  Score=78.03  Aligned_cols=55  Identities=20%  Similarity=0.326  Sum_probs=45.1

Q ss_pred             cccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHH
Q psy7786           3 TYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ   67 (252)
Q Consensus         3 ~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~   67 (252)
                      .+.+|+++++.+|||||||..+...++......          +.++++++|+++|+.|.++.+.
T Consensus         3 ~l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~----------~~~vli~~p~~~l~~q~~~~~~   57 (140)
T d1yksa1           3 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR----------RLRTLVLAPTRVVLSEMKEAFH   57 (140)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT----------TCCEEEEESSHHHHHHHHHHTT
T ss_pred             HHHcCCcEEEEcCCCCChhHHHHHHHHHHhhhc----------CceeeeeecchhHHHHHHHHhh
Confidence            567899999999999999988776666655442          4579999999999999887653

>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=98.73  E-value=7.5e-09  Score=82.41  Aligned_cols=109  Identities=18%  Similarity=0.171  Sum_probs=64.9

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeC
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIG   84 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g   84 (252)
                      ++.+..++.+|||+|||+.... ++..+....         ..++||++|+++|+.|..+.+.+++....  ..+....+
T Consensus       126 l~~~~~il~~pTGsGKT~i~~~-i~~~~~~~~---------~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~--~~~~~~~~  193 (282)
T d1rifa_         126 LVNRRRILNLPTSAGRSLIQAL-LARYYLENY---------EGKILIIVPTTALTTQMADDFVDYRLFSH--AMIKKIGG  193 (282)
T ss_dssp             HHHSEEEECCCTTSCHHHHHHH-HHHHHHHHC---------SSEEEEECSSHHHHHHHHHHHHHHTSCCG--GGEEECST
T ss_pred             HhcCCceeEEEcccCccHHHHH-HHHHhhhcc---------cceEEEEEcCchhHHHHHHHHHHhhcccc--ccceeecc
Confidence            4456688999999999976443 333333332         34799999999999999999988754322  34444555


Q ss_pred             CcccCcchhhhhhcccccCCccccccCCccccCCChhHHHHHhhhhceeeccCC
Q psy7786          85 GVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDD  138 (252)
Q Consensus        85 ~~~~~~~~~~l~~~~~i~~~i~t~~~~p~~l~~~~~~~~~~l~~~~~~~V~de~  138 (252)
                      |.......   ....++.  +    ++...+......    +.+...++|.||+
T Consensus       194 g~~~~~~~---~~~~~i~--i----~t~qs~~~~~~~----~~~~f~~VIvDEa  234 (282)
T d1rifa_         194 GASKDDKY---KNDAPVV--V----GTWQTVVKQPKE----WFSQFGMMMNDEC  234 (282)
T ss_dssp             TCSSTTCC---CTTCSEE--E----ECHHHHTTSCGG----GGGGEEEEEEETG
T ss_pred             eecccccc---cccceEE--E----Eeeehhhhhccc----ccCCCCEEEEECC
Confidence            54332221   1111220  1    224444444332    2234789999997

>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=98.61  E-value=2.8e-08  Score=70.14  Aligned_cols=50  Identities=22%  Similarity=0.088  Sum_probs=37.2

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      .+..++.+|||||||..+  +.+  +..          .+-+++|++|+++|++|..+.+.+..
T Consensus         8 ~~~~ll~apTGsGKT~~~--~~~--~~~----------~~~~vli~~P~~~l~~q~~~~~~~~~   57 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKV--PAA--YAA----------QGYKVLVLNPSVAATLGFGAYMSKAH   57 (136)
T ss_dssp             CEEEEEECCTTSCTTTHH--HHH--HHT----------TTCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHH--HHH--HHH----------cCCcEEEEcChHHHHHHHHHHHHHHh
Confidence            345689999999999643  322  211          24579999999999999998887653

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=98.39  E-value=3.3e-07  Score=68.64  Aligned_cols=70  Identities=19%  Similarity=0.162  Sum_probs=55.9

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .|...|..++.... +++.+++++||+|||..++..+...+...          +.++++++|++.+++|.++.++++..
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~----------~~~il~i~P~~~L~~q~~~~~~~~~~   77 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY----------GGKVLMLAPTKPLVLQHAESFRRLFN   77 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS----------CSCEEEECSSHHHHHHHHHHHHHHBC
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc----------CCcEEEEcCchHHHHHHHHHHHHhhc
Confidence            68999999887665 55789999999999998777665544321          45799999999999999999988754


Q ss_pred             h
Q psy7786         246 A  246 (252)
Q Consensus       246 ~  246 (252)
                      .
T Consensus        78 ~   78 (200)
T d1wp9a1          78 L   78 (200)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=98.33  E-value=2.6e-07  Score=69.84  Aligned_cols=53  Identities=25%  Similarity=0.213  Sum_probs=40.3

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      +++++..++.+|||+|||+..+. ++..+             +.++||++|+++|+.|..+.++.++
T Consensus        82 ~~~~~~~ll~~~tG~GKT~~a~~-~~~~~-------------~~~~Liv~p~~~L~~q~~~~~~~~~  134 (206)
T d2fz4a1          82 WLVDKRGCIVLPTGSGKTHVAMA-AINEL-------------STPTLIVVPTLALAEQWKERLGIFG  134 (206)
T ss_dssp             HTTTSEEEEEESSSTTHHHHHHH-HHHHS-------------CSCEEEEESSHHHHHHHHHHHGGGC
T ss_pred             HHhCCCcEEEeCCCCCceehHHh-HHHHh-------------cCceeEEEcccchHHHHHHHHHhhc
Confidence            45677788999999999976543 22221             2358999999999999998887663

>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=98.23  E-value=2.4e-07  Score=73.99  Aligned_cols=57  Identities=23%  Similarity=0.270  Sum_probs=47.6

Q ss_pred             hhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         178 ALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       178 ~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ...+++.++.++||+|||.+|+.+++......          +.++||++|||+||+|+++.++.++
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~----------~~~~lvi~Ptr~La~q~~~~l~~~~   62 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR----------GLRTLILAPTRVVAAEMEEALRGLP   62 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH----------TCCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc----------CCEEEEEccHHHHHHHHHHHHhcCC
Confidence            34678999999999999999988888766553          4579999999999999999887543

>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=97.93  E-value=4e-05  Score=58.31  Aligned_cols=89  Identities=24%  Similarity=0.148  Sum_probs=68.7

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHhhhhhhh----cC--CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEE
Q psy7786         150 KLPESLVRALEAKGIKKPTPIQVQGIPAAL----SG--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG  223 (252)
Q Consensus       150 ~l~~~l~~~l~~~~~~~p~~iQ~~~~p~~~----~~--~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~  223 (252)
                      ..+.+..+.+....--.+++-|..++....    .+  .+.++++++|+|||..|+..+..-+.           .+.|+
T Consensus        39 ~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~-----------~g~qv  107 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD-----------NHKQV  107 (233)
T ss_dssp             CCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT-----------TTCEE
T ss_pred             CCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH-----------cCCce
Confidence            345666666666655567777877775543    22  47899999999999999888776543           36789


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCCC
Q psy7786         224 LIICPSRELARQTHDIIQYYCAALPI  249 (252)
Q Consensus       224 LIf~~tr~~a~~i~~~l~~l~~~~~i  249 (252)
                      ++++||.-||.|.++.++++-..+++
T Consensus       108 ~~l~Pt~~La~Q~~~~~~~~~~~~~~  133 (233)
T d2eyqa3         108 AVLVPTTLLAQQHYDNFRDRFANWPV  133 (233)
T ss_dssp             EEECSSHHHHHHHHHHHHHHSTTTTC
T ss_pred             EEEccHHHhHHHHHHHHHHHHhhCCC
Confidence            99999999999999999988777764

>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=97.64  E-value=0.00013  Score=56.55  Aligned_cols=84  Identities=23%  Similarity=0.115  Sum_probs=64.4

Q ss_pred             HHHHH-HHCCCCCChHHHHhhhhhhhc----C--CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEc
Q psy7786         155 LVRAL-EAKGIKKPTPIQVQGIPAALS----G--RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC  227 (252)
Q Consensus       155 l~~~l-~~~~~~~p~~iQ~~~~p~~~~----~--~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~  227 (252)
                      +.+.+ +...| .+|.-|..++.....    +  .+.++++.+|+|||..++..+...+..           +.|+++++
T Consensus        72 l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~-----------g~q~~~m~  139 (264)
T d1gm5a3          72 LAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA-----------GFQTAFMV  139 (264)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH-----------TSCEEEEC
T ss_pred             HHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc-----------ccceeEEe
Confidence            33443 33333 678889888866532    2  367999999999999999888765544           56899999


Q ss_pred             CcHHHHHHHHHHHHHHHhhCCCC
Q psy7786         228 PSRELARQTHDIIQYYCAALPIG  250 (252)
Q Consensus       228 ~tr~~a~~i~~~l~~l~~~~~i~  250 (252)
                      ||.-+|.|.++.++++-+.+++.
T Consensus       140 Pt~~La~Qh~~~~~~~f~~~~~~  162 (264)
T d1gm5a3         140 PTSILAIQHYRRTVESFSKFNIH  162 (264)
T ss_dssp             SCHHHHHHHHHHHHHHHTCSSCC
T ss_pred             ehHhhhHHHHHHHHHhhhhcccc
Confidence            99999999999999888876653

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.60  E-value=5.5e-05  Score=56.55  Aligned_cols=67  Identities=22%  Similarity=0.163  Sum_probs=52.1

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      .+.+.|..++...+.+...++.+++|+|||...+. .+..    .         ..++||+||++.+++|..+.+++++.
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~-~~~~----~---------~~~~Liv~p~~~L~~q~~~~~~~~~~  135 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMA-AINE----L---------STPTLIVVPTLALAEQWKERLGIFGE  135 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHH-HHHH----S---------CSCEEEEESSHHHHHHHHHHHGGGCG
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHh-HHHH----h---------cCceeEEEcccchHHHHHHHHHhhcc
Confidence            46778888888888888888999999999986432 2221    1         34699999999999999999887654


Q ss_pred             h
Q psy7786         246 A  246 (252)
Q Consensus       246 ~  246 (252)
                      .
T Consensus       136 ~  136 (206)
T d2fz4a1         136 E  136 (206)
T ss_dssp             G
T ss_pred             c
Confidence            3

>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=97.50  E-value=0.00012  Score=57.53  Aligned_cols=69  Identities=28%  Similarity=0.275  Sum_probs=54.5

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      .|...|..++...+.++..++.++||+|||..... ++..+....         ..++||++|++++++|.++.+.+++
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~-i~~~~~~~~---------~~k~Liivp~~~Lv~Q~~~~f~~~~  181 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQAL-LARYYLENY---------EGKILIIVPTTALTTQMADDFVDYR  181 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHH-HHHHHHHHC---------SSEEEEECSSHHHHHHHHHHHHHHT
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHH-HHHHhhhcc---------cceEEEEEcCchhHHHHHHHHHHhh
Confidence            58889999998888888899999999999975332 333333321         3479999999999999999998775

>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=97.40  E-value=9.2e-05  Score=51.04  Aligned_cols=53  Identities=23%  Similarity=0.335  Sum_probs=41.5

Q ss_pred             cCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHH
Q psy7786         180 SGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQY  242 (252)
Q Consensus       180 ~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~  242 (252)
                      .|++.++.++||+|||..++...+......          +.++++++|++.+++|..+.+..
T Consensus         6 ~~~~~il~~~tGsGKT~~~~~~~~~~~~~~----------~~~vli~~p~~~l~~q~~~~~~~   58 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFLPQILAECARR----------RLRTLVLAPTRVVLSEMKEAFHG   58 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHHT----------TCCEEEEESSHHHHHHHHHHTTT
T ss_pred             cCCcEEEEcCCCCChhHHHHHHHHHHhhhc----------CceeeeeecchhHHHHHHHHhhh
Confidence            578999999999999987655555544332          45799999999999999887643

>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=97.15  E-value=0.00039  Score=54.57  Aligned_cols=57  Identities=18%  Similarity=0.083  Sum_probs=39.5

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      ...++|.|+.|||||.+.+-=+.. +......      ..-+.|++++|+.+|..+.+.+.++.
T Consensus        14 ~~~~lI~g~aGTGKTt~l~~rv~~-ll~~~~~------~~~~ILvlt~tn~a~~~i~~~~~~~~   70 (306)
T d1uaaa1          14 TGPCLVLAGAGSGKTRVITNKIAH-LIRGCGY------QARHIAAVTFTNKAAREMKERVGQTL   70 (306)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHH-HHHHHCC------CGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEeeCCccHHHHHHHHHHH-HHHhcCC------ChhHEEEEeCcHHHHHHHHHHHHHhc
Confidence            356899999999999765433333 3332211      12369999999999999888776653

>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=97.08  E-value=0.00049  Score=47.36  Aligned_cols=49  Identities=20%  Similarity=0.057  Sum_probs=36.9

Q ss_pred             CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       182 ~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +..++.++||+|||......+     ..         .+.+++|.+|++.+++|.++.+.+..
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~-----~~---------~~~~vli~~P~~~l~~q~~~~~~~~~   57 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAY-----AA---------QGYKVLVLNPSVAATLGFGAYMSKAH   57 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHH-----HT---------TTCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHH-----HH---------cCCcEEEEcChHHHHHHHHHHHHHHh
Confidence            457889999999997532211     11         25579999999999999999887653

>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=97.06  E-value=0.00061  Score=53.88  Aligned_cols=59  Identities=22%  Similarity=0.175  Sum_probs=41.1

Q ss_pred             CCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHh
Q psy7786           7 SRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA   72 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~   72 (252)
                      +..++|.|+.|||||.+.+-=+.+.+ .....      ..-+.+++++|+..|..+.+.+......
T Consensus        24 ~g~~lV~g~aGSGKTt~l~~ri~~ll-~~~~~------~p~~il~lt~t~~aa~~~~~~~~~~~~~   82 (318)
T d1pjra1          24 EGPLLIMAGAGSGKTRVLTHRIAYLM-AEKHV------APWNILAITFTNKAAREMRERVQSLLGG   82 (318)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHH-HTTCC------CGGGEEEEESSHHHHHHHHHHHHHHHGG
T ss_pred             CCCEEEEecCCccHHHHHHHHHHHHH-HcCCC------CHHHeEeEeccHHHHHHHHHHHHhhccc
Confidence            34699999999999976644333333 22210      1236899999999999998888766544

>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=95.70  E-value=0.017  Score=43.89  Aligned_cols=76  Identities=21%  Similarity=0.256  Sum_probs=59.7

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCc
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQ   90 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~   90 (252)
                      ++.-+||=|||+...+|+.-..+.           |-.+=|++..--||..=.+++..+-+.+|  +++.+...+.+..+
T Consensus        97 iaem~TGEGKTL~a~l~a~l~al~-----------g~~vhvvTvNdyLA~RDae~m~~iy~~lG--lsvg~~~~~~~~~~  163 (273)
T d1tf5a3          97 IAEMKTGEGKTLTSTLPVYLNALT-----------GKGVHVVTVNEYLASRDAEQMGKIFEFLG--LTVGLNLNSMSKDE  163 (273)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTT-----------SSCEEEEESSHHHHHHHHHHHHHHHHHTT--CCEEECCTTSCHHH
T ss_pred             heeecCCCcchhHHHHHHHHHHhc-----------CCCceEEecCccccchhhhHHhHHHHHcC--CCccccccccCHHH
Confidence            788899999999999998866554           33588899999999999999999999999  78887776655444


Q ss_pred             chhhhhhcccc
Q psy7786          91 SLDVIKKGIQY  101 (252)
Q Consensus        91 ~~~~l~~~~~i  101 (252)
                      +.+..  .+||
T Consensus       164 r~~~Y--~~di  172 (273)
T d1tf5a3         164 KREAY--AADI  172 (273)
T ss_dssp             HHHHH--HSSE
T ss_pred             HHHHh--hCCc
Confidence            44333  3455

>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=95.51  E-value=0.018  Score=46.14  Aligned_cols=64  Identities=19%  Similarity=0.148  Sum_probs=43.0

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCC
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~   74 (252)
                      +++++=.+++++.|||||... .-++..+.....      ..+.+.++.+||.--|..+.+.........+
T Consensus       160 al~~~~~vI~G~pGTGKTt~i-~~~l~~l~~~~~------~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~  223 (359)
T d1w36d1         160 ALTRRISVISGGPGTGKTTTV-AKLLAALIQMAD------GERCRIRLAAPTGKAAARLTESLGKALRQLP  223 (359)
T ss_dssp             HHTBSEEEEECCTTSTHHHHH-HHHHHHHHHTCS------SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSS
T ss_pred             HHcCCeEEEEcCCCCCceehH-HHHHHHHHHHHh------ccCCeEEEecCcHHHHHHHHHHHHHHHhhcC
Confidence            346777899999999999663 233333332211      1366799999999988888777666555443

>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=95.49  E-value=0.0014  Score=52.22  Aligned_cols=43  Identities=26%  Similarity=0.308  Sum_probs=29.8

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHH
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSREL   58 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreL   58 (252)
                      +..+++++++++||||||. ++-.++..+.           ..-+.+.+--++||
T Consensus       163 v~~~~nili~G~tgSGKTT-~l~al~~~i~-----------~~~rivtiEd~~El  205 (323)
T d1g6oa_         163 IAIGKNVIVCGGTGSGKTT-YIKSIMEFIP-----------KEERIISIEDTEEI  205 (323)
T ss_dssp             HHHTCCEEEEESTTSSHHH-HHHHHGGGSC-----------TTCCEEEEESSCCC
T ss_pred             HHhCCCEEEEeeccccchH-HHHHHhhhcc-----------cccceeeccchhhh
Confidence            4568899999999999994 3333333221           23467888888887

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

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: Bacillus caldotenax [TaxId: 1395]

Probab=95.27  E-value=0.016  Score=47.30  Aligned_cols=49  Identities=22%  Similarity=0.308  Sum_probs=37.1

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      ++.++.+-||||||+... -++.    ..         +-.+|||+|+..+|.|+++.++.|.
T Consensus        32 ~~q~l~GltGS~ka~~iA-~l~~----~~---------~rp~LVVt~n~~~A~qL~~dL~~~l   80 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTIS-NVIA----QV---------NKPTLVIAHNKTLAGQLYSELKEFF   80 (413)
T ss_dssp             SEEEEEECTTSCHHHHHH-HHHH----HH---------TCCEEEECSSHHHHHHHHHHHHHHC
T ss_pred             CcEEEeCCCCcHHHHHHH-HHHH----Hh---------CCCEEEEeCCHHHHHHHHHHHHHHc
Confidence            578899999999995442 2222    21         1138999999999999999998874

>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=94.59  E-value=0.057  Score=41.48  Aligned_cols=69  Identities=19%  Similarity=0.085  Sum_probs=45.6

Q ss_pred             hHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         168 TPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       168 ~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      ++-|..++..  ....+++.++.|+|||...+.-+.. +..+..      ....+++|++.|+..|+.+...+.++..
T Consensus         3 ~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~-ll~~~~------~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           3 NPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAH-LIRGCG------YQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHH-HHHHHC------CCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHH-HHHhcC------CChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            3456665532  2345888999999999875543332 333221      1124699999999999999888876554

>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=94.57  E-value=0.023  Score=46.44  Aligned_cols=47  Identities=19%  Similarity=0.296  Sum_probs=33.3

Q ss_pred             CcccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHH
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELA   59 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa   59 (252)
                      |.=...+++++.++||||||.++ ..++..+...          +..++|+=|.-|+.
T Consensus        45 ~~~~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~----------g~~~iiiD~kge~~   91 (433)
T d1e9ra_          45 PRDAEPRHLLVNGATGTGKSVLL-RELAYTGLLR----------GDRMVIVDPNGDML   91 (433)
T ss_dssp             CGGGGGGCEEEEECTTSSHHHHH-HHHHHHHHHT----------TCEEEEEEETTHHH
T ss_pred             CCCcccceEEEEeCCCCcHHHHH-HHHHHHHHhC----------CCCEEEEeCChhHH
Confidence            34455689999999999999654 4455444432          44688888988864

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=94.50  E-value=0.013  Score=40.16  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=22.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +.++||||+|++.|+++++.|++.+
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~G   59 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVALG   59 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhccc
Confidence            4579999999999999999998765

>d1s2ma2 c.37.1.19 (A:252-422) 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=94.25  E-value=0.046  Score=38.64  Aligned_cols=25  Identities=16%  Similarity=0.094  Sum_probs=22.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..++||||+|++.|+.++..|+..+
T Consensus        32 ~~k~iVF~~~~~~~~~l~~~L~~~g   56 (171)
T d1s2ma2          32 INQAIIFCNSTNRVELLAKKITDLG   56 (171)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEeeeehhhHhHHhhhccc
Confidence            4689999999999999999998764

>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=94.18  E-value=0.021  Score=40.22  Aligned_cols=26  Identities=19%  Similarity=0.156  Sum_probs=19.5

Q ss_pred             CcEEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786           8 RDIIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      |++++.+|+|||||. .+--++..+..
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            789999999999995 44455555544

>d1hv8a2 c.37.1.19 (A:211-365) 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=93.99  E-value=0.038  Score=38.41  Aligned_cols=25  Identities=16%  Similarity=0.456  Sum_probs=21.8

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..++||||+|++.|+++++.|++.+
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~g   52 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDIG   52 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEECchHHHHHHHhhhcccc
Confidence            4579999999999999999998754

>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=93.96  E-value=0.046  Score=40.52  Aligned_cols=55  Identities=20%  Similarity=0.247  Sum_probs=36.1

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      .+...+++.+.|.|||...+ .++..+....        ...++||++|.. +..|-.+++.++.
T Consensus        30 ~~~g~iLaDe~GlGKT~~~i-~~~~~~~~~~--------~~~~~LIv~p~~-l~~~W~~e~~~~~   84 (230)
T d1z63a1          30 LGFGICLADDMGLGKTLQTI-AVFSDAKKEN--------ELTPSLVICPLS-VLKNWEEELSKFA   84 (230)
T ss_dssp             TTCCEEECCCTTSCHHHHHH-HHHHHHHHTT--------CCSSEEEEECST-THHHHHHHHHHHC
T ss_pred             cCCCEEEEeCCCCChHHHHH-Hhhhhhhhcc--------cccccceecchh-hhhHHHHHHHhhc
Confidence            35568899999999998753 3344443332        134589999854 6666666666654

>d1fuka_ 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=93.93  E-value=0.035  Score=39.00  Aligned_cols=37  Identities=11%  Similarity=0.088  Sum_probs=27.2

Q ss_pred             HHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         200 LPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       200 ~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +..+..++++.        ...++||||+|+..++++++.|+..+
T Consensus        15 ~~~L~~ll~~~--------~~~k~iIF~~s~~~~~~l~~~L~~~~   51 (162)
T d1fuka_          15 YECLTDLYDSI--------SVTQAVIFCNTRRKVEELTTKLRNDK   51 (162)
T ss_dssp             HHHHHHHHHHT--------TCSCEEEEESSHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhC--------CCCcEEEEEEEEchHHHHHHHHhhcC
Confidence            45555555442        24579999999999999999987653

>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=93.64  E-value=0.014  Score=48.18  Aligned_cols=18  Identities=39%  Similarity=0.565  Sum_probs=15.6

Q ss_pred             CCCcEEEEcCCCchHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a   23 (252)
                      ..+|+++.+|||||||+-
T Consensus        48 ~ksNILliGPTGvGKTlL   65 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCCCEEEECCTTSSHHHH
T ss_pred             ccccEEEECCCCCCHHHH
Confidence            467999999999999953

>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=93.64  E-value=0.13  Score=39.63  Aligned_cols=72  Identities=24%  Similarity=0.247  Sum_probs=43.3

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCC
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGG   85 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~   85 (252)
                      ++...+++-..|+|||+.-+ .++..+......   .......+|||+|.. |..|=.++++++....   ......+|+
T Consensus        78 ~~~g~iLaDemGlGKT~qai-a~l~~l~~~~~~---~~~~~~~~LIV~P~s-l~~qW~~Ei~k~~~~~---~~~v~~~~~  149 (298)
T d1z3ix2          78 NSYGCIMADEMGLGKTLQCI-TLIWTLLKQSPD---CKPEIDKVIVVSPSS-LVRNWYNEVGKWLGGR---VQPVAIDGG  149 (298)
T ss_dssp             TCCEEEECCCTTSCHHHHHH-HHHHHHHHCCTT---SSCSCSCEEEEECHH-HHHHHHHHHHHHHGGG---CCEEEECSS
T ss_pred             cCCceEEEeCCCCCHHHHHH-HHHHHHHHhccc---ccCCCCcEEEEccch-hhHHHHHHHHhhcCCc---eeEEEEeCc
Confidence            45668899999999997532 233333332211   111233589999986 7777777777665431   444555555

>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=93.35  E-value=0.12  Score=40.05  Aligned_cols=71  Identities=21%  Similarity=0.155  Sum_probs=48.0

Q ss_pred             CChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       166 ~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      ..++-|..++..  .+..+++.++.|+|||...+--+...+....       ....++++++.|+..|..+...+.....
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~-------~~p~~il~lt~t~~aa~~~~~~~~~~~~   81 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKH-------VAPWNILAITFTNKAAREMRERVQSLLG   81 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTC-------CCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCC-------CCHHHeEeEeccHHHHHHHHHHHHhhcc
Confidence            355666666643  2345899999999999876554443332211       1123699999999999999998876543

>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=93.22  E-value=0.18  Score=36.82  Aligned_cols=60  Identities=18%  Similarity=0.164  Sum_probs=32.3

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc-Cc-HHHHHHHHHHHHHHHHhCCCCcceeeeeCC
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC-PS-RELARQTHDIIQYYCAALPIPLRTCLAIGG   85 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~-pt-reLa~q~~~~~~~l~~~~~~~~~~~~~~g~   85 (252)
                      +++.+|||+|||.+-.==. .++...          +-++.+++ -| |.=|   .+.++.+++.++  +.+.....+
T Consensus        12 i~lvGptGvGKTTTiAKLA-~~~~~~----------g~kV~lit~Dt~R~gA---~eQL~~~a~~l~--v~~~~~~~~   73 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLA-RQFEQQ----------GKSVMLAAGDTFRAAA---VEQLQVWGQRNN--IPVIAQHTG   73 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HHHHTT----------TCCEEEECCCTTCHHH---HHHHHHHHHHTT--CCEECCSTT
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHC----------CCcEEEEecccccccc---hhhhhhhhhhcC--CcccccccC
Confidence            5569999999996643212 222211          22344444 34 4444   344677778887  444333333

>d2j0sa2 c.37.1.19 (A:244-411) 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=92.87  E-value=0.097  Score=36.82  Aligned_cols=25  Identities=8%  Similarity=0.105  Sum_probs=22.1

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..++||||++++.|+.+++.++..+
T Consensus        34 ~~k~iiF~~~~~~~~~~~~~l~~~~   58 (168)
T d2j0sa2          34 ITQAVIFCNTKRKVDWLTEKMREAN   58 (168)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTT
T ss_pred             CCceEEEeeeHHHHHHHHHHhhhcc
Confidence            4589999999999999999998654

>d1t5ia_ 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=92.56  E-value=0.1  Score=36.65  Aligned_cols=26  Identities=8%  Similarity=-0.162  Sum_probs=22.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      ..++||||++++.++.+++.|++.+.
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~~~   52 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQNF   52 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             CCeEEEEEeeeecchhhhhhhccccc
Confidence            45799999999999999999987543

>d1c4oa2 c.37.1.19 (A:410-583) 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=92.09  E-value=0.099  Score=37.04  Aligned_cols=25  Identities=12%  Similarity=0.121  Sum_probs=22.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +.++||||+|++.|+.+++.|++.+
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~G   55 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEHG   55 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHTT
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhcC
Confidence            6689999999999999999998653

>d1a1va2 c.37.1.14 (A:326-624) 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=91.75  E-value=0.052  Score=41.84  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=22.3

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +.++||||+||+.|+++++.|++.+
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~G   60 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALG   60 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTT
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCC
Confidence            5689999999999999999998754

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=91.12  E-value=0.14  Score=38.72  Aligned_cols=39  Identities=21%  Similarity=0.123  Sum_probs=25.6

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC   53 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~   53 (252)
                      ..|.=+++.|+||+||| +|++-+..++...         .+..+++++
T Consensus        33 ~~G~l~vi~G~~G~GKT-~~~~~la~~~a~~---------~g~~v~~~s   71 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKS-TFVRQQALQWGTA---------MGKKVGLAM   71 (277)
T ss_dssp             CTTCEEEEECSTTSSHH-HHHHHHHHHHHHT---------SCCCEEEEE
T ss_pred             CCCeEEEEEeCCCCCHH-HHHHHHHHhhhhh---------cccceeEee
Confidence            45667899999999999 5555554433222         244577776

>d1oywa3 c.37.1.19 (A:207-406) 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=91.08  E-value=0.21  Score=36.12  Aligned_cols=25  Identities=32%  Similarity=0.429  Sum_probs=21.8

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +.++||||+|+..|+.++..|+..+
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~~~   54 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQSKG   54 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEEeeehhhHHhhhhhccCC
Confidence            4579999999999999999988654

>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=90.74  E-value=0.056  Score=37.04  Aligned_cols=17  Identities=29%  Similarity=0.499  Sum_probs=14.9

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      +.|++++.+++|||||.
T Consensus         1 ~~k~I~l~G~~GsGKST   17 (169)
T d1kaga_           1 EKRNIFLVGPMGAGKST   17 (169)
T ss_dssp             CCCCEEEECCTTSCHHH
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            35789999999999994

>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=90.66  E-value=0.052  Score=42.37  Aligned_cols=19  Identities=37%  Similarity=0.496  Sum_probs=15.9

Q ss_pred             CCCcEEEEcCCCchHHHHh
Q psy7786           6 NSRDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~   24 (252)
                      .++.++..+|||+|||+..
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999543

>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=90.40  E-value=0.17  Score=34.79  Aligned_cols=24  Identities=21%  Similarity=0.319  Sum_probs=17.4

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      +.++++.||||| +++--++..+..
T Consensus         5 i~itG~~GSGKT-TL~~~L~~~l~~   28 (170)
T d1np6a_           5 LAFAAWSGTGKT-TLLKKLIPALCA   28 (170)
T ss_dssp             EEEECCTTSCHH-HHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHH-HHHHHHHHHHHH
Confidence            578999999999 555555555543

>d2p6ra4 c.37.1.19 (A:203-403) 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=90.30  E-value=0.26  Score=35.56  Aligned_cols=27  Identities=19%  Similarity=0.025  Sum_probs=22.5

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHHhh
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYCAA  246 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~~~  246 (252)
                      +.++|||||||..|+.++..|.+....
T Consensus        40 ~~~~LVF~~sRk~~~~~A~~L~~~~~~   66 (201)
T d2p6ra4          40 NGGVLVFESTRRGAEKTAVKLSAITAK   66 (201)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            346999999999999999998876543

>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=90.25  E-value=0.066  Score=39.17  Aligned_cols=58  Identities=21%  Similarity=0.308  Sum_probs=31.5

Q ss_pred             CcccCCCc-EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc--CcHHHHHHHHHHHHHHHHhCC
Q psy7786           2 VTYRNSRD-IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC--PSRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         2 ~~~~~g~d-~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~--ptreLa~q~~~~~~~l~~~~~   74 (252)
                      |... .++ +++.+|||+|||.+-.-=.. ++...          +-++.+++  ..|.=|.+   .++.+++.++
T Consensus         5 p~~~-~~~vi~lvGp~GvGKTTTiaKLA~-~~~~~----------g~kV~lit~Dt~R~gA~e---QL~~~a~~l~   65 (207)
T d1ls1a2           5 PVLK-DRNLWFLVGLQGSGKTTTAAKLAL-YYKGK----------GRRPLLVAADTQRPAARE---QLRLLGEKVG   65 (207)
T ss_dssp             CCCC-SSEEEEEECCTTTTHHHHHHHHHH-HHHHT----------TCCEEEEECCSSCHHHHH---HHHHHHHHHT
T ss_pred             CCCC-CCcEEEEECCCCCCHHHHHHHHHH-HHHHC----------CCcEEEEecccccchHHH---HHHHHHHhcC
Confidence            4444 445 45699999999965332111 22221          22355555  35655544   4556666666

>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=89.52  E-value=0.076  Score=39.33  Aligned_cols=17  Identities=24%  Similarity=0.249  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCchHHHHh
Q psy7786           8 RDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~   24 (252)
                      .++++.+|+|+|||.+.
T Consensus        36 ~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            47999999999999643

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {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: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=89.40  E-value=0.25  Score=37.17  Aligned_cols=67  Identities=10%  Similarity=-0.023  Sum_probs=36.1

Q ss_pred             ccCCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHHh
Q psy7786           4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA   72 (252)
Q Consensus         4 ~~~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~~~   72 (252)
                      ++.|.=+++.+++|+||| +|++-+...+.............+..++|+.- -+-..++...+..+...
T Consensus        26 ~~pg~~~~i~G~~G~GKS-~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~-E~~~~~~~~Rl~~~~~~   92 (274)
T d1nlfa_          26 MVAGTVGALVSPGGAGKS-MLALQLAAQIAGGPDLLEVGELPTGPVIYLPA-EDPPTAIHHRLHALGAH   92 (274)
T ss_dssp             EETTSEEEEEESTTSSHH-HHHHHHHHHHHTCCCTTCCCCCCCCCEEEEES-SSCHHHHHHHHHHHHTT
T ss_pred             ccCCcEEEEEeCCCCCHH-HHHHHHHHHHHcCCCcccccccCCCceEEEec-cchHHHHHHHHHHHhhc
Confidence            445777899999999999 55555444443322111122223445777652 22233455555555443

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal 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: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.20  E-value=0.5  Score=38.28  Aligned_cols=58  Identities=17%  Similarity=0.100  Sum_probs=33.5

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCC-cEEEEEcCcHHHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEG-PYGLIICPSRELARQTHDII   66 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~-~~~lil~ptreLa~q~~~~~   66 (252)
                      .++|.|..|||||.+-+-=++..+............-. -+.|+|+=|+.=|..+.+++
T Consensus        18 ~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI   76 (485)
T d1w36b1          18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRI   76 (485)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHH
T ss_pred             CeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHH
Confidence            47889999999997655444444432211000000001 14888999987777766555

>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=89.16  E-value=0.4  Score=38.65  Aligned_cols=52  Identities=25%  Similarity=0.363  Sum_probs=36.7

Q ss_pred             cCCC-cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786           5 RNSR-DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC   70 (252)
Q Consensus         5 ~~g~-d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~~~~~l~   70 (252)
                      .+|+ ...+.+-+||+|++..  ..+   ....         +-..|||+|+.+.|.++++.++.+.
T Consensus        25 ~~g~~~~~L~GlsgS~ka~~~--A~l---~~~~---------~rp~LvVt~~~~~A~~l~~dL~~~l   77 (408)
T d1c4oa1          25 RDGERFVTLLGATGTGKTVTM--AKV---IEAL---------GRPALVLAPNKILAAQLAAEFRELF   77 (408)
T ss_dssp             HTTCSEEEEEECTTSCHHHHH--HHH---HHHH---------TCCEEEEESSHHHHHHHHHHHHHHC
T ss_pred             hcCCCcEEEecCCCCHHHHHH--HHH---HHHh---------CCCEEEEeCCHHHHHHHHHHHHHhc
Confidence            3454 4688899999999432  222   1221         1137999999999999999998874

>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=89.13  E-value=0.082  Score=36.75  Aligned_cols=17  Identities=29%  Similarity=0.382  Sum_probs=14.8

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      .+.++++.+++|||||.
T Consensus         4 k~~~I~i~G~~GsGKTT   20 (174)
T d1y63a_           4 KGINILITGTPGTGKTS   20 (174)
T ss_dssp             SSCEEEEECSTTSSHHH
T ss_pred             CCCEEEEEeCCCCCHHH
Confidence            35679999999999995

>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=89.07  E-value=1.7  Score=32.52  Aligned_cols=73  Identities=26%  Similarity=0.261  Sum_probs=58.5

Q ss_pred             CCChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       165 ~~p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      ..|..+|...--++..|  -+....||.|||+...+|..-..+.           +..+=|++.+-.||.+=++++..+-
T Consensus        79 ~RhyDVQLiGgi~L~~G--~iaem~TGEGKTL~a~l~a~l~al~-----------g~~vhvvTvNdyLA~RDae~m~~iy  145 (273)
T d1tf5a3          79 MFPFKVQLMGGVALHDG--NIAEMKTGEGKTLTSTLPVYLNALT-----------GKGVHVVTVNEYLASRDAEQMGKIF  145 (273)
T ss_dssp             CCCCHHHHHHHHHHHTT--SEEECCTTSCHHHHHHHHHHHHHTT-----------SSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             eEEehhHHHHHHHHHhh--hheeecCCCcchhHHHHHHHHHHhc-----------CCCceEEecCccccchhhhHHhHHH
Confidence            37888888666556555  4778899999999888777654443           4458899999999999999999999


Q ss_pred             hhCCCC
Q psy7786         245 AALPIG  250 (252)
Q Consensus       245 ~~~~i~  250 (252)
                      +.+|++
T Consensus       146 ~~lGls  151 (273)
T d1tf5a3         146 EFLGLT  151 (273)
T ss_dssp             HHTTCC
T ss_pred             HHcCCC
Confidence            999875

>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=88.85  E-value=0.069  Score=37.42  Aligned_cols=15  Identities=20%  Similarity=0.317  Sum_probs=13.5

Q ss_pred             CcEEEEcCCCchHHH
Q psy7786           8 RDIIGIAFTGSGKTL   22 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~   22 (252)
                      |.|++.+++|||||.
T Consensus         8 K~I~i~G~~GsGKTT   22 (192)
T d1lw7a2           8 KTVAILGGESSGKSV   22 (192)
T ss_dssp             EEEEEECCTTSHHHH
T ss_pred             eEEEEECCCCCCHHH
Confidence            579999999999993

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

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: Bacillus caldotenax [TaxId: 1395]

Probab=88.70  E-value=0.64  Score=37.47  Aligned_cols=50  Identities=22%  Similarity=0.307  Sum_probs=37.0

Q ss_pred             CcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHh
Q psy7786         182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCA  245 (252)
Q Consensus       182 ~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~  245 (252)
                      ++..+...+|++|++.  +..+.   .+.         +..+||+||+...|.++++.|+.+..
T Consensus        32 ~~q~l~GltGS~ka~~--iA~l~---~~~---------~rp~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          32 KHQTLLGATGTGKTFT--ISNVI---AQV---------NKPTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             SEEEEEECTTSCHHHH--HHHHH---HHH---------TCCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CcEEEeCCCCcHHHHH--HHHHH---HHh---------CCCEEEEeCCHHHHHHHHHHHHHHcC
Confidence            5677888999999754  32222   221         22489999999999999999998754

>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=88.55  E-value=0.096  Score=38.80  Aligned_cols=17  Identities=24%  Similarity=0.292  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCchHHHHh
Q psy7786           8 RDIIGIAFTGSGKTLVF   24 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a~   24 (252)
                      .++++.+|+|+|||.+.
T Consensus        36 ~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            47999999999999543

>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=88.46  E-value=0.61  Score=33.92  Aligned_cols=52  Identities=15%  Similarity=0.162  Sum_probs=28.2

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcC-cHHHHHHHHHHHHHHHHhCC
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICP-SRELARQTHDIIQYYCAALP   74 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~p-treLa~q~~~~~~~l~~~~~   74 (252)
                      ++..+|||+|||.+-.==. .++....         ..-+||-+- .|.=|.   +.++.+++.++
T Consensus        14 i~lvGptGvGKTTTiAKLA-a~~~~~~---------~kV~lit~Dt~R~gA~---eQL~~~a~~l~   66 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLA-KMFVDEG---------KSVVLAAADTFRAAAI---EQLKIWGERVG   66 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHH-HHHHHTT---------CCEEEEEECTTCHHHH---HHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCC---------CceEEEeecccccchh---HHHHHHhhhcC
Confidence            5669999999997643212 2222221         112444444 444443   34566777777

>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=88.27  E-value=0.093  Score=35.67  Aligned_cols=13  Identities=46%  Similarity=0.726  Sum_probs=11.6

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      +++++++|||||.
T Consensus         5 Iii~G~pGsGKTT   17 (152)
T d1ly1a_           5 ILTIGCPGSGKST   17 (152)
T ss_dssp             EEEECCTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            6789999999995

>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=88.19  E-value=0.082  Score=36.80  Aligned_cols=18  Identities=22%  Similarity=0.257  Sum_probs=15.8

Q ss_pred             cCCCcEEEEcCCCchHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~   22 (252)
                      +.|+=+++.+++|||||.
T Consensus         2 ~~g~iI~l~G~~GsGKST   19 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKST   19 (176)
T ss_dssp             CTTEEEEEEECTTSCHHH
T ss_pred             CCCeEEEEECCCCCCHHH
Confidence            467889999999999995

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=88.06  E-value=0.098  Score=42.33  Aligned_cols=23  Identities=30%  Similarity=0.195  Sum_probs=16.8

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHH
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCL   33 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~   33 (252)
                      +++.+|||||||.+. -.+++.+.
T Consensus       161 iLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         161 ILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             EEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             EEEEcCCCCCccHHH-HHHhhhhc
Confidence            899999999999554 33455553

>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=87.72  E-value=0.12  Score=38.65  Aligned_cols=16  Identities=25%  Similarity=0.322  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCchHHHH
Q psy7786           8 RDIIGIAFTGSGKTLV   23 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a   23 (252)
                      .++++.+|+|+|||..
T Consensus        44 ~~lll~GppGtGKT~l   59 (276)
T d1fnna2          44 PRATLLGRPGTGKTVT   59 (276)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             CceEEECCCCCCHHHH
Confidence            5899999999999954

>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=86.87  E-value=0.15  Score=35.37  Aligned_cols=16  Identities=44%  Similarity=0.798  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCchHHHH
Q psy7786           8 RDIIGIAFTGSGKTLV   23 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a   23 (252)
                      |++++.+++|||||..
T Consensus         1 k~I~liG~~GsGKsTi   16 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTL   16 (161)
T ss_dssp             CCEEEECCTTSCHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            6899999999999943

>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=86.68  E-value=0.14  Score=35.43  Aligned_cols=15  Identities=33%  Similarity=0.403  Sum_probs=13.3

Q ss_pred             CcEEEEcCCCchHHH
Q psy7786           8 RDIIGIAFTGSGKTL   22 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~   22 (252)
                      -.+++.+++|||||.
T Consensus         5 ~~I~i~G~pGsGKTT   19 (173)
T d1rkba_           5 PNILLTGTPGVGKTT   19 (173)
T ss_dssp             CCEEEECSTTSSHHH
T ss_pred             CEEEEECCCCCCHHH
Confidence            468999999999994

>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=86.65  E-value=0.18  Score=36.78  Aligned_cols=55  Identities=15%  Similarity=0.174  Sum_probs=30.6

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEc-C-cHHHHHHHHHHHHHHHHhCC
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC-P-SRELARQTHDIIQYYCAALP   74 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~-p-treLa~q~~~~~~~l~~~~~   74 (252)
                      +++=+++.+|||+|||.+-.==. .++...          +.++.+++ - -|.=|.++   ++.+++.++
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA-~~~~~~----------g~kV~lit~Dt~R~gA~eQ---L~~~a~~l~   61 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLG-RYYQNL----------GKKVMFCAGDTFRAAGGTQ---LSEWGKRLS   61 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHH-HHHHTT----------TCCEEEECCCCSSTTHHHH---HHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH-HHHHHC----------CCcEEEEEeccccccchhh---HhhcccccC
Confidence            34557789999999997643211 122211          22344444 3 36655444   455666666

>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=86.43  E-value=0.44  Score=34.50  Aligned_cols=17  Identities=29%  Similarity=0.378  Sum_probs=14.8

Q ss_pred             cCCCcEEEEcCCCchHH
Q psy7786           5 RNSRDIIGIAFTGSGKT   21 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT   21 (252)
                      -.|.=+++.+++|+|||
T Consensus        24 ~~G~~~~I~G~~G~GKT   40 (242)
T d1tf7a1          24 PIGRSTLVSGTSGTGKT   40 (242)
T ss_dssp             ETTSEEEEEESTTSSHH
T ss_pred             cCCeEEEEEeCCCCCHH
Confidence            35677899999999999

>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=86.14  E-value=0.15  Score=37.83  Aligned_cols=16  Identities=31%  Similarity=0.287  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCchHHHH
Q psy7786           8 RDIIGIAFTGSGKTLV   23 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a   23 (252)
                      +.+++.+|+|+|||.+
T Consensus        53 ~~lll~GPpG~GKTt~   68 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTA   68 (253)
T ss_dssp             SEEEEECSTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            4699999999999944

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=85.94  E-value=0.42  Score=34.99  Aligned_cols=26  Identities=27%  Similarity=0.354  Sum_probs=18.5

Q ss_pred             CCCcEEEEcCCCchHHHHhHHHHHHHH
Q psy7786           6 NSRDIIGIAFTGSGKTLVFVLPILMFC   32 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~a~~lp~~~~~   32 (252)
                      .|.=+++.+++|+||| .|++=+....
T Consensus        25 ~gsl~li~G~pGsGKT-~l~~qia~~~   50 (242)
T d1tf7a2          25 KDSIILATGATGTGKT-LLVSRFVENA   50 (242)
T ss_dssp             SSCEEEEEECTTSSHH-HHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHH-HHHHHHHHHH
Confidence            4667899999999999 4444444333

>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=85.87  E-value=0.16  Score=35.23  Aligned_cols=21  Identities=19%  Similarity=0.156  Sum_probs=17.9

Q ss_pred             CcccCCCcEEEEcCCCchHHH
Q psy7786           2 VTYRNSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         2 ~~~~~g~d~~~~a~tgsGKT~   22 (252)
                      |.-.+|.=|++++.+|||||.
T Consensus         1 ~~~~~g~~I~l~G~~GsGKTT   21 (183)
T d1m8pa3           1 PRATQGFTIFLTGYMNSGKDA   21 (183)
T ss_dssp             CTTTCCEEEEEECSTTSSHHH
T ss_pred             CCCCCCeEEEEECCCCCCHHH
Confidence            455678889999999999994

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=85.81  E-value=0.17  Score=40.24  Aligned_cols=17  Identities=53%  Similarity=0.675  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCchHHHH
Q psy7786           7 SRDIIGIAFTGSGKTLV   23 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~a   23 (252)
                      -.+++..+|||+|||..
T Consensus        68 ~~niLfiGPTGvGKTEl   84 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLM   84 (364)
T ss_dssp             CCCEEEECCTTSSHHHH
T ss_pred             CcceeeeCCCCccHHHH
Confidence            35799999999999954

>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=85.80  E-value=0.15  Score=35.06  Aligned_cols=13  Identities=31%  Similarity=0.286  Sum_probs=11.9

Q ss_pred             EEEEcCCCchHHH
Q psy7786          10 IIGIAFTGSGKTL   22 (252)
Q Consensus        10 ~~~~a~tgsGKT~   22 (252)
                      +++.+++|||||.
T Consensus         5 I~i~G~~GsGKTT   17 (176)
T d2bdta1           5 YIITGPAGVGKST   17 (176)
T ss_dssp             EEEECSTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            7899999999995

>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=85.70  E-value=1.7  Score=34.09  Aligned_cols=75  Identities=20%  Similarity=0.159  Sum_probs=53.0

Q ss_pred             ChHHHHhhhhhhhcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHHHHHHHHHhh
Q psy7786         167 PTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAA  246 (252)
Q Consensus       167 p~~iQ~~~~p~~~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~~~l~~l~~~  246 (252)
                      ...-|..++...+.++-.++..++|+|||.... ..+..+....      ...+.++++.+||-.-|..+.+.+......
T Consensus       149 ~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~-~~l~~l~~~~------~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~  221 (359)
T d1w36d1         149 EINWQKVAAAVALTRRISVISGGPGTGKTTTVA-KLLAALIQMA------DGERCRIRLAAPTGKAAARLTESLGKALRQ  221 (359)
T ss_dssp             SCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHH-HHHHHHHHTC------SSCCCCEEEEBSSHHHHHHHHHHHTHHHHH
T ss_pred             cccHHHHHHHHHHcCCeEEEEcCCCCCceehHH-HHHHHHHHHH------hccCCeEEEecCcHHHHHHHHHHHHHHHhh
Confidence            355788888888888888889999999987632 2222222211      123567999999999999999888766655


Q ss_pred             CC
Q psy7786         247 LP  248 (252)
Q Consensus       247 ~~  248 (252)
                      ++
T Consensus       222 ~~  223 (359)
T d1w36d1         222 LP  223 (359)
T ss_dssp             SS
T ss_pred             cC
Confidence            54

>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=85.55  E-value=0.18  Score=36.93  Aligned_cols=16  Identities=25%  Similarity=0.264  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCchHHHH
Q psy7786           8 RDIIGIAFTGSGKTLV   23 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a   23 (252)
                      .++++.+|+|+|||.+
T Consensus        46 ~~lll~Gp~G~GKTtl   61 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTA   61 (231)
T ss_dssp             CEEEEESCTTSSHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            4689999999999944

>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=85.35  E-value=0.17  Score=35.99  Aligned_cols=15  Identities=33%  Similarity=0.470  Sum_probs=13.5

Q ss_pred             CcEEEEcCCCchHHH
Q psy7786           8 RDIIGIAFTGSGKTL   22 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~   22 (252)
                      |-+++.+|+|||||.
T Consensus         2 rpIvl~GpsG~GK~t   16 (186)
T d1gkya_           2 RPIVISGPSGTGKST   16 (186)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            568999999999995

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

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: Bacillus caldotenax [TaxId: 1395]

Probab=85.33  E-value=0.32  Score=34.48  Aligned_cols=25  Identities=12%  Similarity=0.167  Sum_probs=22.1

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHH
Q psy7786         220 GPYGLIICPSRELARQTHDIIQYYC  244 (252)
Q Consensus       220 ~~~~LIf~~tr~~a~~i~~~l~~l~  244 (252)
                      +.++||||+|++.++.++..|++.+
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~g   55 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEAG   55 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTTT
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhCC
Confidence            4589999999999999999998654

>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=85.16  E-value=0.15  Score=38.28  Aligned_cols=16  Identities=25%  Similarity=0.164  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCchHHHH
Q psy7786           8 RDIIGIAFTGSGKTLV   23 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a   23 (252)
                      +.+++.+|+|||||..
T Consensus        41 ~~vLL~GppGtGKT~l   56 (246)
T d1d2na_          41 VSVLLEGPPHSGKTAL   56 (246)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             eEEEEECcCCCCHHHH
Confidence            3589999999999954

>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=84.90  E-value=0.12  Score=40.50  Aligned_cols=22  Identities=27%  Similarity=0.277  Sum_probs=17.4

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        70 ~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          70 DVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHcCCCcceeeecccCCCCceec
Confidence            4567886  677899999999764

>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=84.80  E-value=0.2  Score=36.77  Aligned_cols=14  Identities=29%  Similarity=0.356  Sum_probs=12.7

Q ss_pred             cEEEEcCCCchHHH
Q psy7786           9 DIIGIAFTGSGKTL   22 (252)
Q Consensus         9 d~~~~a~tgsGKT~   22 (252)
                      ++++.+|+|+|||.
T Consensus        35 ~lll~Gp~G~GKTt   48 (237)
T d1sxjd2          35 HMLFYGPPGTGKTS   48 (237)
T ss_dssp             CEEEECSTTSSHHH
T ss_pred             eEEEECCCCCChHH
Confidence            58999999999994

>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=84.60  E-value=0.17  Score=36.92  Aligned_cols=52  Identities=21%  Similarity=0.242  Sum_probs=24.3

Q ss_pred             EEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcE-EEEEcCc-HHHHHHHHHHHHHHHHhCCC
Q psy7786          10 IIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY-GLIICPS-RELARQTHDIIQYYCAALPI   75 (252)
Q Consensus        10 ~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~-~lil~pt-reLa~q~~~~~~~l~~~~~~   75 (252)
                      ++..+|||+|||.+-.==. .++...          +-+ ++|-+-| |.=|.   +.++.+++.++.
T Consensus        15 i~lvGptGvGKTTTiAKLA-~~~~~~----------g~kV~lit~Dt~R~ga~---eQL~~~a~~l~v   68 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLA-YFYKKK----------GFKVGLVGADVYRPAAL---EQLQQLGQQIGV   68 (211)
T ss_dssp             EEEECSCCC----HHHHHH-HHHHHT----------TCCEEEEECCCSSHHHH---HHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHC----------CCceEEEEeeccccchh---HHHHHhccccCc
Confidence            4558999999996533111 222221          223 4444433 44333   456677777773

>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=84.38  E-value=0.33  Score=34.58  Aligned_cols=23  Identities=13%  Similarity=-0.009  Sum_probs=17.3

Q ss_pred             cCCCcEEEEcCCCchHHHHhHHHH
Q psy7786           5 RNSRDIIGIAFTGSGKTLVFVLPI   28 (252)
Q Consensus         5 ~~g~d~~~~a~tgsGKT~a~~lp~   28 (252)
                      ..|+=+++.+++||||| +|++-+
T Consensus        21 ~~G~v~~i~G~~GsGKT-~l~l~l   43 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKT-QICHTL   43 (242)
T ss_dssp             ETTSEEEEECCTTSSHH-HHHHHH
T ss_pred             cCCEEEEEEeCCCCCHH-HHHHHH
Confidence            45777899999999999 344433

>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=83.80  E-value=0.18  Score=37.72  Aligned_cols=16  Identities=31%  Similarity=0.277  Sum_probs=13.5

Q ss_pred             CcEEEEcCCCchHHHH
Q psy7786           8 RDIIGIAFTGSGKTLV   23 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~a   23 (252)
                      +-+++.+|+|||||..
T Consensus        33 ~~ilL~GpPGtGKT~l   48 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSL   48 (273)
T ss_dssp             EEEEEECCTTSCTHHH
T ss_pred             EEEEEECCCCCCHHHH
Confidence            3489999999999953

>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=83.58  E-value=0.16  Score=40.34  Aligned_cols=22  Identities=23%  Similarity=0.404  Sum_probs=17.5

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        74 ~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          74 DILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HhhccCceeEEecccCCCCcceee
Confidence            4578888  667799999999764

>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=83.43  E-value=0.24  Score=38.95  Aligned_cols=24  Identities=29%  Similarity=0.426  Sum_probs=18.6

Q ss_pred             CcccCCCc--EEEEcCCCchHHHHhH
Q psy7786           2 VTYRNSRD--IIGIAFTGSGKTLVFV   25 (252)
Q Consensus         2 ~~~~~g~d--~~~~a~tgsGKT~a~~   25 (252)
                      +.+++|.|  +++-++||||||.+..
T Consensus        76 ~~~l~G~n~~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          76 QSSLDGYNVCIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             GGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             cchhcccccceeeeeccCCccccccc
Confidence            45678887  5567899999997763

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=83.37  E-value=0.77  Score=31.42  Aligned_cols=23  Identities=17%  Similarity=0.242  Sum_probs=15.5

Q ss_pred             EEEcCCCchHHHHhHHHHHHHHHH
Q psy7786          11 IGIAFTGSGKTLVFVLPILMFCLE   34 (252)
Q Consensus        11 ~~~a~tgsGKT~a~~lp~~~~~~~   34 (252)
                      -+.+..||||| +++--++..+..
T Consensus         5 ~I~G~~gSGKT-Tli~~l~~~L~~   27 (165)
T d1xjca_           5 QVVGYKHSGKT-TLMEKWVAAAVR   27 (165)
T ss_dssp             EEECCTTSSHH-HHHHHHHHHHHH
T ss_pred             EEEeCCCCCHH-HHHHHHHHHHHh
Confidence            48899999999 444444444433

>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=83.21  E-value=0.24  Score=35.95  Aligned_cols=17  Identities=29%  Similarity=0.239  Sum_probs=15.0

Q ss_pred             CCCcEEEEcCCCchHHH
Q psy7786           6 NSRDIIGIAFTGSGKTL   22 (252)
Q Consensus         6 ~g~d~~~~a~tgsGKT~   22 (252)
                      +|+=+++++|+|+|||.
T Consensus         1 ~G~livi~GPSG~GK~t   17 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSS   17 (205)
T ss_dssp             CCCEEEEECCTTSCHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            47778999999999994

>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=82.70  E-value=1.2  Score=32.08  Aligned_cols=44  Identities=16%  Similarity=0.123  Sum_probs=25.0

Q ss_pred             cEEEEcCCCchHHHHhHHHHHHHHHHhhcCCCCCCCCCcEEEEEcCcHHHHHHHHH
Q psy7786           9 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD   64 (252)
Q Consensus         9 d~~~~a~tgsGKT~a~~lp~~~~~~~~~~~~~~~~~~~~~~lil~ptreLa~q~~~   64 (252)
                      .+++.+++|||||. .+-.+-+.+...          +..++++ +..++..+...
T Consensus        38 ~l~l~G~~G~GKTH-Ll~A~~~~~~~~----------~~~~~~~-~~~~~~~~~~~   81 (213)
T d1l8qa2          38 PIFIYGSVGTGKTH-LLQAAGNEAKKR----------GYRVIYS-SADDFAQAMVE   81 (213)
T ss_dssp             SEEEECSSSSSHHH-HHHHHHHHHHHT----------TCCEEEE-EHHHHHHHHHH
T ss_pred             cEEEECCCCCcHHH-HHHHHHHHhccC----------ccceEEe-chHHHHHHHHH
Confidence            38999999999993 222333333322          3345555 55555555443

>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=82.65  E-value=0.26  Score=35.14  Aligned_cols=15  Identities=27%  Similarity=0.443  Sum_probs=13.2

Q ss_pred             CcEEEEcCCCchHHH
Q psy7786           8 RDIIGIAFTGSGKTL   22 (252)
Q Consensus         8 ~d~~~~a~tgsGKT~   22 (252)
                      |-+++.+|+|||||.
T Consensus         1 rpIvl~GPsGsGK~t   15 (190)
T d1lvga_           1 RPVVLSGPSGAGKST   15 (190)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            458999999999995

>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=82.53  E-value=0.25  Score=34.26  Aligned_cols=14  Identities=43%  Similarity=0.399  Sum_probs=12.4

Q ss_pred             cEEEEcCCCchHHH
Q psy7786           9 DIIGIAFTGSGKTL   22 (252)
Q Consensus         9 d~~~~a~tgsGKT~   22 (252)
                      .+++.+|+|+|||.
T Consensus         2 ki~I~G~~G~GKST   15 (178)
T d1ye8a1           2 KIIITGEPGVGKTT   15 (178)
T ss_dssp             EEEEECCTTSSHHH
T ss_pred             EEEEECCCCcHHHH
Confidence            37899999999995

>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=82.48  E-value=3.6  Score=30.95  Aligned_cols=74  Identities=22%  Similarity=0.192  Sum_probs=44.4

Q ss_pred             ChHHHHhhhhhh---------hcCCcEEEEccCCCchhHHhHHHHHHHHHhhhccCCCCCCCCcEEEEEcCcHHHHHHHH
Q psy7786         167 PTPIQVQGIPAA---------LSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH  237 (252)
Q Consensus       167 p~~iQ~~~~p~~---------~~~~~~~~~~~~g~gKt~~~~~~~l~~i~~~~~~~~~~~~~~~~~LIf~~tr~~a~~i~  237 (252)
                      ..+.|...+..+         -.+...++....|.|||+..+ .++..+..+..   .......++||+||.. +..+-.
T Consensus        56 Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qai-a~l~~l~~~~~---~~~~~~~~~LIV~P~s-l~~qW~  130 (298)
T d1z3ix2          56 LRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCI-TLIWTLLKQSP---DCKPEIDKVIVVSPSS-LVRNWY  130 (298)
T ss_dssp             CCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHH-HHHHHHHHCCT---TSSCSCSCEEEEECHH-HHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHH-HHHHHHHHhcc---cccCCCCcEEEEccch-hhHHHH
Confidence            455666665432         234567888888999997532 33333333221   1112234699999986 666777


Q ss_pred             HHHHHHHh
Q psy7786         238 DIIQYYCA  245 (252)
Q Consensus       238 ~~l~~l~~  245 (252)
                      ++++++..
T Consensus       131 ~Ei~k~~~  138 (298)
T d1z3ix2         131 NEVGKWLG  138 (298)
T ss_dssp             HHHHHHHG
T ss_pred             HHHHhhcC
Confidence            77877664

>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=82.24  E-value=0.16  Score=38.10  Aligned_cols=14  Identities=36%  Similarity=0.337  Sum_probs=11.4

Q ss_pred             EEEEcCCCchHHHH
Q psy7786          10 IIGIAFTGSGKTLV   23 (252)
Q Consensus        10 ~~~~a~tgsGKT~a   23 (252)
                      +++.+|+|+|||..
T Consensus        49 l~l~GppGtGKT~l   62 (287)
T d1w5sa2          49 YGSIGRVGIGKTTL   62 (287)
T ss_dssp             EECTTCCSSSHHHH
T ss_pred             EEeECCCCCCHHHH
Confidence            45679999999955

>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=81.73  E-value=0.19  Score=39.75  Aligned_cols=22  Identities=23%  Similarity=0.332  Sum_probs=17.2

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        81 ~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          81 HAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhccCceeeeeccCCCCCceee
Confidence            3567876  677889999999774

>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=81.65  E-value=0.31  Score=35.51  Aligned_cols=14  Identities=29%  Similarity=0.363  Sum_probs=12.7

Q ss_pred             cEEEEcCCCchHHH
Q psy7786           9 DIIGIAFTGSGKTL   22 (252)
Q Consensus         9 d~~~~a~tgsGKT~   22 (252)
                      ++++.+|+|+|||.
T Consensus        37 ~lLl~Gp~G~GKtt   50 (227)
T d1sxjc2          37 HLLFYGPPGTGKTS   50 (227)
T ss_dssp             CEEEECSSSSSHHH
T ss_pred             eEEEECCCCCChhH
Confidence            58999999999994

>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=81.65  E-value=0.18  Score=40.12  Aligned_cols=22  Identities=32%  Similarity=0.314  Sum_probs=16.5

Q ss_pred             cccCCCcE--EEEcCCCchHHHHh
Q psy7786           3 TYRNSRDI--IGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d~--~~~a~tgsGKT~a~   24 (252)
                      .+++|.|.  ++-++||||||.+.
T Consensus       108 ~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         108 TIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHhccCceEEeeccCCCCCceee
Confidence            35678874  45589999999774

>d1c4oa2 c.37.1.19 (A:410-583) 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=81.25  E-value=1.2  Score=31.11  Aligned_cols=46  Identities=11%  Similarity=0.113  Sum_probs=36.6

Q ss_pred             CcEEEEEcCcHHHHHHHHHHHHHHHHhCCCCcceeeeeCCcccCcchhhhhh
Q psy7786          46 GPYGLIICPSRELARQTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKK   97 (252)
Q Consensus        46 ~~~~lil~ptreLa~q~~~~~~~l~~~~~~~~~~~~~~g~~~~~~~~~~l~~   97 (252)
                      +-++||.|+|+.-|..+.+.++..    |  +++..++|+.+..++.+.+++
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~----G--i~a~~~Hg~~~~~eR~~~l~~   76 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEH----G--IRARYLHHELDAFKRQALIRD   76 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----T--CCEEEECTTCCHHHHHHHHHH
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhc----C--CceEEEecccchHHHHHHHHH
Confidence            567999999999998887777653    4  889999999887776555544

>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=81.23  E-value=0.3  Score=33.54  Aligned_cols=14  Identities=36%  Similarity=0.593  Sum_probs=12.0

Q ss_pred             EEEEcCCCchHHHH
Q psy7786          10 IIGIAFTGSGKTLV   23 (252)
Q Consensus        10 ~~~~a~tgsGKT~a   23 (252)
                      +++.+++|||||..
T Consensus         9 ivl~G~~GsGKsT~   22 (171)
T d1knqa_           9 YVLMGVSGSGKSAV   22 (171)
T ss_dssp             EEEECSTTSCHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67899999999954

>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=80.92  E-value=0.34  Score=35.23  Aligned_cols=15  Identities=33%  Similarity=0.392  Sum_probs=13.3

Q ss_pred             cEEEEcCCCchHHHH
Q psy7786           9 DIIGIAFTGSGKTLV   23 (252)
Q Consensus         9 d~~~~a~tgsGKT~a   23 (252)
                      ++++.+|+|+|||.+
T Consensus        38 ~~ll~Gp~G~GKTt~   52 (224)
T d1sxjb2          38 HMIISGMPGIGKTTS   52 (224)
T ss_dssp             CEEEECSTTSSHHHH
T ss_pred             eEEEECCCCCCchhh
Confidence            689999999999954

>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=80.72  E-value=0.19  Score=40.04  Aligned_cols=22  Identities=32%  Similarity=0.450  Sum_probs=16.9

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus        69 ~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          69 SAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHhcCCceeeeccccCCCCccccc
Confidence            3567776  566789999999774

>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=80.53  E-value=0.2  Score=39.91  Aligned_cols=22  Identities=32%  Similarity=0.425  Sum_probs=17.1

Q ss_pred             cccCCCc--EEEEcCCCchHHHHh
Q psy7786           3 TYRNSRD--IIGIAFTGSGKTLVF   24 (252)
Q Consensus         3 ~~~~g~d--~~~~a~tgsGKT~a~   24 (252)
                      .+++|.|  +++-++||||||.+.
T Consensus       119 ~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         119 SALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHhcccceeEEeeccCCCccceEe
Confidence            3567776  677789999999774

>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=80.17  E-value=0.35  Score=33.98  Aligned_cols=16  Identities=19%  Similarity=0.208  Sum_probs=14.2

Q ss_pred             CCcEEEEcCCCchHHH
Q psy7786           7 SRDIIGIAFTGSGKTL   22 (252)
Q Consensus         7 g~d~~~~a~tgsGKT~   22 (252)
                      |+=+++.+|+|||||.
T Consensus         2 G~iivl~GpsG~GK~t   17 (182)
T d1znwa1           2 GRVVVLSGPSAVGKST   17 (182)
T ss_dssp             CCEEEEECSTTSSHHH
T ss_pred             CeEEEEECCCCCCHHH
Confidence            6668999999999995