Citrus Sinensis ID: 022383

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------30
Protein Sequence
MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWIG
Secondary Structure (PSIPRED)
cHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHcccccccEEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHcccccEEEcccHHHHHHccccccccccccEEEEEccccccccccHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHcccccEEEEEccccccccEEEEEEEEccccHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccEEEEccccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHccEEEEEcHHHHHHHHcccccccccccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEcEcccEEcccEEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
MAAATAMRrrgggggmdddkMVFETTEGVeaitsfdamgiKDDLLRGIYQygfekpsaiqqravmpiikgrDVIAqaqsgtgktSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFiniqahacvggksvgedIRKLehgvhvvsgtpgrvcdmIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTkfmtdpvkILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWIG
Flexible Loop (DISEMBL)
maaatamrrrgggggmdddkMVFETTEGVEaitsfdamgiKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAqsgtgktsmIALTVCQTVDTSSREVQALIlsptrelatQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEhgvhvvsgtpgrvcdmikrkTLRTRAIKLlvldesdemlSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMttkfmtdpVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWIG
Low Complexity Region (SEG)
maaatamrrrgggggmdddKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWIG
Disordered region (IsUnstruct)
***********************ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI*
Disordered Region (DISOPRED)
*************************TEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW**
Disordered Region (DISEMBL)
*************GGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWIG
Disordered Region (DISPRO)
******************DKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWIG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	298	2.2.26 [Sep-21-2011]
Q5VNM3	404	DEAD-box ATP-dependent RN	yes	no	0.949	0.700	0.859	1e-145
Q10I26	404	DEAD-box ATP-dependent RN	yes	no	0.949	0.700	0.852	1e-144
Q94A52	408	DEAD-box ATP-dependent RN	yes	no	0.916	0.669	0.882	1e-143
P41380	391	Eukaryotic initiation fac	N/A	no	0.906	0.690	0.885	1e-141
Q4P184	397	ATP-dependent RNA helicas	N/A	no	0.922	0.692	0.730	1e-123
P0CQ72	396	ATP-dependent RNA helicas	yes	no	0.919	0.691	0.718	1e-121
P0CQ73	396	ATP-dependent RNA helicas	N/A	no	0.919	0.691	0.718	1e-121
Q3B8Q2	411	Eukaryotic initiation fac	yes	no	0.956	0.693	0.717	1e-121
A6M931	411	Eukaryotic initiation fac	yes	no	0.956	0.693	0.717	1e-121
Q2NL22	411	Eukaryotic initiation fac	yes	no	0.956	0.693	0.717	1e-121

>sp|Q5VNM3|RH2_ORYSJ DEAD-box ATP-dependent RNA helicase 2 OS=Oryza sativa subsp. japonica GN=Os01g0639100 PE=2 SV=1

 Score =  513 bits (1321), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 245/285 (85%), Positives = 266/285 (93%), Gaps = 2/285 (0%)

Query: 1   MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQ 60
           MAAAT  RR  G G MDD+ + FET+ GVE I+SFD MGI+DDLLRGIY YGFEKPSAIQ
Sbjct: 1   MAAATTSRR--GPGAMDDENLTFETSPGVEVISSFDQMGIRDDLLRGIYAYGFEKPSAIQ 58

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV 120
           QRAV+PII GRDVIAQAQSGTGKTSMI+L+VCQ VDT+ REVQALILSPTRELA QTE+V
Sbjct: 59  QRAVLPIISGRDVIAQAQSGTGKTSMISLSVCQIVDTAVREVQALILSPTRELAAQTERV 118

Query: 121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV 180
           +LAIGDFINIQ HAC+GGKS+GEDIRKLEHGVHVVSGTPGRVCDMIKR+TLRTRAIKLL+
Sbjct: 119 MLAIGDFINIQVHACIGGKSIGEDIRKLEHGVHVVSGTPGRVCDMIKRRTLRTRAIKLLI 178

Query: 181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE 240
           LDE+DEML RGFKDQIYDVYRYLPP+LQV LISATLPHEILEMT+KFMTDPV+ILVKRDE
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVCLISATLPHEILEMTSKFMTDPVRILVKRDE 238

Query: 241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 239 LTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKV 283

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.
Oryza sativa subsp. japonica (taxid: 39947)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q10I26|RH34_ORYSJ DEAD-box ATP-dependent RNA helicase 34 OS=Oryza sativa subsp. japonica GN=Os03g0566800 PE=2 SV=1

 Score =  510 bits (1313), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 243/285 (85%), Positives = 266/285 (93%), Gaps = 2/285 (0%)

Query: 1   MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQ 60
           MAAAT  RR  G G MDD+ + FET+ GVE I+SFD MGI++DLLRGIY YGFEKPSAIQ
Sbjct: 1   MAAATTSRR--GPGAMDDENLTFETSPGVEVISSFDQMGIREDLLRGIYAYGFEKPSAIQ 58

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV 120
           QRAV+PII GRDVIAQAQSGTGKTSMI+L+VCQ VDT+ REVQALILSPTRELA QTE+V
Sbjct: 59  QRAVLPIISGRDVIAQAQSGTGKTSMISLSVCQIVDTAVREVQALILSPTRELAAQTERV 118

Query: 121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV 180
           +LAIGD+INIQ HAC+GGKS+GEDIRKLEHGVHVVSGTPGRVCDMIKR+TLRTRAIKLL+
Sbjct: 119 MLAIGDYINIQVHACIGGKSIGEDIRKLEHGVHVVSGTPGRVCDMIKRRTLRTRAIKLLI 178

Query: 181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE 240
           LDE+DEML RGFKDQIYDVYRYLPP+LQV LISATLPHEILEMT+KFMTDPV+ILVKRDE
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVCLISATLPHEILEMTSKFMTDPVRILVKRDE 238

Query: 241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 239 LTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKV 283

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

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q94A52|RH2_ARATH DEAD-box ATP-dependent RNA helicase 2 OS=Arabidopsis thaliana GN=RH2 PE=2 SV=2

 Score =  509 bits (1310), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 241/273 (88%), Positives = 261/273 (95%)

Query: 15  GMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVI 74
            MDDDK+VFETT+G+E ITSF+ MGIK+D+LRG+Y+YGFEKPSAIQQRAVMPI++GRDVI
Sbjct: 17  AMDDDKLVFETTDGIEPITSFNDMGIKEDVLRGVYEYGFEKPSAIQQRAVMPILQGRDVI 76

Query: 75  AQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA 134
           AQAQSGTGKTSMIAL+VCQ VDTSSREVQALILSPTRELATQTEK I AIG   NIQAHA
Sbjct: 77  AQAQSGTGKTSMIALSVCQVVDTSSREVQALILSPTRELATQTEKTIQAIGLHANIQAHA 136

Query: 135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD 194
           C+GG SVGEDIRKLEHGVHVVSGTPGRVCDMIKR++LRTRAIKLL+LDESDEMLSRGFKD
Sbjct: 137 CIGGNSVGEDIRKLEHGVHVVSGTPGRVCDMIKRRSLRTRAIKLLILDESDEMLSRGFKD 196

Query: 195 QIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVE 254
           QIYDVYRYLPPDLQV L+SATLPHEILEMT+KFMT+PVKILVKRDELTLEGIKQFFVAVE
Sbjct: 197 QIYDVYRYLPPDLQVCLVSATLPHEILEMTSKFMTEPVKILVKRDELTLEGIKQFFVAVE 256

Query: 255 REEWKFDTLCDLYDTLTITQAVIFCNTKRKIYY 287
           +EEWKFDTLCDLYDTLTITQAVIFCNTKRK+ Y
Sbjct: 257 KEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDY 289

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

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P41380|IF4A3_NICPL Eukaryotic initiation factor 4A-3 OS=Nicotiana plumbaginifolia PE=2 SV=1

 Score =  502 bits (1293), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 239/270 (88%), Positives = 259/270 (95%)

Query: 16  MDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIA 75
           M++D++VFET++GVE I SF  MGIKDDLLRG+YQYGFEKPSAIQQRAV+PII GRDVIA
Sbjct: 1   MEEDRLVFETSKGVEPIASFAEMGIKDDLLRGVYQYGFEKPSAIQQRAVLPIISGRDVIA 60

Query: 76  QAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC 135
           QAQSGTGKTSMIALTVCQ VDT S EVQALILSPTRELA QTEKVILAIGD+IN+QAHAC
Sbjct: 61  QAQSGTGKTSMIALTVCQIVDTKSSEVQALILSPTRELAAQTEKVILAIGDYINVQAHAC 120

Query: 136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQ 195
           +GGKSVGEDIRKLEHGV VVSGTPGRVCDMIKR+TLRTR IKLL+LDESDEMLSRGFKDQ
Sbjct: 121 IGGKSVGEDIRKLEHGVQVVSGTPGRVCDMIKRRTLRTRGIKLLILDESDEMLSRGFKDQ 180

Query: 196 IYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER 255
           IYDVYRYLPP+LQVVLISATLP+EILE+T+KFMTDPV+ILVKRDELTLEGIKQFFVAVE+
Sbjct: 181 IYDVYRYLPPELQVVLISATLPNEILEITSKFMTDPVRILVKRDELTLEGIKQFFVAVEK 240

Query: 256 EEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           EEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 241 EEWKFDTLCDLYDTLTITQAVIFCNTKRKV 270

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Nicotiana plumbaginifolia (taxid: 4092)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4P184|FAL1_USTMA ATP-dependent RNA helicase FAL1 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=FAL1 PE=3 SV=1

 Score =  442 bits (1138), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 201/275 (73%), Positives = 245/275 (89%)

Query: 11  GGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG 70
            GG    D K+ FE++E V+  T+FDAMG+K+DLLRGIY Y FEKPSAIQQRA++PII+G
Sbjct: 2   SGGINAGDSKLAFESSEHVKVATTFDAMGLKEDLLRGIYAYNFEKPSAIQQRAILPIIRG 61

Query: 71  RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI 130
           RDVIAQAQSGTGKT+  ++++ Q++DT+ RE QAL+LSPTRELA Q + V+LA+GD++N+
Sbjct: 62  RDVIAQAQSGTGKTATFSISMLQSIDTTLRETQALVLSPTRELAIQIQSVVLALGDYLNV 121

Query: 131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR 190
           Q HAC+GG SVGEDIRKL++G H+VSGTPGRV DMI+R+ LRT+ IK+L+LDESDE+L+ 
Sbjct: 122 QCHACIGGTSVGEDIRKLDYGQHIVSGTPGRVYDMIRRRHLRTKNIKMLILDESDELLNM 181

Query: 191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFF 250
           GFKDQIYDVYRYLPP  QVVL+SATLP ++LEMT+KFMTDPV+ILVKRDELTLEGIKQFF
Sbjct: 182 GFKDQIYDVYRYLPPSTQVVLLSATLPQDVLEMTSKFMTDPVRILVKRDELTLEGIKQFF 241

Query: 251 VAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           VAVE+EEWKFDTLCDLYDTLTITQAVIFCNT+RK+
Sbjct: 242 VAVEKEEWKFDTLCDLYDTLTITQAVIFCNTRRKV 276

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

Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P0CQ72|FAL1_CRYNJ ATP-dependent RNA helicase FAL1 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=FAL1 PE=3 SV=1

 Score =  435 bits (1119), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 197/274 (71%), Positives = 243/274 (88%)

Query: 12  GGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR 71
            G  + DDK+VFE++E V    +F+A+ +K+DLLRGIY Y FEKPSAIQQRA++PII+GR
Sbjct: 2   AGVNVGDDKLVFESSEAVTVAPTFEALNLKEDLLRGIYAYNFEKPSAIQQRAIIPIIRGR 61

Query: 72  DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ 131
           DVIAQAQSGTGKT+  ++++ Q++DT+ RE QAL+LSPTRELA Q + V+LA+GD++N+ 
Sbjct: 62  DVIAQAQSGTGKTATFSISMLQSIDTNLRETQALVLSPTRELAVQIQTVVLALGDYMNVS 121

Query: 132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG 191
            HAC+GG SVGEDIRKLE G  VVSGTPGRV DMI+R+ LRT+ IK+L+LDESDE+L++G
Sbjct: 122 CHACIGGTSVGEDIRKLEAGQQVVSGTPGRVFDMIRRRNLRTKDIKMLILDESDELLNKG 181

Query: 192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV 251
           FKDQIYD+YRYLPP  QVV++SATLPH++LEMTTKFMTDPV+ILVKRDELTLEGIKQFFV
Sbjct: 182 FKDQIYDIYRYLPPATQVVVVSATLPHDVLEMTTKFMTDPVRILVKRDELTLEGIKQFFV 241

Query: 252 AVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           AVE+E+WKFDTLCDLYDTLTITQAVIFCNT+RK+
Sbjct: 242 AVEKEDWKFDTLCDLYDTLTITQAVIFCNTRRKV 275

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

Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (taxid: 214684)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P0CQ73|FAL1_CRYNB ATP-dependent RNA helicase FAL1 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=FAL1 PE=3 SV=1

 Score =  435 bits (1119), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 197/274 (71%), Positives = 243/274 (88%)

Query: 12  GGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR 71
            G  + DDK+VFE++E V    +F+A+ +K+DLLRGIY Y FEKPSAIQQRA++PII+GR
Sbjct: 2   AGVNVGDDKLVFESSEAVTVAPTFEALNLKEDLLRGIYAYNFEKPSAIQQRAIIPIIRGR 61

Query: 72  DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ 131
           DVIAQAQSGTGKT+  ++++ Q++DT+ RE QAL+LSPTRELA Q + V+LA+GD++N+ 
Sbjct: 62  DVIAQAQSGTGKTATFSISMLQSIDTNLRETQALVLSPTRELAVQIQTVVLALGDYMNVS 121

Query: 132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG 191
            HAC+GG SVGEDIRKLE G  VVSGTPGRV DMI+R+ LRT+ IK+L+LDESDE+L++G
Sbjct: 122 CHACIGGTSVGEDIRKLEAGQQVVSGTPGRVFDMIRRRNLRTKDIKMLILDESDELLNKG 181

Query: 192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV 251
           FKDQIYD+YRYLPP  QVV++SATLPH++LEMTTKFMTDPV+ILVKRDELTLEGIKQFFV
Sbjct: 182 FKDQIYDIYRYLPPATQVVVVSATLPHDVLEMTTKFMTDPVRILVKRDELTLEGIKQFFV 241

Query: 252 AVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           AVE+E+WKFDTLCDLYDTLTITQAVIFCNT+RK+
Sbjct: 242 AVEKEDWKFDTLCDLYDTLTITQAVIFCNTRRKV 275

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

Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) (taxid: 283643)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q3B8Q2|IF4A3_RAT Eukaryotic initiation factor 4A-III OS=Rattus norvegicus GN=Eif4a3 PE=1 SV=1

 Score =  435 bits (1118), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 208/290 (71%), Positives = 245/290 (84%), Gaps = 5/290 (1%)

Query: 1   MAAATAMRRRGGGGGM-----DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEK 55
           MAA   M   G          D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEK
Sbjct: 1   MAATATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEK 60

Query: 56  PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT 115
           PSAIQQRA+  IIKGRDVIAQ+QSGTGKT+  +++V Q +D   RE QALIL+PTRELA 
Sbjct: 61  PSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAV 120

Query: 116 QTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA 175
           Q +K +LA+GD++N+Q HAC+GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRA
Sbjct: 121 QIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA 180

Query: 176 IKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKIL 235
           IK+LVLDE+DEML++GFK+QIYDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++IL
Sbjct: 181 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRIL 240

Query: 236 VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 241 VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 290

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A6M931|IF4A3_PIG Eukaryotic initiation factor 4A-III OS=Sus scrofa GN=EIF4A3 PE=2 SV=1

 Score =  435 bits (1118), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 208/290 (71%), Positives = 245/290 (84%), Gaps = 5/290 (1%)

Query: 1   MAAATAMRRRGGGGGM-----DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEK 55
           MAA   M   G          D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEK
Sbjct: 1   MAATATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEK 60

Query: 56  PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT 115
           PSAIQQRA+  IIKGRDVIAQ+QSGTGKT+  +++V Q +D   RE QALIL+PTRELA 
Sbjct: 61  PSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAV 120

Query: 116 QTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA 175
           Q +K +LA+GD++N+Q HAC+GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRA
Sbjct: 121 QIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA 180

Query: 176 IKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKIL 235
           IK+LVLDE+DEML++GFK+QIYDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++IL
Sbjct: 181 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRIL 240

Query: 236 VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 241 VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 290

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.

Sus scrofa (taxid: 9823)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2NL22|IF4A3_BOVIN Eukaryotic initiation factor 4A-III OS=Bos taurus GN=EIF4A3 PE=2 SV=3

 Score =  435 bits (1118), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 208/290 (71%), Positives = 245/290 (84%), Gaps = 5/290 (1%)

Query: 1   MAAATAMRRRGGGGGM-----DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEK 55
           MAA   M   G          D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEK
Sbjct: 1   MAATATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEK 60

Query: 56  PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT 115
           PSAIQQRA+  IIKGRDVIAQ+QSGTGKT+  +++V Q +D   RE QALIL+PTRELA 
Sbjct: 61  PSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAV 120

Query: 116 QTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA 175
           Q +K +LA+GD++N+Q HAC+GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRA
Sbjct: 121 QIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA 180

Query: 176 IKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKIL 235
           IK+LVLDE+DEML++GFK+QIYDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++IL
Sbjct: 181 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRIL 240

Query: 236 VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 241 VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 290

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.

Bos taurus (taxid: 9913)

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	298
225464928	412	PREDICTED: eukaryotic initiation factor	0.953	0.689	0.889	1e-146
255559772	407	dead box ATP-dependent RNA helicase, put	0.902	0.660	0.925	1e-144
356530272	407	PREDICTED: DEAD-box ATP-dependent RNA he	0.932	0.683	0.903	1e-144
356556161	406	PREDICTED: DEAD-box ATP-dependent RNA he	0.942	0.692	0.887	1e-143
115438787	404	Os01g0639100 [Oryza sativa Japonica Grou	0.949	0.700	0.859	1e-143
118574850	406	DH [Medicago sativa]	0.946	0.694	0.881	1e-142
297830638	408	hypothetical protein ARALYDRAFT_479492 [	0.912	0.666	0.893	1e-142
125586856	394	hypothetical protein OsJ_11472 [Oryza sa	0.949	0.718	0.852	1e-142
147785805	398	hypothetical protein VITISV_037577 [Viti	0.889	0.665	0.924	1e-142
115453811	404	Os03g0566800 [Oryza sativa Japonica Grou	0.949	0.700	0.852	1e-142

>gi|225464928|ref|XP_002275011.1| PREDICTED: eukaryotic initiation factor 4A-3-like [Vitis vinifera]

 Score =  523 bits (1348), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 257/289 (88%), Positives = 273/289 (94%), Gaps = 5/289 (1%)

Query: 2   AAATAM---RRRGG--GGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKP 56
           AAATA      RGG   G +DD+K+VFETTEGVE I SFD MGIKDDLLRGIY YGFEKP
Sbjct: 3   AAATASVVPANRGGRRNGAVDDEKLVFETTEGVEPIMSFDQMGIKDDLLRGIYAYGFEKP 62

Query: 57  SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ 116
           SAIQQRAV+PII+GRDVIAQAQSGTGKTSMIALTVCQ VDTS+REVQALILSPTRELA+Q
Sbjct: 63  SAIQQRAVLPIIQGRDVIAQAQSGTGKTSMIALTVCQMVDTSNREVQALILSPTRELASQ 122

Query: 117 TEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI 176
           TEKVILAIGDFINIQAHAC+GGKSVGEDIRKLE+GVH+VSGTPGRVCDMIKR+TLRTRAI
Sbjct: 123 TEKVILAIGDFINIQAHACIGGKSVGEDIRKLEYGVHIVSGTPGRVCDMIKRRTLRTRAI 182

Query: 177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
           KLLVLDESDEMLSRGFKDQIYDVYRYLPP+LQVVLISATLP+EILE+T KFMTDPV+ILV
Sbjct: 183 KLLVLDESDEMLSRGFKDQIYDVYRYLPPELQVVLISATLPNEILEITNKFMTDPVRILV 242

Query: 237 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 243 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 291

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559772|ref|XP_002520905.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223539871|gb|EEF41450.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  518 bits (1333), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 249/269 (92%), Positives = 263/269 (97%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           +D+K+VFETTEG+E ITSFD MGIK+DLLRGIY YGFEKPSAIQQRAVMPIIKGRDVIAQ
Sbjct: 18  EDEKLVFETTEGIEPITSFDEMGIKNDLLRGIYAYGFEKPSAIQQRAVMPIIKGRDVIAQ 77

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           AQSGTGKTSMIALT CQ VDTSSREVQALILSPTRELA QTEKVILAIGD+INIQAHAC+
Sbjct: 78  AQSGTGKTSMIALTACQLVDTSSREVQALILSPTRELAAQTEKVILAIGDYINIQAHACI 137

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GGKSVGEDIRKLE+GVHVVSGTPGRVCDMIKR+TLRTRAIKLLVLDESDEMLSRGFKDQI
Sbjct: 138 GGKSVGEDIRKLEYGVHVVSGTPGRVCDMIKRRTLRTRAIKLLVLDESDEMLSRGFKDQI 197

Query: 197 YDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
           YDVYRYLPP+LQVVLISATLP+EILEMT+KFMTDP+KILVKRDELTLEGIKQFFVAVERE
Sbjct: 198 YDVYRYLPPELQVVLISATLPNEILEMTSKFMTDPIKILVKRDELTLEGIKQFFVAVERE 257

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           EWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 258 EWKFDTLCDLYDTLTITQAVIFCNTKRKV 286

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530272|ref|XP_003533706.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 2-like [Glycine max]

 Score =  516 bits (1330), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 253/280 (90%), Positives = 263/280 (93%), Gaps = 2/280 (0%)

Query: 6   AMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVM 65
           A RRR      +D  M FETTEGV+AI SF+ MGIKDDLLRGIYQYGFEKPSAIQQRAV 
Sbjct: 9   ANRRRAAANPAED--MDFETTEGVKAIASFEEMGIKDDLLRGIYQYGFEKPSAIQQRAVT 66

Query: 66  PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG 125
           PII+GRDVIAQAQSGTGKTSMIALTVCQ VDTS REVQALILSPTRELA+QTEKVILAIG
Sbjct: 67  PIIQGRDVIAQAQSGTGKTSMIALTVCQVVDTSVREVQALILSPTRELASQTEKVILAIG 126

Query: 126 DFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD 185
           DFINIQAHACVGGKSVGEDIRKLE+GVHVVSGTPGRVCDMIKR+TLRTRAIK+LVLDESD
Sbjct: 127 DFINIQAHACVGGKSVGEDIRKLEYGVHVVSGTPGRVCDMIKRRTLRTRAIKMLVLDESD 186

Query: 186 EMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEG 245
           EMLSRGFKDQIYDVYRYLPPDLQV LISATLPHEILEMT KFMTDPV+ILVKRDELTLEG
Sbjct: 187 EMLSRGFKDQIYDVYRYLPPDLQVCLISATLPHEILEMTNKFMTDPVRILVKRDELTLEG 246

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 247 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 286

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556161|ref|XP_003546395.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 2-like [Glycine max]

 Score =  514 bits (1325), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 252/284 (88%), Positives = 264/284 (92%), Gaps = 3/284 (1%)

Query: 2   AAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQ 61
           +   A RRR        ++M FETTEGV+AI SF+ MGIKDDLLRGIYQYGFEKPSAIQQ
Sbjct: 5   SVVPANRRRAANPA---EEMDFETTEGVKAIASFEEMGIKDDLLRGIYQYGFEKPSAIQQ 61

Query: 62  RAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI 121
           RAV PII+GRDVIAQAQSGTGKTSMIALTVCQ VDTS REVQALILSPTRELA+QTEKVI
Sbjct: 62  RAVTPIIQGRDVIAQAQSGTGKTSMIALTVCQVVDTSVREVQALILSPTRELASQTEKVI 121

Query: 122 LAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVL 181
           LAIGDFINIQAHACVGGKSVGEDIRKLE+GVHVVSGTPGRVCDMIKR+TLRTRAIK+LVL
Sbjct: 122 LAIGDFINIQAHACVGGKSVGEDIRKLEYGVHVVSGTPGRVCDMIKRRTLRTRAIKMLVL 181

Query: 182 DESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDEL 241
           DESDEMLSRGFKDQIYDVYRYLPPDLQV LISATLPHEILEMT KFMTDPV+ILVKRDEL
Sbjct: 182 DESDEMLSRGFKDQIYDVYRYLPPDLQVCLISATLPHEILEMTNKFMTDPVRILVKRDEL 241

Query: 242 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 242 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115438787|ref|NP_001043673.1| Os01g0639100 [Oryza sativa Japonica Group] gi|75321708|sp|Q5VNM3.1|RH2_ORYSJ RecName: Full=DEAD-box ATP-dependent RNA helicase 2 gi|55297015|dbj|BAD68586.1| putative nicotiana eukaryotic translation initiation factor 4A [Oryza sativa Japonica Group] gi|55297606|dbj|BAD68952.1| putative nicotiana eukaryotic translation initiation factor 4A [Oryza sativa Japonica Group] gi|113533204|dbj|BAF05587.1| Os01g0639100 [Oryza sativa Japonica Group] gi|215707106|dbj|BAG93566.1| unnamed protein product [Oryza sativa Japonica Group] gi|222618929|gb|EEE55061.1| hypothetical protein OsJ_02769 [Oryza sativa Japonica Group]

 Score =  513 bits (1321), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 245/285 (85%), Positives = 266/285 (93%), Gaps = 2/285 (0%)

Query: 1   MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQ 60
           MAAAT  RR  G G MDD+ + FET+ GVE I+SFD MGI+DDLLRGIY YGFEKPSAIQ
Sbjct: 1   MAAATTSRR--GPGAMDDENLTFETSPGVEVISSFDQMGIRDDLLRGIYAYGFEKPSAIQ 58

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV 120
           QRAV+PII GRDVIAQAQSGTGKTSMI+L+VCQ VDT+ REVQALILSPTRELA QTE+V
Sbjct: 59  QRAVLPIISGRDVIAQAQSGTGKTSMISLSVCQIVDTAVREVQALILSPTRELAAQTERV 118

Query: 121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV 180
           +LAIGDFINIQ HAC+GGKS+GEDIRKLEHGVHVVSGTPGRVCDMIKR+TLRTRAIKLL+
Sbjct: 119 MLAIGDFINIQVHACIGGKSIGEDIRKLEHGVHVVSGTPGRVCDMIKRRTLRTRAIKLLI 178

Query: 181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE 240
           LDE+DEML RGFKDQIYDVYRYLPP+LQV LISATLPHEILEMT+KFMTDPV+ILVKRDE
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVCLISATLPHEILEMTSKFMTDPVRILVKRDE 238

Query: 241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 239 LTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKV 283

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118574850|gb|ABL07003.1| DH [Medicago sativa]

 Score =  511 bits (1317), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 254/288 (88%), Positives = 265/288 (92%), Gaps = 6/288 (2%)

Query: 1   MAAAT---AMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPS 57
           MA A+   A RRR      D   M FETTEGV+AI SF+ MGIKDDLLRGIY YGFEKPS
Sbjct: 1   MATASVVPANRRRTVTANED---MDFETTEGVKAIGSFEEMGIKDDLLRGIYNYGFEKPS 57

Query: 58  AIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT 117
           AIQQRAV PII+GRDVIAQAQSGTGKTSMIALTVCQ VDTS REVQALI+SPTRELA+QT
Sbjct: 58  AIQQRAVAPIIQGRDVIAQAQSGTGKTSMIALTVCQVVDTSVREVQALIVSPTRELASQT 117

Query: 118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIK 177
           EKVILAIGD+INIQAHAC+GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR+TLRTRAIK
Sbjct: 118 EKVILAIGDYINIQAHACIGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRRTLRTRAIK 177

Query: 178 LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK 237
           LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV LISATLPHEILEMT KFMTDPV+ILVK
Sbjct: 178 LLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVCLISATLPHEILEMTNKFMTDPVRILVK 237

Query: 238 RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 238 RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKV 285

Source: Medicago sativa

Species: Medicago sativa

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830638|ref|XP_002883201.1| hypothetical protein ARALYDRAFT_479492 [Arabidopsis lyrata subsp. lyrata] gi|297329041|gb|EFH59460.1| hypothetical protein ARALYDRAFT_479492 [Arabidopsis lyrata subsp. lyrata]

 Score =  511 bits (1317), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 243/272 (89%), Positives = 262/272 (96%)

Query: 16  MDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIA 75
           MDDDK+VFETTEG+E ITSF+ MGIK+D+LRG+Y+YGFEKPSAIQQRAVMPI++GRDVIA
Sbjct: 18  MDDDKLVFETTEGIEPITSFNDMGIKEDVLRGVYEYGFEKPSAIQQRAVMPILQGRDVIA 77

Query: 76  QAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC 135
           QAQSGTGKTSMIAL+VCQ VDTSSREVQALILSPTRELATQTEK I AIG   NIQAHAC
Sbjct: 78  QAQSGTGKTSMIALSVCQVVDTSSREVQALILSPTRELATQTEKTIQAIGLHANIQAHAC 137

Query: 136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQ 195
           +GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR++LRTRAIKLL+LDESDEMLSRGFKDQ
Sbjct: 138 IGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRRSLRTRAIKLLILDESDEMLSRGFKDQ 197

Query: 196 IYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER 255
           IYDVYRYLPPDLQV L+SATLPHEILEMT+KFMT+PVKILVKRDELTLEGIKQFFVAVE+
Sbjct: 198 IYDVYRYLPPDLQVCLVSATLPHEILEMTSKFMTEPVKILVKRDELTLEGIKQFFVAVEK 257

Query: 256 EEWKFDTLCDLYDTLTITQAVIFCNTKRKIYY 287
           EEWKFDTLCDLYDTLTITQAVIFCNTKRK+ Y
Sbjct: 258 EEWKFDTLCDLYDTLTITQAVIFCNTKRKVDY 289

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125586856|gb|EAZ27520.1| hypothetical protein OsJ_11472 [Oryza sativa Japonica Group]

 Score =  511 bits (1315), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 243/285 (85%), Positives = 266/285 (93%), Gaps = 2/285 (0%)

Query: 1   MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQ 60
           MAAAT  RR  G G MDD+ + FET+ GVE I+SFD MGI++DLLRGIY YGFEKPSAIQ
Sbjct: 1   MAAATTSRR--GPGAMDDENLTFETSPGVEVISSFDQMGIREDLLRGIYAYGFEKPSAIQ 58

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV 120
           QRAV+PII GRDVIAQAQSGTGKTSMI+L+VCQ VDT+ REVQALILSPTRELA QTE+V
Sbjct: 59  QRAVLPIISGRDVIAQAQSGTGKTSMISLSVCQIVDTAVREVQALILSPTRELAAQTERV 118

Query: 121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV 180
           +LAIGD+INIQ HAC+GGKS+GEDIRKLEHGVHVVSGTPGRVCDMIKR+TLRTRAIKLL+
Sbjct: 119 MLAIGDYINIQVHACIGGKSIGEDIRKLEHGVHVVSGTPGRVCDMIKRRTLRTRAIKLLI 178

Query: 181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE 240
           LDE+DEML RGFKDQIYDVYRYLPP+LQV LISATLPHEILEMT+KFMTDPV+ILVKRDE
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVCLISATLPHEILEMTSKFMTDPVRILVKRDE 238

Query: 241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 239 LTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKV 283

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147785805|emb|CAN62124.1| hypothetical protein VITISV_037577 [Vitis vinifera]

 Score =  510 bits (1314), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 245/265 (92%), Positives = 259/265 (97%)

Query: 21  MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSG 80
           +VFETTEGVE I SFD MGIKDDLLRGIY YGFEKPSAIQQRAV+PII+GRDVIAQAQSG
Sbjct: 10  LVFETTEGVEPIMSFDQMGIKDDLLRGIYAYGFEKPSAIQQRAVLPIIQGRDVIAQAQSG 69

Query: 81  TGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKS 140
           TGKTSMIALTVCQ VDTS+REVQALILSPTRELA+QTEKVILAIGDFINIQAHAC+GGKS
Sbjct: 70  TGKTSMIALTVCQMVDTSNREVQALILSPTRELASQTEKVILAIGDFINIQAHACIGGKS 129

Query: 141 VGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY 200
           VGEDIRKLE+GVH+VSGTPGRVCDMIKR+TLRTRAIKLLVLDESDEMLSRGFKDQIYDVY
Sbjct: 130 VGEDIRKLEYGVHIVSGTPGRVCDMIKRRTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY 189

Query: 201 RYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF 260
           RYLPP+LQVVLISATLP+EILE+T KFMTDPV+ILVKRDELTLEGIKQFFVAVEREEWKF
Sbjct: 190 RYLPPELQVVLISATLPNEILEITNKFMTDPVRILVKRDELTLEGIKQFFVAVEREEWKF 249

Query: 261 DTLCDLYDTLTITQAVIFCNTKRKI 285
           DTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 250 DTLCDLYDTLTITQAVIFCNTKRKV 274

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115453811|ref|NP_001050506.1| Os03g0566800 [Oryza sativa Japonica Group] gi|122246919|sp|Q10I26.1|RH34_ORYSJ RecName: Full=DEAD-box ATP-dependent RNA helicase 34 gi|13957631|gb|AAK50586.1|AC084404_11 putative translation initiation factor [Oryza sativa Japonica Group] gi|108709369|gb|ABF97164.1| Eukaryotic initiation factor 4A-3, putative, expressed [Oryza sativa Japonica Group] gi|113548977|dbj|BAF12420.1| Os03g0566800 [Oryza sativa Japonica Group]

 Score =  510 bits (1313), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 243/285 (85%), Positives = 266/285 (93%), Gaps = 2/285 (0%)

Query: 1   MAAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQ 60
           MAAAT  RR  G G MDD+ + FET+ GVE I+SFD MGI++DLLRGIY YGFEKPSAIQ
Sbjct: 1   MAAATTSRR--GPGAMDDENLTFETSPGVEVISSFDQMGIREDLLRGIYAYGFEKPSAIQ 58

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV 120
           QRAV+PII GRDVIAQAQSGTGKTSMI+L+VCQ VDT+ REVQALILSPTRELA QTE+V
Sbjct: 59  QRAVLPIISGRDVIAQAQSGTGKTSMISLSVCQIVDTAVREVQALILSPTRELAAQTERV 118

Query: 121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV 180
           +LAIGD+INIQ HAC+GGKS+GEDIRKLEHGVHVVSGTPGRVCDMIKR+TLRTRAIKLL+
Sbjct: 119 MLAIGDYINIQVHACIGGKSIGEDIRKLEHGVHVVSGTPGRVCDMIKRRTLRTRAIKLLI 178

Query: 181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE 240
           LDE+DEML RGFKDQIYDVYRYLPP+LQV LISATLPHEILEMT+KFMTDPV+ILVKRDE
Sbjct: 179 LDEADEMLGRGFKDQIYDVYRYLPPELQVCLISATLPHEILEMTSKFMTDPVRILVKRDE 238

Query: 241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           LTLEGIKQFFVAVE+EEWKFDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 239 LTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKV 283

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	298
TAIR|locus:2091191	408	EIF4A-III "eukaryotic initiati	0.899	0.656	0.884	1.3e-125
FB|FBgn0037573	399	eIF4AIII "eIF4AIII" [Drosophil	0.882	0.659	0.768	6.1e-110
UNIPROTKB|Q5ZM36	412	EIF4A3 "Eukaryotic initiation	0.892	0.645	0.759	7e-109
UNIPROTKB|Q2NL22	411	EIF4A3 "Eukaryotic initiation	0.892	0.647	0.759	7e-109
UNIPROTKB|E2RDZ4	411	EIF4A3 "Uncharacterized protei	0.892	0.647	0.759	7e-109
UNIPROTKB|P38919	411	EIF4A3 "Eukaryotic initiation	0.892	0.647	0.759	7e-109
UNIPROTKB|A6M931	411	EIF4A3 "Eukaryotic initiation	0.892	0.647	0.759	7e-109
RGD|1591139	411	Eif4a3 "eukaryotic translation	0.892	0.647	0.759	7e-109
ZFIN|ZDB-GENE-040426-915	406	eif4a3 "eukaryotic translation	0.892	0.655	0.759	1.1e-108
WB|WBGene00018007	399	F33D11.10 [Caenorhabditis eleg	0.882	0.659	0.752	1.3e-107

TAIR|locus:2091191 EIF4A-III "eukaryotic initiation factor 4A-III" [Arabidopsis thaliana (taxid:3702)]

 Score = 1234 (439.4 bits), Expect = 1.3e-125, P = 1.3e-125
 Identities = 237/268 (88%), Positives = 257/268 (95%)

Query:    20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
             K+VFETT+G+E ITSF+ MGIK+D+LRG+Y+YGFEKPSAIQQRAVMPI++GRDVIAQAQS
Sbjct:    22 KLVFETTDGIEPITSFNDMGIKEDVLRGVYEYGFEKPSAIQQRAVMPILQGRDVIAQAQS 81

Query:    80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             GTGKTSMIAL+VCQ VDTSSREVQALILSPTRELATQTEK I AIG   NIQAHAC+GG 
Sbjct:    82 GTGKTSMIALSVCQVVDTSSREVQALILSPTRELATQTEKTIQAIGLHANIQAHACIGGN 141

Query:   140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
             SVGEDIRKLEHGVHVVSGTPGRVCDMIKR++LRTRAIKLL+LDESDEMLSRGFKDQIYDV
Sbjct:   142 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRRSLRTRAIKLLILDESDEMLSRGFKDQIYDV 201

Query:   200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
             YRYLPPDLQV L+SATLPHEILEMT+KFMT+PVKILVKRDELTLEGIKQFFVAVE+EEWK
Sbjct:   202 YRYLPPDLQVCLVSATLPHEILEMTSKFMTEPVKILVKRDELTLEGIKQFFVAVEKEEWK 261

Query:   260 FDTLCDLYDTLTITQAVIFCNTKRKIYY 287
             FDTLCDLYDTLTITQAVIFCNTKRK+ Y
Sbjct:   262 FDTLCDLYDTLTITQAVIFCNTKRKVDY 289

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005730 "nucleolus" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0001666 "response to hypoxia" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=IDA

GO:0006397 "mRNA processing" evidence=IPI

GO:0016607 "nuclear speck" evidence=IDA

GO:0035145 "exon-exon junction complex" evidence=IDA

FB|FBgn0037573 eIF4AIII "eIF4AIII" [Drosophila melanogaster (taxid:7227)]

 Score = 1086 (387.4 bits), Expect = 6.1e-110, P = 6.1e-110
 Identities = 202/263 (76%), Positives = 239/263 (90%)

Query:    23 FETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTG 82
             FET+E VE I +F+AM +K++LLRGIY YGFEKPSAIQQR++ PI+KGRDVIAQAQSGTG
Sbjct:    16 FETSEDVEVIPTFNAMNLKEELLRGIYAYGFEKPSAIQQRSITPIVKGRDVIAQAQSGTG 75

Query:    83 KTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVG 142
             KT+  ++++ Q++DT+ RE Q L LSPTRELA Q +KVILA+GD +N+Q H C+GG ++G
Sbjct:    76 KTATFSISILQSLDTTLRETQVLCLSPTRELAVQIQKVILALGDMMNVQCHVCIGGTNLG 135

Query:   143 EDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY 202
             EDIRKL++G H+VSGTPGRV DMIKR+ LRTRAIK+LVLDE+DEML++GFK+QIYDVYRY
Sbjct:   136 EDIRKLDYGQHIVSGTPGRVFDMIKRRVLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY 195

Query:   203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT 262
             LPP  QVVLISATLPHEILEMT+KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWKFDT
Sbjct:   196 LPPATQVVLISATLPHEILEMTSKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDT 255

Query:   263 LCDLYDTLTITQAVIFCNTKRKI 285
             LCDLYDTLTITQAVIFCNTKRK+
Sbjct:   256 LCDLYDTLTITQAVIFCNTKRKV 278

GO:0016281 "eukaryotic translation initiation factor 4F complex" evidence=ISS

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

GO:0006413 "translational initiation" evidence=ISS

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

GO:0005524 "ATP binding" evidence=IEA

GO:0045495 "pole plasm" evidence=IDA

GO:0045451 "pole plasm oskar mRNA localization" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

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

GO:0006974 "response to DNA damage stimulus" evidence=IMP

GO:0008380 "RNA splicing" evidence=IMP

UNIPROTKB|Q5ZM36 EIF4A3 "Eukaryotic initiation factor 4A-III" [Gallus gallus (taxid:9031)]

 Score = 1076 (383.8 bits), Expect = 7.0e-109, P = 7.0e-109
 Identities = 202/266 (75%), Positives = 239/266 (89%)

Query:    20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
             K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct:    26 KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 85

Query:    80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct:    86 GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 145

Query:   140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
             +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct:   146 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 205

Query:   200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
             YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct:   206 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 265

Query:   260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
             FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct:   266 FDTLCDLYDTLTITQAVIFCNTKRKV 291

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

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

UNIPROTKB|Q2NL22 EIF4A3 "Eukaryotic initiation factor 4A-III" [Bos taurus (taxid:9913)]

 Score = 1076 (383.8 bits), Expect = 7.0e-109, P = 7.0e-109
 Identities = 202/266 (75%), Positives = 239/266 (89%)

Query:    20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
             K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct:    25 KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 84

Query:    80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct:    85 GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 144

Query:   140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
             +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct:   145 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 204

Query:   200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
             YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct:   205 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 264

Query:   260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
             FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct:   265 FDTLCDLYDTLTITQAVIFCNTKRKV 290

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

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

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

GO:0035145 "exon-exon junction complex" evidence=IEA

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

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

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

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E2RDZ4 EIF4A3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1076 (383.8 bits), Expect = 7.0e-109, P = 7.0e-109
 Identities = 202/266 (75%), Positives = 239/266 (89%)

Query:    20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
             K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct:    25 KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 84

Query:    80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct:    85 GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 144

Query:   140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
             +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct:   145 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 204

Query:   200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
             YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct:   205 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 264

Query:   260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
             FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct:   265 FDTLCDLYDTLTITQAVIFCNTKRKV 290

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

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

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

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

GO:0035145 "exon-exon junction complex" evidence=IEA

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

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|P38919 EIF4A3 "Eukaryotic initiation factor 4A-III" [Homo sapiens (taxid:9606)]

 Score = 1076 (383.8 bits), Expect = 7.0e-109, P = 7.0e-109
 Identities = 202/266 (75%), Positives = 239/266 (89%)

Query:    20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
             K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct:    25 KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 84

Query:    80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct:    85 GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 144

Query:   140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
             +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct:   145 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 204

Query:   200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
             YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct:   205 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 264

Query:   260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
             FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct:   265 FDTLCDLYDTLTITQAVIFCNTKRKV 290

GO:0006364 "rRNA processing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

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

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

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

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

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

GO:0035145 "exon-exon junction complex" evidence=IDA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IMP;TAS

GO:0005515 "protein binding" evidence=IPI

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

GO:0005524 "ATP binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019221 "cytokine-mediated signaling pathway" evidence=TAS

UNIPROTKB|A6M931 EIF4A3 "Eukaryotic initiation factor 4A-III" [Sus scrofa (taxid:9823)]

 Score = 1076 (383.8 bits), Expect = 7.0e-109, P = 7.0e-109
 Identities = 202/266 (75%), Positives = 239/266 (89%)

Query:    20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
             K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct:    25 KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 84

Query:    80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct:    85 GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 144

Query:   140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
             +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct:   145 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 204

Query:   200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
             YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct:   205 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 264

Query:   260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
             FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct:   265 FDTLCDLYDTLTITQAVIFCNTKRKV 290

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

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

RGD|1591139 Eif4a3 "eukaryotic translation initiation factor 4A, isoform 3" [Rattus norvegicus (taxid:10116)]

 Score = 1076 (383.8 bits), Expect = 7.0e-109, P = 7.0e-109
 Identities = 202/266 (75%), Positives = 239/266 (89%)

Query:    20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
             K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct:    25 KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 84

Query:    80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct:    85 GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 144

Query:   140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
             +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct:   145 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 204

Query:   200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
             YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct:   205 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 264

Query:   260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
             FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct:   265 FDTLCDLYDTLTITQAVIFCNTKRKV 290

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

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

GO:0035145 "exon-exon junction complex" evidence=IEA

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

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

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

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

ZFIN|ZDB-GENE-040426-915 eif4a3 "eukaryotic translation initiation factor 4A, isoform 3" [Danio rerio (taxid:7955)]

 Score = 1074 (383.1 bits), Expect = 1.1e-108, P = 1.1e-108
 Identities = 202/266 (75%), Positives = 238/266 (89%)

Query:    20 KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
             K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct:    20 KIEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 79

Query:    80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             GTGKT+   ++V Q +D   RE QALIL+PTRELA Q +KV+LA+GD++N+Q HAC+GG 
Sbjct:    80 GTGKTATFCVSVLQCLDIQVRETQALILAPTRELAGQIQKVLLALGDYMNVQCHACIGGT 139

Query:   140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
             +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct:   140 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 199

Query:   200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
             YRYLPP  QV LISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct:   200 YRYLPPATQVCLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 259

Query:   260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
             FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct:   260 FDTLCDLYDTLTITQAVIFCNTKRKV 285

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

WB|WBGene00018007 F33D11.10 [Caenorhabditis elegans (taxid:6239)]

 Score = 1064 (379.6 bits), Expect = 1.3e-107, P = 1.3e-107
 Identities = 198/263 (75%), Positives = 238/263 (90%)

Query:    23 FETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTG 82
             FE++E V  I +FD MG+++DLLRGIY YGFEKPSAIQQRAV  I+K RDVIAQAQSGTG
Sbjct:    16 FESSEEVNVIPTFDKMGLREDLLRGIYAYGFEKPSAIQQRAVPAILKARDVIAQAQSGTG 75

Query:    83 KTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVG 142
             KT+  +++V Q++DT  RE QALILSPTRELA Q +KV+LA+GD++N+Q HAC+GG ++G
Sbjct:    76 KTATFSISVLQSLDTQVRETQALILSPTRELAVQIQKVVLALGDYMNVQCHACIGGTNLG 135

Query:   143 EDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY 202
             EDIRKL++G HVVSGTPGRV DMI+R+ LRTRAIKLLVLDE+DEML++GFK+Q+YD+YRY
Sbjct:   136 EDIRKLDYGQHVVSGTPGRVFDMIRRRNLRTRAIKLLVLDEADEMLNKGFKEQLYDIYRY 195

Query:   203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT 262
             LPP  QVVL+SATLPHEILEMT+KFMTDP++ILVKRDELTLEGIKQFFVAV+REEWKFDT
Sbjct:   196 LPPGAQVVLLSATLPHEILEMTSKFMTDPIRILVKRDELTLEGIKQFFVAVDREEWKFDT 255

Query:   263 LCDLYDTLTITQAVIFCNTKRKI 285
             L DLYDTLTITQAV+FCNT+RK+
Sbjct:   256 LIDLYDTLTITQAVLFCNTRRKV 278

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0001703 "gastrulation with mouth forming first" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0051301 "cell division" evidence=IMP

GO:0000910 "cytokinesis" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040010 "positive regulation of growth rate" evidence=IMP

---

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)
P0CQ73	FAL1_CRYNB	3, ., 6, ., 4, ., 1, 3	0.7189	0.9194	0.6919	N/A	no
P0CQ72	FAL1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.7189	0.9194	0.6919	yes	no
Q4IAA0	FAL1_GIBZE	3, ., 6, ., 4, ., 1, 3	0.6630	0.9161	0.6807	yes	no
Q2NL22	IF4A3_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7172	0.9563	0.6934	yes	no
Q5VNM3	RH2_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8596	0.9496	0.7004	yes	no
B5FZY7	IF4A3_TAEGU	3, ., 6, ., 4, ., 1, 3	0.7546	0.9026	0.6560	yes	no
Q55D61	IF4A_DICDI	3, ., 6, ., 4, ., 1, 3	0.6628	0.8758	0.6444	yes	no
O42226	I4A3B_XENLA	3, ., 6, ., 4, ., 1, 3	0.7528	0.8825	0.6352	N/A	no
P41380	IF4A3_NICPL	3, ., 6, ., 4, ., 1, 3	0.8851	0.9060	0.6905	N/A	no
A6M931	IF4A3_PIG	3, ., 6, ., 4, ., 1, 3	0.7172	0.9563	0.6934	yes	no
Q6BT27	FAL1_DEBHA	3, ., 6, ., 4, ., 1, 3	0.6066	0.9060	0.6766	yes	no
Q2UAK1	FAL1_ASPOR	3, ., 6, ., 4, ., 1, 3	0.6826	0.9093	0.6809	yes	no
B5DG42	IF4A3_SALSA	3, ., 6, ., 4, ., 1, 3	0.7263	0.9563	0.7019	N/A	no
Q91VC3	IF4A3_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7546	0.9026	0.6545	yes	no
A5AAE5	FAL1_ASPNC	3, ., 6, ., 4, ., 1, 3	0.6902	0.8993	0.6716	yes	no
Q5U526	I4A3A_XENLA	3, ., 6, ., 4, ., 1, 3	0.7546	0.9026	0.6481	N/A	no
Q7ZVA6	IF4A3_DANRE	3, ., 6, ., 4, ., 1, 3	0.7263	0.9563	0.7019	yes	no
P38919	IF4A3_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7546	0.9026	0.6545	yes	no
Q5ZM36	IF4A3_CHICK	3, ., 6, ., 4, ., 1, 3	0.7546	0.9026	0.6529	yes	no
B7ZTW1	IF4A3_XENTR	3, ., 6, ., 4, ., 1, 3	0.7546	0.9026	0.6481	yes	no
Q4R3Q1	IF4A3_MACFA	3, ., 6, ., 4, ., 1, 3	0.7472	0.9026	0.6545	N/A	no
Q6C347	FAL1_YARLI	3, ., 6, ., 4, ., 1, 3	0.6679	0.8993	0.6750	yes	no
Q10I26	RH34_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8526	0.9496	0.7004	yes	no
Q94A52	RH2_ARATH	3, ., 6, ., 4, ., 1, 3	0.8827	0.9161	0.6691	yes	no
Q4P184	FAL1_USTMA	3, ., 6, ., 4, ., 1, 3	0.7309	0.9228	0.6926	N/A	no
Q3B8Q2	IF4A3_RAT	3, ., 6, ., 4, ., 1, 3	0.7172	0.9563	0.6934	yes	no
Q10055	FAL1_SCHPO	3, ., 6, ., 4, ., 1, 3	0.6858	0.8758	0.6624	yes	no
Q5AUL4	FAL1_EMENI	3, ., 6, ., 4, ., 1, 3	0.6940	0.8993	0.6716	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.991
3rd Layer	3.6.4	0.976

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00037338001	SubName- Full=Chromosome undetermined scaffold_87, whole genome shotgun sequence; (415 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00034829001	SubName- Full=Chromosome chr4 scaffold_73, whole genome shotgun sequence; (202 aa)				•	•	•			0.821

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	298
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-138
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-93
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	6e-86
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	8e-62
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	1e-50
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	3e-47
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	3e-46
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-44
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	4e-35
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	6e-34
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	4e-33
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	3e-31
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	4e-30
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-29
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-27
COG1205	851	COG1205, COG1205, Distinct helicase family with a	6e-07

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

 Score =  396 bits (1019), Expect = e-138
 Identities = 169/258 (65%), Positives = 210/258 (81%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           E + SFDA+ + +DLLRGIY YGFEKPSAIQQR + PI+ G D I QAQSGTGKT+   +
Sbjct: 25  EIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVI 84

Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
              Q +D      QALIL+PTRELA Q +KV+LA+GD++ ++ HACVGG  V +DI KL+
Sbjct: 85  AALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLK 144

Query: 150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
            GVH+V GTPGRV DMI ++ LR   +KL +LDE+DEMLSRGFK QIYDV++ LPPD+QV
Sbjct: 145 AGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQV 204

Query: 210 VLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDT 269
            L SAT+P+EILE+TTKFM DP +ILVK+DELTLEGI+QF+VAVE+EEWKFDTLCDLY+T
Sbjct: 205 ALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYET 264

Query: 270 LTITQAVIFCNTKRKIYY 287
           LTITQA+I+CNT+RK+ Y
Sbjct: 265 LTITQAIIYCNTRRKVDY 282

Length = 401

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

 Score =  275 bits (705), Expect = 1e-93
 Identities = 94/203 (46%), Positives = 137/203 (67%), Gaps = 2/203 (0%)

Query: 35  FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQT 94
           F+ +G+  +LLRGIY  GFEKP+ IQ RA+ P++ GRDVI QAQ+G+GKT+   + + + 
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 95  VDTSSR--EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV 152
           +D S +    QALIL+PTRELA Q  +V   +G   N++     GG S+ + IRKL+ G 
Sbjct: 61  LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120

Query: 153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI 212
           H+V  TPGR+ D+++R  L    +K LVLDE+D ML  GF+DQI ++ + LP D Q +L 
Sbjct: 121 HIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLF 180

Query: 213 SATLPHEILEMTTKFMTDPVKIL 235
           SAT+P E+ ++  KF+ +PV+IL
Sbjct: 181 SATMPKEVRDLARKFLRNPVRIL 203

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 =  266 bits (681), Expect = 6e-86
 Identities = 104/256 (40%), Positives = 153/256 (59%), Gaps = 5/256 (1%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
             F ++G+  +LL+ +   GFE+P+ IQ  A+  I+ GRDV+ QAQ+GTGKT+   L + 
Sbjct: 29  PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLL 88

Query: 93  QTVDTSSR--EVQALILSPTRELATQTEKVILAIGDF-INIQAHACVGGKSVGEDIRKLE 149
           Q +  S     V ALIL+PTRELA Q  + +  +G     ++     GG S+ + I  L+
Sbjct: 89  QKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALK 148

Query: 150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
            GV +V  TPGR+ D+IKR  L    ++ LVLDE+D ML  GF D I  + + LPPD Q 
Sbjct: 149 RGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQT 208

Query: 210 VLISATLPHEILEMTTKFMTDPVKILVKRDEL--TLEGIKQFFVAVEREEWKFDTLCDLY 267
           +L SAT+P +I E+  +++ DPV+I V  ++L  TL+ IKQF++ VE EE K + L  L 
Sbjct: 209 LLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLL 268

Query: 268 DTLTITQAVIFCNTKR 283
                 + ++F  TKR
Sbjct: 269 KDEDEGRVIVFVRTKR 284

Length = 513

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

 Score =  202 bits (516), Expect = 8e-62
 Identities = 98/254 (38%), Positives = 141/254 (55%), Gaps = 7/254 (2%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           T+F  + +   LL  + + G+ + + IQ +++  I+ G+DVIAQA++G+GKT+   L + 
Sbjct: 4   TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL 63

Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHG 151
           Q +D     VQAL+L PTRELA Q  K I  +  FI NI+     GG  +G  I  LEHG
Sbjct: 64  QKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHG 123

Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
            H++ GTPGR+ D +++ TL   A+  LVLDE+D ML  GF+D I  + R  P   Q +L
Sbjct: 124 AHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQTLL 183

Query: 212 ISATLPHEILEMTTKFMTDP--VKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDT 269
            SAT P  I  ++ +F  DP  VK+    D      I+Q F  V  +E +   L  L   
Sbjct: 184 FSATYPEGIAAISQRFQRDPVEVKVESTHDLPA---IEQRFYEVSPDE-RLPALQRLLLH 239

Query: 270 LTITQAVIFCNTKR 283
                 V+FCNTK+
Sbjct: 240 HQPESCVVFCNTKK 253

Length = 460

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

 Score =  164 bits (418), Expect = 1e-50
 Identities = 64/168 (38%), Positives = 103/168 (61%), Gaps = 2/168 (1%)

Query: 57  SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ 116
           + IQ +A+  I+ G+DV+ QA +G+GKT    L + Q +       QAL+L+PTRELA Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 117 TEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRT-R 174
             + +  +   + ++     GG S+ E  RKL+ G   ++ GTPGR+ D+++R  L+  +
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120

Query: 175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILE 222
            +KLLVLDE+  +L  GF D + ++   LPPD Q++L+SATLP  + +
Sbjct: 121 NLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLED 168

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|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score =  156 bits (397), Expect = 3e-47
 Identities = 72/204 (35%), Positives = 114/204 (55%), Gaps = 5/204 (2%)

Query: 48  IYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI 106
           I ++GFE     Q+ A+  ++ G RDVI  A +G+GKT    L   + +    +  + L+
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALK-RGKGGRVLV 59

Query: 107 LSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV-HVVSGTPGRVCDM 165
           L PTRELA Q  + +  +G  + ++     GG S  E +RKLE G   ++  TPGR+ D+
Sbjct: 60  LVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDL 119

Query: 166 IKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTT 225
           ++   L    + L++LDE+  +L  GF DQ+  + + LP ++Q++L+SAT P EI  +  
Sbjct: 120 LENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLE 179

Query: 226 KFMTDPVKILVKRDELTLEGIKQF 249
            F+ DPV I V      LE I+QF
Sbjct: 180 LFLNDPVFIDVGF--TPLEPIEQF 201

Length = 201

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

 Score =  161 bits (408), Expect = 3e-46
 Identities = 89/255 (34%), Positives = 144/255 (56%), Gaps = 7/255 (2%)

Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQ 93
           SFD++G+  D+LR + + G+ +P+ IQQ+A+  +++GRD++A AQ+GTGKT+   L + Q
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 94  TVDTSS------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK 147
            + T        R V+ALIL+PTRELA Q  + +     ++NI++    GG S+   + K
Sbjct: 62  HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121

Query: 148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDL 207
           L  GV V+  TPGR+ D+  +  ++   +++LVLDE+D ML  GF   I  V   LP   
Sbjct: 122 LRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKR 181

Query: 208 QVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY 267
           Q +L SAT   +I  +  K + +P++I V R     E + Q    V+++  K + L  + 
Sbjct: 182 QNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKR-KRELLSQMI 240

Query: 268 DTLTITQAVIFCNTK 282
                 Q ++F  TK
Sbjct: 241 GKGNWQQVLVFTRTK 255

Length = 456

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

 Score =  159 bits (403), Expect = 2e-44
 Identities = 90/257 (35%), Positives = 134/257 (52%), Gaps = 8/257 (3%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           E  T+F  +G+K  +L  +   G+EKPS IQ   +  ++ GRDV+  AQ+G+GKT+  +L
Sbjct: 3   EFETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSL 62

Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI----NIQAHACVGGKSVGEDI 145
            +   +D   +  Q L+L+PTRELA Q   V  A+ DF      +   A  GG+     +
Sbjct: 63  PLLHNLDPELKAPQILVLAPTRELAVQ---VAEAMTDFSKHMRGVNVVALYGGQRYDVQL 119

Query: 146 RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP 205
           R L  G  +V GTPGR+ D +KR TL    +  LVLDE+DEML  GF + +  +   +P 
Sbjct: 120 RALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPE 179

Query: 206 DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 265
             Q  L SAT+P  I  +T +FM +P ++ ++    T   I Q +  V     K + L  
Sbjct: 180 GHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMR-KNEALVR 238

Query: 266 LYDTLTITQAVIFCNTK 282
             +      A+IF  TK
Sbjct: 239 FLEAEDFDAAIIFVRTK 255

Length = 629

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

 Score =  131 bits (331), Expect = 4e-35
 Identities = 77/273 (28%), Positives = 136/273 (49%), Gaps = 14/273 (5%)

Query: 27  EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSM 86
           E  E  T F    +  +L+  I+  GF   + IQ + +   + G D I +AQ+GTGKT+ 
Sbjct: 81  EPQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAA 140

Query: 87  IALTVC----QTVDTSSR---EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
             +++     QT     R   E +ALI++PTREL  Q  K   A+  +  +     VGG 
Sbjct: 141 FLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGM 200

Query: 140 SVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD 198
              + +++LE     ++  TPGR+ D  +R  +    ++++VLDE+D ML  GF  Q+  
Sbjct: 201 DFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQ 260

Query: 199 VYRYLPP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
           + R  P   + Q +L SAT   +++ +  ++ TDP  + ++ + +  + ++Q   AV   
Sbjct: 261 IIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGS 320

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTK---RKIY 286
           + K+  L +L       + ++F N K   R+I 
Sbjct: 321 D-KYKLLYNLVTQNPWERVMVFANRKDEVRRIE 352

Length = 475

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

 Score =  129 bits (325), Expect = 6e-34
 Identities = 78/263 (29%), Positives = 139/263 (52%), Gaps = 17/263 (6%)

Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTV 91
           I SF + G+   LL  +   G+E P+ IQ +A+   + GR ++  A +G+GKT+   + +
Sbjct: 120 ILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPI 179

Query: 92  ---CQTV----DTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED 144
              C T+     +  R   A++L+PTREL  Q E     +G  +  +    VGG ++ + 
Sbjct: 180 ISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQ 239

Query: 145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP 204
           + +++ GV ++ GTPGR+ D++ +  +    + +LVLDE D ML RGF+DQ+  +++ L 
Sbjct: 240 LYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS 299

Query: 205 PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLC 264
              QV+L SAT+  E+ +  +    D + I +       + +KQ  + VE ++ K     
Sbjct: 300 QP-QVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKK----Q 354

Query: 265 DLYDTLTITQ-----AVIFCNTK 282
            L+D L   Q     AV+F +++
Sbjct: 355 KLFDILKSKQHFKPPAVVFVSSR 377

Length = 518

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

 Score =  118 bits (298), Expect = 4e-33
 Identities = 51/146 (34%), Positives = 82/146 (56%), Gaps = 2/146 (1%)

Query: 71  RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI 130
           RDV+  A +G+GKT    L + + +D+     Q L+L+PTRELA Q  + +  +     I
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKG-GQVLVLAPTRELANQVAERLKELFGE-GI 58

Query: 131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR 190
           +    +GG S+ +  + L     +V GTPGR+ D ++R  L  + + LL+LDE+  +L++
Sbjct: 59  KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQ 118

Query: 191 GFKDQIYDVYRYLPPDLQVVLISATL 216
           GF      +   LP D QV+L+SAT 
Sbjct: 119 GFGLLGLKILLKLPKDRQVLLLSATP 144

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

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

 Score =  122 bits (307), Expect = 3e-31
 Identities = 84/261 (32%), Positives = 130/261 (49%), Gaps = 15/261 (5%)

Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQ 93
           +F +  +   LL G+   GF + + IQ   +   + G DV  QAQ+GTGKT    + V  
Sbjct: 10  TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 94  T-------VDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR 146
                    D    + +ALIL+PTRELA Q  K  +  G  + ++     GG    +   
Sbjct: 70  RLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRE 129

Query: 147 KLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP 205
            L+ GV V+  TPGR+ D +K+ K +   A ++ VLDE+D M   GF   I  + R +P 
Sbjct: 130 LLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPE 189

Query: 206 --DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQ--FFVAVEREEWKFD 261
               Q +L SATL H +LE+  + M +P K++V+ + +T   ++Q  +F A   +E K  
Sbjct: 190 RGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPA---DEEKQT 246

Query: 262 TLCDLYDTLTITQAVIFCNTK 282
            L  L       + ++F NTK
Sbjct: 247 LLLGLLSRSEGARTMVFVNTK 267

Length = 572

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

 Score =  118 bits (298), Expect = 4e-30
 Identities = 82/264 (31%), Positives = 126/264 (47%), Gaps = 16/264 (6%)

Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPI-IKGRDVIAQAQSGTGKTSMIALT 90
           + SF+     D +L+ +   GF +P+ IQ +   PI + GRD+I  A++G+GKT  +A  
Sbjct: 129 VVSFEYTSFPDYILKSLKNAGFTEPTPIQVQG-WPIALSGRDMIGIAETGSGKT--LAFL 185

Query: 91  VCQTVDTSSREVQ-------ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE 143
           +   V  +++ +         L+L+PTRELA Q  +     G    I+     GG     
Sbjct: 186 LPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRG 245

Query: 144 DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL 203
            I  L  GV ++   PGR+ D ++      R +  LVLDE+D ML  GF+ QI  +   +
Sbjct: 246 QIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQI 305

Query: 204 PPDLQVVLISATLPHEILEMTTKFMTD-PVKILVKRDELTL-EGIKQFFVAVEREEWKFD 261
            PD Q ++ SAT P E+  +      + PV + V   +LT    IKQ    VE  E K  
Sbjct: 306 RPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHE-KRG 364

Query: 262 TLCDLYDTLTI--TQAVIFCNTKR 283
            L  L   +     + +IF  TK+
Sbjct: 365 KLKMLLQRIMRDGDKILIFVETKK 388

Length = 545

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

 Score =  116 bits (292), Expect = 1e-29
 Identities = 81/275 (29%), Positives = 130/275 (47%), Gaps = 38/275 (13%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA---- 88
             F    +   ++  + + GF   + IQ  A+   + GRDV  QAQ+GTGKT  +A    
Sbjct: 8   QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKT--MAFLTA 65

Query: 89  -----LTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE 143
                L+     D    + +ALI++PTRELA Q       +     ++     GG    +
Sbjct: 66  TFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDK 125

Query: 144 DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL 203
            ++ LE GV ++ GT GR+ D  K+  +   AI+++VLDE+D M   GF   I  ++R +
Sbjct: 126 QLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRM 185

Query: 204 PPDLQ--VVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQ--FFVAVE----- 254
           PP  Q   +L SATL + + E+  + M +P  + V+ ++ T   IK+  F+ + E     
Sbjct: 186 PPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRL 245

Query: 255 -----REEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
                 EEW               +A+IF NTK +
Sbjct: 246 LQTLIEEEWP-------------DRAIIFANTKHR 267

Length = 423

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

 Score =  110 bits (278), Expect = 1e-27
 Identities = 75/258 (29%), Positives = 123/258 (47%), Gaps = 11/258 (4%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           T+F  + + + LL  +   G+ +P+AIQ  A+ P + GRDV+  A +GTGKT+   L   
Sbjct: 1   TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPAL 60

Query: 93  QTVDTSSRE----VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL 148
           Q +    R      + LIL+PTRELA Q       +    ++      GG +        
Sbjct: 61  QHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVF 120

Query: 149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK---DQIYDVYRYLPP 205
                +V  TPGR+   IK +    RA++ L+LDE+D ML  GF    + I    R+   
Sbjct: 121 SENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRK- 179

Query: 206 DLQVVLISATLPHE-ILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLC 264
             Q +L SATL  + + +   + + DPV++  +      + I Q++   +  E K   LC
Sbjct: 180 --QTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLC 237

Query: 265 DLYDTLTITQAVIFCNTK 282
            L     +T++++F  T+
Sbjct: 238 HLLKQPEVTRSIVFVRTR 255

Length = 434

>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 = 50.1 bits (120), Expect = 6e-07
 Identities = 51/213 (23%), Positives = 82/213 (38%), Gaps = 29/213 (13%)

Query: 24  ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGK 83
              E     TS       + L   + + G E+  + Q  A+  I +GR+V+    +G+GK
Sbjct: 39  PEIEARPGKTSEFPELRDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGK 98

Query: 84  TSMIALTVCQTVDTSSREVQALILSPTRELAT-QTEKVILAIGDF-INIQAHACVGGKSV 141
           T    L +   +       +AL+L PT  LA  Q E++   I D    +      G    
Sbjct: 99  TESFLLPILDHL-LRDPSARALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPP 157

Query: 142 GEDIRKLEHGVHVVSGTPGRVCDMIKRKTLR--------TRAIKLLVLDE---------S 184
            E    + +   ++   P    DM+    LR         R +K LV+DE         S
Sbjct: 158 EERRAIIRNPPDILLTNP----DMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGS 213

Query: 185 D-EMLSRGFKDQIYDVYRYLPPDLQVVLISATL 216
           +  +L R    ++    R     LQ++  SATL
Sbjct: 214 EVALLLRRLLRRL----RRYGSPLQIICTSATL 242

Length = 851

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	298
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.98
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.98
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.98
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.97
PRK14701	1638	reverse gyrase; Provisional	99.97
COG1205	851	Distinct helicase family with a unique C-terminal	99.97
COG1204	766	Superfamily II helicase [General function predicti	99.97
COG1202	830	Superfamily II helicase, archaea-specific [General	99.96
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.96
PRK10689	1147	transcription-repair coupling factor; Provisional	99.96
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.96
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.96
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.95
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.95
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.95
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.95
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.94
PHA02653	675	RNA helicase NPH-II; Provisional	99.94
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.94
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.93
PHA02558	501	uvsW UvsW helicase; Provisional	99.92
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.92
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.92
PRK13766	773	Hef nuclease; Provisional	99.91
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.91
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.9
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.9
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.9
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.89
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.88
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.88
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.88
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.87
PRK09694	878	helicase Cas3; Provisional	99.87
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.87
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.87
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.87
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.86
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.86
KOG0354	746	consensus DEAD-box like helicase [General function	99.85
PRK05580	679	primosome assembly protein PriA; Validated	99.85
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.82
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.82
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.82
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.81
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.81
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.8
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.78
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.77
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.77
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.76
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.76
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.75
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.75
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.73
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.72
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.7
COG4096	875	HsdR Type I site-specific restriction-modification	99.69
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.65
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.63
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.61
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.57
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.56
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.51
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.51
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.44
PRK04914	956	ATP-dependent helicase HepA; Validated	99.44
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.42
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.42
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.41
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.4
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.35
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.34
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.34
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.33
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.32
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.28
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.28
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.27
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.23
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.19
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.19
KOG1123	776	consensus RNA polymerase II transcription initiati	99.18
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.16
PRK14873	665	primosome assembly protein PriA; Provisional	99.11
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.11
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.06
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.04
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.02
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.0
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	98.99
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.97
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.86
COG4889	1518	Predicted helicase [General function prediction on	98.85
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.81
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.8
PRK15483	986	type III restriction-modification system StyLTI en	98.79
COG0610	962	Type I site-specific restriction-modification syst	98.78
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.75
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.74
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	98.66
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.65
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	98.63
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	98.63
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.61
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.57
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.55
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.54
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.36
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.32
KOG1002	791	consensus Nucleotide excision repair protein RAD16	98.31
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.31
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.31
PRK10536	262	hypothetical protein; Provisional	98.31
KOG2340	698	consensus Uncharacterized conserved protein [Funct	98.3
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.29
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.28
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.26
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.24
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.21
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.21
PF13245	76	AAA_19: Part of AAA domain	98.21
KOG1803	649	consensus DNA helicase [Replication, recombination	98.11
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.11
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.09
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	98.06
KOG4439	901	consensus RNA polymerase II transcription terminat	98.04
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.95
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.92
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.9
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.86
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	97.85
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.84
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.82
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.81
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.81
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.79
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.79
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.73
PRK04296	190	thymidine kinase; Provisional	97.69
PRK08181	269	transposase; Validated	97.64
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	97.63
PRK06526	254	transposase; Provisional	97.63
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.6
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.58
smart00382	148	AAA ATPases associated with a variety of cellular	97.54
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.54
PRK14974	336	cell division protein FtsY; Provisional	97.52
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.51
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	97.51
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.51
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.38
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.32
PRK06921	266	hypothetical protein; Provisional	97.32
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.32
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	97.3
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	97.3
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	97.28
PRK11054	684	helD DNA helicase IV; Provisional	97.27
PRK05642	234	DNA replication initiation factor; Validated	97.27
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	97.25
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.23
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.23
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.22
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.22
PHA02533	534	17 large terminase protein; Provisional	97.2
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.2
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.19
PRK08727	233	hypothetical protein; Validated	97.18
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	97.16
PRK07952	244	DNA replication protein DnaC; Validated	97.15
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.15
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	97.07
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.07
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.06
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.06
PLN03025	319	replication factor C subunit; Provisional	97.06
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.04
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.03
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.01
PRK06835	329	DNA replication protein DnaC; Validated	97.0
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.0
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.99
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.98
PRK12377	248	putative replication protein; Provisional	96.98
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	96.97
COG4626	546	Phage terminase-like protein, large subunit [Gener	96.97
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	96.94
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.93
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.92
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.92
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.91
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	96.88
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.88
PRK08084	235	DNA replication initiation factor; Provisional	96.87
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.85
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.85
PF00004	132	AAA: ATPase family associated with various cellula	96.84
PRK08116	268	hypothetical protein; Validated	96.83
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.82
PF13173	128	AAA_14: AAA domain	96.82
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.82
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.81
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.81
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	96.79
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.78
PRK06893	229	DNA replication initiation factor; Validated	96.78
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.78
PRK12402	337	replication factor C small subunit 2; Reviewed	96.78
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.77
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	96.74
PHA02544	316	44 clamp loader, small subunit; Provisional	96.74
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.72
CHL00181	287	cbbX CbbX; Provisional	96.72
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	96.71
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.7
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.7
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.7
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.7
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.66
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.64
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.62
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.61
PRK12422	445	chromosomal replication initiation protein; Provis	96.6
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.58
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.57
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.57
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	96.57
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.56
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.55
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.55
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.54
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.52
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.52
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.49
KOG0298	1394	consensus DEAD box-containing helicase-like transc	96.49
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.48
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.47
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.47
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.46
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.44
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.42
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.41
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.41
PRK09183	259	transposase/IS protein; Provisional	96.4
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.4
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	96.4
PRK05973	237	replicative DNA helicase; Provisional	96.4
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.38
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.37
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.36
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.36
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.35
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.31
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.31
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	96.3
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.29
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	96.24
PRK11823	446	DNA repair protein RadA; Provisional	96.23
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.23
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	96.23
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	96.22
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.22
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	96.19
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.19
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	96.18
PRK08939	306	primosomal protein DnaI; Reviewed	96.17
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.15
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.15
PRK04195	482	replication factor C large subunit; Provisional	96.14
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.14
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.13
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	96.12
PTZ00293	211	thymidine kinase; Provisional	96.12
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.12
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.11
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.1
PRK05298	652	excinuclease ABC subunit B; Provisional	96.1
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.09
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.09
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.07
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.01
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.01
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	96.01
PRK13342	413	recombination factor protein RarA; Reviewed	95.99
PHA00729	226	NTP-binding motif containing protein	95.98
PF05729	166	NACHT: NACHT domain	95.97
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.97
PRK07993	334	DNA polymerase III subunit delta'; Validated	95.95
PHA03372	668	DNA packaging terminase subunit 1; Provisional	95.95
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.95
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	95.92
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	95.9
PRK04841	903	transcriptional regulator MalT; Provisional	95.9
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.89
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	95.86
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	95.82
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.82
PRK13851	344	type IV secretion system protein VirB11; Provision	95.8
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.79
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	95.77
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.74
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	95.74
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	95.73
PRK10867	433	signal recognition particle protein; Provisional	95.7
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.7
PRK13341	725	recombination factor protein RarA/unknown domain f	95.69
TIGR00959	428	ffh signal recognition particle protein. This mode	95.63
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.62
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.58
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.57
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.56
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.56
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.56
PRK04328	249	hypothetical protein; Provisional	95.54
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	95.54
PRK07940	394	DNA polymerase III subunit delta'; Validated	95.53
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	95.5
PRK06904	472	replicative DNA helicase; Validated	95.49
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.47
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	95.46
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	95.43
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	95.41
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	95.39
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	95.39
PRK03992	389	proteasome-activating nucleotidase; Provisional	95.35
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	95.35
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	95.35
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	95.34
TIGR00767	415	rho transcription termination factor Rho. Members	95.33
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	95.33
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	95.32
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.32
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.3
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	95.28
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.26
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	95.25
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.22
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.21
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	95.19
PRK06620	214	hypothetical protein; Validated	95.15
PRK09354	349	recA recombinase A; Provisional	95.13
PRK06090	319	DNA polymerase III subunit delta'; Validated	95.13
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	95.1
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.1
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.09
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	95.09
KOG2028	554	consensus ATPase related to the helicase subunit o	95.08
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	95.08
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	95.07
PRK06067	234	flagellar accessory protein FlaH; Validated	95.07
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	95.0
PRK13764	602	ATPase; Provisional	94.97
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	94.93
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	94.87
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	94.84
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.83
PRK08058	329	DNA polymerase III subunit delta'; Validated	94.8
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	94.8
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.76
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	94.76
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.71
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	94.69
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	94.67
TIGR02237	209	recomb_radB DNA repair and recombination protein R	94.63
COG1221	403	PspF Transcriptional regulators containing an AAA-	94.58
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	94.56
PRK09165	497	replicative DNA helicase; Provisional	94.53
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	94.5
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.5
PRK08840	464	replicative DNA helicase; Provisional	94.49
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	94.49
cd01128	249	rho_factor Transcription termination factor rho is	94.47
PRK08506	472	replicative DNA helicase; Provisional	94.43
TIGR00665	434	DnaB replicative DNA helicase. This model describe	94.42
PRK10416	318	signal recognition particle-docking protein FtsY;	94.41
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	94.4
PRK07004	460	replicative DNA helicase; Provisional	94.38
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	94.37
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	94.34
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	94.33
PRK09376	416	rho transcription termination factor Rho; Provisio	94.31
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	94.28
PRK13897	606	type IV secretion system component VirD4; Provisio	94.27
PRK08006	471	replicative DNA helicase; Provisional	94.27
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	94.24
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	94.23
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	94.2
KOG1131	755	consensus RNA polymerase II transcription initiati	94.19
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	94.18
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.18
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	94.17
PRK10689	1147	transcription-repair coupling factor; Provisional	94.15
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	94.13
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	94.13
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	94.09
PF12846	304	AAA_10: AAA-like domain	94.06
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	94.02
PRK05748	448	replicative DNA helicase; Provisional	94.02
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	93.99
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	93.95
CHL00176	638	ftsH cell division protein; Validated	93.94
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	93.85
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	93.84
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	93.8
PRK08760	476	replicative DNA helicase; Provisional	93.8
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	93.76
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.73
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	93.72
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	93.71
PRK09087	226	hypothetical protein; Validated	93.66
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	93.61
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	93.61
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	93.59
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	93.58
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	93.53
TIGR02533	486	type_II_gspE general secretory pathway protein E.	93.53
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	93.49
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	93.47
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	93.45
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	93.45
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	93.4
PRK05595	444	replicative DNA helicase; Provisional	93.39
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	93.39
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	93.39
PRK07399	314	DNA polymerase III subunit delta'; Validated	93.37
PRK12608	380	transcription termination factor Rho; Provisional	93.34
PRK10436	462	hypothetical protein; Provisional	93.33
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	93.32
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	93.31
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	93.19
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	93.17
PRK13850	670	type IV secretion system protein VirD4; Provisiona	93.17
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	93.13
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	93.1
KOG1969	877	consensus DNA replication checkpoint protein CHL12	93.09
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	93.08
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	93.05
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	92.99
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	92.94
COG3972	660	Superfamily I DNA and RNA helicases [General funct	92.83
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.79
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	92.72
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	92.69
PRK05917	290	DNA polymerase III subunit delta'; Validated	92.68
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	92.65
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	92.62
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	92.58
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	92.57
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	92.56
PRK05636	505	replicative DNA helicase; Provisional	92.51
PRK10865	857	protein disaggregation chaperone; Provisional	92.5
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	92.41
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	92.35

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

Probab=100.00  E-value=5.2e-50  Score=322.43  Aligned_cols=288  Identities=72%  Similarity=1.097  Sum_probs=276.1

Q ss_pred             cCCCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHH
Q 022383           10 RGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~   89 (298)
                      |..+....++..++|.++..+++++|+++||.++++++.+..||+.|+..|+.+++++++|+|++.++..|+|||.+|.+
T Consensus         4 r~~~~~~~~~~~~feTs~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si   83 (400)
T KOG0328|consen    4 RELFTMEDMDTVEFETSEKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSI   83 (400)
T ss_pred             hhhcccccccceeEeeccCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEe
Confidence            44566778888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc
Q 022383           90 TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK  169 (298)
Q Consensus        90 ~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~  169 (298)
                      .++..+.-..+..++++++||+||+.|+.+.+..++...++++..+.||.+..+..+.+..+++++.+||+++..+++.+
T Consensus        84 ~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~  163 (400)
T KOG0328|consen   84 SVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRR  163 (400)
T ss_pred             eeeeecccccceeeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhc
Confidence            99998887777789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEE
Q 022383          170 TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQF  249 (298)
Q Consensus       170 ~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  249 (298)
                      .+..+.++++|+||+|.|++.+|..++-.+.+++|+..|++++|||+|.++.+....++.+|+.+.+.+++.+..++.++
T Consensus       164 ~L~tr~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf  243 (400)
T KOG0328|consen  164 SLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQF  243 (400)
T ss_pred             cccccceeEEEeccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          250 FVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       250 ~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ++.++.++||.+.+.++.......+++|||||+..+.++.+.+++..+
T Consensus       244 ~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVdwLtekm~~~nf  291 (400)
T KOG0328|consen  244 FVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANF  291 (400)
T ss_pred             eeeechhhhhHhHHHHHhhhhehheEEEEecccchhhHHHHHHHhhCc
Confidence            999999999999999999999889999999999999999999987654

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

Probab=100.00  E-value=2.5e-49  Score=331.07  Aligned_cols=268  Identities=30%  Similarity=0.487  Sum_probs=257.0

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        29 ~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      .+...+|.+|++++.+.+++.+.||..|+++|++++|.++.|+|++..|.||||||.+|++|+++++...+..++++|++
T Consensus        57 ~e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLt  136 (476)
T KOG0330|consen   57 DESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLT  136 (476)
T ss_pred             hhhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEec
Confidence            45667999999999999999999999999999999999999999999999999999999999999999988889999999


Q ss_pred             CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEEechhhHh
Q 022383          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       109 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE~h~~  187 (298)
                      |||||+.|+.++++.++...|+++..+.||.+...+...+...++|+|+||++|...+.+ +.+++..++++|+||||.+
T Consensus       137 PtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrl  216 (476)
T KOG0330|consen  137 PTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRL  216 (476)
T ss_pred             CcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhh
Confidence            999999999999999999999999999999999999999999999999999999999985 8899999999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHH
Q 022383          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll  267 (298)
                      ++..|...+..|++.+|...|.+++|||++..+..+....+.+|..+.+.....+.+.+.|.|..++... |...+..++
T Consensus       217 Ld~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~-K~~yLV~ll  295 (476)
T KOG0330|consen  217 LDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKD-KDTYLVYLL  295 (476)
T ss_pred             hhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccc-cchhHHHHH
Confidence            9999999999999999999999999999999999999999999999999888888899999999999887 999999999


Q ss_pred             hhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          268 DTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       268 ~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +...+..+||||++...+..++-.|+..|+
T Consensus       296 ~e~~g~s~iVF~~t~~tt~~la~~L~~lg~  325 (476)
T KOG0330|consen  296 NELAGNSVIVFCNTCNTTRFLALLLRNLGF  325 (476)
T ss_pred             HhhcCCcEEEEEeccchHHHHHHHHHhcCc
Confidence            998889999999999999999999998886

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

Probab=100.00  E-value=9.7e-47  Score=345.14  Aligned_cols=265  Identities=39%  Similarity=0.625  Sum_probs=247.6

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc--CCCCeEEEEEcCc
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPT  110 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~--~~~~~~~lil~p~  110 (298)
                      .+|+++++++.+.+++.++||..|+|+|..++|.++.|+|+++.++||+|||++|++|+++.+..  ......+||++||
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PT  108 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCC
Confidence            68999999999999999999999999999999999999999999999999999999999999873  2222229999999


Q ss_pred             HHHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          111 RELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                      ||||.|+.+.++++.... ++++..++||.+...+...+..+++|+|+||+++.++++.+.+++.++.++|+||||.|++
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd  188 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLD  188 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhc
Confidence            999999999999999988 7999999999999988888888899999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCcc--CcCCceEEEEEecCccchHHHHHHHH
Q 022383          190 RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDEL--TLEGIKQFFVAVEREEWKFDTLCDLY  267 (298)
Q Consensus       190 ~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~~k~~~l~~ll  267 (298)
                      .||.+.+..+++.++.+.|++++|||++..+..+...++.+|..+.+.....  ....+.|.++.++....|...+..++
T Consensus       189 ~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll  268 (513)
T COG0513         189 MGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLL  268 (513)
T ss_pred             CCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999888875555  78899999999998766999999999


Q ss_pred             hhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          268 DTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       268 ~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +.....++||||+|+..|+.++..|+..|+
T Consensus       269 ~~~~~~~~IVF~~tk~~~~~l~~~l~~~g~  298 (513)
T COG0513         269 KDEDEGRVIVFVRTKRLVEELAESLRKRGF  298 (513)
T ss_pred             hcCCCCeEEEEeCcHHHHHHHHHHHHHCCC
Confidence            988888999999999999999999999875

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

Probab=100.00  E-value=1.5e-47  Score=338.76  Aligned_cols=262  Identities=31%  Similarity=0.541  Sum_probs=243.1

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc------CCCCeEEEEE
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT------SSREVQALIL  107 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~------~~~~~~~lil  107 (298)
                      .|++++|++.+..+|+..||+.|+|+|.+.||.+++|+|++..+.||||||++|++|++.++..      ...+|++|+|
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL  171 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVL  171 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEE
Confidence            6888999999999999999999999999999999999999999999999999999999999875      4557899999


Q ss_pred             cCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       108 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      +||||||.|+...+++++...+++...++||.+...+...+.++++|+|+||++|..++..+.++++++.++|+||||.|
T Consensus       172 ~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrM  251 (519)
T KOG0331|consen  172 APTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRM  251 (519)
T ss_pred             cCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccHHHHHHHHHhC-CCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCc--cCcCCceEEEEEecCccchHHHHH
Q 022383          188 LSRGFKDQIYDVYRYL-PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE--LTLEGIKQFFVAVEREEWKFDTLC  264 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~-~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~~~~~~~~~~~~k~~~l~  264 (298)
                      ++.+|..+++.|++.+ ++..|++++|||||..+..+...++.+|..+.+....  ....++.|....|+... |...+.
T Consensus       252 ldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~-K~~~l~  330 (519)
T KOG0331|consen  252 LDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETA-KLRKLG  330 (519)
T ss_pred             hccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHH-HHHHHH
Confidence            9999999999999999 5566899999999999999999999999998887543  55678999999999555 888888


Q ss_pred             HHHhhC---CCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          265 DLYDTL---TITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       265 ~ll~~~---~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      .++...   ..+|+||||+|++.|+.++..|+..+
T Consensus       331 ~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~  365 (519)
T KOG0331|consen  331 KLLEDISSDSEGKVIIFCETKRTCDELARNLRRKG  365 (519)
T ss_pred             HHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcC
Confidence            888765   35699999999999999999999875

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=1.2e-45  Score=340.90  Aligned_cols=273  Identities=28%  Similarity=0.416  Sum_probs=241.7

Q ss_pred             ecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-----
Q 022383           24 ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----   98 (298)
Q Consensus        24 ~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-----   98 (298)
                      +....|+++.+|+++++++++.++|+++||..|+++|.++||.+++|+|+++++|||||||++|++|++.++...     
T Consensus       121 ~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~  200 (545)
T PTZ00110        121 AGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRY  200 (545)
T ss_pred             cCCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccC
Confidence            456678899999999999999999999999999999999999999999999999999999999999999876432     


Q ss_pred             CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccE
Q 022383           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (298)
Q Consensus        99 ~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~  178 (298)
                      ..++.+|||+||++||.|+.+.+++++...++++..++|+.....+...+..+++|+|+||++|.+++.....+++++++
T Consensus       201 ~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~  280 (545)
T PTZ00110        201 GDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTY  280 (545)
T ss_pred             CCCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcE
Confidence            24678999999999999999999999988889999999999888888888889999999999999999988889999999


Q ss_pred             EEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCC-CCEEEEecCCc-cCcCCceEEEEEecCc
Q 022383          179 LVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMT-DPVKILVKRDE-LTLEGIKQFFVAVERE  256 (298)
Q Consensus       179 vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~i~~~~~~~~~~  256 (298)
                      ||+||||++++++|...+..++..+++..|++++|||++..+..+...++. +|..+.+...+ .....+.+.+..++..
T Consensus       281 lViDEAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~  360 (545)
T PTZ00110        281 LVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEH  360 (545)
T ss_pred             EEeehHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEech
Confidence            999999999999999999999999999999999999999999988887775 57777665443 2335677777777665


Q ss_pred             cchHHHHHHHHhhC--CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          257 EWKFDTLCDLYDTL--TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       257 ~~k~~~l~~ll~~~--~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      + |...+..++...  ...++||||++++.|+.++..|+..|+
T Consensus       361 ~-k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~  402 (545)
T PTZ00110        361 E-KRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGW  402 (545)
T ss_pred             h-HHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCC
Confidence            5 888888888754  456999999999999999999987664

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=4.4e-45  Score=329.82  Aligned_cols=265  Identities=29%  Similarity=0.392  Sum_probs=236.6

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-------CCCeEE
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-------SREVQA  104 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-------~~~~~~  104 (298)
                      ..+|++++|++++.++|.++||..|+++|.++||.+++|+|++++||||+|||++|++|+++.+...       ..++++
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~   86 (423)
T PRK04837          7 EQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRA   86 (423)
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceE
Confidence            4689999999999999999999999999999999999999999999999999999999999887532       235789


Q ss_pred             EEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechh
Q 022383          105 LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDES  184 (298)
Q Consensus       105 lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~  184 (298)
                      |||+||++|+.|+.+.++.+....++++..++||.....+...+..+++|+|+||+++..++..+.+.+++++++|+|||
T Consensus        87 lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEa  166 (423)
T PRK04837         87 LIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEA  166 (423)
T ss_pred             EEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecH
Confidence            99999999999999999999998899999999998888777788888999999999999999988899999999999999


Q ss_pred             hHhhccccHHHHHHHHHhCCC--CccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHH
Q 022383          185 DEMLSRGFKDQIYDVYRYLPP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT  262 (298)
Q Consensus       185 h~~~~~~~~~~i~~i~~~~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~  262 (298)
                      |++++++|...+..+++.++.  ..+.+++|||++..+..+....+.+|..+.+.........+.+.+....... |...
T Consensus       167 d~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~-k~~~  245 (423)
T PRK04837        167 DRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEE-KMRL  245 (423)
T ss_pred             HHHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHH-HHHH
Confidence            999999999999999999874  4668999999999999888888889988887766655566777666555444 8888


Q ss_pred             HHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          263 LCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       263 l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +..+++.....++||||++++.|+.+++.|...|+
T Consensus       246 l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~  280 (423)
T PRK04837        246 LQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGH  280 (423)
T ss_pred             HHHHHHhcCCCeEEEEECCHHHHHHHHHHHHhCCC
Confidence            98998877778999999999999999999988764

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=3.7e-45  Score=333.66  Aligned_cols=264  Identities=37%  Similarity=0.589  Sum_probs=242.1

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ..+|++++|++.+.++|.++||..|+|+|.++++.+++|+|++++||||+|||++|++|+++.+......++++|++||+
T Consensus         3 ~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~Ptr   82 (460)
T PRK11776          3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTR   82 (460)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCH
Confidence            35899999999999999999999999999999999999999999999999999999999999987665567899999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      +|+.|+.+.++.+.... ++++..++|+.+...+...+..+++|+|+||+++..++..+.+.++++++||+||+|++++.
T Consensus        83 eLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~  162 (460)
T PRK11776         83 ELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDM  162 (460)
T ss_pred             HHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCc
Confidence            99999999999987654 68899999999988888888889999999999999999988888999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  270 (298)
                      +|...+..+++.++...|++++|||+++.+..+...++.+|..+.+.... ....+.+.++.++..+ |...+..++...
T Consensus       163 g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~~~-k~~~l~~ll~~~  240 (460)
T PRK11776        163 GFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSPDE-RLPALQRLLLHH  240 (460)
T ss_pred             CcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCcHH-HHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999888776543 3456888888888777 999999999888


Q ss_pred             CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          271 TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       271 ~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ...++||||++++.|+.+++.|+..|+
T Consensus       241 ~~~~~lVF~~t~~~~~~l~~~L~~~~~  267 (460)
T PRK11776        241 QPESCVVFCNTKKECQEVADALNAQGF  267 (460)
T ss_pred             CCCceEEEECCHHHHHHHHHHHHhCCC
Confidence            888999999999999999999988775

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=9.3e-45  Score=329.97  Aligned_cols=263  Identities=34%  Similarity=0.540  Sum_probs=238.1

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC------CCeEEEEE
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS------REVQALIL  107 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~------~~~~~lil  107 (298)
                      +|++++|++++.++|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....      ..+++|||
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            699999999999999999999999999999999999999999999999999999999999875432      23589999


Q ss_pred             cCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       108 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      +||++|+.|+.+.++.+....++++..++|+.+...+...+..+++|+|+||++|..++....+.++++++|||||+|++
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~l  161 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRM  161 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHH
Confidence            99999999999999999988899999999999888887788888999999999999999888889999999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHH
Q 022383          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll  267 (298)
                      ++++|...+..++..++...|++++|||+++.+..+...++.+|..+.+.........+.+.+..++... +...+..++
T Consensus       162 l~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~l~  240 (456)
T PRK10590        162 LDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKR-KRELLSQMI  240 (456)
T ss_pred             hccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCHHH-HHHHHHHHH
Confidence            9999999999999999999999999999999999998888999988877666666667788877776655 777888888


Q ss_pred             hhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          268 DTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       268 ~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ......++||||++++.|+.+++.|...|+
T Consensus       241 ~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~  270 (456)
T PRK10590        241 GKGNWQQVLVFTRTKHGANHLAEQLNKDGI  270 (456)
T ss_pred             HcCCCCcEEEEcCcHHHHHHHHHHHHHCCC
Confidence            877778999999999999999999987764

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=1e-44  Score=337.77  Aligned_cols=265  Identities=32%  Similarity=0.509  Sum_probs=243.0

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ..+|++++|++.++++|.++||..|+|+|.++|+.++.|+|++++||||+|||++|++|+++.+......+++|||+||+
T Consensus         5 ~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTr   84 (629)
T PRK11634          5 ETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTR   84 (629)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcH
Confidence            45799999999999999999999999999999999999999999999999999999999999887665677999999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      +|+.|+.+.++.+.... ++.+..++|+.+...+...+..+++|+|+||+++.+++....++++++++||+||+|.|++.
T Consensus        85 eLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~  164 (629)
T PRK11634         85 ELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRM  164 (629)
T ss_pred             HHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhc
Confidence            99999999999887654 78899999999888888888889999999999999999988889999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  270 (298)
                      +|...+..++..++...|++++|||+++.+..+...++.+|..+.+.........+.+.+..+.... |...+..++...
T Consensus       165 gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~~~-k~~~L~~~L~~~  243 (629)
T PRK11634        165 GFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMR-KNEALVRFLEAE  243 (629)
T ss_pred             ccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEechhh-HHHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999988887766666677888888777666 888999999887


Q ss_pred             CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          271 TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       271 ~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ...++||||+|+..++.+++.|...|+
T Consensus       244 ~~~~~IVF~~tk~~a~~l~~~L~~~g~  270 (629)
T PRK11634        244 DFDAAIIFVRTKNATLEVAEALERNGY  270 (629)
T ss_pred             CCCCEEEEeccHHHHHHHHHHHHhCCC
Confidence            778999999999999999999998775

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2e-44  Score=333.85  Aligned_cols=264  Identities=31%  Similarity=0.436  Sum_probs=235.9

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-------CCCeEEE
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-------SREVQAL  105 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-------~~~~~~l  105 (298)
                      .+|++++|++.+.++|.++||..|+++|.++||.+++|+|+++++|||+|||++|++|+++.+...       ...+++|
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raL   88 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            479999999999999999999999999999999999999999999999999999999999987432       1246899


Q ss_pred             EEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc-CccCCCccEEEechh
Q 022383          106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDES  184 (298)
Q Consensus       106 il~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~-~~~~~~l~~vViDE~  184 (298)
                      ||+||++|+.|+.+.+++++...++++..++|+.....+...+..+++|+|+||++|..++... .+.+..+++|||||+
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEA  168 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEA  168 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCH
Confidence            9999999999999999999998899999999999888877778888999999999999998764 577899999999999


Q ss_pred             hHhhccccHHHHHHHHHhCCC--CccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHH
Q 022383          185 DEMLSRGFKDQIYDVYRYLPP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT  262 (298)
Q Consensus       185 h~~~~~~~~~~i~~i~~~~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~  262 (298)
                      |++++++|...+..+++.++.  ..|++++|||++..+..+...++.+|..+.+.........+.+.++...... |...
T Consensus       169 h~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~~~-k~~~  247 (572)
T PRK04537        169 DRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEE-KQTL  247 (572)
T ss_pred             HHHhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecCHHH-HHHH
Confidence            999999999999999999986  6899999999999999998888888887777655556666778777666555 8888


Q ss_pred             HHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          263 LCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       263 l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +..++......++||||||++.|+.+++.|...|+
T Consensus       248 L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~  282 (572)
T PRK04537        248 LLGLLSRSEGARTMVFVNTKAFVERVARTLERHGY  282 (572)
T ss_pred             HHHHHhcccCCcEEEEeCCHHHHHHHHHHHHHcCC
Confidence            88888887778999999999999999999988764

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

Probab=100.00  E-value=5e-44  Score=329.09  Aligned_cols=270  Identities=28%  Similarity=0.474  Sum_probs=238.6

Q ss_pred             eecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc-----
Q 022383           23 FETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-----   97 (298)
Q Consensus        23 ~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~-----   97 (298)
                      +.+...+.++.+|+++++++.+.++|.+.||..|+|+|.++||.+++|+|+++++|||+|||++|++|++.++..     
T Consensus       111 ~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~  190 (518)
T PLN00206        111 VKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGH  190 (518)
T ss_pred             ecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhcccc
Confidence            345566789999999999999999999999999999999999999999999999999999999999999987642     


Q ss_pred             --CCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCC
Q 022383           98 --SSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus        98 --~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                        ...++++|||+||++|+.|+.+.++.+....+++...+.||.....+...+..+++|+|+||++|..++....+.+++
T Consensus       191 ~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~  270 (518)
T PLN00206        191 PSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDN  270 (518)
T ss_pred             ccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchh
Confidence              224679999999999999999999999888888898999998888888888888999999999999999988889999


Q ss_pred             ccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecC
Q 022383          176 IKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER  255 (298)
Q Consensus       176 l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  255 (298)
                      +++||+||||+|++++|...+..+++.++ +.|++++|||+++.+..+...++.++..+...........+.+.+..++.
T Consensus       271 v~~lViDEad~ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~  349 (518)
T PLN00206        271 VSVLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVET  349 (518)
T ss_pred             eeEEEeecHHHHhhcchHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccc
Confidence            99999999999999999999999998885 68999999999999999998888888888876655555667777777776


Q ss_pred             ccchHHHHHHHHhhCC--CCcEEEEecchhhHHHHHHHHhh
Q 022383          256 EEWKFDTLCDLYDTLT--ITQAVIFCNTKRKIYYSVFYFWI  294 (298)
Q Consensus       256 ~~~k~~~l~~ll~~~~--~~k~lIf~~s~~~~~~l~~~L~~  294 (298)
                      .. |...+.+++....  ..++||||+++..|+.+++.|..
T Consensus       350 ~~-k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~  389 (518)
T PLN00206        350 KQ-KKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITV  389 (518)
T ss_pred             hh-HHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhh
Confidence            65 7777777776433  35899999999999999999875

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=1.4e-43  Score=321.30  Aligned_cols=264  Identities=28%  Similarity=0.458  Sum_probs=239.0

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC----CCCeEEEEEcC
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQALILSP  109 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~----~~~~~~lil~p  109 (298)
                      +|+++++++.+.++|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+...    ...+++||++|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~P   81 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTP   81 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECC
Confidence            69999999999999999999999999999999999999999999999999999999999987532    23468999999


Q ss_pred             cHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                      |++|+.|+.+.++.+....++++..++|+.....+...+.++++|+|+||++|..++....+.+.++++|||||||++.+
T Consensus        82 t~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~  161 (434)
T PRK11192         82 TRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLD  161 (434)
T ss_pred             cHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhC
Confidence            99999999999999999999999999999988887777788899999999999999999889999999999999999999


Q ss_pred             cccHHHHHHHHHhCCCCccEEEEEeeCch-hHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh
Q 022383          190 RGFKDQIYDVYRYLPPDLQVVLISATLPH-EILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (298)
Q Consensus       190 ~~~~~~i~~i~~~~~~~~~~v~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  268 (298)
                      ++|...+..+....+...|++++|||++. .+..+...++.+|..+...........+.+.+..++....|...+..+++
T Consensus       162 ~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~  241 (434)
T PRK11192        162 MGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLK  241 (434)
T ss_pred             CCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHh
Confidence            99999999999999988999999999975 57778888888898888776666667788888888776668889999988


Q ss_pred             hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          269 TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       269 ~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .....++||||++++.|+.+++.|+..|+
T Consensus       242 ~~~~~~~lVF~~s~~~~~~l~~~L~~~~~  270 (434)
T PRK11192        242 QPEVTRSIVFVRTRERVHELAGWLRKAGI  270 (434)
T ss_pred             cCCCCeEEEEeCChHHHHHHHHHHHhCCC
Confidence            76778999999999999999999988764

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

Probab=100.00  E-value=1.6e-44  Score=311.23  Aligned_cols=265  Identities=28%  Similarity=0.459  Sum_probs=243.2

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC---CeEEEEEc
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR---EVQALILS  108 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~---~~~~lil~  108 (298)
                      ..+|.+++|+..+++++..+||..|+|+|..+||..+-|+|+..||.||+|||.||++|++.++.=.+.   ..++||||
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~  259 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLV  259 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEe
Confidence            458999999999999999999999999999999999999999999999999999999999999854433   34999999


Q ss_pred             CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEEechhhHh
Q 022383          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       109 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE~h~~  187 (298)
                      ||++|+.|++.+.++++.+.++.++++.||.+...+...+..++||+|+||++|...+++ ..+++.++..+|+||||+|
T Consensus       260 PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRM  339 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRM  339 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHH
Confidence            999999999999999999999999999999999999999999999999999999999988 6899999999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecC--ccchHHHHHH
Q 022383          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER--EEWKFDTLCD  265 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~--~~~k~~~l~~  265 (298)
                      ++.+|.+.+..|++.+++++|.++||||++..+.++....+..|+.+.+++.........|.|+-+.+  +..+...+..
T Consensus       340 LeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~  419 (691)
T KOG0338|consen  340 LEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLAS  419 (691)
T ss_pred             HHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHH
Confidence            99999999999999999999999999999999999999999999999999888888888887776653  3457778888


Q ss_pred             HHhhCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          266 LYDTLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       266 ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      ++...-..+++||+.|++.|+.+.-.|--.|
T Consensus       420 l~~rtf~~~~ivFv~tKk~AHRl~IllGLlg  450 (691)
T KOG0338|consen  420 LITRTFQDRTIVFVRTKKQAHRLRILLGLLG  450 (691)
T ss_pred             HHHHhcccceEEEEehHHHHHHHHHHHHHhh
Confidence            8886667899999999999999987764433

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.5e-44  Score=303.13  Aligned_cols=264  Identities=28%  Similarity=0.429  Sum_probs=233.3

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc------CCCCeEEEE
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT------SSREVQALI  106 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~------~~~~~~~li  106 (298)
                      .+|++++|++.+++++.+.||+.|+.+|+.+||.++.|+|++..|.||||||.||++|+++.+..      ...++.++|
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~i   98 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVI   98 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEE
Confidence            69999999999999999999999999999999999999999999999999999999999998743      345789999


Q ss_pred             EcCcHHHHHHHHHHHHHhhccCC--ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccC-ccCCCccEEEech
Q 022383          107 LSPTRELATQTEKVILAIGDFIN--IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT-LRTRAIKLLVLDE  183 (298)
Q Consensus       107 l~p~~~l~~q~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~-~~~~~l~~vViDE  183 (298)
                      ++||+|||+|++..+.++....+  +++.-+.++.+.......+.+.++|+|+||.++..++..+. ..+..+.++|+||
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDE  178 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDE  178 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEech
Confidence            99999999999999998876543  45555555555555556677889999999999999998865 6789999999999


Q ss_pred             hhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccC-cCCceEEEEEecCccchHHH
Q 022383          184 SDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELT-LEGIKQFFVAVEREEWKFDT  262 (298)
Q Consensus       184 ~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~~~~~~~~~~~~k~~~  262 (298)
                      ||.+++.||.+++..+.+.+|+..|.++||||++.++..+-..++.+|..+.....+.. ...+.|+++.|..++ |.-.
T Consensus       179 ADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~D-Kfll  257 (569)
T KOG0346|consen  179 ADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEED-KFLL  257 (569)
T ss_pred             hhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEeccch-hHHH
Confidence            99999999999999999999999999999999999999999999999999877655443 366889999999555 9999


Q ss_pred             HHHHHhhC-CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          263 LCDLYDTL-TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       263 l~~ll~~~-~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ++.+++.. -.+|.|||+||...|..+.-+|...|+
T Consensus       258 lyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGi  293 (569)
T KOG0346|consen  258 LYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGI  293 (569)
T ss_pred             HHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCc
Confidence            99998843 457999999999999999999998876

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=3.3e-42  Score=309.88  Aligned_cols=267  Identities=63%  Similarity=1.042  Sum_probs=241.0

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      ...+|+++++++.+.++|.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+.....+.++||++|+
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt  105 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPT  105 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCC
Confidence            45799999999999999999999999999999999999999999999999999999999999988765567789999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      ++|+.|+.+.++.++...++.+..+.|+.........+..+++|+|+||+++..++......++++++|||||+|++.++
T Consensus       106 ~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~  185 (401)
T PTZ00424        106 RELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSR  185 (401)
T ss_pred             HHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhc
Confidence            99999999999999888888888889998877777777788999999999999999888888999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  270 (298)
                      ++...+..+++.++++.|++++|||+++....+...++.+|..+.+........++.+.+..++....+...+..+++..
T Consensus       186 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  265 (401)
T PTZ00424        186 GFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETL  265 (401)
T ss_pred             chHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999888888888888888776666667778888888877666778888888877


Q ss_pred             CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          271 TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       271 ~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ...++||||++++.|+.+++.|+..++
T Consensus       266 ~~~~~ivF~~t~~~~~~l~~~l~~~~~  292 (401)
T PTZ00424        266 TITQAIIYCNTRRKVDYLTKKMHERDF  292 (401)
T ss_pred             CCCeEEEEecCcHHHHHHHHHHHHCCC
Confidence            778999999999999999999987764

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=1.1e-43  Score=308.65  Aligned_cols=267  Identities=28%  Similarity=0.452  Sum_probs=244.3

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc----CCCCeEEE
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT----SSREVQAL  105 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~----~~~~~~~l  105 (298)
                      ..+..|.+|+|+..++++|++.+|..++.+|+.+||..+.|+|++-.|.||||||+||++|+++++..    ...|.-+|
T Consensus        66 ~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGal  145 (758)
T KOG0343|consen   66 TTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGAL  145 (758)
T ss_pred             hhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeE
Confidence            34569999999999999999999999999999999999999999999999999999999999998743    23566899


Q ss_pred             EEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEEechh
Q 022383          106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDES  184 (298)
Q Consensus       106 il~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE~  184 (298)
                      ||+|||+||.|+++.+.++++.+++..+++.||.....+...+ ++++|+||||++|+..+.+ ..++..++.++|+|||
T Consensus       146 IISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi-~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEA  224 (758)
T KOG0343|consen  146 IISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERI-SQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEA  224 (758)
T ss_pred             EecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhh-hcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccH
Confidence            9999999999999999999999999999999998877666655 4579999999999998877 5788899999999999


Q ss_pred             hHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEec--CCccCcCCceEEEEEecCccchHHH
Q 022383          185 DEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK--RDELTLEGIKQFFVAVEREEWKFDT  262 (298)
Q Consensus       185 h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~i~~~~~~~~~~~~k~~~  262 (298)
                      |++++.||...+..|+.++|+.+|.++||||.+..+.++++..+.+|..+.+.  ....++.+..|+|+.++..+ |++.
T Consensus       225 DR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~-Ki~~  303 (758)
T KOG0343|consen  225 DRMLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLED-KIDM  303 (758)
T ss_pred             HHHHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhh-HHHH
Confidence            99999999999999999999999999999999999999999999999887765  33567788999999999888 9999


Q ss_pred             HHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcCC
Q 022383          263 LCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWIG  298 (298)
Q Consensus       263 l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~~  298 (298)
                      +..+++.+...|.|||+.|++++..+++.+.+.-+|
T Consensus       304 L~sFI~shlk~K~iVF~SscKqvkf~~e~F~rlrpg  339 (758)
T KOG0343|consen  304 LWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRPG  339 (758)
T ss_pred             HHHHHHhccccceEEEEehhhHHHHHHHHHHhcCCC
Confidence            999999999999999999999999999999876543

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

Probab=100.00  E-value=7.5e-45  Score=297.26  Aligned_cols=264  Identities=35%  Similarity=0.597  Sum_probs=251.9

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ...|+++.|..+++....+.||+.|+|+|.+++|..+.|+|++..|..|+|||.+|.+|+++.+.......+++|++|++
T Consensus        84 G~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtr  163 (459)
T KOG0326|consen   84 GNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTR  163 (459)
T ss_pred             CccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecc
Confidence            35899999999999999999999999999999999999999999999999999999999999999988889999999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~  191 (298)
                      +||.|+...++.+++..++.+....||++..+.+-.+.+..+++|+||++++.+...+--.+++..++|+||||.+++..
T Consensus       164 elALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~  243 (459)
T KOG0326|consen  164 ELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVD  243 (459)
T ss_pred             hhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchh
Confidence            99999999999999999999999999999998888888999999999999999999998899999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCC
Q 022383          192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT  271 (298)
Q Consensus       192 ~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~  271 (298)
                      |...++.++..+|++.|++++|||+|-.+..+...++.+|..+..- ++.++.++.|+|.++.+.. |...+..++....
T Consensus       244 F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM-~eLtl~GvtQyYafV~e~q-KvhCLntLfskLq  321 (459)
T KOG0326|consen  244 FQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLM-EELTLKGVTQYYAFVEERQ-KVHCLNTLFSKLQ  321 (459)
T ss_pred             hhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehh-hhhhhcchhhheeeechhh-hhhhHHHHHHHhc
Confidence            9999999999999999999999999999999999999999998866 5688899999999999988 9999999999888


Q ss_pred             CCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          272 ITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       272 ~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..+.||||||.+.+|.+|+.+-+.|+
T Consensus       322 INQsIIFCNS~~rVELLAkKITelGy  347 (459)
T KOG0326|consen  322 INQSIIFCNSTNRVELLAKKITELGY  347 (459)
T ss_pred             ccceEEEeccchHhHHHHHHHHhccc
Confidence            89999999999999999999877764

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.8e-42  Score=314.78  Aligned_cols=265  Identities=27%  Similarity=0.458  Sum_probs=234.6

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC-------CCeEE
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-------REVQA  104 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-------~~~~~  104 (298)
                      ...|.+++|++.+.++|.++||..|+++|.++|+.+.+|+|+++++|||+|||++|++|+++.+....       ..+++
T Consensus        86 ~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~a  165 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRA  165 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceE
Confidence            45788999999999999999999999999999999999999999999999999999999999876542       14689


Q ss_pred             EEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEech
Q 022383          105 LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (298)
Q Consensus       105 lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE  183 (298)
                      |||+||++|+.|+.+.++.+.+..++++..++||.+...+...+. ..++|+|+||++|..++......++++++|||||
T Consensus       166 Lil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDE  245 (475)
T PRK01297        166 LIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDE  245 (475)
T ss_pred             EEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEech
Confidence            999999999999999999999888999999999987776666654 5689999999999999888888899999999999


Q ss_pred             hhHhhccccHHHHHHHHHhCCC--CccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHH
Q 022383          184 SDEMLSRGFKDQIYDVYRYLPP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFD  261 (298)
Q Consensus       184 ~h~~~~~~~~~~i~~i~~~~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~  261 (298)
                      +|.+.+.+|...+..+++..+.  +.|++++|||++..+..+...++.+|..+.+.........+.+.+..+...+ +..
T Consensus       246 ah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~-k~~  324 (475)
T PRK01297        246 ADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSD-KYK  324 (475)
T ss_pred             HHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecchh-HHH
Confidence            9999999999999999998864  5799999999999999999999889988877666665566777777766665 888


Q ss_pred             HHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          262 TLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       262 ~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .+..++......++||||++++.|+.+++.|...|+
T Consensus       325 ~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~  360 (475)
T PRK01297        325 LLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGI  360 (475)
T ss_pred             HHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcCC
Confidence            888888887778999999999999999999987764

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

Probab=100.00  E-value=1e-42  Score=297.71  Aligned_cols=262  Identities=31%  Similarity=0.507  Sum_probs=236.0

Q ss_pred             cCcccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc--CC---CCeEEE
Q 022383           33 TSFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT--SS---REVQAL  105 (298)
Q Consensus        33 ~~~~~l~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~--~~---~~~~~l  105 (298)
                      ..|++++  |+++++.++..+||...||+|..++|.+++++|+++.++||||||+||++|+++.+..  ..   ....++
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgal   83 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGAL   83 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEE
Confidence            3678775  6699999999999999999999999999999999999999999999999999999832  11   123699


Q ss_pred             EEcCcHHHHHHHHHHHHHhhcc-CCceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhcc--CccCCCccEEEe
Q 022383          106 ILSPTRELATQTEKVILAIGDF-INIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRK--TLRTRAIKLLVL  181 (298)
Q Consensus       106 il~p~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~--~~~~~~l~~vVi  181 (298)
                      ||+|||||+.||.+++..+... ..+.+.++.||....+.+..+. +++.|+||||++|..++...  .+++++++++|+
T Consensus        84 IIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVL  163 (567)
T KOG0345|consen   84 IISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVL  163 (567)
T ss_pred             EecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEe
Confidence            9999999999999999988766 5788999999988887777664 67889999999999999884  466779999999


Q ss_pred             chhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCcc--CcCCceEEEEEecCccch
Q 022383          182 DESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDEL--TLEGIKQFFVAVEREEWK  259 (298)
Q Consensus       182 DE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~~k  259 (298)
                      ||||.+++.||...++.|++.+|+.++.=+||||...++.++.+..+.+|..+.+.....  ++++...+|..|+..+ |
T Consensus       164 DEADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~e-K  242 (567)
T KOG0345|consen  164 DEADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADE-K  242 (567)
T ss_pred             cchHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHH-H
Confidence            999999999999999999999999999999999999999999999999999999876655  7788999999999988 9


Q ss_pred             HHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          260 FDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       260 ~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ...+..++.....+|+|||..|...+++.+..|...
T Consensus       243 ~~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~~~~  278 (567)
T KOG0345|consen  243 LSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFSRL  278 (567)
T ss_pred             HHHHHHHHhccccccEEEEecCcchHHHHHHHHHHH
Confidence            999999999999999999999999999999888653

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

Probab=100.00  E-value=1.4e-42  Score=300.32  Aligned_cols=290  Identities=25%  Similarity=0.357  Sum_probs=263.4

Q ss_pred             HHhcCCCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHH
Q 022383            7 MRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~   86 (298)
                      |..|+-+.-..+-.....+..-+.|+.+|++.+++.++++.+.+.||..|+|+|..++|..++.+|+|.++.||||||.+
T Consensus       219 m~~rdwri~redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaa  298 (673)
T KOG0333|consen  219 MTERDWRIFREDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAA  298 (673)
T ss_pred             cCCccceeeecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCcccc
Confidence            34444444444444455667778999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccC---------CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEe
Q 022383           87 IALTVCQTVDTS---------SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSG  157 (298)
Q Consensus        87 ~~~~~~~~~~~~---------~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~  157 (298)
                      |++|++..+...         ..+|+++++.||++|++|+.+.-.++++..+++++.+.||.+..++-.++..+|+|+|+
T Consensus       299 f~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceivia  378 (673)
T KOG0333|consen  299 FLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIA  378 (673)
T ss_pred             chhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeec
Confidence            999999876432         34789999999999999999999999999999999999999999988889999999999


Q ss_pred             ChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCC-------------------------CccEEEE
Q 022383          158 TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-------------------------DLQVVLI  212 (298)
Q Consensus       158 Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~-------------------------~~~~v~~  212 (298)
                      ||++|...+.+..+-++.+.+||+||||.|.+.+|.+++..++..+|.                         -.|.++|
T Consensus       379 tPgrLid~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mf  458 (673)
T KOG0333|consen  379 TPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMF  458 (673)
T ss_pred             CchHHHHHHHHHHHHhccCceEeccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEE
Confidence            999999999999999999999999999999999999999999999873                         1689999


Q ss_pred             EeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHH
Q 022383          213 SATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYF  292 (298)
Q Consensus       213 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L  292 (298)
                      |||+++.++.+++.|+.+|..+.+.......+.+.|.++.+..++ |...|..+++.....++|||+|+++.|+.+|+.|
T Consensus       459 tatm~p~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~-k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~L  537 (673)
T KOG0333|consen  459 TATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDE-KRKKLIEILESNFDPPIIIFVNTKKGADALAKIL  537 (673)
T ss_pred             ecCCChHHHHHHHHHhhCCeEEEeccCCCCccchheEEEEecchH-HHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHH
Confidence            999999999999999999999999988888889999999999888 8999999999887789999999999999999999


Q ss_pred             hhhcC
Q 022383          293 WIRWI  297 (298)
Q Consensus       293 ~~~~~  297 (298)
                      .+.|+
T Consensus       538 eK~g~  542 (673)
T KOG0333|consen  538 EKAGY  542 (673)
T ss_pred             hhccc
Confidence            88775

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

Probab=100.00  E-value=1.2e-41  Score=292.74  Aligned_cols=264  Identities=27%  Similarity=0.439  Sum_probs=238.3

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC----CCCeEEEE
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQALI  106 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~----~~~~~~li  106 (298)
                      ....|++..|++...++++++||+..+++|+..++.++.|+|+++.|.||+|||+||++|+++.+...    +.+..++|
T Consensus        80 ~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlI  159 (543)
T KOG0342|consen   80 TTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLI  159 (543)
T ss_pred             hhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEE
Confidence            35578889999999999999999999999999999999999999999999999999999999987543    24568999


Q ss_pred             EcCcHHHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEEechh
Q 022383          107 LSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDES  184 (298)
Q Consensus       107 l~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE~  184 (298)
                      +||||+|+.|++...+++.+.+ ++.+....||.....+...+..+++|+|+||++|...+.+ ..+.+++++++|+|||
T Consensus       160 i~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEA  239 (543)
T KOG0342|consen  160 ICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEA  239 (543)
T ss_pred             ecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecc
Confidence            9999999999999999999988 8999999999999988888888999999999999999988 5677788899999999


Q ss_pred             hHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCC-CCEEEEecCC--ccCcCCceEEEEEecCccchHH
Q 022383          185 DEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMT-DPVKILVKRD--ELTLEGIKQFFVAVEREEWKFD  261 (298)
Q Consensus       185 h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~--~~~~~~i~~~~~~~~~~~~k~~  261 (298)
                      |++++.||...++.|++.+|...|.++||||.++.+.++++-.+. +|..+.+...  ..+..++.|.|+.++... ++-
T Consensus       240 DrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~-~f~  318 (543)
T KOG0342|consen  240 DRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDS-RFS  318 (543)
T ss_pred             hhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccc-hHH
Confidence            999999999999999999999999999999999999999887665 4777766543  455688999999888887 688


Q ss_pred             HHHHHHhhCCC-CcEEEEecchhhHHHHHHHHhhh
Q 022383          262 TLCDLYDTLTI-TQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       262 ~l~~ll~~~~~-~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      .+..+++.+.. .|+||||+|...+..+++.|+..
T Consensus       319 ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~  353 (543)
T KOG0342|consen  319 LLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYI  353 (543)
T ss_pred             HHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhc
Confidence            89999987766 79999999999999999999743

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

Probab=100.00  E-value=8.8e-42  Score=294.25  Aligned_cols=274  Identities=29%  Similarity=0.412  Sum_probs=256.4

Q ss_pred             ecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-----
Q 022383           24 ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----   98 (298)
Q Consensus        24 ~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-----   98 (298)
                      -+..+++++.+|+.+++++.+..+.++..|.+|+|.|.+++|..++|++++-.|.||||||.||++|++.++...     
T Consensus       214 ~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~  293 (731)
T KOG0339|consen  214 SGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKP  293 (731)
T ss_pred             ccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcC
Confidence            466788999999999999999999999999999999999999999999999999999999999999999988542     


Q ss_pred             CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccE
Q 022383           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (298)
Q Consensus        99 ~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~  178 (298)
                      ..+|..+|+|||++|+.|++..++++++..+++++.++||.+..++.+.+..++.|+||||++|..++.-+..++.++.+
T Consensus       294 g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~  373 (731)
T KOG0339|consen  294 GEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSY  373 (731)
T ss_pred             CCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeE
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccc
Q 022383          179 LVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEW  258 (298)
Q Consensus       179 vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  258 (298)
                      +|+||+|.|.+.||...++.|...+++..|.++||||++..++.+.+..+.+|+.+...........|.|.+..|+.++.
T Consensus       374 LV~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~  453 (731)
T KOG0339|consen  374 LVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEK  453 (731)
T ss_pred             EEEechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHH
Confidence            99999999999999999999999999999999999999999999999999999999888778888999999999999988


Q ss_pred             hHHHHHHHHh-hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          259 KFDTLCDLYD-TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       259 k~~~l~~ll~-~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      |+.-+..-|- ....+++|||+..+.++++++..|.-+++
T Consensus       454 Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~  493 (731)
T KOG0339|consen  454 KLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGF  493 (731)
T ss_pred             HHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccc
Confidence            8887655544 44557999999999999999999988776

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

Probab=100.00  E-value=8.8e-42  Score=297.41  Aligned_cols=286  Identities=29%  Similarity=0.395  Sum_probs=254.6

Q ss_pred             CCCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHH
Q 022383           11 GGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT   90 (298)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~   90 (298)
                      ..+.+..+-.+...+...|.++.+|++-.+.+.+...++..++..|+|+|+.++|.+..|+++++||+||+|||.||++|
T Consensus        52 ~nfd~~~~i~v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiP  131 (482)
T KOG0335|consen   52 INFDKYNDIPVKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIP  131 (482)
T ss_pred             hccCCccceeeeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHH
Confidence            34555555566667777788889999989999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhccCC----------CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChH
Q 022383           91 VCQTVDTSS----------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPG  160 (298)
Q Consensus        91 ~~~~~~~~~----------~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~  160 (298)
                      ++..+....          ..|+++|++||++|+.|++++.+++.-..+++....+|+.+...+...+.++|+|+|+||+
T Consensus       132 ii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpG  211 (482)
T KOG0335|consen  132 IISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPG  211 (482)
T ss_pred             HHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCc
Confidence            999875432          3589999999999999999999999988899999999999998999999999999999999


Q ss_pred             HHHHHHhccCccCCCccEEEechhhHhhc-cccHHHHHHHHHhCC----CCccEEEEEeeCchhHHHHHHhcCCC-CEEE
Q 022383          161 RVCDMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLP----PDLQVVLISATLPHEILEMTTKFMTD-PVKI  234 (298)
Q Consensus       161 ~l~~~~~~~~~~~~~l~~vViDE~h~~~~-~~~~~~i~~i~~~~~----~~~~~v~~SAT~~~~~~~~~~~~~~~-~~~~  234 (298)
                      +|..++..+.+.+.++.++|+||||.|++ .+|.+.|+.++....    .+.|.++||||+|..+..+...++.+ ...+
T Consensus       212 rL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~l  291 (482)
T KOG0335|consen  212 RLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFL  291 (482)
T ss_pred             hhhhhhhcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEE
Confidence            99999999999999999999999999999 799999999998875    37899999999999999987777765 6677


Q ss_pred             EecCCccCcCCceEEEEEecCccchHHHHHHHHhhCC----CC-----cEEEEecchhhHHHHHHHHhhhcC
Q 022383          235 LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT----IT-----QAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       235 ~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~----~~-----k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .+........++.|.+..+.... |...+.+++....    .+     +++|||.+++.|..++.+|...++
T Consensus       292 aV~rvg~~~~ni~q~i~~V~~~~-kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~  362 (482)
T KOG0335|consen  292 AVGRVGSTSENITQKILFVNEME-KRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGY  362 (482)
T ss_pred             EEeeeccccccceeEeeeecchh-hHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCC
Confidence            77778888899999999999888 7788888776322    23     899999999999999999988765

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

Probab=100.00  E-value=2.8e-41  Score=279.75  Aligned_cols=267  Identities=29%  Similarity=0.421  Sum_probs=238.2

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      .....|+.|||++|+.+-|+.+|+..|+|+|..++|.|+.|+|++-+|.||||||.+|.+|+++++...+.+..++|++|
T Consensus         4 ~t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTP   83 (442)
T KOG0340|consen    4 KTAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTP   83 (442)
T ss_pred             cccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecc
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc----CccCCCccEEEechhh
Q 022383          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK----TLRTRAIKLLVLDESD  185 (298)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~----~~~~~~l~~vViDE~h  185 (298)
                      |++|+-|+.++|..+++..++++.+++||.+.-.+...+..+++++|+||+++...+..+    ...++++.++|+||||
T Consensus        84 TrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEAD  163 (442)
T KOG0340|consen   84 TRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEAD  163 (442)
T ss_pred             hHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchh
Confidence            999999999999999999999999999999998888999999999999999999998875    3457999999999999


Q ss_pred             HhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCC--CEEEEecCCccCcCCceEEEEEecCccchHHHH
Q 022383          186 EMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTD--PVKILVKRDELTLEGIKQFFVAVEREEWKFDTL  263 (298)
Q Consensus       186 ~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l  263 (298)
                      .+++..|.+.+.-+.+.+|..+|.+++|||+++.+..+.......  .......+.........+.|+.++... |...+
T Consensus       164 rvL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~v-kdaYL  242 (442)
T KOG0340|consen  164 RVLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDV-KDAYL  242 (442)
T ss_pred             hhhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhh-hHHHH
Confidence            999999999999999999999999999999998877765544443  333444455666777889999998877 77778


Q ss_pred             HHHHhhCC---CCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          264 CDLYDTLT---ITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       264 ~~ll~~~~---~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +.++....   .+.++||+|+..+|+.++..|+...+
T Consensus       243 v~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~  279 (442)
T KOG0340|consen  243 VHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEV  279 (442)
T ss_pred             HHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhce
Confidence            88876543   35899999999999999999987654

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

Probab=100.00  E-value=2.5e-40  Score=278.91  Aligned_cols=272  Identities=29%  Similarity=0.443  Sum_probs=239.9

Q ss_pred             ecccCCccccCccc-CCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc-----
Q 022383           24 ETTEGVEAITSFDA-MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-----   97 (298)
Q Consensus        24 ~~~~~~~~~~~~~~-l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~-----   97 (298)
                      +...-|.|.-+|++ +.-.+++...+++.||..|+|+|+++||.+++|+|++.+|.||+|||++|++|.+.++..     
T Consensus       210 ekrpIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~  289 (629)
T KOG0336|consen  210 EKRPIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRR  289 (629)
T ss_pred             CcccCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhh
Confidence            33445677778887 578999999999999999999999999999999999999999999999999998887643     


Q ss_pred             -CCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383           98 -SSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus        98 -~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                       ...++.+|++.||++|+.|+.-.+.++. ..++....++|+.+..++...+..+.+|+++||++|..+...+.+++..+
T Consensus       290 ~qr~~p~~lvl~ptreLalqie~e~~kys-yng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~si  368 (629)
T KOG0336|consen  290 EQRNGPGVLVLTPTRELALQIEGEVKKYS-YNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASI  368 (629)
T ss_pred             hccCCCceEEEeccHHHHHHHHhHHhHhh-hcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeee
Confidence             2457899999999999999999888765 34778888899999999999999999999999999999999999999999


Q ss_pred             cEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCc-CCceEEEEEecC
Q 022383          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTL-EGIKQFFVAVER  255 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~~~~~~~~~  255 (298)
                      .++|+||||.|++.+|...+++++--+++..|+++.|||||+.+..+...|+.+|..+.+...+... ..+.|.+ .+..
T Consensus       369 TYlVlDEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i-~v~~  447 (629)
T KOG0336|consen  369 TYLVLDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNI-IVTT  447 (629)
T ss_pred             EEEEecchhhhhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeE-Eecc
Confidence            9999999999999999999999999999999999999999999999999999999999988766444 5567776 5666


Q ss_pred             ccchHHHHHHHHhhCCC-CcEEEEecchhhHHHHHHHHhhhcC
Q 022383          256 EEWKFDTLCDLYDTLTI-TQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       256 ~~~k~~~l~~ll~~~~~-~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +..|.+.+..+++.... .|+||||.++..|..+...|.-+|+
T Consensus       448 d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi  490 (629)
T KOG0336|consen  448 DSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGI  490 (629)
T ss_pred             cHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhccc
Confidence            66699999988887654 5999999999999988777655554

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

Probab=100.00  E-value=1.2e-40  Score=277.65  Aligned_cols=288  Identities=34%  Similarity=0.534  Sum_probs=255.5

Q ss_pred             hhhHHHhcCCCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC--CcEEEEcCCC
Q 022383            3 AATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSG   80 (298)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~pTG   80 (298)
                      +.+++.+.-...+....    +.+++.....+|++|+|.|++++++..|+|..|+.+|..++|.++..  +|.|.++..|
T Consensus        64 ~~~~ll~~~~~~~vk~~----dpnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsG  139 (477)
T KOG0332|consen   64 ADSSLLNKFIESNVKLA----DPNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSG  139 (477)
T ss_pred             chhhhhcchhhhceeec----CCCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCC
Confidence            44455555444444444    37778888899999999999999999999999999999999999865  7999999999


Q ss_pred             CchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChH
Q 022383           81 TGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPG  160 (298)
Q Consensus        81 ~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~  160 (298)
                      +|||.||.+.++.++......|+++.|+|+++||.|+.+.+.+++++.++...+...+........ +  ..+|+|+||+
T Consensus       140 tGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG~~-i--~eqIviGTPG  216 (477)
T KOG0332|consen  140 TGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRGNK-L--TEQIVIGTPG  216 (477)
T ss_pred             CchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCcccccCCc-c--hhheeeCCCc
Confidence            999999999999999988888999999999999999999999999999888877766552221111 1  1379999999


Q ss_pred             HHHHHHhc-cCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecC
Q 022383          161 RVCDMIKR-KTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (298)
Q Consensus       161 ~l~~~~~~-~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~  238 (298)
                      .+..+... ..+++.+++.+|+||||.|.+. ||+++-..+.+.+|++.|++++|||+.+.+..+.....+++..+...+
T Consensus       217 tv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~  296 (477)
T KOG0332|consen  217 TVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKR  296 (477)
T ss_pred             cHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeeh
Confidence            99998877 7889999999999999999765 799999999999999999999999999999999999999999999999


Q ss_pred             CccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          239 DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       239 ~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ++..+.+|.++|..|..+++|++.+..+......++.||||.|++.|.+++..++..|.
T Consensus       297 eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh  355 (477)
T KOG0332|consen  297 EELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEMRAEGH  355 (477)
T ss_pred             hhccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHHHhcCc
Confidence            99999999999999999999999999999988889999999999999999999998874

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

Probab=100.00  E-value=1.9e-39  Score=281.46  Aligned_cols=270  Identities=25%  Similarity=0.424  Sum_probs=226.8

Q ss_pred             ecccCCccccCcccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc-----
Q 022383           24 ETTEGVEAITSFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-----   97 (298)
Q Consensus        24 ~~~~~~~~~~~~~~l~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~-----   97 (298)
                      +.++.+-....|.+|||++.+...|.+ |++..||.+|+++||.++.|+|++|.++||||||++|++|+++.+..     
T Consensus       127 ~v~e~~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki  206 (708)
T KOG0348|consen  127 QVSEAPFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKI  206 (708)
T ss_pred             cccccccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccc
Confidence            344444455689999999999999987 79999999999999999999999999999999999999999998743     


Q ss_pred             -CCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceE-EEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCC
Q 022383           98 -SSREVQALILSPTRELATQTEKVILAIGDFINIQA-HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTR  174 (298)
Q Consensus        98 -~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~  174 (298)
                       ...|+.++||+||||||.|+++.++++.+....-+ +.+.||...+.+...+..+++|+|+||++|++.+.+ ..+.++
T Consensus       207 ~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s  286 (708)
T KOG0348|consen  207 QRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFS  286 (708)
T ss_pred             cccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheee
Confidence             34588999999999999999999999987755433 667888888888889999999999999999999987 678899


Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCC-------------CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCC--
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLP-------------PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD--  239 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-------------~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~--  239 (298)
                      ++.++|+||+|.+++-||...+..|++.+.             +..|-+++|||++..+.++....+.+|..+..+..  
T Consensus       287 ~LRwlVlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~  366 (708)
T KOG0348|consen  287 RLRWLVLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHS  366 (708)
T ss_pred             eeeEEEecchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhh
Confidence            999999999999999999999999988872             13678999999999999999999999988872110  


Q ss_pred             -----------------------ccCcCCceEEEEEecCccchHHHHHHHHhh----CCCCcEEEEecchhhHHHHHHHH
Q 022383          240 -----------------------ELTLEGIKQFFVAVEREEWKFDTLCDLYDT----LTITQAVIFCNTKRKIYYSVFYF  292 (298)
Q Consensus       240 -----------------------~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~----~~~~k~lIf~~s~~~~~~l~~~L  292 (298)
                                             ...+....+.|..++..- ++..+..++..    ....|+|||..+.+.++.=+..|
T Consensus       367 ~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKL-RLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf  445 (708)
T KOG0348|consen  367 QLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKL-RLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLF  445 (708)
T ss_pred             hcCcchhhhhhcCCcccccccccccCcHHhhhceEecCCch-hHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHH
Confidence                                   122344567777777776 77777777653    34459999999999999888887


Q ss_pred             hh
Q 022383          293 WI  294 (298)
Q Consensus       293 ~~  294 (298)
                      ..
T Consensus       446 ~~  447 (708)
T KOG0348|consen  446 SE  447 (708)
T ss_pred             Hh
Confidence            64

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.4e-39  Score=302.23  Aligned_cols=277  Identities=30%  Similarity=0.473  Sum_probs=253.9

Q ss_pred             ceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC--
Q 022383           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--   98 (298)
Q Consensus        21 ~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~--   98 (298)
                      ..+.+..-++|+.+|...|++..|+..++++||..|+++|.++||++.+|+|+|.+|.||||||++|++|++.++...  
T Consensus       353 i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~  432 (997)
T KOG0334|consen  353 IKVKGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRP  432 (997)
T ss_pred             eeeccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCC
Confidence            566788889999999999999999999999999999999999999999999999999999999999999999876432  


Q ss_pred             ---CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccC---cc
Q 022383           99 ---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT---LR  172 (298)
Q Consensus        99 ---~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~---~~  172 (298)
                         ..||.+||++||++|+.|+.+.++++.+..+++++..+|+.....++..+.+++.|+||||+++..++-.+.   .+
T Consensus       433 ~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtn  512 (997)
T KOG0334|consen  433 LEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTN  512 (997)
T ss_pred             hhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCcccc
Confidence               358999999999999999999999999999999999999999999999999999999999999999875544   45


Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVA  252 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  252 (298)
                      +.++.++|+||+|.|.+.+|.+.+..|++.+++..|.+++|||++..++.+....+..|+.+.+........++.+.+..
T Consensus       513 lrR~t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V  592 (997)
T KOG0334|consen  513 LRRVTYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRV  592 (997)
T ss_pred             ccccceeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEE
Confidence            56666999999999999999999999999999999999999999999999999999999999988777778899999999


Q ss_pred             ecCccchHHHHHHHHhhC-CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          253 VEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       253 ~~~~~~k~~~l~~ll~~~-~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +..+..|...+.+++... ...++||||.+...|..+.+.|++.|+
T Consensus       593 ~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~  638 (997)
T KOG0334|consen  593 CAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQKAGY  638 (997)
T ss_pred             ecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHHhcCc
Confidence            996666999999999743 457999999999999999999998774

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

Probab=100.00  E-value=2.4e-39  Score=273.66  Aligned_cols=266  Identities=30%  Similarity=0.469  Sum_probs=244.7

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-CCCeEEEEEcCc
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPT  110 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~  110 (298)
                      .-.|+++||+..+.+++.+-||..|+|.|+..+|.++++++++-.+-||+|||.||++|+++++... ..+.++++++|+
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilspt   99 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPT   99 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCc
Confidence            5689999999999999999999999999999999999999999999999999999999999998654 346799999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      ++|+.|+.+..+.+++..+++..+++|+....++...+..++|||++||+++..+.-+..+.++.+.||||||+|.+++.
T Consensus       100 reLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfem  179 (529)
T KOG0337|consen  100 RELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEM  179 (529)
T ss_pred             HHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhh
Confidence            99999999999999999999999999999999999999999999999999999988887789999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  270 (298)
                      ||+..+..++..++.+.|.++||||+|+.+.++.+..+.+|..+..+.+..........+..+...+ |...|..++...
T Consensus       180 gfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~-K~aaLl~il~~~  258 (529)
T KOG0337|consen  180 GFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAE-KEAALLSILGGR  258 (529)
T ss_pred             hhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHH-HHHHHHHHHhcc
Confidence            9999999999999999999999999999999999999999999997766666666777777777777 888888888754


Q ss_pred             C-CCcEEEEecchhhHHHHHHHHhhhcCC
Q 022383          271 T-ITQAVIFCNTKRKIYYSVFYFWIRWIG  298 (298)
Q Consensus       271 ~-~~k~lIf~~s~~~~~~l~~~L~~~~~~  298 (298)
                      - .++++|||.|+..++.+...|+..|++
T Consensus       259 ~~~~~t~vf~~tk~hve~~~~ll~~~g~~  287 (529)
T KOG0337|consen  259 IKDKQTIVFVATKHHVEYVRGLLRDFGGE  287 (529)
T ss_pred             ccccceeEEecccchHHHHHHHHHhcCCC
Confidence            3 468999999999999999999988864

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

Probab=100.00  E-value=1.2e-40  Score=279.02  Aligned_cols=274  Identities=30%  Similarity=0.477  Sum_probs=244.4

Q ss_pred             eeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhc-----
Q 022383           22 VFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVD-----   96 (298)
Q Consensus        22 ~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~-----   96 (298)
                      .+++...+.|+.+|.++.++..+++.|++.|+.+|+|.|.+-+|.+++|+|.+-.|-||||||++|.+|++....     
T Consensus       159 ~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~  238 (610)
T KOG0341|consen  159 LVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMM  238 (610)
T ss_pred             EeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhc
Confidence            457788899999999999999999999999999999999999999999999999999999999999999877531     


Q ss_pred             ---cCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC------CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHh
Q 022383           97 ---TSSREVQALILSPTRELATQTEKVILAIGDFI------NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIK  167 (298)
Q Consensus        97 ---~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~  167 (298)
                         ....+|..+|+||+++|+.|+++.+..+...+      .++..++.||.+..++...+..+.+|+|+||++|..++.
T Consensus       239 lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~  318 (610)
T KOG0341|consen  239 LPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLA  318 (610)
T ss_pred             CccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHH
Confidence               23568899999999999999999988775433      468889999999999999999999999999999999999


Q ss_pred             ccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCce
Q 022383          168 RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIK  247 (298)
Q Consensus       168 ~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  247 (298)
                      ...+++.-+.++++||+|+|.+.||.++++.++..+...+|.++||||+|..++.+.+..+-.|+.+.+.+.....-++.
T Consensus       319 KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldVi  398 (610)
T KOG0341|consen  319 KKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVI  398 (610)
T ss_pred             HhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchhHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998888777777


Q ss_pred             EEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          248 QFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       248 ~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      |.+..+..+. |...+.+.++. ...++||||..+.++..++++|--+|.
T Consensus       399 QevEyVkqEa-KiVylLeCLQK-T~PpVLIFaEkK~DVD~IhEYLLlKGV  446 (610)
T KOG0341|consen  399 QEVEYVKQEA-KIVYLLECLQK-TSPPVLIFAEKKADVDDIHEYLLLKGV  446 (610)
T ss_pred             HHHHHHHhhh-hhhhHHHHhcc-CCCceEEEeccccChHHHHHHHHHccc
Confidence            7666666555 55555555543 346999999999999999999987774

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

Probab=100.00  E-value=9.1e-39  Score=267.93  Aligned_cols=265  Identities=60%  Similarity=0.979  Sum_probs=247.0

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      +...+|++++|++.+++.++..||+.|+..|+.++.++.+|.|+.+.+++|+|||.+|.+++++.+........+++++|
T Consensus        23 evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaP  102 (397)
T KOG0327|consen   23 EVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAP  102 (397)
T ss_pred             HHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcc
Confidence            45569999999999999999999999999999999999999999999999999999999999999877777789999999


Q ss_pred             cHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh-hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      +++|+.|+.++.+.++...++++..+.|+.....+...+ ...++|+|+||+++..+++.+.+..+.++++|+||+|.++
T Consensus       103 treLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmL  182 (397)
T KOG0327|consen  103 TRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEML  182 (397)
T ss_pred             hHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhhh
Confidence            999999999999999999999999999998877555444 4568999999999999999988888899999999999999


Q ss_pred             ccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh
Q 022383          189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (298)
Q Consensus       189 ~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  268 (298)
                      +.+|.+.+..+++.+|++.|++++|||+|.++......++.+|..+.+...+.+..++.++++....++ |+..+..+.+
T Consensus       183 s~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~-k~~~l~dl~~  261 (397)
T KOG0327|consen  183 SRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEE-KLDTLCDLYR  261 (397)
T ss_pred             ccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccc-cccHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999888 9999999998


Q ss_pred             hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          269 TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       269 ~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                        ...+.+||||+++.+..+...|.+++.
T Consensus       262 --~~~q~~if~nt~r~v~~l~~~L~~~~~  288 (397)
T KOG0327|consen  262 --RVTQAVIFCNTRRKVDNLTDKLRAHGF  288 (397)
T ss_pred             --hhhcceEEecchhhHHHHHHHHhhCCc
Confidence              457999999999999999999977653

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.5e-38  Score=276.72  Aligned_cols=268  Identities=25%  Similarity=0.394  Sum_probs=229.4

Q ss_pred             CCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC-CcEEEEcCCCCchHHHHHHHHHHhhccC--------
Q 022383           28 GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTS--------   98 (298)
Q Consensus        28 ~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~--------   98 (298)
                      ....+..|..|+++..++.+|.++||..|+++|.-.+|++..| .|++--|.||||||+||-+|+++.+...        
T Consensus       176 ~~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~  255 (731)
T KOG0347|consen  176 SKVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELS  255 (731)
T ss_pred             cccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhh
Confidence            3445678999999999999999999999999999999999988 7999999999999999999999955322        


Q ss_pred             ---CCCe--EEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccC---
Q 022383           99 ---SREV--QALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT---  170 (298)
Q Consensus        99 ---~~~~--~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~---  170 (298)
                         ..++  .+||++|||+||.|+..-+..+....++++..+.||.....+...+...++|+|+||++|..++.+..   
T Consensus       256 ~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l  335 (731)
T KOG0347|consen  256 NTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHL  335 (731)
T ss_pred             hHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhh
Confidence               1233  49999999999999999999999999999999999998888888888899999999999999998743   


Q ss_pred             ccCCCccEEEechhhHhhccccHHHHHHHHHhCC-----CCccEEEEEeeCchh---------------------HHHHH
Q 022383          171 LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-----PDLQVVLISATLPHE---------------------ILEMT  224 (298)
Q Consensus       171 ~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-----~~~~~v~~SAT~~~~---------------------~~~~~  224 (298)
                      -++.++.++|+||+|+|.+.|+-..+..+++.+.     ...|.++||||++-.                     ++.++
T Consensus       336 ~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lm  415 (731)
T KOG0347|consen  336 GNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLM  415 (731)
T ss_pred             hhhhhceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHH
Confidence            4689999999999999999998888888888775     357999999997431                     33333


Q ss_pred             Hh--cCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          225 TK--FMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       225 ~~--~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..  +.+.|..+...+...+...+....+.|+..+ |.-.+++++..++ +++|||||+...+..++-+|...++
T Consensus       416 k~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~e-KD~ylyYfl~ryP-GrTlVF~NsId~vKRLt~~L~~L~i  488 (731)
T KOG0347|consen  416 KKIGFRGKPKIIDLTPQSATASTLTESLIECPPLE-KDLYLYYFLTRYP-GRTLVFCNSIDCVKRLTVLLNNLDI  488 (731)
T ss_pred             HHhCccCCCeeEecCcchhHHHHHHHHhhcCCccc-cceeEEEEEeecC-CceEEEechHHHHHHHHHHHhhcCC
Confidence            33  3457777887777777777888888897777 8888888888876 8999999999999999999987665

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=5.8e-38  Score=277.44  Aligned_cols=268  Identities=28%  Similarity=0.495  Sum_probs=248.1

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      .....|+++.|...++..|+..+|..|+++|..+||+++.+-|+||++..|+|||++|...+++.+......++.+|++|
T Consensus        22 ~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~P  101 (980)
T KOG4284|consen   22 NCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTP  101 (980)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEec
Confidence            34568999999999999999999999999999999999999999999999999999999999998888888889999999


Q ss_pred             cHHHHHHHHHHHHHhhcc-CCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          110 TRELATQTEKVILAIGDF-INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      ||+++-|+.+.+.+++.. .|.++..+.||+.-......+. .++|+||||+++..++..+.++.++++++|+||||.+.
T Consensus       102 TREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk-~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~  180 (980)
T KOG4284|consen  102 TREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLK-QTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLM  180 (980)
T ss_pred             chhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhh-hceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhh
Confidence            999999999999999864 4899999999998877666664 46899999999999999999999999999999999999


Q ss_pred             c-cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCcc-------chH
Q 022383          189 S-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREE-------WKF  260 (298)
Q Consensus       189 ~-~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------~k~  260 (298)
                      + ..|+..+..|+..+|..+|++.+|||.+..+...+..++.+|..+.....+..+-++.|+++..+...       -|+
T Consensus       181 ~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlkl  260 (980)
T KOG4284|consen  181 DTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKL  260 (980)
T ss_pred             chhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHH
Confidence            8 47999999999999999999999999999999999999999999999999999999999999887652       367


Q ss_pred             HHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcCC
Q 022383          261 DTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWIG  298 (298)
Q Consensus       261 ~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~~  298 (298)
                      ..|..+++..+..+.||||+....|+.++..|...|+|
T Consensus       261 q~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d  298 (980)
T KOG4284|consen  261 QKLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLD  298 (980)
T ss_pred             HHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCC
Confidence            78888899999999999999999999999999999986

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=1.3e-35  Score=242.68  Aligned_cols=200  Identities=47%  Similarity=0.812  Sum_probs=184.6

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC--CCCeEEEEEcCcHH
Q 022383           35 FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--SREVQALILSPTRE  112 (298)
Q Consensus        35 ~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~--~~~~~~lil~p~~~  112 (298)
                      |+++++++.+.+.|.++|+..|+++|.++++.+.+|+|+++++|||+|||++|+++++..+...  ..+++++|++|+++
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~   80 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRE   80 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHH
Confidence            7899999999999999999999999999999999999999999999999999999999998776  46779999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc
Q 022383          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~  192 (298)
                      |+.|+...++++....++.+..++|+.........+.++++|+|+||+++..++......+++++++|+||+|.+.+.++
T Consensus        81 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~~  160 (203)
T cd00268          81 LALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGF  160 (203)
T ss_pred             HHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccCh
Confidence            99999999999988778889999998887776666767899999999999999988888889999999999999988889


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEE
Q 022383          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKI  234 (298)
Q Consensus       193 ~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~  234 (298)
                      ...+..+.+.++..+|++++|||+++....++..++.+|..+
T Consensus       161 ~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         161 EDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             HHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            999999999999899999999999999999998888887765

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 ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.7e-37  Score=244.06  Aligned_cols=264  Identities=34%  Similarity=0.590  Sum_probs=236.4

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      .-|.++-|.|++++++.++||++|+..|.+++|...-|-|++.+|.+|.|||.+|.+.-++++........++++|+|++
T Consensus        42 sgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtre  121 (387)
T KOG0329|consen   42 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRE  121 (387)
T ss_pred             cchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHH
Confidence            46778889999999999999999999999999999999999999999999999999999999988877889999999999


Q ss_pred             HHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-
Q 022383          113 LATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-  190 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-  190 (298)
                      |+-|+.+...++.++. ++++..++||...+.....+.+.++|+|+||++++.+.+++.+++++++.+|+||||.|+++ 
T Consensus       122 lafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~l  201 (387)
T KOG0329|consen  122 LAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQL  201 (387)
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHH
Confidence            9999999888887765 78999999999888777778888999999999999999999999999999999999999876 


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCC-ccCcCCceEEEEEecCccchHHHHHHHHhh
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDT  269 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~  269 (298)
                      ..+.+++.+.+.-|...|++++|||++.++...++.++.+|..+.++.+ ..++.+.+|+|+..+..+ |-..+.+++..
T Consensus       202 DMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~e-KNrkl~dLLd~  280 (387)
T KOG0329|consen  202 DMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENE-KNRKLNDLLDV  280 (387)
T ss_pred             HHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhh-hhhhhhhhhhh
Confidence            6889999999999999999999999999999999999999999888754 456688999999998887 88888888888


Q ss_pred             CCCCcEEEEecchhhHH----HHHHHHhhhcC
Q 022383          270 LTITQAVIFCNTKRKIY----YSVFYFWIRWI  297 (298)
Q Consensus       270 ~~~~k~lIf~~s~~~~~----~l~~~L~~~~~  297 (298)
                      ...++++||+.++....    -++..|--+|+
T Consensus       281 LeFNQVvIFvKsv~Rl~f~kr~vat~lfgrgm  312 (387)
T KOG0329|consen  281 LEFNQVVIFVKSVQRLSFQKRLVATDLFGRGM  312 (387)
T ss_pred             hhhcceeEeeehhhhhhhhhhhHHhhhhcccc
Confidence            88899999999987643    24444444443

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

Probab=100.00  E-value=3.1e-35  Score=279.25  Aligned_cols=247  Identities=19%  Similarity=0.224  Sum_probs=187.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      +++.+.++|++.||+.|+++|.++++.+++|+|+++++|||||||+||++|+++.+..+ .+.++|||+||++|++|+.+
T Consensus        21 l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~-~~~~aL~l~PtraLa~q~~~   99 (742)
T TIGR03817        21 AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD-PRATALYLAPTKALAADQLR   99 (742)
T ss_pred             CCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC-CCcEEEEEcChHHHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999998653 35699999999999999999


Q ss_pred             HHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-c---CccCCCccEEEechhhHhhccccHHH
Q 022383          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-K---TLRTRAIKLLVLDESDEMLSRGFKDQ  195 (298)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~---~~~~~~l~~vViDE~h~~~~~~~~~~  195 (298)
                      .++++. ..++++..+.|+.+.. +...+..+++|+|+||+++...+.. .   ...++++++||+||+|.+.+ .|...
T Consensus       100 ~l~~l~-~~~i~v~~~~Gdt~~~-~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g-~fg~~  176 (742)
T TIGR03817       100 AVRELT-LRGVRPATYDGDTPTE-ERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG-VFGSH  176 (742)
T ss_pred             HHHHhc-cCCeEEEEEeCCCCHH-HHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC-ccHHH
Confidence            999987 4478888888887754 3355666789999999999753322 1   12378999999999999854 46655


Q ss_pred             HHHHHHh-------CCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecC-------------
Q 022383          196 IYDVYRY-------LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER-------------  255 (298)
Q Consensus       196 i~~i~~~-------~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-------------  255 (298)
                      +..+++.       .+.++|++++|||+++..+ ....+++.|..+. .... .+....+.....+.             
T Consensus       177 ~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~i-~~~~-~~~~~~~~~~~~p~~~~~~~~~~~~~r  253 (742)
T TIGR03817       177 VALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVAV-TEDG-SPRGARTVALWEPPLTELTGENGAPVR  253 (742)
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEEE-CCCC-CCcCceEEEEecCCccccccccccccc
Confidence            5444433       3567899999999988744 5667777776543 2222 22222222222111             


Q ss_pred             ---ccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          256 ---EEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       256 ---~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                         ...+...+..+++.  +.++||||||++.|+.++..|++.
T Consensus       254 ~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l~~~  294 (742)
T TIGR03817       254 RSASAEAADLLADLVAE--GARTLTFVRSRRGAELVAAIARRL  294 (742)
T ss_pred             cchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHHHHH
Confidence               01234455555553  479999999999999999998753

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.

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=8.8e-35  Score=278.34  Aligned_cols=252  Identities=18%  Similarity=0.235  Sum_probs=186.4

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      .|++++|++.+.+++++.||..|+|+|.++++. +.+|+|+++++|||+|||++|.++++..+..   +.++||++|+++
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~---~~kal~i~P~ra   78 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR---GGKALYIVPLRA   78 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc---CCcEEEEeChHH
Confidence            588999999999999999999999999999998 7799999999999999999999999998853   558999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc
Q 022383          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~  192 (298)
                      |+.|+.+.++++.. .++++..++|+......   ....++|+|+||+++..++++....++++++||+||+|.+.+.++
T Consensus        79 La~q~~~~~~~~~~-~g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~r  154 (737)
T PRK02362         79 LASEKFEEFERFEE-LGVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANR  154 (737)
T ss_pred             HHHHHHHHHHHhhc-CCCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcc
Confidence            99999999998654 47889999988654332   224579999999999999988767789999999999999988888


Q ss_pred             HHHHHHHHHhC---CCCccEEEEEeeCch--hHHHHHHhcCC----CCEEEE--ecCC-ccCcCCceEEEEEecCccchH
Q 022383          193 KDQIYDVYRYL---PPDLQVVLISATLPH--EILEMTTKFMT----DPVKIL--VKRD-ELTLEGIKQFFVAVEREEWKF  260 (298)
Q Consensus       193 ~~~i~~i~~~~---~~~~~~v~~SAT~~~--~~~~~~~~~~~----~~~~~~--~~~~-~~~~~~i~~~~~~~~~~~~k~  260 (298)
                      +..++.++.++   ++..|++++|||+++  ++..|+.....    .|..+.  +... ...... .+............
T Consensus       155 g~~le~il~rl~~~~~~~qii~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~-~~~~~~~~~~~~~~  233 (737)
T PRK02362        155 GPTLEVTLAKLRRLNPDLQVVALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDD-SQREVEVPSKDDTL  233 (737)
T ss_pred             hHHHHHHHHHHHhcCCCCcEEEEcccCCCHHHHHHHhCCCcccCCCCCCCCeeeEecCCeecccc-ccccCCCccchHHH
Confidence            88877765554   467999999999976  33333321110    111111  0000 000000 00111111111123


Q ss_pred             HHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          261 DTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       261 ~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ..+...++  .++++||||+|++.|+.++..|...
T Consensus       234 ~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~  266 (737)
T PRK02362        234 NLVLDTLE--EGGQCLVFVSSRRNAEGFAKRAASA  266 (737)
T ss_pred             HHHHHHHH--cCCCeEEEEeCHHHHHHHHHHHHHH
Confidence            33333333  4579999999999999999998654

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=6.3e-34  Score=271.85  Aligned_cols=247  Identities=15%  Similarity=0.201  Sum_probs=189.9

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      +|+++++++.+.+.|++.||..|+|+|.++++. +.+|+|+++++|||+|||++|.+|++..+...  +.++|||+|+++
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~--~~~~l~l~P~~a   79 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--GGKAVYLVPLKA   79 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc--CCeEEEEeChHH
Confidence            578999999999999999999999999999986 78999999999999999999999999987643  458999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc
Q 022383          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~  192 (298)
                      |+.|+.+.++.+. ..++++..++|+.+....   ....++|+|+||+++..+++.....++++++||+||+|.+.+.++
T Consensus        80 La~q~~~~~~~~~-~~g~~v~~~~Gd~~~~~~---~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~r  155 (720)
T PRK00254         80 LAEEKYREFKDWE-KLGLRVAMTTGDYDSTDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDR  155 (720)
T ss_pred             HHHHHHHHHHHHh-hcCCEEEEEeCCCCCchh---hhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccc
Confidence            9999999998764 358899999998765432   235689999999999999987777789999999999999988888


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceE-----EEEEecCcc------chHH
Q 022383          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQ-----FFVAVEREE------WKFD  261 (298)
Q Consensus       193 ~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~-----~~~~~~~~~------~k~~  261 (298)
                      ...++.++..+..+.|++++|||+++. .++.. ++......    ....+.....     .+.......      ....
T Consensus       156 g~~le~il~~l~~~~qiI~lSATl~n~-~~la~-wl~~~~~~----~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (720)
T PRK00254        156 GATLEMILTHMLGRAQILGLSATVGNA-EELAE-WLNAELVV----SDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWES  229 (720)
T ss_pred             hHHHHHHHHhcCcCCcEEEEEccCCCH-HHHHH-HhCCcccc----CCCCCCcceeeEecCCeeeccCcchhcchHHHHH
Confidence            999999999998899999999999763 44443 33222110    0111111111     111111110      0112


Q ss_pred             HHHHHHhhCCCCcEEEEecchhhHHHHHHHHhh
Q 022383          262 TLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWI  294 (298)
Q Consensus       262 ~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~  294 (298)
                      .+...++  .++++||||+|++.|+.++..|..
T Consensus       230 ~~~~~i~--~~~~vLVF~~sr~~~~~~a~~l~~  260 (720)
T PRK00254        230 LVYDAVK--KGKGALVFVNTRRSAEKEALELAK  260 (720)
T ss_pred             HHHHHHH--hCCCEEEEEcChHHHHHHHHHHHH
Confidence            3334443  357999999999999999887753

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

Probab=100.00  E-value=5.6e-34  Score=245.78  Aligned_cols=261  Identities=20%  Similarity=0.325  Sum_probs=212.7

Q ss_pred             ccCcccCCCCHH----------HHHHHHHCCCCCChHHHHHHHHHhh---------cCCcEEEEcCCCCchHHHHHHHHH
Q 022383           32 ITSFDAMGIKDD----------LLRGIYQYGFEKPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIALTVC   92 (298)
Q Consensus        32 ~~~~~~l~l~~~----------i~~~l~~~~~~~~~~~Q~~~~~~~~---------~~~~~li~~pTG~GKT~~~~~~~~   92 (298)
                      ...|+.++++..          +.+++.++++....|+|..++|.++         .++|+.|.||||||||+||.+|+.
T Consensus       126 lq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIV  205 (620)
T KOG0350|consen  126 LQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIV  205 (620)
T ss_pred             eeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHH
Confidence            345666666554          4445899999999999999999885         258999999999999999999999


Q ss_pred             HhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcC-----CcEEEeChHHHHHHH
Q 022383           93 QTVDTSS-REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG-----VHVVSGTPGRVCDMI  166 (298)
Q Consensus        93 ~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~ilV~Tp~~l~~~~  166 (298)
                      +.+.... .-.+++||+|+++|+.|+++.|.++....|+.++.+.|..+...+..++.+.     .||+|+||++|...+
T Consensus       206 Q~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl  285 (620)
T KOG0350|consen  206 QLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHL  285 (620)
T ss_pred             HHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhc
Confidence            9997753 2369999999999999999999999999999999999999888887777532     389999999999999


Q ss_pred             hc-cCccCCCccEEEechhhHhhccccHHHHHHHHHhC----------------------------------CCCccEEE
Q 022383          167 KR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL----------------------------------PPDLQVVL  211 (298)
Q Consensus       167 ~~-~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~----------------------------------~~~~~~v~  211 (298)
                      ++ ..+++++++++||||+|++++..|+..+-.+...+                                  .+..+.++
T Consensus       286 ~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~  365 (620)
T KOG0350|consen  286 NNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLV  365 (620)
T ss_pred             cCCCCcchhhceEEEechHHHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhh
Confidence            96 78999999999999999999887765544433222                                  12345788


Q ss_pred             EEeeCchhHHHHHHhcCCCCEEEEec----CCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHH
Q 022383          212 ISATLPHEILEMTTKFMTDPVKILVK----RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYY  287 (298)
Q Consensus       212 ~SAT~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~  287 (298)
                      +|||+......+...-+..|-...+.    .....+..+.+..+.++... |.-.++.++...+..++|+|+++.+.+.+
T Consensus       366 ~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~~-kpl~~~~lI~~~k~~r~lcf~~S~~sa~R  444 (620)
T KOG0350|consen  366 FSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPKF-KPLAVYALITSNKLNRTLCFVNSVSSANR  444 (620)
T ss_pred             cchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeeccccc-chHhHHHHHHHhhcceEEEEecchHHHHH
Confidence            99999776666666666777544443    23344566778888888777 88899999999999999999999999999


Q ss_pred             HHHHHh
Q 022383          288 SVFYFW  293 (298)
Q Consensus       288 l~~~L~  293 (298)
                      ++..|.
T Consensus       445 l~~~L~  450 (620)
T KOG0350|consen  445 LAHVLK  450 (620)
T ss_pred             HHHHHH
Confidence            999886

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

Probab=100.00  E-value=3.3e-33  Score=260.56  Aligned_cols=249  Identities=17%  Similarity=0.197  Sum_probs=197.0

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-----CCCeEEEEEcCcHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----SREVQALILSPTRELA  114 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-----~~~~~~lil~p~~~l~  114 (298)
                      |++.+.+.++.. |..||+.|.++||.+.+|+|+++.||||||||+|+.+|+++.+...     ..+..+|||+|.++|.
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn   86 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN   86 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHH
Confidence            789999999998 9999999999999999999999999999999999999999998665     2357999999999999


Q ss_pred             HHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc--CccCCCccEEEechhhHhhcccc
Q 022383          115 TQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK--TLRTRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       115 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~--~~~~~~l~~vViDE~h~~~~~~~  192 (298)
                      +++.++++.++...|+.+...+|+++..+..+...+.+||+|+|||.|.-++...  .-.+.++.+|||||+|.+.....
T Consensus        87 ~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKR  166 (814)
T COG1201          87 NDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKR  166 (814)
T ss_pred             HHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhcccc
Confidence            9999999999999999999999999999998899999999999999999988764  33579999999999999976643


Q ss_pred             HH----HHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCC--CEEEEecCCccCcCCceEEEEEecCc--------cc
Q 022383          193 KD----QIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTD--PVKILVKRDELTLEGIKQFFVAVERE--------EW  258 (298)
Q Consensus       193 ~~----~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~i~~~~~~~~~~--------~~  258 (298)
                      +.    .++++....+ +.|.|++|||..+. ....+...+.  +..+..... ..  ..+..+......        ..
T Consensus       167 G~~Lsl~LeRL~~l~~-~~qRIGLSATV~~~-~~varfL~g~~~~~~Iv~~~~-~k--~~~i~v~~p~~~~~~~~~~~~~  241 (814)
T COG1201         167 GVQLALSLERLRELAG-DFQRIGLSATVGPP-EEVAKFLVGFGDPCEIVDVSA-AK--KLEIKVISPVEDLIYDEELWAA  241 (814)
T ss_pred             chhhhhhHHHHHhhCc-ccEEEeehhccCCH-HHHHHHhcCCCCceEEEEccc-CC--cceEEEEecCCccccccchhHH
Confidence            33    3344444444 89999999999753 3344443333  444443322 11  122222222222        12


Q ss_pred             hHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          259 KFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       259 k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      -+..+.++++.+  ..+|||+||+..+|.++..|++.+
T Consensus       242 ~~~~i~~~v~~~--~ttLIF~NTR~~aE~l~~~L~~~~  277 (814)
T COG1201         242 LYERIAELVKKH--RTTLIFTNTRSGAERLAFRLKKLG  277 (814)
T ss_pred             HHHHHHHHHhhc--CcEEEEEeChHHHHHHHHHHHHhc
Confidence            355566666665  499999999999999999998876

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

Probab=100.00  E-value=4.7e-32  Score=254.14  Aligned_cols=242  Identities=19%  Similarity=0.208  Sum_probs=182.7

Q ss_pred             HHHHH-CCCCCChHHHHHHHHHhhcCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCe-EEEEEcCcHHHHHHHHHHHH
Q 022383           46 RGIYQ-YGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREV-QALILSPTRELATQTEKVIL  122 (298)
Q Consensus        46 ~~l~~-~~~~~~~~~Q~~~~~~~~~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~-~~lil~p~~~l~~q~~~~~~  122 (298)
                      +.+++ .||+ |+|+|.++++.++.|+ ++++.+|||+|||.++..+++.. ......+ +.++++|+++|+.|+.+.++
T Consensus         6 ~ff~~~~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~~~~~~rLv~~vPtReLa~Qi~~~~~   83 (844)
T TIGR02621         6 EWYQGLHGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIGAKVPRRLVYVVNRRTVVDQVTEEAE   83 (844)
T ss_pred             HHHHHHhCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cccccccceEEEeCchHHHHHHHHHHHH
Confidence            34444 5888 9999999999999998 57788999999999776555533 2223334 45557799999999999999


Q ss_pred             HhhccC-----------------------CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCc--------
Q 022383          123 AIGDFI-----------------------NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL--------  171 (298)
Q Consensus       123 ~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~--------  171 (298)
                      ++++.+                       .+++..++||.+...+...+..+++|+|+|++.+.    ++.+        
T Consensus        84 ~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~----sr~L~~gYg~~~  159 (844)
T TIGR02621        84 KIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIG----SRLLFSGYGCGF  159 (844)
T ss_pred             HHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHc----CCcccccccccc
Confidence            988754                       47889999999998998989999999999975443    3332        


Q ss_pred             --------cCCCccEEEechhhHhhccccHHHHHHHHHhC--CC---CccEEEEEeeCchhHHHHHHhcCCCCEEEEecC
Q 022383          172 --------RTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PP---DLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (298)
Q Consensus       172 --------~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~--~~---~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~  238 (298)
                              .+++++++|+||||  ++.+|...+..|++.+  ++   +.|+++||||++..+......++.++..+.+..
T Consensus       160 ~~~pi~ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~  237 (844)
T TIGR02621       160 KSRPLHAGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLK  237 (844)
T ss_pred             ccccchhhhhccceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeeccc
Confidence                    26889999999999  5788999999999975  33   269999999999888877777776777666655


Q ss_pred             CccCcCCceEEEEEecCccchHHHHHHHH---hhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          239 DELTLEGIKQFFVAVEREEWKFDTLCDLY---DTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       239 ~~~~~~~i~~~~~~~~~~~~k~~~l~~ll---~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ......++.++ +..+... |...+...+   ....++++||||||++.|+.+++.|+..++
T Consensus       238 ~~l~a~ki~q~-v~v~~e~-Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~  297 (844)
T TIGR02621       238 KRLAAKKIVKL-VPPSDEK-FLSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF  297 (844)
T ss_pred             ccccccceEEE-EecChHH-HHHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC
Confidence            55555566664 3333332 433322221   123457999999999999999999987664

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.

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=6.5e-32  Score=261.30  Aligned_cols=252  Identities=19%  Similarity=0.257  Sum_probs=177.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC------CCCeEEEEEcCcHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS------SREVQALILSPTREL  113 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~------~~~~~~lil~p~~~l  113 (298)
                      +++.+.+.+++ +|..|+|+|.++|+.+.+|+|++++||||+|||++|.+|+++.+...      ..+.++|||+|+++|
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraL   96 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL   96 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHH
Confidence            67788888776 78899999999999999999999999999999999999999887532      235689999999999


Q ss_pred             HHHHHHHHHH-------hh----ccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCc--cCCCccEE
Q 022383          114 ATQTEKVILA-------IG----DFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL--RTRAIKLL  179 (298)
Q Consensus       114 ~~q~~~~~~~-------~~----~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~--~~~~l~~v  179 (298)
                      ++|+.+.+..       +.    ... ++++...+|+.+..+....+.+.++|+|+||++|..++....+  .++++++|
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~V  176 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWV  176 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEE
Confidence            9999886652       22    222 6788999999988877777778899999999999888866543  57899999


Q ss_pred             EechhhHhhccccHHHHH----HHHHhCCCCccEEEEEeeCch--hHHHHHHhcC----CCCEEEEecCCccCcCCceEE
Q 022383          180 VLDESDEMLSRGFKDQIY----DVYRYLPPDLQVVLISATLPH--EILEMTTKFM----TDPVKILVKRDELTLEGIKQF  249 (298)
Q Consensus       180 ViDE~h~~~~~~~~~~i~----~i~~~~~~~~~~v~~SAT~~~--~~~~~~~~~~----~~~~~~~~~~~~~~~~~i~~~  249 (298)
                      ||||+|.+.+..+...+.    .+....+...|++++|||+++  .+..++....    ..+..+... .......+...
T Consensus       177 VIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~~~va~~L~~~~~~~~~r~~~iv~~-~~~k~~~i~v~  255 (876)
T PRK13767        177 IVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEPLEEVAKFLVGYEDDGEPRDCEIVDA-RFVKPFDIKVI  255 (876)
T ss_pred             EEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCCHHHHHHHhcCccccCCCCceEEEcc-CCCccceEEEe
Confidence            999999998766555444    333444467899999999976  3333332221    112222211 11111111100


Q ss_pred             -----EEEecCcc---chHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          250 -----FVAVEREE---WKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       250 -----~~~~~~~~---~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                           ........   .....+..+++  ..+++||||||++.|+.++..|+..
T Consensus       256 ~p~~~l~~~~~~~~~~~l~~~L~~~i~--~~~~~LVF~nTr~~ae~la~~L~~~  307 (876)
T PRK13767        256 SPVDDLIHTPAEEISEALYETLHELIK--EHRTTLIFTNTRSGAERVLYNLRKR  307 (876)
T ss_pred             ccCccccccccchhHHHHHHHHHHHHh--cCCCEEEEeCCHHHHHHHHHHHHHh
Confidence                 00011111   11223333333  2479999999999999999999874

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=4.4e-32  Score=257.99  Aligned_cols=248  Identities=17%  Similarity=0.225  Sum_probs=183.2

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      .|++++|++.+.+.+.+.+|. ++++|.++++.+.+|+|+++++|||+|||+++.++++..+..   +.++||++|+++|
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~---~~k~v~i~P~raL   77 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA---GLKSIYIVPLRSL   77 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh---CCcEEEEechHHH
Confidence            578899999999999999988 999999999999999999999999999999999999988764   4589999999999


Q ss_pred             HHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccH
Q 022383          114 ATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (298)
Q Consensus       114 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~  193 (298)
                      +.|+++.++++. ..+.++....|+......   ....++|+|+||+++..+++.....++++++||+||+|.+.+.+++
T Consensus        78 a~q~~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg  153 (674)
T PRK01172         78 AMEKYEELSRLR-SLGMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRG  153 (674)
T ss_pred             HHHHHHHHHHHh-hcCCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCcc
Confidence            999999998764 357888888887654322   2245799999999999998887677899999999999999887777


Q ss_pred             HHHHHHHH---hCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEE-----EecCccchHHHHHH
Q 022383          194 DQIYDVYR---YLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV-----AVEREEWKFDTLCD  265 (298)
Q Consensus       194 ~~i~~i~~---~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~-----~~~~~~~k~~~l~~  265 (298)
                      ..++.++.   ..+++.|++++|||+++. .++..+ +..+. +.   ....+..+.....     ..+........+..
T Consensus       154 ~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la~w-l~~~~-~~---~~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~  227 (674)
T PRK01172        154 PTLETVLSSARYVNPDARILALSATVSNA-NELAQW-LNASL-IK---SNFRPVPLKLGILYRKRLILDGYERSQVDINS  227 (674)
T ss_pred             HHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHHHH-hCCCc-cC---CCCCCCCeEEEEEecCeeeecccccccccHHH
Confidence            77776654   445689999999999764 344332 22111 00   0011111111010     01111101111223


Q ss_pred             HHhh--CCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          266 LYDT--LTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       266 ll~~--~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ++..  ..++++||||++++.|+.++..|...
T Consensus       228 ~i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~  259 (674)
T PRK01172        228 LIKETVNDGGQVLVFVSSRKNAEDYAEMLIQH  259 (674)
T ss_pred             HHHHHHhCCCcEEEEeccHHHHHHHHHHHHHh
Confidence            3332  34579999999999999999998764

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

Probab=100.00  E-value=3.9e-31  Score=251.84  Aligned_cols=251  Identities=15%  Similarity=0.183  Sum_probs=182.0

Q ss_pred             Ccc--cCCCCHHHHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           34 SFD--AMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        34 ~~~--~l~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      .|.  .+++...+...+++ +|+..++|.|.++|+.++.|+|+++++|||+|||+||++|++..      +..+|||+|+
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISPL  509 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISPL  509 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeCH
Confidence            455  46777788888777 78999999999999999999999999999999999999999864      3479999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh------cCCcEEEeChHHHHH---HHhc--cCccCCCccEE
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE------HGVHVVSGTPGRVCD---MIKR--KTLRTRAIKLL  179 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~ilV~Tp~~l~~---~~~~--~~~~~~~l~~v  179 (298)
                      ++|+.++...+..    .++....+.++....++...+.      ..++|+++||+++..   +++.  .......+.+|
T Consensus       510 iSLmqDQV~~L~~----~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslI  585 (1195)
T PLN03137        510 VSLIQDQIMNLLQ----ANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARF  585 (1195)
T ss_pred             HHHHHHHHHHHHh----CCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhcccccee
Confidence            9999876665554    3788888999887665544332      468999999999863   2221  11123568999


Q ss_pred             EechhhHhhccc--cHHHHHHH--HHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecC
Q 022383          180 VLDESDEMLSRG--FKDQIYDV--YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER  255 (298)
Q Consensus       180 ViDE~h~~~~~~--~~~~i~~i--~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  255 (298)
                      ||||||++.+||  |+..+..+  ++...+..|++++|||+++.+...+...+......... .....+++.  +...+.
T Consensus       586 VIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr-~Sf~RpNL~--y~Vv~k  662 (1195)
T PLN03137        586 VIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFR-QSFNRPNLW--YSVVPK  662 (1195)
T ss_pred             ccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEee-cccCccceE--EEEecc
Confidence            999999999997  77777653  33334578899999999988777555544322111111 222333332  222333


Q ss_pred             ccchHHHHHHHHhhC-CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          256 EEWKFDTLCDLYDTL-TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       256 ~~~k~~~l~~ll~~~-~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .......+..++... ...+.||||+|+++|+.+++.|+..|+
T Consensus       663 ~kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gi  705 (1195)
T PLN03137        663 TKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGH  705 (1195)
T ss_pred             chhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCC
Confidence            222345566666543 356899999999999999999998775

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=3.9e-31  Score=241.44  Aligned_cols=232  Identities=16%  Similarity=0.244  Sum_probs=169.2

Q ss_pred             HCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .+||..|+|+|.++++.+++|+|+++++|||+|||+||++|++..      +..+||++|+++|+.|+.+.++..    +
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~~~l~~~----g   75 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQVLQLKAS----G   75 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHHc----C
Confidence            379999999999999999999999999999999999999998863      347999999999999999888764    6


Q ss_pred             ceEEEEEcCCchHHHHH---Hh-hcCCcEEEeChHHHHHHHh-ccCc-cCCCccEEEechhhHhhccc--cHHHHHHH--
Q 022383          130 IQAHACVGGKSVGEDIR---KL-EHGVHVVSGTPGRVCDMIK-RKTL-RTRAIKLLVLDESDEMLSRG--FKDQIYDV--  199 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~---~~-~~~~~ilV~Tp~~l~~~~~-~~~~-~~~~l~~vViDE~h~~~~~~--~~~~i~~i--  199 (298)
                      +....+.++....+...   .+ ...++|+++||+++..... ...+ ...++++|||||||++.+|+  |...+..+  
T Consensus        76 i~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~~  155 (470)
T TIGR00614        76 IPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGS  155 (470)
T ss_pred             CcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHHH
Confidence            77777777766543322   22 3458999999999764221 1112 56789999999999999886  56665543  


Q ss_pred             -HHhCCCCccEEEEEeeCchhHHHHHHhcC--CCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh-hCCCCcE
Q 022383          200 -YRYLPPDLQVVLISATLPHEILEMTTKFM--TDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD-TLTITQA  275 (298)
Q Consensus       200 -~~~~~~~~~~v~~SAT~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~-~~~~~k~  275 (298)
                       .+.+ ++.+++++|||+++.+...+...+  .+|..+...   ....++...+  ..........+..++. ..+++++
T Consensus       156 l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s---~~r~nl~~~v--~~~~~~~~~~l~~~l~~~~~~~~~  229 (470)
T TIGR00614       156 LKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCTS---FDRPNLYYEV--RRKTPKILEDLLRFIRKEFKGKSG  229 (470)
T ss_pred             HHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCC---CCCCCcEEEE--EeCCccHHHHHHHHHHHhcCCCce
Confidence             3334 578899999999988766554443  344443322   2222332222  2222224555666665 4555677


Q ss_pred             EEEecchhhHHHHHHHHhhhcC
Q 022383          276 VIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       276 lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ||||+|+++|+.+++.|+..|+
T Consensus       230 IIF~~s~~~~e~la~~L~~~g~  251 (470)
T TIGR00614       230 IIYCPSRKKSEQVTASLQNLGI  251 (470)
T ss_pred             EEEECcHHHHHHHHHHHHhcCC
Confidence            9999999999999999998775

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

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=1.2e-30  Score=256.06  Aligned_cols=241  Identities=19%  Similarity=0.220  Sum_probs=184.6

Q ss_pred             HHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH
Q 022383           44 LLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (298)
Q Consensus        44 i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~  122 (298)
                      ..+.+++ .|+ .|+++|..+++.++.|+|++++||||+|||. |.+++...+..  .+.+++||+||++|+.|+.+.++
T Consensus        69 ~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~  144 (1176)
T PRK09401         69 FEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLE  144 (1176)
T ss_pred             HHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHH
Confidence            3334444 466 6999999999999999999999999999996 44455444433  36789999999999999999999


Q ss_pred             HhhccCCceEEEEEcCCch-----HHHHHHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc-------
Q 022383          123 AIGDFINIQAHACVGGKSV-----GEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS-------  189 (298)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~-----~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~-------  189 (298)
                      +++...++.+..+.++...     ......+. ++++|+|+||++|.+.+.  .+...+++++|+||||++++       
T Consensus       145 ~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~  222 (1176)
T PRK09401        145 KFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDK  222 (1176)
T ss_pred             HHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhh
Confidence            9998888887777766432     22233344 468999999999998776  45566799999999999986       


Q ss_pred             ----cccH-HHHHHHHHhCCC------------------------CccEEEEEeeCchh-HHHHHHhcCCCCEEEEecCC
Q 022383          190 ----RGFK-DQIYDVYRYLPP------------------------DLQVVLISATLPHE-ILEMTTKFMTDPVKILVKRD  239 (298)
Q Consensus       190 ----~~~~-~~i~~i~~~~~~------------------------~~~~v~~SAT~~~~-~~~~~~~~~~~~~~~~~~~~  239 (298)
                          .||. ..+..+++.++.                        ..|++++|||+++. +..   ..+.++..+.+...
T Consensus       223 ~l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~~  299 (1176)
T PRK09401        223 LLYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGSP  299 (1176)
T ss_pred             HHHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecCc
Confidence                4564 567777766654                        68999999999864 332   12334555666555


Q ss_pred             ccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhh---HHHHHHHHhhhcC
Q 022383          240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK---IYYSVFYFWIRWI  297 (298)
Q Consensus       240 ~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~---~~~l~~~L~~~~~  297 (298)
                      .....++.+.++.++   ++...+..+++... .++||||++++.   |+.++++|+..|+
T Consensus       300 ~~~~rnI~~~yi~~~---~k~~~L~~ll~~l~-~~~LIFv~t~~~~~~ae~l~~~L~~~gi  356 (1176)
T PRK09401        300 VFYLRNIVDSYIVDE---DSVEKLVELVKRLG-DGGLIFVPSDKGKEYAEELAEYLEDLGI  356 (1176)
T ss_pred             ccccCCceEEEEEcc---cHHHHHHHHHHhcC-CCEEEEEecccChHHHHHHHHHHHHCCC
Confidence            566678888888765   37778888887654 689999999888   9999999999886

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.98  E-value=2.1e-30  Score=243.10  Aligned_cols=235  Identities=16%  Similarity=0.232  Sum_probs=177.0

Q ss_pred             HHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           46 RGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        46 ~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      +.|++ +||..+++.|.++++.+++|+|+++++|||+|||+||++|++..      +..++|++|+++|+.|+.+.++.+
T Consensus         3 ~~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~------~g~~lVisPl~sL~~dq~~~l~~~   76 (591)
T TIGR01389         3 QVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL------KGLTVVISPLISLMKDQVDQLRAA   76 (591)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc------CCcEEEEcCCHHHHHHHHHHHHHc
Confidence            34555 79999999999999999999999999999999999999998853      336899999999999999988875


Q ss_pred             hccCCceEEEEEcCCchHHHHHH----hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc--cHHHHHH
Q 022383          125 GDFINIQAHACVGGKSVGEDIRK----LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYD  198 (298)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~--~~~~i~~  198 (298)
                          ++.+..++++.+..+....    ..+.++|+++||+++........+...++++|||||+|++.+|+  |+..+..
T Consensus        77 ----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~  152 (591)
T TIGR01389        77 ----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQR  152 (591)
T ss_pred             ----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHH
Confidence                6778888888766544322    23568999999999875433334556789999999999999886  6666555


Q ss_pred             H---HHhCCCCccEEEEEeeCchhHHHHHHhcCC--CCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCC
Q 022383          199 V---YRYLPPDLQVVLISATLPHEILEMTTKFMT--DPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT  273 (298)
Q Consensus       199 i---~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~  273 (298)
                      +   ...++ ..+++++|||.++.....+...+.  ++..+. .  .....++.  +...... .+...+..++....+.
T Consensus       153 l~~l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~-~--~~~r~nl~--~~v~~~~-~~~~~l~~~l~~~~~~  225 (591)
T TIGR01389       153 LGSLAERFP-QVPRIALTATADAETRQDIRELLRLADANEFI-T--SFDRPNLR--FSVVKKN-NKQKFLLDYLKKHRGQ  225 (591)
T ss_pred             HHHHHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEe-c--CCCCCCcE--EEEEeCC-CHHHHHHHHHHhcCCC
Confidence            4   33444 456999999999887765555543  333322 1  12222332  2222223 3677788888877778


Q ss_pred             cEEEEecchhhHHHHHHHHhhhcC
Q 022383          274 QAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       274 k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ++||||+|++.|+.+++.|+..|+
T Consensus       226 ~~IIf~~sr~~~e~la~~L~~~g~  249 (591)
T TIGR01389       226 SGIIYASSRKKVEELAERLESQGI  249 (591)
T ss_pred             CEEEEECcHHHHHHHHHHHHhCCC
Confidence            999999999999999999988765

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

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.98  E-value=4.2e-30  Score=240.69  Aligned_cols=242  Identities=17%  Similarity=0.255  Sum_probs=176.1

Q ss_pred             CCCHHHHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHH
Q 022383           39 GIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (298)
Q Consensus        39 ~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~  117 (298)
                      +.+......|++ +||..++|+|.++++.+++|+|+++++|||+|||+||++|++..      ...+||++|+++|+.|+
T Consensus         8 ~~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~------~g~tlVisPl~sL~~dq   81 (607)
T PRK11057          8 NLESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL------DGLTLVVSPLISLMKDQ   81 (607)
T ss_pred             CchhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc------CCCEEEEecHHHHHHHH
Confidence            344455556655 69999999999999999999999999999999999999999864      33689999999999999


Q ss_pred             HHHHHHhhccCCceEEEEEcCCchHHHHHH---h-hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc--
Q 022383          118 EKVILAIGDFINIQAHACVGGKSVGEDIRK---L-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--  191 (298)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~--  191 (298)
                      .+.++..    ++....+.++.........   + .+..+++++||+++........+...++++|||||||++.+|+  
T Consensus        82 v~~l~~~----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~  157 (607)
T PRK11057         82 VDQLLAN----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHD  157 (607)
T ss_pred             HHHHHHc----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCc
Confidence            9988765    5677777777665543322   2 2457899999999874222223344588999999999999886  


Q ss_pred             cHHHHHHH---HHhCCCCccEEEEEeeCchhHHHHHHhc--CCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHH
Q 022383          192 FKDQIYDV---YRYLPPDLQVVLISATLPHEILEMTTKF--MTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL  266 (298)
Q Consensus       192 ~~~~i~~i---~~~~~~~~~~v~~SAT~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  266 (298)
                      |...+..+   ...+ ++.+++++|||+++.....+...  +.+|......   ...+++..  ....... +...+..+
T Consensus       158 fr~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~~---~~r~nl~~--~v~~~~~-~~~~l~~~  230 (607)
T PRK11057        158 FRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISS---FDRPNIRY--TLVEKFK-PLDQLMRY  230 (607)
T ss_pred             ccHHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEEECC---CCCCccee--eeeeccc-hHHHHHHH
Confidence            55555443   3344 47899999999988765544333  3344433321   22223322  2222222 56667777


Q ss_pred             HhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          267 YDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       267 l~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +....++++||||+|+++|+.+++.|++.|+
T Consensus       231 l~~~~~~~~IIFc~tr~~~e~la~~L~~~g~  261 (607)
T PRK11057        231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGI  261 (607)
T ss_pred             HHhcCCCCEEEEECcHHHHHHHHHHHHhCCC
Confidence            7777778999999999999999999998775

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

Probab=99.98  E-value=1.9e-31  Score=234.71  Aligned_cols=270  Identities=24%  Similarity=0.329  Sum_probs=232.9

Q ss_pred             eecccCCccccCcccC----CCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC
Q 022383           23 FETTEGVEAITSFDAM----GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS   98 (298)
Q Consensus        23 ~~~~~~~~~~~~~~~l----~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~   98 (298)
                      +.+...+.++.+|.++    ..+..+++.+...+|..|+|.|.+++|.++.+++++.|+|||+|||++|.+|++.++...
T Consensus       122 v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~  201 (593)
T KOG0344|consen  122 VDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDL  201 (593)
T ss_pred             ccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHh
Confidence            3566668888899974    689999999999999999999999999999999999999999999999999999988543


Q ss_pred             -----CCCeEEEEEcCcHHHHHHHHHHHHHhh--ccCCceEEEEEcCCchHHH-HHHhhcCCcEEEeChHHHHHHHhccC
Q 022383           99 -----SREVQALILSPTRELATQTEKVILAIG--DFINIQAHACVGGKSVGED-IRKLEHGVHVVSGTPGRVCDMIKRKT  170 (298)
Q Consensus        99 -----~~~~~~lil~p~~~l~~q~~~~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ilV~Tp~~l~~~~~~~~  170 (298)
                           ..+.+++|+.|+++|+.|++..+.++.  ...+.+...+......... .......++++|+||.++...+....
T Consensus       202 ~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~  281 (593)
T KOG0344|consen  202 SQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGK  281 (593)
T ss_pred             hcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCC
Confidence                 346799999999999999999999998  5555555554444222221 11222457999999999999888764


Q ss_pred             --ccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCC-CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCc
Q 022383          171 --LRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGI  246 (298)
Q Consensus       171 --~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  246 (298)
                        +++.++.++|+||+|++.+. .|..++..++..+. ++..+-+||||++..+++|+.....++..+.+.........+
T Consensus       282 ~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V  361 (593)
T KOG0344|consen  282 LNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETV  361 (593)
T ss_pred             ccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhh
Confidence              78999999999999999999 88888888887765 567788999999999999999999999999998888888889


Q ss_pred             eEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHH
Q 022383          247 KQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYF  292 (298)
Q Consensus       247 ~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L  292 (298)
                      .|..++|..+..|.-++.+++...-..++|||+.+.+.|..|++.|
T Consensus       362 ~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L  407 (593)
T KOG0344|consen  362 DQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEEL  407 (593)
T ss_pred             hhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHh
Confidence            9999999999989999999999887789999999999999999998

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

Probab=99.97  E-value=3.5e-30  Score=204.35  Aligned_cols=165  Identities=27%  Similarity=0.474  Sum_probs=144.0

Q ss_pred             hHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEE
Q 022383           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV  136 (298)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (298)
                      ||+|.++++.+.+|+++++.+|||+|||++|+++++..+... ...++++++|+++|++|+.+.++++....++++..++
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~   79 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLH   79 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEES
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccccccccccc
Confidence            689999999999999999999999999999999999988776 4458999999999999999999999888788999999


Q ss_pred             cCCchH-HHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCC--CCccEEEEE
Q 022383          137 GGKSVG-EDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDLQVVLIS  213 (298)
Q Consensus       137 ~~~~~~-~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~--~~~~~v~~S  213 (298)
                      ++.... .....+.++++|+|+||++|..++.....++.++++|||||+|.+..+.+...+..+.+.+.  .+.|++++|
T Consensus        80 ~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~~~~~~i~~S  159 (169)
T PF00270_consen   80 GGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRFKNIQIILLS  159 (169)
T ss_dssp             TTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTTTTSEEEEEE
T ss_pred             ccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHHhcCCCCCcEEEEe
Confidence            988765 33444556799999999999999988656778899999999999998888888888888873  368999999


Q ss_pred             eeCchhHHH
Q 022383          214 ATLPHEILE  222 (298)
Q Consensus       214 AT~~~~~~~  222 (298)
                      ||+++.++.
T Consensus       160 AT~~~~~~~  168 (169)
T PF00270_consen  160 ATLPSNVEK  168 (169)
T ss_dssp             SSSTHHHHH
T ss_pred             eCCChhHhh
Confidence            999966553

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 ....

>PRK14701 reverse gyrase; Provisional

Probab=99.97  E-value=5.2e-29  Score=249.57  Aligned_cols=244  Identities=17%  Similarity=0.187  Sum_probs=183.3

Q ss_pred             HHHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHH
Q 022383           43 DLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        43 ~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      ++.+.+++ +|| .|++.|+.+++.+++|+|++++||||+|||++++++++....   .+.+++||+||++|+.|+.+.+
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~---~g~~aLVl~PTreLa~Qi~~~l  142 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL---KGKKCYIILPTTLLVKQTVEKI  142 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh---cCCeEEEEECHHHHHHHHHHHH
Confidence            55556666 799 599999999999999999999999999999976666554422   3568999999999999999999


Q ss_pred             HHhhccC--CceEEEEEcCCchHHHH---HHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-----
Q 022383          122 LAIGDFI--NIQAHACVGGKSVGEDI---RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-----  190 (298)
Q Consensus       122 ~~~~~~~--~~~~~~~~~~~~~~~~~---~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-----  190 (298)
                      +.++...  ++++..++|+.+..++.   ..+. +.++|+|+||+++...+... . ..+++++|+||||+|+++     
T Consensus       143 ~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l-~-~~~i~~iVVDEAD~ml~~~knid  220 (1638)
T PRK14701        143 ESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM-K-HLKFDFIFVDDVDAFLKASKNID  220 (1638)
T ss_pred             HHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH-h-hCCCCEEEEECceeccccccccc
Confidence            9988765  45677888988766553   2333 35899999999988766542 2 278999999999999873     


Q ss_pred             ------ccHHHHHH----HHH----------------------hCCCCcc-EEEEEeeCchhHHHHHHhcCCCCEEEEec
Q 022383          191 ------GFKDQIYD----VYR----------------------YLPPDLQ-VVLISATLPHEILEMTTKFMTDPVKILVK  237 (298)
Q Consensus       191 ------~~~~~i~~----i~~----------------------~~~~~~~-~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  237 (298)
                            ||.+.+..    +++                      .+++..| .+++|||+++...  ...++.++..+.+.
T Consensus       221 ~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~--~~~l~~~~l~f~v~  298 (1638)
T PRK14701        221 RSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGD--RVKLYRELLGFEVG  298 (1638)
T ss_pred             hhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhH--HHHHhhcCeEEEec
Confidence                  67666653    322                      2344455 5779999986311  11234567777777


Q ss_pred             CCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhh---HHHHHHHHhhhcC
Q 022383          238 RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK---IYYSVFYFWIRWI  297 (298)
Q Consensus       238 ~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~---~~~l~~~L~~~~~  297 (298)
                      .......++.+.++..+... + ..+..+++.. +.++||||+|++.   |+.+++.|+..|+
T Consensus       299 ~~~~~lr~i~~~yi~~~~~~-k-~~L~~ll~~~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi  358 (1638)
T PRK14701        299 SGRSALRNIVDVYLNPEKII-K-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGF  358 (1638)
T ss_pred             CCCCCCCCcEEEEEECCHHH-H-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCC
Confidence            66666778888888765443 4 4677777765 4789999999886   5899999999886

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

Probab=99.97  E-value=7e-29  Score=237.07  Aligned_cols=248  Identities=19%  Similarity=0.261  Sum_probs=189.7

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      ....+..+|.+.|+..|+++|.+++..+.+|+|++|++|||||||+||++|+++++...+.. ++|+|.||++|++++.+
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a-~AL~lYPtnALa~DQ~~  133 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAE  133 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc-cEEEEechhhhHhhHHH
Confidence            34566889999999999999999999999999999999999999999999999998876555 89999999999999999


Q ss_pred             HHHHhhccCC--ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc----CccCCCccEEEechhhHhhccccH
Q 022383          120 VILAIGDFIN--IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK----TLRTRAIKLLVLDESDEMLSRGFK  193 (298)
Q Consensus       120 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~----~~~~~~l~~vViDE~h~~~~~~~~  193 (298)
                      +++++....+  +....+.|++...+....+.+.++|+++||++|..++...    ...++++++||+||+|.+ ...++
T Consensus       134 rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtY-rGv~G  212 (851)
T COG1205         134 RLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTY-RGVQG  212 (851)
T ss_pred             HHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceec-cccch
Confidence            9999988776  7888889998887777778899999999999999965442    234588999999999986 33355


Q ss_pred             HHHHHHHHhC-------CCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecC--------ccc
Q 022383          194 DQIYDVYRYL-------PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER--------EEW  258 (298)
Q Consensus       194 ~~i~~i~~~~-------~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~--------~~~  258 (298)
                      .++..+++++       +.+.|+|+.|||+.+. .++...+.+......+. .+..+.+....+..-+.        ...
T Consensus       213 S~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~v~-~~g~~~~~~~~~~~~p~~~~~~~~~r~s  290 (851)
T COG1205         213 SEVALLLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVPVD-EDGSPRGLRYFVRREPPIRELAESIRRS  290 (851)
T ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceeecc-CCCCCCCceEEEEeCCcchhhhhhcccc
Confidence            5444443333       4579999999999876 55666677766666432 22333333333333330        112


Q ss_pred             hHHHHHHHHhhC--CCCcEEEEecchhhHHHHHHH
Q 022383          259 KFDTLCDLYDTL--TITQAVIFCNTKRKIYYSVFY  291 (298)
Q Consensus       259 k~~~l~~ll~~~--~~~k~lIf~~s~~~~~~l~~~  291 (298)
                      +...+..+....  .+-++|+|+.+++.++.++..
T Consensus       291 ~~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~  325 (851)
T COG1205         291 ALAELATLAALLVRNGIQTLVFFRSRKQVELLYLS  325 (851)
T ss_pred             hHHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhc
Confidence            444444444432  446999999999999999743

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.97  E-value=4.2e-29  Score=235.58  Aligned_cols=249  Identities=17%  Similarity=0.192  Sum_probs=184.4

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHHHHHHhh-cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHH
Q 022383           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (298)
Q Consensus        39 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~-~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~  117 (298)
                      .+.+.+...++..++.++.+.|+.++.... +++|+++++|||+|||+.+++.+++.+...  +.+++|+||+++|+.+.
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~Ek   92 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAEEK   92 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHH
Confidence            477888888888999888888888887754 569999999999999999999999998875  45899999999999999


Q ss_pred             HHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHH
Q 022383          118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (298)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~  197 (298)
                      ++.++ ....+|+++...+|+......   ...+++|+|+|||++..++++.......+++|||||+|.+.+...+..++
T Consensus        93 ~~~~~-~~~~~GirV~~~TgD~~~~~~---~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE  168 (766)
T COG1204          93 YEEFS-RLEELGIRVGISTGDYDLDDE---RLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLE  168 (766)
T ss_pred             HHHhh-hHHhcCCEEEEecCCcccchh---hhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceeh
Confidence            99999 445669999999999775442   22458999999999999999987788999999999999998876666666


Q ss_pred             HHHHhCC---CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccC-cCCceEEEEEecCcc-----chHH-HHHHHH
Q 022383          198 DVYRYLP---PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELT-LEGIKQFFVAVEREE-----WKFD-TLCDLY  267 (298)
Q Consensus       198 ~i~~~~~---~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~~~~~~~~~~~-----~k~~-~l~~ll  267 (298)
                      .++.+.+   ...|++++|||+|+. .++..+...++..-...+.... .....+.+.......     ...+ .+..++
T Consensus       169 ~iv~r~~~~~~~~rivgLSATlpN~-~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~  247 (766)
T COG1204         169 SIVARMRRLNELIRIVGLSATLPNA-EEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVL  247 (766)
T ss_pred             hHHHHHHhhCcceEEEEEeeecCCH-HHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHH
Confidence            6665554   348999999999986 4445444434332111111111 111222222222111     0122 233333


Q ss_pred             hh-CCCCcEEEEecchhhHHHHHHHHhh
Q 022383          268 DT-LTITQAVIFCNTKRKIYYSVFYFWI  294 (298)
Q Consensus       268 ~~-~~~~k~lIf~~s~~~~~~l~~~L~~  294 (298)
                      .. ..++++||||+|++.+...|+.|++
T Consensus       248 ~~~~~~~qvLvFv~sR~~a~~~A~~l~~  275 (766)
T COG1204         248 ESLAEGGQVLVFVHSRKEAEKTAKKLRI  275 (766)
T ss_pred             HHHhcCCeEEEEEecCchHHHHHHHHHH
Confidence            32 3457999999999999999999984

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

Probab=99.96  E-value=9.2e-29  Score=217.06  Aligned_cols=257  Identities=18%  Similarity=0.198  Sum_probs=204.1

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ...++|.++++....|+..|++.+.|+|.-++.. ++.|+|.+++++|+||||+...++-+..+...  +.+.+|++|..
T Consensus       194 ~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~--g~KmlfLvPLV  271 (830)
T COG1202         194 VPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSG--GKKMLFLVPLV  271 (830)
T ss_pred             ccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhC--CCeEEEEehhH
Confidence            5778999999999999999999999999999987 88999999999999999999998888887765  55899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHH----HHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDI----RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      +||+|-++.|+.--..+++.+..-.|........    ..-..+.||||+|-+-+..+++.+ .++.++..|||||+|.+
T Consensus       272 ALANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL  350 (830)
T COG1202         272 ALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTL  350 (830)
T ss_pred             HhhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeeeeeec
Confidence            9999999999876677788887777643222111    111245799999999999999987 77899999999999998


Q ss_pred             hccccH---HHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHH
Q 022383          188 LSRGFK---DQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLC  264 (298)
Q Consensus       188 ~~~~~~---~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  264 (298)
                      -+...+   +-+..-++++-+..|+|.+|||+.+. +.+.+.+..+++.+.     ..+..++...+++.++..|.+.+.
T Consensus       351 ~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp-~elA~~l~a~lV~y~-----~RPVplErHlvf~~~e~eK~~ii~  424 (830)
T COG1202         351 EDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNP-EELAKKLGAKLVLYD-----ERPVPLERHLVFARNESEKWDIIA  424 (830)
T ss_pred             cchhcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHhCCeeEeec-----CCCCChhHeeeeecCchHHHHHHH
Confidence            765433   33444455666789999999999776 555655544444332     334456777778887766999888


Q ss_pred             HHHhhC------C--CCcEEEEecchhhHHHHHHHHhhhcCC
Q 022383          265 DLYDTL------T--ITQAVIFCNTKRKIYYSVFYFWIRWIG  298 (298)
Q Consensus       265 ~ll~~~------~--~~k~lIf~~s~~~~~~l~~~L~~~~~~  298 (298)
                      .+.+..      +  .++||||.+|++.|+.+|.+|..+|+.
T Consensus       425 ~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~  466 (830)
T COG1202         425 RLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLK  466 (830)
T ss_pred             HHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcc
Confidence            887532      1  359999999999999999999988863

>TIGR01054 rgy reverse gyrase

Probab=99.96  E-value=6e-28  Score=237.44  Aligned_cols=242  Identities=17%  Similarity=0.231  Sum_probs=176.7

Q ss_pred             HHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH
Q 022383           43 DLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (298)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~  122 (298)
                      +..+.+.+.....|+++|+.+++.++.|+|++++||||+|||. |.+++...+..  .+++++||+||++|+.|+.+.++
T Consensus        66 ~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l~  142 (1171)
T TIGR01054        66 EFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK--KGKRCYIILPTTLLVIQVAEKIS  142 (1171)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeCHHHHHHHHHHHHH
Confidence            4555555544457999999999999999999999999999996 66666655543  26789999999999999999999


Q ss_pred             HhhccCCceEE---EEEcCCchHHHH---HHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc------
Q 022383          123 AIGDFINIQAH---ACVGGKSVGEDI---RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS------  189 (298)
Q Consensus       123 ~~~~~~~~~~~---~~~~~~~~~~~~---~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~------  189 (298)
                      ++....++...   .++|+.+..++.   ..+. ++++|+|+||++|...+..-  .. +++++|+||||.|++      
T Consensus       143 ~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l--~~-~~~~iVvDEaD~~L~~~k~vd  219 (1171)
T TIGR01054       143 SLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDEL--GP-KFDFIFVDDVDALLKASKNVD  219 (1171)
T ss_pred             HHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHh--cC-CCCEEEEeChHhhhhccccHH
Confidence            99887666543   467887765432   2333 45899999999998876641  12 899999999999987      


Q ss_pred             -----cccHHH-HHHHH----------------------HhCCCCcc--EEEEEee-CchhHHHHHHhcCCCCEEEEecC
Q 022383          190 -----RGFKDQ-IYDVY----------------------RYLPPDLQ--VVLISAT-LPHEILEMTTKFMTDPVKILVKR  238 (298)
Q Consensus       190 -----~~~~~~-i~~i~----------------------~~~~~~~~--~v~~SAT-~~~~~~~~~~~~~~~~~~~~~~~  238 (298)
                           .||... +..++                      +.+++..|  ++++||| .|.....   .++.++..+.+..
T Consensus       220 ~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~~v~~  296 (1171)
T TIGR01054       220 KLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGFEVGG  296 (1171)
T ss_pred             HHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccceEecC
Confidence                 356543 44432                      23444455  5678999 4554432   2344555566665


Q ss_pred             CccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecch---hhHHHHHHHHhhhcC
Q 022383          239 DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTK---RKIYYSVFYFWIRWI  297 (298)
Q Consensus       239 ~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~---~~~~~l~~~L~~~~~  297 (298)
                      ......++.+.+...+.   +...+..+++.. +.++||||+++   +.|+.+++.|++.|+
T Consensus       297 ~~~~~r~I~~~~~~~~~---~~~~L~~ll~~l-~~~~IVFv~t~~~~~~a~~l~~~L~~~g~  354 (1171)
T TIGR01054       297 GSDTLRNVVDVYVEDED---LKETLLEIVKKL-GTGGIVYVSIDYGKEKAEEIAEFLENHGV  354 (1171)
T ss_pred             ccccccceEEEEEeccc---HHHHHHHHHHHc-CCCEEEEEeccccHHHHHHHHHHHHhCCc
Confidence            55566778887765442   244566777654 36899999999   999999999998876

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.96  E-value=1.3e-27  Score=234.43  Aligned_cols=237  Identities=17%  Similarity=0.160  Sum_probs=178.9

Q ss_pred             CHHHHHHHHHCCCCCChHHHHHHHHHhhcC------CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHH
Q 022383           41 KDDLLRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (298)
Q Consensus        41 ~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~  114 (298)
                      ..+..+....+.| .|++.|.++++.+..+      .|++++|+||+|||.+|+.+++..+..   +.+++|++||++|+
T Consensus       587 ~~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~---g~qvlvLvPT~eLA  662 (1147)
T PRK10689        587 REQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN---HKQVAVLVPTTLLA  662 (1147)
T ss_pred             HHHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHH
Confidence            3455666677888 5999999999999876      799999999999999999888777643   56899999999999


Q ss_pred             HHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          115 TQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       115 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      .|+++.+++.....++++..++|+.+..++...+.    +.++|+|+||+.+    . ..+.+++++++||||+|++   
T Consensus       663 ~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~-~~v~~~~L~lLVIDEahrf---  734 (1147)
T PRK10689        663 QQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----Q-SDVKWKDLGLLIVDEEHRF---  734 (1147)
T ss_pred             HHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----h-CCCCHhhCCEEEEechhhc---
Confidence            99999999877666788888888877666554332    4689999999643    2 3456789999999999997   


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  270 (298)
                      ++.  ....++.++.++|++++|||+.+....+....+.++..+...+..  ...+.+.+........+...+..+.   
T Consensus       735 G~~--~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~--r~~v~~~~~~~~~~~~k~~il~el~---  807 (1147)
T PRK10689        735 GVR--HKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPAR--RLAVKTFVREYDSLVVREAILREIL---  807 (1147)
T ss_pred             chh--HHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCC--CCCceEEEEecCcHHHHHHHHHHHh---
Confidence            222  234456777899999999999887777777777788777654332  2335555444332221223333332   


Q ss_pred             CCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          271 TITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       271 ~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      .+++++||||+++.++.+++.|+...
T Consensus       808 r~gqv~vf~n~i~~ie~la~~L~~~~  833 (1147)
T PRK10689        808 RGGQVYYLYNDVENIQKAAERLAELV  833 (1147)
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhC
Confidence            35799999999999999999998764

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.96  E-value=1.5e-27  Score=229.37  Aligned_cols=237  Identities=18%  Similarity=0.147  Sum_probs=173.8

Q ss_pred             CCHHHHHHHHH-CCCCCChHHHHHHHHHhhcC------CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           40 IKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        40 l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~------~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      .+..+...+.+ ++|+ |++.|.++++.+.++      .|.+++||||+|||.+|+.+++..+..   +.+++|++||++
T Consensus       436 ~~~~~~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~---g~qvlvLvPT~~  511 (926)
T TIGR00580       436 PDLEWQQEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD---GKQVAVLVPTTL  511 (926)
T ss_pred             CCHHHHHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh---CCeEEEEeCcHH
Confidence            34455555544 6785 999999999999874      799999999999999999999988765   468999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH---Hhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---KLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      |+.|+++.++++....++++..++|+.+..+...   .+. +.++|+||||..    + ...+.+++++++||||+|++.
T Consensus       512 LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~l----l-~~~v~f~~L~llVIDEahrfg  586 (926)
T TIGR00580       512 LAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKL----L-QKDVKFKDLGLLIIDEEQRFG  586 (926)
T ss_pred             HHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHH----h-hCCCCcccCCEEEeecccccc
Confidence            9999999999988888889988888876544332   333 358999999942    2 345678999999999999852


Q ss_pred             ccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh
Q 022383          189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (298)
Q Consensus       189 ~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  268 (298)
                           ......++.++.++|+++||||+.+....+......++..+...+..  ...+..++....... ....+..-  
T Consensus       587 -----v~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~--R~~V~t~v~~~~~~~-i~~~i~~e--  656 (926)
T TIGR00580       587 -----VKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPED--RLPVRTFVMEYDPEL-VREAIRRE--  656 (926)
T ss_pred             -----hhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCC--ccceEEEEEecCHHH-HHHHHHHH--
Confidence                 23345566677789999999998776666555555666666554322  223454444322111 11122221  


Q ss_pred             hCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          269 TLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       269 ~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ...+++++||||+++.++.+++.|+..
T Consensus       657 l~~g~qv~if~n~i~~~e~l~~~L~~~  683 (926)
T TIGR00580       657 LLRGGQVFYVHNRIESIEKLATQLREL  683 (926)
T ss_pred             HHcCCeEEEEECCcHHHHHHHHHHHHh
Confidence            224579999999999999999999875

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.96  E-value=4.2e-27  Score=232.46  Aligned_cols=218  Identities=16%  Similarity=0.174  Sum_probs=154.5

Q ss_pred             EEcCCCCchHHHHHHHHHHhhccC----------CCCeEEEEEcCcHHHHHHHHHHHHHhh------------ccCCceE
Q 022383           75 AQAQSGTGKTSMIALTVCQTVDTS----------SREVQALILSPTRELATQTEKVILAIG------------DFINIQA  132 (298)
Q Consensus        75 i~~pTG~GKT~~~~~~~~~~~~~~----------~~~~~~lil~p~~~l~~q~~~~~~~~~------------~~~~~~~  132 (298)
                      |++|||||||+||.+|+++.+...          ..+.++|||+|+++|++|+.+.++...            ...++++
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            579999999999999999987542          235799999999999999999887521            1247889


Q ss_pred             EEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc-CccCCCccEEEechhhHhhcccc----HHHHHHHHHhCCCCc
Q 022383          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDESDEMLSRGF----KDQIYDVYRYLPPDL  207 (298)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~-~~~~~~l~~vViDE~h~~~~~~~----~~~i~~i~~~~~~~~  207 (298)
                      ...+|+++..++.+.+.+.++|+|+||++|..++.++ ...++++++|||||+|.+.+..+    ...+..+...++.+.
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~~  160 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSA  160 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCCC
Confidence            9999999988887777788999999999999987653 34689999999999999986543    345566666667789


Q ss_pred             cEEEEEeeCchhHHHHHHhcCC-CCEEEEecCCccCcCCceEEEEEecCcc-------------------chH-HHHHHH
Q 022383          208 QVVLISATLPHEILEMTTKFMT-DPVKILVKRDELTLEGIKQFFVAVEREE-------------------WKF-DTLCDL  266 (298)
Q Consensus       208 ~~v~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------------------~k~-~~l~~l  266 (298)
                      |+|++|||+++. +.....+.. .+..+.. ........+. .++......                   ... .....+
T Consensus       161 QrIgLSATI~n~-eevA~~L~g~~pv~Iv~-~~~~r~~~l~-v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~i  237 (1490)
T PRK09751        161 QRIGLSATVRSA-SDVAAFLGGDRPVTVVN-PPAMRHPQIR-IVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETGI  237 (1490)
T ss_pred             eEEEEEeeCCCH-HHHHHHhcCCCCEEEEC-CCCCcccceE-EEEecCchhhccccccccccccchhhhhhhhHHHHHHH
Confidence            999999999873 444443333 3555432 2222222222 222221100                   000 011122


Q ss_pred             Hhh-CCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          267 YDT-LTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       267 l~~-~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      +.. ....++||||||++.|+.++..|++.
T Consensus       238 l~~i~~~~stLVFvNSR~~AE~La~~L~~~  267 (1490)
T PRK09751        238 LDEVLRHRSTIVFTNSRGLAEKLTARLNEL  267 (1490)
T ss_pred             HHHHhcCCCEEEECCCHHHHHHHHHHHHHh
Confidence            322 23479999999999999999999764

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.95  E-value=3.5e-26  Score=216.62  Aligned_cols=234  Identities=19%  Similarity=0.175  Sum_probs=162.3

Q ss_pred             HHHHHHCCCCCChHHHHHHHHHhhcC------CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           45 LRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      ......++|. |++.|.++++.+.++      .+.+++||||||||++|++|++..+..   +.+++|++||++|+.|++
T Consensus       252 ~~~~~~l~f~-lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~---g~q~lilaPT~~LA~Q~~  327 (681)
T PRK10917        252 KKFLASLPFE-LTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA---GYQAALMAPTEILAEQHY  327 (681)
T ss_pred             HHHHHhCCCC-CCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEeccHHHHHHHH
Confidence            3344556775 999999999999876      489999999999999999999988754   668999999999999999


Q ss_pred             HHHHHhhccCCceEEEEEcCCchHHHH---HHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHH
Q 022383          119 KVILAIGDFINIQAHACVGGKSVGEDI---RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD  194 (298)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~  194 (298)
                      +.++++....++++..++|+.+..+..   ..+. +.++|+||||+.+..     .+.+++++++|+||+|++...    
T Consensus       328 ~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~~----  398 (681)
T PRK10917        328 ENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGVE----  398 (681)
T ss_pred             HHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhHH----
Confidence            999999988899999999998764433   3333 359999999977642     456789999999999996322    


Q ss_pred             HHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCc
Q 022383          195 QIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ  274 (298)
Q Consensus       195 ~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k  274 (298)
                       .+..+......+++++||||+.+....+......+...+...+  .....+...+.........++.+...+  ..+.+
T Consensus       399 -qr~~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~p--~~r~~i~~~~~~~~~~~~~~~~i~~~~--~~g~q  473 (681)
T PRK10917        399 -QRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELP--PGRKPITTVVIPDSRRDEVYERIREEI--AKGRQ  473 (681)
T ss_pred             -HHHHHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecCC--CCCCCcEEEEeCcccHHHHHHHHHHHH--HcCCc
Confidence             2233444455789999999987655444332222333222211  112234444443222221122222222  34579


Q ss_pred             EEEEecchh--------hHHHHHHHHhhhc
Q 022383          275 AVIFCNTKR--------KIYYSVFYFWIRW  296 (298)
Q Consensus       275 ~lIf~~s~~--------~~~~l~~~L~~~~  296 (298)
                      ++|||+.++        .++.+++.|+..+
T Consensus       474 ~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~  503 (681)
T PRK10917        474 AYVVCPLIEESEKLDLQSAEETYEELQEAF  503 (681)
T ss_pred             EEEEEcccccccchhHHHHHHHHHHHHHHC
Confidence            999999654        4567777777653

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.95  E-value=4.6e-26  Score=200.70  Aligned_cols=230  Identities=13%  Similarity=0.094  Sum_probs=155.2

Q ss_pred             HHHHHHHHhhcCCc--EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc----CCceE
Q 022383           59 IQQRAVMPIIKGRD--VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF----INIQA  132 (298)
Q Consensus        59 ~Q~~~~~~~~~~~~--~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~----~~~~~  132 (298)
                      +|.++++.+.++.+  +++++|||+|||.+|++|++..      ..+++|++|+++|++|+.+.++++...    .+..+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v   74 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG------ENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            59999999998864  7889999999999999998852      336899999999999999999887633    24556


Q ss_pred             EEEEcCCchH--HHH------------------HHhhcCCcEEEeChHHHHHHHhcc----C-c---cCCCccEEEechh
Q 022383          133 HACVGGKSVG--EDI------------------RKLEHGVHVVSGTPGRVCDMIKRK----T-L---RTRAIKLLVLDES  184 (298)
Q Consensus       133 ~~~~~~~~~~--~~~------------------~~~~~~~~ilV~Tp~~l~~~~~~~----~-~---~~~~l~~vViDE~  184 (298)
                      ..+.|.+..+  ...                  ......+.|+++||+.+..+++..    . .   .+.++++|||||+
T Consensus        75 ~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~  154 (357)
T TIGR03158        75 LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEF  154 (357)
T ss_pred             EEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecc
Confidence            6666653222  000                  011235788999999998776541    1 1   2478999999999


Q ss_pred             hHhhcccc-----HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhc--CCCCEEEEecC-----C-------------
Q 022383          185 DEMLSRGF-----KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKF--MTDPVKILVKR-----D-------------  239 (298)
Q Consensus       185 h~~~~~~~-----~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~--~~~~~~~~~~~-----~-------------  239 (298)
                      |.+..+..     ......+++......+++++|||+++.+...+...  ++.+.......     +             
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~  234 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSF  234 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhcccccccc
Confidence            99864431     12333444444445799999999999877777664  45554332222     0             


Q ss_pred             ccCcCCceEEEEEecCccchHHHHHHHH-------hhCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          240 ELTLEGIKQFFVAVEREEWKFDTLCDLY-------DTLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       240 ~~~~~~i~~~~~~~~~~~~k~~~l~~ll-------~~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      ....+.+++.+.. .. ..+...+..++       +..+++++||||||++.|+.+++.|+..+
T Consensus       235 ~~~~~~i~~~~~~-~~-~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~  296 (357)
T TIGR03158       235 RPVLPPVELELIP-AP-DFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQG  296 (357)
T ss_pred             ceeccceEEEEEe-CC-chhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhC
Confidence            0011245555554 22 22433333222       22356799999999999999999998754

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.

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

Probab=99.95  E-value=2.7e-26  Score=207.48  Aligned_cols=238  Identities=18%  Similarity=0.199  Sum_probs=176.1

Q ss_pred             HHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           46 RGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        46 ~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      ..|+. +||..+++-|.++|..+++|+|+++..|||+||++||.+|++-.      ..-+|||+|..+|..++.+.++..
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~------~G~TLVVSPLiSLM~DQV~~l~~~   80 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL------EGLTLVVSPLISLMKDQVDQLEAA   80 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc------CCCEEEECchHHHHHHHHHHHHHc
Confidence            44555 69999999999999999999999999999999999999999775      226999999999999999988876


Q ss_pred             hccCCceEEEEEcCCchHHHHHHh---h-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc--cHHHHHH
Q 022383          125 GDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYD  198 (298)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~--~~~~i~~  198 (298)
                          |+.+..+++..+..+....+   . +..+++..+||++..---...+.-..+.++||||||++.+||  |++.+..
T Consensus        81 ----Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~  156 (590)
T COG0514          81 ----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRR  156 (590)
T ss_pred             ----CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHH
Confidence                68888888886666554332   2 447999999999876432223335688999999999999997  8888776


Q ss_pred             HHHhCC--CCccEEEEEeeCchhHHHHHHhcCC--CCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCc
Q 022383          199 VYRYLP--PDLQVVLISATLPHEILEMTTKFMT--DPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ  274 (298)
Q Consensus       199 i~~~~~--~~~~~v~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k  274 (298)
                      +.....  ++++++.+|||-++.+..-+...+.  .+..+..   ...++++...+........++..+.. ......+.
T Consensus       157 lg~l~~~~~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~---sfdRpNi~~~v~~~~~~~~q~~fi~~-~~~~~~~~  232 (590)
T COG0514         157 LGRLRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRG---SFDRPNLALKVVEKGEPSDQLAFLAT-VLPQLSKS  232 (590)
T ss_pred             HHHHHhhCCCCCEEEEeCCCChHHHHHHHHHhcCCCcceEEe---cCCCchhhhhhhhcccHHHHHHHHHh-hccccCCC
Confidence            644432  3789999999999887776666544  3323322   23334444443333322223332222 12444567


Q ss_pred             EEEEecchhhHHHHHHHHhhhcC
Q 022383          275 AVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       275 ~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .||||.|++.++.++++|+..|+
T Consensus       233 GIIYc~sRk~~E~ia~~L~~~g~  255 (590)
T COG0514         233 GIIYCLTRKKVEELAEWLRKNGI  255 (590)
T ss_pred             eEEEEeeHHhHHHHHHHHHHCCC
Confidence            99999999999999999998875

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

Probab=99.95  E-value=3e-26  Score=212.89  Aligned_cols=240  Identities=14%  Similarity=0.215  Sum_probs=179.8

Q ss_pred             HCCCCCChHHHHHHHHHhh-cCCcEEEEcCCCCchHHHHHHHHHHhhcc-------CCCCeEEEEEcCcHHHHHHHHHHH
Q 022383           50 QYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDT-------SSREVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~-~~~~~li~~pTG~GKT~~~~~~~~~~~~~-------~~~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      -++|..++..|++++|.+. +..|.+||||||+|||..|++.+++.+..       ...+.++|||+|+++||.++.+.+
T Consensus       105 ~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~  184 (1230)
T KOG0952|consen  105 FFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKF  184 (1230)
T ss_pred             cccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHH
Confidence            3578899999999999876 56799999999999999999999998864       234579999999999999999999


Q ss_pred             HHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccC---ccCCCccEEEechhhHhhccccHHHHHH
Q 022383          122 LAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT---LRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (298)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~---~~~~~l~~vViDE~h~~~~~~~~~~i~~  198 (298)
                      .+-....|+.+..++|++......   ...++|+|+|||+..-.-+...   ..++.+.+|||||+|.+.++ .++.++.
T Consensus       185 ~kkl~~~gi~v~ELTGD~ql~~te---i~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~-RGpvlEt  260 (1230)
T KOG0952|consen  185 SKKLAPLGISVRELTGDTQLTKTE---IADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDD-RGPVLET  260 (1230)
T ss_pred             hhhcccccceEEEecCcchhhHHH---HHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCc-ccchHHH
Confidence            887777799999999998765432   2348999999999887666532   23588999999999998655 4555555


Q ss_pred             HHHhC-------CCCccEEEEEeeCchhHHHHHHhcCCC-CEEEEecCCccCcCCceEEEEEecCc---c-------chH
Q 022383          199 VYRYL-------PPDLQVVLISATLPHEILEMTTKFMTD-PVKILVKRDELTLEGIKQFFVAVERE---E-------WKF  260 (298)
Q Consensus       199 i~~~~-------~~~~~~v~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~i~~~~~~~~~~---~-------~k~  260 (298)
                      ++.+.       ....++|++|||+|+- ++...++.-+ +..+........+..+.+.++-++..   .       -.+
T Consensus       261 iVaRtlr~vessqs~IRivgLSATlPN~-eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~~~  339 (1230)
T KOG0952|consen  261 IVARTLRLVESSQSMIRIVGLSATLPNY-EDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEVCY  339 (1230)
T ss_pred             HHHHHHHHHHhhhhheEEEEeeccCCCH-HHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHHHH
Confidence            54433       3578999999999985 4444433333 33444444455666677777766654   1       112


Q ss_pred             HHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          261 DTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       261 ~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      +.+.+++.  .+.+++|||.++.++...|+.|.+.+
T Consensus       340 ~kv~e~~~--~g~qVlvFvhsR~~Ti~tA~~l~~~a  373 (1230)
T KOG0952|consen  340 DKVVEFLQ--EGHQVLVFVHSRNETIRTAKKLRERA  373 (1230)
T ss_pred             HHHHHHHH--cCCeEEEEEecChHHHHHHHHHHHHH
Confidence            33333333  34699999999999999999998764

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.94  E-value=5.8e-25  Score=206.96  Aligned_cols=234  Identities=18%  Similarity=0.172  Sum_probs=159.9

Q ss_pred             HHHHHHHHCCCCCChHHHHHHHHHhhcC------CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHH
Q 022383           43 DLLRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ  116 (298)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q  116 (298)
                      .+...+...+| .|++.|+++++.+.++      .+.+++||||||||.+|+++++..+..   +.+++|++||++|+.|
T Consensus       224 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~---g~qvlilaPT~~LA~Q  299 (630)
T TIGR00643       224 LLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA---GYQVALMAPTEILAEQ  299 (630)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEECCHHHHHHH
Confidence            44556677888 5999999999999865      268999999999999999999988764   5689999999999999


Q ss_pred             HHHHHHHhhccCCceEEEEEcCCchHHHH---HHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc
Q 022383          117 TEKVILAIGDFINIQAHACVGGKSVGEDI---RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~  192 (298)
                      +++.++++....++++..++|+....+..   ..+. +.++|+|+||+.+..     .+.++++++|||||+|++.... 
T Consensus       300 ~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~q-  373 (630)
T TIGR00643       300 HYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVEQ-  373 (630)
T ss_pred             HHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHHH-
Confidence            99999999888899999999998765533   2332 458999999987653     4567899999999999863221 


Q ss_pred             HHHHHHHHHhCC--CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh-h
Q 022383          193 KDQIYDVYRYLP--PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD-T  269 (298)
Q Consensus       193 ~~~i~~i~~~~~--~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~-~  269 (298)
                      .   ..+.....  ..+++++||||+.+....+......+...+...+  .....+...+...  .. + ..+...+. .
T Consensus       374 r---~~l~~~~~~~~~~~~l~~SATp~prtl~l~~~~~l~~~~i~~~p--~~r~~i~~~~~~~--~~-~-~~~~~~i~~~  444 (630)
T TIGR00643       374 R---KKLREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELP--PGRKPITTVLIKH--DE-K-DIVYEFIEEE  444 (630)
T ss_pred             H---HHHHHhcccCCCCCEEEEeCCCCcHHHHHHhcCCcceeeeccCC--CCCCceEEEEeCc--ch-H-HHHHHHHHHH
Confidence            1   12223322  2688999999986654433221111111111111  1112233333322  22 2 23333333 2


Q ss_pred             -CCCCcEEEEecch--------hhHHHHHHHHhhh
Q 022383          270 -LTITQAVIFCNTK--------RKIYYSVFYFWIR  295 (298)
Q Consensus       270 -~~~~k~lIf~~s~--------~~~~~l~~~L~~~  295 (298)
                       ..+.+++|||+..        ..++.+++.|.+.
T Consensus       445 l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~  479 (630)
T TIGR00643       445 IAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKA  479 (630)
T ss_pred             HHhCCcEEEEEccccccccchHHHHHHHHHHHHhh
Confidence             3457999999876        4566777777654

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.94  E-value=5.7e-25  Score=205.11  Aligned_cols=226  Identities=19%  Similarity=0.143  Sum_probs=159.8

Q ss_pred             hHHHHHHHHHhhcCCcEEEEcCCCCchHHH---------HHHHHHHhhc---cCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSM---------IALTVCQTVD---TSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~---------~~~~~~~~~~---~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      ...|.++++.+.+|++++++|+||+|||.+         |++|.+..+.   ....+.++++++|+++|+.|+...+.+.
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~  245 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKS  245 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHH
Confidence            347889999999999999999999999987         4455555442   1334568999999999999999988765


Q ss_pred             hcc---CCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHH
Q 022383          125 GDF---INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR  201 (298)
Q Consensus       125 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~  201 (298)
                      ...   .+.++...+|+... ..........+++|+|+..       ....++++++||+||+|.+...+  +.+..+++
T Consensus       246 vg~~~~~g~~v~v~~Gg~~~-~~~~t~~k~~~Ilv~T~~L-------~l~~L~~v~~VVIDEaHEr~~~~--DllL~llk  315 (675)
T PHA02653        246 LGFDEIDGSPISLKYGSIPD-ELINTNPKPYGLVFSTHKL-------TLNKLFDYGTVIIDEVHEHDQIG--DIIIAVAR  315 (675)
T ss_pred             hCccccCCceEEEEECCcch-HHhhcccCCCCEEEEeCcc-------cccccccCCEEEccccccCccch--hHHHHHHH
Confidence            433   35677888998763 2222222367999999742       12357889999999999985553  55555665


Q ss_pred             hCC-CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCc---------cchHHHHHHHHhh--
Q 022383          202 YLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE---------EWKFDTLCDLYDT--  269 (298)
Q Consensus       202 ~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~---------~~k~~~l~~ll~~--  269 (298)
                      ... ...|+++||||++.++..+ ..++.+|..+.+.  ......+++.+......         ..+...+..+...  
T Consensus       316 ~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~--grt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~  392 (675)
T PHA02653        316 KHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIP--GGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTP  392 (675)
T ss_pred             HhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeC--CCcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhc
Confidence            443 3458999999999887766 5678888877764  23345677777644311         1122223333222  


Q ss_pred             CCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          270 LTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       270 ~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ..++++||||+++.+++.+++.|++.
T Consensus       393 ~~~g~iLVFlpg~~ei~~l~~~L~~~  418 (675)
T PHA02653        393 PKGSSGIVFVASVSQCEEYKKYLEKR  418 (675)
T ss_pred             ccCCcEEEEECcHHHHHHHHHHHHhh
Confidence            23468999999999999999999876

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.94  E-value=2.1e-25  Score=197.84  Aligned_cols=220  Identities=17%  Similarity=0.093  Sum_probs=143.5

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchH---------
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVG---------  142 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---------  142 (298)
                      ++++++|||+|||++|+.+++..+.. ..+.+++|++|+++|+.|+.++++.+...   .+...+++....         
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~-~~~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~~~~~~   76 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKS-QKADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKEMGDSE   76 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhh-CCCCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhccCCch
Confidence            58999999999999999999988654 34568999999999999999999887421   334444432210         


Q ss_pred             --HHH-HHh------hcCCcEEEeChHHHHHHHhccC----ccC--CCccEEEechhhHhhccccHHHHHHHHHhCC-CC
Q 022383          143 --EDI-RKL------EHGVHVVSGTPGRVCDMIKRKT----LRT--RAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PD  206 (298)
Q Consensus       143 --~~~-~~~------~~~~~ilV~Tp~~l~~~~~~~~----~~~--~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-~~  206 (298)
                        ... ...      ....+|+|+||+++...+..+.    ..+  -..++|||||+|.+.+.++.. +..+++.+. .+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l~~l~~~~  155 (358)
T TIGR01587        77 EFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVLEVLKDND  155 (358)
T ss_pred             hHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHHHHHHHcC
Confidence              000 001      1235799999999988765421    111  233799999999997765433 555555443 47


Q ss_pred             ccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEe-cCccchHHHHHHHHhh-CCCCcEEEEecchhh
Q 022383          207 LQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAV-EREEWKFDTLCDLYDT-LTITQAVIFCNTKRK  284 (298)
Q Consensus       207 ~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~-~~~~~k~~~l~~ll~~-~~~~k~lIf~~s~~~  284 (298)
                      .|++++|||+++.+..+.......+........... ....+.+..+ .....+...+..+++. ..++++||||||++.
T Consensus       156 ~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~  234 (358)
T TIGR01587       156 VPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEER-RFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDR  234 (358)
T ss_pred             CCEEEEecCchHHHHHHHhcCCCcccccCCCCcccc-ccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHH
Confidence            899999999998877776654332211111111100 0112222222 2222356666666654 345799999999999


Q ss_pred             HHHHHHHHhhhcC
Q 022383          285 IYYSVFYFWIRWI  297 (298)
Q Consensus       285 ~~~l~~~L~~~~~  297 (298)
                      |+.+++.|++.++
T Consensus       235 ~~~~~~~L~~~~~  247 (358)
T TIGR01587       235 AQEFYQQLKENAP  247 (358)
T ss_pred             HHHHHHHHHhhcC
Confidence            9999999988765

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.

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

Probab=99.93  E-value=2.6e-25  Score=189.62  Aligned_cols=196  Identities=27%  Similarity=0.371  Sum_probs=151.8

Q ss_pred             eEEEEEcCcHHHHHHHHHHHHHhhc---cCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccE
Q 022383          102 VQALILSPTRELATQTEKVILAIGD---FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (298)
Q Consensus       102 ~~~lil~p~~~l~~q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~  178 (298)
                      +.++|+-|+++|++|+.+.++++..   ...++..++.||.....+.+.+.++.+|+|+||+++..++..+.+.+.++.+
T Consensus       287 p~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crF  366 (725)
T KOG0349|consen  287 PEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRF  366 (725)
T ss_pred             cceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEE
Confidence            5699999999999999997766543   3356667888888888899999999999999999999999999999999999


Q ss_pred             EEechhhHhhccccHHHHHHHHHhCC------CCccEEEEEeeCch-hHHHHHHhcCCCCEEEEecCCccCcCCceEEEE
Q 022383          179 LVLDESDEMLSRGFKDQIYDVYRYLP------PDLQVVLISATLPH-EILEMTTKFMTDPVKILVKRDELTLEGIKQFFV  251 (298)
Q Consensus       179 vViDE~h~~~~~~~~~~i~~i~~~~~------~~~~~v~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  251 (298)
                      +|+||+|.++..+|.+.|.++...+|      ...|.+++|||+.. ++.....+.+.-|.++....++..+..+.+.+.
T Consensus       367 lvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHhvv~  446 (725)
T KOG0349|consen  367 LVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHVVK  446 (725)
T ss_pred             EEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhcccee
Confidence            99999999999999999999988887      36899999999853 334444455666777776655555555555544


Q ss_pred             EecCcc-----------------------------chHHHHHHH---------HhhCCCCcEEEEecchhhHHHHHHHHh
Q 022383          252 AVEREE-----------------------------WKFDTLCDL---------YDTLTITQAVIFCNTKRKIYYSVFYFW  293 (298)
Q Consensus       252 ~~~~~~-----------------------------~k~~~l~~l---------l~~~~~~k~lIf~~s~~~~~~l~~~L~  293 (298)
                      .+.+..                             ........+         ++.+...+.||||.|+.+|..+-.+++
T Consensus       447 lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~~~  526 (725)
T KOG0349|consen  447 LVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMMN  526 (725)
T ss_pred             ecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHHHH
Confidence            443321                             111122222         334456799999999999999999999


Q ss_pred             hhcC
Q 022383          294 IRWI  297 (298)
Q Consensus       294 ~~~~  297 (298)
                      ++|-
T Consensus       527 qkgg  530 (725)
T KOG0349|consen  527 QKGG  530 (725)
T ss_pred             HcCC
Confidence            8873

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.92  E-value=4.6e-24  Score=196.10  Aligned_cols=151  Identities=17%  Similarity=0.133  Sum_probs=114.9

Q ss_pred             CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceE
Q 022383           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  132 (298)
                      ...|+++|.++++.++.+++.++++|||+|||+++...+...+..  ...++|||+|+++|+.|+.+.++++.......+
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~--~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~  189 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN--YEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAM  189 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc--CCCeEEEEECcHHHHHHHHHHHHHhccccccce
Confidence            357999999999999999999999999999998765432222222  234899999999999999999998865444445


Q ss_pred             EEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      ..+.+|....       .+.+|+|+|++++.+...   ..+.++++||+||||++...    .+..++..+++..+++++
T Consensus       190 ~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~----~~~~il~~~~~~~~~lGL  255 (501)
T PHA02558        190 HKIYSGTAKD-------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGK----SLTSIITKLDNCKFKFGL  255 (501)
T ss_pred             eEEecCcccC-------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccch----hHHHHHHhhhccceEEEE
Confidence            4555554322       346999999999875432   24678999999999998654    345666777667889999


Q ss_pred             EeeCchh
Q 022383          213 SATLPHE  219 (298)
Q Consensus       213 SAT~~~~  219 (298)
                      |||+...
T Consensus       256 TATp~~~  262 (501)
T PHA02558        256 TGSLRDG  262 (501)
T ss_pred             eccCCCc
Confidence            9999654

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.92  E-value=3.1e-23  Score=198.11  Aligned_cols=218  Identities=18%  Similarity=0.253  Sum_probs=158.2

Q ss_pred             HHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH-HhhccCCceEEEEEc
Q 022383           59 IQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHACVG  137 (298)
Q Consensus        59 ~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~-~~~~~~~~~~~~~~~  137 (298)
                      +-.+++..+.++++++++||||||||.+|.+++++....   ..+++++.|++++|.|+++++. .++...+..+++..+
T Consensus         9 ~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~---~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr   85 (812)
T PRK11664          9 VLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI---NGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMR   85 (812)
T ss_pred             HHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc---CCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEec
Confidence            334667777789999999999999999999999986432   2489999999999999999885 455555667777666


Q ss_pred             CCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh-hcccc-HHHHHHHHHhCCCCccEEEEEee
Q 022383          138 GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-LSRGF-KDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       138 ~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~-~~~~~-~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      +...      .....+|+|+||++|.+++.. ...++++++|||||+|.. .+.++ ...+..+.+.++++.|+++||||
T Consensus        86 ~~~~------~~~~t~I~v~T~G~Llr~l~~-d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSAT  158 (812)
T PRK11664         86 AESK------VGPNTRLEVVTEGILTRMIQR-DPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSAT  158 (812)
T ss_pred             Cccc------cCCCCcEEEEChhHHHHHHhh-CCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecC
Confidence            5432      123458999999999998876 357899999999999972 33222 23345566777888999999999


Q ss_pred             CchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHH-----HHHHHHhhCCCCcEEEEecchhhHHHHHH
Q 022383          216 LPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFD-----TLCDLYDTLTITQAVIFCNTKRKIYYSVF  290 (298)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~-----~l~~ll~~~~~~k~lIf~~s~~~~~~l~~  290 (298)
                      ++...   +..++.++..+.....   ...+.+.|...+... +..     .+..++.. ..+++||||++..+++.+++
T Consensus       159 l~~~~---l~~~~~~~~~I~~~gr---~~pV~~~y~~~~~~~-~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~~l~~  230 (812)
T PRK11664        159 LDNDR---LQQLLPDAPVIVSEGR---SFPVERRYQPLPAHQ-RFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQRVQE  230 (812)
T ss_pred             CCHHH---HHHhcCCCCEEEecCc---cccceEEeccCchhh-hHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHHHHHH
Confidence            98652   2456655544443321   234677777665444 332     23334433 35799999999999999999


Q ss_pred             HHhh
Q 022383          291 YFWI  294 (298)
Q Consensus       291 ~L~~  294 (298)
                      .|++
T Consensus       231 ~L~~  234 (812)
T PRK11664        231 QLAS  234 (812)
T ss_pred             HHHH
Confidence            9986

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.92  E-value=7.2e-23  Score=195.28  Aligned_cols=220  Identities=17%  Similarity=0.205  Sum_probs=159.0

Q ss_pred             HHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH-HhhccCCceEEEEEc
Q 022383           59 IQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHACVG  137 (298)
Q Consensus        59 ~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~-~~~~~~~~~~~~~~~  137 (298)
                      +-.+++..+.++++++++|+||||||.+|..++++....   +.+++++.|++++|.|+++++. .++...+..+++..+
T Consensus         6 ~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~---~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr   82 (819)
T TIGR01970         6 VLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGI---GGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVR   82 (819)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhcc---CCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEc
Confidence            345667777789999999999999999999999987632   4589999999999999999885 444445556665554


Q ss_pred             CCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhH-hhccccHH-HHHHHHHhCCCCccEEEEEee
Q 022383          138 GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGFKD-QIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       138 ~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~-~~~~~~~~-~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      +..      ....+.+|+|+||+.|.+++.. ...++++++|||||+|. .++.++.. .+..+.+.++++.|+++||||
T Consensus        83 ~~~------~~s~~t~I~v~T~G~Llr~l~~-d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSAT  155 (819)
T TIGR01970        83 GEN------KVSRRTRLEVVTEGILTRMIQD-DPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSAT  155 (819)
T ss_pred             ccc------ccCCCCcEEEECCcHHHHHHhh-CcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCC
Confidence            432      2234578999999999998876 35789999999999995 55555433 344566667788999999999


Q ss_pred             CchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchH----HHHHHHHhhCCCCcEEEEecchhhHHHHHHH
Q 022383          216 LPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF----DTLCDLYDTLTITQAVIFCNTKRKIYYSVFY  291 (298)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~----~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~  291 (298)
                      ++...   +..++.++..+.....   ...++++|......+...    ..+..+++. ..+++||||++..+++.+++.
T Consensus       156 l~~~~---l~~~l~~~~vI~~~gr---~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~eI~~l~~~  228 (819)
T TIGR01970       156 LDGER---LSSLLPDAPVVESEGR---SFPVEIRYLPLRGDQRLEDAVSRAVEHALAS-ETGSILVFLPGQAEIRRVQEQ  228 (819)
T ss_pred             CCHHH---HHHHcCCCcEEEecCc---ceeeeeEEeecchhhhHHHHHHHHHHHHHHh-cCCcEEEEECCHHHHHHHHHH
Confidence            98653   3456655544443321   234667776665443221    233334433 357899999999999999999


Q ss_pred             Hhhh
Q 022383          292 FWIR  295 (298)
Q Consensus       292 L~~~  295 (298)
                      |++.
T Consensus       229 L~~~  232 (819)
T TIGR01970       229 LAER  232 (819)
T ss_pred             HHhh
Confidence            9863

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

>PRK13766 Hef nuclease; Provisional

Probab=99.91  E-value=1.3e-22  Score=196.45  Aligned_cols=163  Identities=18%  Similarity=0.200  Sum_probs=129.8

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .+...+++||.+++..++.+ |+++++|||+|||.++++++...+..  .+.++|||+|+++|+.|+.+.++++....+.
T Consensus        11 ~~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~--~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~   87 (773)
T PRK13766         11 PNTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK--KGGKVLILAPTKPLVEQHAEFFRKFLNIPEE   87 (773)
T ss_pred             cCcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh--CCCeEEEEeCcHHHHHHHHHHHHHHhCCCCc
Confidence            34457999999999888877 99999999999999999888887742  3458999999999999999999987654445


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEE
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v  210 (298)
                      .+..++|+....... .+..+++|+|+||+.+...+..+.+.+.++++|||||||++........+........+..+++
T Consensus        88 ~v~~~~g~~~~~~r~-~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~~~~il  166 (773)
T PRK13766         88 KIVVFTGEVSPEKRA-ELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLVL  166 (773)
T ss_pred             eEEEEeCCCCHHHHH-HHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCCCCEEE
Confidence            777788877765433 3344679999999999888877778889999999999999865543444444444445567899


Q ss_pred             EEEeeCc
Q 022383          211 LISATLP  217 (298)
Q Consensus       211 ~~SAT~~  217 (298)
                      ++|||+.
T Consensus       167 ~lTaTP~  173 (773)
T PRK13766        167 GLTASPG  173 (773)
T ss_pred             EEEcCCC
Confidence            9999984

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

Probab=99.91  E-value=4.8e-22  Score=173.30  Aligned_cols=164  Identities=16%  Similarity=0.192  Sum_probs=135.5

Q ss_pred             CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      +..+++.||.......+.+ |.+++.|||-|||+.+++-+...+...+.  ++|+++||+.|+.|..+.|++......-.
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~--kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~   88 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVTGIPEDE   88 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC--eEEEecCCchHHHHHHHHHHHHhCCChhh
Confidence            3456889999888777765 99999999999999999989888877644  89999999999999999999988776668


Q ss_pred             EEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc-cHHHHHHHHHhCCCCccEE
Q 022383          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPPDLQVV  210 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~~~~~~~~v  210 (298)
                      ++.+.|.....+....+.. .+|+|+||+.+.+-+..+.+++.++.++||||||+-.... |.......++. .+++.++
T Consensus        89 i~~ltGev~p~~R~~~w~~-~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~-~k~~~il  166 (542)
T COG1111          89 IAALTGEVRPEEREELWAK-KKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRS-AKNPLIL  166 (542)
T ss_pred             eeeecCCCChHHHHHHHhh-CCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHh-ccCceEE
Confidence            8899999888777666655 4999999999999999999999999999999999975443 33333334433 3578899


Q ss_pred             EEEeeCchhH
Q 022383          211 LISATLPHEI  220 (298)
Q Consensus       211 ~~SAT~~~~~  220 (298)
                      ++|||+..+.
T Consensus       167 gLTASPGs~~  176 (542)
T COG1111         167 GLTASPGSDL  176 (542)
T ss_pred             EEecCCCCCH
Confidence            9999996643

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.90  E-value=5.7e-22  Score=160.62  Aligned_cols=187  Identities=35%  Similarity=0.595  Sum_probs=151.3

Q ss_pred             HCCCCCChHHHHHHHHHhhcC-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC
Q 022383           50 QYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (298)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~  128 (298)
                      ..++..++++|.++++.+..+ +++++.+|||+|||.+++.+++..+.... ..+++|++|+..++.|+...+.+.....
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~   81 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSL   81 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            356788999999999999988 99999999999999999999988876542 3479999999999999999998877554


Q ss_pred             CceEEEEEcCCchHHHHHHhhcCC-cEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCc
Q 022383          129 NIQAHACVGGKSVGEDIRKLEHGV-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDL  207 (298)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~-~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~  207 (298)
                      ........++.........+..+. +++++|++.+............+++++|+||+|.+....+...+..+++.+++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~  161 (201)
T smart00487       82 GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNV  161 (201)
T ss_pred             CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhCCccc
Confidence            423334444444344444455555 9999999999999988777788999999999999976577888888998888889


Q ss_pred             cEEEEEeeCchhHHHHHHhcCCCCEEEEec
Q 022383          208 QVVLISATLPHEILEMTTKFMTDPVKILVK  237 (298)
Q Consensus       208 ~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  237 (298)
                      +++++|||+++........+......+...
T Consensus       162 ~~v~~saT~~~~~~~~~~~~~~~~~~~~~~  191 (201)
T smart00487      162 QLLLLSATPPEEIENLLELFLNDPVFIDVG  191 (201)
T ss_pred             eEEEEecCCchhHHHHHHHhcCCCEEEeCC
Confidence            999999999988888777777655555443

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

Probab=99.90  E-value=1.3e-22  Score=170.75  Aligned_cols=253  Identities=16%  Similarity=0.216  Sum_probs=182.1

Q ss_pred             cCcccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           33 TSFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ..-++++++....+.|++ +..+.++|.|..+++....|++++++.|||.||++||.+|++..      ...++++||..
T Consensus        71 wdkd~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a------dg~alvi~pli  144 (695)
T KOG0353|consen   71 WDKDDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA------DGFALVICPLI  144 (695)
T ss_pred             cccCCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc------CCceEeechhH
Confidence            445678899999999987 46788999999999999999999999999999999999998764      44799999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh-------hcCCcEEEeChHHHHH---HHhc--cCccCCCccEE
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-------EHGVHVVSGTPGRVCD---MIKR--KTLRTRAIKLL  179 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~ilV~Tp~~l~~---~~~~--~~~~~~~l~~v  179 (298)
                      .|++++.-+++.+    |+....+....+. +..+.+       .....++..||+++..   +++.  ..+....+.++
T Consensus       145 slmedqil~lkql----gi~as~lnanssk-e~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~i  219 (695)
T KOG0353|consen  145 SLMEDQILQLKQL----GIDASMLNANSSK-EEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLI  219 (695)
T ss_pred             HHHHHHHHHHHHh----CcchhhccCcccH-HHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEE
Confidence            9999988888887    4444444443332 222222       1345789999999875   2222  45667889999


Q ss_pred             EechhhHhhccc--cHHHHHH--HHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecC
Q 022383          180 VLDESDEMLSRG--FKDQIYD--VYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER  255 (298)
Q Consensus       180 ViDE~h~~~~~~--~~~~i~~--i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  255 (298)
                      -+||+|+-.+||  |+.++..  ++++.-++.++++++||-++.+.+-....+.-...+.+ +....+++....+.--+.
T Consensus       220 aidevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf-~a~fnr~nl~yev~qkp~  298 (695)
T KOG0353|consen  220 AIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTF-RAGFNRPNLKYEVRQKPG  298 (695)
T ss_pred             eecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhhee-ecccCCCCceeEeeeCCC
Confidence            999999999996  6665543  45555578999999999988776655544321111111 122333333333332222


Q ss_pred             -ccchHHHHHHHHh-hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          256 -EEWKFDTLCDLYD-TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       256 -~~~k~~~l~~ll~-~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                       +++-.+.+..+++ ...+...||||-+.++|++++..|+..|+
T Consensus       299 n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi  342 (695)
T KOG0353|consen  299 NEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGI  342 (695)
T ss_pred             ChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCc
Confidence             2234555666665 45667899999999999999999999886

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.90  E-value=5.4e-22  Score=182.90  Aligned_cols=236  Identities=16%  Similarity=0.184  Sum_probs=175.4

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|.. |++.|..+++.++.|+  +..+.||+|||++|++|++.....   ++.++|++||++||.|.++.+..+...+++
T Consensus       100 lg~~-p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~---G~~v~VvTptreLA~qdae~~~~l~~~lGl  173 (656)
T PRK12898        100 LGQR-HFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA---GLPVHVITVNDYLAERDAELMRPLYEALGL  173 (656)
T ss_pred             hCCC-CChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc---CCeEEEEcCcHHHHHHHHHHHHHHHhhcCC
Confidence            4544 9999999999999999  999999999999999999987554   568999999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhccC-------------------------ccCCCccEEEechh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT-------------------------LRTRAIKLLVLDES  184 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~~-------------------------~~~~~l~~vViDE~  184 (298)
                      ++..++|+.+..  .+....+++|+++|...| .++++.+.                         ...+.+.+.||||+
T Consensus       174 sv~~i~gg~~~~--~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEv  251 (656)
T PRK12898        174 TVGCVVEDQSPD--ERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDEA  251 (656)
T ss_pred             EEEEEeCCCCHH--HHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEeecc
Confidence            999999997643  344556789999999887 44444321                         12366889999999


Q ss_pred             hHhhcc-c-----------------cH--------------------------------HHHHHHHHhCCC---------
Q 022383          185 DEMLSR-G-----------------FK--------------------------------DQIYDVYRYLPP---------  205 (298)
Q Consensus       185 h~~~~~-~-----------------~~--------------------------------~~i~~i~~~~~~---------  205 (298)
                      |.++=+ .                 ..                                ..++.++..++.         
T Consensus       252 DSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~~~~~~~~~  331 (656)
T PRK12898        252 DSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPAWRGAVRRE  331 (656)
T ss_pred             cceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhhcccchHHH
Confidence            986511 0                 00                                001111100000         


Q ss_pred             ----------------------------------------------------------------------------CccE
Q 022383          206 ----------------------------------------------------------------------------DLQV  209 (298)
Q Consensus       206 ----------------------------------------------------------------------------~~~~  209 (298)
                                                                                                  -.++
T Consensus       332 ~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~~Fr~Y~kl  411 (656)
T PRK12898        332 ELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQRFFRRYLRL  411 (656)
T ss_pred             HHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHHHHHhhHHH
Confidence                                                                                        1258


Q ss_pred             EEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC--CCCcEEEEecchhhHHH
Q 022383          210 VLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL--TITQAVIFCNTKRKIYY  287 (298)
Q Consensus       210 v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~--~~~k~lIf~~s~~~~~~  287 (298)
                      .+||||.+.....+...|..++..+......  .....+.++.++..+ |...+...++..  .+.++||||+|++.++.
T Consensus       412 ~GmTGTa~~~~~El~~~y~l~vv~IPt~kp~--~r~~~~~~v~~t~~~-K~~aL~~~i~~~~~~~~pvLIft~t~~~se~  488 (656)
T PRK12898        412 AGMTGTAREVAGELWSVYGLPVVRIPTNRPS--QRRHLPDEVFLTAAA-KWAAVAARVRELHAQGRPVLVGTRSVAASER  488 (656)
T ss_pred             hcccCcChHHHHHHHHHHCCCeEEeCCCCCc--cceecCCEEEeCHHH-HHHHHHHHHHHHHhcCCCEEEEeCcHHHHHH
Confidence            8999999988777888887777666554332  222344455555444 888888888753  35689999999999999


Q ss_pred             HHHHHhhhcC
Q 022383          288 SVFYFWIRWI  297 (298)
Q Consensus       288 l~~~L~~~~~  297 (298)
                      +++.|...|+
T Consensus       489 L~~~L~~~gi  498 (656)
T PRK12898        489 LSALLREAGL  498 (656)
T ss_pred             HHHHHHHCCC
Confidence            9999998876

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

Probab=99.89  E-value=3.9e-22  Score=189.47  Aligned_cols=179  Identities=22%  Similarity=0.292  Sum_probs=146.0

Q ss_pred             HHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           47 GIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      .-...+|+ |.++|++++..+..|.+++++||||+|||++...++...+..   +.+++|.+|.++|.+|.++.+.....
T Consensus       112 ~~~~~~F~-LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~---~qrviYTsPIKALsNQKyrdl~~~fg  187 (1041)
T COG4581         112 PAREYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD---GQRVIYTSPIKALSNQKYRDLLAKFG  187 (1041)
T ss_pred             HHHhCCCC-cCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc---CCceEeccchhhhhhhHHHHHHHHhh
Confidence            33556777 999999999999999999999999999999988888777766   34599999999999999998876543


Q ss_pred             cCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCC
Q 022383          127 FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (298)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~  206 (298)
                      ...-.+++.+|+.+       ++.+..++|.|.|.|.+|+..+...+..+..|||||+|.|.+...+..++.++-.+|..
T Consensus       188 dv~~~vGL~TGDv~-------IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~  260 (1041)
T COG4581         188 DVADMVGLMTGDVS-------INPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDH  260 (1041)
T ss_pred             hhhhhccceeccee-------eCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCC
Confidence            22123456666654       34567999999999999999999999999999999999999988999999999999999


Q ss_pred             ccEEEEEeeCchh--HHHHHHhcCCCCEEEEe
Q 022383          207 LQVVLISATLPHE--ILEMTTKFMTDPVKILV  236 (298)
Q Consensus       207 ~~~v~~SAT~~~~--~~~~~~~~~~~~~~~~~  236 (298)
                      .++|++|||+++.  ...|+...-..|..+..
T Consensus       261 v~~v~LSATv~N~~EF~~Wi~~~~~~~~~vv~  292 (1041)
T COG4581         261 VRFVFLSATVPNAEEFAEWIQRVHSQPIHVVS  292 (1041)
T ss_pred             CcEEEEeCCCCCHHHHHHHHHhccCCCeEEEe
Confidence            9999999999875  33344443445555544

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

Probab=99.88  E-value=1.5e-21  Score=186.32  Aligned_cols=237  Identities=15%  Similarity=0.146  Sum_probs=171.4

Q ss_pred             HHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           47 GIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      ....+|...+++-|.+++..++.|+|+++.+|||.||++||.+|++-.      ++.+|+|.|..+|+.++...+.+   
T Consensus       256 l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv~~L~~---  326 (941)
T KOG0351|consen  256 LKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQVTHLSK---  326 (941)
T ss_pred             HHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHHHhhhh---
Confidence            445579999999999999999999999999999999999999888653      44899999999999988876633   


Q ss_pred             cCCceEEEEEcCCchHHHHH---Hhhc---CCcEEEeChHHHHHHH--hccCccCCC---ccEEEechhhHhhccc--cH
Q 022383          127 FINIQAHACVGGKSVGEDIR---KLEH---GVHVVSGTPGRVCDMI--KRKTLRTRA---IKLLVLDESDEMLSRG--FK  193 (298)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~---~~~~---~~~ilV~Tp~~l~~~~--~~~~~~~~~---l~~vViDE~h~~~~~~--~~  193 (298)
                       .++....+.++....++..   .+..   .++|+..|||++...-  ......+..   +.++||||||+...|+  |+
T Consensus       327 -~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFR  405 (941)
T KOG0351|consen  327 -KGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFR  405 (941)
T ss_pred             -cCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhccccc
Confidence             3688888888877654432   3332   5789999999997632  223334444   8999999999999996  77


Q ss_pred             HHHHHHHHh--CCCCccEEEEEeeCchhHHHHHHhcCC--CCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHH-h
Q 022383          194 DQIYDVYRY--LPPDLQVVLISATLPHEILEMTTKFMT--DPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY-D  268 (298)
Q Consensus       194 ~~i~~i~~~--~~~~~~~v~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll-~  268 (298)
                      +.+..+...  ..+..+++++|||.+..+..-+-..++  ++..+.   ....+.++...+..-.... ....+...+ .
T Consensus       406 p~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~---~sfnR~NL~yeV~~k~~~~-~~~~~~~~~~~  481 (941)
T KOG0351|consen  406 PSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFK---SSFNRPNLKYEVSPKTDKD-ALLDILEESKL  481 (941)
T ss_pred             HHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceec---ccCCCCCceEEEEeccCcc-chHHHHHHhhh
Confidence            777765333  234589999999998877665555443  444222   2233334444333322222 333333344 4


Q ss_pred             hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          269 TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       269 ~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .++....||||.++.+|+.++..|+..|.
T Consensus       482 ~~~~~s~IIYC~sr~~ce~vs~~L~~~~~  510 (941)
T KOG0351|consen  482 RHPDQSGIIYCLSRKECEQVSAVLRSLGK  510 (941)
T ss_pred             cCCCCCeEEEeCCcchHHHHHHHHHHhch
Confidence            55667999999999999999999998763

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

Probab=99.88  E-value=1e-21  Score=185.37  Aligned_cols=251  Identities=15%  Similarity=0.211  Sum_probs=184.6

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC-CcEEEEcCCCCchHHHHHHHHHHhhccCCC--------CeEEEEEcC
Q 022383           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSR--------EVQALILSP  109 (298)
Q Consensus        39 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--------~~~~lil~p  109 (298)
                      .++.|-..++.  |..++++.|+.+.+..+.+ .++++|||||+|||-.+++.+++.+....+        ..+++|++|
T Consensus       295 elP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAP  372 (1674)
T KOG0951|consen  295 ELPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAP  372 (1674)
T ss_pred             CCcchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEee
Confidence            45556666553  5567999999999998866 689999999999999999999998855322        348999999


Q ss_pred             cHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccC--ccCCCccEEEechhhHh
Q 022383          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEM  187 (298)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~--~~~~~l~~vViDE~h~~  187 (298)
                      .++|++.+...|.+....+|+++...+|+.....+  + ..+..++|||||+..-.-++..  -..+-++++||||+|++
T Consensus       373 mKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~--q-ieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLL  449 (1674)
T KOG0951|consen  373 MKALVQEMVGSFSKRLAPLGITVLELTGDSQLGKE--Q-IEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLL  449 (1674)
T ss_pred             HHHHHHHHHHHHHhhccccCcEEEEecccccchhh--h-hhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhc
Confidence            99999999999999888999999999998664432  1 1346999999999876666532  12346788999999998


Q ss_pred             hccccHHHHHHHHHhC-------CCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccch-
Q 022383          188 LSRGFKDQIYDVYRYL-------PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK-  259 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~-------~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k-  259 (298)
                      .+. .++.++.+..+.       ...++.+++|||+|+- ++......-++..++....+..+..+.|.++.+.....- 
T Consensus       450 hDd-RGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy-~DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~  527 (1674)
T KOG0951|consen  450 HDD-RGPVLESIVARTFRRSESTEEGSRLVGLSATLPNY-EDVASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLK  527 (1674)
T ss_pred             ccc-cchHHHHHHHHHHHHhhhcccCceeeeecccCCch-hhhHHHhccCcccccccCcccCcCCccceEeccccCCchH
Confidence            655 355555443332       2468899999999986 222222233444455555567777788888887765411 


Q ss_pred             H------HHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          260 F------DTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       260 ~------~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      .      ......++.....++|||+.+++++-+.|.++|++.
T Consensus       528 ~~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aIRd~~  570 (1674)
T KOG0951|consen  528 RFQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAIRDKA  570 (1674)
T ss_pred             HHHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHHHHHH
Confidence            1      123334555555799999999999999999999754

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.88  E-value=5.6e-21  Score=178.27  Aligned_cols=130  Identities=15%  Similarity=0.201  Sum_probs=100.0

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      ++|+|.+++..+.-++..+++++||+|||++|++|++.....   +..++|++|+++||.|..+.+..+...+|+.+...
T Consensus        69 lrpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL~---g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~~  145 (762)
T TIGR03714        69 MFPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNALT---GKGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSLG  145 (762)
T ss_pred             CCccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhhc---CCceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEEE
Confidence            455555566555545557999999999999999998766544   44699999999999999999999999999999887


Q ss_pred             EcCCc---hHHHHHHhhcCCcEEEeChHHH-HHHHhc------cCccCCCccEEEechhhHhh
Q 022383          136 VGGKS---VGEDIRKLEHGVHVVSGTPGRV-CDMIKR------KTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       136 ~~~~~---~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~------~~~~~~~l~~vViDE~h~~~  188 (298)
                      .++..   ..........+++|+++||++| ..+++.      ....++.+.++|+||||.++
T Consensus       146 ~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsIL  208 (762)
T TIGR03714       146 VVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVL  208 (762)
T ss_pred             ECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHh
Confidence            76522   2223334446799999999999 455533      23456889999999999985

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.

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

Probab=99.87  E-value=1e-21  Score=167.52  Aligned_cols=242  Identities=17%  Similarity=0.198  Sum_probs=164.0

Q ss_pred             HHHHHHHHH-CCCC-CChHHHHHHHHHhhcC-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           42 DDLLRGIYQ-YGFE-KPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        42 ~~i~~~l~~-~~~~-~~~~~Q~~~~~~~~~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      ..+..+|++ +|+. .-++.|..++..+.++ +||.|++|||+||++||.+|.+..      +..+|+++|..+|..++.
T Consensus         5 r~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~------~gITIV~SPLiALIkDQi   78 (641)
T KOG0352|consen    5 RKVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH------GGITIVISPLIALIKDQI   78 (641)
T ss_pred             HHHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh------CCeEEEehHHHHHHHHHH
Confidence            356677777 4554 3578999999998765 799999999999999999998875      337999999999999988


Q ss_pred             HHHHHhhccCCceEEEEEcCCchHHHHHHh------hcCCcEEEeChHHHHHHH----hccCccCCCccEEEechhhHhh
Q 022383          119 KVILAIGDFINIQAHACVGGKSVGEDIRKL------EHGVHVVSGTPGRVCDMI----KRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~ilV~Tp~~l~~~~----~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      +-+.++    .+++..+.+..+..+....+      .....++..|||....-.    .+...+-+.+.++|+||+|+..
T Consensus        79 DHL~~L----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVS  154 (641)
T KOG0352|consen   79 DHLKRL----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVS  154 (641)
T ss_pred             HHHHhc----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHh
Confidence            877765    45665666655544432222      234578999999876422    2233445678999999999999


Q ss_pred             ccc--cHHHHHHHHHhC--CCCccEEEEEeeCchhHHHHHHh--cCCCCEEEEecCCccCcCCceEEEEEecC---ccch
Q 022383          189 SRG--FKDQIYDVYRYL--PPDLQVVLISATLPHEILEMTTK--FMTDPVKILVKRDELTLEGIKQFFVAVER---EEWK  259 (298)
Q Consensus       189 ~~~--~~~~i~~i~~~~--~~~~~~v~~SAT~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~i~~~~~~~~~---~~~k  259 (298)
                      +||  |++++..+-...  -+....+.+|||-++.+++-+-.  .+.+|+-++-.+...     .+.++....   -.+-
T Consensus       155 QWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR-----~NLFYD~~~K~~I~D~  229 (641)
T KOG0352|consen  155 QWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFR-----DNLFYDNHMKSFITDC  229 (641)
T ss_pred             hhccccCcchhhhhhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcchh-----hhhhHHHHHHHHhhhH
Confidence            996  777777664333  35788999999998887664433  345666554322111     111111100   0112


Q ss_pred             HHHHHHHHhh----------CC---CCcEEEEecchhhHHHHHHHHhhhcCC
Q 022383          260 FDTLCDLYDT----------LT---ITQAVIFCNTKRKIYYSVFYFWIRWIG  298 (298)
Q Consensus       260 ~~~l~~ll~~----------~~---~~k~lIf~~s~~~~~~l~~~L~~~~~~  298 (298)
                      +..+.++-..          .+   .+-.||||.|++.|+.+|-.|..+|++
T Consensus       230 ~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~  281 (641)
T KOG0352|consen  230 LTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIP  281 (641)
T ss_pred             hHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcc
Confidence            3333333211          11   236899999999999999999988874

>PRK09694 helicase Cas3; Provisional

Probab=99.87  E-value=2.2e-20  Score=178.57  Aligned_cols=242  Identities=14%  Similarity=0.056  Sum_probs=147.8

Q ss_pred             CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC--Cc
Q 022383           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI--NI  130 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~--~~  130 (298)
                      ...|+|+|..+......+..+++.+|||+|||.+++.++...... ....+++|..||++++++++++++++....  ..
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~-~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~  362 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQ-GLADSIIFALPTQATANAMLSRLEALASKLFPSP  362 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHh-CCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCC
Confidence            346999999886554456779999999999999988776544433 334589999999999999999998644321  34


Q ss_pred             eEEEEEcCCchHHHH--------------------HHhhc-------CCcEEEeChHHHHHHHhc-cCccCCCc----cE
Q 022383          131 QAHACVGGKSVGEDI--------------------RKLEH-------GVHVVSGTPGRVCDMIKR-KTLRTRAI----KL  178 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~--------------------~~~~~-------~~~ilV~Tp~~l~~~~~~-~~~~~~~l----~~  178 (298)
                      .+.+.+|........                    .....       -.+|+|||+.+++...-. +...++.+    ++
T Consensus       363 ~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~La~sv  442 (878)
T PRK09694        363 NLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFGLGRSV  442 (878)
T ss_pred             ceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHhhccCe
Confidence            567777654321110                    01111       158999999998854332 22222333    48


Q ss_pred             EEechhhHhhccccHHHHHHHHHhCC-CCccEEEEEeeCchhHHHHHHh-cCCC---------CEEEEecCC---c----
Q 022383          179 LVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTK-FMTD---------PVKILVKRD---E----  240 (298)
Q Consensus       179 vViDE~h~~~~~~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~~~~~~~~-~~~~---------~~~~~~~~~---~----  240 (298)
                      |||||+|.+ +..+...+..+++.+. ...++|+||||+|......+.. +-..         |........   .    
T Consensus       443 vIiDEVHAy-D~ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~~~~~~~~~~~~~  521 (878)
T PRK09694        443 LIVDEVHAY-DAYMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITWRGVNGAQRFDLS  521 (878)
T ss_pred             EEEechhhC-CHHHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhccccccccccccccccccccccceeeecc
Confidence            999999997 3444555666666643 3577999999999887654433 2111         000000000   0    


Q ss_pred             cCc--CCceEEE--EEe--cCccchHHHHHHHHhh-CCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          241 LTL--EGIKQFF--VAV--EREEWKFDTLCDLYDT-LTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       241 ~~~--~~i~~~~--~~~--~~~~~k~~~l~~ll~~-~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      ...  ....+.+  ...  .........+..+++. ..+++++|||||++.|+.+++.|++.+
T Consensus       522 ~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~  584 (878)
T PRK09694        522 AHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELN  584 (878)
T ss_pred             ccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhC
Confidence            000  0011111  111  1111123334444443 345799999999999999999998764

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.87  E-value=2.4e-21  Score=181.98  Aligned_cols=149  Identities=18%  Similarity=0.298  Sum_probs=130.4

Q ss_pred             ccCCCCHHHHHHHH-----HCCCCCC---hHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEE
Q 022383           36 DAMGIKDDLLRGIY-----QYGFEKP---SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (298)
Q Consensus        36 ~~l~l~~~i~~~l~-----~~~~~~~---~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (298)
                      +.+++...+...+.     .+||..|   +|+|.++++.+..+++++.+++||+|||++|++|++..+...   ..++||
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g---~~v~IV  141 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG---KPVHLV  141 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc---CCeEEE
Confidence            45678888888776     6899988   999999999999999999999999999999999999877543   248899


Q ss_pred             cCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhccCccCC-------CccEE
Q 022383          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKTLRTR-------AIKLL  179 (298)
Q Consensus       108 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~~~~~~-------~l~~v  179 (298)
                      +|+++||.|+.+.+..+.+.+++++..+.||.+...+...+  +++|+|+||++| ..+++.+.+.++       .+.++
T Consensus       142 TpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~  219 (970)
T PRK12899        142 TVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFYFA  219 (970)
T ss_pred             eCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcccccEE
Confidence            99999999999999999999999999999998887776554  589999999999 999988766654       55899


Q ss_pred             EechhhHhhc
Q 022383          180 VLDESDEMLS  189 (298)
Q Consensus       180 ViDE~h~~~~  189 (298)
                      |+||||.|+-
T Consensus       220 IIDEADsmLi  229 (970)
T PRK12899        220 IIDEVDSILI  229 (970)
T ss_pred             EEechhhhhh
Confidence            9999999873

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

Probab=99.87  E-value=2.7e-21  Score=174.65  Aligned_cols=225  Identities=15%  Similarity=0.210  Sum_probs=174.0

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .+.|+|+.++..+-++.++++.|.|.+|||.++..++...+..   .-++||-+|-++|.+|-++.+..-.+    .+++
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~---kQRVIYTSPIKALSNQKYREl~~EF~----DVGL  201 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE---KQRVIYTSPIKALSNQKYRELLEEFK----DVGL  201 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh---cCeEEeeChhhhhcchhHHHHHHHhc----ccce
Confidence            4899999999999999999999999999999988888777755   34899999999999999998765433    3556


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      .+|+....       .....+|.|.+.|.+|+.++..-.+.+.+|||||+|.|-+...+-.|+..+-.+|.+.+.+++||
T Consensus       202 MTGDVTIn-------P~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VFLSA  274 (1041)
T KOG0948|consen  202 MTGDVTIN-------PDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVFLSA  274 (1041)
T ss_pred             eecceeeC-------CCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEEEec
Confidence            67765543       33689999999999999999888999999999999999888788888888889999999999999


Q ss_pred             eCchhH--HHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCcc-------------c---------------------
Q 022383          215 TLPHEI--LEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREE-------------W---------------------  258 (298)
Q Consensus       215 T~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------------~---------------------  258 (298)
                      |+|+..  .+|+...-..|.++....  ..+-..+|+..+...+.             +                     
T Consensus       275 TiPNA~qFAeWI~~ihkQPcHVVYTd--yRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~~~~~  352 (1041)
T KOG0948|consen  275 TIPNARQFAEWICHIHKQPCHVVYTD--YRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDGKKKA  352 (1041)
T ss_pred             cCCCHHHHHHHHHHHhcCCceEEeec--CCCCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCcccccc
Confidence            999863  446666666777776543  33333455544422110             0                     


Q ss_pred             -----------------hHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          259 -----------------KFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       259 -----------------k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                                       .+..+...+-.....++|||+-|+++|+.+|..+...
T Consensus       353 ~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kl  406 (1041)
T KOG0948|consen  353 NKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKL  406 (1041)
T ss_pred             ccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccC
Confidence                             1112333333445568999999999999999887654

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.87  E-value=2.8e-20  Score=172.70  Aligned_cols=130  Identities=20%  Similarity=0.328  Sum_probs=109.2

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHH-HhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC-QTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~-~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .|.. |++.|......+..|+  +.+++||+|||+++.+|++ +.+.    +..+.|++||.+||.|.++.+..+.+.+|
T Consensus        53 lg~~-p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~----G~~V~VvTpt~~LA~qdae~~~~l~~~LG  125 (745)
T TIGR00963        53 LGMR-PFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT----GKGVHVVTVNDYLAQRDAEWMGQVYRFLG  125 (745)
T ss_pred             hCCC-ccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh----CCCEEEEcCCHHHHHHHHHHHHHHhccCC
Confidence            4544 8999999888887776  9999999999999999995 4443    33699999999999999999999999999


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhcc------CccCCCccEEEechhhHhhc
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~------~~~~~~l~~vViDE~h~~~~  189 (298)
                      +++..+.|+.+........  .++|+++||.+| ..+++.+      ...++.+.++|+||+|.++-
T Consensus       126 Lsv~~i~g~~~~~~r~~~y--~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LI  190 (745)
T TIGR00963       126 LSVGLILSGMSPEERREAY--ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILI  190 (745)
T ss_pred             CeEEEEeCCCCHHHHHHhc--CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhH
Confidence            9999999988765443333  479999999999 8888765      35679999999999999864

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.

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

Probab=99.86  E-value=1.6e-20  Score=173.52  Aligned_cols=155  Identities=19%  Similarity=0.259  Sum_probs=132.1

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      ..|+ +..+|++++-++.+|.+++|.|+|.+|||+++..++.....+   +.+++|-+|-++|.+|-++-|+.....   
T Consensus       294 ~pFe-lD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h---~TR~iYTSPIKALSNQKfRDFk~tF~D---  366 (1248)
T KOG0947|consen  294 YPFE-LDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKH---MTRTIYTSPIKALSNQKFRDFKETFGD---  366 (1248)
T ss_pred             CCCC-ccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhh---ccceEecchhhhhccchHHHHHHhccc---
Confidence            4555 999999999999999999999999999998866555443323   558999999999999999988876443   


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEE
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v  210 (298)
                       +++++|+....       ....++|.|.|.|-+|+.++.--.+++.+|||||+|.+.+...+-.++.++-++|+.+++|
T Consensus       367 -vgLlTGDvqin-------PeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~~I  438 (1248)
T KOG0947|consen  367 -VGLLTGDVQIN-------PEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVNFI  438 (1248)
T ss_pred             -cceeecceeeC-------CCcceEeehHHHHHHHHhcccchhhccceEEEeeeeecccccccccceeeeeeccccceEE
Confidence             33777775543       3368999999999999999888889999999999999988888999999999999999999


Q ss_pred             EEEeeCchhH
Q 022383          211 LISATLPHEI  220 (298)
Q Consensus       211 ~~SAT~~~~~  220 (298)
                      ++|||+|+..
T Consensus       439 lLSATVPN~~  448 (1248)
T KOG0947|consen  439 LLSATVPNTL  448 (1248)
T ss_pred             EEeccCCChH
Confidence            9999998863

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=6.4e-20  Score=172.65  Aligned_cols=131  Identities=16%  Similarity=0.268  Sum_probs=108.2

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|. .|++.|..+.+.+.+|+  +.++.||+|||+++++|++.....   +..+.|++||++||.|.++.+..+...+|+
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~---G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl  148 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE---GKGVHLITVNDYLAKRDAEEMGQVYEFLGL  148 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc---CCCeEEEeCCHHHHHHHHHHHHHHHhhcCC
Confidence            465 59999999999888887  999999999999999999865444   568999999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhccC------ccCCCccEEEechhhHhh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT------LRTRAIKLLVLDESDEML  188 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~~------~~~~~l~~vViDE~h~~~  188 (298)
                      ++....|+.+...+.+ ...+++|+++||+++ .++++.+.      ..++.+.++|+||+|.++
T Consensus       149 ~v~~i~g~~~~~~~r~-~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiL  212 (790)
T PRK09200        149 TVGLNFSDIDDASEKK-AIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSIL  212 (790)
T ss_pred             eEEEEeCCCCcHHHHH-HhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccce
Confidence            9999999987323322 234589999999999 45554422      356889999999999975

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

Probab=99.85  E-value=9.8e-21  Score=173.79  Aligned_cols=163  Identities=17%  Similarity=0.201  Sum_probs=130.6

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEE
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  133 (298)
                      -.++.||.++....+ |+|+++++|||+|||+.++..+++++...+. .++||++|++-|+.|+.+.++.++..  ..+.
T Consensus        61 ~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a~~~~~~~~--~~~T  136 (746)
T KOG0354|consen   61 LELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIACFSIYLIP--YSVT  136 (746)
T ss_pred             ccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHHHHhhccCc--ccce
Confidence            469999999999999 9999999999999999999999999988666 58999999999999999888777654  4555


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCcc-CCCccEEEechhhHhhccc-cHHHHHHHHHhCCCCccEEE
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLR-TRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPPDLQVVL  211 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~-~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~~~~~~~~v~  211 (298)
                      ...||.........+-...+|+|.||+.+...+.++..+ ++.+.++||||||+-.... |...++..+..-....|+++
T Consensus       137 ~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~l~~k~~~~qILg  216 (746)
T KOG0354|consen  137 GQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMREYLDLKNQGNQILG  216 (746)
T ss_pred             eeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHHHHHHhhhccccEEE
Confidence            555664333333344455799999999999988875443 5999999999999976654 55566577766666669999


Q ss_pred             EEeeCchhH
Q 022383          212 ISATLPHEI  220 (298)
Q Consensus       212 ~SAT~~~~~  220 (298)
                      +|||++...
T Consensus       217 LTASpG~~~  225 (746)
T KOG0354|consen  217 LTASPGSKL  225 (746)
T ss_pred             EecCCCccH
Confidence            999997643

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.85  E-value=2.7e-19  Score=169.32  Aligned_cols=156  Identities=24%  Similarity=0.238  Sum_probs=119.0

Q ss_pred             CChHHHHHHHHHhhcC---CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           55 KPSAIQQRAVMPIIKG---RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~---~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      .+++.|+++++.+.++   +++++.|+||+|||.+|+.++...+..   +.++||++|+++|+.|+.+.+++..   +.+
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~---g~~vLvLvPt~~L~~Q~~~~l~~~f---g~~  217 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ---GKQALVLVPEIALTPQMLARFRARF---GAP  217 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHHh---CCC
Confidence            5899999999999874   789999999999999999887776654   5589999999999999999998753   568


Q ss_pred             EEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc---cHHHHHH--HHHh
Q 022383          132 AHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG---FKDQIYD--VYRY  202 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~---~~~~i~~--i~~~  202 (298)
                      +..++|+.+..+....+    .+.++|+|+|+..+.       ..++++++||+||+|...-..   ...+.+.  +.+.
T Consensus       218 v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~ra  290 (679)
T PRK05580        218 VAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRA  290 (679)
T ss_pred             EEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHHHHHHHHh
Confidence            88999987765544332    356899999997764       457899999999999754221   1111222  2333


Q ss_pred             CCCCccEEEEEeeCchhHHHH
Q 022383          203 LPPDLQVVLISATLPHEILEM  223 (298)
Q Consensus       203 ~~~~~~~v~~SAT~~~~~~~~  223 (298)
                      ...+.+++++|||++......
T Consensus       291 ~~~~~~~il~SATps~~s~~~  311 (679)
T PRK05580        291 KLENIPVVLGSATPSLESLAN  311 (679)
T ss_pred             hccCCCEEEEcCCCCHHHHHH
Confidence            446789999999987554443

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.82  E-value=5.2e-19  Score=165.07  Aligned_cols=222  Identities=17%  Similarity=0.125  Sum_probs=141.7

Q ss_pred             CChHHHHHHHHHhh-cC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           55 KPSAIQQRAVMPII-KG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~-~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      .+++||.+++..+. .|  ++.++++|||+|||+..+..+.. +     +.++|||||+..|+.|+.+.|.++.......
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l-----~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~  328 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-V-----KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQ  328 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-h-----CCCEEEEeCcHHHHHHHHHHHHHhcCCCCce
Confidence            59999999999877 34  47899999999999887755443 2     2369999999999999999999886444455


Q ss_pred             EEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc--------cCccCCCccEEEechhhHhhccccHHHHHHHHHhC
Q 022383          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~--------~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~  203 (298)
                      +..+.|+....     .....+|+|+|.+.+......        ..+.-...++||+||+|++...    .+..++..+
T Consensus       329 I~~~tg~~k~~-----~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~----~fr~il~~l  399 (732)
T TIGR00603       329 ICRFTSDAKER-----FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAA----MFRRVLTIV  399 (732)
T ss_pred             EEEEecCcccc-----cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHH----HHHHHHHhc
Confidence            55666653321     122368999999877543221        1233357889999999998543    344455555


Q ss_pred             CCCccEEEEEeeCchhH--HHHHHhcCCCCEEEEecCCccC----cCCceEEEEEec----------------------C
Q 022383          204 PPDLQVVLISATLPHEI--LEMTTKFMTDPVKILVKRDELT----LEGIKQFFVAVE----------------------R  255 (298)
Q Consensus       204 ~~~~~~v~~SAT~~~~~--~~~~~~~~~~~~~~~~~~~~~~----~~~i~~~~~~~~----------------------~  255 (298)
                      . ....+++|||+....  ...+..+++ |..+.....+..    ...+...-+.|+                      .
T Consensus       400 ~-a~~RLGLTATP~ReD~~~~~L~~LiG-P~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~l~~~  477 (732)
T TIGR00603       400 Q-AHCKLGLTATLVREDDKITDLNFLIG-PKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVM  477 (732)
T ss_pred             C-cCcEEEEeecCcccCCchhhhhhhcC-CeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhHHhhh
Confidence            4 345799999995421  122222222 333322211111    011111111111                      1


Q ss_pred             ccchHHHHHHHHhhC--CCCcEEEEecchhhHHHHHHHHh
Q 022383          256 EEWKFDTLCDLYDTL--TITQAVIFCNTKRKIYYSVFYFW  293 (298)
Q Consensus       256 ~~~k~~~l~~ll~~~--~~~k~lIf~~s~~~~~~l~~~L~  293 (298)
                      ...|+..+..+++.+  .+.++||||++...++.++..|.
T Consensus       478 np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~  517 (732)
T TIGR00603       478 NPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG  517 (732)
T ss_pred             ChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC
Confidence            123566666677654  56799999999999999988874

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

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.82  E-value=4.9e-18  Score=166.18  Aligned_cols=220  Identities=20%  Similarity=0.240  Sum_probs=137.2

Q ss_pred             hHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHH-HHhhccCCCCeEEEEEcCcH----HHHHHHHHHHHH-hhccCCc
Q 022383           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTV-CQTVDTSSREVQALILSPTR----ELATQTEKVILA-IGDFINI  130 (298)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~-~~~~~~~~~~~~~lil~p~~----~l~~q~~~~~~~-~~~~~~~  130 (298)
                      +.+-.+++..+.+++.++++|+||||||.  .+|. +...... ....+++.-|.+    +++.++.+.+.. ++...|+
T Consensus        76 ~~~r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~g-~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY  152 (1294)
T PRK11131         76 SQKKQDILEAIRDHQVVIVAGETGSGKTT--QLPKICLELGRG-VKGLIGHTQPRRLAARTVANRIAEELETELGGCVGY  152 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCC-CCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceece
Confidence            34444666777788889999999999998  4563 3322221 112333344754    666666666553 3322222


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhH-hhccccHH-HHHHHHHhCCCCcc
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGFKD-QIYDVYRYLPPDLQ  208 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~-~~~~~~~~-~i~~i~~~~~~~~~  208 (298)
                      .    ...   ..   ....+++|+|+||++|++.+.... .++++++|||||+|. +++.+|.. .+..++... ++.|
T Consensus       153 ~----vrf---~~---~~s~~t~I~v~TpG~LL~~l~~d~-~Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~r-pdlK  220 (1294)
T PRK11131        153 K----VRF---ND---QVSDNTMVKLMTDGILLAEIQQDR-LLMQYDTIIIDEAHERSLNIDFILGYLKELLPRR-PDLK  220 (1294)
T ss_pred             e----ecC---cc---ccCCCCCEEEEChHHHHHHHhcCC-ccccCcEEEecCccccccccchHHHHHHHhhhcC-CCce
Confidence            2    111   11   123567999999999999887654 489999999999994 66666553 344443332 4689


Q ss_pred             EEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCcc-----chHHHHHHHHh---hCCCCcEEEEec
Q 022383          209 VVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREE-----WKFDTLCDLYD---TLTITQAVIFCN  280 (298)
Q Consensus       209 ~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-----~k~~~l~~ll~---~~~~~k~lIf~~  280 (298)
                      +|+||||++.  ..+...+...|. +.+...   ...+...|.......     +....+...+.   ....+++||||+
T Consensus       221 vILmSATid~--e~fs~~F~~apv-I~V~Gr---~~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLp  294 (1294)
T PRK11131        221 VIITSATIDP--ERFSRHFNNAPI-IEVSGR---TYPVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMS  294 (1294)
T ss_pred             EEEeeCCCCH--HHHHHHcCCCCE-EEEcCc---cccceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcC
Confidence            9999999974  355555544553 444322   234666666654322     12223332222   234579999999


Q ss_pred             chhhHHHHHHHHhhhcC
Q 022383          281 TKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       281 s~~~~~~l~~~L~~~~~  297 (298)
                      +..+++.+++.|+..++
T Consensus       295 g~~EIe~lae~L~~~~~  311 (1294)
T PRK11131        295 GEREIRDTADALNKLNL  311 (1294)
T ss_pred             CHHHHHHHHHHHHhcCC
Confidence            99999999999987654

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.82  E-value=1.8e-18  Score=132.13  Aligned_cols=144  Identities=35%  Similarity=0.523  Sum_probs=112.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (298)
                      +++++.+|||+|||..++..+...... ....+++|++|++.++.|..+.+...... +..+..+.+.............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~-~~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   78 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS-LKGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSG   78 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc-ccCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHHHHhcC
Confidence            478999999999999988888877655 23458999999999999999999887654 5677777777666555555567


Q ss_pred             CCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeC
Q 022383          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       151 ~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      ..+++++|++.+............+.+++|+||+|.+....................+++++|||+
T Consensus        79 ~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          79 KTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            789999999999988777655667899999999999876654443223344445678899999996

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

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

Probab=99.81  E-value=4.3e-19  Score=160.37  Aligned_cols=224  Identities=18%  Similarity=0.159  Sum_probs=138.5

Q ss_pred             CCChHHHHHHHHHhhc----CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           54 EKPSAIQQRAVMPIIK----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~----~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      ..++++|.+++..+.+    ++..++++|||+|||..++..+...      ...++||||+++|+.|+.+.+.+..... 
T Consensus        35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~------~~~~Lvlv~~~~L~~Qw~~~~~~~~~~~-  107 (442)
T COG1061          35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL------KRSTLVLVPTKELLDQWAEALKKFLLLN-  107 (442)
T ss_pred             CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh------cCCEEEEECcHHHHHHHHHHHHHhcCCc-
Confidence            4599999999999987    8999999999999998876555443      2249999999999999987766654321 


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccE
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~  209 (298)
                      -.+..+.|+......       ..|.|+|-+.+.+.-....+...+.++|||||||++....+.....    .+.....+
T Consensus       108 ~~~g~~~~~~~~~~~-------~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~~----~~~~~~~~  176 (442)
T COG1061         108 DEIGIYGGGEKELEP-------AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILE----LLSAAYPR  176 (442)
T ss_pred             cccceecCceeccCC-------CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHHHHHH----hhhcccce
Confidence            123334443332110       3699999988887432223334478999999999987666553333    33322228


Q ss_pred             EEEEeeCchhHH---HHHHhcCCCCEEEEecCCc----cCcCCceEEEEEec----------------------------
Q 022383          210 VLISATLPHEIL---EMTTKFMTDPVKILVKRDE----LTLEGIKQFFVAVE----------------------------  254 (298)
Q Consensus       210 v~~SAT~~~~~~---~~~~~~~~~~~~~~~~~~~----~~~~~i~~~~~~~~----------------------------  254 (298)
                      +++|||++....   ..+..+++ |..+.....+    ..........+.+.                            
T Consensus       177 LGLTATp~R~D~~~~~~l~~~~g-~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (442)
T COG1061         177 LGLTATPEREDGGRIGDLFDLIG-PIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRA  255 (442)
T ss_pred             eeeccCceeecCCchhHHHHhcC-CeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhhhhhhhH
Confidence            999999864321   11222221 2232222110    00111111111111                            


Q ss_pred             ---------CccchHHHHHHHHhhC-CCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          255 ---------REEWKFDTLCDLYDTL-TITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       255 ---------~~~~k~~~l~~ll~~~-~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                               ..+.+...+..++..+ ...+++|||.++..++.++..+...|
T Consensus       256 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~  307 (442)
T COG1061         256 ENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPG  307 (442)
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCC
Confidence                     0112334444445444 35699999999999999999987654

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=2.9e-18  Score=161.60  Aligned_cols=126  Identities=20%  Similarity=0.257  Sum_probs=102.5

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      +++.|--.--.+.  +.-+..++||+|||++|.+|++.....   +..+.|++|+++||.|.++.+..+...+|+++..+
T Consensus        83 ~ydvQliGg~~Lh--~G~Iaem~TGeGKTL~a~Lpa~~~al~---G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~i  157 (896)
T PRK13104         83 HFDVQLIGGMVLH--EGNIAEMRTGEGKTLVATLPAYLNAIS---GRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGVI  157 (896)
T ss_pred             cchHHHhhhhhhc--cCccccccCCCCchHHHHHHHHHHHhc---CCCEEEEcCCHHHHHHHHHHHHHHhcccCceEEEE
Confidence            5565554443333  444889999999999999999977654   34689999999999999999999999999999999


Q ss_pred             EcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhcc-CccC-----CCccEEEechhhHhh
Q 022383          136 VGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK-TLRT-----RAIKLLVLDESDEML  188 (298)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~-~~~~-----~~l~~vViDE~h~~~  188 (298)
                      .|+.+........  .++|+++||++| ..+++.+ .+++     +.+.++|+||+|.++
T Consensus       158 ~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiL  215 (896)
T PRK13104        158 YPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSIL  215 (896)
T ss_pred             eCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhh
Confidence            9997766554443  589999999999 8888876 3444     689999999999986

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.80  E-value=5.2e-18  Score=159.63  Aligned_cols=129  Identities=19%  Similarity=0.315  Sum_probs=105.5

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHH-HhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC-QTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~-~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .|.. |++.|--.--.+.+|+  +..++||+|||+++.+|++ +.+..    ..+-|++|+..||.|.++.+..+...+|
T Consensus        78 lg~~-~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G----~~V~IvTpn~yLA~rd~e~~~~l~~~LG  150 (830)
T PRK12904         78 LGMR-HFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTG----KGVHVVTVNDYLAKRDAEWMGPLYEFLG  150 (830)
T ss_pred             hCCC-CCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcC----CCEEEEecCHHHHHHHHHHHHHHHhhcC
Confidence            4544 7777877665565664  8899999999999999996 55532    2467999999999999999999999999


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhccC------ccCCCccEEEechhhHhh
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRKT------LRTRAIKLLVLDESDEML  188 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~~------~~~~~l~~vViDE~h~~~  188 (298)
                      +++..+.|+.+..++...+  .++|+++||.+| .++++.+.      ...+.+.+.|+||+|.++
T Consensus       151 lsv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiL  214 (830)
T PRK12904        151 LSVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSIL  214 (830)
T ss_pred             CeEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhhe
Confidence            9999999998877665554  489999999999 88887653      346889999999999976

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

Probab=99.78  E-value=5.5e-17  Score=147.39  Aligned_cols=237  Identities=18%  Similarity=0.162  Sum_probs=166.0

Q ss_pred             CCCHHHHHHH-HHCCCCCChHHHHHHHHHhhcC------CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           39 GIKDDLLRGI-YQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        39 ~l~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      +....+.+.+ ....|. +|..|++++..|...      -+-+++|.-|||||.+++++++..+..   |.++..++||.
T Consensus       246 ~~~~~l~~~~~~~LPF~-LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~---G~Q~ALMAPTE  321 (677)
T COG1200         246 PANGELLAKFLAALPFK-LTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA---GYQAALMAPTE  321 (677)
T ss_pred             CccHHHHHHHHHhCCCC-ccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc---CCeeEEeccHH
Confidence            3444555544 556777 999999999998854      367999999999999999999998876   67899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH---Hhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---KLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      -||.|.++.+.++....++++..+.|.........   .+. +..+++|||..-+     .....++++.++|+||=|++
T Consensus       322 ILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALi-----Qd~V~F~~LgLVIiDEQHRF  396 (677)
T COG1200         322 ILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALI-----QDKVEFHNLGLVIIDEQHRF  396 (677)
T ss_pred             HHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhh-----hcceeecceeEEEEeccccc
Confidence            99999999999999999999999999876654433   333 4589999997333     34677899999999999985


Q ss_pred             hccccHHHHHHHHHhCCC-CccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHH
Q 022383          188 LSRGFKDQIYDVYRYLPP-DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL  266 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~~~-~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  266 (298)
                           +-.-+..++.-.. .+.+++||||+-+....+....-.+-..+..-+  .-+..|...++..+..    ..+.+.
T Consensus       397 -----GV~QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt~fgDldvS~IdElP--~GRkpI~T~~i~~~~~----~~v~e~  465 (677)
T COG1200         397 -----GVHQRLALREKGEQNPHVLVMTATPIPRTLALTAFGDLDVSIIDELP--PGRKPITTVVIPHERR----PEVYER  465 (677)
T ss_pred             -----cHHHHHHHHHhCCCCCcEEEEeCCCchHHHHHHHhccccchhhccCC--CCCCceEEEEeccccH----HHHHHH
Confidence                 3334445555555 688999999986654444332222222222211  1223355555544333    333333


Q ss_pred             Hh--hCCCCcEEEEecchhhH--------HHHHHHHhhh
Q 022383          267 YD--TLTITQAVIFCNTKRKI--------YYSVFYFWIR  295 (298)
Q Consensus       267 l~--~~~~~k~lIf~~s~~~~--------~~l~~~L~~~  295 (298)
                      +.  ...+.++.+.|+-+++.        +.+++.|+..
T Consensus       466 i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~  504 (677)
T COG1200         466 IREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSF  504 (677)
T ss_pred             HHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHH
Confidence            32  23567999999877654        4566666643

>TIGR00595 priA primosomal protein N'

Probab=99.77  E-value=3.5e-17  Score=149.85  Aligned_cols=134  Identities=22%  Similarity=0.211  Sum_probs=97.2

Q ss_pred             EEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----h
Q 022383           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----E  149 (298)
Q Consensus        74 li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  149 (298)
                      ++.||||+|||.+|+..+...+..   +.++||++|+++|+.|+.+.+++..   +.++..++|+.+..+....+    .
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~---g~~vLvlvP~i~L~~Q~~~~l~~~f---~~~v~vlhs~~~~~er~~~~~~~~~   74 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL---GKSVLVLVPEIALTPQMIQRFKYRF---GSQVAVLHSGLSDSEKLQAWRKVKN   74 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHHh---CCcEEEEECCCCHHHHHHHHHHHHc
Confidence            478999999999997766555543   5589999999999999999998753   56788889987765543332    3


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc-----c-HHHHHHHHHhCCCCccEEEEEeeCchhHH
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----F-KDQIYDVYRYLPPDLQVVLISATLPHEIL  221 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-----~-~~~i~~i~~~~~~~~~~v~~SAT~~~~~~  221 (298)
                      +..+|+|||+..+.       ..++++++|||||.|...-+.     | ...+... +....+.+++++|||++.+..
T Consensus        75 g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~-ra~~~~~~vil~SATPsles~  144 (505)
T TIGR00595        75 GEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVY-RAKKFNCPVVLGSATPSLESY  144 (505)
T ss_pred             CCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHHHH-HHHhcCCCEEEEeCCCCHHHH
Confidence            56799999997664       357889999999999864221     1 1222222 233357899999999775433

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).

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

Probab=99.77  E-value=1e-17  Score=164.58  Aligned_cols=160  Identities=16%  Similarity=0.129  Sum_probs=108.0

Q ss_pred             CChHHHHHHHHHhh----c-CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           55 KPSAIQQRAVMPII----K-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~-~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .++++|.+++..+.    + .+..++++|||+|||.+++. ++..+.......++|||+|+++|+.|..+.|+.+.....
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~-li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIA-LMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHH-HHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            48999999998765    3 36899999999999987543 334444333456899999999999999999987632211


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-----cCccCCCccEEEechhhHhhc------c--------
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-----KTLRTRAIKLLVLDESDEMLS------R--------  190 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-----~~~~~~~l~~vViDE~h~~~~------~--------  190 (298)
                      ......++......  .......+|+|+|.+++...+..     ....+.++++||+||||+-..      .        
T Consensus       492 ~~~~~i~~i~~L~~--~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~~  569 (1123)
T PRK11448        492 QTFASIYDIKGLED--KFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRDQ  569 (1123)
T ss_pred             cchhhhhchhhhhh--hcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccchh
Confidence            11111111100000  11123468999999998776432     124568899999999998531      0        


Q ss_pred             -ccHHHHHHHHHhCCCCccEEEEEeeCchh
Q 022383          191 -GFKDQIYDVYRYLPPDLQVVLISATLPHE  219 (298)
Q Consensus       191 -~~~~~i~~i~~~~~~~~~~v~~SAT~~~~  219 (298)
                       .+...++.++.++.  ...|++|||+...
T Consensus       570 ~~~~~~yr~iL~yFd--A~~IGLTATP~r~  597 (1123)
T PRK11448        570 LDYVSKYRRVLDYFD--AVKIGLTATPALH  597 (1123)
T ss_pred             hhHHHHHHHHHhhcC--ccEEEEecCCccc
Confidence             12466778888763  5689999999643

>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=99.76  E-value=8.5e-18  Score=134.80  Aligned_cols=152  Identities=19%  Similarity=0.190  Sum_probs=103.0

Q ss_pred             CChHHHHHHHHHhhc-------CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           55 KPSAIQQRAVMPIIK-------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~-------~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      .|+++|.+++..+.+       ++++++.+|||+|||.+++..+.....      +++|++|+..|+.|+.+.+..+...
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~~~~~~   76 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFDDFGSE   76 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHHHHSTT
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHHHhhhh
Confidence            389999999998873       689999999999999988755544433      8999999999999999999666433


Q ss_pred             CCceEEE------------EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc-----------CccCCCccEEEechh
Q 022383          128 INIQAHA------------CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-----------TLRTRAIKLLVLDES  184 (298)
Q Consensus       128 ~~~~~~~------------~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~-----------~~~~~~l~~vViDE~  184 (298)
                      .. ....            ..................+++++|.+++.......           .......++||+||+
T Consensus        77 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEa  155 (184)
T PF04851_consen   77 KY-NFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEA  155 (184)
T ss_dssp             SE-EEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETG
T ss_pred             hh-hhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehh
Confidence            21 1100            01111111222333456789999999999876541           123457789999999


Q ss_pred             hHhhccccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          185 DEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       185 h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      |++....-   +..+++  .+...++++|||+.+
T Consensus       156 H~~~~~~~---~~~i~~--~~~~~~l~lTATp~r  184 (184)
T PF04851_consen  156 HHYPSDSS---YREIIE--FKAAFILGLTATPFR  184 (184)
T ss_dssp             GCTHHHHH---HHHHHH--SSCCEEEEEESS-S-
T ss_pred             hhcCCHHH---HHHHHc--CCCCeEEEEEeCccC
Confidence            99754431   444444  456779999999863

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 ....

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.76  E-value=2.7e-16  Score=154.60  Aligned_cols=220  Identities=18%  Similarity=0.170  Sum_probs=138.1

Q ss_pred             HHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH-hhccCCceEEEEEcCC
Q 022383           61 QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA-IGDFINIQAHACVGGK  139 (298)
Q Consensus        61 ~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~~~~~~~~~~~~~~~  139 (298)
                      .+++..+.+++.++++|+||||||..  +|.+-.-.......++++.-|++--+..++.++.+ ++...|-.+++.....
T Consensus        73 ~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~vR~~  150 (1283)
T TIGR01967        73 EDIAEAIAENQVVIIAGETGSGKTTQ--LPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFH  150 (1283)
T ss_pred             HHHHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeEEcCC
Confidence            35666677788899999999999984  34332211111222455566998888888776644 3323333333322211


Q ss_pred             chHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhH-hhccccHHH-HHHHHHhCCCCccEEEEEeeCc
Q 022383          140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE-MLSRGFKDQ-IYDVYRYLPPDLQVVLISATLP  217 (298)
Q Consensus       140 ~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~-~~~~~~~~~-i~~i~~~~~~~~~~v~~SAT~~  217 (298)
                      +      ....+..|.++|++.|++.+.... .+.++++|||||+|. .++.++... +..++... ++.|+|+||||+.
T Consensus       151 ~------~~s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~r-pdLKlIlmSATld  222 (1283)
T TIGR01967       151 D------QVSSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRR-PDLKIIITSATID  222 (1283)
T ss_pred             c------ccCCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccchhHHHHHHHHHhhC-CCCeEEEEeCCcC
Confidence            1      123457899999999999887643 478999999999994 666665543 55555544 4789999999997


Q ss_pred             hhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCc-----cchHHHHHHHHh---hCCCCcEEEEecchhhHHHHH
Q 022383          218 HEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE-----EWKFDTLCDLYD---TLTITQAVIFCNTKRKIYYSV  289 (298)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-----~~k~~~l~~ll~---~~~~~k~lIf~~s~~~~~~l~  289 (298)
                      .  ..+...+...|. +.+...   ...+...|......     .++...+...+.   ....+++|||+++..+++.++
T Consensus       223 ~--~~fa~~F~~apv-I~V~Gr---~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~~l~  296 (1283)
T TIGR01967       223 P--ERFSRHFNNAPI-IEVSGR---TYPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGEREIRDAA  296 (1283)
T ss_pred             H--HHHHHHhcCCCE-EEECCC---cccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHHHHHH
Confidence            4  455554444454 333321   12345555544321     123333333332   124579999999999999999


Q ss_pred             HHHhhhc
Q 022383          290 FYFWIRW  296 (298)
Q Consensus       290 ~~L~~~~  296 (298)
                      +.|+..+
T Consensus       297 ~~L~~~~  303 (1283)
T TIGR01967       297 EILRKRN  303 (1283)
T ss_pred             HHHHhcC
Confidence            9998765

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.

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

Probab=99.75  E-value=2.6e-16  Score=131.38  Aligned_cols=221  Identities=18%  Similarity=0.120  Sum_probs=149.6

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .+++.|+.+-+.+.    +.++.++.|-||+|||.+..-.+-..+..   |.++.+.+|+...|.+++.++++...  +.
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~---G~~vciASPRvDVclEl~~Rlk~aF~--~~  171 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQ---GGRVCIASPRVDVCLELYPRLKQAFS--NC  171 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhc---CCeEEEecCcccchHHHHHHHHHhhc--cC
Confidence            58999998876654    67899999999999998744344333333   66899999999999999999988744  46


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEE
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v  210 (298)
                      .+..++|+.+...+       .+++|+|..+|.++-.       .++++||||+|.+.=..-......+-+...++.-.|
T Consensus       172 ~I~~Lyg~S~~~fr-------~plvVaTtHQLlrFk~-------aFD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~I  237 (441)
T COG4098         172 DIDLLYGDSDSYFR-------APLVVATTHQLLRFKQ-------AFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATI  237 (441)
T ss_pred             CeeeEecCCchhcc-------ccEEEEehHHHHHHHh-------hccEEEEeccccccccCCHHHHHHHHHhhcccCceE
Confidence            67788887665432       5899999988887654       678999999998632221222233344444567799


Q ss_pred             EEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchH------HHHHHHHhhC--CCCcEEEEecch
Q 022383          211 LISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF------DTLCDLYDTL--TITQAVIFCNTK  282 (298)
Q Consensus       211 ~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~------~~l~~ll~~~--~~~k~lIf~~s~  282 (298)
                      .+|||+++.++..+...-..+..+........+  ..-.++.+.+-..++      -.+..+++.+  .+.+++||+++.
T Consensus       238 ylTATp~k~l~r~~~~g~~~~~klp~RfH~~pL--pvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~I  315 (441)
T COG4098         238 YLTATPTKKLERKILKGNLRILKLPARFHGKPL--PVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPEI  315 (441)
T ss_pred             EEecCChHHHHHHhhhCCeeEeecchhhcCCCC--CCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEecch
Confidence            999999988877665433222322222222221  222223233222132      2566666533  456999999999


Q ss_pred             hhHHHHHHHHhhhc
Q 022383          283 RKIYYSVFYFWIRW  296 (298)
Q Consensus       283 ~~~~~l~~~L~~~~  296 (298)
                      +..+++++.|+.+.
T Consensus       316 ~~~eq~a~~lk~~~  329 (441)
T COG4098         316 ETMEQVAAALKKKL  329 (441)
T ss_pred             HHHHHHHHHHHhhC
Confidence            99999999997654

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

Probab=99.75  E-value=1.3e-16  Score=149.36  Aligned_cols=239  Identities=17%  Similarity=0.212  Sum_probs=157.3

Q ss_pred             HHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           45 LRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .+.+++.....|+..|+-+...+..|++.-+.||||.|||.--++..+- +  ...+.+++||+||..|+.|+.+.++++
T Consensus        72 ~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~-~--a~kgkr~yii~PT~~Lv~Q~~~kl~~~  148 (1187)
T COG1110          72 EEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLY-L--AKKGKRVYIIVPTTTLVRQVYERLKKF  148 (1187)
T ss_pred             HHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHH-H--HhcCCeEEEEecCHHHHHHHHHHHHHH
Confidence            3344444334799999999999999999999999999999533222211 1  123569999999999999999999999


Q ss_pred             hccCC-ceEEE-EEcCCchHHH---HHHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc-------
Q 022383          125 GDFIN-IQAHA-CVGGKSVGED---IRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-------  191 (298)
Q Consensus       125 ~~~~~-~~~~~-~~~~~~~~~~---~~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-------  191 (298)
                      +...+ ..+.. +|+..+..+.   ..++. ++.||+|+|.+-|..-...  +.-.++++|++|++|.++..+       
T Consensus       149 ~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~--L~~~kFdfifVDDVDA~LkaskNvDriL  226 (1187)
T COG1110         149 AEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE--LSKLKFDFIFVDDVDAILKASKNVDRLL  226 (1187)
T ss_pred             HhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH--hcccCCCEEEEccHHHHHhccccHHHHH
Confidence            86655 33322 6666444332   33333 5789999998555543332  111478999999999987543       


Q ss_pred             ----cHH-------HHHHHHHhC------------------------CCCccEEEEEeeCchhH--HHHHHhcCCCCEEE
Q 022383          192 ----FKD-------QIYDVYRYL------------------------PPDLQVVLISATLPHEI--LEMTTKFMTDPVKI  234 (298)
Q Consensus       192 ----~~~-------~i~~i~~~~------------------------~~~~~~v~~SAT~~~~~--~~~~~~~~~~~~~~  234 (298)
                          |..       .+..+...+                        .+..++++.|||..+.-  ..+.+..++    +
T Consensus       227 ~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlg----F  302 (1187)
T COG1110         227 RLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLG----F  302 (1187)
T ss_pred             HHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhC----C
Confidence                111       011111111                        13468999999985432  223333332    3


Q ss_pred             EecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecc---hhhHHHHHHHHhhhcC
Q 022383          235 LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNT---KRKIYYSVFYFWIRWI  297 (298)
Q Consensus       235 ~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s---~~~~~~l~~~L~~~~~  297 (298)
                      .+......+.+|...|...   + -...+..+++... .-.|||++.   ++.+++++++|++.|+
T Consensus       303 evG~~~~~LRNIvD~y~~~---~-~~e~~~elvk~lG-~GgLIfV~~d~G~e~aeel~e~Lr~~Gi  363 (1187)
T COG1110         303 EVGSGGEGLRNIVDIYVES---E-SLEKVVELVKKLG-DGGLIFVPIDYGREKAEELAEYLRSHGI  363 (1187)
T ss_pred             ccCccchhhhheeeeeccC---c-cHHHHHHHHHHhC-CCeEEEEEcHHhHHHHHHHHHHHHhcCc
Confidence            3333444455666666654   2 4556666666653 478999999   9999999999999986

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

Probab=99.73  E-value=2.5e-17  Score=153.21  Aligned_cols=172  Identities=14%  Similarity=0.143  Sum_probs=138.0

Q ss_pred             CHHHHHHHHHCCCCCChHHHHHHH--HHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           41 KDDLLRGIYQYGFEKPSAIQQRAV--MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        41 ~~~i~~~l~~~~~~~~~~~Q~~~~--~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      +....-..+..|...++.||.+++  +.++.++|++..+||+.|||++..+-++..+...  ...++++.|....+.+-.
T Consensus       209 ~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~--rr~~llilp~vsiv~Ek~  286 (1008)
T KOG0950|consen  209 TKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCR--RRNVLLILPYVSIVQEKI  286 (1008)
T ss_pred             hHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHH--hhceeEecceeehhHHHH
Confidence            334444556678899999999997  4578999999999999999999998888876654  337899999999999988


Q ss_pred             HHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc--cCccCCCccEEEechhhHhhccccHHHH
Q 022383          119 KVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQI  196 (298)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~--~~~~~~~l~~vViDE~h~~~~~~~~~~i  196 (298)
                      ..+..+....|+++-.+.|........    ..-++.|||.|+-..+++.  ..-++..+++||+||.|++.+.+.+..+
T Consensus       287 ~~l~~~~~~~G~~ve~y~g~~~p~~~~----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~l  362 (1008)
T KOG0950|consen  287 SALSPFSIDLGFPVEEYAGRFPPEKRR----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAIL  362 (1008)
T ss_pred             hhhhhhccccCCcchhhcccCCCCCcc----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHH
Confidence            888888888899887777665544332    2358999999999887765  3456778999999999999999888887


Q ss_pred             HHHHHhC-----CCCccEEEEEeeCch
Q 022383          197 YDVYRYL-----PPDLQVVLISATLPH  218 (298)
Q Consensus       197 ~~i~~~~-----~~~~~~v~~SAT~~~  218 (298)
                      +.++.++     ....|+|+||||+++
T Consensus       363 E~~l~k~~y~~~~~~~~iIGMSATi~N  389 (1008)
T KOG0950|consen  363 ELLLAKILYENLETSVQIIGMSATIPN  389 (1008)
T ss_pred             HHHHHHHHHhccccceeEeeeecccCC
Confidence            7776654     234679999999986

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=99.72  E-value=2.2e-15  Score=144.24  Aligned_cols=236  Identities=19%  Similarity=0.172  Sum_probs=174.7

Q ss_pred             CHHHHHHHHH-CCCCCChHHHHHHHHHhhc----C--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           41 KDDLLRGIYQ-YGFEKPSAIQQRAVMPIIK----G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        41 ~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~----~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      +......+.. +.|+ -|+-|..+|..+.+    +  -|-++||--|-|||.+++-+++..+..   +.+|.++|||.-|
T Consensus       580 d~~~q~~F~~~FPye-ET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~---GKQVAvLVPTTlL  655 (1139)
T COG1197         580 DTEWQEEFEASFPYE-ETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMD---GKQVAVLVPTTLL  655 (1139)
T ss_pred             ChHHHHHHHhcCCCc-CCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcC---CCeEEEEcccHHh
Confidence            3444444444 4555 89999999999874    3  388999999999999999999998876   5799999999999


Q ss_pred             HHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          114 ATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       114 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                      |+|.++.|++......+++..++.-.+.+++...+.    +..||+|||.    +++. ..+.++++.++||||-|++.-
T Consensus       656 A~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTH----rLL~-kdv~FkdLGLlIIDEEqRFGV  730 (1139)
T COG1197         656 AQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTH----RLLS-KDVKFKDLGLLIIDEEQRFGV  730 (1139)
T ss_pred             HHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEech----HhhC-CCcEEecCCeEEEechhhcCc
Confidence            999999999998888999988888777666654432    6789999997    3333 467789999999999999632


Q ss_pred             cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHH-h
Q 022383          190 RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY-D  268 (298)
Q Consensus       190 ~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll-~  268 (298)
                      .     -..-++.+..++-++-+|||+-+....+.-..+.+...+..++.+.  ..++.++..-++.     .+.+.+ .
T Consensus       731 k-----~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R--~pV~T~V~~~d~~-----~ireAI~R  798 (1139)
T COG1197         731 K-----HKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDR--LPVKTFVSEYDDL-----LIREAILR  798 (1139)
T ss_pred             c-----HHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCC--cceEEEEecCChH-----HHHHHHHH
Confidence            2     2344455566788999999997766776666666666665554332  2345544433322     222222 2


Q ss_pred             -hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          269 -TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       269 -~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                       ...++++-..+|.+++.+.+++.|+..-|
T Consensus       799 El~RgGQvfYv~NrV~~Ie~~~~~L~~LVP  828 (1139)
T COG1197         799 ELLRGGQVFYVHNRVESIEKKAERLRELVP  828 (1139)
T ss_pred             HHhcCCEEEEEecchhhHHHHHHHHHHhCC
Confidence             23567999999999999999999987644

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.70  E-value=3.6e-16  Score=149.52  Aligned_cols=242  Identities=15%  Similarity=0.122  Sum_probs=149.9

Q ss_pred             CChHHHHHHHHHhhcC---C-cEEEEcCCCCchHHHHHHHHHHhhcc-CCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           55 KPSAIQQRAVMPIIKG---R-DVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~---~-~~li~~pTG~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      ...++|..++..+...   . .+++.||||+|||.+.+.++...... .....+++++.|++.+++++.++++.+....+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~  274 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFS  274 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccc
Confidence            3589999999887743   4 78999999999999999999888766 34567999999999999999999998766544


Q ss_pred             ceEEEEEcCCchHHHHHH-----h---------hcCCcEEEeChHHHHHHHhc-cCcc-C--CCccEEEechhhHhhccc
Q 022383          130 IQAHACVGGKSVGEDIRK-----L---------EHGVHVVSGTPGRVCDMIKR-KTLR-T--RAIKLLVLDESDEMLSRG  191 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~-----~---------~~~~~ilV~Tp~~l~~~~~~-~~~~-~--~~l~~vViDE~h~~~~~~  191 (298)
                      +.....++..........     .         .....+.++||......... ..+. +  --.+.+|+||+|.+.+..
T Consensus       275 ~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~  354 (733)
T COG1203         275 VIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET  354 (733)
T ss_pred             cccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc
Confidence            333323333222211110     0         01134555666555542211 1111 1  133679999999987664


Q ss_pred             cHHHHHHHHHhCC-CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCc---cCcCCceEE-EEEecCccchHHHHHHH
Q 022383          192 FKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE---LTLEGIKQF-FVAVEREEWKFDTLCDL  266 (298)
Q Consensus       192 ~~~~i~~i~~~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~i~~~-~~~~~~~~~k~~~l~~l  266 (298)
                      ....+..++..+. .+..+|+||||+|+.....+.........+......   ..-..+.+. ........ ........
T Consensus       355 ~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~-~~~~~~~~  433 (733)
T COG1203         355 MLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGP-QEELIELI  433 (733)
T ss_pred             hHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhh-hHhhhhcc
Confidence            4444444444443 468899999999999999888876654444332110   000001100 00000000 00111111


Q ss_pred             H-hhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          267 Y-DTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       267 l-~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      . ....+++++|.|||+..|.++++.|+..++
T Consensus       434 ~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~  465 (733)
T COG1203         434 SEEVKEGKKVLVIVNTVDRAIELYEKLKEKGP  465 (733)
T ss_pred             hhhhccCCcEEEEEecHHHHHHHHHHHHhcCC
Confidence            2 233457999999999999999999998764

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=99.69  E-value=8e-16  Score=141.87  Aligned_cols=153  Identities=20%  Similarity=0.228  Sum_probs=111.3

Q ss_pred             CCChHHHHHHHHHhh----cC-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC
Q 022383           54 EKPSAIQQRAVMPII----KG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~----~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~  128 (298)
                      ..++.+|..++..+.    +| +-+++++.||+|||.++ +.++.++.....-.++|||+-+++|+.|....+..+....
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~  242 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFG  242 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCc
Confidence            369999999997654    44 35999999999999763 4566677666667799999999999999999888876543


Q ss_pred             CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc-----CccCCCccEEEechhhHhhccccHHHHHHHHHhC
Q 022383          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-----TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (298)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~-----~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~  203 (298)
                      . .+..+.+...        ...++|.|+|-+.+...+...     .+...++++|||||||+    |.......++.++
T Consensus       243 ~-~~n~i~~~~~--------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHR----gi~~~~~~I~dYF  309 (875)
T COG4096         243 T-KMNKIEDKKG--------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR----GIYSEWSSILDYF  309 (875)
T ss_pred             c-ceeeeecccC--------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhh----hHHhhhHHHHHHH
Confidence            2 2222222111        124799999999988776543     46668899999999996    3455666888888


Q ss_pred             CCCccEEEEEeeCchhHHH
Q 022383          204 PPDLQVVLISATLPHEILE  222 (298)
Q Consensus       204 ~~~~~~v~~SAT~~~~~~~  222 (298)
                      ..-  .+++|||+...+..
T Consensus       310 dA~--~~gLTATP~~~~d~  326 (875)
T COG4096         310 DAA--TQGLTATPKETIDR  326 (875)
T ss_pred             HHH--HHhhccCccccccc
Confidence            532  34559998764443

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.65  E-value=4.3e-15  Score=140.09  Aligned_cols=127  Identities=19%  Similarity=0.249  Sum_probs=100.3

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      |++.|--.--.+  .+.-+..++||.|||+++.+|++.....   +..+.|++|+..||.+..+.+..+...+|+++...
T Consensus        83 ~ydVQliGgl~L--~~G~IaEm~TGEGKTL~a~lp~~l~al~---g~~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv~~i  157 (908)
T PRK13107         83 HFDVQLLGGMVL--DSNRIAEMRTGEGKTLTATLPAYLNALT---GKGVHVITVNDYLARRDAENNRPLFEFLGLTVGIN  157 (908)
T ss_pred             cCchHHhcchHh--cCCccccccCCCCchHHHHHHHHHHHhc---CCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEEe
Confidence            566555433333  3455889999999999999999876654   33599999999999999999999999999999999


Q ss_pred             EcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhcc-CccC-----CCccEEEechhhHhhc
Q 022383          136 VGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK-TLRT-----RAIKLLVLDESDEMLS  189 (298)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~-~~~~-----~~l~~vViDE~h~~~~  189 (298)
                      .++.+.....  -.-.++|+++||..| +.+++.+ .++.     +.+.+.||||+|.++-
T Consensus       158 ~~~~~~~~r~--~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLi  216 (908)
T PRK13107        158 VAGLGQQEKK--AAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILI  216 (908)
T ss_pred             cCCCCHHHHH--hcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhcc
Confidence            8887754332  223689999999999 8888775 3333     7889999999999863

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

Probab=99.63  E-value=1.5e-14  Score=137.16  Aligned_cols=151  Identities=17%  Similarity=0.163  Sum_probs=99.7

Q ss_pred             ChHHHHHHHHHhh----c------CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           56 PSAIQQRAVMPII----K------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        56 ~~~~Q~~~~~~~~----~------~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      ++++|.+++..+.    .      ++..+++.|||||||++.+..+...+ .....+++|||+|+.+|..|+.+.+..++
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            7899999998763    2      25799999999999988765554433 33446799999999999999999998875


Q ss_pred             ccCCceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhcc--CccCCCc-cEEEechhhHhhccccHHHHHHHH-
Q 022383          126 DFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRK--TLRTRAI-KLLVLDESDEMLSRGFKDQIYDVY-  200 (298)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~--~~~~~~l-~~vViDE~h~~~~~~~~~~i~~i~-  200 (298)
                      ... .     .+..+.......+. ...+|+|+|.++|...+...  .+...+- .+||+||||+.....+.    ..+ 
T Consensus       318 ~~~-~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~~~~----~~l~  387 (667)
T TIGR00348       318 KDC-A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYGELA----KNLK  387 (667)
T ss_pred             CCC-C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccchHHH----HHHH
Confidence            310 0     11112222222232 34689999999998644331  1211111 28999999986433333    333 


Q ss_pred             HhCCCCccEEEEEeeCch
Q 022383          201 RYLPPDLQVVLISATLPH  218 (298)
Q Consensus       201 ~~~~~~~~~v~~SAT~~~  218 (298)
                      +.+ ++...+++|||+-.
T Consensus       388 ~~~-p~a~~lGfTaTP~~  404 (667)
T TIGR00348       388 KAL-KNASFFGFTGTPIF  404 (667)
T ss_pred             hhC-CCCcEEEEeCCCcc
Confidence            344 46789999999853

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

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

Probab=99.61  E-value=4.8e-14  Score=131.92  Aligned_cols=215  Identities=20%  Similarity=0.183  Sum_probs=144.2

Q ss_pred             CCChHHHHHHHHHhhcC----CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           54 EKPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~----~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      ..+++-|+.++..+.+.    +..++.|.||||||.+|+-.+-..+..   |..+|+|+|-.+|..|+.++|+...   +
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~---GkqvLvLVPEI~Ltpq~~~rf~~rF---g  270 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ---GKQVLVLVPEIALTPQLLARFKARF---G  270 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc---CCEEEEEeccccchHHHHHHHHHHh---C
Confidence            36789999999998755    679999999999999999888777766   5689999999999999999998764   5


Q ss_pred             ceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh---ccc---cHHHHHHH
Q 022383          130 IQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML---SRG---FKDQIYDV  199 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~---~~~---~~~~i~~i  199 (298)
                      .++..++++.+..+....+    .+...|+|||-..++       ..++++.+||+||-|--.   +++   ...++ .+
T Consensus       271 ~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdv-A~  342 (730)
T COG1198         271 AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEDGPRYHARDV-AV  342 (730)
T ss_pred             CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-------CchhhccEEEEeccccccccCCcCCCcCHHHH-HH
Confidence            7888899887766554443    467899999975554       457899999999999632   111   12222 23


Q ss_pred             HHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchH-----HHHHHHHh--hCCC
Q 022383          200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF-----DTLCDLYD--TLTI  272 (298)
Q Consensus       200 ~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~-----~~l~~ll~--~~~~  272 (298)
                      .+....++++|+-|||++  ++++....-+....+..........-....++.+..+..+.     ..+.+.++  ...+
T Consensus       343 ~Ra~~~~~pvvLgSATPS--LES~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~g  420 (730)
T COG1198         343 LRAKKENAPVVLGSATPS--LESYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERG  420 (730)
T ss_pred             HHHHHhCCCEEEecCCCC--HHHHHhhhcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcC
Confidence            333335789999999966  55555443332233333222222212233334444333222     23444442  3356


Q ss_pred             CcEEEEecchhh
Q 022383          273 TQAVIFCNTKRK  284 (298)
Q Consensus       273 ~k~lIf~~s~~~  284 (298)
                      +++|+|.|++--
T Consensus       421 eQ~llflnRRGy  432 (730)
T COG1198         421 EQVLLFLNRRGY  432 (730)
T ss_pred             CeEEEEEccCCc
Confidence            799999998753

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=99.57  E-value=6.6e-13  Score=126.15  Aligned_cols=224  Identities=16%  Similarity=0.207  Sum_probs=147.6

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH-HhhccCCceEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHA  134 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~-~~~~~~~~~~~~  134 (298)
                      .+....+...++.+.+-++|+||||+|||...-.-+++.-..  .+..+.+.-|+|--|..+++++- .++...|-.|++
T Consensus        51 v~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~--~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY  128 (845)
T COG1643          51 VTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLG--IAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGY  128 (845)
T ss_pred             cHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhcc--cCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeE
Confidence            455666777888889999999999999998765555555432  23356667799988888887774 344444544544


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh-ccc-cHHHHHHHHHhCCCCccEEEE
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRG-FKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~-~~~-~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      .....+      ....+..|-+.|.+.|++.+..... ++.+++|||||+|.=. +.+ ..-.+..++..++...++|+|
T Consensus       129 ~iRfe~------~~s~~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIim  201 (845)
T COG1643         129 SIRFES------KVSPRTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIM  201 (845)
T ss_pred             EEEeec------cCCCCceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEE
Confidence            332211      1223468999999999999987544 7899999999999721 111 223445556666767999999


Q ss_pred             EeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccc-hHHHHHHHHh---hCCCCcEEEEecchhhHHHH
Q 022383          213 SATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEW-KFDTLCDLYD---TLTITQAVIFCNTKRKIYYS  288 (298)
Q Consensus       213 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~-k~~~l~~ll~---~~~~~k~lIf~~s~~~~~~l  288 (298)
                      |||+..+  .+. .++++.-.+.+..   ....++.+|......++ -...+...+.   ....+.+|||.+...+.+..
T Consensus       202 SATld~~--rfs-~~f~~apvi~i~G---R~fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~  275 (845)
T COG1643         202 SATLDAE--RFS-AYFGNAPVIEIEG---RTYPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERT  275 (845)
T ss_pred             ecccCHH--HHH-HHcCCCCEEEecC---CccceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHH
Confidence            9999853  333 3455333333321   22345555544443333 3344444443   33467999999999999999


Q ss_pred             HHHHhh
Q 022383          289 VFYFWI  294 (298)
Q Consensus       289 ~~~L~~  294 (298)
                      ++.|++
T Consensus       276 ~~~L~~  281 (845)
T COG1643         276 AEWLEK  281 (845)
T ss_pred             HHHHHh
Confidence            999987

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

Probab=99.56  E-value=1.6e-14  Score=134.56  Aligned_cols=160  Identities=15%  Similarity=0.166  Sum_probs=119.6

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc-eEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI-QAH  133 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~-~~~  133 (298)
                      .|..||.+.+...-.+.+++|+|||.+|||++--..+ +.+.......-+|++.|+++|++|+............+ +..
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~i-EKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~  589 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAI-EKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLRGV  589 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHH-HHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccccch
Confidence            4889999999999999999999999999997644334 44444444558999999999999999888765432222 122


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc---cCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEE
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR---KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~---~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v  210 (298)
                      .+.|....+++..  .-.|+|+|+.|+.+.+++..   ...+..+++++|+||+|.++...-...++.++-..  .++++
T Consensus       590 sl~g~ltqEYsin--p~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li--~CP~L  665 (1330)
T KOG0949|consen  590 SLLGDLTQEYSIN--PWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI--PCPFL  665 (1330)
T ss_pred             hhHhhhhHHhcCC--chhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc--CCCee
Confidence            2333333332222  23589999999999999877   45677999999999999998776566666776666  48899


Q ss_pred             EEEeeCchh
Q 022383          211 LISATLPHE  219 (298)
Q Consensus       211 ~~SAT~~~~  219 (298)
                      ++|||+.+.
T Consensus       666 ~LSATigN~  674 (1330)
T KOG0949|consen  666 VLSATIGNP  674 (1330)
T ss_pred             EEecccCCH
Confidence            999999653

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.51  E-value=1.2e-12  Score=123.36  Aligned_cols=130  Identities=17%  Similarity=0.259  Sum_probs=101.1

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|. .|++.|--.--.+..|+  +....||+|||+++.+|++-....   |..+-+++|+.-||.|-++.+..+...+|+
T Consensus        77 ~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~---G~~v~vvT~neyLA~Rd~e~~~~~~~~LGl  150 (796)
T PRK12906         77 LGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT---GKGVHVVTVNEYLSSRDATEMGELYRWLGL  150 (796)
T ss_pred             hCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc---CCCeEEEeccHHHHHhhHHHHHHHHHhcCC
Confidence            454 48888877766666666  899999999999998888776655   557889999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHH-HHhcc------CccCCCccEEEechhhHhh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~-~~~~~------~~~~~~l~~vViDE~h~~~  188 (298)
                      ++....++.+..+.....  .+||+.+|...|.- +++.+      ....+.+.+.||||+|.++
T Consensus       151 ~vg~i~~~~~~~~r~~~y--~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiL  213 (796)
T PRK12906        151 TVGLNLNSMSPDEKRAAY--NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSIL  213 (796)
T ss_pred             eEEEeCCCCCHHHHHHHh--cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchhee
Confidence            999998877665544333  57999999877652 33332      1223678899999999875

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

Probab=99.51  E-value=6e-13  Score=129.88  Aligned_cols=94  Identities=22%  Similarity=0.237  Sum_probs=71.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHH----HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~----~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~  115 (298)
                      +++.....+...||+ +++.|.++++    .+.+++++++.||||+|||++|++|++....   .+.+++|.+||++|..
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~---~~~~vvi~t~t~~Lq~  306 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI---TEKPVVISTNTKVLQS  306 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc---CCCeEEEEeCcHHHHH
Confidence            445677778788888 8899998666    4557899999999999999999999988665   2448999999999999


Q ss_pred             HHHH-HHHHhhccCC--ceEEEEEc
Q 022383          116 QTEK-VILAIGDFIN--IQAHACVG  137 (298)
Q Consensus       116 q~~~-~~~~~~~~~~--~~~~~~~~  137 (298)
                      |+.. .+..+.+..+  +++..+.|
T Consensus       307 Ql~~~~~~~l~~~~~~~~~~~~~kG  331 (850)
T TIGR01407       307 QLLEKDIPLLNEILNFKINAALIKG  331 (850)
T ss_pred             HHHHHHHHHHHHHcCCCceEEEEEc
Confidence            9865 4544444333  55555543

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.

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=99.44  E-value=2.9e-11  Score=109.63  Aligned_cols=221  Identities=14%  Similarity=0.207  Sum_probs=140.0

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH-HhhccCCceEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQAHA  134 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~-~~~~~~~~~~~~  134 (298)
                      ...+-.+.+..+.+++-+++.|+||||||.-.--.+.+.-... .+ ++-+.-|+|--|..++.+.. .++...|-.+++
T Consensus        52 I~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~-~g-~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY  129 (674)
T KOG0922|consen   52 IYKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFAS-SG-KIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGY  129 (674)
T ss_pred             HHHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhccccc-CC-cEEeecCchHHHHHHHHHHHHHhCCCcCceeee
Confidence            3444556777788889999999999999965433333332222 22 46667799987777776553 444444545544


Q ss_pred             EE--cCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh--hccccHHHHHHHHHhCCCCccEE
Q 022383          135 CV--GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM--LSRGFKDQIYDVYRYLPPDLQVV  210 (298)
Q Consensus       135 ~~--~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~--~~~~~~~~i~~i~~~~~~~~~~v  210 (298)
                      ..  .+...        ....|...|.+.|++-+.... .++++++||+||||.=  ..+-..-.++.++++. +..++|
T Consensus       130 ~IRFed~ts--------~~TrikymTDG~LLRE~l~Dp-~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R-~~LklI  199 (674)
T KOG0922|consen  130 TIRFEDSTS--------KDTRIKYMTDGMLLREILKDP-LLSKYSVIILDEAHERSLHTDILLGLLKKILKKR-PDLKLI  199 (674)
T ss_pred             EEEecccCC--------CceeEEEecchHHHHHHhcCC-ccccccEEEEechhhhhhHHHHHHHHHHHHHhcC-CCceEE
Confidence            33  22211        235899999999998665432 3679999999999961  1111222333344433 467899


Q ss_pred             EEEeeCchhHHHHHHhcCCC-CEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh---hCCCCcEEEEecchhhHH
Q 022383          211 LISATLPHEILEMTTKFMTD-PVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD---TLTITQAVIFCNTKRKIY  286 (298)
Q Consensus       211 ~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~---~~~~~k~lIf~~s~~~~~  286 (298)
                      ++|||+..   +....|+.. |....-.    ....++..|..-+..++-...+...++   ..+.+-+|||....++.+
T Consensus       200 imSATlda---~kfS~yF~~a~i~~i~G----R~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe  272 (674)
T KOG0922|consen  200 IMSATLDA---EKFSEYFNNAPILTIPG----RTFPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIE  272 (674)
T ss_pred             EEeeeecH---HHHHHHhcCCceEeecC----CCCceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHH
Confidence            99999983   333345544 4433322    223466666665555544445555444   345679999999999999


Q ss_pred             HHHHHHhhh
Q 022383          287 YSVFYFWIR  295 (298)
Q Consensus       287 ~l~~~L~~~  295 (298)
                      .+++.|++.
T Consensus       273 ~~~~~l~e~  281 (674)
T KOG0922|consen  273 AACELLRER  281 (674)
T ss_pred             HHHHHHHHH
Confidence            999999765

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.44  E-value=1.4e-11  Score=119.49  Aligned_cols=158  Identities=18%  Similarity=0.083  Sum_probs=97.2

Q ss_pred             CChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceE
Q 022383           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  132 (298)
                      .|.|||.++...+...  ..+++.-.+|.|||.-+.+.+...+.. ....++|||||. .|..|+...+.+..   ++..
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~-g~~~rvLIVvP~-sL~~QW~~El~~kF---~l~~  226 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLT-GRAERVLILVPE-TLQHQWLVEMLRRF---NLRF  226 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHc-CCCCcEEEEcCH-HHHHHHHHHHHHHh---CCCe
Confidence            4999999998776543  478999999999997765544444333 333479999997 89999988875432   3444


Q ss_pred             EEEEcCCchHHHH--HHhhcCCcEEEeChHHHHHHH-hccCccCCCccEEEechhhHhhcc--ccHHHHHHHHHhCCCCc
Q 022383          133 HACVGGKSVGEDI--RKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLSR--GFKDQIYDVYRYLPPDL  207 (298)
Q Consensus       133 ~~~~~~~~~~~~~--~~~~~~~~ilV~Tp~~l~~~~-~~~~~~~~~l~~vViDE~h~~~~~--~~~~~i~~i~~~~~~~~  207 (298)
                      ..+.++.......  .......+++|+|.+.+...- ....+.-...++||+||||++-..  .-...+..+........
T Consensus       227 ~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~~  306 (956)
T PRK04914        227 SLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVIP  306 (956)
T ss_pred             EEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhccC
Confidence            4443332111000  011123589999987776421 111222347899999999998521  11122333322222345


Q ss_pred             cEEEEEeeCc
Q 022383          208 QVVLISATLP  217 (298)
Q Consensus       208 ~~v~~SAT~~  217 (298)
                      .++++|||+.
T Consensus       307 ~~LLLTATP~  316 (956)
T PRK04914        307 GVLLLTATPE  316 (956)
T ss_pred             CEEEEEcCcc
Confidence            6899999974

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

Probab=99.42  E-value=3.6e-12  Score=118.46  Aligned_cols=61  Identities=18%  Similarity=0.201  Sum_probs=51.5

Q ss_pred             HHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           64 VMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        64 ~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      ...+.+++.+++.||||+|||++|++|++..+... .+.++||++||++|.+|+.+.+..+.
T Consensus        10 ~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~-~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117        10 LTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER-PDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             HHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc-cCceEEEECCcHHHHHHHHHHHHHHH
Confidence            34455788999999999999999999998876532 24689999999999999999888776

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.

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

Probab=99.42  E-value=2.9e-12  Score=122.46  Aligned_cols=221  Identities=14%  Similarity=0.202  Sum_probs=149.6

Q ss_pred             CCChHHHHHHHHHhh-cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH-HhhccCCce
Q 022383           54 EKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQ  131 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~-~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~-~~~~~~~~~  131 (298)
                      ...++.|.++++.+. .+.++++.+|+|+|||.|+-++++.    .....+++++.|..+.+..++..+. ++.+..|..
T Consensus      1142 ~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~ 1217 (1674)
T KOG0951|consen 1142 QDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLR 1217 (1674)
T ss_pred             cccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccccCce
Confidence            344899999999876 4678999999999999999888877    2234589999999999988877664 566667888


Q ss_pred             EEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHH------HHHHHHHhCCC
Q 022383          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD------QIYDVYRYLPP  205 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~------~i~~i~~~~~~  205 (298)
                      ++.+.|..+.+-..   ...-+++|+||++...+ +    ..+.++++|.||.|.+... ++.      .++.+-+.+-+
T Consensus      1218 ~~~l~ge~s~~lkl---~~~~~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~igg~-~g~v~evi~S~r~ia~q~~k 1288 (1674)
T KOG0951|consen 1218 IVKLTGETSLDLKL---LQKGQVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIGGV-YGAVYEVICSMRYIASQLEK 1288 (1674)
T ss_pred             EEecCCccccchHH---hhhcceEEechhHHHHH-h----hhhhcceEeeehhhhhccc-CCceEEEEeeHHHHHHHHHh
Confidence            88888877655332   23359999999998776 2    5778999999999998733 221      15666666667


Q ss_pred             CccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCcc----------chHHHHHHHHhhCCCCcE
Q 022383          206 DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREE----------WKFDTLCDLYDTLTITQA  275 (298)
Q Consensus       206 ~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~----------~k~~~l~~ll~~~~~~k~  275 (298)
                      +.+++.+|..+.+. .+++  ++ .+..+.....+..+....-.+...+-..          .-+.++...  ...+++.
T Consensus      1289 ~ir~v~ls~~lana-~d~i--g~-s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~--a~~~k~~ 1362 (1674)
T KOG0951|consen 1289 KIRVVALSSSLANA-RDLI--GA-SSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRH--AGNRKPA 1362 (1674)
T ss_pred             heeEEEeehhhccc-hhhc--cc-cccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHH--hcCCCCe
Confidence            88999999998765 3332  11 2222322222333323222222222211          111122211  2345799


Q ss_pred             EEEecchhhHHHHHHHHh
Q 022383          276 VIFCNTKRKIYYSVFYFW  293 (298)
Q Consensus       276 lIf~~s~~~~~~l~~~L~  293 (298)
                      +||+++++.|..++..|-
T Consensus      1363 ~vf~p~rk~~~~~a~~~~ 1380 (1674)
T KOG0951|consen 1363 IVFLPTRKHARLVAVDLV 1380 (1674)
T ss_pred             EEEeccchhhhhhhhccc
Confidence            999999999999887653

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

Probab=99.41  E-value=5.8e-12  Score=121.74  Aligned_cols=83  Identities=25%  Similarity=0.321  Sum_probs=65.3

Q ss_pred             CCCCCChHHHHHHHHHh----hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH-HHHHHhh
Q 022383           51 YGFEKPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-KVILAIG  125 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~----~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~-~~~~~~~  125 (298)
                      .||+ .++-|.+....+    .+++.++++|+||+|||++|++|++...    .+.++||++||++|++|+. ..+..+.
T Consensus       242 ~~~e-~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~----~~~~vvI~t~T~~Lq~Ql~~~~i~~l~  316 (820)
T PRK07246        242 LGLE-ERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKAIQ  316 (820)
T ss_pred             CCCc-cCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHHHH
Confidence            3555 899999866554    4678999999999999999999988754    2458999999999999994 6677777


Q ss_pred             ccCCceEEEEEcC
Q 022383          126 DFINIQAHACVGG  138 (298)
Q Consensus       126 ~~~~~~~~~~~~~  138 (298)
                      +..++++..+.|+
T Consensus       317 ~~~~~~~~~~kg~  329 (820)
T PRK07246        317 EVFHIDCHSLKGP  329 (820)
T ss_pred             HhcCCcEEEEECC
Confidence            6667766665544

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.40  E-value=6.4e-11  Score=109.88  Aligned_cols=130  Identities=15%  Similarity=0.234  Sum_probs=102.0

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|.. |++.|--..-.+..|+  +....||.|||+++.+|++.....   |..+-+++|+.-||.+-++.+..+...+|+
T Consensus        75 lg~r-~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~---G~~VhvvT~NdyLA~RDae~m~~ly~~LGL  148 (764)
T PRK12326         75 LGLR-PFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ---GRRVHVITVNDYLARRDAEWMGPLYEALGL  148 (764)
T ss_pred             cCCC-cchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc---CCCeEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            4544 8888988887787775  679999999999999888776544   557899999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHH-HHHhcc------CccCCCccEEEechhhHhh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRK------TLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~~~~~------~~~~~~l~~vViDE~h~~~  188 (298)
                      ++....++.+..+....+  .|||+.+|...|. .+++.+      ....+.+.+.||||+|.++
T Consensus       149 svg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiL  211 (764)
T PRK12326        149 TVGWITEESTPEERRAAY--ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVL  211 (764)
T ss_pred             EEEEECCCCCHHHHHHHH--cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhe
Confidence            999988887765444443  4799999987754 233322      2234678999999999875

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.35  E-value=5.7e-11  Score=112.69  Aligned_cols=126  Identities=18%  Similarity=0.231  Sum_probs=96.5

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      +++.|--.--.+  .+.-+..+.||.|||+++.+|++-....   |..+-+++|+..||.+-++.+..+...+|+++..+
T Consensus        83 ~ydVQliGg~~L--h~G~iaEM~TGEGKTLvA~l~a~l~al~---G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~i  157 (913)
T PRK13103         83 HFDVQLIGGMTL--HEGKIAEMRTGEGKTLVGTLAVYLNALS---GKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIV  157 (913)
T ss_pred             cchhHHHhhhHh--ccCccccccCCCCChHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEEE
Confidence            666665443333  4455789999999999999888765544   55789999999999999999999999999999998


Q ss_pred             EcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhcc------CccCCCccEEEechhhHhh
Q 022383          136 VGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~------~~~~~~l~~vViDE~h~~~  188 (298)
                      .++.+..+....+.  ++|++||...| +.+++.+      ....+.+.++||||+|.++
T Consensus       158 ~~~~~~~err~~Y~--~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        158 TPFQPPEEKRAAYA--ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             CCCCCHHHHHHHhc--CCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            88776655444443  89999999876 2333332      1224889999999999975

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=99.34  E-value=3.2e-12  Score=95.41  Aligned_cols=136  Identities=15%  Similarity=0.239  Sum_probs=81.2

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      +|+-.++...+|+|||.-.+.-++..-...  +.++|+|.|||.++.++.+.++..    .+++.   ...-.    ...
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~--~~rvLvL~PTRvva~em~~aL~~~----~~~~~---t~~~~----~~~   69 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKR--RLRVLVLAPTRVVAEEMYEALKGL----PVRFH---TNARM----RTH   69 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHT--T--EEEEESSHHHHHHHHHHTTTS----SEEEE---STTSS-------
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHc--cCeEEEecccHHHHHHHHHHHhcC----CcccC---ceeee----ccc
Confidence            456678899999999987666555544332  558999999999999999977543    22221   11110    122


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc--cHHHHHHHHHhCCCCccEEEEEeeCchhH
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG--FKDQIYDVYRYLPPDLQVVLISATLPHEI  220 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~--~~~~i~~i~~~~~~~~~~v~~SAT~~~~~  220 (298)
                      .++.-|-|.|-..+.+.+.+ .....++++||+||+|..-...  +...+..... . ....+|++|||+|-..
T Consensus        70 ~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~~~-~-g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   70 FGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTSIAARGYLRELAE-S-GEAKVIFMTATPPGSE  140 (148)
T ss_dssp             -SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHHHHHHHHHHHHHH-T-TS-EEEEEESS-TT--
T ss_pred             cCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHHHhhheeHHHhhh-c-cCeeEEEEeCCCCCCC
Confidence            34557888898888887766 5557899999999999852221  2222222211 1 2467999999998653

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 ....

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.34  E-value=2.3e-10  Score=108.98  Aligned_cols=245  Identities=16%  Similarity=0.120  Sum_probs=152.6

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      .++...+.+....--..+..+.+.++++.+.+.++++|.||+|||.-.---+++....+....++++--|+|--|..+++
T Consensus       158 ~s~~~~~~~~~R~~LPa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAe  237 (924)
T KOG0920|consen  158 KSESYKEMLRFRESLPAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAE  237 (924)
T ss_pred             hhhHHHHHHHHHHhCccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHH
Confidence            33444444444433457788899999999999999999999999977665666665444445567777799988888888


Q ss_pred             HHHH-hhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHH
Q 022383          120 VILA-IGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIY  197 (298)
Q Consensus       120 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~  197 (298)
                      +..+ .+...|-.+++-.+..+      .......+++||.+.|++.+.. .-.+..+..+|+||+|.=.-+ +|.-.+.
T Consensus       238 RVa~ER~~~~g~~VGYqvrl~~------~~s~~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~l  310 (924)
T KOG0920|consen  238 RVAKERGESLGEEVGYQVRLES------KRSRETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILL  310 (924)
T ss_pred             HHHHHhccccCCeeeEEEeeec------ccCCceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHH
Confidence            7743 33334444444332211      1112358999999999999887 455789999999999973222 3433333


Q ss_pred             HHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCc----------------cCcCCceEE------------
Q 022383          198 DVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE----------------LTLEGIKQF------------  249 (298)
Q Consensus       198 ~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~i~~~------------  249 (298)
                      +.+-..++..++|+||||+..  +. ...|++....+.+....                .......+.            
T Consensus       311 k~lL~~~p~LkvILMSAT~da--e~-fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~  387 (924)
T KOG0920|consen  311 KDLLPRNPDLKVILMSATLDA--EL-FSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLAR  387 (924)
T ss_pred             HHHhhhCCCceEEEeeeecch--HH-HHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCcccccc
Confidence            333334478999999999983  33 33444433333222110                000000011            


Q ss_pred             EEEecCccchHHHHHHHHh----hCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          250 FVAVEREEWKFDTLCDLYD----TLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       250 ~~~~~~~~~k~~~l~~ll~----~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ......+ ..++.+.+++.    ....+.+|||.+...+...+++.|...
T Consensus       388 ~~~~~~~-id~~Li~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~  436 (924)
T KOG0920|consen  388 LKLWEPE-IDYDLIEDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVN  436 (924)
T ss_pred             chhcccc-ccHHHHHHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhc
Confidence            0001111 24555555553    333569999999999999999999653

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.33  E-value=3.3e-10  Score=99.26  Aligned_cols=250  Identities=15%  Similarity=0.139  Sum_probs=150.1

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      +.+..|+..+.++...+.|++..---.+..+.+.+..+.+++-++++|.||||||.-.--+.+.......  ..+..--|
T Consensus        22 k~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~--~~v~CTQp   99 (699)
T KOG0925|consen   22 KAINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL--TGVACTQP   99 (699)
T ss_pred             hhcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhc--cceeecCc
Confidence            3488999999999999999997555566666777777888999999999999999544333333322221  24566668


Q ss_pred             cHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh--
Q 022383          110 TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM--  187 (298)
Q Consensus       110 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~--  187 (298)
                      .+.-+-+++.+.-.   ..++..+--.|-.-..+.+..  .+.-+-.+|.++|++-.-. .-.+.+.+++|+||+|.=  
T Consensus       100 rrvaamsva~RVad---EMDv~lG~EVGysIrfEdC~~--~~T~Lky~tDgmLlrEams-~p~l~~y~viiLDeahERtl  173 (699)
T KOG0925|consen  100 RRVAAMSVAQRVAD---EMDVTLGEEVGYSIRFEDCTS--PNTLLKYCTDGMLLREAMS-DPLLGRYGVIILDEAHERTL  173 (699)
T ss_pred             hHHHHHHHHHHHHH---HhccccchhccccccccccCC--hhHHHHHhcchHHHHHHhh-CcccccccEEEechhhhhhH
Confidence            88877777664432   112222111111000010000  0000112444444443322 233678999999999972  


Q ss_pred             hccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHH
Q 022383          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll  267 (298)
                      ..+...-.+..+++.. +..++|.||||+-.   .....|++++-.+.+..    ...++.+|..-.+.+.-..++...+
T Consensus       174 ATDiLmGllk~v~~~r-pdLk~vvmSatl~a---~Kfq~yf~n~Pll~vpg----~~PvEi~Yt~e~erDylEaairtV~  245 (699)
T KOG0925|consen  174 ATDILMGLLKEVVRNR-PDLKLVVMSATLDA---EKFQRYFGNAPLLAVPG----THPVEIFYTPEPERDYLEAAIRTVL  245 (699)
T ss_pred             HHHHHHHHHHHHHhhC-CCceEEEeecccch---HHHHHHhCCCCeeecCC----CCceEEEecCCCChhHHHHHHHHHH
Confidence            1222344555566665 48999999999863   33445667666666543    2234555544444443333444444


Q ss_pred             h---hCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          268 D---TLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       268 ~---~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      +   ....+-+|+|....++.+..++.+.+.
T Consensus       246 qih~~ee~GDilvFLtgeeeIe~aC~~i~re  276 (699)
T KOG0925|consen  246 QIHMCEEPGDILVFLTGEEEIEDACRKISRE  276 (699)
T ss_pred             HHHhccCCCCEEEEecCHHHHHHHHHHHHHH
Confidence            4   234578999999999999998887643

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.32  E-value=7.7e-11  Score=108.59  Aligned_cols=224  Identities=17%  Similarity=0.211  Sum_probs=131.0

Q ss_pred             HHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC---CCCeEEEEEcCcHHHHHHHHHHHH-HhhccCCceE--EE
Q 022383           61 QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTRELATQTEKVIL-AIGDFINIQA--HA  134 (298)
Q Consensus        61 ~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~l~~q~~~~~~-~~~~~~~~~~--~~  134 (298)
                      +++..+|..+.-++|||.||||||.-.---++..-...   ..+..+=|--|+|--|..++.+.- .++. ++-.+  .+
T Consensus       262 q~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~-~~~eVsYqI  340 (1172)
T KOG0926|consen  262 QRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGV-LGSEVSYQI  340 (1172)
T ss_pred             HHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhcc-CccceeEEE
Confidence            45667777788899999999999965333333332111   122234455598877777766553 3333 33333  33


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh--cc---ccHHHHHHHHHhCCC----
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML--SR---GFKDQIYDVYRYLPP----  205 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~--~~---~~~~~i~~i~~~~~~----  205 (298)
                      .+.++        +.....|.+.|.+-|++-+.+ .+.+.+++.||+||||.=.  .+   |+...+-.+.....+    
T Consensus       341 Rfd~t--------i~e~T~IkFMTDGVLLrEi~~-DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~  411 (1172)
T KOG0926|consen  341 RFDGT--------IGEDTSIKFMTDGVLLREIEN-DFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQ  411 (1172)
T ss_pred             Eeccc--------cCCCceeEEecchHHHHHHHH-hHhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcc
Confidence            33332        223468999999999987775 4668899999999999621  00   122222222222222    


Q ss_pred             --CccEEEEEeeCchhHHHHHHhcCCC-CEEEEecCCccCcCCceEEEEEecCccchHHHHHHHH---hhCCCCcEEEEe
Q 022383          206 --DLQVVLISATLPHEILEMTTKFMTD-PVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY---DTLTITQAVIFC  279 (298)
Q Consensus       206 --~~~~v~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll---~~~~~~k~lIf~  279 (298)
                        ..+.|+||||+--......+.+++. |-.+.++....   .+.-.+..-...++-.++.....   +..+.+-+|||+
T Consensus       412 ~kpLKLIIMSATLRVsDFtenk~LFpi~pPlikVdARQf---PVsIHF~krT~~DYi~eAfrKtc~IH~kLP~G~ILVFv  488 (1172)
T KOG0926|consen  412 IKPLKLIIMSATLRVSDFTENKRLFPIPPPLIKVDARQF---PVSIHFNKRTPDDYIAEAFRKTCKIHKKLPPGGILVFV  488 (1172)
T ss_pred             cCceeEEEEeeeEEecccccCceecCCCCceeeeecccC---ceEEEeccCCCchHHHHHHHHHHHHhhcCCCCcEEEEE
Confidence              5679999999864333333344442 22333332221   12211111112222333333333   355778999999


Q ss_pred             cchhhHHHHHHHHhhhcC
Q 022383          280 NTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       280 ~s~~~~~~l~~~L~~~~~  297 (298)
                      ...+++..+++.|+++++
T Consensus       489 TGQqEV~qL~~kLRK~~p  506 (1172)
T KOG0926|consen  489 TGQQEVDQLCEKLRKRFP  506 (1172)
T ss_pred             eChHHHHHHHHHHHhhCc
Confidence            999999999999999865

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.28  E-value=7.6e-11  Score=101.00  Aligned_cols=72  Identities=19%  Similarity=0.221  Sum_probs=57.8

Q ss_pred             CCCCChHHHHHHHH----HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC---CeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           52 GFEKPSAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR---EVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~----~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~---~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      -|. ++|.|.+.+.    .+..|+++++.+|||+|||++++.|++..+.....   +.+++|.++|..+..|....++++
T Consensus         6 Py~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        6 PYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            344 6999999554    45578999999999999999999999876554322   237999999999999988777765

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.28  E-value=7.6e-11  Score=101.00  Aligned_cols=72  Identities=19%  Similarity=0.221  Sum_probs=57.8

Q ss_pred             CCCCChHHHHHHHH----HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC---CeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           52 GFEKPSAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR---EVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~----~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~---~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      -|. ++|.|.+.+.    .+..|+++++.+|||+|||++++.|++..+.....   +.+++|.++|..+..|....++++
T Consensus         6 Py~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        6 PYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            344 6999999554    45578999999999999999999999876554322   237999999999999988777765

>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=99.27  E-value=1e-10  Score=101.04  Aligned_cols=143  Identities=19%  Similarity=0.156  Sum_probs=84.2

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCC--CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (298)
                      .+..++.-.+|+|||...+..+.......+.  ...+||+||. .+..++...+.++.....+++..+.|+.........
T Consensus        25 ~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~~~  103 (299)
T PF00176_consen   25 PRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLSKN  103 (299)
T ss_dssp             T-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTTSS
T ss_pred             CCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhcccccccccccccccccccccccccc
Confidence            4689999999999997765444322222111  1259999999 888999999999876546677666665522222223


Q ss_pred             hhcCCcEEEeChHHHHHHHhc---cCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeC
Q 022383          148 LEHGVHVVSGTPGRVCDMIKR---KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~~~~---~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      .....+++|+|.+.+......   ..+...+.++||+||+|.+-+.  .......+..+. ...++++|||+
T Consensus       104 ~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~~--~s~~~~~l~~l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  104 QLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKNK--DSKRYKALRKLR-ARYRWLLSGTP  172 (299)
T ss_dssp             SCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTTT--TSHHHHHHHCCC-ECEEEEE-SS-
T ss_pred             ccccceeeeccccccccccccccccccccccceeEEEecccccccc--cccccccccccc-cceEEeecccc
Confidence            345678999999998811110   1111234899999999998333  223333344454 56688899997

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.

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

Probab=99.23  E-value=2.5e-10  Score=112.39  Aligned_cols=65  Identities=22%  Similarity=0.229  Sum_probs=53.9

Q ss_pred             CCCCChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           52 GFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      ||+ +++-|.+....+.    +++.+++.||||+|||++|++|++......  +.+++|-++|+.|-+|+..
T Consensus       255 ~~e-~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~--~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        255 KYE-KREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKK--EEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             CCc-CCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhcc--CCeEEEEcCCHHHHHHHHH
Confidence            444 9999999766544    678999999999999999999998655433  4589999999999999876

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.19  E-value=9.3e-10  Score=104.15  Aligned_cols=130  Identities=19%  Similarity=0.236  Sum_probs=96.8

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|+. |++.|--..  +.-.+.-+..+.||.|||+++.+|++-....   |..|-|++++..||.+-.+.+..+...+|+
T Consensus        73 lG~r-~ydvQlig~--l~L~~G~IaEm~TGEGKTL~a~l~ayl~aL~---G~~VhVvT~NdyLA~RD~e~m~pvy~~LGL  146 (870)
T CHL00122         73 LGLR-HFDVQLIGG--LVLNDGKIAEMKTGEGKTLVATLPAYLNALT---GKGVHIVTVNDYLAKRDQEWMGQIYRFLGL  146 (870)
T ss_pred             hCCC-CCchHhhhh--HhhcCCccccccCCCCchHHHHHHHHHHHhc---CCceEEEeCCHHHHHHHHHHHHHHHHHcCC
Confidence            4544 667666554  4435667889999999999999888543222   446899999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHH-HHHhcc------CccCCCccEEEechhhHhh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRK------TLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~~~~~------~~~~~~l~~vViDE~h~~~  188 (298)
                      .+....++.+..+.....  .+||+.+|...|. ++++.+      ....+.+.+.||||+|.++
T Consensus       147 svg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        147 TVGLIQEGMSSEERKKNY--LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             ceeeeCCCCChHHHHHhc--CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            999887777665544433  4799999987654 334332      1234678999999999975

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.19  E-value=8.4e-10  Score=107.78  Aligned_cols=153  Identities=14%  Similarity=0.125  Sum_probs=102.5

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhc-cCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVD-TSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~-~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .+.+||.+.+..+.    .|.+.|+.-.+|.|||+..+..+ ..+. .......+|||||. .++.++.+.++++..  .
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL-~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p--~  244 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLL-GYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCP--V  244 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHH-HHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCC--C
Confidence            68999999998764    57889999999999997643322 2222 11223368999995 667889999998864  4


Q ss_pred             ceEEEEEcCCchHHHHH-H--hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCC
Q 022383          130 IQAHACVGGKSVGEDIR-K--LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~-~--~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~  206 (298)
                      +++..++|......... .  ....++|+|+|.+.+.....  .+.--+.++||+||+|.+-..  .......++.+. .
T Consensus       245 l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~--~L~k~~W~~VIvDEAHrIKN~--~Sklskalr~L~-a  319 (1033)
T PLN03142        245 LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT--ALKRFSWRYIIIDEAHRIKNE--NSLLSKTMRLFS-T  319 (1033)
T ss_pred             CceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH--HhccCCCCEEEEcCccccCCH--HHHHHHHHHHhh-c
Confidence            56777777544322211 1  12467999999988765332  222235689999999998443  333444555554 3


Q ss_pred             ccEEEEEeeC
Q 022383          207 LQVVLISATL  216 (298)
Q Consensus       207 ~~~v~~SAT~  216 (298)
                      ...+++|+|+
T Consensus       320 ~~RLLLTGTP  329 (1033)
T PLN03142        320 NYRLLITGTP  329 (1033)
T ss_pred             CcEEEEecCC
Confidence            4568899997

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=99.18  E-value=1.1e-10  Score=102.67  Aligned_cols=223  Identities=19%  Similarity=0.171  Sum_probs=137.6

Q ss_pred             CChHHHHHHHHHhh-cC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           55 KPSAIQQRAVMPII-KG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~-~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      .++|+|...+.... +|  ++-+|+.|-|+|||++-..+++.      -..++|+||.+.-.+.|+..+++.+....+-.
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t------ikK~clvLcts~VSVeQWkqQfk~wsti~d~~  375 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT------IKKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQ  375 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee------ecccEEEEecCccCHHHHHHHHHhhcccCccc
Confidence            68999999998876 34  68999999999999764433322      13479999999999999999999987666666


Q ss_pred             EEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc--------CccCCCccEEEechhhHhhccccHHHHHHHHHhC
Q 022383          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK--------TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~--------~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~  203 (298)
                      ++.+.++...     ....++.|+|+|-.++..--++.        .+.-+...++++||+|.+...-|+..+.-+-...
T Consensus       376 i~rFTsd~Ke-----~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVlsiv~aHc  450 (776)
T KOG1123|consen  376 ICRFTSDAKE-----RFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLSIVQAHC  450 (776)
T ss_pred             eEEeeccccc-----cCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHHHHHHHHh
Confidence            7777765443     12356899999976665322211        1223567899999999986555665554443333


Q ss_pred             CCCccEEEEEeeCchhHHHHHH-hcCCCCEEEEecCCccC----------------------------cCCceEEEEEec
Q 022383          204 PPDLQVVLISATLPHEILEMTT-KFMTDPVKILVKRDELT----------------------------LEGIKQFFVAVE  254 (298)
Q Consensus       204 ~~~~~~v~~SAT~~~~~~~~~~-~~~~~~~~~~~~~~~~~----------------------------~~~i~~~~~~~~  254 (298)
                           .+++|||+-++...... .++-.|..+....-+..                            ...-....+.++
T Consensus       451 -----KLGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr~lLyvMN  525 (776)
T KOG1123|consen  451 -----KLGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKRMLLYVMN  525 (776)
T ss_pred             -----hccceeEEeeccccccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhhheeeecC
Confidence                 58999998433111111 01111211111100000                            000112222222


Q ss_pred             CccchHHHHHHHHh--hCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          255 REEWKFDTLCDLYD--TLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       255 ~~~~k~~~l~~ll~--~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      +.  |..+-..+++  ...+.|+|||..++-....+|-.|.+-
T Consensus       526 P~--KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~Kp  566 (776)
T KOG1123|consen  526 PN--KFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLGKP  566 (776)
T ss_pred             cc--hhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcCCc
Confidence            22  4555445554  335679999999998888888777543

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.16  E-value=3.1e-09  Score=96.40  Aligned_cols=228  Identities=15%  Similarity=0.160  Sum_probs=142.6

Q ss_pred             CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHH-HHhhccCCce
Q 022383           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI-LAIGDFINIQ  131 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~-~~~~~~~~~~  131 (298)
                      .-..+++-.+.+.++..++-++|+|.||||||.-.--.+...-.. ..+.++-+--|+|--|..++.+. +.++..+|-.
T Consensus       263 sLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGyt-k~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG~e  341 (902)
T KOG0923|consen  263 SLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYT-KGGKKIGCTQPRRVAAMSVAARVAEEMGVKLGHE  341 (902)
T ss_pred             cCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhcccc-cCCceEeecCcchHHHHHHHHHHHHHhCcccccc
Confidence            334667777888889999999999999999996432223222111 22334556669998888887765 4555555444


Q ss_pred             EEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh--ccccHHHHHHHHHhCCCCccE
Q 022383          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML--SRGFKDQIYDVYRYLPPDLQV  209 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~--~~~~~~~i~~i~~~~~~~~~~  209 (298)
                      +++-..-    +.+  ..+..-+=+.|.++|++-+.. ..++...++|||||||.=.  .+-.-..+..|.+ +++...+
T Consensus       342 VGYsIRF----Edc--TSekTvlKYMTDGmLlREfL~-epdLasYSViiiDEAHERTL~TDILfgLvKDIar-~RpdLKl  413 (902)
T KOG0923|consen  342 VGYSIRF----EDC--TSEKTVLKYMTDGMLLREFLS-EPDLASYSVIIVDEAHERTLHTDILFGLVKDIAR-FRPDLKL  413 (902)
T ss_pred             cceEEEe----ccc--cCcceeeeeecchhHHHHHhc-cccccceeEEEeehhhhhhhhhhHHHHHHHHHHh-hCCcceE
Confidence            4332211    000  012235668999999876554 3567899999999999621  1111222333333 3468899


Q ss_pred             EEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh---hCCCCcEEEEecchhhHH
Q 022383          210 VLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD---TLTITQAVIFCNTKRKIY  286 (298)
Q Consensus       210 v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~---~~~~~k~lIf~~s~~~~~  286 (298)
                      ++.|||+..+  .+ ..++.+.-.+.++   -....++-+|...+..++-..++..+++   ..+.+-+|||....++.+
T Consensus       414 lIsSAT~DAe--kF-S~fFDdapIF~iP---GRRyPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIE  487 (902)
T KOG0923|consen  414 LISSATMDAE--KF-SAFFDDAPIFRIP---GRRYPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIE  487 (902)
T ss_pred             EeeccccCHH--HH-HHhccCCcEEecc---CcccceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHH
Confidence            9999999742  33 3455443333332   2234567777777776655555555555   345678999999999888


Q ss_pred             HHHHHHhhh
Q 022383          287 YSVFYFWIR  295 (298)
Q Consensus       287 ~l~~~L~~~  295 (298)
                      ...+.|.++
T Consensus       488 t~~e~l~~~  496 (902)
T KOG0923|consen  488 TVKENLKER  496 (902)
T ss_pred             HHHHHHHHH
Confidence            888877654

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.11  E-value=2.2e-09  Score=101.24  Aligned_cols=137  Identities=16%  Similarity=0.150  Sum_probs=96.2

Q ss_pred             EEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----h
Q 022383           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----E  149 (298)
Q Consensus        74 li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  149 (298)
                      +..+.+|||||..|+-.+-..+..   +..+|+++|...|..|+.+.++....  +-.+..++++.+..+....+    .
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~---Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~lhS~l~~~~R~~~w~~~~~  238 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRA---GRGALVVVPDQRDVDRLEAALRALLG--AGDVAVLSAGLGPADRYRRWLAVLR  238 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHc---CCeEEEEecchhhHHHHHHHHHHHcC--CCcEEEECCCCCHHHHHHHHHHHhC
Confidence            334446999999999888777665   55799999999999999999987642  25688899987776554433    3


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh-cc--ccHHHHHHH--HHhCCCCccEEEEEeeCchhHHH
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SR--GFKDQIYDV--YRYLPPDLQVVLISATLPHEILE  222 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~-~~--~~~~~i~~i--~~~~~~~~~~v~~SAT~~~~~~~  222 (298)
                      +..+|+|||-..++       ..+.++.+||+||-|.-. ..  ..+.+.+.+  .+....+..+|+.|||++-+...
T Consensus       239 G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~~  309 (665)
T PRK14873        239 GQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQA  309 (665)
T ss_pred             CCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHHH
Confidence            55799999964433       457899999999988532 11  111222222  23333578899999998755443

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.11  E-value=6.3e-09  Score=98.63  Aligned_cols=130  Identities=19%  Similarity=0.233  Sum_probs=95.8

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|.. |++.|--.--.+  .+.-+..+.||-|||+++.+|++-....   |..|-|++++..||..=.+.+..+...+|+
T Consensus        82 lG~r-~ydVQliGgl~L--h~G~IAEM~TGEGKTL~atlpaylnAL~---GkgVhVVTvNdYLA~RDae~m~~vy~~LGL  155 (939)
T PRK12902         82 LGMR-HFDVQLIGGMVL--HEGQIAEMKTGEGKTLVATLPSYLNALT---GKGVHVVTVNDYLARRDAEWMGQVHRFLGL  155 (939)
T ss_pred             hCCC-cchhHHHhhhhh--cCCceeeecCCCChhHHHHHHHHHHhhc---CCCeEEEeCCHHHHHhHHHHHHHHHHHhCC
Confidence            3433 666665444333  4556889999999999998888764433   446889999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHH-HHHhc------cCccCCCccEEEechhhHhh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKR------KTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~~~~------~~~~~~~l~~vViDE~h~~~  188 (298)
                      .+....++.+..+.  ...-.+||+.+|+..|. .+++.      .....+.+.+.||||+|.++
T Consensus       156 tvg~i~~~~~~~er--r~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        156 SVGLIQQDMSPEER--KKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             eEEEECCCCChHHH--HHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            99988776655433  33346899999998872 22222      22345788999999999875

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=99.06  E-value=1.4e-08  Score=95.29  Aligned_cols=152  Identities=12%  Similarity=0.128  Sum_probs=99.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh-
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-  149 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  149 (298)
                      .-.++.+|.|+|||.+..-++-..+..  ...++++++.++.|+.++.++++..+-. ++.   .+.+....    .+. 
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~~--~~~~VLvVShRrSL~~sL~~rf~~~~l~-gFv---~Y~d~~~~----~i~~  119 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALKN--PDKSVLVVSHRRSLTKSLAERFKKAGLS-GFV---NYLDSDDY----IIDG  119 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhccC--CCCeEEEEEhHHHHHHHHHHHHhhcCCC-cce---eeeccccc----cccc
Confidence            346788999999998876666555433  2458999999999999999988765211 221   11111110    111 


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHH-------HHHHHHHhCCCCccEEEEEeeCchhHHH
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD-------QIYDVYRYLPPDLQVVLISATLPHEILE  222 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~-------~i~~i~~~~~~~~~~v~~SAT~~~~~~~  222 (298)
                      ...+-+++..+.|.++..   -.+.+.++||+||+-..+..-|..       .+..+...+.....+|++-|+++....+
T Consensus       120 ~~~~rLivqIdSL~R~~~---~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvd  196 (824)
T PF02399_consen  120 RPYDRLIVQIDSLHRLDG---SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVD  196 (824)
T ss_pred             cccCeEEEEehhhhhccc---ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHH
Confidence            134667777777766543   245678999999998876543322       2222334445678899999999999999


Q ss_pred             HHHhcCCC-CEEEE
Q 022383          223 MTTKFMTD-PVKIL  235 (298)
Q Consensus       223 ~~~~~~~~-~~~~~  235 (298)
                      ++....++ ++.++
T Consensus       197 Fl~~~Rp~~~i~vI  210 (824)
T PF02399_consen  197 FLASCRPDENIHVI  210 (824)
T ss_pred             HHHHhCCCCcEEEE
Confidence            99887653 34443

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

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.04  E-value=2.7e-08  Score=94.20  Aligned_cols=130  Identities=15%  Similarity=0.180  Sum_probs=95.1

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|. .|++.|--.--.+..|  -+..+.||-|||+++.+|++-....   |..|-|++.+.-||..=.+.+..+...+|+
T Consensus        75 lG~-r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL~---GkgVhVVTvNdYLA~RDae~mg~vy~fLGL  148 (925)
T PRK12903         75 LGK-RPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNALT---GKGVIVSTVNEYLAERDAEEMGKVFNFLGL  148 (925)
T ss_pred             hCC-CcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHhc---CCceEEEecchhhhhhhHHHHHHHHHHhCC
Confidence            344 4777777666555555  4789999999999998887543323   335778889999999989999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHH-HHhcc------CccCCCccEEEechhhHhh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~-~~~~~------~~~~~~l~~vViDE~h~~~  188 (298)
                      .++....+....+....  -.|||+.+|...|.- +++.+      ....+.+.+.||||+|.++
T Consensus       149 svG~i~~~~~~~~rr~a--Y~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        149 SVGINKANMDPNLKREA--YACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             ceeeeCCCCChHHHHHh--ccCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            99888776555443333  348999999877643 44432      1234778899999999875

>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=99.02  E-value=1.9e-08  Score=84.30  Aligned_cols=130  Identities=20%  Similarity=0.324  Sum_probs=95.6

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|+ .|++.|.-+.-.+.+|+  +++..||-|||++..+|+.-....   |..|=|++.+..|+..=.+.+..+...+|+
T Consensus        74 ~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~---G~~V~vvT~NdyLA~RD~~~~~~~y~~LGl  147 (266)
T PF07517_consen   74 LGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ---GKGVHVVTSNDYLAKRDAEEMRPFYEFLGL  147 (266)
T ss_dssp             TS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT---SS-EEEEESSHHHHHHHHHHHHHHHHHTT-
T ss_pred             cCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh---cCCcEEEeccHHHhhccHHHHHHHHHHhhh
Confidence            454 48888888887776666  999999999999887776555443   457889999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHH-HHhcc------CccCCCccEEEechhhHhh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRK------TLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~-~~~~~------~~~~~~l~~vViDE~h~~~  188 (298)
                      .+....++.+..+.....  .++|+.+|...+.- +++.+      ....+.++++||||+|.++
T Consensus       148 sv~~~~~~~~~~~r~~~Y--~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  148 SVGIITSDMSSEERREAY--AADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             -EEEEETTTEHHHHHHHH--HSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             ccccCccccCHHHHHHHH--hCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            999999887755443333  36899999988764 44432      1124788999999999975

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 ....

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.00  E-value=5.8e-09  Score=100.37  Aligned_cols=175  Identities=19%  Similarity=0.149  Sum_probs=108.2

Q ss_pred             HHHHHCCCCCChHHHHHHHHHhhc------CCc--EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHH
Q 022383           46 RGIYQYGFEKPSAIQQRAVMPIIK------GRD--VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (298)
Q Consensus        46 ~~l~~~~~~~~~~~Q~~~~~~~~~------~~~--~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~  117 (298)
                      +.|++..-..-..||-.+++.+..      ...  ++=.|.||+|||++=+-.+ ..+.....+.+..|..-.|.|-.|+
T Consensus       399 k~~~~r~~~~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNARIm-yaLsd~~~g~RfsiALGLRTLTLQT  477 (1110)
T TIGR02562       399 KYFCQRSAHPRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANARAM-YALRDDKQGARFAIALGLRSLTLQT  477 (1110)
T ss_pred             hhhccCCCCCCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHHHH-HHhCCCCCCceEEEEccccceeccc
Confidence            344443334567799999998763      122  4555999999998855433 3445556677888888899999998


Q ss_pred             HHHHHHhhccCCceEEEEEcCCchHHHH-------------------------------------------HHhh-----
Q 022383          118 EKVILAIGDFINIQAHACVGGKSVGEDI-------------------------------------------RKLE-----  149 (298)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------~~~~-----  149 (298)
                      -+.+++.....+-...++.|+....+-.                                           ..+.     
T Consensus       478 Gda~r~rL~L~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~  557 (1110)
T TIGR02562       478 GHALKTRLNLSDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKE  557 (1110)
T ss_pred             hHHHHHhcCCCccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhh
Confidence            8888765443333445555442211100                                           0000     


Q ss_pred             ---cCCcEEEeChHHHHHHHhc---cCccCC----CccEEEechhhHhhccccHHHHHHHHHhCC-CCccEEEEEeeCch
Q 022383          150 ---HGVHVVSGTPGRVCDMIKR---KTLRTR----AIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATLPH  218 (298)
Q Consensus       150 ---~~~~ilV~Tp~~l~~~~~~---~~~~~~----~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-~~~~~v~~SAT~~~  218 (298)
                         -..+++|||++.++.....   +...+.    .=+.|||||+|.+ +......+..+++... ...+++++|||+|+
T Consensus       558 ~rll~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaY-D~~~~~~L~rlL~w~~~lG~~VlLmSATLP~  636 (1110)
T TIGR02562       558 KTLLAAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDY-EPEDLPALLRLVQLAGLLGSRVLLSSATLPP  636 (1110)
T ss_pred             hhhhcCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccC-CHHHHHHHHHHHHHHHHcCCCEEEEeCCCCH
Confidence               0146999999999887622   122111    2256999999986 3333344445554332 35789999999998


Q ss_pred             hHHH
Q 022383          219 EILE  222 (298)
Q Consensus       219 ~~~~  222 (298)
                      .+..
T Consensus       637 ~l~~  640 (1110)
T TIGR02562       637 ALVK  640 (1110)
T ss_pred             HHHH
Confidence            7655

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.99  E-value=7.1e-08  Score=88.12  Aligned_cols=224  Identities=14%  Similarity=0.138  Sum_probs=137.4

Q ss_pred             CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH-HhhccCCce
Q 022383           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL-AIGDFINIQ  131 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~-~~~~~~~~~  131 (298)
                      +-....++.+.+..+..++-++|++.||||||.-..-.++..-...  ...+-+--|++.-|..++.+.. .++..+|-.
T Consensus       354 ~LPvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~--~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~  431 (1042)
T KOG0924|consen  354 YLPVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYAD--NGMIGCTQPRRVAAISVAKRVAEEMGVTLGDT  431 (1042)
T ss_pred             hcchHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhccccc--CCeeeecCchHHHHHHHHHHHHHHhCCccccc
Confidence            4445667778888888889999999999999976444444432222  2233444599999988887765 454444444


Q ss_pred             EEEEE--cCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-c-cHHHHHHHHHhCCCCc
Q 022383          132 AHACV--GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-G-FKDQIYDVYRYLPPDL  207 (298)
Q Consensus       132 ~~~~~--~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~-~~~~i~~i~~~~~~~~  207 (298)
                      +++..  .+...        ....|=..|.+.|++-.-. .-.+.++++||+||||.=.-. . ..-.+..++.. +.+.
T Consensus       432 VGYsIRFEdvT~--------~~T~IkymTDGiLLrEsL~-d~~L~kYSviImDEAHERslNtDilfGllk~~lar-Rrdl  501 (1042)
T KOG0924|consen  432 VGYSIRFEDVTS--------EDTKIKYMTDGILLRESLK-DRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLAR-RRDL  501 (1042)
T ss_pred             cceEEEeeecCC--------CceeEEEeccchHHHHHhh-hhhhhheeEEEechhhhcccchHHHHHHHHHHHHh-hccc
Confidence            43322  12111        1235667888888764332 234678999999999973211 1 11222233333 3478


Q ss_pred             cEEEEEeeCchhHHHHHHhcCC-CCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC---CCCcEEEEecchh
Q 022383          208 QVVLISATLPHEILEMTTKFMT-DPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL---TITQAVIFCNTKR  283 (298)
Q Consensus       208 ~~v~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~---~~~k~lIf~~s~~  283 (298)
                      ++|..|||+..  +.+. .+++ .|...+-.+    ...++..+...+-+++...++.+.+.-+   ..+-.|||....+
T Consensus       502 KliVtSATm~a--~kf~-nfFgn~p~f~IpGR----TyPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqe  574 (1042)
T KOG0924|consen  502 KLIVTSATMDA--QKFS-NFFGNCPQFTIPGR----TYPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQE  574 (1042)
T ss_pred             eEEEeeccccH--HHHH-HHhCCCceeeecCC----ccceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCc
Confidence            89999999974  3333 3444 555544322    2335666666665665555566555432   4468999999998


Q ss_pred             hHHHHHHHHhhh
Q 022383          284 KIYYSVFYFWIR  295 (298)
Q Consensus       284 ~~~~l~~~L~~~  295 (298)
                      +.+..+..+..+
T Consensus       575 diE~t~~~i~~~  586 (1042)
T KOG0924|consen  575 DIECTCDIIKEK  586 (1042)
T ss_pred             chhHHHHHHHHH
Confidence            888777776544

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.97  E-value=1.5e-08  Score=96.90  Aligned_cols=64  Identities=27%  Similarity=0.330  Sum_probs=52.0

Q ss_pred             CCCCChHHHHHHHHHhh----c-----CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           52 GFEKPSAIQQRAVMPII----K-----GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~----~-----~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      ||+ .++-|.+....+.    +     ++.+++.||||+|||++|++|++......  +.++||-++|++|-+|+.
T Consensus        23 ~~e-~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~--~k~vVIST~T~~LQeQL~   95 (697)
T PRK11747         23 GFI-PRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAE--KKKLVISTATVALQEQLV   95 (697)
T ss_pred             CCC-cCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHc--CCeEEEEcCCHHHHHHHH
Confidence            554 9999999776654    3     36789999999999999999998754433  447999999999999986

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

Probab=98.86  E-value=1.4e-09  Score=103.07  Aligned_cols=231  Identities=13%  Similarity=0.156  Sum_probs=140.5

Q ss_pred             CChHHHHHHHHHhhc-CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEE
Q 022383           55 KPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~-~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  133 (298)
                      ...|.|.+.+-.+.. ..++++-+|||+|||.+|...++..+...+. .+++++.|.++|+..-.+.+++.....|+++.
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~-~kvvyIap~kalvker~~Dw~~r~~~~g~k~i 1005 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPG-SKVVYIAPDKALVKERSDDWSKRDELPGIKVI 1005 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCC-ccEEEEcCCchhhcccccchhhhcccCCceeE
Confidence            445556555543332 3678999999999999999999888776554 58999999999999988888766555588899


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc--cCccCCCccEEEechhhHhhccccHHHHHHHHH-------hCC
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR-------YLP  204 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~--~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~-------~~~  204 (298)
                      -+.|+...+.  ..+ ...+++|+||++.....++  ..-.++++..+|+||.|++.+. +.+.++.+..       ...
T Consensus      1006 e~tgd~~pd~--~~v-~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~-rgPVle~ivsr~n~~s~~t~ 1081 (1230)
T KOG0952|consen 1006 ELTGDVTPDV--KAV-READIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED-RGPVLEVIVSRMNYISSQTE 1081 (1230)
T ss_pred             eccCccCCCh--hhe-ecCceEEcccccccCccccccchhhhccccceeecccccccCC-CcceEEEEeeccccCccccC
Confidence            8888876652  222 3469999999999988874  4556789999999999998655 3333322221       122


Q ss_pred             CCccEEEEEeeCchhHHHHHHhcCCCCE--E---EEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC-CCCcEEEE
Q 022383          205 PDLQVVLISATLPHEILEMTTKFMTDPV--K---ILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIF  278 (298)
Q Consensus       205 ~~~~~v~~SAT~~~~~~~~~~~~~~~~~--~---~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~k~lIf  278 (298)
                      +..+.+++|.-+.+. .++..+....+.  .   +.-.+.+....+..- ...|++...+-.-..+.++.+ +..+++||
T Consensus      1082 ~~vr~~glsta~~na-~dla~wl~~~~~~nf~~svrpvp~~~~i~gfp~-~~~cprm~smnkpa~qaik~~sp~~p~lif 1159 (1230)
T KOG0952|consen 1082 EPVRYLGLSTALANA-NDLADWLNIKDMYNFRPSVRPVPLEVHIDGFPG-QHYCPRMMSMNKPAFQAIKTHSPIKPVLIF 1159 (1230)
T ss_pred             cchhhhhHhhhhhcc-HHHHHHhCCCCcCCCCcccccCCceEeecCCCc-hhcchhhhhcccHHHHHHhcCCCCCceEEE
Confidence            346666665544322 222222222222  0   000000000001111 112232221222334444544 45699999


Q ss_pred             ecchhhHHHHHHHH
Q 022383          279 CNTKRKIYYSVFYF  292 (298)
Q Consensus       279 ~~s~~~~~~l~~~L  292 (298)
                      +.++.....-+..|
T Consensus      1160 v~srrqtrlta~~l 1173 (1230)
T KOG0952|consen 1160 VSSRRQTRLTALDL 1173 (1230)
T ss_pred             eecccccccchHhH
Confidence            99988665555444

>COG4889 Predicted helicase [General function prediction only]

Probab=98.85  E-value=2.8e-09  Score=99.44  Aligned_cols=140  Identities=21%  Similarity=0.201  Sum_probs=92.4

Q ss_pred             HHHHHHHHCCCCCChHHHHHHHHHhhcC----CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           43 DLLRGIYQYGFEKPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~----~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      ++..++.-..-..|+|+|+.+++...+|    ..-=+.+..|+|||+..+-.+ +.+..    .++|+|+|+.+|..|..
T Consensus       149 e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLkis-Eala~----~~iL~LvPSIsLLsQTl  223 (1518)
T COG4889         149 ELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLKIS-EALAA----ARILFLVPSISLLSQTL  223 (1518)
T ss_pred             ccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHHHH-HHHhh----hheEeecchHHHHHHHH
Confidence            4444444455578999999999998765    112334457999998876433 33322    48999999999999988


Q ss_pred             HHHHHhhccCCceEEEEEcCCchHHHH--------------------HH-----hhcCCcEEEeChHHHHHHHhccCccC
Q 022383          119 KVILAIGDFINIQAHACVGGKSVGEDI--------------------RK-----LEHGVHVVSGTPGRVCDMIKRKTLRT  173 (298)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~-----~~~~~~ilV~Tp~~l~~~~~~~~~~~  173 (298)
                      +.+..-. ...++.....++...+...                    ..     -..+--|+++|-+.+...-.-+..-+
T Consensus       224 rew~~~~-~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eAQe~G~  302 (1518)
T COG4889         224 REWTAQK-ELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEAQEAGL  302 (1518)
T ss_pred             HHHhhcc-CccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHHHHHcCC
Confidence            8765422 2344444444332221110                    00     11234588899988888776666778


Q ss_pred             CCccEEEechhhHhh
Q 022383          174 RAIKLLVLDESDEML  188 (298)
Q Consensus       174 ~~l~~vViDE~h~~~  188 (298)
                      ..+++||.||||+..
T Consensus       303 ~~fDliicDEAHRTt  317 (1518)
T COG4889         303 DEFDLIICDEAHRTT  317 (1518)
T ss_pred             CCccEEEecchhccc
Confidence            899999999999964

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

Probab=98.81  E-value=7.4e-08  Score=79.99  Aligned_cols=69  Identities=22%  Similarity=0.346  Sum_probs=50.4

Q ss_pred             CChHHHHHHHHHhhcCCc-EEEEcCCCCchHHHHHHHHHHhh-----ccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           55 KPSAIQQRAVMPIIKGRD-VIAQAQSGTGKTSMIALTVCQTV-----DTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~-~li~~pTG~GKT~~~~~~~~~~~-----~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      ++++.|.+++..+++... .+|.||.|+|||....-.+...+     .....+.++++++|+..-++++.+.+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            368899999999999988 99999999999955443333321     1234566899999999999999998877

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

Probab=98.80  E-value=3.7e-08  Score=94.36  Aligned_cols=73  Identities=21%  Similarity=0.221  Sum_probs=59.5

Q ss_pred             HHCCCCCChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           49 YQYGFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        49 ~~~~~~~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      ..+....+++.|.+++..+.    +++.+++.||||+|||++|+.|++......  +.+++|.++|+.+-+|+.+....
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~--~~~viist~t~~lq~q~~~~~~~   85 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE--GKKVIISTRTKALQEQLLEEDLP   85 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHc--CCcEEEECCCHHHHHHHHHhhcc
Confidence            33455669999999986654    456799999999999999999999986654  35899999999999998876644

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=98.79  E-value=7.1e-08  Score=93.07  Aligned_cols=143  Identities=15%  Similarity=0.254  Sum_probs=87.1

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH-hh--------ccCCceEEEEEcCC--
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA-IG--------DFINIQAHACVGGK--  139 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~--------~~~~~~~~~~~~~~--  139 (298)
                      .++.+.++||+|||.+|+-.++...... ...+.||+||+.+....+...++. ..        ....++...+.++.  
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~-~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~  138 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKY-GLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKK  138 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHc-CCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCccc
Confidence            4799999999999999998887765443 234799999999999888876651 11        11124444444432  


Q ss_pred             -----chHHHHHHhh-------cCCcEEEeChHHHHHHHh--cc-------Cc--cC----CCccEEEechhhHhhcccc
Q 022383          140 -----SVGEDIRKLE-------HGVHVVSGTPGRVCDMIK--RK-------TL--RT----RAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       140 -----~~~~~~~~~~-------~~~~ilV~Tp~~l~~~~~--~~-------~~--~~----~~l~~vViDE~h~~~~~~~  192 (298)
                           .....+....       +...|+|.|.+.|..-..  ..       ..  .+    ..=-.||+||.|++-..  
T Consensus       139 k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~~--  216 (986)
T PRK15483        139 KSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPRD--  216 (986)
T ss_pred             ccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCcc--
Confidence                 1122222221       146899999998875221  10       00  11    11135999999998442  


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          193 KDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       193 ~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      ...+..+ ..+.+.. ++.+|||.+.
T Consensus       217 ~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        217 NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             hHHHHHH-HhcCccc-EEEEeeecCC
Confidence            2344444 4443322 5679999976

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=98.78  E-value=8.7e-08  Score=94.36  Aligned_cols=137  Identities=16%  Similarity=0.180  Sum_probs=92.9

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (298)
                      +..+|+--||||||+.....+-..+.. ...+.++||+-++.|-.|+.+.+..+........    ...+..+....+.+
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~~~-~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~Lk~~l~~  348 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLEL-PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSELKELLED  348 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHHhc-cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHHHHHHhc
Confidence            568999999999998866554333333 6678999999999999999999998865432211    23333444444553


Q ss_pred             C-CcEEEeChHHHHHHHhcc-C-ccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeC
Q 022383          151 G-VHVVSGTPGRVCDMIKRK-T-LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       151 ~-~~ilV~Tp~~l~~~~~~~-~-~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      + -.|+|+|.++|....... . ..-++==+||+||||+-   .++..-..+...++ +...++||.|+
T Consensus       349 ~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS---Q~G~~~~~~~~~~~-~a~~~gFTGTP  413 (962)
T COG0610         349 GKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS---QYGELAKLLKKALK-KAIFIGFTGTP  413 (962)
T ss_pred             CCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhc---cccHHHHHHHHHhc-cceEEEeeCCc
Confidence            3 389999999999888664 1 11223336889999983   22333333333343 47899999998

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=98.75  E-value=1.7e-06  Score=77.40  Aligned_cols=67  Identities=22%  Similarity=0.279  Sum_probs=51.5

Q ss_pred             ChHHHHHHHHHhhcC-----CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC
Q 022383           56 PSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~-----~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~  128 (298)
                      |.--|-+||..+..|     +.-.+.|.||||||+...-.+ ..+     +.-+||++|.+.||.|++..++.+....
T Consensus        13 PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI-~~~-----~rPtLV~AhNKTLAaQLy~Efk~fFP~N   84 (663)
T COG0556          13 PAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVI-AKV-----QRPTLVLAHNKTLAAQLYSEFKEFFPEN   84 (663)
T ss_pred             CCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHH-HHh-----CCCeEEEecchhHHHHHHHHHHHhCcCc
Confidence            666788888776644     578899999999998755433 222     2258999999999999999999987543

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=98.74  E-value=2.8e-07  Score=85.31  Aligned_cols=158  Identities=16%  Similarity=0.196  Sum_probs=105.3

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhc--cCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQALILSPTRELATQTEKVILAIGDFI  128 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~--~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~  128 (298)
                      .++++|.+.++.+.    .|-+.|+.-..|-|||+-. ++.+..+.  .+-.|| -+|+||...| ..+.+.++++..  
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQt-Is~l~yl~~~~~~~GP-fLVi~P~StL-~NW~~Ef~rf~P--  241 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQT-ISLLGYLKGRKGIPGP-FLVIAPKSTL-DNWMNEFKRFTP--  241 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHH-HHHHHHHHHhcCCCCC-eEEEeeHhhH-HHHHHHHHHhCC--
Confidence            68999999887754    5778999999999999542 22222222  222343 6889997765 556777888864  


Q ss_pred             CceEEEEEcCCchHHHH-HHh--hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCC
Q 022383          129 NIQAHACVGGKSVGEDI-RKL--EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (298)
Q Consensus       129 ~~~~~~~~~~~~~~~~~-~~~--~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~  205 (298)
                      ++++..++|+....... +.+  ....+|+|+|-+....--  ..+.--..+++||||+|++-..  ...+..+++.+..
T Consensus       242 ~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk--~~lk~~~W~ylvIDEaHRiKN~--~s~L~~~lr~f~~  317 (971)
T KOG0385|consen  242 SLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDK--SFLKKFNWRYLVIDEAHRIKNE--KSKLSKILREFKT  317 (971)
T ss_pred             CcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhH--HHHhcCCceEEEechhhhhcch--hhHHHHHHHHhcc
Confidence            58899999986544332 222  246899999998877531  1222335689999999998444  4555577777764


Q ss_pred             CccEEEEEeeC-chhHHH
Q 022383          206 DLQVVLISATL-PHEILE  222 (298)
Q Consensus       206 ~~~~v~~SAT~-~~~~~~  222 (298)
                      .. .+++|.|+ .+.+.+
T Consensus       318 ~n-rLLlTGTPLQNNL~E  334 (971)
T KOG0385|consen  318 DN-RLLLTGTPLQNNLHE  334 (971)
T ss_pred             cc-eeEeeCCcccccHHH
Confidence            33 56777776 444443

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=98.66  E-value=1.2e-07  Score=87.86  Aligned_cols=162  Identities=14%  Similarity=0.151  Sum_probs=100.9

Q ss_pred             ChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           56 PSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        56 ~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      +.+||.-.++.+.    .+-+.|+.-..|-|||.- .++-+..+...+....-|||||...| +.+.+.+.+++.  .++
T Consensus       400 LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQ-vIaFlayLkq~g~~gpHLVVvPsSTl-eNWlrEf~kwCP--sl~  475 (941)
T KOG0389|consen  400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQ-VIAFLAYLKQIGNPGPHLVVVPSSTL-ENWLREFAKWCP--SLK  475 (941)
T ss_pred             ccchhhhhHHHHHHHHHccccceehhhccCcchhH-HHHHHHHHHHcCCCCCcEEEecchhH-HHHHHHHHHhCC--ceE
Confidence            8899998887653    455778999999999932 22222322222222346889998765 456666777754  578


Q ss_pred             EEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhc-cCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCC
Q 022383          132 AHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~  206 (298)
                      +..++|......+.....    .+++|+|+|-..+..--.. .-+.-.+++++|+||+|.+-... ...+..+..--  .
T Consensus       476 Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~-SeRy~~LM~I~--A  552 (941)
T KOG0389|consen  476 VEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT-SERYKHLMSIN--A  552 (941)
T ss_pred             EEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc-hHHHHHhcccc--c
Confidence            888999887666554332    3689999997555421111 11233577899999999875442 33333333222  3


Q ss_pred             ccEEEEEeeC-chhHHHHH
Q 022383          207 LQVVLISATL-PHEILEMT  224 (298)
Q Consensus       207 ~~~v~~SAT~-~~~~~~~~  224 (298)
                      .+.+++|.|+ .+.+.+++
T Consensus       553 n~RlLLTGTPLQNNL~ELi  571 (941)
T KOG0389|consen  553 NFRLLLTGTPLQNNLKELI  571 (941)
T ss_pred             cceEEeeCCcccccHHHHH
Confidence            4567888886 55444443

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.65  E-value=9.2e-07  Score=83.46  Aligned_cols=164  Identities=16%  Similarity=0.120  Sum_probs=106.6

Q ss_pred             CChHHHHHHHHHhhc---C-------CcEEEEcCCCCchHHHHHHHHHHhhccCCC----CeEEEEEcCcHHHHHHHHHH
Q 022383           55 KPSAIQQRAVMPIIK---G-------RDVIAQAQSGTGKTSMIALTVCQTVDTSSR----EVQALILSPTRELATQTEKV  120 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~---~-------~~~li~~pTG~GKT~~~~~~~~~~~~~~~~----~~~~lil~p~~~l~~q~~~~  120 (298)
                      .++|+|++.+..+.+   |       ...++.=..|+|||+-...-+-..+...+.    -.++|||+| ..|+..+.+.
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P-~sLv~nWkkE  316 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAP-SSLVNNWKKE  316 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEcc-HHHHHHHHHH
Confidence            589999999987652   2       246777779999997643333333333222    147899999 5789999999


Q ss_pred             HHHhhccCCceEEEEEcCCchH-HHHHHhh------cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccH
Q 022383          121 ILAIGDFINIQAHACVGGKSVG-EDIRKLE------HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (298)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~------~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~  193 (298)
                      |.++.....+....+++..... .....+.      ....+++.+-+.+.+..+.  +....++++|+||.|..-  +-.
T Consensus       317 F~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrlk--N~~  392 (776)
T KOG0390|consen  317 FGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRLK--NSD  392 (776)
T ss_pred             HHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCcc--chh
Confidence            9998765567777777766541 0011111      1235677777777655443  445688999999999863  334


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeC-chhHHHHH
Q 022383          194 DQIYDVYRYLPPDLQVVLISATL-PHEILEMT  224 (298)
Q Consensus       194 ~~i~~i~~~~~~~~~~v~~SAT~-~~~~~~~~  224 (298)
                      ..+...+..+. -.+.|++|.|+ .+.+.++.
T Consensus       393 s~~~kaL~~l~-t~rRVLLSGTp~QNdl~EyF  423 (776)
T KOG0390|consen  393 SLTLKALSSLK-TPRRVLLTGTPIQNDLKEYF  423 (776)
T ss_pred             hHHHHHHHhcC-CCceEEeeCCcccccHHHHH
Confidence            55556666665 45578889997 55555543

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=98.63  E-value=6.7e-06  Score=72.98  Aligned_cols=152  Identities=15%  Similarity=0.129  Sum_probs=94.6

Q ss_pred             CCCChHHHHHHHHHh-hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           53 FEKPSAIQQRAVMPI-IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~-~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      ++.+.|+|.+.+... .+|..+++.-..|-|||.-++-.+ .....   ..-.+|+||.. +--.+.+.+.++..... .
T Consensus       196 vs~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA-~yyra---EwplliVcPAs-vrftWa~al~r~lps~~-p  269 (689)
T KOG1000|consen  196 VSRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIA-RYYRA---EWPLLIVCPAS-VRFTWAKALNRFLPSIH-P  269 (689)
T ss_pred             HHhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHH-HHHhh---cCcEEEEecHH-HhHHHHHHHHHhccccc-c
Confidence            456789999998875 467788888999999997654221 22222   22478899953 44566777777654332 2


Q ss_pred             EEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEE
Q 022383          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL  211 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~  211 (298)
                      +.+..++.+...   .+.....|.|.+.+.+..+-..  +.-....+||+||.|++-+. -....+.+...+..-.++|+
T Consensus       270 i~vv~~~~D~~~---~~~t~~~v~ivSye~ls~l~~~--l~~~~~~vvI~DEsH~Lk~s-ktkr~Ka~~dllk~akhvIL  343 (689)
T KOG1000|consen  270 IFVVDKSSDPLP---DVCTSNTVAIVSYEQLSLLHDI--LKKEKYRVVIFDESHMLKDS-KTKRTKAATDLLKVAKHVIL  343 (689)
T ss_pred             eEEEecccCCcc---ccccCCeEEEEEHHHHHHHHHH--HhcccceEEEEechhhhhcc-chhhhhhhhhHHHHhhheEE
Confidence            444444433221   1222346888888776643321  22345789999999997433 33445555555555567899


Q ss_pred             EEeeC
Q 022383          212 ISATL  216 (298)
Q Consensus       212 ~SAT~  216 (298)
                      +|.|+
T Consensus       344 LSGTP  348 (689)
T KOG1000|consen  344 LSGTP  348 (689)
T ss_pred             ecCCc
Confidence            99986

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.63  E-value=4.2e-07  Score=81.69  Aligned_cols=248  Identities=10%  Similarity=-0.017  Sum_probs=153.2

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           44 LLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        44 i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      +...+.++..+....+|.++++.+-.|+++++...|.+||.++|.......+...+. ...+++.|++++++...+-+..
T Consensus       275 ~~~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~-s~~~~~~~~~~~~~~~~~~~~V  353 (1034)
T KOG4150|consen  275 IRSLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHA-TNSLLPSEMVEHLRNGSKGQVV  353 (1034)
T ss_pred             HHHHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCcc-cceecchhHHHHhhccCCceEE
Confidence            334445566678899999999999999999999999999999998888776554333 3578899999998876553321


Q ss_pred             hhccC-Cc--eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCc----cCCCccEEEechhhHhhccc---cH
Q 022383          124 IGDFI-NI--QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL----RTRAIKLLVLDESDEMLSRG---FK  193 (298)
Q Consensus       124 ~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~----~~~~l~~vViDE~h~~~~~~---~~  193 (298)
                      ..... ..  -++-.+.+........-+..+.+++.+.|..+.....-+..    .+-+..++++||+|.+.-.-   -.
T Consensus       354 ~~~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~  433 (1034)
T KOG4150|consen  354 HVEVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQ  433 (1034)
T ss_pred             EEEehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHH
Confidence            11110 11  12233444444444445556789999999988875543322    23455779999999864331   23


Q ss_pred             HHHHHHHHhC-----CCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCcc--------chH
Q 022383          194 DQIYDVYRYL-----PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREE--------WKF  260 (298)
Q Consensus       194 ~~i~~i~~~~-----~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~--------~k~  260 (298)
                      ..++.+.+..     +.+.|++-.+||+.....-....+..+-..+..  .+-.+.+-.+.++..++-.        .+.
T Consensus       434 ~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~--~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i  511 (1034)
T KOG4150|consen  434 DQLRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVT--IDGSPSSEKLFVLWNPSAPPTSKSEKSSKV  511 (1034)
T ss_pred             HHHHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEE--ecCCCCccceEEEeCCCCCCcchhhhhhHH
Confidence            4444444443     257899999999977655444333222222222  2233334445555443211        122


Q ss_pred             HHHHHHHhh--CCCCcEEEEecchhhHHHHHHHHhh
Q 022383          261 DTLCDLYDT--LTITQAVIFCNTKRKIYYSVFYFWI  294 (298)
Q Consensus       261 ~~l~~ll~~--~~~~k~lIf~~s~~~~~~l~~~L~~  294 (298)
                      .....++.+  ..+-++|-||.+++-|+.+-..-++
T Consensus       512 ~E~s~~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~  547 (1034)
T KOG4150|consen  512 VEVSHLFAEMVQHGLRCIAFCPSRKLCELVLCLTRE  547 (1034)
T ss_pred             HHHHHHHHHHHHcCCcEEEeccHHHHHHHHHHHHHH
Confidence            223333322  2335999999999999988665543

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

Probab=98.61  E-value=3.8e-07  Score=73.50  Aligned_cols=150  Identities=12%  Similarity=0.170  Sum_probs=72.4

Q ss_pred             CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH----HHHHhhccC
Q 022383           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK----VILAIGDFI  128 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~----~~~~~~~~~  128 (298)
                      +...+..|..++.++.+.+-+++.||.|+|||+.++-.+++.+.. ....+++|+-|..+..+++--    .-+++..+.
T Consensus         2 I~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~-g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~   80 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKE-GEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYL   80 (205)
T ss_dssp             ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT-TS-SEEEEEE-S--TT----SS---------TTT
T ss_pred             ccCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHh-CCCcEEEEEecCCCCccccccCCCCHHHHHHHHH
Confidence            345688999999999988899999999999999998888888876 344477888787754222110    000000000


Q ss_pred             CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCcc
Q 022383          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (298)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~  208 (298)
                      . .+.-.....-.......+.....|-+..+    .+++..  .++ -.+||+|||..+    -...+..++.++..+.+
T Consensus        81 ~-p~~d~l~~~~~~~~~~~~~~~~~Ie~~~~----~~iRGr--t~~-~~~iIvDEaQN~----t~~~~k~ilTR~g~~sk  148 (205)
T PF02562_consen   81 R-PIYDALEELFGKEKLEELIQNGKIEIEPL----AFIRGR--TFD-NAFIIVDEAQNL----TPEELKMILTRIGEGSK  148 (205)
T ss_dssp             H-HHHHHHTTTS-TTCHHHHHHTTSEEEEEG----GGGTT----B--SEEEEE-SGGG------HHHHHHHHTTB-TT-E
T ss_pred             H-HHHHHHHHHhChHhHHHHhhcCeEEEEeh----hhhcCc--ccc-ceEEEEecccCC----CHHHHHHHHcccCCCcE
Confidence            0 00000000000001111112223333333    222222  222 289999999865    35678888999988888


Q ss_pred             EEEEEee
Q 022383          209 VVLISAT  215 (298)
Q Consensus       209 ~v~~SAT  215 (298)
                      ++++--.
T Consensus       149 ii~~GD~  155 (205)
T PF02562_consen  149 IIITGDP  155 (205)
T ss_dssp             EEEEE--
T ss_pred             EEEecCc
Confidence            8876544

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

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=98.57  E-value=9.3e-06  Score=72.65  Aligned_cols=196  Identities=17%  Similarity=0.226  Sum_probs=120.5

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccC-Cc----eEEEEEc--------------CCchHHHHHHhh-----------
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFI-NI----QAHACVG--------------GKSVGEDIRKLE-----------  149 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~-~~----~~~~~~~--------------~~~~~~~~~~~~-----------  149 (298)
                      ..|+||||+|++..|-++.+.+-++.... .+    +...-+|              ......+...+.           
T Consensus        36 tRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~FrlG  115 (442)
T PF06862_consen   36 TRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCFRLG  115 (442)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceEEEe
Confidence            35799999999999999998887765431 00    0000000              000011111111           


Q ss_pred             --------------cCCcEEEeChHHHHHHHhc------cCccCCCccEEEechhhHhhccccHHHHHHHHHhC---CC-
Q 022383          150 --------------HGVHVVSGTPGRVCDMIKR------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL---PP-  205 (298)
Q Consensus       150 --------------~~~~ilV~Tp~~l~~~~~~------~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~---~~-  205 (298)
                                    ..+||||++|=-|...+..      ..-.++.+.++|+|.+|.+.-. ..+++..+++.+   |+ 
T Consensus       116 ik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQ-NW~Hv~~v~~~lN~~P~~  194 (442)
T PF06862_consen  116 IKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQ-NWEHVLHVFEHLNLQPKK  194 (442)
T ss_pred             EEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHh-hHHHHHHHHHHhccCCCC
Confidence                          1378999999888887764      1223689999999999997532 234444554444   32 


Q ss_pred             --------------------CccEEEEEeeCchhHHHHHHhcCCCCE-EEEecC--C-----ccCcCCceEEEEEecCcc
Q 022383          206 --------------------DLQVVLISATLPHEILEMTTKFMTDPV-KILVKR--D-----ELTLEGIKQFFVAVEREE  257 (298)
Q Consensus       206 --------------------~~~~v~~SAT~~~~~~~~~~~~~~~~~-~~~~~~--~-----~~~~~~i~~~~~~~~~~~  257 (298)
                                          -+|.|++|+...+.+..+....+.+.. .+....  .     .....++.|.+...+...
T Consensus       195 ~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s  274 (442)
T PF06862_consen  195 SHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSS  274 (442)
T ss_pred             CCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCC
Confidence                                369999999999999998887555432 222211  1     133456777777655432


Q ss_pred             ------chHHHHHH-H---Hh-hCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          258 ------WKFDTLCD-L---YD-TLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       258 ------~k~~~l~~-l---l~-~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                            .+.+.... +   +. ....+.+|||++|--+=-.+.++|+...
T Consensus       275 ~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~  324 (442)
T PF06862_consen  275 PADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKEN  324 (442)
T ss_pred             cchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcC
Confidence                  12222221 1   22 3445699999999998888888887654

; GO: 0005634 nucleus

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

Probab=98.55  E-value=5.7e-07  Score=72.75  Aligned_cols=123  Identities=20%  Similarity=0.273  Sum_probs=72.2

Q ss_pred             CChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceE
Q 022383           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  132 (298)
                      .+++-|.+++..++..  +-.+++||.|+|||.+ +..+...+...  +.++++++||...+..+.+..       +...
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~~-------~~~a   70 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL-LKALAEALEAA--GKRVIGLAPTNKAAKELREKT-------GIEA   70 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH-HHHHHHHHHHT--T--EEEEESSHHHHHHHHHHH-------TS-E
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH-HHHHHHHHHhC--CCeEEEECCcHHHHHHHHHhh-------Ccch
Confidence            3788999999998643  3577889999999965 33344555443  468999999999888866642       1111


Q ss_pred             EEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccC----ccCCCccEEEechhhHhhccccHHHHHHHHHhCCC-Cc
Q 022383          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT----LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP-DL  207 (298)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~----~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~-~~  207 (298)
                                              .|-.+++.......    ..+...++|||||+-++.    ...+..+++..+. ..
T Consensus        71 ------------------------~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~----~~~~~~ll~~~~~~~~  122 (196)
T PF13604_consen   71 ------------------------QTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVD----SRQLARLLRLAKKSGA  122 (196)
T ss_dssp             ------------------------EEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-B----HHHHHHHHHHS-T-T-
T ss_pred             ------------------------hhHHHHHhcCCcccccccccCCcccEEEEecccccC----HHHHHHHHHHHHhcCC
Confidence                                    11111111111100    114566899999998763    3456667777765 66


Q ss_pred             cEEEEEee
Q 022383          208 QVVLISAT  215 (298)
Q Consensus       208 ~~v~~SAT  215 (298)
                      ++|++--+
T Consensus       123 klilvGD~  130 (196)
T PF13604_consen  123 KLILVGDP  130 (196)
T ss_dssp             EEEEEE-T
T ss_pred             EEEEECCc
Confidence            77776554

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.54  E-value=1.3e-06  Score=81.24  Aligned_cols=159  Identities=16%  Similarity=0.118  Sum_probs=101.8

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHH---HHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTS---MIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~---~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      .+.++|++.+..+.    ++..-|+--.+|-|||.   +|+-.+.+. .  .....+|||||. .++.|+...+..+.. 
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S-~--k~~~paLIVCP~-Tii~qW~~E~~~w~p-  279 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHS-G--KLTKPALIVCPA-TIIHQWMKEFQTWWP-  279 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhc-c--cccCceEEEccH-HHHHHHHHHHHHhCc-
Confidence            57899999877654    56778888899999993   333333322 1  223479999994 678999999999854 


Q ss_pred             CCceEEEEEcCCchH--------HHHHH-----hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHH
Q 022383          128 INIQAHACVGGKSVG--------EDIRK-----LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD  194 (298)
Q Consensus       128 ~~~~~~~~~~~~~~~--------~~~~~-----~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~  194 (298)
                       .+++..+++..+..        .....     ...+..|+|+|-+.+--.  ...+.-...+++|+||.|.+-.+.  .
T Consensus       280 -~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~--~d~l~~~~W~y~ILDEGH~IrNpn--s  354 (923)
T KOG0387|consen  280 -PFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ--GDDLLGILWDYVILDEGHRIRNPN--S  354 (923)
T ss_pred             -ceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc--CcccccccccEEEecCcccccCCc--c
Confidence             46777777754420        11111     123456899997555321  122333566899999999985553  4


Q ss_pred             HHHHHHHhCCCCccEEEEEeeC-chhHHHHH
Q 022383          195 QIYDVYRYLPPDLQVVLISATL-PHEILEMT  224 (298)
Q Consensus       195 ~i~~i~~~~~~~~~~v~~SAT~-~~~~~~~~  224 (298)
                      .+...+..++ ..+.+++|.|+ .+.+.++.
T Consensus       355 ~islackki~-T~~RiILSGTPiQNnL~ELw  384 (923)
T KOG0387|consen  355 KISLACKKIR-TVHRIILSGTPIQNNLTELW  384 (923)
T ss_pred             HHHHHHHhcc-ccceEEeeCccccchHHHHH
Confidence            4445556665 45677778886 45444443

>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=98.36  E-value=8.9e-06  Score=66.27  Aligned_cols=128  Identities=20%  Similarity=0.279  Sum_probs=83.0

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhc---CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIK---GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      +|+-...+.++.-.+.. ++. +++.|.++...+.+   |+|.+.+.-+|.|||.+.+ |++..+.++.. .-+.+++| 
T Consensus         4 ~w~p~~~P~wLl~E~e~-~il-iR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~-Pmla~~LAdg~-~LvrviVp-   78 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIES-NIL-IRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIV-PMLALALADGS-RLVRVIVP-   78 (229)
T ss_pred             CCCchhChHHHHHHHHc-Cce-eeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHH-HHHHHHHcCCC-cEEEEEcC-
Confidence            56666667777777654 454 89999999888764   6899999999999997754 55555444322 25666666 


Q ss_pred             HHHHHHHHHHHHH-hhccCCceEEE--EEcCCchHH-H---HH----HhhcCCcEEEeChHHHHHHH
Q 022383          111 RELATQTEKVILA-IGDFINIQAHA--CVGGKSVGE-D---IR----KLEHGVHVVSGTPGRVCDMI  166 (298)
Q Consensus       111 ~~l~~q~~~~~~~-~~~~~~~~~~~--~~~~~~~~~-~---~~----~~~~~~~ilV~Tp~~l~~~~  166 (298)
                      ++|..|....++. ++.-.+-++..  +..+..... .   ..    .....-.|+++||+.+.++-
T Consensus        79 k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~  145 (229)
T PF12340_consen   79 KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFK  145 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHH
Confidence            5799999988864 44333444433  333333221 1   11    12234479999999988753

There are two conserved sequence motifs: LLE and NMG.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.32  E-value=4.3e-06  Score=74.03  Aligned_cols=108  Identities=13%  Similarity=0.185  Sum_probs=67.1

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcC
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (298)
                      -++|.|..|+|||+..+-.+ ..+.....+..++++++..+|...+...+......                      ..
T Consensus         3 v~~I~G~aGTGKTvla~~l~-~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~----------------------~~   59 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLA-KELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNP----------------------KL   59 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHH-HHhhccccCCceEEEEecchHHHHHHHHHhhhccc----------------------ch
Confidence            47889999999997654333 33322334568999999999999888877653200                      00


Q ss_pred             CcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc-------cHHHHHHHHHh
Q 022383          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-------FKDQIYDVYRY  202 (298)
Q Consensus       152 ~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-------~~~~i~~i~~~  202 (298)
                      ....+..+..+..............++|||||||.+...+       ....+..+++.
T Consensus        60 ~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   60 KKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             hhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence            1122233333333222223456788999999999997732       23556666665

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=98.31  E-value=8e-06  Score=72.50  Aligned_cols=168  Identities=19%  Similarity=0.220  Sum_probs=103.2

Q ss_pred             CChHHHHHHHHHhhcC-----CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-----~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .+-|+|.+.+..+...     ..-++.-..|+|||.-.+-.++..+.    +...|+++|+.+| .|+.+.+..... ..
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~~----ra~tLVvaP~VAl-mQW~nEI~~~T~-gs  257 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEVD----RAPTLVVAPTVAL-MQWKNEIERHTS-GS  257 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhccc----cCCeeEEccHHHH-HHHHHHHHHhcc-Cc
Confidence            5789999988765533     34567778999999765544555433    3358999999996 577888877766 35


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc--Cc-----------cCCCccE--EEechhhHhhccccHH
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK--TL-----------RTRAIKL--LVLDESDEMLSRGFKD  194 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~--~~-----------~~~~l~~--vViDE~h~~~~~~~~~  194 (298)
                      +++..++|.... ...+.+ .++|++++|-..+.+..+.+  ++           .+..+++  ||+||||.+-+.. ..
T Consensus       258 lkv~~YhG~~R~-~nikel-~~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R~-sn  334 (791)
T KOG1002|consen  258 LKVYIYHGAKRD-KNIKEL-MNYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDRQ-SN  334 (791)
T ss_pred             eEEEEEeccccc-CCHHHh-hcCcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhccccccc-cc
Confidence            677777775332 233333 35799999998888877652  11           1234444  9999999985442 11


Q ss_pred             HHHHHHHhCCCCccEEEEEeeC-chh---HHHHHHhcCCCCEE
Q 022383          195 QIYDVYRYLPPDLQVVLISATL-PHE---ILEMTTKFMTDPVK  233 (298)
Q Consensus       195 ~i~~i~~~~~~~~~~v~~SAT~-~~~---~~~~~~~~~~~~~~  233 (298)
                      .-+.+...-  ......+|.|+ .+.   +-.+++.+.-+|..
T Consensus       335 TArAV~~L~--tt~rw~LSGTPLQNrigElySLiRFL~i~Pfs  375 (791)
T KOG1002|consen  335 TARAVFALE--TTYRWCLSGTPLQNRIGELYSLIRFLNINPFS  375 (791)
T ss_pred             HHHHHHhhH--hhhhhhccCCcchhhHHHHHHHHHHHccCcch
Confidence            122222111  23356778876 333   33344433345543

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.31  E-value=3.3e-06  Score=81.51  Aligned_cols=75  Identities=19%  Similarity=0.196  Sum_probs=63.2

Q ss_pred             CCCCCChHHHHHHHHHh----hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           51 YGFEKPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~----~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      +-|..++|.|.+....+    ..|++.++.+|||+|||++.+.+++......+..++++|.+.|..=..|+.+.+++..
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhhh
Confidence            35676799999887664    4789999999999999999999999977654445689999999999999999998853

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).

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

Probab=98.31  E-value=2.6e-06  Score=77.95  Aligned_cols=76  Identities=22%  Similarity=0.190  Sum_probs=63.2

Q ss_pred             HHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           47 GIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .+...++..++.-|..|+.+++.+.-.+|+||.|+|||.+..-.+++.+..  ....+|+.+|+..-++|+++.+.+-
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~--~~~~VLvcApSNiAVDqLaeKIh~t  477 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--HAGPVLVCAPSNIAVDQLAEKIHKT  477 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh--cCCceEEEcccchhHHHHHHHHHhc
Confidence            445567788999999999999999999999999999998766656555544  2447999999999999999988764

>PRK10536 hypothetical protein; Provisional

Probab=98.31  E-value=2.4e-05  Score=65.07  Aligned_cols=143  Identities=13%  Similarity=0.140  Sum_probs=81.6

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHH-------HHHHH--
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ-------TEKVI--  121 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q-------~~~~~--  121 (298)
                      .++...+..|...+..+.++..+++.||+|+|||+......++.+... .-.++++.=|..+..+.       ..+.+  
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~-~~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p  133 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK-DVDRIIVTRPVLQADEDLGFLPGDIAEKFAP  133 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC-CeeEEEEeCCCCCchhhhCcCCCCHHHHHHH
Confidence            456678899999999999888999999999999988777677665442 23345555566543221       11111  


Q ss_pred             --HHhhccCCceEEEEEcCCchHHHHHHh-h-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHH
Q 022383          122 --LAIGDFINIQAHACVGGKSVGEDIRKL-E-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (298)
Q Consensus       122 --~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~  197 (298)
                        +.+...+..    +.+.    .....+ . +.-.|-|...    .+++...+   .-++||+||++.+.    ...+.
T Consensus       134 ~~~pi~D~L~~----~~~~----~~~~~~~~~~~~~Iei~~l----~ymRGrtl---~~~~vIvDEaqn~~----~~~~k  194 (262)
T PRK10536        134 YFRPVYDVLVR----RLGA----SFMQYCLRPEIGKVEIAPF----AYMRGRTF---ENAVVILDEAQNVT----AAQMK  194 (262)
T ss_pred             HHHHHHHHHHH----HhCh----HHHHHHHHhccCcEEEecH----HHhcCCcc---cCCEEEEechhcCC----HHHHH
Confidence              111111100    0010    011111 0 1112333322    33343333   33899999998762    36777


Q ss_pred             HHHHhCCCCccEEEEE
Q 022383          198 DVYRYLPPDLQVVLIS  213 (298)
Q Consensus       198 ~i~~~~~~~~~~v~~S  213 (298)
                      .++..++.+.++|++-
T Consensus       195 ~~ltR~g~~sk~v~~G  210 (262)
T PRK10536        195 MFLTRLGENVTVIVNG  210 (262)
T ss_pred             HHHhhcCCCCEEEEeC
Confidence            8888888888777653

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.30  E-value=2.3e-05  Score=70.16  Aligned_cols=177  Identities=16%  Similarity=0.194  Sum_probs=113.4

Q ss_pred             CCCChHHHHHHHHHhhcCCcEEEEcCC-CCch--HHHHHHHHHHhhccC----------------------------CCC
Q 022383           53 FEKPSAIQQRAVMPIIKGRDVIAQAQS-GTGK--TSMIALTVCQTVDTS----------------------------SRE  101 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~li~~pT-G~GK--T~~~~~~~~~~~~~~----------------------------~~~  101 (298)
                      -..+++.|.+.+....+.+|++....| +.|+  +-.|++.+++++.+.                            -..
T Consensus       214 s~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tR  293 (698)
T KOG2340|consen  214 SEPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTR  293 (698)
T ss_pred             cCcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCC
Confidence            357999999999999999998765332 3344  466888888876211                            123


Q ss_pred             eEEEEEcCcHHHHHHHHHHHHHhhccCCc---------eE-EEE---------------------EcCCchHHH------
Q 022383          102 VQALILSPTRELATQTEKVILAIGDFINI---------QA-HAC---------------------VGGKSVGED------  144 (298)
Q Consensus       102 ~~~lil~p~~~l~~q~~~~~~~~~~~~~~---------~~-~~~---------------------~~~~~~~~~------  144 (298)
                      |+|||+||+++-|-.+.+.+..+..+.+-         +. .-+                     .|.++..-.      
T Consensus       294 pkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ft  373 (698)
T KOG2340|consen  294 PKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFT  373 (698)
T ss_pred             ceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHH
Confidence            78999999999999999999877432211         00 001                     111110000      


Q ss_pred             ---H--HHhhcCCcEEEeChHHHHHHHhcc-----Cc-cCCCccEEEechhhHhhccccHHHHHHHHHhCC---C-----
Q 022383          145 ---I--RKLEHGVHVVSGTPGRVCDMIKRK-----TL-RTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP---P-----  205 (298)
Q Consensus       145 ---~--~~~~~~~~ilV~Tp~~l~~~~~~~-----~~-~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~---~-----  205 (298)
                         +  ..-....||+||+|--|..++.+.     .+ .++.+.++|||-+|.++... ..++..++..+.   .     
T Consensus       374 kKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QN-wEhl~~ifdHLn~~P~k~h~~  452 (698)
T KOG2340|consen  374 KKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQN-WEHLLHIFDHLNLQPSKQHDV  452 (698)
T ss_pred             HHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhh-HHHHHHHHHHhhcCcccccCC
Confidence               0  000135799999998888877642     22 25889999999999986543 344445554442   1     


Q ss_pred             ----------------CccEEEEEeeCchhHHHHHHhcCCC
Q 022383          206 ----------------DLQVVLISATLPHEILEMTTKFMTD  230 (298)
Q Consensus       206 ----------------~~~~v~~SAT~~~~~~~~~~~~~~~  230 (298)
                                      -.|.+++|+--.+.+..+...++.+
T Consensus       453 DfSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N  493 (698)
T KOG2340|consen  453 DFSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQN  493 (698)
T ss_pred             ChhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhh
Confidence                            2578888888777777666665543

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.29  E-value=1.5e-05  Score=74.81  Aligned_cols=141  Identities=17%  Similarity=0.200  Sum_probs=85.3

Q ss_pred             hHHHHHHHHHhhcCCcEEEEcCCCCchHHHHH--HHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA--LTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~--~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      ..+|+.++...+.++-+++.|+.|+|||....  +..+..........++++.+||-.-+..+.+.+......++..   
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~~~---  223 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNLAAA---  223 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhcccccc---
Confidence            37999999999999999999999999996533  2223222221123578999999988888887665533221110   


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc------cCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCcc
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~------~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~  208 (298)
                             ...    ......-..|-.+++.....      ...+...+++|||||+-++.    ...+..+++.+++..+
T Consensus       224 -------~~~----~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd----~~l~~~ll~al~~~~r  288 (586)
T TIGR01447       224 -------EAL----IAALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVD----LPLMAKLLKALPPNTK  288 (586)
T ss_pred             -------hhh----hhccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCC----HHHHHHHHHhcCCCCE
Confidence                   000    00011112333333221110      11223467999999997652    3456677888888888


Q ss_pred             EEEEEee
Q 022383          209 VVLISAT  215 (298)
Q Consensus       209 ~v~~SAT  215 (298)
                      +|++--.
T Consensus       289 lIlvGD~  295 (586)
T TIGR01447       289 LILLGDK  295 (586)
T ss_pred             EEEECCh
Confidence            8877554

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.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.28  E-value=2.8e-05  Score=73.22  Aligned_cols=140  Identities=16%  Similarity=0.199  Sum_probs=85.1

Q ss_pred             hHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHH--HHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL--TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~--~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .++|+.++...+.++-.+|.|++|+|||....-  ..+..... ....++.+..||..-+..+.+.+.......+..   
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~-~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~---  229 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLAD-GERCRIRLAAPTGKAAARLTESLGKALRQLPLT---  229 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC-CCCcEEEEECCcHHHHHHHHHHHHhhhhccccc---
Confidence            589999999999999999999999999966422  22222211 123478888999998888888776543322210   


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHh------ccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCcc
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIK------RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~------~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~  208 (298)
                             ......    ...-..|-.+++....      ....+....++|||||+-++-    ...+..+++.+++..+
T Consensus       230 -------~~~~~~----~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd----~~lm~~ll~al~~~~r  294 (615)
T PRK10875        230 -------DEQKKR----IPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVD----LPMMARLIDALPPHAR  294 (615)
T ss_pred             -------hhhhhc----CCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhccc----HHHHHHHHHhcccCCE
Confidence                   000000    0111122222221111      111233456899999997752    4556677888888888


Q ss_pred             EEEEEee
Q 022383          209 VVLISAT  215 (298)
Q Consensus       209 ~v~~SAT  215 (298)
                      +|++--.
T Consensus       295 lIlvGD~  301 (615)
T PRK10875        295 VIFLGDR  301 (615)
T ss_pred             EEEecch
Confidence            8887655

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.26  E-value=1.8e-05  Score=66.92  Aligned_cols=160  Identities=21%  Similarity=0.141  Sum_probs=101.9

Q ss_pred             CChHHHHHHHHHhh----------cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           55 KPSAIQQRAVMPII----------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----------~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .++..|-+++-...          .+...++-=.||.||--...-.+++......  .++|+++.+..|..+..+-++.+
T Consensus        37 ~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr--~r~vwvS~s~dL~~Da~RDl~DI  114 (303)
T PF13872_consen   37 LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGR--KRAVWVSVSNDLKYDAERDLRDI  114 (303)
T ss_pred             cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCC--CceEEEECChhhhhHHHHHHHHh
Confidence            46888888876543          2356777778999998766666777766643  37899999999999999999888


Q ss_pred             hccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc---Ccc---------CCCccEEEechhhHhhcccc
Q 022383          125 GDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK---TLR---------TRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~---~~~---------~~~l~~vViDE~h~~~~~~~  192 (298)
                      +.. .+.+..+..-...    ....-.-.|+.+|-..|......+   .-.         -..=.+||+||||..-...-
T Consensus       115 G~~-~i~v~~l~~~~~~----~~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~  189 (303)
T PF13872_consen  115 GAD-NIPVHPLNKFKYG----DIIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSS  189 (303)
T ss_pred             CCC-cccceechhhccC----cCCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCc
Confidence            644 3333222211000    001123468999988877664321   000         13345899999999754421


Q ss_pred             --------HHHHHHHHHhCCCCccEEEEEeeCchhHHH
Q 022383          193 --------KDQIYDVYRYLPPDLQVVLISATLPHEILE  222 (298)
Q Consensus       193 --------~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~  222 (298)
                              ...+..+-+.+| +.+++.+|||--.+..+
T Consensus       190 ~~~~~sk~g~avl~LQ~~LP-~ARvvY~SATgasep~N  226 (303)
T PF13872_consen  190 GSKKPSKTGIAVLELQNRLP-NARVVYASATGASEPRN  226 (303)
T ss_pred             cCccccHHHHHHHHHHHhCC-CCcEEEecccccCCCce
Confidence                    234444555664 67799999997544333

>TIGR00376 DNA helicase, putative

Probab=98.24  E-value=1.6e-05  Score=75.57  Aligned_cols=67  Identities=18%  Similarity=0.207  Sum_probs=53.2

Q ss_pred             CCChHHHHHHHHHhhcC-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           54 EKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      ..+++.|..++..++.. ..++|.||+|+|||....-.+.+.+..   +.++++++||..-++++.+.+..
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~---g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR---GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEEcCcHHHHHHHHHHHHh
Confidence            35799999999998866 678899999999996654444443333   44899999999999999998875

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.21  E-value=2.5e-05  Score=75.24  Aligned_cols=126  Identities=22%  Similarity=0.233  Sum_probs=78.7

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEE
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  133 (298)
                      ..+++.|.+++..+..++-+++.|+.|+|||... -.++..+........+++++||-.-+..+.+..       +....
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~-------g~~a~  393 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT-------GLTAS  393 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc-------CCccc
Confidence            4599999999999998899999999999999653 233343333221246788899987776554421       21111


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-----cCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCcc
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-----KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ  208 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-----~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~  208 (298)
                                              |-.+++.....     ..-.....++|||||++++..    ..+..+++.++...+
T Consensus       394 ------------------------Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd~----~~~~~Ll~~~~~~~r  445 (720)
T TIGR01448       394 ------------------------TIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDT----WLALSLLAALPDHAR  445 (720)
T ss_pred             ------------------------cHHHHhhccCCccchhhhhccccCCEEEEeccccCCH----HHHHHHHHhCCCCCE
Confidence                                    11111110000     001124578999999998732    345666777887888


Q ss_pred             EEEEEee
Q 022383          209 VVLISAT  215 (298)
Q Consensus       209 ~v~~SAT  215 (298)
                      +|++--+
T Consensus       446 lilvGD~  452 (720)
T TIGR01448       446 LLLVGDT  452 (720)
T ss_pred             EEEECcc
Confidence            8887554

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

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.21  E-value=1.2e-05  Score=78.29  Aligned_cols=161  Identities=18%  Similarity=0.205  Sum_probs=105.2

Q ss_pred             CChHHHHHHHHHhh--c--CCcEEEEcCCCCchHHHHHHHHHH-hhccC----CCCe-EEEEEcCcHHHHHHHHHHHHHh
Q 022383           55 KPSAIQQRAVMPII--K--GRDVIAQAQSGTGKTSMIALTVCQ-TVDTS----SREV-QALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~--~--~~~~li~~pTG~GKT~~~~~~~~~-~~~~~----~~~~-~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .++.||++.++.+.  +  +-+-|+|--.|-|||+-.+-.+.. +....    .... -.||+||+ .|+..+...++++
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf 1053 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKF 1053 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHh
Confidence            57899999887653  2  358899999999999764433322 22221    1112 38999995 6899999999998


Q ss_pred             hccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCC
Q 022383          125 GDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (298)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~  204 (298)
                      ...  +++..+.|+.......+.-.++.+|+|++-+.+..-+..  +.-....|.|+||-|-+-..  ...+.+..+.+.
T Consensus      1054 ~pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVikN~--ktkl~kavkqL~ 1127 (1549)
T KOG0392|consen 1054 FPF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVIKNS--KTKLTKAVKQLR 1127 (1549)
T ss_pred             cch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH--HHhcccceEEecCcceecch--HHHHHHHHHHHh
Confidence            776  566667776666555555556789999998776532221  11134569999999987332  444555555554


Q ss_pred             CCccEEEEEeeC-chhHHHH
Q 022383          205 PDLQVVLISATL-PHEILEM  223 (298)
Q Consensus       205 ~~~~~v~~SAT~-~~~~~~~  223 (298)
                      .+ ..+++|.|+ .+.+.++
T Consensus      1128 a~-hRLILSGTPIQNnvleL 1146 (1549)
T KOG0392|consen 1128 AN-HRLILSGTPIQNNVLEL 1146 (1549)
T ss_pred             hc-ceEEeeCCCcccCHHHH
Confidence            33 356678886 4544443

>PF13245 AAA_19: Part of AAA domain

Probab=98.21  E-value=8.2e-06  Score=55.05  Aligned_cols=51  Identities=25%  Similarity=0.429  Sum_probs=38.4

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhc--cCCCCeEEEEEcCcHHHHHHHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~--~~~~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      ++-++|.||.|+|||...+-.+...+.  ... +.++++++|++..++++.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCC-CCeEEEECCCHHHHHHHHHHH
Confidence            344556999999999766555555552  222 568999999999999999877

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

Probab=98.11  E-value=1.6e-05  Score=72.40  Aligned_cols=65  Identities=22%  Similarity=0.294  Sum_probs=53.0

Q ss_pred             CCChHHHHHHHHHhhcCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHH
Q 022383           54 EKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      ..+.+.|..++....+.+ -.++.||+|+|||.+....+.+.+..   +.++++..||.+-++.+.+++
T Consensus       184 ~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~---~k~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  184 KNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ---KKRVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             ccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc---CCeEEEEcCchHHHHHHHHHh
Confidence            468899999999888775 47888999999998766666665555   458999999999999999864

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.11  E-value=1.3e-05  Score=78.09  Aligned_cols=159  Identities=16%  Similarity=0.152  Sum_probs=103.6

Q ss_pred             CCChHHHHHHHHHhh----cCCcEEEEcCCCCchH---HHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           54 EKPSAIQQRAVMPII----KGRDVIAQAQSGTGKT---SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT---~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      ..++.+|-+.++.++    .+.++|+.-..|-|||   .+|+-.+++...-  .|| .|+++|...+ ..+.+.|..++ 
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~--~gp-flvvvplst~-~~W~~ef~~w~-  443 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQI--HGP-FLVVVPLSTI-TAWEREFETWT-  443 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhc--cCC-eEEEeehhhh-HHHHHHHHHHh-
Confidence            679999999887654    6899999999999999   4566666665422  244 5778886553 34455555554 


Q ss_pred             cCCceEEEEEcCCchHHHHHHhh----c-----CCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHH
Q 022383          127 FINIQAHACVGGKSVGEDIRKLE----H-----GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (298)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~----~-----~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~  197 (298)
                        +++++.++|+....+.++...    .     ..+++++|.+.++.--.  .+.--...+++|||||++-... ...+.
T Consensus       444 --~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~--~L~~i~w~~~~vDeahrLkN~~-~~l~~  518 (1373)
T KOG0384|consen  444 --DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA--ELSKIPWRYLLVDEAHRLKNDE-SKLYE  518 (1373)
T ss_pred             --hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHh--hhccCCcceeeecHHhhcCchH-HHHHH
Confidence              788999999877766655543    2     36899999988764221  1222355789999999984331 22233


Q ss_pred             HHHHhCCCCccEEEEEeeC-chhHHHHH
Q 022383          198 DVYRYLPPDLQVVLISATL-PHEILEMT  224 (298)
Q Consensus       198 ~i~~~~~~~~~~v~~SAT~-~~~~~~~~  224 (298)
                      . +..+.- ...+++|.|+ .+.+..+.
T Consensus       519 ~-l~~f~~-~~rllitgTPlQNsikEL~  544 (1373)
T KOG0384|consen  519 S-LNQFKM-NHRLLITGTPLQNSLKELW  544 (1373)
T ss_pred             H-HHHhcc-cceeeecCCCccccHHHHH
Confidence            3 444432 3356667775 55555544

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.09  E-value=2e-05  Score=74.32  Aligned_cols=146  Identities=14%  Similarity=0.144  Sum_probs=83.6

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC------CceEEEEEcCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI------NIQAHACVGGKSVGED  144 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~------~~~~~~~~~~~~~~~~  144 (298)
                      -++-|.+.||+|||.||+-.++..-..-. -.+-||+||+.+.-.-+.-..+.....+      +.+.-.+.-+......
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~YG-~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~~~~~~~  153 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKKYG-LFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYDEDIEKF  153 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHHhC-ceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeechHHHHH
Confidence            47889999999999999988877544432 2367999999988777554444332222      2333333222111111


Q ss_pred             HHHhhcCCcEEEeChHHHHHH------HhccCccCCC-----------c----cEEEechhhHhhccccHHHHHHHHHhC
Q 022383          145 IRKLEHGVHVVSGTPGRVCDM------IKRKTLRTRA-----------I----KLLVLDESDEMLSRGFKDQIYDVYRYL  203 (298)
Q Consensus       145 ~~~~~~~~~ilV~Tp~~l~~~------~~~~~~~~~~-----------l----~~vViDE~h~~~~~~~~~~i~~i~~~~  203 (298)
                      .....+.+.+++.|...+..-      ++.......+           +    -.||+||-|.+..+  -..+..+....
T Consensus       154 ~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~--~k~~~~i~~l~  231 (985)
T COG3587         154 KFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGD--DKTYGAIKQLN  231 (985)
T ss_pred             hhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccc--hHHHHHHHhhC
Confidence            122235677888776555432      2221111111           1    25999999999764  23333333333


Q ss_pred             CCCccEEEEEeeCchhHH
Q 022383          204 PPDLQVVLISATLPHEIL  221 (298)
Q Consensus       204 ~~~~~~v~~SAT~~~~~~  221 (298)
                      |  .-++=++||.+....
T Consensus       232 p--l~ilRfgATfkd~y~  247 (985)
T COG3587         232 P--LLILRFGATFKDEYN  247 (985)
T ss_pred             c--eEEEEecccchhhhc
Confidence            2  336678999876543

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=98.06  E-value=0.00012  Score=69.84  Aligned_cols=127  Identities=17%  Similarity=0.252  Sum_probs=92.3

Q ss_pred             hHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEE
Q 022383           57 SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV  136 (298)
Q Consensus        57 ~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (298)
                      +|+=.+.+-.+.-+..-+..+-||-|||++..+|+.-.-..   +..+-++.-..-|+..-.+.+..+..++|+.++...
T Consensus        80 ~~~dVQliG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~---gkgVhvVTvNdYLA~RDae~m~~l~~~LGlsvG~~~  156 (822)
T COG0653          80 RHFDVQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALA---GKGVHVVTVNDYLARRDAEWMGPLYEFLGLSVGVIL  156 (822)
T ss_pred             ChhhHHHhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcC---CCCcEEeeehHHhhhhCHHHHHHHHHHcCCceeecc
Confidence            33334455555556667889999999999988887554333   335788888999999999999999999999999988


Q ss_pred             cCCchHHHHHHhhcCCcEEEeChHHHH-HHHhc------cCccCCCccEEEechhhHhh
Q 022383          137 GGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKR------KTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       137 ~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~~~~------~~~~~~~l~~vViDE~h~~~  188 (298)
                      .+.+..+....+  .|||..+|...|- .+++.      .......+.+-|+||+|.++
T Consensus       157 ~~m~~~ek~~aY--~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         157 AGMSPEEKRAAY--ACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             CCCChHHHHHHH--hcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            887665554444  4899999987663 12221      22334568899999999865

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=98.04  E-value=1.5e-05  Score=73.48  Aligned_cols=134  Identities=17%  Similarity=0.105  Sum_probs=86.8

Q ss_pred             CChHHHHHHHHHhhc-----CCcEEEEcCCCCchHHHHHHHHHHhhc-----cC--CCCeEEEEEcCcHHHHHHHHHHHH
Q 022383           55 KPSAIQQRAVMPIIK-----GRDVIAQAQSGTGKTSMIALTVCQTVD-----TS--SREVQALILSPTRELATQTEKVIL  122 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~-----~~~~li~~pTG~GKT~~~~~~~~~~~~-----~~--~~~~~~lil~p~~~l~~q~~~~~~  122 (298)
                      .+.|+|..++..+..     +...|+....|-|||+..+-.++++=.     ..  .....+||||| ..|..|+...+.
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~P-aSli~qW~~Ev~  403 (901)
T KOG4439|consen  325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICP-ASLIHQWEAEVA  403 (901)
T ss_pred             ecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCc-HHHHHHHHHHHH
Confidence            578999998876652     246788889999999875555544321     11  11124899999 467889988887


Q ss_pred             HhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHH----HHhcc--CccCC--CccEEEechhhHhhcc
Q 022383          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD----MIKRK--TLRTR--AIKLLVLDESDEMLSR  190 (298)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~----~~~~~--~~~~~--~l~~vViDE~h~~~~~  190 (298)
                      +......+++..++|.....-. ......+||+|+|..-+..    -...+  .-.+.  ....||+||||.+-+.
T Consensus       404 ~rl~~n~LsV~~~HG~n~r~i~-~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~  478 (901)
T KOG4439|consen  404 RRLEQNALSVYLYHGPNKREIS-AKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNS  478 (901)
T ss_pred             HHHhhcceEEEEecCCccccCC-HHHHhhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhccc
Confidence            6666667899999987642222 2223568999999755544    11111  11122  2355999999998544

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.95  E-value=1.8e-05  Score=76.53  Aligned_cols=126  Identities=17%  Similarity=0.232  Sum_probs=89.4

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      ++++|-  +-.+.-++.-+..+.||-|||+++.+|++-....   |..|=+|+.+--||..=.+.+..+..++|+.+...
T Consensus       139 ~ydVQL--iGgivLh~G~IAEM~TGEGKTLvatlp~yLnAL~---G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~i  213 (1025)
T PRK12900        139 PYDVQL--IGGIVLHSGKISEMATGEGKTLVSTLPTFLNALT---GRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGVI  213 (1025)
T ss_pred             ccchHH--hhhHHhhcCCccccCCCCCcchHhHHHHHHHHHc---CCCcEEEeechHhhhhhHHHHHHHHHHhCCeeeee
Confidence            555554  4444434455789999999999998887655444   33466778888999988889999999999999887


Q ss_pred             EcCCchHHHHHHhhcCCcEEEeChHHHH-HHHhcc------CccCCCccEEEechhhHhh
Q 022383          136 VGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRK------TLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~~~~~------~~~~~~l~~vViDE~h~~~  188 (298)
                      ..+.+....  .-.-.|||..||...|- .+++.+      ..-.+.+.+.||||+|.++
T Consensus       214 ~~~~~~~~R--r~aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        214 LNTMRPEER--REQYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             CCCCCHHHH--HHhCCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            665554443  33445899999987663 233332      2234778999999999975

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.92  E-value=0.00033  Score=62.33  Aligned_cols=129  Identities=19%  Similarity=0.203  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhcc-CCCCeEEEEEc--CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~-~~~~~~~lil~--p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (298)
                      +.++++||||+|||.+..-.+...... ...+.++.++.  +.+.-+..+   ++.++...++++...            
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQ---L~~~a~~lgvpv~~~------------  239 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQ---IQTYGDIMGIPVKAI------------  239 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHH---HHHHhhcCCcceEee------------
Confidence            568999999999997765444322211 12234555555  333333332   444554445543221            


Q ss_pred             hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc-cHHHHHHHHHhCCCC-ccEEEEEeeCch-hHHHHH
Q 022383          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPPD-LQVVLISATLPH-EILEMT  224 (298)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~~~~~-~~~v~~SAT~~~-~~~~~~  224 (298)
                               -+++.+...+..    +.+.++|+||++.+..... ....+..+++...+. -.++.+|||... .+....
T Consensus       240 ---------~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~  306 (388)
T PRK12723        240 ---------ESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIF  306 (388)
T ss_pred             ---------CcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHH
Confidence                     123334343332    3578999999998765332 234555555555433 356888999864 445455


Q ss_pred             Hhc
Q 022383          225 TKF  227 (298)
Q Consensus       225 ~~~  227 (298)
                      ..+
T Consensus       307 ~~~  309 (388)
T PRK12723        307 HQF  309 (388)
T ss_pred             HHh
Confidence            555

>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=97.90  E-value=4.1e-05  Score=66.45  Aligned_cols=122  Identities=16%  Similarity=0.155  Sum_probs=74.4

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      +++-|.+++..  ..++++|.|+.|||||.+.+--+...+... -...+++++++|+..+.++..++...........  
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~~~~~~--   76 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEEEQQES--   76 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHCC--
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCcccccc--
Confidence            46789998877  788999999999999988766655555443 2345899999999999999999987643321100  


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHH-HhccCccC-CCccEEEechhh
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDM-IKRKTLRT-RAIKLLVLDESD  185 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~-~~~~~~~~-~~l~~vViDE~h  185 (298)
                          ...............+.|+|-..+..- ++...... -.-.+-++|+..
T Consensus        77 ----~~~~~~~~~~~~~~~~~i~T~hsf~~~ll~~~~~~~~~~~~~~i~~~~~  125 (315)
T PF00580_consen   77 ----SDNERLRRQLSNIDRIYISTFHSFCYRLLREYGYEIGIDPNFEILDEEE  125 (315)
T ss_dssp             ----TT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHH
T ss_pred             ----cccccccccccccchheeehhhhhhhhhhhhhhhhhhccccceeecchh
Confidence                000011112223346788888777653 33321111 123456666665

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 ....

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.86  E-value=0.00036  Score=68.98  Aligned_cols=123  Identities=20%  Similarity=0.118  Sum_probs=75.5

Q ss_pred             CChHHHHHHHHHhhcCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEE
Q 022383           55 KPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  133 (298)
                      .+++-|.+++..++.++ -++++|+.|+|||.+ +-.+...+..  .+.+++.++||-.-+..+.+       ..++.. 
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~--~G~~V~~~ApTGkAA~~L~e-------~tGi~a-  414 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA--AGYEVRGAALSGIAAENLEG-------GSGIAS-  414 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH--cCCeEEEecCcHHHHHHHhh-------ccCcch-
Confidence            49999999999999865 478999999999975 3344444433  25689999999866655432       112211 


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhC-CCCccEEEE
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLI  212 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~-~~~~~~v~~  212 (298)
                                             .|..++..-...+...+...++|||||+-++...    .+..+++.. +...++|++
T Consensus       415 -----------------------~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~~~----~m~~LL~~a~~~garvVLV  467 (988)
T PRK13889        415 -----------------------RTIASLEHGWGQGRDLLTSRDVLVIDEAGMVGTR----QLERVLSHAADAGAKVVLV  467 (988)
T ss_pred             -----------------------hhHHHHHhhhcccccccccCcEEEEECcccCCHH----HHHHHHHhhhhCCCEEEEE
Confidence                                   1222221111122234567789999999876433    334455443 346677776


Q ss_pred             Eee
Q 022383          213 SAT  215 (298)
Q Consensus       213 SAT  215 (298)
                      --+
T Consensus       468 GD~  470 (988)
T PRK13889        468 GDP  470 (988)
T ss_pred             CCH
Confidence            555

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=97.85  E-value=0.00014  Score=70.90  Aligned_cols=159  Identities=15%  Similarity=0.196  Sum_probs=103.9

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCC--CCeEEEEEcCcHHHHHHHHHHHHHhhccC
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS--REVQALILSPTRELATQTEKVILAIGDFI  128 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~--~~~~~lil~p~~~l~~q~~~~~~~~~~~~  128 (298)
                      .++.||...++.+.    ++-|-|+.-..|-|||.- .+.++.++..+.  =|+ -|||+||-.+. .+.=.|++++.  
T Consensus       615 qLReYQkiGLdWLatLYeknlNGILADEmGLGKTIQ-tISllAhLACeegnWGP-HLIVVpTsviL-nWEMElKRwcP--  689 (1958)
T KOG0391|consen  615 QLREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQ-TISLLAHLACEEGNWGP-HLIVVPTSVIL-NWEMELKRWCP--  689 (1958)
T ss_pred             HHHHHHHhhHHHHHHHHHhcccceehhhhcccchhH-HHHHHHHHHhcccCCCC-ceEEeechhhh-hhhHHHhhhCC--
Confidence            58889998887654    445889999999999943 344555554432  233 57888887654 34445777754  


Q ss_pred             CceEEEEEcCCchHHHH-HHhh--cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCC
Q 022383          129 NIQAHACVGGKSVGEDI-RKLE--HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (298)
Q Consensus       129 ~~~~~~~~~~~~~~~~~-~~~~--~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~  205 (298)
                      ++++..++|........ +.+.  +..+|-|++...+..-+.  .|.-.+..|+|+||+|.+-.+. ...|+.++...  
T Consensus       690 glKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~--AFkrkrWqyLvLDEaqnIKnfk-sqrWQAllnfn--  764 (1958)
T KOG0391|consen  690 GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLT--AFKRKRWQYLVLDEAQNIKNFK-SQRWQALLNFN--  764 (1958)
T ss_pred             cceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHH--HHHhhccceeehhhhhhhcchh-HHHHHHHhccc--
Confidence            68899999986654333 2232  345677777665555433  2444677899999999985442 55677776664  


Q ss_pred             CccEEEEEeeC-chhHHHH
Q 022383          206 DLQVVLISATL-PHEILEM  223 (298)
Q Consensus       206 ~~~~v~~SAT~-~~~~~~~  223 (298)
                      ..+.++++.|+ .+.+.++
T Consensus       765 sqrRLLLtgTPLqNslmEL  783 (1958)
T KOG0391|consen  765 SQRRLLLTGTPLQNSLMEL  783 (1958)
T ss_pred             hhheeeecCCchhhHHHHH
Confidence            34567777775 5554443

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.84  E-value=0.00042  Score=67.21  Aligned_cols=121  Identities=18%  Similarity=0.160  Sum_probs=73.2

Q ss_pred             CChHHHHHHHHHhhcC-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEE
Q 022383           55 KPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  133 (298)
                      .+++-|.+++..+..+ +-+++.|+.|+|||... -.+...+...  +.++++++||-.-+..+.+       ..++...
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~~--g~~V~~~ApTg~Aa~~L~~-------~~g~~a~  421 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEAA--GYRVIGAALSGKAAEGLQA-------ESGIESR  421 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHhC--CCeEEEEeCcHHHHHHHHh-------ccCCcee
Confidence            4899999999998874 67899999999999653 2344444332  5588999999766655543       1122111


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhC-CCCccEEEE
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLI  212 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~-~~~~~~v~~  212 (298)
                                              |-.++..-.......+...++|||||+-++....+    ..+++.. ....++|++
T Consensus       422 ------------------------Ti~~~~~~~~~~~~~~~~~~llIvDEasMv~~~~~----~~Ll~~~~~~~~kliLV  473 (744)
T TIGR02768       422 ------------------------TLASLEYAWANGRDLLSDKDVLVIDEAGMVGSRQM----ARVLKEAEEAGAKVVLV  473 (744)
T ss_pred             ------------------------eHHHHHhhhccCcccCCCCcEEEEECcccCCHHHH----HHHHHHHHhcCCEEEEE
Confidence                                    11122111122223356789999999987643333    3344422 245666666


Q ss_pred             E
Q 022383          213 S  213 (298)
Q Consensus       213 S  213 (298)
                      -
T Consensus       474 G  474 (744)
T TIGR02768       474 G  474 (744)
T ss_pred             C
Confidence            5

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

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.82  E-value=0.0001  Score=62.03  Aligned_cols=59  Identities=20%  Similarity=0.300  Sum_probs=41.4

Q ss_pred             CccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeC---chhHHHHHHhcCC
Q 022383          170 TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL---PHEILEMTTKFMT  229 (298)
Q Consensus       170 ~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~---~~~~~~~~~~~~~  229 (298)
                      ....+.++.||+||||.|.... +..+++.++..+...+++++..-+   ++.+..-+.++.-
T Consensus       124 ~~~~~~fKiiIlDEcdsmtsda-q~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrF  185 (346)
T KOG0989|consen  124 GYPCPPFKIIILDECDSMTSDA-QAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRF  185 (346)
T ss_pred             CCCCCcceEEEEechhhhhHHH-HHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcC
Confidence            3445677899999999997654 667777888887788888887765   3444555555443

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.81  E-value=0.00027  Score=60.99  Aligned_cols=144  Identities=16%  Similarity=0.234  Sum_probs=89.6

Q ss_pred             CCCCCChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC
Q 022383           51 YGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~  128 (298)
                      +|+...+..|.-+++.+++.  +=|.+.|+.|+|||+-++-+.+.++...+...++|+-=|+..+.+++-          
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIG----------  293 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIG----------  293 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccC----------
Confidence            68888888999999999876  457888999999999888888888777666667777778876554321          


Q ss_pred             CceEEEEEcCCc--hHHHHHHhhcCCcEEE----eChHHHHHHHhccCccC--------C--CccEEEechhhHhhcccc
Q 022383          129 NIQAHACVGGKS--VGEDIRKLEHGVHVVS----GTPGRVCDMIKRKTLRT--------R--AIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       129 ~~~~~~~~~~~~--~~~~~~~~~~~~~ilV----~Tp~~l~~~~~~~~~~~--------~--~l~~vViDE~h~~~~~~~  192 (298)
                           .+-|...  ...+.+.+...-.++.    ++-+.+...+....+.+        +  .=.+||||||+.+    -
T Consensus       294 -----fLPG~eEeKm~PWmq~i~DnLE~L~~~~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNL----T  364 (436)
T COG1875         294 -----FLPGTEEEKMGPWMQAIFDNLEVLFSPNEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNL----T  364 (436)
T ss_pred             -----cCCCchhhhccchHHHHHhHHHHHhcccccchHHHHHHHhccceeeeeeeeecccccccceEEEehhhcc----C
Confidence                 1111100  0111111111111111    12333444433322211        1  2268999999876    3


Q ss_pred             HHHHHHHHHhCCCCccEEEEE
Q 022383          193 KDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       193 ~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...+..++.+..+..++|++.
T Consensus       365 pheikTiltR~G~GsKIVl~g  385 (436)
T COG1875         365 PHELKTILTRAGEGSKIVLTG  385 (436)
T ss_pred             HHHHHHHHHhccCCCEEEEcC
Confidence            677888999998888877753

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.81  E-value=0.00018  Score=53.90  Aligned_cols=20  Identities=30%  Similarity=0.556  Sum_probs=12.9

Q ss_pred             cCCcEEEEcCCCCchHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~   88 (298)
                      +++.+++.||+|+|||....
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~   22 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIK   22 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHH
Confidence            35678999999999997644

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.79  E-value=4.6e-05  Score=73.95  Aligned_cols=128  Identities=17%  Similarity=0.211  Sum_probs=89.5

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      +.++-.+.+-.+.-.+.-+..+.||-|||+++.+|++-....   |..|-+++.+--||..=.+.+..+..++|+.+...
T Consensus       168 m~~yDVQliGgivLh~G~IAEM~TGEGKTLvAtlp~yLnAL~---GkgVHvVTVNDYLA~RDaewmgply~fLGLsvg~i  244 (1112)
T PRK12901        168 MVHYDVQLIGGVVLHQGKIAEMATGEGKTLVATLPVYLNALT---GNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDCI  244 (1112)
T ss_pred             CcccchHHhhhhhhcCCceeeecCCCCchhHHHHHHHHHHHc---CCCcEEEEechhhhhccHHHHHHHHHHhCCceeec
Confidence            344444555555545666889999999999998887665444   33467778888999888888888888999999876


Q ss_pred             Ec-CCchHHHHHHhhcCCcEEEeChHHHH-HHHhcc------CccCCCccEEEechhhHhh
Q 022383          136 VG-GKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRK------TLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       136 ~~-~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~~~~~------~~~~~~l~~vViDE~h~~~  188 (298)
                      .. +.+..+  ++-.-.|||..+|...|- ++++.+      ....+.+.+.||||+|.++
T Consensus       245 ~~~~~~~~~--rr~aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        245 DKHQPNSEA--RRKAYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             CCCCCCHHH--HHHhCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            54 223322  333445899999987653 333332      2234678999999999975

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.79  E-value=7.1e-05  Score=62.24  Aligned_cols=87  Identities=21%  Similarity=0.321  Sum_probs=67.9

Q ss_pred             CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCC-chHHHHHHhh-cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK-SVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus        99 ~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      ...|.+||||.+---|-++.+.++.+.. .+..++.++... ...+++..+. ...+|.||||+|+..++..+.+.++++
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~-k~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l  202 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKG-KDCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNL  202 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhcc-CCchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccC
Confidence            3568999999998888888888877631 124455555543 6667777676 578999999999999999999999999


Q ss_pred             cEEEechhhH
Q 022383          177 KLLVLDESDE  186 (298)
Q Consensus       177 ~~vViDE~h~  186 (298)
                      .+||+|--|.
T Consensus       203 ~~ivlD~s~~  212 (252)
T PF14617_consen  203 KRIVLDWSYL  212 (252)
T ss_pred             eEEEEcCCcc
Confidence            9999996543

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

Probab=97.73  E-value=0.00075  Score=51.09  Aligned_cols=17  Identities=29%  Similarity=0.616  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCCchHHH
Q 022383           70 GRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~   86 (298)
                      ++.+++.||+|+|||..
T Consensus        19 ~~~v~i~G~~G~GKT~l   35 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            67899999999999954

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.

>PRK04296 thymidine kinase; Provisional

Probab=97.69  E-value=0.00011  Score=59.15  Aligned_cols=37  Identities=11%  Similarity=0.231  Sum_probs=24.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      |.-.++.||+|+|||...+-.+......   +.+++++-|
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~~---g~~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEER---GMKVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHHc---CCeEEEEec
Confidence            3457889999999997655444333222   457777766

>PRK08181 transposase; Validated

Probab=97.64  E-value=0.00086  Score=56.83  Aligned_cols=58  Identities=21%  Similarity=0.262  Sum_probs=32.7

Q ss_pred             hHHHHHHHH----HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           57 SAIQQRAVM----PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        57 ~~~Q~~~~~----~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      .+.|..++.    .+..++++++.||+|+|||....- +...+..  .+..++|+ +..+|+.++.
T Consensus        89 ~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~A-ia~~a~~--~g~~v~f~-~~~~L~~~l~  150 (269)
T PRK08181         89 SKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAA-IGLALIE--NGWRVLFT-RTTDLVQKLQ  150 (269)
T ss_pred             CHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHH-HHHHHHH--cCCceeee-eHHHHHHHHH
Confidence            445555442    234678999999999999954332 2222222  13345544 4455555554

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=97.63  E-value=7.1e-05  Score=67.54  Aligned_cols=104  Identities=18%  Similarity=0.118  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (298)
                      ++-++=+|||.||||--    +++++...+   ..+|-.|.+-||.++++++.+.    |+.+.+++|.........  .
T Consensus       191 RkIi~H~GPTNSGKTy~----ALqrl~~ak---sGvycGPLrLLA~EV~~r~na~----gipCdL~TGeE~~~~~~~--~  257 (700)
T KOG0953|consen  191 RKIIMHVGPTNSGKTYR----ALQRLKSAK---SGVYCGPLRLLAHEVYDRLNAL----GIPCDLLTGEERRFVLDN--G  257 (700)
T ss_pred             heEEEEeCCCCCchhHH----HHHHHhhhc---cceecchHHHHHHHHHHHhhhc----CCCccccccceeeecCCC--C
Confidence            35567789999999965    556665533   4589999999999999998876    577777776433221110  1


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHH
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKD  194 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~  194 (298)
                      +.+..+=||.|+..-        -..+++.||||+++|.+...+.
T Consensus       258 ~~a~hvScTVEM~sv--------~~~yeVAViDEIQmm~Dp~RGw  294 (700)
T KOG0953|consen  258 NPAQHVSCTVEMVSV--------NTPYEVAVIDEIQMMRDPSRGW  294 (700)
T ss_pred             CcccceEEEEEEeec--------CCceEEEEehhHHhhcCcccch
Confidence            234566677655431        2356789999999987665443

>PRK06526 transposase; Provisional

Probab=97.63  E-value=0.00019  Score=60.33  Aligned_cols=22  Identities=27%  Similarity=0.434  Sum_probs=17.8

Q ss_pred             hhcCCcEEEEcCCCCchHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      +..+++++++||+|+|||....
T Consensus        95 i~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHHH
Confidence            3456899999999999996544

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.60  E-value=0.00046  Score=66.31  Aligned_cols=138  Identities=16%  Similarity=0.167  Sum_probs=84.1

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHH
Q 022383           38 MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ  116 (298)
Q Consensus        38 l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q  116 (298)
                      ..+.+++...    -...++.-|++|+..++.-+ ..+|.|=+|+|||...... +..+...  +.++|+.+=|..-++.
T Consensus       656 ~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~L-IkiL~~~--gkkVLLtsyThsAVDN  728 (1100)
T KOG1805|consen  656 KVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLL-IKILVAL--GKKVLLTSYTHSAVDN  728 (1100)
T ss_pred             cccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHH-HHHHHHc--CCeEEEEehhhHHHHH
Confidence            3455555554    23468889999998877554 5788899999999654332 2222222  5578888888888888


Q ss_pred             HHHHHHHhhccCCceEEEEEcCCch-----------------HHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEE
Q 022383          117 TEKVILAIGDFINIQAHACVGGKSV-----------------GEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (298)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~v  179 (298)
                      +.-.++...    +.+.-+..+...                 -+......+.+.|+.||=--+    ....+..+.+++.
T Consensus       729 ILiKL~~~~----i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi----~~plf~~R~FD~c  800 (1100)
T KOG1805|consen  729 ILIKLKGFG----IYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGI----NHPLFVNRQFDYC  800 (1100)
T ss_pred             HHHHHhccC----cceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCC----CchhhhccccCEE
Confidence            887766542    222211111111                 122233445667777773211    2223445678999


Q ss_pred             EechhhHhhcc
Q 022383          180 VLDESDEMLSR  190 (298)
Q Consensus       180 ViDE~h~~~~~  190 (298)
                      |||||-++...
T Consensus       801 IiDEASQI~lP  811 (1100)
T KOG1805|consen  801 IIDEASQILLP  811 (1100)
T ss_pred             EEccccccccc
Confidence            99999887543

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.58  E-value=0.0002  Score=63.69  Aligned_cols=60  Identities=23%  Similarity=0.340  Sum_probs=43.3

Q ss_pred             CChHHHHHHHHHh------hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHH
Q 022383           55 KPSAIQQRAVMPI------IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (298)
Q Consensus        55 ~~~~~Q~~~~~~~------~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~  117 (298)
                      ++++-|+++++.+      ..+.++++.||-|+|||..+- .+.+.+..  .+..+++++||-.-|..+
T Consensus         1 ~Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~-~i~~~~~~--~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    1 KLNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIK-AIIDYLRS--RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHH-HHHHHhcc--ccceEEEecchHHHHHhc
Confidence            3678899998888      578899999999999996532 23333333  345788888987655555

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.54  E-value=0.00035  Score=52.51  Aligned_cols=41  Identities=15%  Similarity=0.281  Sum_probs=25.2

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      ++.+++.||+|+|||...... ...+....  ..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l-~~~~~~~~--~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARAL-ARELGPPG--GGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHH-HhccCCCC--CCEEEECCEEcc
Confidence            567999999999999654322 22222211  246777766543

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.

>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=97.54  E-value=0.00099  Score=53.81  Aligned_cols=128  Identities=18%  Similarity=0.235  Sum_probs=66.4

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--cHHHH-HHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELA-TQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~-~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      -++++||||+|||.+..-.+......   +.++.+++-  .|.=+ +|+.    .+++..++++.......+..+.    
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~ga~eQL~----~~a~~l~vp~~~~~~~~~~~~~----   71 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRIGAVEQLK----TYAEILGVPFYVARTESDPAEI----   71 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSSTHHHHHHH----HHHHHHTEEEEESSTTSCHHHH----
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCccHHHHHH----HHHHHhccccchhhcchhhHHH----
Confidence            36899999999997765544443333   334555553  33333 3333    3333345554432222211111    


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc-cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHH
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~-~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~  225 (298)
                                   +...++.  ...++.++|+||-+-+... ......+..+.+...+..-.+.+|||..........
T Consensus        72 -------------~~~~l~~--~~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~  134 (196)
T PF00448_consen   72 -------------AREALEK--FRKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQAL  134 (196)
T ss_dssp             -------------HHHHHHH--HHHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHH
T ss_pred             -------------HHHHHHH--HhhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHH
Confidence                         1111111  1224567888887754322 234566667777776666678899999765444333

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 ....

>PRK14974 cell division protein FtsY; Provisional

Probab=97.52  E-value=0.0015  Score=57.08  Aligned_cols=130  Identities=19%  Similarity=0.268  Sum_probs=72.7

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc---HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT---RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~---~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      -++++|++|+|||......+ ..+..  .+.+++++...   .+-..|+.....    ..++.+.....+.+....    
T Consensus       142 vi~~~G~~GvGKTTtiakLA-~~l~~--~g~~V~li~~Dt~R~~a~eqL~~~a~----~lgv~v~~~~~g~dp~~v----  210 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLA-YYLKK--NGFSVVIAAGDTFRAGAIEQLEEHAE----RLGVKVIKHKYGADPAAV----  210 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHH-HHHHH--cCCeEEEecCCcCcHHHHHHHHHHHH----HcCCceecccCCCCHHHH----
Confidence            47889999999997654333 22322  23456666543   333445444333    335544321111111110    


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhc
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKF  227 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~  227 (298)
                                   +...+..  ......++|+||.+..+... .+...+..+.+...+...++.++|+...........+
T Consensus       211 -------------~~~ai~~--~~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~f  275 (336)
T PRK14974        211 -------------AYDAIEH--AKARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAREF  275 (336)
T ss_pred             -------------HHHHHHH--HHhCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHHH
Confidence                         1111111  11235689999999887533 4567777777777777778889998876655555544

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.51  E-value=0.0024  Score=63.73  Aligned_cols=137  Identities=18%  Similarity=0.160  Sum_probs=81.1

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhc-CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      +++.........++ .+++-|.+++..+.. ++-++++|+.|+|||.+. -.+...+..  .+.+++.++||-.-+..+.
T Consensus       367 v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~--~G~~V~g~ApTgkAA~~L~  442 (1102)
T PRK13826        367 VREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEA--AGYRVVGGALAGKAAEGLE  442 (1102)
T ss_pred             CCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHH--cCCeEEEEcCcHHHHHHHH
Confidence            34444444333333 499999999998864 567899999999999653 334443333  2558899999977665554


Q ss_pred             HHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHH
Q 022383          119 KVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (298)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~  198 (298)
                      +       ..|+...                        |-.++..-...+...+..-++|||||+.++..    ..+..
T Consensus       443 e-------~~Gi~a~------------------------TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~~----~~m~~  487 (1102)
T PRK13826        443 K-------EAGIQSR------------------------TLSSWELRWNQGRDQLDNKTVFVLDEAGMVAS----RQMAL  487 (1102)
T ss_pred             H-------hhCCCee------------------------eHHHHHhhhccCccCCCCCcEEEEECcccCCH----HHHHH
Confidence            3       1232221                        11111111111223455678999999987633    33344


Q ss_pred             HHHhCC-CCccEEEEEee
Q 022383          199 VYRYLP-PDLQVVLISAT  215 (298)
Q Consensus       199 i~~~~~-~~~~~v~~SAT  215 (298)
                      +++... ...++|++.-+
T Consensus       488 Ll~~~~~~garvVLVGD~  505 (1102)
T PRK13826        488 FVEAVTRAGAKLVLVGDP  505 (1102)
T ss_pred             HHHHHHhcCCEEEEECCH
Confidence            555553 46777777655

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

Probab=97.51  E-value=0.00099  Score=63.48  Aligned_cols=71  Identities=17%  Similarity=0.185  Sum_probs=49.4

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhh---c-----------c--------C----------
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTV---D-----------T--------S----------   98 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~---~-----------~--------~----------   98 (298)
                      +|++.|...+..++    .+.+.++..|||+|||++.+-..+...   .           .        .          
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~  100 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEA  100 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhh
Confidence            48999998877665    457899999999999987665544422   1           0        0          


Q ss_pred             --C-----CCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           99 --S-----REVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        99 --~-----~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                        +     .-|++.|-+-|..-..|+.+.+++..
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~  134 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTG  134 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcC
Confidence              0     12566666677777788888777653

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.51  E-value=0.0011  Score=58.73  Aligned_cols=131  Identities=17%  Similarity=0.192  Sum_probs=61.6

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (298)
                      |..++++||||+|||......+........ ..++.++....-. .--.++++.++...++.+....             
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G-~~~V~lit~D~~R-~ga~EqL~~~a~~~gv~~~~~~-------------  201 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFG-ASKVALLTTDSYR-IGGHEQLRIFGKILGVPVHAVK-------------  201 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEeccccc-ccHHHHHHHHHHHcCCceEecC-------------
Confidence            578999999999999776544433222211 1244444422111 1112333344434444433322             


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc-cHHHHHHHHHhCCCCccEEEEEeeCchhH-HHHHHhc
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPPDLQVVLISATLPHEI-LEMTTKF  227 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~~~~~~~~v~~SAT~~~~~-~~~~~~~  227 (298)
                              ++..+...+..    +.+.++|+||.+-....+. ....+..+.....+...++.+|||..... ......|
T Consensus       202 --------~~~~l~~~l~~----l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~evi~~f  269 (374)
T PRK14722        202 --------DGGDLQLALAE----LRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNEVVQAY  269 (374)
T ss_pred             --------CcccHHHHHHH----hcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHHHHHHHH
Confidence                    23333332221    3455888899885432111 22223222222222344778899985543 3333433

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.38  E-value=0.0078  Score=53.26  Aligned_cols=131  Identities=17%  Similarity=0.263  Sum_probs=66.1

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc-H-HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT-R-ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~-~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (298)
                      ++.+.++||||.|||...+-.+-..........-+||-.-| | .-+.|+.    .+++..++++..+.           
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk----~Ya~im~vp~~vv~-----------  267 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLK----TYADIMGVPLEVVY-----------  267 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHH----HHHHHhCCceEEec-----------
Confidence            78899999999999976544333322122223345555542 2 2233333    33434455544444           


Q ss_pred             hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh-hccccHHHHHHHHHhCCCCccEEEEEeeCc-hhHHHHHH
Q 022383          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-LSRGFKDQIYDVYRYLPPDLQVVLISATLP-HEILEMTT  225 (298)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~-~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~-~~~~~~~~  225 (298)
                                +|.-|...+..    +.+.++|.||=+-+- .+......+..+++.-.+---.+.+|||-. ..+.+...
T Consensus       268 ----------~~~el~~ai~~----l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~  333 (407)
T COG1419         268 ----------SPKELAEAIEA----LRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIK  333 (407)
T ss_pred             ----------CHHHHHHHHHH----hhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHH
Confidence                      34444433332    334466666644321 111234445555554433344677788874 44555555


Q ss_pred             hcCC
Q 022383          226 KFMT  229 (298)
Q Consensus       226 ~~~~  229 (298)
                      .|..
T Consensus       334 ~f~~  337 (407)
T COG1419         334 QFSL  337 (407)
T ss_pred             Hhcc
Confidence            5543

>TIGR01075 uvrD DNA helicase II

Probab=97.32  E-value=0.0014  Score=63.79  Aligned_cols=70  Identities=17%  Similarity=0.207  Sum_probs=54.3

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      ..+++-|.+++.+  ...+++|.|..|||||.+..--+...+.... ...++++++.|+..|.++.+++.++.
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~   73 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALL   73 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHh
Confidence            4689999999865  3568999999999999875554544443322 33489999999999999999998864

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK06921 hypothetical protein; Provisional

Probab=97.32  E-value=0.0038  Score=52.96  Aligned_cols=46  Identities=17%  Similarity=0.252  Sum_probs=27.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~  117 (298)
                      .+.++++.||+|+|||.... .+...+... .+..++|+. ..++..++
T Consensus       116 ~~~~l~l~G~~G~GKThLa~-aia~~l~~~-~g~~v~y~~-~~~l~~~l  161 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLT-AAANELMRK-KGVPVLYFP-FVEGFGDL  161 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHH-HHHHHHhhh-cCceEEEEE-HHHHHHHH
Confidence            35789999999999995432 333443332 134566655 34444443

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.32  E-value=0.0045  Score=54.91  Aligned_cols=129  Identities=14%  Similarity=0.244  Sum_probs=66.4

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--cH-HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TR-ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK  147 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (298)
                      +.+.++||||+|||......+... ..  .+.++.++..  .+ +.+.|+..    ++...++.+..             
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L-~~--~GkkVglI~aDt~RiaAvEQLk~----yae~lgipv~v-------------  301 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQF-HG--KKKTVGFITTDHSRIGTVQQLQD----YVKTIGFEVIA-------------  301 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH-HH--cCCcEEEEecCCcchHHHHHHHH----HhhhcCCcEEe-------------
Confidence            568999999999997655443332 22  2334555553  33 23333333    32222332221             


Q ss_pred             hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCCCCccEEEEEeeCc-hhHHHHHH
Q 022383          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLP-HEILEMTT  225 (298)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~~~~~~v~~SAT~~-~~~~~~~~  225 (298)
                              +.+|..+...+..-. ...+.++|+||-+=+.... .....+..+++...+..-++.+|||.. +.+.....
T Consensus       302 --------~~d~~~L~~aL~~lk-~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~  372 (436)
T PRK11889        302 --------VRDEAAMTRALTYFK-EEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIIT  372 (436)
T ss_pred             --------cCCHHHHHHHHHHHH-hccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHH
Confidence                    235555555443211 0125789999977543322 223444455554444444666888764 45566665


Q ss_pred             hcC
Q 022383          226 KFM  228 (298)
Q Consensus       226 ~~~  228 (298)
                      .+-
T Consensus       373 ~F~  375 (436)
T PRK11889        373 NFK  375 (436)
T ss_pred             Hhc
Confidence            543

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=97.30  E-value=0.00067  Score=65.37  Aligned_cols=155  Identities=14%  Similarity=0.135  Sum_probs=91.5

Q ss_pred             CCChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHhhccC
Q 022383           54 EKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGDFI  128 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~~~  128 (298)
                      ..+.+||...+....    ++-+-++.-.+|-|||..-.-.+...+.... .|| -+|++|+-.|.+=.. .|..++.  
T Consensus       393 G~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP-~LvivPlstL~NW~~-Ef~kWaP--  468 (1157)
T KOG0386|consen  393 GELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGP-FLIIVPLSTLVNWSS-EFPKWAP--  468 (1157)
T ss_pred             CCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCC-eEEeccccccCCchh-hcccccc--
Confidence            368999998887654    3457888899999999654433333332222 344 588899988765433 3444432  


Q ss_pred             CceEEEEEcCCchHHHH--HHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCC
Q 022383          129 NIQAHACVGGKSVGEDI--RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (298)
Q Consensus       129 ~~~~~~~~~~~~~~~~~--~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~  206 (298)
                      .+..+.+.|........  +......+|+++|-+.+..  ....+.--+..++||||.|+|-.  ....+...+.-....
T Consensus       469 Sv~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik--dk~lLsKI~W~yMIIDEGHRmKN--a~~KLt~~L~t~y~~  544 (1157)
T KOG0386|consen  469 SVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK--DKALLSKISWKYMIIDEGHRMKN--AICKLTDTLNTHYRA  544 (1157)
T ss_pred             ceeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC--CHHHHhccCCcceeecccccccc--hhhHHHHHhhccccc
Confidence            34444444432222211  2223678999999877764  11122223557899999999832  234444444433334


Q ss_pred             ccEEEEEeeC
Q 022383          207 LQVVLISATL  216 (298)
Q Consensus       207 ~~~v~~SAT~  216 (298)
                      ...+++|.|+
T Consensus       545 q~RLLLTGTP  554 (1157)
T KOG0386|consen  545 QRRLLLTGTP  554 (1157)
T ss_pred             hhhhhhcCCh
Confidence            5567778886

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=97.30  E-value=0.00072  Score=62.45  Aligned_cols=148  Identities=15%  Similarity=0.106  Sum_probs=84.1

Q ss_pred             HHHHHHHHHhh-----cC----CcEEEEcCCCCchHHHHHHHHHHh-hccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           58 AIQQRAVMPII-----KG----RDVIAQAQSGTGKTSMIALTVCQT-VDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        58 ~~Q~~~~~~~~-----~~----~~~li~~pTG~GKT~~~~~~~~~~-~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      |||..++-.+.     .|    +.+++..|=|.|||......++.. +.....+..+++.+++++-+..+++.++++...
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~~   80 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIEA   80 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            67887777665     22    468999999999996654443333 344445678999999999999999999887543


Q ss_pred             CCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHh--ccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCC
Q 022383          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIK--RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (298)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~--~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~  205 (298)
                      ..... ....     ...... ..-.|.....+.....+.  ....+-.+.+++|+||+|.+.+......+..-....+ 
T Consensus        81 ~~~l~-~~~~-----~~~~~~-~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~~~~~~l~~g~~~r~-  152 (477)
T PF03354_consen   81 SPELR-KRKK-----PKIIKS-NKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKDDELYDALESGMGARP-  152 (477)
T ss_pred             Chhhc-cchh-----hhhhhh-hceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCCHHHHHHHHhhhccCC-
Confidence            21100 0000     000000 011222221122221111  1233445779999999999865445555555555533 


Q ss_pred             CccEEEEE
Q 022383          206 DLQVVLIS  213 (298)
Q Consensus       206 ~~~~v~~S  213 (298)
                      +++++.+|
T Consensus       153 ~pl~~~IS  160 (477)
T PF03354_consen  153 NPLIIIIS  160 (477)
T ss_pred             CceEEEEe
Confidence            45555543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=97.28  E-value=0.003  Score=62.77  Aligned_cols=164  Identities=18%  Similarity=0.120  Sum_probs=99.9

Q ss_pred             CCChHHHHHHHHHhh-----cCCcEEEEcCCCCchHHHHHHHHHHhhccCCC-CeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           54 EKPSAIQQRAVMPII-----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR-EVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~-----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~-~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      ..+.++|.+.++.+.     .+.+.++.-..|.|||+..+..+......... .+.++++||+ +++.++.+.+.++...
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~-s~~~nw~~e~~k~~~~  415 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPA-SLLSNWKREFEKFAPD  415 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecH-HHHHHHHHHHhhhCcc
Confidence            567888999886644     25778888999999997655444432222222 3468899996 4567777777777554


Q ss_pred             CCceEEEEEcCCch----HHHHHHhhcC-----CcEEEeChHHHHHHH-hccCccCCCccEEEechhhHhhccccHHHHH
Q 022383          128 INIQAHACVGGKSV----GEDIRKLEHG-----VHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (298)
Q Consensus       128 ~~~~~~~~~~~~~~----~~~~~~~~~~-----~~ilV~Tp~~l~~~~-~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~  197 (298)
                      ... +...+|....    .+....+...     .+++++|-+.+.... ....+.-...+.+|+||+|.+-... .....
T Consensus       416 ~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~~-s~~~~  493 (866)
T COG0553         416 LRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQ-SSEGK  493 (866)
T ss_pred             ccc-eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhhh-hHHHH
Confidence            332 5566665541    2333333322     689999998888742 1123444577899999999964432 22222


Q ss_pred             HHHHhCCCCccEEEEEeeC-chhHHH
Q 022383          198 DVYRYLPPDLQVVLISATL-PHEILE  222 (298)
Q Consensus       198 ~i~~~~~~~~~~v~~SAT~-~~~~~~  222 (298)
                      .+. .+.... .+.+|.|+ .+.+.+
T Consensus       494 ~l~-~~~~~~-~~~LtgTPlen~l~e  517 (866)
T COG0553         494 ALQ-FLKALN-RLDLTGTPLENRLGE  517 (866)
T ss_pred             HHH-HHhhcc-eeeCCCChHhhhHHH
Confidence            333 333222 37778887 444333

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.27  E-value=0.0015  Score=62.69  Aligned_cols=81  Identities=22%  Similarity=0.215  Sum_probs=56.3

Q ss_pred             CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           53 FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      -..+++-|++++..  ...+++|.|..|||||.+..--+...+... ..+.++++++.++..+..+.+++.......++.
T Consensus       194 ~~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg~~~v~  271 (684)
T PRK11054        194 SSPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLGTEDIT  271 (684)
T ss_pred             CCCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcCCCCcE
Confidence            35699999999853  346789999999999977544433333222 224489999999999999999887654322344


Q ss_pred             EEEE
Q 022383          132 AHAC  135 (298)
Q Consensus       132 ~~~~  135 (298)
                      +.++
T Consensus       272 v~TF  275 (684)
T PRK11054        272 ARTF  275 (684)
T ss_pred             EEeH
Confidence            4443

>PRK05642 DNA replication initiation factor; Validated

Probab=97.27  E-value=0.002  Score=53.61  Aligned_cols=44  Identities=16%  Similarity=0.399  Sum_probs=27.7

Q ss_pred             CccEEEechhhHhhcc-ccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      ..+++|+|++|.+... .....+-.+++.+..+...++++++.++
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            5578999999987432 3345566666665543345666676544

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=97.25  E-value=0.0021  Score=59.97  Aligned_cols=158  Identities=18%  Similarity=0.200  Sum_probs=97.6

Q ss_pred             ChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCCC--CeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           56 PSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        56 ~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      +..+|-..++.+.    +|-|-|+.-..|-|||.-. +..+.++.....  || -|+++|...| ..+...+.++..  +
T Consensus       568 LKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQs-isvlAhLaE~~nIwGP-FLVVtpaStL-~NWaqEisrFlP--~  642 (1185)
T KOG0388|consen  568 LKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQS-ISVLAHLAETHNIWGP-FLVVTPASTL-HNWAQEISRFLP--S  642 (1185)
T ss_pred             hHHHhhccHHHHHHHHHccccceehhhhccchhHHH-HHHHHHHHHhccCCCc-eEEeehHHHH-hHHHHHHHHhCc--c
Confidence            4567777666544    6789999999999999654 344444433221  33 5777786554 455566666643  5


Q ss_pred             ceEEEEEcCCchHHHHHH---------hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHH
Q 022383          130 IQAHACVGGKSVGEDIRK---------LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY  200 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~---------~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~  200 (298)
                      +++..+-|+.+......+         -..+.+|+|++-+.+..--  +.+.--+..++|+|||..+-+. ....+..++
T Consensus       643 ~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDe--ky~qkvKWQYMILDEAQAIKSS-sS~RWKtLL  719 (1185)
T KOG0388|consen  643 FKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDE--KYLQKVKWQYMILDEAQAIKSS-SSSRWKTLL  719 (1185)
T ss_pred             ceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechH--HHHHhhhhhheehhHHHHhhhh-hhhHHHHHh
Confidence            778888887776555444         2346789998876554211  1111124578999999987443 355566665


Q ss_pred             HhCCCCccEEEEEeeC-chhHHHH
Q 022383          201 RYLPPDLQVVLISATL-PHEILEM  223 (298)
Q Consensus       201 ~~~~~~~~~v~~SAT~-~~~~~~~  223 (298)
                      ..-  .+-.+++|.|+ .+.++++
T Consensus       720 sF~--cRNRLLLTGTPIQNsMqEL  741 (1185)
T KOG0388|consen  720 SFK--CRNRLLLTGTPIQNSMQEL  741 (1185)
T ss_pred             hhh--ccceeeecCCccchHHHHH
Confidence            543  33368888887 4555543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.23  E-value=0.0066  Score=55.04  Aligned_cols=128  Identities=14%  Similarity=0.222  Sum_probs=65.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhh-ccCCCCeEEEEEcC--cHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTV-DTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~-~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (298)
                      ++.++++||||+|||......+.... ..  .+.++.++.-  .+.-+.   +.++.++...++.+..            
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~--~g~~V~li~~D~~r~~a~---eqL~~~a~~~~vp~~~------------  283 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLY--GKKKVALITLDTYRIGAV---EQLKTYAKIMGIPVEV------------  283 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhc--CCCeEEEEECCccHHHHH---HHHHHHHHHhCCceEc------------
Confidence            46789999999999976554333322 12  1335555552  232221   2333333333333221            


Q ss_pred             HhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhC-CCCccEEEEEeeCch-hHHHH
Q 022383          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYL-PPDLQVVLISATLPH-EILEM  223 (298)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~-~~~~~~v~~SAT~~~-~~~~~  223 (298)
                               +.++..+...+..    +.+.++|+||.+-..... .....+..+++.. .+....+++|||... .+...
T Consensus       284 ---------~~~~~~l~~~l~~----~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~  350 (424)
T PRK05703        284 ---------VYDPKELAKALEQ----LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDI  350 (424)
T ss_pred             ---------cCCHHhHHHHHHH----hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHH
Confidence                     2334444444442    235789999987443221 2234455555522 233447788998864 44444


Q ss_pred             HHhc
Q 022383          224 TTKF  227 (298)
Q Consensus       224 ~~~~  227 (298)
                      ...+
T Consensus       351 ~~~f  354 (424)
T PRK05703        351 YKHF  354 (424)
T ss_pred             HHHh
Confidence            4444

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.23  E-value=0.003  Score=57.99  Aligned_cols=47  Identities=9%  Similarity=0.204  Sum_probs=27.1

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      ..+++.||+|+|||... .++.+.+.....+.+++++ +...+..+...
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~~~~~~~v~yi-~~~~~~~~~~~  195 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILEKNPNAKVVYV-TSEKFTNDFVN  195 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhCCCCeEEEE-EHHHHHHHHHH
Confidence            46899999999999543 2333444332223456666 43444544433

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.22  E-value=0.0077  Score=46.53  Aligned_cols=38  Identities=16%  Similarity=0.300  Sum_probs=23.2

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      +++.||+|+|||......+.... .  .+..++++......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~-~--~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIA-T--KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHH-h--cCCEEEEEECCcch
Confidence            68899999999965433322222 2  24467777665443

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>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=97.22  E-value=0.0018  Score=53.35  Aligned_cols=106  Identities=19%  Similarity=0.324  Sum_probs=58.2

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcC
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (298)
                      .+++.||+|+|||- .+.++.+.+.....+.+++|+... +........++.                            
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~~~~~~~v~y~~~~-~f~~~~~~~~~~----------------------------   85 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQKQHPGKRVVYLSAE-EFIREFADALRD----------------------------   85 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHHCTTS-EEEEEHH-HHHHHHHHHHHT----------------------------
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHhccccccceeecHH-HHHHHHHHHHHc----------------------------
Confidence            58999999999996 344455544433334466666532 333333332221                            


Q ss_pred             CcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCC-CCccEEEEEeeCchh
Q 022383          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPHE  219 (298)
Q Consensus       152 ~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~  219 (298)
                           ...+.+...       +...++++||++|.+... ..+..+..++..+. .+.++|+.|...|..
T Consensus        86 -----~~~~~~~~~-------~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~  143 (219)
T PF00308_consen   86 -----GEIEEFKDR-------LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSE  143 (219)
T ss_dssp             -----TSHHHHHHH-------HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTT
T ss_pred             -----ccchhhhhh-------hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCcc
Confidence                 011112111       346799999999998544 23455555555543 356666666566554

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.

>PHA02533 17 large terminase protein; Provisional

Probab=97.20  E-value=0.0036  Score=58.28  Aligned_cols=148  Identities=15%  Similarity=0.177  Sum_probs=85.8

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC--ceE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQA  132 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~--~~~  132 (298)
                      .+.|+|..++..+..++-.++..+=..|||.+....++...... .+..+++++|+..-+..+++.++.+.....  .+.
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~-~~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l~~~  137 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN-KDKNVGILAHKASMAAEVLDRTKQAIELLPDFLQP  137 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC-CCCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHhhc
Confidence            48899999998876677778999999999987764443332222 245899999999999999988876543221  011


Q ss_pred             EEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCC--CccEE
Q 022383          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP--DLQVV  210 (298)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~--~~~~v  210 (298)
                      .. ...   ....-.+.++..|.+.|.+       .....-.+.+++++||+|.+.+  +...+..+...+..  ..+++
T Consensus       138 ~i-~~~---~~~~I~l~NGS~I~~lss~-------~~t~rG~~~~~liiDE~a~~~~--~~e~~~ai~p~lasg~~~r~i  204 (534)
T PHA02533        138 GI-VEW---NKGSIELENGSKIGAYASS-------PDAVRGNSFAMIYIDECAFIPN--FIDFWLAIQPVISSGRSSKII  204 (534)
T ss_pred             ce-eec---CccEEEeCCCCEEEEEeCC-------CCccCCCCCceEEEeccccCCC--HHHHHHHHHHHHHcCCCceEE
Confidence            00 000   0000112355566555432       1112234668999999997633  23333333333322  23455


Q ss_pred             EEEeeC
Q 022383          211 LISATL  216 (298)
Q Consensus       211 ~~SAT~  216 (298)
                      ++|.+.
T Consensus       205 iiSTp~  210 (534)
T PHA02533        205 ITSTPN  210 (534)
T ss_pred             EEECCC
Confidence            555553

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.20  E-value=0.0018  Score=63.03  Aligned_cols=71  Identities=15%  Similarity=0.186  Sum_probs=54.2

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-CCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      ..+++-|.+++.+.  ..+++|.|+.|||||.+..--+...+... -...++++|+-|+..|.++.+++.++..
T Consensus         8 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          8 DSLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             HhcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            45899999998643  46899999999999977555444444322 2234899999999999999999988643

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.19  E-value=0.041  Score=59.08  Aligned_cols=209  Identities=12%  Similarity=0.110  Sum_probs=110.2

Q ss_pred             CChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceE
Q 022383           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  132 (298)
                      .+++-|.+++..++..  +-.++.|+.|+|||.+. -.+...+..  .+.+++.++||..-+..+.+...       ...
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~--~G~~V~~lAPTgrAA~~L~e~~g-------~~A  498 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASE--QGYEIQIITAGSLSAQELRQKIP-------RLA  498 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHh--cCCeEEEEeCCHHHHHHHHHHhc-------chh
Confidence            4889999999998764  57899999999999653 233333333  25689999999877666655321       110


Q ss_pred             EEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhC-CCCccEEE
Q 022383          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVL  211 (298)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~-~~~~~~v~  211 (298)
                      ..      .......+..  ..-..|...+.    .....+..-++|||||+-++.    ...+..+++.. +.+.++|+
T Consensus       499 ~T------i~~~l~~l~~--~~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl~----~~~~~~Ll~~a~~~garvVl  562 (1960)
T TIGR02760       499 ST------FITWVKNLFN--DDQDHTVQGLL----DKSSPFSNKDIFVVDEANKLS----NNELLKLIDKAEQHNSKLIL  562 (1960)
T ss_pred             hh------HHHHHHhhcc--cccchhHHHhh----cccCCCCCCCEEEEECCCCCC----HHHHHHHHHHHhhcCCEEEE
Confidence            00      0011111111  01112222222    122334577899999998763    34455666554 35788888


Q ss_pred             EEeeC--ch----hHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHH-HHHHHhhC-CCCcEEEEecchh
Q 022383          212 ISATL--PH----EILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT-LCDLYDTL-TITQAVIFCNTKR  283 (298)
Q Consensus       212 ~SAT~--~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~-l~~ll~~~-~~~k~lIf~~s~~  283 (298)
                      +.-+-  +.    .....+... +-+...... .......+  .+...+ ...++.. ...++... ...+++|+..+..
T Consensus       563 vGD~~QL~sV~aG~~f~~L~~~-gv~t~~l~~-i~rq~~~v--~i~~~~-~~~r~~~ia~~y~~L~~~r~~tliv~~t~~  637 (1960)
T TIGR02760       563 LNDSAQRQGMSAGSAIDLLKEG-GVTTYAWVD-TKQQKASV--EISEAV-DKLRVDYIASAWLDLTPDRQNSQVLATTHR  637 (1960)
T ss_pred             EcChhhcCccccchHHHHHHHC-CCcEEEeec-ccccCcce--eeeccC-chHHHHHHHHHHHhcccccCceEEEcCCcH
Confidence            87652  11    222233332 112211111 00111111  112111 2223333 33344433 3347999999999


Q ss_pred             hHHHHHHHHhh
Q 022383          284 KIYYSVFYFWI  294 (298)
Q Consensus       284 ~~~~l~~~L~~  294 (298)
                      +.+.+....+.
T Consensus       638 dr~~Ln~~iR~  648 (1960)
T TIGR02760       638 EQQDLTQIIRN  648 (1960)
T ss_pred             HHHHHHHHHHH
Confidence            98888877654

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK08727 hypothetical protein; Validated

Probab=97.18  E-value=0.0028  Score=52.74  Aligned_cols=35  Identities=20%  Similarity=0.356  Sum_probs=21.3

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      ..+++.||+|+|||.... .+...+...  +.+++|+.
T Consensus        42 ~~l~l~G~~G~GKThL~~-a~~~~~~~~--~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLAL-ALCAAAEQA--GRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHc--CCcEEEEe
Confidence            459999999999994332 222332222  34666654

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=97.16  E-value=0.0037  Score=64.23  Aligned_cols=123  Identities=15%  Similarity=0.174  Sum_probs=79.7

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      .|+-|.+++.  ..+++++|.|..|||||.+..--++..+..+....++++++=|++-+.++.+++++..... +.    
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~~~-~~----   74 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQKA-LQ----   74 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHHHH-Hh----
Confidence            5788999997  4688999999999999988766666665543223479999999999999999887643221 00    


Q ss_pred             EcCCchHHHHHHhhcCCcEEEeChHHHHH-HHhccCccC-CCccEEEechhhH
Q 022383          136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRT-RAIKLLVLDESDE  186 (298)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~-~~~~~~~~~-~~l~~vViDE~h~  186 (298)
                       ...........+..-...-|+|-..+.. +++.....+ -...+=|.||...
T Consensus        75 -~~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        75 -QEPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             -cCchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence             0001111222333334678999888875 444432211 1335566887765

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.15  E-value=0.0068  Score=50.63  Aligned_cols=44  Identities=14%  Similarity=0.112  Sum_probs=25.7

Q ss_pred             CCCccEEEechhhHhhccccH-HHHHHHHHhCCC-CccEEEEEeeCc
Q 022383          173 TRAIKLLVLDESDEMLSRGFK-DQIYDVYRYLPP-DLQVVLISATLP  217 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~-~~i~~i~~~~~~-~~~~v~~SAT~~  217 (298)
                      +...+++||||++......+. ..+..++..... ..++++ |.-++
T Consensus       160 l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tii-tSNl~  205 (244)
T PRK07952        160 LSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGM-LTNSN  205 (244)
T ss_pred             hccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEE-eCCCC
Confidence            347789999999886533333 244456655433 444555 44443

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.15  E-value=0.0011  Score=63.78  Aligned_cols=69  Identities=17%  Similarity=0.162  Sum_probs=53.5

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      .+++-|.+++.+  .+.+++|.|+.|||||.+..--+...+.... ...++++++.|+..|.++.+++.+..
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            378999999865  3567899999999999876655555554322 23479999999999999999998764

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=97.07  E-value=0.0015  Score=62.34  Aligned_cols=146  Identities=22%  Similarity=0.246  Sum_probs=88.9

Q ss_pred             HHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCC--eEEEEEcCcHHHHHHHHHHHHH-hhccCCceEEE-
Q 022383           59 IQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSRE--VQALILSPTRELATQTEKVILA-IGDFINIQAHA-  134 (298)
Q Consensus        59 ~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~--~~~lil~p~~~l~~q~~~~~~~-~~~~~~~~~~~-  134 (298)
                      +-..++..+.+.+-+++-+.||+|||.-+.--+++.+..+..+  ..+.+--|++..+..+++++-+ .....+-.+++ 
T Consensus       382 ~~~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~  461 (1282)
T KOG0921|consen  382 YRSEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYN  461 (1282)
T ss_pred             HHHHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhccccccc
Confidence            3345566677788899999999999988888888887665443  2455555899888888876632 22111111111 


Q ss_pred             --EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHh---CCCCccE
Q 022383          135 --CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY---LPPDLQV  209 (298)
Q Consensus       135 --~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~---~~~~~~~  209 (298)
                        +.+..+..        .-.|+.||.+-+++++....   ..+..+++||+|..--.  .+.+..+++-   ..+...+
T Consensus       462 vRf~Sa~prp--------yg~i~fctvgvllr~~e~gl---rg~sh~i~deiherdv~--~dfll~~lr~m~~ty~dl~v  528 (1282)
T KOG0921|consen  462 VRFDSATPRP--------YGSIMFCTVGVLLRMMENGL---RGISHVIIDEIHERDVD--TDFVLIVLREMISTYRDLRV  528 (1282)
T ss_pred             cccccccccc--------ccceeeeccchhhhhhhhcc---cccccccchhhhhhccc--hHHHHHHHHhhhccchhhhh
Confidence              01111111        11588999999999988764   35678999999985222  2222222222   2234555


Q ss_pred             EEEEeeCc
Q 022383          210 VLISATLP  217 (298)
Q Consensus       210 v~~SAT~~  217 (298)
                      +++|||+.
T Consensus       529 ~lmsatId  536 (1282)
T KOG0921|consen  529 VLMSATID  536 (1282)
T ss_pred             hhhhcccc
Confidence            66666654

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.07  E-value=0.0054  Score=55.52  Aligned_cols=37  Identities=14%  Similarity=0.267  Sum_probs=23.5

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      ..+++.||+|+|||... ..+.+.+.....+..++++.
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhCCCCcEEEEE
Confidence            45899999999999543 33444443332244667764

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).

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.06  E-value=0.003  Score=53.78  Aligned_cols=117  Identities=14%  Similarity=0.266  Sum_probs=59.5

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhcc-C---CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDT-S---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~-~---~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (298)
                      .+++++|+||.|||...---.-.+-.. +   ..-|-+.+-+|...-....+..+-.   .++.....    ........
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~---~lgaP~~~----~~~~~~~~  134 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILE---ALGAPYRP----RDRVAKLE  134 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHH---HhCcccCC----CCCHHHHH
Confidence            589999999999997432111111100 0   1124555566776655555554422   12222111    00000000


Q ss_pred             HhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc--HHHHHHHHHhCCCC--ccEEEE
Q 022383          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPD--LQVVLI  212 (298)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~--~~~v~~  212 (298)
                                   .+..++++     --.++++||||+|.++....  +.....+++++.+.  ..+|++
T Consensus       135 -------------~~~~~llr-----~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~v  186 (302)
T PF05621_consen  135 -------------QQVLRLLR-----RLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGV  186 (302)
T ss_pred             -------------HHHHHHHH-----HcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEe
Confidence                         11223333     34678999999999876643  34455666666654  344443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.06  E-value=0.0064  Score=53.22  Aligned_cols=33  Identities=15%  Similarity=0.166  Sum_probs=26.5

Q ss_pred             ChHHHHHHHHHhhcC----CcEEEEcCCCCchHHHHH
Q 022383           56 PSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~----~~~li~~pTG~GKT~~~~   88 (298)
                      .+|||...|..+...    +-.++.||.|.|||..+.
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~   40 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAE   40 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHH
Confidence            579999999988743    258899999999996543

>PLN03025 replication factor C subunit; Provisional

Probab=97.06  E-value=0.011  Score=51.71  Aligned_cols=39  Identities=21%  Similarity=0.307  Sum_probs=25.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...+++|+||+|.+.... +..+...++..+....+++.+
T Consensus        98 ~~~kviiiDE~d~lt~~a-q~aL~~~lE~~~~~t~~il~~  136 (319)
T PLN03025         98 GRHKIVILDEADSMTSGA-QQALRRTMEIYSNTTRFALAC  136 (319)
T ss_pred             CCeEEEEEechhhcCHHH-HHHHHHHHhcccCCceEEEEe
Confidence            357899999999986543 455566666655555555543

>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=97.04  E-value=0.0054  Score=48.95  Aligned_cols=48  Identities=15%  Similarity=0.160  Sum_probs=32.1

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      +++.||+|+|||...+--+......   +..++|++. .+...++.+.++.+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~---g~~v~~~s~-e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLAR---GEPGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHC---CCcEEEEEC-CCCHHHHHHHHHHc
Confidence            6899999999996554444443322   456777754 45677777777665

A related protein is found in archaea.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.03  E-value=0.0071  Score=54.47  Aligned_cols=36  Identities=22%  Similarity=0.374  Sum_probs=22.1

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEE
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (298)
                      .++++.||+|+|||.... .++..+.....+..++++
T Consensus        56 ~~~lI~G~~GtGKT~l~~-~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVK-KVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHhcCCcEEEEE
Confidence            679999999999996533 333443332223345555

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.01  E-value=0.0052  Score=50.70  Aligned_cols=20  Identities=25%  Similarity=0.424  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCCchHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~   88 (298)
                      .+.++++.||+|+|||....
T Consensus        37 ~~~~lll~G~~G~GKT~la~   56 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQ   56 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            45789999999999996543

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.00  E-value=0.01  Score=51.84  Aligned_cols=46  Identities=15%  Similarity=0.233  Sum_probs=27.7

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      .++++++.||||+|||.... .+...+...  +..++++. ..++..++.
T Consensus       182 ~~~~Lll~G~~GtGKThLa~-aIa~~l~~~--g~~V~y~t-~~~l~~~l~  227 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSN-CIAKELLDR--GKSVIYRT-ADELIEILR  227 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHH-HHHHHHHHC--CCeEEEEE-HHHHHHHHH
Confidence            45899999999999996432 333333332  44565544 445544443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.00  E-value=0.0062  Score=55.55  Aligned_cols=19  Identities=26%  Similarity=0.366  Sum_probs=15.3

Q ss_pred             cEEEEcCCCCchHHHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIALT   90 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~   90 (298)
                      .++++||.|+|||.++.+.
T Consensus        42 a~Lf~GP~GtGKTTlAriL   60 (484)
T PRK14956         42 AYIFFGPRGVGKTTIARIL   60 (484)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3799999999999765533

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.99  E-value=0.0071  Score=55.36  Aligned_cols=108  Identities=13%  Similarity=0.255  Sum_probs=58.1

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (298)
                      ..+++.|++|+|||... ..+.+.+.....+.+++++.+ .++..++...+..-.                         
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l~~~~-------------------------  194 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVDILQKTH-------------------------  194 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHHhh-------------------------
Confidence            45899999999999432 344444443333456776655 556655555443210                         


Q ss_pred             CCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCC-CCccEEEEEeeCch
Q 022383          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPH  218 (298)
Q Consensus       151 ~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~-~~~~~v~~SAT~~~  218 (298)
                               +.+..+..    .+.+.+++|+||+|.+... .....+..++..+. ...|+|+.|-..|.
T Consensus       195 ---------~~~~~~~~----~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~  251 (450)
T PRK14087        195 ---------KEIEQFKN----EICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPE  251 (450)
T ss_pred             ---------hHHHHHHH----HhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHH
Confidence                     01111111    1346789999999987432 23344555555543 33455554444443

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.98  E-value=0.0091  Score=57.11  Aligned_cols=67  Identities=22%  Similarity=0.301  Sum_probs=51.3

Q ss_pred             CChHHHHHHHHHhhcC-----CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-----~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      .|+--|..++..+.++     +..++.|.||||||+...- ++..+     +..+|||+|++.+|.|+++.++.+...
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~-~~~~~-----~~p~Lvi~~n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN-VIAQV-----NRPTLVIAHNKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH-HHHHh-----CCCEEEEECCHHHHHHHHHHHHHhCCC
Confidence            3888899888887543     3667999999999977543 33322     225899999999999999999988643

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

>PRK12377 putative replication protein; Provisional

Probab=96.98  E-value=0.0049  Score=51.59  Aligned_cols=46  Identities=9%  Similarity=0.240  Sum_probs=27.6

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      ..++++.||+|+|||... .++.+.+...  +..+++ ++..++..++..
T Consensus       101 ~~~l~l~G~~GtGKThLa-~AIa~~l~~~--g~~v~~-i~~~~l~~~l~~  146 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLA-AAIGNRLLAK--GRSVIV-VTVPDVMSRLHE  146 (248)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHHc--CCCeEE-EEHHHHHHHHHH
Confidence            368999999999999432 2333444332  334444 455566666554

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=96.97  E-value=0.013  Score=56.65  Aligned_cols=147  Identities=14%  Similarity=0.116  Sum_probs=80.6

Q ss_pred             CCcEEEEcCCCCchHH---HHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC----CceEEEEEcCCc--
Q 022383           70 GRDVIAQAQSGTGKTS---MIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI----NIQAHACVGGKS--  140 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~---~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~--  140 (298)
                      |-..|+.-=.|-|||+   +|+..++.+...  .-.++|||||... +..+...|.++...+    .+.+.-+..-..  
T Consensus       696 GsGcILAHcMGLGKTlQVvtflhTvL~c~kl--g~ktaLvV~PlNt-~~NW~~EFekWm~~~e~~~~leV~eL~~vkr~e  772 (1567)
T KOG1015|consen  696 GSGCILAHCMGLGKTLQVVTFLHTVLLCDKL--GFKTALVVCPLNT-ALNWMNEFEKWMEGLEDDEKLEVSELATVKRPE  772 (1567)
T ss_pred             CcchHHHHhhcccceehhhHHHHHHHHhhcc--CCceEEEEcchHH-HHHHHHHHHHhcccccccccceeehhhhccChH
Confidence            4456776779999995   344444444332  2238999999765 566777888887642    234433332222  


Q ss_pred             -hHHHHHHhhcCCcEEEeChHHHHHHHhcc-------------CccCCCccEEEechhhHhhccccHHHHHHHHHhCCCC
Q 022383          141 -VGEDIRKLEHGVHVVSGTPGRVCDMIKRK-------------TLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD  206 (298)
Q Consensus       141 -~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~-------------~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~  206 (298)
                       .......+.+.-.|.|.-.+.+-.+....             .+--...++||.||+|.+-..  ...+...+..+. .
T Consensus       773 ~R~~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNe--ksa~Skam~~ir-t  849 (1567)
T KOG1015|consen  773 ERSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNE--KSAVSKAMNSIR-T  849 (1567)
T ss_pred             HHHHHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhccc--hHHHHHHHHHHH-h
Confidence             22233444433355555544443332221             111256799999999998544  233333333333 2


Q ss_pred             ccEEEEEeeC-chhHHH
Q 022383          207 LQVVLISATL-PHEILE  222 (298)
Q Consensus       207 ~~~v~~SAT~-~~~~~~  222 (298)
                      .+.|++|.|+ .+.+..
T Consensus       850 kRRI~LTGTPLQNNLmE  866 (1567)
T KOG1015|consen  850 KRRIILTGTPLQNNLME  866 (1567)
T ss_pred             heeEEeecCchhhhhHH
Confidence            3356677775 444333

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=96.97  E-value=0.0071  Score=55.36  Aligned_cols=148  Identities=16%  Similarity=0.159  Sum_probs=86.9

Q ss_pred             CCChHHHHHHHHHhhc------C----CcEEEEcCCCCchHHHHH-HHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH
Q 022383           54 EKPSAIQQRAVMPIIK------G----RDVIAQAQSGTGKTSMIA-LTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~------~----~~~li~~pTG~GKT~~~~-~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~  122 (298)
                      ..+-|||.-++-.+..      |    +..+|..|-+-|||.... +.....+.....+....|++|+.+-+.+.++.++
T Consensus        60 ~~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F~~ar  139 (546)
T COG4626          60 ESLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSFNPAR  139 (546)
T ss_pred             cccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhhHHHH
Confidence            3589999999988871      1    468999999999995433 3333333333456678899999999999988887


Q ss_pred             HhhccCCceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhc--cCccCCCccEEEechhhHhhccccHHHHHHH
Q 022383          123 AIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (298)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~--~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i  199 (298)
                      .+.....          +.. ....+. +...|...--......+..  +..+-.+..+.|+||.|.....+  ..+..+
T Consensus       140 ~mv~~~~----------~l~-~~~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~--~~~~~~  206 (546)
T COG4626         140 DMVKRDD----------DLR-DLCNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE--DMYSEA  206 (546)
T ss_pred             HHHHhCc----------chh-hhhccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHH--HHHHHH
Confidence            6643322          000 000010 1111222111112222222  34566788999999999976552  344444


Q ss_pred             HHhC--CCCccEEEEEe
Q 022383          200 YRYL--PPDLQVVLISA  214 (298)
Q Consensus       200 ~~~~--~~~~~~v~~SA  214 (298)
                      ..-+  +++.+++.+|.
T Consensus       207 ~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         207 KGGLGARPEGLVVYITT  223 (546)
T ss_pred             HhhhccCcCceEEEEec
Confidence            3333  24667777665

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=96.94  E-value=0.0041  Score=56.14  Aligned_cols=135  Identities=16%  Similarity=0.206  Sum_probs=76.7

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH-HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhc
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE-LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (298)
                      -.++.|+.|||||.+....++..+.....+.+++++-++.. +...+...+.......++....-....+.  .. .+.+
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~~~~~~~~~~--~i-~~~~   79 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIEGINYEFKKSKSSM--EI-KILN   79 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChhheeecCCcc--EE-EecC
Confidence            35788999999998887777766655323457888888776 77778887776655545432111111110  00 0111


Q ss_pred             -CCcEEEeCh-HHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCC--CCccEEEEEeeCch
Q 022383          151 -GVHVVSGTP-GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDLQVVLISATLPH  218 (298)
Q Consensus       151 -~~~ilV~Tp-~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~--~~~~~v~~SAT~~~  218 (298)
                       +..|++..- +....+.     ....++++.+||+..+...    .+..+...++  .....+++|.++..
T Consensus        80 ~g~~i~f~g~~d~~~~ik-----~~~~~~~~~idEa~~~~~~----~~~~l~~rlr~~~~~~~i~~t~NP~~  142 (396)
T TIGR01547        80 TGKKFIFKGLNDKPNKLK-----SGAGIAIIWFEEASQLTFE----DIKELIPRLRETGGKKFIIFSSNPES  142 (396)
T ss_pred             CCeEEEeecccCChhHhh-----CcceeeeehhhhhhhcCHH----HHHHHHHHhhccCCccEEEEEcCcCC
Confidence             345555443 2222211     1233689999999987433    3344444443  22224788888754

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.

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=96.93  E-value=0.018  Score=45.01  Aligned_cols=44  Identities=16%  Similarity=0.356  Sum_probs=32.2

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      ...+++||||+|.|... -...+.+.++.-+.+..++++|..+..
T Consensus       101 ~~~KviiI~~ad~l~~~-a~NaLLK~LEepp~~~~fiL~t~~~~~  144 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEE-AQNALLKTLEEPPENTYFILITNNPSK  144 (162)
T ss_dssp             SSSEEEEEETGGGS-HH-HHHHHHHHHHSTTTTEEEEEEES-GGG
T ss_pred             CCceEEEeehHhhhhHH-HHHHHHHHhcCCCCCEEEEEEECChHH
Confidence            57899999999998554 366777788887777877777766543

...

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.92  E-value=0.012  Score=53.80  Aligned_cols=45  Identities=11%  Similarity=0.278  Sum_probs=26.5

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~  117 (298)
                      ..+++.||+|+|||... ..+.+.+.....+.+++|+.. ..+..++
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~~~~~~~v~yi~~-~~f~~~~  175 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQNEPDLRVMYITS-EKFLNDL  175 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHH
Confidence            46999999999999543 234444433323446777653 3333333

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.92  E-value=0.012  Score=51.38  Aligned_cols=40  Identities=18%  Similarity=0.401  Sum_probs=27.1

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ....+||+||+|.|... -...+...+..-+.+..+++.+-
T Consensus       108 ~~~kviiidead~mt~~-A~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470         108 GGYKVVIIDEADKLTED-AANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             CCceEEEeCcHHHHhHH-HHHHHHHHhccCCCCeEEEEEcC
Confidence            67899999999998653 34555555555555665555544

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.91  E-value=0.017  Score=54.67  Aligned_cols=39  Identities=10%  Similarity=0.264  Sum_probs=26.0

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|++.... ...+.++++.-+....+|+.+
T Consensus       117 gk~KV~IIDEVh~LS~~A-~NALLKtLEEPP~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHS-FNALLKTLEEPPEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCHHH-HHHHHHHHhcCCCCcEEEEEE
Confidence            456899999999985544 345556666655556555544

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.88  E-value=0.0029  Score=58.05  Aligned_cols=149  Identities=15%  Similarity=0.208  Sum_probs=80.6

Q ss_pred             EEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh-h-ccCCceEEEEEcCCchH----HHHHHh
Q 022383           75 AQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI-G-DFINIQAHACVGGKSVG----EDIRKL  148 (298)
Q Consensus        75 i~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~-~-~~~~~~~~~~~~~~~~~----~~~~~~  148 (298)
                      +.+.||||||++.+-.|+.....+  ...-|+.|.....++-+...+..- . +.+ ..-.+..++....    .....-
T Consensus         2 f~matgsgkt~~ma~lil~~y~kg--yr~flffvnq~nilekt~~nftd~~s~kyl-f~e~i~~~d~~i~ikkvn~fseh   78 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKG--YRNFLFFVNQANILEKTKLNFTDSVSSKYL-FSENININDENIEIKKVNNFSEH   78 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhc--hhhEEEEecchhHHHHHHhhcccchhhhHh-hhhhhhcCCceeeeeeecccCcc
Confidence            568899999999888888887664  335678887766666655443210 0 000 0000111111100    000112


Q ss_pred             hcCCcEEEeChHHHHHHHhcc---C---ccCCCccE-EEechhhHhhccc---------cHHHHHHHHHh---CCCCccE
Q 022383          149 EHGVHVVSGTPGRVCDMIKRK---T---LRTRAIKL-LVLDESDEMLSRG---------FKDQIYDVYRY---LPPDLQV  209 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~---~---~~~~~l~~-vViDE~h~~~~~~---------~~~~i~~i~~~---~~~~~~~  209 (298)
                      .++..|..+|.+.|...+.+.   .   .++.+..+ ++-||+|++-...         -...++..+..   -.+..-+
T Consensus        79 nd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~  158 (812)
T COG3421          79 NDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLL  158 (812)
T ss_pred             CCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCcee
Confidence            345789999999998876542   2   23444444 5669999985431         11122222111   1234557


Q ss_pred             EEEEeeCchhHHHHHHhc
Q 022383          210 VLISATLPHEILEMTTKF  227 (298)
Q Consensus       210 v~~SAT~~~~~~~~~~~~  227 (298)
                      +.+|||.+.. .+....|
T Consensus       159 lef~at~~k~-k~v~~ky  175 (812)
T COG3421         159 LEFSATIPKE-KSVEDKY  175 (812)
T ss_pred             ehhhhcCCcc-ccHHHHh
Confidence            7899999843 4444444

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.88  E-value=0.032  Score=51.35  Aligned_cols=39  Identities=13%  Similarity=0.307  Sum_probs=24.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|.+.... .+.+.+.++.-++...+|+.+
T Consensus       115 ~~~KVvIIDEah~Ls~~A-~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964        115 SKFKVYIIDEVHMLSNSA-FNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             CCceEEEEeChHhCCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            578899999999985543 234444555555555555544

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.87  E-value=0.01  Score=49.48  Aligned_cols=37  Identities=8%  Similarity=0.240  Sum_probs=22.2

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      +..+++.||+|+|||.... .+.+.+...  +.+++|+.-
T Consensus        45 ~~~l~l~Gp~G~GKThLl~-a~~~~~~~~--~~~v~y~~~   81 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLH-AACAELSQR--GRAVGYVPL   81 (235)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHhC--CCeEEEEEH
Confidence            4689999999999995433 222222221  345666543

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.85  E-value=0.008  Score=50.62  Aligned_cols=67  Identities=15%  Similarity=0.306  Sum_probs=40.7

Q ss_pred             CCCCChHHHHHHHHHhh-------cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH
Q 022383           52 GFEKPSAIQQRAVMPII-------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~-------~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~  122 (298)
                      .|......+..++..+.       ++.++++.||+|+|||..+.- +-+.+..  .+ .-++.+++.+++.++...+.
T Consensus        80 d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~A-i~~~l~~--~g-~sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484          80 DFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIA-IGNELLK--AG-ISVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             cccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHH-HHHHHHH--cC-CeEEEEEHHHHHHHHHHHHh
Confidence            34444444555443332       678999999999999965432 2233332  23 34556677888888777543

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.85  E-value=0.0033  Score=60.68  Aligned_cols=68  Identities=18%  Similarity=0.153  Sum_probs=53.2

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-CCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      +++-|.+++.+  ...+++|.|+.|||||.+..--+...+... -...++++|+.|+..+.++.+++.+..
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            78889998864  356899999999999988666666666432 234478999999999999999987654

Designed to identify rep members of the uvrD/rep subfamily.

>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=96.84  E-value=0.017  Score=42.95  Aligned_cols=17  Identities=24%  Similarity=0.464  Sum_probs=13.7

Q ss_pred             CccEEEechhhHhhccc
Q 022383          175 AIKLLVLDESDEMLSRG  191 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~  191 (298)
                      ...+++|||+|.+....
T Consensus        58 ~~~vl~iDe~d~l~~~~   74 (132)
T PF00004_consen   58 KPCVLFIDEIDKLFPKS   74 (132)
T ss_dssp             TSEEEEEETGGGTSHHC
T ss_pred             cceeeeeccchhccccc
Confidence            35899999999986554

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 ....

>PRK08116 hypothetical protein; Validated

Probab=96.83  E-value=0.012  Score=50.03  Aligned_cols=45  Identities=18%  Similarity=0.264  Sum_probs=27.0

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      ..+++.|++|+|||..+. ++.+.+...  +..++++ +..++...+..
T Consensus       115 ~gl~l~G~~GtGKThLa~-aia~~l~~~--~~~v~~~-~~~~ll~~i~~  159 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAA-CIANELIEK--GVPVIFV-NFPQLLNRIKS  159 (268)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHHc--CCeEEEE-EHHHHHHHHHH
Confidence            359999999999995433 344554433  3344444 44555555444

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.82  E-value=0.0098  Score=54.12  Aligned_cols=59  Identities=10%  Similarity=0.317  Sum_probs=37.8

Q ss_pred             cCCCccEEEechhhHhhcc-c--------cHHHHHHHHHhCC-----CCccEEEEEeeCchhHHHHHHhcCCCCEEEE
Q 022383          172 RTRAIKLLVLDESDEMLSR-G--------FKDQIYDVYRYLP-----PDLQVVLISATLPHEILEMTTKFMTDPVKIL  235 (298)
Q Consensus       172 ~~~~l~~vViDE~h~~~~~-~--------~~~~i~~i~~~~~-----~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  235 (298)
                      .-+.++.|||||+|.+... |        .-..+..++.+..     ++.-+|+||--     .+++...+..|..+.
T Consensus       321 ~~SgLHIIIFDEiDAICKqRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR-----~DlIDEALLRPGRlE  393 (744)
T KOG0741|consen  321 ANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNR-----KDLIDEALLRPGRLE  393 (744)
T ss_pred             ccCCceEEEehhhHHHHHhcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCc-----hhhHHHHhcCCCceE
Confidence            3468899999999998643 1        2345666776664     46667777544     455555555665443

>PF13173 AAA_14: AAA domain

Probab=96.82  E-value=0.03  Score=41.78  Aligned_cols=38  Identities=16%  Similarity=0.347  Sum_probs=25.8

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEee
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      .-.+|++||+|.+.  ++...+..+.+.. ++.++++.+..
T Consensus        61 ~~~~i~iDEiq~~~--~~~~~lk~l~d~~-~~~~ii~tgS~   98 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP--DWEDALKFLVDNG-PNIKIILTGSS   98 (128)
T ss_pred             CCcEEEEehhhhhc--cHHHHHHHHHHhc-cCceEEEEccc
Confidence            45689999999984  4567777777755 45666554443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.012  Score=57.28  Aligned_cols=38  Identities=13%  Similarity=0.253  Sum_probs=25.2

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      .+.+++||||+|+|.... ...+.++++.-+....+|+.
T Consensus       118 gk~KViIIDEAh~LT~eA-qNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRSS-FNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CCcEEEEEechHhcCHHH-HHHHHHHHhccCCCeEEEEE
Confidence            467899999999985433 44455566655555655554

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.81  E-value=0.01  Score=56.87  Aligned_cols=40  Identities=15%  Similarity=0.359  Sum_probs=26.2

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      .+.+++||||+|.|.... .+.+.++++.-+.+..+|+.|-
T Consensus       118 gr~KVIIIDEah~LT~~A-~NALLKtLEEPP~~v~FILaTt  157 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHA-FNAMLKTLEEPPPHVKFILATT  157 (830)
T ss_pred             CCceEEEEeChhhCCHHH-HHHHHHHHHhcCCCeEEEEEEC
Confidence            467899999999986544 3444455666555565555443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.81  E-value=0.018  Score=48.84  Aligned_cols=18  Identities=33%  Similarity=0.514  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      .++++.||+|+|||..+-
T Consensus        43 ~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            578999999999996543

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.

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=96.79  E-value=0.024  Score=45.03  Aligned_cols=107  Identities=14%  Similarity=0.130  Sum_probs=60.6

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (298)
                      |+=.++++|+.||||...+..+-+.-..   +.++++..|-..             .+.+...+...-|...        
T Consensus         4 g~l~~i~gpM~SGKT~eLl~r~~~~~~~---g~~v~vfkp~iD-------------~R~~~~~V~Sr~G~~~--------   59 (201)
T COG1435           4 GWLEFIYGPMFSGKTEELLRRARRYKEA---GMKVLVFKPAID-------------TRYGVGKVSSRIGLSS--------   59 (201)
T ss_pred             EEEEEEEccCcCcchHHHHHHHHHHHHc---CCeEEEEecccc-------------cccccceeeeccCCcc--------
Confidence            3446889999999998644443333222   446777777421             1112222222222221        


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCC
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~  204 (298)
                        .-+.|-.+..+...+....... .+++|.|||++.+ +...-..+..+.+.+.
T Consensus        60 --~A~~i~~~~~i~~~i~~~~~~~-~~~~v~IDEaQF~-~~~~v~~l~~lad~lg  110 (201)
T COG1435          60 --EAVVIPSDTDIFDEIAALHEKP-PVDCVLIDEAQFF-DEELVYVLNELADRLG  110 (201)
T ss_pred             --cceecCChHHHHHHHHhcccCC-CcCEEEEehhHhC-CHHHHHHHHHHHhhcC
Confidence              2455666666777666543333 2899999999875 3344556666666653

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.78  E-value=0.044  Score=50.33  Aligned_cols=22  Identities=27%  Similarity=0.303  Sum_probs=17.4

Q ss_pred             CCcEEEEcCCCCchHHHHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTV   91 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~   91 (298)
                      |+-+.++||||+|||.+....+
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA  277 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLA  277 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHH
Confidence            4568899999999998765444

>PRK06893 DNA replication initiation factor; Validated

Probab=96.78  E-value=0.008  Score=49.87  Aligned_cols=46  Identities=20%  Similarity=0.387  Sum_probs=28.5

Q ss_pred             CCccEEEechhhHhhcc-ccHHHHHHHHHhCC-CCccEEEEEeeCchh
Q 022383          174 RAIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPHE  219 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~  219 (298)
                      .+.+++|+||+|.+... .....+..+++... ...+++++|++.++.
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            46689999999987533 23334445555443 245567788876543

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.78  E-value=0.093  Score=48.58  Aligned_cols=21  Identities=33%  Similarity=0.501  Sum_probs=17.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~   89 (298)
                      .|+.+.++||+|+|||.....
T Consensus       349 ~G~vIaLVGPtGvGKTTtaak  369 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAK  369 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            467889999999999976543

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.78  E-value=0.025  Score=49.67  Aligned_cols=39  Identities=8%  Similarity=0.234  Sum_probs=25.6

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...++||+||+|.+... ....+..+++..+...++|+.+
T Consensus       124 ~~~~vlilDe~~~l~~~-~~~~L~~~le~~~~~~~~Il~~  162 (337)
T PRK12402        124 ADYKTILLDNAEALRED-AQQALRRIMEQYSRTCRFIIAT  162 (337)
T ss_pred             CCCcEEEEeCcccCCHH-HHHHHHHHHHhccCCCeEEEEe
Confidence            45679999999987433 3445566666666666665544

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.77  E-value=0.023  Score=51.62  Aligned_cols=36  Identities=14%  Similarity=0.224  Sum_probs=22.7

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      ..++++|++|+|||......+. .+...  +.+++++..
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~-~L~~~--g~kV~lV~~  131 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLAR-YFKKK--GLKVGLVAA  131 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHH-HHHHc--CCeEEEecC
Confidence            3588999999999976554332 23322  345666653

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=96.74  E-value=0.0014  Score=51.59  Aligned_cols=123  Identities=15%  Similarity=0.200  Sum_probs=51.8

Q ss_pred             EEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHH-HHHhhcCC
Q 022383           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED-IRKLEHGV  152 (298)
Q Consensus        74 li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  152 (298)
                      ++.|+-|-|||.+.-+.+...+...  ..++++.+|+.+-++.+++.+..-.+..+++...    ...... .....++.
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~--~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~----~~~~~~~~~~~~~~~   74 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKG--KIRILVTAPSPENVQTLFEFAEKGLKALGYKEEK----KKRIGQIIKLRFNKQ   74 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC------------------------------CC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhc--CceEEEecCCHHHHHHHHHHHHhhcccccccccc----ccccccccccccccc
Confidence            5789999999976544333333332  2478999999999988888665544333332200    000000 00111234


Q ss_pred             cEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCc
Q 022383          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLP  217 (298)
Q Consensus       153 ~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~  217 (298)
                      .|-...|+.+...       ....+++|||||=.+.    ...+..+++..    ..+++|.|..
T Consensus        75 ~i~f~~Pd~l~~~-------~~~~DlliVDEAAaIp----~p~L~~ll~~~----~~vv~stTi~  124 (177)
T PF05127_consen   75 RIEFVAPDELLAE-------KPQADLLIVDEAAAIP----LPLLKQLLRRF----PRVVFSTTIH  124 (177)
T ss_dssp             C--B--HHHHCCT-----------SCEEECTGGGS-----HHHHHHHHCCS----SEEEEEEEBS
T ss_pred             eEEEECCHHHHhC-------cCCCCEEEEechhcCC----HHHHHHHHhhC----CEEEEEeecc
Confidence            5555666544421       1234899999996542    34444444333    3677888873

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.74  E-value=0.012  Score=51.20  Aligned_cols=40  Identities=10%  Similarity=0.191  Sum_probs=27.0

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ..++|||||+|.+........+..+++..+...++|+.+.
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n  139 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITAN  139 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcC
Confidence            4579999999988333345566666777666676666443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.72  E-value=0.015  Score=56.94  Aligned_cols=39  Identities=15%  Similarity=0.405  Sum_probs=28.0

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|+|.... .+.+.++++..+....+|+.+
T Consensus       119 ~~~KV~IIDEad~lt~~a-~NaLLK~LEEpP~~~~fIl~t  157 (824)
T PRK07764        119 SRYKIFIIDEAHMVTPQG-FNALLKIVEEPPEHLKFIFAT  157 (824)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            567899999999996543 445666677666666666655

>CHL00181 cbbX CbbX; Provisional

Probab=96.72  E-value=0.014  Score=50.17  Aligned_cols=19  Identities=32%  Similarity=0.455  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      |.++++.||+|+|||..+-
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4568999999999997654

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.71  E-value=0.023  Score=49.82  Aligned_cols=56  Identities=25%  Similarity=0.479  Sum_probs=36.1

Q ss_pred             cccCcccCCCCHHHHHHHHHC--------CCC------CChHHHHHH------HHHhhcC-----CcEEEEcCCCCchHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQY--------GFE------KPSAIQQRA------VMPIIKG-----RDVIAQAQSGTGKTS   85 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~--------~~~------~~~~~Q~~~------~~~~~~~-----~~~li~~pTG~GKT~   85 (298)
                      ....|+.++...++.++|+.-        .|.      ..-..=+++      +|.+.+|     +.++..||.|+|||+
T Consensus       181 ~~~~f~~~~~d~~Lve~lerdIl~~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTl  260 (491)
T KOG0738|consen  181 EDKKFDSLGYDADLVEALERDILQRNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTL  260 (491)
T ss_pred             ccCCCCcccchHHHHHHHHHHHhccCCCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHH
Confidence            556888888888888888661        111      111122222      2334455     789999999999995


Q ss_pred             H
Q 022383           86 M   86 (298)
Q Consensus        86 ~   86 (298)
                      .
T Consensus       261 L  261 (491)
T KOG0738|consen  261 L  261 (491)
T ss_pred             H
Confidence            3

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.70  E-value=0.0086  Score=52.09  Aligned_cols=64  Identities=22%  Similarity=0.279  Sum_probs=41.0

Q ss_pred             HHHHCCCCCChHHHHHHHHH-hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           47 GIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      .+.+.|.  +++.|...+.. +..+++++++|+||||||.. +-.++..+...+...+++.+=...||
T Consensus       122 ~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTl-l~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        122 DYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTL-ANAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             HHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHHhcCCCCceEEEecCCccc
Confidence            4445444  55667766555 45678999999999999953 34555555332233466666666665

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

Probab=96.70  E-value=0.015  Score=49.56  Aligned_cols=121  Identities=17%  Similarity=0.171  Sum_probs=59.1

Q ss_pred             HHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHH
Q 022383           65 MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED  144 (298)
Q Consensus        65 ~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (298)
                      .-+..|.-+++.|++|+|||....-.+.+....  .+..++|++- ..-..++..++........+........ .....
T Consensus        25 gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~--~g~~vl~iS~-E~~~~~~~~r~~~~~~~~~~~~~~~~~~-~~~~~  100 (271)
T cd01122          25 KGLRKGELIILTAGTGVGKTTFLREYALDLITQ--HGVRVGTISL-EEPVVRTARRLLGQYAGKRLHLPDTVFI-YTLEE  100 (271)
T ss_pred             EEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh--cCceEEEEEc-ccCHHHHHHHHHHHHhCCCcccCCcccc-ccHHH
Confidence            345567889999999999996444333333222  1446777763 2234555555543322212211000001 11111


Q ss_pred             H----HHhhcCCcEEE-e-----ChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          145 I----RKLEHGVHVVS-G-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       145 ~----~~~~~~~~ilV-~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      .    ..+.....+.+ -     |++.+...++... .-..+++||||.++.+...
T Consensus       101 ~~~~~~~~~~~~~l~i~d~~~~~~~~~i~~~i~~~~-~~~~~~~vvID~l~~l~~~  155 (271)
T cd01122         101 FDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMA-VSHGIQHIIIDNLSIMVSD  155 (271)
T ss_pred             HHHHHHHhcCCCcEEEEcCCCccCHHHHHHHHHHHH-hcCCceEEEECCHHHHhcc
Confidence            1    12222122322 1     4455555444311 1236789999999988543

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

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.70  E-value=0.011  Score=51.04  Aligned_cols=67  Identities=21%  Similarity=0.386  Sum_probs=41.4

Q ss_pred             HHHHHHHCCCCCChHHHHHHHH-HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           44 LLRGIYQYGFEKPSAIQQRAVM-PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        44 i~~~l~~~~~~~~~~~Q~~~~~-~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      -.+.|.+.|.  +++.|...+. .+..+++++++||||||||.. +-.++..+.......+++.+=...|+
T Consensus       107 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       107 TLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTL-ANALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHhhccCCCceEEEECCchhh
Confidence            3444555453  3444555544 455678999999999999954 44455555442223467777777665

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.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.70  E-value=0.015  Score=54.05  Aligned_cols=39  Identities=15%  Similarity=0.378  Sum_probs=26.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|++....+ ..+.+.++.-|....+|+.+
T Consensus       118 ~~~kV~iIDE~~~ls~~a~-naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHSF-NALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHHHH-HHHHHHHhccCCCeEEEEEE
Confidence            4678999999999865543 44555666666666666654

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.66  E-value=0.027  Score=53.90  Aligned_cols=158  Identities=15%  Similarity=0.210  Sum_probs=94.3

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCC--cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHH
Q 022383           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ  116 (298)
Q Consensus        39 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~--~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q  116 (298)
                      +.++.....+.....+....-|.+.+..+.+++  -+++.|.-|=|||.+.=+++........ ..++++.+|+.+-++.
T Consensus       198 ~~~~~~~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~~-~~~iiVTAP~~~nv~~  276 (758)
T COG1444         198 PLDPVFPRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLAG-SVRIIVTAPTPANVQT  276 (758)
T ss_pred             CCCCCCCHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhcC-CceEEEeCCCHHHHHH
Confidence            344444555667666667777777777777553  5888899999999776555422222211 4488999999999999


Q ss_pred             HHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHH
Q 022383          117 TEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI  196 (298)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i  196 (298)
                      +...+.+-....|++.............  .-.+...|=.-+|....          ..-+++|||||=.+    -.+.+
T Consensus       277 Lf~fa~~~l~~lg~~~~v~~d~~g~~~~--~~~~~~~i~y~~P~~a~----------~~~DllvVDEAAaI----plplL  340 (758)
T COG1444         277 LFEFAGKGLEFLGYKRKVAPDALGEIRE--VSGDGFRIEYVPPDDAQ----------EEADLLVVDEAAAI----PLPLL  340 (758)
T ss_pred             HHHHHHHhHHHhCCccccccccccceee--ecCCceeEEeeCcchhc----------ccCCEEEEehhhcC----ChHHH
Confidence            9988877666655443222111100000  00011223344553322          11589999999654    24555


Q ss_pred             HHHHHhCCCCccEEEEEeeCc
Q 022383          197 YDVYRYLPPDLQVVLISATLP  217 (298)
Q Consensus       197 ~~i~~~~~~~~~~v~~SAT~~  217 (298)
                      ..+++..    +.++||.|+.
T Consensus       341 ~~l~~~~----~rv~~sTTIh  357 (758)
T COG1444         341 HKLLRRF----PRVLFSTTIH  357 (758)
T ss_pred             HHHHhhc----CceEEEeeec
Confidence            5555554    3688999984

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.64  E-value=0.011  Score=53.42  Aligned_cols=33  Identities=21%  Similarity=0.361  Sum_probs=26.5

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHH
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      +......++..+..++++++.||+|+|||..+.
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            455556677778889999999999999996654

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.62  E-value=0.0058  Score=59.59  Aligned_cols=71  Identities=15%  Similarity=0.208  Sum_probs=54.3

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      ..+++-|.+++.+  ...+++|.|+.|||||.+..--+...+.... ...+++.++-|+.-+.++.+++.++..
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         3 AHLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             cccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            4589999999875  3578999999999999876555555443322 234799999999999999999887643

Designed to identify pcrA members of the uvrD/rep subfamily.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.61  E-value=0.018  Score=54.31  Aligned_cols=41  Identities=15%  Similarity=0.365  Sum_probs=26.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEee
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      .+.+++||||+|+|....+ +.+.+.++.-+.+..+|+.|-.
T Consensus       123 gr~KViIIDEah~Ls~~Aa-NALLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNHAF-NAMLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             CCceEEEEEChHhcCHHHH-HHHHHhhccCCCCceEEEEeCC
Confidence            4678999999999865543 3344455554556666666543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.60  E-value=0.021  Score=52.15  Aligned_cols=48  Identities=15%  Similarity=0.430  Sum_probs=27.3

Q ss_pred             CCccEEEechhhHhhccc-cHHHHHHHHHhC-CCCccEEEEEeeCchhHH
Q 022383          174 RAIKLLVLDESDEMLSRG-FKDQIYDVYRYL-PPDLQVVLISATLPHEIL  221 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~-~~~~i~~i~~~~-~~~~~~v~~SAT~~~~~~  221 (298)
                      ...++++|||+|.+.... ....+..++..+ ....++++.|.+.|..+.
T Consensus       201 ~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~  250 (445)
T PRK12422        201 RNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLK  250 (445)
T ss_pred             ccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHh
Confidence            367899999999975432 234444444433 234555555544454443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.58  E-value=0.019  Score=53.93  Aligned_cols=107  Identities=17%  Similarity=0.250  Sum_probs=56.3

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (298)
                      ..+++.|++|+|||.. +..+.+.+.....+.+++|+. ..+++++....++.-                          
T Consensus       315 NpL~LyG~sGsGKTHL-L~AIa~~a~~~~~g~~V~Yit-aeef~~el~~al~~~--------------------------  366 (617)
T PRK14086        315 NPLFIYGESGLGKTHL-LHAIGHYARRLYPGTRVRYVS-SEEFTNEFINSIRDG--------------------------  366 (617)
T ss_pred             CcEEEECCCCCCHHHH-HHHHHHHHHHhCCCCeEEEee-HHHHHHHHHHHHHhc--------------------------
Confidence            3489999999999953 223344433322344566654 344555444322210                          


Q ss_pred             CCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc-cHHHHHHHHHhCCC-CccEEEEEeeCchh
Q 022383          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPP-DLQVVLISATLPHE  219 (298)
Q Consensus       151 ~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~~~~-~~~~v~~SAT~~~~  219 (298)
                             ..+.+..       .+.++++|||||+|.+.... ....+..+++.+.. +.++|+.|-..+..
T Consensus       367 -------~~~~f~~-------~y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~e  423 (617)
T PRK14086        367 -------KGDSFRR-------RYREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQ  423 (617)
T ss_pred             -------cHHHHHH-------HhhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHh
Confidence                   0011111       13457899999999875432 23444455555433 46666655444443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.57  E-value=0.018  Score=47.70  Aligned_cols=43  Identities=7%  Similarity=0.254  Sum_probs=25.6

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCCCC-ccEEEEEeeCch
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD-LQVVLISATLPH  218 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~-~~~v~~SAT~~~  218 (298)
                      ..+++||||+|.+..+ ....+..+++..... ..+++++++.++
T Consensus        90 ~~~~liiDdi~~l~~~-~~~~L~~~~~~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903         90 EAELYAVDDVERLDDA-QQIALFNLFNRVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             cCCEEEEeChhhcCch-HHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence            4578999999987433 344454555444323 335667776543

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.57  E-value=0.032  Score=53.11  Aligned_cols=38  Identities=13%  Similarity=0.260  Sum_probs=25.3

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      .+.+++||||+|+|.... .+.+.++++.-+....+|+.
T Consensus       118 g~~KV~IIDEah~Ls~~a-~NALLKtLEEPp~~v~FIL~  155 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLA  155 (647)
T ss_pred             CCCEEEEEechHhCCHHH-HHHHHHHHHcCCCCeEEEEe
Confidence            467899999999986544 44444566665555555554

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.57  E-value=0.029  Score=59.00  Aligned_cols=64  Identities=25%  Similarity=0.301  Sum_probs=45.2

Q ss_pred             CCChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhc--cCCCCeEEEEEcCcHHHHHHHH
Q 022383           54 EKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~--~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      ..+++.|.+++..++.+  +-++|.|..|+|||... -.++..+.  ....+..++.++||-.-+..+.
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~ 1033 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEMR 1033 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHHH
Confidence            35899999999998864  57899999999999653 22222222  1223457888999987666543

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.56  E-value=0.028  Score=48.92  Aligned_cols=141  Identities=17%  Similarity=0.174  Sum_probs=69.3

Q ss_pred             CCCChHHHHHHHHHhh----cCC---cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh-
Q 022383           53 FEKPSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI-  124 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~----~~~---~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~-  124 (298)
                      +..++|||..+|..+.    +|+   -.++.||.|.||+..+.. +...+.........  -|+          .++.+ 
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~-lA~~LlC~~~~~~~--~c~----------~c~~~~   68 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALA-LAEHVLASGPDPAA--AQR----------TRQLIA   68 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH-HHHHHhCCCCCCCC--cch----------HHHHHh
Confidence            3568999999998865    343   489999999999965432 22222221111000  111          12222 


Q ss_pred             -hccCCceEEEEEc-CCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHh
Q 022383          125 -GDFINIQAHACVG-GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY  202 (298)
Q Consensus       125 -~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~  202 (298)
                       +...++....... +...+       ....|.|-....+...+..... ....+++|||++|.|.... ...+.++++-
T Consensus        69 ~g~HPD~~~i~~~p~~~~~k-------~~~~I~idqIR~l~~~~~~~p~-~g~~kV~iI~~ae~m~~~A-aNaLLKtLEE  139 (319)
T PRK08769         69 AGTHPDLQLVSFIPNRTGDK-------LRTEIVIEQVREISQKLALTPQ-YGIAQVVIVDPADAINRAA-CNALLKTLEE  139 (319)
T ss_pred             cCCCCCEEEEecCCCccccc-------ccccccHHHHHHHHHHHhhCcc-cCCcEEEEeccHhhhCHHH-HHHHHHHhhC
Confidence             2223433331110 00000       0001222122222222222211 2467899999999995443 4555566666


Q ss_pred             CCCCccEEEEEee
Q 022383          203 LPPDLQVVLISAT  215 (298)
Q Consensus       203 ~~~~~~~v~~SAT  215 (298)
                      -+.+..+|++|..
T Consensus       140 Pp~~~~fiL~~~~  152 (319)
T PRK08769        140 PSPGRYLWLISAQ  152 (319)
T ss_pred             CCCCCeEEEEECC
Confidence            6666666666653

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.55  E-value=0.019  Score=51.14  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=17.6

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTV   95 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~   95 (298)
                      .++++.||+|+|||... ..++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            58999999999999653 3344443

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.55  E-value=0.029  Score=50.55  Aligned_cols=20  Identities=30%  Similarity=0.318  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCCchHHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~   89 (298)
                      |+-+.++||||+|||.....
T Consensus       191 g~vi~lvGpnG~GKTTtlak  210 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAK  210 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45689999999999976543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.54  E-value=0.021  Score=49.05  Aligned_cols=18  Identities=28%  Similarity=0.370  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      +.++++.||+|+|||..+
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            458999999999999765

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.52  E-value=0.021  Score=47.61  Aligned_cols=53  Identities=15%  Similarity=0.226  Sum_probs=36.6

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      .|..+++.||+|+|||.-.+-.+...+..   +..++|++ +.+-..++.+.+..++
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~---ge~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc---CCcEEEEE-eeCCHHHHHHHHHHhC
Confidence            45789999999999997554444444432   45678877 4566777777776654

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.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.52  E-value=0.038  Score=42.84  Aligned_cols=53  Identities=28%  Similarity=0.538  Sum_probs=41.4

Q ss_pred             CCCccEEEechhhHhhcccc--HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHH
Q 022383          173 TRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~  225 (298)
                      ...++++|+||+-.....++  ...+..+++..|...-+|+.+-..|+.+.+...
T Consensus        93 ~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD  147 (159)
T cd00561          93 SGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAAD  147 (159)
T ss_pred             cCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence            46789999999988766664  567778888888888888887788877766544

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.49  E-value=0.072  Score=52.06  Aligned_cols=28  Identities=18%  Similarity=0.674  Sum_probs=18.7

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHh
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRY  202 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~  202 (298)
                      ....+||+||+|.+.... ...+..+++.
T Consensus       868 r~v~IIILDEID~L~kK~-QDVLYnLFR~  895 (1164)
T PTZ00112        868 RNVSILIIDEIDYLITKT-QKVLFTLFDW  895 (1164)
T ss_pred             ccceEEEeehHhhhCccH-HHHHHHHHHH
Confidence            456789999999987542 3444445544

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=96.49  E-value=0.017  Score=57.55  Aligned_cols=149  Identities=15%  Similarity=0.071  Sum_probs=90.9

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccC-----------C----CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEE
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS-----------S----REVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-----------~----~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  133 (298)
                      .|+.++..-..|+|||.+-+...+......           .    ..+-+|||||. ++..|+...+.+-.... +.+.
T Consensus       373 ~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~-lKv~  450 (1394)
T KOG0298|consen  373 HGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSL-LKVL  450 (1394)
T ss_pred             CCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhcccc-ceEE
Confidence            356778888899999988766554433110           0    12468999995 67789998887765443 6777


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc--------------CccC----CCccE--EEechhhHhhccccH
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK--------------TLRT----RAIKL--LVLDESDEMLSRGFK  193 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~--------------~~~~----~~l~~--vViDE~h~~~~~~~~  193 (298)
                      .+.|-.............+||+++|-..|..-+...              ..+.    -.+.+  |++||+.++..  -.
T Consensus       451 ~Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMves--ss  528 (1394)
T KOG0298|consen  451 LYFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVES--SS  528 (1394)
T ss_pred             EEechhhhcccCchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcc--hH
Confidence            776643322221233346899999998887644321              1111    11111  89999988744  34


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeCchhHHH
Q 022383          194 DQIYDVYRYLPPDLQVVLISATLPHEILE  222 (298)
Q Consensus       194 ~~i~~i~~~~~~~~~~v~~SAT~~~~~~~  222 (298)
                      ........+++ ....-.+|.|+-..+.+
T Consensus       529 S~~a~M~~rL~-~in~W~VTGTPiq~Idd  556 (1394)
T KOG0298|consen  529 SAAAEMVRRLH-AINRWCVTGTPIQKIDD  556 (1394)
T ss_pred             HHHHHHHHHhh-hhceeeecCCchhhhhh
Confidence            55555666664 34467788996443444

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.48  E-value=0.048  Score=43.64  Aligned_cols=39  Identities=13%  Similarity=0.416  Sum_probs=24.1

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ....++||||+|.+.... ...+...++.-++..-+|+++
T Consensus        95 ~~~kviiide~~~l~~~~-~~~Ll~~le~~~~~~~~il~~  133 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAA-ANALLKTLEEPPPNTLFILIT  133 (188)
T ss_pred             CCeEEEEEechhhhCHHH-HHHHHHHhcCCCCCeEEEEEE
Confidence            567899999999985432 344445555544444455443

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.47  E-value=0.02  Score=59.45  Aligned_cols=63  Identities=22%  Similarity=0.291  Sum_probs=45.6

Q ss_pred             CChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHH--HHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           55 KPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMI--ALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~--~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      .+++-|.+++..++..  +-++|.|..|+|||...  ++.++..+.. ..+..++.++||-.-+..+.
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e-~~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE-SERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh-ccCceEEEEechHHHHHHHH
Confidence            6899999999998854  77999999999999763  2222332222 23457888999987766654

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.47  E-value=0.056  Score=44.88  Aligned_cols=54  Identities=17%  Similarity=0.196  Sum_probs=33.9

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      +..|.-+++.|++|+|||...+-.+...+..   +.++++++ +.+-..+..+.+..+
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~---g~~~~yi~-~e~~~~~~~~~~~~~   74 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGFLQN---GYSVSYVS-TQLTTTEFIKQMMSL   74 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEEe-CCCCHHHHHHHHHHh
Confidence            3457789999999999996543333333222   45678888 444445655555544

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.46  E-value=0.037  Score=50.96  Aligned_cols=18  Identities=33%  Similarity=0.484  Sum_probs=14.7

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~   89 (298)
                      .+++.||.|+|||..+..
T Consensus        38 ~~Lf~GPpGtGKTTlA~~   55 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARI   55 (472)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            379999999999976543

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.44  E-value=0.033  Score=53.76  Aligned_cols=131  Identities=15%  Similarity=0.153  Sum_probs=61.7

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (298)
                      ++-+.++||||+|||.+....+-...... .+.++.++.-...-+- ..++++.++...++.+.                
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~-G~kkV~lit~Dt~Rig-A~eQL~~~a~~~gvpv~----------------  246 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVARE-GADQLALLTTDSFRIG-ALEQLRIYGRILGVPVH----------------  246 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHc-CCCeEEEecCcccchH-HHHHHHHHHHhCCCCcc----------------
Confidence            34578999999999977654433221111 1224555543222100 12333344434444322                


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCCCCccEEEEEeeCch-hHHHHHHhc
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPH-EILEMTTKF  227 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~~~~~~v~~SAT~~~-~~~~~~~~~  227 (298)
                           .+.+|+.+...+..    +.+.++|+||=+=+.... .....+..+.+...+...++.+|||... .+.+....|
T Consensus       247 -----~~~~~~~l~~al~~----~~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l~~i~~~f  317 (767)
T PRK14723        247 -----AVKDAADLRFALAA----LGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTLNEVVHAY  317 (767)
T ss_pred             -----ccCCHHHHHHHHHH----hcCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHHHHHHHHH
Confidence                 12245454444442    234467777765433211 1233333333333344556777888643 333344444

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.42  E-value=0.016  Score=54.53  Aligned_cols=136  Identities=14%  Similarity=0.140  Sum_probs=81.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  148 (298)
                      .+-.++..|--.|||+... +++..+...-.+.++++.+|.+..++.+++.+....+.. .-...-...|...   .-..
T Consensus       254 qk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkGe~I---~i~f  329 (738)
T PHA03368        254 QRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKGETI---SFSF  329 (738)
T ss_pred             ccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecCcEE---EEEe
Confidence            3678899999999997655 555554444347799999999999999999887764321 1111111111100   0011


Q ss_pred             hcC--CcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          149 EHG--VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       149 ~~~--~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      .++  ..|.+.+-      -+.+...-..++++|||||+.+-+..+...+-.+..   .+.++|++|.|-+.
T Consensus       330 ~nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk~~al~~ilp~l~~---~n~k~I~ISS~Ns~  392 (738)
T PHA03368        330 PDGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIRPDAVQTIMGFLNQ---TNCKIIFVSSTNTG  392 (738)
T ss_pred             cCCCccEEEEEec------cCCCCccCCcccEEEEechhhCCHHHHHHHHHHHhc---cCccEEEEecCCCC
Confidence            112  23444321      122345556889999999998855444433322222   37889999998643

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.41  E-value=0.016  Score=50.56  Aligned_cols=66  Identities=20%  Similarity=0.352  Sum_probs=42.4

Q ss_pred             HHHHHHCCCCCChHHHHHHHHH-hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           45 LRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      +..|.+.|.  +++.|.+.+.. +..+++++++|+||+||| .++-.++..+.......+++.+-.+.|+
T Consensus       124 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        124 LDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            445555554  45667777664 557889999999999999 4445555544222223467776676665

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.41  E-value=0.056  Score=47.02  Aligned_cols=38  Identities=18%  Similarity=0.388  Sum_probs=25.0

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ..++|++||+|.+.... ...+..+++..+....+|+.+
T Consensus       102 ~~~vviiDe~~~l~~~~-~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTSDA-QQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCHHH-HHHHHHHHhcCCCCCeEEEEe
Confidence            45799999999875432 445556666666666666644

>PRK09183 transposase/IS protein; Provisional

Probab=96.40  E-value=0.015  Score=49.10  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=17.9

Q ss_pred             hhcCCcEEEEcCCCCchHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      +..|.++++.||+|+|||....
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~  120 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAI  120 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHH
Confidence            4467899999999999995433

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.40  E-value=0.04  Score=48.23  Aligned_cols=33  Identities=21%  Similarity=0.214  Sum_probs=25.8

Q ss_pred             ChHHHHHHHHHhhc--CC---cEEEEcCCCCchHHHHH
Q 022383           56 PSAIQQRAVMPIIK--GR---DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~--~~---~~li~~pTG~GKT~~~~   88 (298)
                      .+|||+..|..+..  ++   ..++.||.|.|||..+.
T Consensus         2 ~yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~   39 (325)
T PRK08699          2 IYPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFAR   39 (325)
T ss_pred             CCCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHH
Confidence            47899999988763  32   58899999999996544

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.40  E-value=0.031  Score=49.80  Aligned_cols=39  Identities=15%  Similarity=0.383  Sum_probs=24.1

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|.+....+ ..+...++.-+....+++.+
T Consensus       118 ~~~kviIIDEa~~l~~~a~-naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSF-NALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHHHH-HHHHHHHhcCCCCeEEEEEc
Confidence            4568999999999854332 23444445445555555544

>PRK05973 replicative DNA helicase; Provisional

Probab=96.40  E-value=0.04  Score=45.76  Aligned_cols=84  Identities=14%  Similarity=0.194  Sum_probs=51.3

Q ss_pred             ccCCCCHHHHHHHHHCCCCC----------ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEE
Q 022383           36 DAMGIKDDLLRGIYQYGFEK----------PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL  105 (298)
Q Consensus        36 ~~l~l~~~i~~~l~~~~~~~----------~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~l  105 (298)
                      ...++++.+-+.-.+-||..          ++| ..+...-+..|.-++|.|++|+|||.-.+--+.+....   +.+++
T Consensus        21 ~~~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p-~~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~---Ge~vl   96 (237)
T PRK05973         21 QNIPLHEALDRIAAEEGFSSWSLLAAKAAATTP-AEELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKS---GRTGV   96 (237)
T ss_pred             cCCcHHHHHHHHHHHhccchHHHHHHhccCCCC-HHHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEE
Confidence            34456666666656666653          344 22233345566789999999999996655444444332   44677


Q ss_pred             EEcCcHHHHHHHHHHHHHh
Q 022383          106 ILSPTRELATQTEKVILAI  124 (298)
Q Consensus       106 il~p~~~l~~q~~~~~~~~  124 (298)
                      |++- .+-..|+.+++..+
T Consensus        97 yfSl-Ees~~~i~~R~~s~  114 (237)
T PRK05973         97 FFTL-EYTEQDVRDRLRAL  114 (237)
T ss_pred             EEEE-eCCHHHHHHHHHHc
Confidence            7753 33457777777665

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.38  E-value=0.085  Score=44.94  Aligned_cols=35  Identities=20%  Similarity=0.262  Sum_probs=22.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      +-++++||+|+|||....-.+... ..  .+.+++++.
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l-~~--~g~~V~li~  107 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKL-KK--QGKSVLLAA  107 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHH-Hh--cCCEEEEEe
Confidence            467888999999997655444332 22  244666666

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.37  E-value=0.1  Score=44.27  Aligned_cols=130  Identities=13%  Similarity=0.225  Sum_probs=67.7

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--c-HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--T-RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (298)
                      +..+.+++|+|+|||..+...+... ..  .+.++.++.-  . .+.+.|+......    .++.+..            
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~~l-~~--~~~~v~~i~~D~~ri~~~~ql~~~~~~----~~~~~~~------------  135 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQF-HG--KKKTVGFITTDHSRIGTVQQLQDYVKT----IGFEVIA------------  135 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHH-HH--cCCeEEEEecCCCCHHHHHHHHHHhhh----cCceEEe------------
Confidence            3678999999999997655433222 22  1334555443  2 2444554443322    2332221            


Q ss_pred             HhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCCCCccEEEEEeeCc-hhHHHHH
Q 022383          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLP-HEILEMT  224 (298)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~~~~~~v~~SAT~~-~~~~~~~  224 (298)
                               ..+++.+...+..- -...+.++++||-+=..... .....+..+++...+..-++.+|||.. ..+...+
T Consensus       136 ---------~~~~~~l~~~l~~l-~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~~  205 (270)
T PRK06731        136 ---------VRDEAAMTRALTYF-KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEII  205 (270)
T ss_pred             ---------cCCHHHHHHHHHHH-HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHHH
Confidence                     12344444433221 11236789999987543222 233444455554444444677899874 4666666


Q ss_pred             HhcC
Q 022383          225 TKFM  228 (298)
Q Consensus       225 ~~~~  228 (298)
                      +.+-
T Consensus       206 ~~f~  209 (270)
T PRK06731        206 TNFK  209 (270)
T ss_pred             HHhC
Confidence            6653

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.36  E-value=0.045  Score=52.24  Aligned_cols=39  Identities=13%  Similarity=0.270  Sum_probs=25.7

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|.+.... ...+.+.+...+....+|+.+
T Consensus       118 gk~KVIIIDEad~Ls~~A-~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKSA-FNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCHHH-HHHHHHHHHhCCCCcEEEEEe
Confidence            467899999999875433 334555555555666666655

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=96.36  E-value=0.011  Score=52.13  Aligned_cols=18  Identities=33%  Similarity=0.516  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      .+.|+.||.|+|||..+-
T Consensus        49 ~SmIl~GPPG~GKTTlA~   66 (436)
T COG2256          49 HSMILWGPPGTGKTTLAR   66 (436)
T ss_pred             ceeEEECCCCCCHHHHHH
Confidence            489999999999996544

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.35  E-value=0.11  Score=46.95  Aligned_cols=59  Identities=12%  Similarity=0.063  Sum_probs=32.3

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--cHHHHHHHHHHHHHhhccCCceEEEEE
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACV  136 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (298)
                      -++++|++|+|||....-.+.. +..  .+.++++++.  .+.-+.   ++++.++...++++....
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~-l~~--~G~kV~lV~~D~~R~aA~---eQLk~~a~~~~vp~~~~~  162 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYY-YQR--KGFKPCLVCADTFRAGAF---DQLKQNATKARIPFYGSY  162 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH-HHH--CCCCEEEEcCcccchhHH---HHHHHHhhccCCeEEeec
Confidence            4789999999999665433322 222  2446666664  343333   333344444566654433

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.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.31  E-value=0.014  Score=54.80  Aligned_cols=126  Identities=15%  Similarity=0.183  Sum_probs=76.1

Q ss_pred             CCChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH-HHHHHhhccC-C
Q 022383           54 EKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-KVILAIGDFI-N  129 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~-~~~~~~~~~~-~  129 (298)
                      ...+|+|.+..+.+.+.  +.+.++.++-+|||.+.+..+...+...+.  .++++.||.+.+.+.. +++..+.... .
T Consensus        15 ~~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P~--~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~   92 (557)
T PF05876_consen   15 TDRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDPG--PMLYVQPTDDAAKDFSKERLDPMIRASPV   92 (557)
T ss_pred             CCCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCCC--CEEEEEEcHHHHHHHHHHHHHHHHHhCHH
Confidence            35889999999998765  689999999999999766555555555443  6899999999998866 4554443221 1


Q ss_pred             ceEEEEEc----CCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          130 IQAHACVG----GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       130 ~~~~~~~~----~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                      ++- .+..    +....-..+... +-.+.++....      -..+.-..++++++||+|.+..
T Consensus        93 l~~-~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~S------~~~l~s~~~r~~~~DEvD~~p~  148 (557)
T PF05876_consen   93 LRR-KLSPSKSRDSGNTILYKRFP-GGFLYLVGANS------PSNLRSRPARYLLLDEVDRYPD  148 (557)
T ss_pred             HHH-HhCchhhcccCCchhheecC-CCEEEEEeCCC------CcccccCCcCEEEEechhhccc
Confidence            110 0111    111111112222 22333332211      1233446778999999999843

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=96.31  E-value=0.029  Score=53.64  Aligned_cols=125  Identities=18%  Similarity=0.130  Sum_probs=76.6

Q ss_pred             HHHHHHHHHhhcC-----CcEEEEcCCCCchHHHHHHHHHHh-hccC-----CCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           58 AIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQT-VDTS-----SREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        58 ~~Q~~~~~~~~~~-----~~~li~~pTG~GKT~~~~~~~~~~-~~~~-----~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      ..|...+-.....     +..|+.--.|-|||...+..++.+ ....     ......+++||+ .+..|+.+.+.+..+
T Consensus       135 ~~~~~~~~~~~~~~~~~~~ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~-s~~~qW~~elek~~~  213 (674)
T KOG1001|consen  135 LKQKYRWSLLKSREQQSLRGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPT-SLLTQWKTELEKVTE  213 (674)
T ss_pred             HHHHHHHHhhcccccCccccceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecch-HHHHHHHHHHhccCC
Confidence            4555555443322     457788889999997755444443 3222     134467888885 456777777766666


Q ss_pred             cCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc
Q 022383          127 FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (298)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~  191 (298)
                      ...+.+..++|..    .......+++|+++|+..+..    ..+..-..-.+|+||+|.+....
T Consensus       214 ~~~l~v~v~~gr~----kd~~el~~~dVVltTy~il~~----~~l~~i~w~Riildea~~ikn~~  270 (674)
T KOG1001|consen  214 EDKLSIYVYHGRT----KDKSELNSYDVVLTTYDILKN----SPLVKIKWLRIVLDEAHTIKNKD  270 (674)
T ss_pred             ccceEEEEecccc----cccchhcCCceEEeeHHHhhc----ccccceeEEEEEeccccccCCcc
Confidence            6566777777611    122233567899999977774    11111233469999999986554

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=96.30  E-value=0.074  Score=42.48  Aligned_cols=140  Identities=17%  Similarity=0.201  Sum_probs=77.6

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHH-HHHHHHHHhhccCCceEEEEEcCCc-----h
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT-QTEKVILAIGDFINIQAHACVGGKS-----V  141 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~-q~~~~~~~~~~~~~~~~~~~~~~~~-----~  141 (298)
                      ..+..+.+.+++|.|||.+++--++..+..   +.+|+++-=.+--.. -=...++++   .++.......+..     .
T Consensus        20 ~~~g~v~v~~g~GkGKtt~a~g~a~ra~g~---G~~V~ivQFlKg~~~~GE~~~l~~l---~~v~~~~~g~~~~~~~~~~   93 (191)
T PRK05986         20 EEKGLLIVHTGNGKGKSTAAFGMALRAVGH---GKKVGVVQFIKGAWSTGERNLLEFG---GGVEFHVMGTGFTWETQDR   93 (191)
T ss_pred             ccCCeEEEECCCCCChHHHHHHHHHHHHHC---CCeEEEEEEecCCCccCHHHHHhcC---CCcEEEECCCCCcccCCCc
Confidence            356789999999999998877666666655   446666643332110 111112221   1222222111100     0


Q ss_pred             HHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc--HHHHHHHHHhCCCCccEEEEEeeCchh
Q 022383          142 GEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHE  219 (298)
Q Consensus       142 ~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~~~~v~~SAT~~~~  219 (298)
                      .+...           .........+ ..+.-..+++||+||+-...+.++  ...+..+++..|...-+|+.--..|++
T Consensus        94 ~e~~~-----------~~~~~~~~a~-~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~  161 (191)
T PRK05986         94 ERDIA-----------AAREGWEEAK-RMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRE  161 (191)
T ss_pred             HHHHH-----------HHHHHHHHHH-HHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHH
Confidence            00000           0011111111 123346789999999988877774  567778888888777777766667777


Q ss_pred             HHHHHH
Q 022383          220 ILEMTT  225 (298)
Q Consensus       220 ~~~~~~  225 (298)
                      +.+...
T Consensus       162 Lie~AD  167 (191)
T PRK05986        162 LIEAAD  167 (191)
T ss_pred             HHHhCc
Confidence            666544

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.29  E-value=0.061  Score=44.50  Aligned_cols=52  Identities=15%  Similarity=0.149  Sum_probs=31.7

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .|..+++.|++|+|||......+.+.+..   +..+++++- .+...++.+..+.+
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~---g~~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRD---GDPVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEEc-cCCHHHHHHHHHHh
Confidence            46789999999999996544333333322   346777764 34445655554444

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.

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=96.24  E-value=0.15  Score=40.11  Aligned_cols=138  Identities=17%  Similarity=0.258  Sum_probs=66.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH-HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcC
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE-LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (298)
                      +.+-...|-|||.|++--++..+..   +.+|+++-=.+. --.   .....+....++....+-.+..........   
T Consensus         6 i~vytG~GKGKTTAAlGlalRA~G~---G~rV~ivQFlKg~~~~---GE~~~l~~l~~~~~~~~g~~f~~~~~~~~~---   76 (172)
T PF02572_consen    6 IQVYTGDGKGKTTAALGLALRAAGH---GMRVLIVQFLKGGRYS---GELKALKKLPNVEIERFGKGFVWRMNEEEE---   76 (172)
T ss_dssp             EEEEESSSS-HHHHHHHHHHHHHCT---T--EEEEESS--SS-----HHHHHHGGGT--EEEE--TT----GGGHHH---
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHhC---CCEEEEEEEecCCCCc---CHHHHHHhCCeEEEEEcCCcccccCCCcHH---
Confidence            4566789999999888777776655   557777765554 111   122222211123322211111000000000   


Q ss_pred             CcEEEeChHHHHHHHhc--cCccCCCccEEEechhhHhhcccc--HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHH
Q 022383          152 VHVVSGTPGRVCDMIKR--KTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (298)
Q Consensus       152 ~~ilV~Tp~~l~~~~~~--~~~~~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~  225 (298)
                       +     .......+..  ..+.-..+++||+||+-...+.++  ...+..+++..|...-+|+.--..|+.+.+...
T Consensus        77 -~-----~~~~~~~~~~a~~~i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~AD  148 (172)
T PF02572_consen   77 -D-----RAAAREGLEEAKEAISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAAD  148 (172)
T ss_dssp             -H-----HHHHHHHHHHHHHHTT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-S
T ss_pred             -H-----HHHHHHHHHHHHHHHhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhCC
Confidence             0     1111122221  233456889999999988877764  467778888888888888777777777766654

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.23  E-value=0.051  Score=49.74  Aligned_cols=89  Identities=19%  Similarity=0.224  Sum_probs=51.3

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      .|.-+++.|++|+|||.-.+..+.. ...  .+.+++|+.- .+...|+..+.++++...+                   
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~-~a~--~g~~vlYvs~-Ees~~qi~~ra~rlg~~~~-------------------  135 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAAR-LAA--AGGKVLYVSG-EESASQIKLRAERLGLPSD-------------------  135 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH-HHh--cCCeEEEEEc-cccHHHHHHHHHHcCCChh-------------------
Confidence            3467899999999999644333322 222  2447888874 4455677666655532111                   


Q ss_pred             hcCCcEEEeC---hHHHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          149 EHGVHVVSGT---PGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       149 ~~~~~ilV~T---p~~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                          ++.+..   .+.+...+..     .+.++||||+++.+..
T Consensus       136 ----~l~~~~e~~l~~i~~~i~~-----~~~~lVVIDSIq~l~~  170 (446)
T PRK11823        136 ----NLYLLAETNLEAILATIEE-----EKPDLVVIDSIQTMYS  170 (446)
T ss_pred             ----cEEEeCCCCHHHHHHHHHh-----hCCCEEEEechhhhcc
Confidence                122222   2333333332     3678999999998764

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.23  E-value=0.083  Score=41.53  Aligned_cols=53  Identities=21%  Similarity=0.454  Sum_probs=41.2

Q ss_pred             CCCccEEEechhhHhhcccc--HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHH
Q 022383          173 TRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~  225 (298)
                      -..+++||+||+-...+.++  ...+..+++..|+...+|+..-..|+.+.+...
T Consensus        95 ~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD  149 (173)
T TIGR00708        95 DPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELAD  149 (173)
T ss_pred             cCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCc
Confidence            46789999999988777764  466778888888888888877777877766554

Alternate name: corrinoid adenosyltransferase.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=96.23  E-value=0.013  Score=57.22  Aligned_cols=67  Identities=12%  Similarity=0.039  Sum_probs=59.3

Q ss_pred             CcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       152 ~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      ..|+++||..+..-+-.+.+++..+..+||||||++....-...+.++.+...+..-+.+|||.+..
T Consensus         8 ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~~   74 (814)
T TIGR00596         8 GGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPEA   74 (814)
T ss_pred             CCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCcc
Confidence            4899999999988888888999999999999999998777778888888888888889999999864

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

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.22  E-value=0.06  Score=48.57  Aligned_cols=40  Identities=10%  Similarity=0.224  Sum_probs=23.2

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .....++||||+|.+.... ...+...++..++...+|+.+
T Consensus       125 ~~~~kvvIIdea~~l~~~~-~~~LLk~LEep~~~t~~Il~t  164 (397)
T PRK14955        125 KGRYRVYIIDEVHMLSIAA-FNAFLKTLEEPPPHAIFIFAT  164 (397)
T ss_pred             cCCeEEEEEeChhhCCHHH-HHHHHHHHhcCCCCeEEEEEe
Confidence            3566899999999985433 233334444444444444443

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.22  E-value=0.08  Score=50.15  Aligned_cols=39  Identities=13%  Similarity=0.371  Sum_probs=25.4

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|.+.... ...+.+.++.-+....+|+.+
T Consensus       118 ~~~KVvIIdev~~Lt~~a-~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTNA-FNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             CCceEEEEEChhhCCHHH-HHHHHHHHHcCCCCeEEEEEe
Confidence            567899999999986443 344555555555555555544

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.19  E-value=0.07  Score=49.89  Aligned_cols=39  Identities=13%  Similarity=0.246  Sum_probs=26.3

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+..++||||+|.+.... ...+...++.-+....+|+.+
T Consensus       118 g~~kViIIDEa~~ls~~a-~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        118 GRYKVYLIDEVHMLSKQS-FNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             CCcEEEEEechhhccHHH-HHHHHHHHhcCCCCceEEEEE
Confidence            466899999999985543 445556666655566666655

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=96.19  E-value=0.13  Score=45.86  Aligned_cols=30  Identities=20%  Similarity=0.395  Sum_probs=19.8

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCC
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~  204 (298)
                      ...-.||+||+|.+..... ..+-.+++.-.
T Consensus       122 ~~~~IvvLDEid~L~~~~~-~~LY~L~r~~~  151 (366)
T COG1474         122 GKTVIVILDEVDALVDKDG-EVLYSLLRAPG  151 (366)
T ss_pred             CCeEEEEEcchhhhccccc-hHHHHHHhhcc
Confidence            3455899999999977753 44445554443

>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=96.18  E-value=0.0069  Score=49.44  Aligned_cols=17  Identities=24%  Similarity=0.438  Sum_probs=14.0

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      .++++.||.|.|||..+
T Consensus        51 ~h~lf~GPPG~GKTTLA   67 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLA   67 (233)
T ss_dssp             -EEEEESSTTSSHHHHH
T ss_pred             ceEEEECCCccchhHHH
Confidence            37999999999999543

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.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.17  E-value=0.049  Score=47.23  Aligned_cols=46  Identities=15%  Similarity=0.309  Sum_probs=26.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      ++++++.||+|+|||.... ++.+.+..  .+..+.++. ..+++.++..
T Consensus       156 ~~gl~L~G~~G~GKThLa~-Aia~~l~~--~g~~v~~~~-~~~l~~~lk~  201 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLA-AIANELAK--KGVSSTLLH-FPEFIRELKN  201 (306)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHH--cCCCEEEEE-HHHHHHHHHH
Confidence            4689999999999995432 33333332  233444443 2345555443

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.15  E-value=0.028  Score=60.22  Aligned_cols=63  Identities=32%  Similarity=0.420  Sum_probs=45.4

Q ss_pred             CCChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHH---HHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           54 EKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIA---LTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~---~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      ..+++.|..++..++.+  +-++|+|+.|+|||....   -++......  .+..++.++||..-+.++.
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~--~g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES--EQLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHHH
Confidence            35899999999998765  567889999999996541   223333332  2557888999977666654

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.15  E-value=0.063  Score=50.66  Aligned_cols=39  Identities=13%  Similarity=0.355  Sum_probs=25.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|.+.... ...+.+.++.-+....+|+.+
T Consensus       117 ~~~KVvIIDEah~Lt~~A-~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTAG-FNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             CCceEEEEECCCcCCHHH-HHHHHHHHhcCCCCeEEEEEe
Confidence            567899999999986553 334455555555555555554

>PRK04195 replication factor C large subunit; Provisional

Probab=96.14  E-value=0.051  Score=50.39  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      .+.+++.||+|+|||...
T Consensus        39 ~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            468999999999999654

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.14  E-value=0.058  Score=47.06  Aligned_cols=33  Identities=24%  Similarity=0.298  Sum_probs=24.5

Q ss_pred             ChHHHHHHHHHhh----cCC---cEEEEcCCCCchHHHHH
Q 022383           56 PSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        56 ~~~~Q~~~~~~~~----~~~---~~li~~pTG~GKT~~~~   88 (298)
                      .+|||+..|..+.    +|+   -.++.||.|.||+..+.
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~   42 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIR   42 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHH
Confidence            4688888887765    443   57799999999996543

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.13  E-value=0.08  Score=46.85  Aligned_cols=40  Identities=20%  Similarity=0.365  Sum_probs=26.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ....++||||+|.|.... ...+.+.++.-+.+..++++|.
T Consensus       140 g~~rVviIDeAd~l~~~a-anaLLk~LEEpp~~~~fiLit~  179 (351)
T PRK09112        140 GNWRIVIIDPADDMNRNA-ANAILKTLEEPPARALFILISH  179 (351)
T ss_pred             CCceEEEEEchhhcCHHH-HHHHHHHHhcCCCCceEEEEEC
Confidence            467899999999985443 4456666666555565666653

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=96.12  E-value=0.094  Score=48.68  Aligned_cols=19  Identities=21%  Similarity=0.324  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCCchHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~   89 (298)
                      +.++++||.|+|||.++.+
T Consensus        44 ~a~Lf~Gp~G~GKTT~Ari   62 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARI   62 (507)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            3689999999999976543

>PTZ00293 thymidine kinase; Provisional

Probab=96.12  E-value=0.056  Score=43.91  Aligned_cols=39  Identities=15%  Similarity=0.164  Sum_probs=25.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      |+-.++.||+++|||.-.+..+-+....   +.+++++-|..
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~y~~a---g~kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKRFTYS---EKKCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHHHHHc---CCceEEEEecc
Confidence            5567889999999996544443333222   34677777753

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.12  E-value=0.048  Score=51.72  Aligned_cols=39  Identities=21%  Similarity=0.370  Sum_probs=23.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|+|....+. .+.+.++.-+....+|+.+
T Consensus       123 g~~KV~IIDEvh~Ls~~a~N-aLLKtLEEPP~~~~fIL~T  161 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTAFN-AMLKTLEEPPEYLKFVLAT  161 (618)
T ss_pred             CCceEEEEEChhhCCHHHHH-HHHHhcccCCCCeEEEEEE
Confidence            46789999999998655432 3334444444445555544

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.11  E-value=0.21  Score=47.49  Aligned_cols=148  Identities=14%  Similarity=0.145  Sum_probs=80.8

Q ss_pred             ChHHHHHHHHHhh---cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC---
Q 022383           56 PSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN---  129 (298)
Q Consensus        56 ~~~~Q~~~~~~~~---~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~---  129 (298)
                      |+|.=.+-++.+.   +.+-.++.+|=|.|||.+..+.+...+..  .+.+++|.+|...-+.++++.++......+   
T Consensus       170 ~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le~lg~~~  247 (752)
T PHA03333        170 PSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVHAYQHKP  247 (752)
T ss_pred             CChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHHHhcccc
Confidence            4555555555544   45678889999999997765444433321  256899999999999999988877665322   


Q ss_pred             -----ceEEEEEcCCchHHHH--HHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHH
Q 022383          130 -----IQAHACVGGKSVGEDI--RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR  201 (298)
Q Consensus       130 -----~~~~~~~~~~~~~~~~--~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~  201 (298)
                           -.+....|+...-...  .... ++..+..++-.       .+...-...+++|+|||..+...    .+..++-
T Consensus       248 ~fp~~~~iv~vkgg~E~I~f~~p~gak~G~sti~F~Ars-------~~s~RG~~~DLLIVDEAAfI~~~----~l~aIlP  316 (752)
T PHA03333        248 WFPEEFKIVTLKGTDENLEYISDPAAKEGKTTAHFLASS-------PNAARGQNPDLVIVDEAAFVNPG----ALLSVLP  316 (752)
T ss_pred             ccCCCceEEEeeCCeeEEEEecCcccccCcceeEEeccc-------CCCcCCCCCCEEEEECcccCCHH----HHHHHHH
Confidence                 0111112211000000  0000 00122222111       12233345689999999887543    3334444


Q ss_pred             hCC-CCccEEEEEeeC
Q 022383          202 YLP-PDLQVVLISATL  216 (298)
Q Consensus       202 ~~~-~~~~~v~~SAT~  216 (298)
                      .+. .+.+++++|.+-
T Consensus       317 ~l~~~~~k~IiISS~~  332 (752)
T PHA03333        317 LMAVKGTKQIHISSPV  332 (752)
T ss_pred             HHccCCCceEEEeCCC
Confidence            433 356677778776

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.10  E-value=0.043  Score=49.07  Aligned_cols=47  Identities=21%  Similarity=0.420  Sum_probs=31.7

Q ss_pred             CccEEEechhhHhhcc-ccHHHHHHHHHhCC-CCccEEEEEeeCchhHH
Q 022383          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPHEIL  221 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~~~  221 (298)
                      ++++++||+++.+... ..+..+-.++..+. .+.|+++.|...|.++.
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~  223 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELN  223 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhc
Confidence            6789999999998554 34555556666655 34577777766666543

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.10  E-value=0.08  Score=50.94  Aligned_cols=67  Identities=24%  Similarity=0.295  Sum_probs=51.6

Q ss_pred             CChHHHHHHHHHhhcC-----CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           55 KPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~-----~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      .|+..|..++..+.++     +..++.|.+|+|||+.+.- ++...     +..+|||+|+...+.++++.++.+...
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia~-l~~~~-----~r~vLIVt~~~~~A~~l~~dL~~~~~~   83 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMAN-VIARL-----QRPTLVLAHNKTLAAQLYSEFKEFFPE   83 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHHH-HHHHh-----CCCEEEEECCHHHHHHHHHHHHHhcCC
Confidence            4999999999887532     2577999999999976442 32222     236899999999999999999888543

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=96.09  E-value=0.013  Score=47.90  Aligned_cols=39  Identities=21%  Similarity=0.347  Sum_probs=27.3

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      ..+-+.||+||||.|.+ +-+..+++..+..++..++.+.
T Consensus       111 ~grhKIiILDEADSMT~-gAQQAlRRtMEiyS~ttRFala  149 (333)
T KOG0991|consen  111 PGRHKIIILDEADSMTA-GAQQALRRTMEIYSNTTRFALA  149 (333)
T ss_pred             CCceeEEEeeccchhhh-HHHHHHHHHHHHHcccchhhhh
Confidence            36678999999999854 4466777777766665555443

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.09  E-value=0.049  Score=50.72  Aligned_cols=39  Identities=13%  Similarity=0.307  Sum_probs=27.2

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...+++||||+|.+.... ...+...+..-++...+|+.+
T Consensus       116 ~~~KVvIIDEad~Lt~~A-~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKEA-FNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             CCeEEEEEECcccCCHHH-HHHHHHHHhhcCCceEEEEEE
Confidence            567899999999986443 444556666666667666655

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.07  E-value=0.066  Score=47.10  Aligned_cols=33  Identities=15%  Similarity=0.169  Sum_probs=25.9

Q ss_pred             ChHHHHHHHHHhhc--C---CcEEEEcCCCCchHHHHH
Q 022383           56 PSAIQQRAVMPIIK--G---RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~--~---~~~li~~pTG~GKT~~~~   88 (298)
                      ++|||...|..+..  +   +-.++.||.|.||+..+.
T Consensus         2 ~yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~   39 (342)
T PRK06964          2 LYPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQ   39 (342)
T ss_pred             CCcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHH
Confidence            47899999988763  3   367899999999996544

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.01  E-value=0.13  Score=45.84  Aligned_cols=41  Identities=20%  Similarity=0.342  Sum_probs=27.0

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEee
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      ....++||||+|.+... -...+.+.++.-+....++++|..
T Consensus       140 ~~~kVviIDead~m~~~-aanaLLK~LEepp~~~~~IL~t~~  180 (365)
T PRK07471        140 GGWRVVIVDTADEMNAN-AANALLKVLEEPPARSLFLLVSHA  180 (365)
T ss_pred             CCCEEEEEechHhcCHH-HHHHHHHHHhcCCCCeEEEEEECC
Confidence            56789999999998433 345555666665555555555544

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.01  E-value=0.17  Score=47.97  Aligned_cols=40  Identities=13%  Similarity=0.339  Sum_probs=26.5

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      +.+.+++||||+|.+.... .+.+.+.++.-+....+|+.+
T Consensus       130 ~a~~KVvIIDEad~Ls~~a-~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        130 SARYKVYIIDEVHMLSTAA-FNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             cCCcEEEEEEChHhCCHHH-HHHHHHHHHhCCCCeEEEEEe
Confidence            3567899999999985433 344445555555666666655

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.01  E-value=0.052  Score=50.80  Aligned_cols=39  Identities=13%  Similarity=0.283  Sum_probs=25.6

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|.+.... ...+.+.++..+....+|+.+
T Consensus       118 ~~~kVvIIDEad~ls~~a-~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKSA-FNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             CCceEEEEcCcccCCHHH-HHHHHHHHhCCCCCEEEEEEe
Confidence            467899999999986543 334445555555566666655

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.99  E-value=0.084  Score=47.94  Aligned_cols=18  Identities=33%  Similarity=0.501  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      .++++.||+|+|||..+.
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            479999999999996543

>PHA00729 NTP-binding motif containing protein

Probab=95.98  E-value=0.043  Score=45.04  Aligned_cols=74  Identities=14%  Similarity=0.229  Sum_probs=38.0

Q ss_pred             cEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc-cH----HHHHHHHHhCCCCccEEEEEeeCchhHHHHHHh
Q 022383          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FK----DQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (298)
Q Consensus       153 ~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-~~----~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~  226 (298)
                      ..++.+.+.+...+....-...+.+++||||+=.-.... +.    .....+...+++.++++.+...-+..+...++.
T Consensus        60 ~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~  138 (226)
T PHA00729         60 NSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLRE  138 (226)
T ss_pred             cEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHHHHHHHh
Confidence            555566666666554321122356889999942211111 01    112223333344566777777766666666655

>PF05729 NACHT: NACHT domain

Probab=95.97  E-value=0.058  Score=41.73  Aligned_cols=38  Identities=29%  Similarity=0.548  Sum_probs=22.9

Q ss_pred             EEEechhhHhhccc-------cHHHHHHHHHh-CCCCccEEEEEee
Q 022383          178 LLVLDESDEMLSRG-------FKDQIYDVYRY-LPPDLQVVLISAT  215 (298)
Q Consensus       178 ~vViDE~h~~~~~~-------~~~~i~~i~~~-~~~~~~~v~~SAT  215 (298)
                      ++|+|-+|.+....       ....+..++.. .+++.++++.|.+
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~  129 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRP  129 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcC
Confidence            49999999886532       22345555555 4456666655544

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=95.97  E-value=0.024  Score=50.44  Aligned_cols=38  Identities=13%  Similarity=0.246  Sum_probs=23.5

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEE
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (298)
                      .+..++++||||||||.. +-.++..+.......+++.+
T Consensus       148 ~~GlilI~G~TGSGKTT~-l~al~~~i~~~~~~~~Ivti  185 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTL-AASIYQHCGETYPDRKIVTY  185 (372)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHHhcCCCceEEEE
Confidence            455789999999999954 34455555432222344444

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).

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=95.95  E-value=0.049  Score=47.85  Aligned_cols=33  Identities=21%  Similarity=0.305  Sum_probs=25.1

Q ss_pred             ChHHHHHHHHHhh----cCC---cEEEEcCCCCchHHHHH
Q 022383           56 PSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        56 ~~~~Q~~~~~~~~----~~~---~~li~~pTG~GKT~~~~   88 (298)
                      .+|||...|..+.    +|+   -.++.||.|.||+..+.
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~   42 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIY   42 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHH
Confidence            5688888887765    343   57899999999996544

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=95.95  E-value=0.061  Score=50.10  Aligned_cols=127  Identities=12%  Similarity=0.163  Sum_probs=81.1

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH-hhccCCce-EEEEEcCCchHHHHHHh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA-IGDFINIQ-AHACVGGKSVGEDIRKL  148 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~  148 (298)
                      |-.++.-|--.||| .++.|++..+..+-.+.++-|+++-+..++-+.+.+.. +.++.+-+ +...-            
T Consensus       203 kaTVFLVPRRHGKT-Wf~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~k------------  269 (668)
T PHA03372        203 KATVFLVPRRHGKT-WFIIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIENK------------  269 (668)
T ss_pred             cceEEEecccCCce-ehHHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeeec------------
Confidence            56788889999999 47888888887777788999999999887776655542 11222211 11110            


Q ss_pred             hcCCcEEEeChHH-----HHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCC-CCccEEEEEeeC
Q 022383          149 EHGVHVVSGTPGR-----VCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATL  216 (298)
Q Consensus       149 ~~~~~ilV~Tp~~-----l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-~~~~~v~~SAT~  216 (298)
                        +-.|.+.-|+.     +....+.+.+.-+..+++++||||-+-.    +.+..++..+. ++.++|++|.|-
T Consensus       270 --~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~~----~a~~tilgfm~q~~~KiIfISS~N  337 (668)
T PHA03372        270 --DNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIKK----DAFNTILGFLAQNTTKIIFISSTN  337 (668)
T ss_pred             --CcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccCH----HHHHHhhhhhcccCceEEEEeCCC
Confidence              11233322211     1122233566778899999999998743    44445555554 578899999885

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=95.95  E-value=0.28  Score=41.47  Aligned_cols=34  Identities=26%  Similarity=0.397  Sum_probs=23.3

Q ss_pred             CChHHHHHHHHHhh----cCC-cEEEEcCCCCchHHHHH
Q 022383           55 KPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~-~~li~~pTG~GKT~~~~   88 (298)
                      .+++.+.+++..+.    .+. .+++.||+|+|||....
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            35566666666543    333 68899999999996543

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=95.92  E-value=0.041  Score=52.93  Aligned_cols=45  Identities=20%  Similarity=0.322  Sum_probs=38.8

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      .+.-++|+|+-|.+.+.....-++.++++.|++...++.|-+-|+
T Consensus       128 ~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         128 EGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             cCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence            344699999999998888889999999999999999998887543

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.90  E-value=0.078  Score=50.18  Aligned_cols=21  Identities=19%  Similarity=0.333  Sum_probs=16.4

Q ss_pred             CcEEEEcCCCCchHHHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTV   91 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~   91 (298)
                      ..+++.||.|+|||.++...+
T Consensus        39 ha~Lf~GPpG~GKTtiArilA   59 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIFA   59 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            357899999999997765433

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.90  E-value=0.083  Score=52.95  Aligned_cols=44  Identities=23%  Similarity=0.361  Sum_probs=35.2

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCc
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLP  217 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~  217 (298)
                      ..--++|+|++|.+-+......+..+++..+.+..+|+.|-+.+
T Consensus       120 ~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~  163 (903)
T PRK04841        120 HQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLP  163 (903)
T ss_pred             CCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCC
Confidence            34568999999998555566788899999998898988887754

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.89  E-value=0.16  Score=45.21  Aligned_cols=36  Identities=19%  Similarity=0.196  Sum_probs=22.9

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      ++.++++||+|+|||....-.+......   +.++.++.
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l~~~---g~~V~lIt  241 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQLLKQ---NRTVGFIT  241 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEe
Confidence            5678999999999997655444332222   33555555

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=95.86  E-value=0.062  Score=50.68  Aligned_cols=20  Identities=30%  Similarity=0.373  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCCchHHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALT   90 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~   90 (298)
                      +-.+++||.|+|||.++-..
T Consensus        39 hayLf~Gp~GtGKTt~Ak~l   58 (559)
T PRK05563         39 HAYLFSGPRGTGKTSAAKIF   58 (559)
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            34788999999999776543

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.82  E-value=0.083  Score=49.11  Aligned_cols=16  Identities=25%  Similarity=0.378  Sum_probs=13.9

Q ss_pred             EEEEcCCCCchHHHHH
Q 022383           73 VIAQAQSGTGKTSMIA   88 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~   88 (298)
                      ++++||.|+|||.++.
T Consensus        39 ~Lf~GppGtGKTTlA~   54 (504)
T PRK14963         39 YLFSGPRGVGKTTTAR   54 (504)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5999999999997754

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.82  E-value=0.042  Score=47.13  Aligned_cols=20  Identities=30%  Similarity=0.451  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchHHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~   89 (298)
                      ++.++++||||+|||.....
T Consensus       194 ~~vi~~vGptGvGKTTt~~k  213 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAK  213 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            34788999999999976543

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.80  E-value=0.02  Score=50.31  Aligned_cols=45  Identities=20%  Similarity=0.334  Sum_probs=30.2

Q ss_pred             HHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           65 MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        65 ~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      ..+..+++++++||||||||.. +-.++..+..   ..+++.+=.+.|+
T Consensus       157 ~~v~~~~nilI~G~tGSGKTTl-l~aLl~~i~~---~~rivtiEd~~El  201 (344)
T PRK13851        157 ACVVGRLTMLLCGPTGSGKTTM-SKTLISAIPP---QERLITIEDTLEL  201 (344)
T ss_pred             HHHHcCCeEEEECCCCccHHHH-HHHHHcccCC---CCCEEEECCCccc
Confidence            3455789999999999999953 3445554433   3356666666665

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

Probab=95.79  E-value=0.023  Score=45.10  Aligned_cols=47  Identities=19%  Similarity=0.355  Sum_probs=26.2

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      .+++++++.||+|+|||..+.- +...+..  .+..++|+ +..+|...+.
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~a-i~~~~~~--~g~~v~f~-~~~~L~~~l~   91 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVA-IANEAIR--KGYSVLFI-TASDLLDELK   91 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHH-HHHHHHH--TT--EEEE-EHHHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHHHH-HHHHhcc--CCcceeEe-ecCceecccc
Confidence            3578999999999999965433 3333333  24455554 4555555543

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.

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=95.77  E-value=0.28  Score=43.35  Aligned_cols=145  Identities=18%  Similarity=0.175  Sum_probs=62.8

Q ss_pred             EEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH---HHHHhhcc-CCceEEEEEcCCchHHHHHHhh
Q 022383           74 IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK---VILAIGDF-INIQAHACVGGKSVGEDIRKLE  149 (298)
Q Consensus        74 li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~---~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  149 (298)
                      ++.++.|+|||.+....++..+...+....+++...+..+...+..   .+..+... ..............      +.
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~   74 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIASTYRQARDIFGRFWKGIIELLPSWFEIKFNEWNDRKII------LP   74 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEEESSHHHHHHHHHHHHHHHHTS-TTTS--EEEE-SSEEE------ET
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEecCHHHHHHHHHHhHHHHHHHHHHhcCcccccCCCCcEE------ec
Confidence            4789999999998877777766554433456666444444454333   33333322 12221111111000      13


Q ss_pred             cCCcEEEeChHHH--HHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeC--chhHHHHHH
Q 022383          150 HGVHVVSGTPGRV--CDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL--PHEILEMTT  225 (298)
Q Consensus       150 ~~~~ilV~Tp~~l--~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~--~~~~~~~~~  225 (298)
                      ++..|.+.+-..-  ..-++     -..++++++||+-.+.+..+...+......... ...+++|.|.  ......+..
T Consensus        75 nG~~i~~~~~~~~~~~~~~~-----G~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~~~-~~~~~~s~p~~~~~~~~~~~~  148 (384)
T PF03237_consen   75 NGSRIQFRGADSPDSGDNIR-----GFEYDLIIIDEAAKVPDDAFSELIRRLRATWGG-SIRMYISTPPNPGGWFYEIFQ  148 (384)
T ss_dssp             TS-EEEEES-----SHHHHH-----TS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT---EEEEEE---SSSHHHHHHH
T ss_pred             CceEEEEecccccccccccc-----ccccceeeeeecccCchHHHHHHHHhhhhcccC-cceEEeecCCCCCCceeeeee
Confidence            4556666553221  11112     257789999999877555445444444433332 2222445544  233344444


Q ss_pred             hcCCC
Q 022383          226 KFMTD  230 (298)
Q Consensus       226 ~~~~~  230 (298)
                      ....+
T Consensus       149 ~~~~~  153 (384)
T PF03237_consen  149 RNLDD  153 (384)
T ss_dssp             HHHCT
T ss_pred             hhhcC
Confidence            33333

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.74  E-value=0.058  Score=44.53  Aligned_cols=134  Identities=13%  Similarity=0.120  Sum_probs=65.9

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC-----ceEEEEEcCCchHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN-----IQAHACVGGKSVGE  143 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~-----~~~~~~~~~~~~~~  143 (298)
                      .|..+++.||+|+|||.-.+-.+.+.+...  +.+++|++ +.+-..++.+.++.++-...     -.............
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~--ge~vlyvs-~ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~~   94 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF--GEKVLYVS-FEEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIG   94 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH--T--EEEEE-SSS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--CCcEEEEE-ecCCHHHHHHHHHHcCCcHHHHhhcCCEEEEeccccccc
Confidence            457899999999999965554454544431  33677777 34445666666665531110     00111111100000


Q ss_pred             HHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc----ccHHHHHHHHHhCCCCccEEEEEeeC
Q 022383          144 DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       144 ~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~----~~~~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      .        .  -..++.+...+... +.-.+.+.+|||-...+...    .+...+..+...+...-.+.++++..
T Consensus        95 ~--------~--~~~~~~l~~~i~~~-i~~~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~~  160 (226)
T PF06745_consen   95 W--------S--PNDLEELLSKIREA-IEELKPDRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSEM  160 (226)
T ss_dssp             ---------T--SCCHHHHHHHHHHH-HHHHTSSEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEEE
T ss_pred             c--------c--ccCHHHHHHHHHHH-HHhcCCCEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEcc
Confidence            0        0  11223333333221 11113389999999887211    24556666666665444566666663

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 ....

>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=95.74  E-value=0.056  Score=45.69  Aligned_cols=138  Identities=18%  Similarity=0.227  Sum_probs=71.4

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc---HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT---RELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~---~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (298)
                      .|.=+++.|.+|.|||...+-.+.+.....  +..++|++.-   .+++..+......      +....+..+.-...+.
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~--~~~vly~SlEm~~~~l~~R~la~~s~------v~~~~i~~g~l~~~e~   89 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNG--GYPVLYFSLEMSEEELAARLLARLSG------VPYNKIRSGDLSDEEF   89 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTT--SSEEEEEESSS-HHHHHHHHHHHHHT------STHHHHHCCGCHHHHH
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhc--CCeEEEEcCCCCHHHHHHHHHHHhhc------chhhhhhccccCHHHH
Confidence            445688889999999966555555554432  3578888753   3443333332211      1111111121111211


Q ss_pred             H-------HhhcCCcEEE-e----ChHHHHHHHhccCccCCCccEEEechhhHhhcc----ccHHHHHHHHHhCC-----
Q 022383          146 R-------KLEHGVHVVS-G----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLP-----  204 (298)
Q Consensus       146 ~-------~~~~~~~ilV-~----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~----~~~~~i~~i~~~~~-----  204 (298)
                      .       .+. ...++| .    |++.+...++.-......+++||||-.|.+...    +....+..+.+.+.     
T Consensus        90 ~~~~~~~~~l~-~~~l~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~~  168 (259)
T PF03796_consen   90 ERLQAAAEKLS-DLPLYIEDTPSLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAKE  168 (259)
T ss_dssp             HHHHHHHHHHH-TSEEEEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh-hCcEEEECCCCCCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            1       222 234444 3    455666665543222378899999999998653    23344444433332     


Q ss_pred             CCccEEEEEee
Q 022383          205 PDLQVVLISAT  215 (298)
Q Consensus       205 ~~~~~v~~SAT  215 (298)
                      .++.++.+|..
T Consensus       169 ~~i~vi~~sQl  179 (259)
T PF03796_consen  169 LNIPVIALSQL  179 (259)
T ss_dssp             HTSEEEEEEEB
T ss_pred             cCCeEEEcccc
Confidence            25667776664

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 ....

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=95.73  E-value=0.032  Score=54.89  Aligned_cols=88  Identities=10%  Similarity=0.068  Sum_probs=57.2

Q ss_pred             ccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC--CCCcEEEEecchhh
Q 022383          207 LQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL--TITQAVIFCNTKRK  284 (298)
Q Consensus       207 ~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~--~~~k~lIf~~s~~~  284 (298)
                      .++-+||.|....-.++...|..+-..+..... ....+....+  ......|+.++...+...  .+.++||||+|++.
T Consensus       534 ~kLaGMTGTA~te~~Ef~~iY~L~Vv~IPTnrP-~~R~D~~d~v--y~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~  610 (1025)
T PRK12900        534 KKLAGMTGTAETEASEFFEIYKLDVVVIPTNKP-IVRKDMDDLV--YKTRREKYNAIVLKVEELQKKGQPVLVGTASVEV  610 (1025)
T ss_pred             hhhcccCCCChhHHHHHHHHhCCcEEECCCCCC-cceecCCCeE--ecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHH
Confidence            357899999877766666666443333222111 1111111122  233334888998888643  56799999999999


Q ss_pred             HHHHHHHHhhhcC
Q 022383          285 IYYSVFYFWIRWI  297 (298)
Q Consensus       285 ~~~l~~~L~~~~~  297 (298)
                      ++.++..|...|+
T Consensus       611 sE~Ls~~L~~~gI  623 (1025)
T PRK12900        611 SETLSRMLRAKRI  623 (1025)
T ss_pred             HHHHHHHHHHcCC
Confidence            9999999998886

>PRK10867 signal recognition particle protein; Provisional

Probab=95.70  E-value=0.16  Score=46.25  Aligned_cols=86  Identities=19%  Similarity=0.293  Sum_probs=42.6

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc--CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH---
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---  146 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~--p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  146 (298)
                      -++++|++|+|||....-.+......  .+.+++++.  +.+.-+.+   +++.++...++.+.....+.+......   
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~--~G~kV~lV~~D~~R~aa~e---QL~~~a~~~gv~v~~~~~~~dp~~i~~~a~  176 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKK--KKKKVLLVAADVYRPAAIE---QLKTLGEQIGVPVFPSGDGQDPVDIAKAAL  176 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHh--cCCcEEEEEccccchHHHH---HHHHHHhhcCCeEEecCCCCCHHHHHHHHH
Confidence            47889999999997655444332222  133555555  34443332   233344444666544322222222111   


Q ss_pred             -H-hhcCCc-EEEeChHHH
Q 022383          147 -K-LEHGVH-VVSGTPGRV  162 (298)
Q Consensus       147 -~-~~~~~~-ilV~Tp~~l  162 (298)
                       . ...+++ |+|=|++++
T Consensus       177 ~~a~~~~~DvVIIDTaGrl  195 (433)
T PRK10867        177 EEAKENGYDVVIVDTAGRL  195 (433)
T ss_pred             HHHHhcCCCEEEEeCCCCc
Confidence             1 123454 566787765

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.70  E-value=0.072  Score=49.44  Aligned_cols=88  Identities=24%  Similarity=0.319  Sum_probs=53.9

Q ss_pred             CCCH-HHHHHHHHCCCCCC----hHHHHHHHHHhh--cCCcEEEEcCCCCchHHHHHHHHHHhh---ccCCCCeEEEEEc
Q 022383           39 GIKD-DLLRGIYQYGFEKP----SAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTV---DTSSREVQALILS  108 (298)
Q Consensus        39 ~l~~-~i~~~l~~~~~~~~----~~~Q~~~~~~~~--~~~~~li~~pTG~GKT~~~~~~~~~~~---~~~~~~~~~lil~  108 (298)
                      ++.+ -+...|++.--.++    ...|.+-=+.+.  .++-++|+|..|||||.+++--+--.+   ...-.+..++++.
T Consensus       188 ~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~  267 (747)
T COG3973         188 GGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLG  267 (747)
T ss_pred             chHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEc
Confidence            4444 44456666433322    224444444444  346689999999999977554322222   2222233499999


Q ss_pred             CcHHHHHHHHHHHHHhhc
Q 022383          109 PTRELATQTEKVILAIGD  126 (298)
Q Consensus       109 p~~~l~~q~~~~~~~~~~  126 (298)
                      |.+-...-+.+.+=.++.
T Consensus       268 PN~vFleYis~VLPeLGe  285 (747)
T COG3973         268 PNRVFLEYISRVLPELGE  285 (747)
T ss_pred             CcHHHHHHHHHhchhhcc
Confidence            999999999888877654

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=95.69  E-value=0.058  Score=52.26  Aligned_cols=39  Identities=21%  Similarity=0.326  Sum_probs=23.5

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      +-.++++||+|.+.... ..   .++..+. +.+++++++|-++
T Consensus       109 ~~~IL~IDEIh~Ln~~q-Qd---aLL~~lE-~g~IiLI~aTTen  147 (725)
T PRK13341        109 KRTILFIDEVHRFNKAQ-QD---ALLPWVE-NGTITLIGATTEN  147 (725)
T ss_pred             CceEEEEeChhhCCHHH-HH---HHHHHhc-CceEEEEEecCCC
Confidence            45689999999974322 22   2333332 4567787777544

>TIGR00959 ffh signal recognition particle protein

Probab=95.63  E-value=0.18  Score=45.84  Aligned_cols=86  Identities=21%  Similarity=0.275  Sum_probs=43.2

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--cHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHH----H
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACVGGKSVGED----I  145 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  145 (298)
                      -++++|++|+|||....-.+.......  +.+++++.-  .+..+.+   +++.++...++.+.....+.+...-    .
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~--g~kV~lV~~D~~R~~a~~---QL~~~a~~~gvp~~~~~~~~~P~~i~~~al  175 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQ--GKKVLLVACDLYRPAAIE---QLKVLGQQVGVPVFALGKGQSPVEIARRAL  175 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhC--CCeEEEEeccccchHHHH---HHHHHHHhcCCceEecCCCCCHHHHHHHHH
Confidence            478999999999977554443322111  335665553  3443333   2333344445555443332222111    1


Q ss_pred             HH-hhcCCc-EEEeChHHH
Q 022383          146 RK-LEHGVH-VVSGTPGRV  162 (298)
Q Consensus       146 ~~-~~~~~~-ilV~Tp~~l  162 (298)
                      .. ..++++ |+|=||+++
T Consensus       176 ~~~~~~~~DvVIIDTaGr~  194 (428)
T TIGR00959       176 EYAKENGFDVVIVDTAGRL  194 (428)
T ss_pred             HHHHhcCCCEEEEeCCCcc
Confidence            11 134454 667787754

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.62  E-value=0.12  Score=43.11  Aligned_cols=41  Identities=20%  Similarity=0.202  Sum_probs=26.6

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      +..|.-+++.|++|+|||...+--+.+.....  +..++|++.
T Consensus        10 l~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~--g~~vly~s~   50 (242)
T cd00984          10 LQPGDLIIIAARPSMGKTAFALNIAENIAKKQ--GKPVLFFSL   50 (242)
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCceEEEeC
Confidence            34567889999999999955443344433321  446778773

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.

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

Probab=95.58  E-value=0.02  Score=48.53  Aligned_cols=25  Identities=12%  Similarity=0.364  Sum_probs=17.6

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhcc
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDT   97 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~   97 (298)
                      =++|.||||||||.. +-++++.+..
T Consensus       127 LILVTGpTGSGKSTT-lAamId~iN~  151 (353)
T COG2805         127 LILVTGPTGSGKSTT-LAAMIDYINK  151 (353)
T ss_pred             eEEEeCCCCCcHHHH-HHHHHHHHhc
Confidence            378899999999955 3345555544

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.57  E-value=0.11  Score=43.94  Aligned_cols=38  Identities=16%  Similarity=0.112  Sum_probs=25.8

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      .|.-++|.|++|+|||.-.+-.+.+....   +.+++|++-
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~---Ge~vlyis~   72 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASR---GNPVLFVTV   72 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhC---CCcEEEEEe
Confidence            45678999999999996544444443322   457788773

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.56  E-value=0.059  Score=47.30  Aligned_cols=44  Identities=18%  Similarity=0.374  Sum_probs=28.6

Q ss_pred             HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      .+..+++++|+|+||||||.. +-.++..+..   ..+++.+=-+.|+
T Consensus       156 ~v~~~~nili~G~tgSGKTTl-l~aL~~~ip~---~~ri~tiEd~~El  199 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKTTF-TNAALREIPA---IERLITVEDAREI  199 (332)
T ss_pred             HHHcCCcEEEECCCCCCHHHH-HHHHHhhCCC---CCeEEEecCCCcc
Confidence            345789999999999999953 4455555533   3355554444443

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.56  E-value=0.17  Score=45.09  Aligned_cols=92  Identities=15%  Similarity=0.194  Sum_probs=50.4

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      .|.-+++.|++|+|||...+..+.. +..  .+.+++|+.-. +...|+..+.++++-..  .-..+...          
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~-~a~--~g~~VlYvs~E-Es~~qi~~Ra~rlg~~~--~~l~l~~e----------  144 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAAR-LAK--RGGKVLYVSGE-ESPEQIKLRADRLGIST--ENLYLLAE----------  144 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH-HHh--cCCeEEEEECC-cCHHHHHHHHHHcCCCc--ccEEEEcc----------
Confidence            3567899999999999654433322 222  23478888653 44566666555543111  00111111          


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                              ...+.+...+..     .+.++||||+++.+..
T Consensus       145 --------~~le~I~~~i~~-----~~~~lVVIDSIq~l~~  172 (372)
T cd01121         145 --------TNLEDILASIEE-----LKPDLVIIDSIQTVYS  172 (372)
T ss_pred             --------CcHHHHHHHHHh-----cCCcEEEEcchHHhhc
Confidence                    112334443332     3678999999998753

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.56  E-value=0.25  Score=44.54  Aligned_cols=126  Identities=13%  Similarity=0.143  Sum_probs=62.3

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc--CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~--p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      .-++++||+|+|||......+......  .+.++.++.  +.+..+..   .++.++...++.....             
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~--~G~~V~Lit~Dt~R~aA~e---QLk~yAe~lgvp~~~~-------------  285 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLH--MGKSVSLYTTDNYRIAAIE---QLKRYADTMGMPFYPV-------------  285 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHh--cCCeEEEecccchhhhHHH---HHHHHHHhcCCCeeeh-------------
Confidence            347899999999997765444333222  133455554  33333332   3333333334332110             


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc-cccHHHHHHHHHhCC---CCccEEEEEeeCch-hHHHH
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRYLP---PDLQVVLISATLPH-EILEM  223 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~-~~~~~~i~~i~~~~~---~~~~~v~~SAT~~~-~~~~~  223 (298)
                              ..+..+...+.     -.+.++|+||=+-.... ......+..+++...   +.-.++.+|||... .+...
T Consensus       286 --------~~~~~l~~~l~-----~~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~  352 (432)
T PRK12724        286 --------KDIKKFKETLA-----RDGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTV  352 (432)
T ss_pred             --------HHHHHHHHHHH-----hCCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHH
Confidence                    01222233332     14568899996543321 123344455555432   22356788999866 44555


Q ss_pred             HHhc
Q 022383          224 TTKF  227 (298)
Q Consensus       224 ~~~~  227 (298)
                      ...+
T Consensus       353 ~~~f  356 (432)
T PRK12724        353 LKAY  356 (432)
T ss_pred             HHHh
Confidence            4444

>PRK04328 hypothetical protein; Provisional

Probab=95.54  E-value=0.16  Score=42.74  Aligned_cols=53  Identities=15%  Similarity=0.213  Sum_probs=34.2

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      .|..+++.|++|+|||.-.+-.+.+.+..   +..++|++ +.+-..++.+.++.++
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~---ge~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEE-eeCCHHHHHHHHHHcC
Confidence            45778999999999996544444444433   44567766 5555666666666553

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=95.54  E-value=0.24  Score=39.11  Aligned_cols=136  Identities=14%  Similarity=0.179  Sum_probs=75.6

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH-HHHHHhhccCCceEEEEEcCC-----chH-HH
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE-KVILAIGDFINIQAHACVGGK-----SVG-ED  144 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~-~~~~~~~~~~~~~~~~~~~~~-----~~~-~~  144 (298)
                      -+.|-...|-|||.+++--++..+..   +.+++|+-=.+.-..+=. ..++++   .++.......+.     ... +.
T Consensus        23 li~VYtGdGKGKTTAAlGlalRAaG~---G~rV~iiQFlKg~~~~GE~~~l~~~---~~v~~~~~g~~~~~~~~~~~~~~   96 (178)
T PRK07414         23 LVQVFTSSQRNFFTSVMAQALRIAGQ---GTPVLIVQFLKGGIQQGPDRPIQLG---QNLDWVRCDLPRCLDTPHLDESE   96 (178)
T ss_pred             EEEEEeCCCCCchHHHHHHHHHHhcC---CCEEEEEEEecCCCcchHHHHHHhC---CCcEEEECCCCCeeeCCCcCHHH
Confidence            35666889999999988777776655   557777654443211111 111221   122222211110     000 00


Q ss_pred             HHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc--HHHHHHHHHhCCCCccEEEEEeeCchhHHH
Q 022383          145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILE  222 (298)
Q Consensus       145 ~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~  222 (298)
                      ...           .+......+ ..+.-..+++||+||+-...+.++  ...+..+++..|....+|+.--..|+.+.+
T Consensus        97 ~~~-----------~~~~~~~a~-~~l~~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie  164 (178)
T PRK07414         97 KKA-----------LQELWQYTQ-AVVDEGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLA  164 (178)
T ss_pred             HHH-----------HHHHHHHHH-HHHhCCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHH
Confidence            000           011111111 123346789999999988877774  567778888888888888777777877666


Q ss_pred             HHH
Q 022383          223 MTT  225 (298)
Q Consensus       223 ~~~  225 (298)
                      ...
T Consensus       165 ~AD  167 (178)
T PRK07414        165 IAD  167 (178)
T ss_pred             hCC
Confidence            543

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=95.53  E-value=0.16  Score=45.66  Aligned_cols=41  Identities=15%  Similarity=0.367  Sum_probs=25.2

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEee
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      .+.+++||||+|.|.... .+.+.+.++.-+++..+|+.|.+
T Consensus       116 ~~~kViiIDead~m~~~a-anaLLk~LEep~~~~~fIL~a~~  156 (394)
T PRK07940        116 GRWRIVVIEDADRLTERA-ANALLKAVEEPPPRTVWLLCAPS  156 (394)
T ss_pred             CCcEEEEEechhhcCHHH-HHHHHHHhhcCCCCCeEEEEECC
Confidence            467899999999995443 34455555554445444444433

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.50  E-value=0.13  Score=48.21  Aligned_cols=57  Identities=23%  Similarity=0.331  Sum_probs=38.6

Q ss_pred             CCccccCcccCCCCHHHHHHHHH---CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           28 GVEAITSFDAMGIKDDLLRGIYQ---YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        28 ~~~~~~~~~~l~l~~~i~~~l~~---~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      ...+..+|++.|=-++++..|++   +...+|-.+....   +..-+.+++.||.|+|||+.+
T Consensus       426 ve~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~G---i~ppkGVLlyGPPGC~KT~lA  485 (693)
T KOG0730|consen  426 VEMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFG---ISPPKGVLLYGPPGCGKTLLA  485 (693)
T ss_pred             ccCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhc---CCCCceEEEECCCCcchHHHH
Confidence            34455699999877788888775   2333444333332   234588999999999999764

>PRK06904 replicative DNA helicase; Validated

Probab=95.49  E-value=0.33  Score=44.81  Aligned_cols=143  Identities=18%  Similarity=0.161  Sum_probs=70.4

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-Ec-CCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VG-GKSVGED  144 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~  144 (298)
                      +..|.=+++-|.+|+|||.-.+-.+.+....  .+..++|++. .--..|+..++-....  ++....+ .| ..+..+.
T Consensus       218 l~~G~LiiIaarPg~GKTafalnia~~~a~~--~g~~Vl~fSl-EMs~~ql~~Rlla~~s--~v~~~~i~~g~~l~~~e~  292 (472)
T PRK06904        218 LQPSDLIIVAARPSMGKTTFAMNLCENAAMA--SEKPVLVFSL-EMPAEQIMMRMLASLS--RVDQTKIRTGQNLDQQDW  292 (472)
T ss_pred             cCCCcEEEEEeCCCCChHHHHHHHHHHHHHh--cCCeEEEEec-cCCHHHHHHHHHHhhC--CCCHHHhccCCCCCHHHH
Confidence            4445567778999999996433233322222  1335666653 2334555554433222  2222111 22 2222221


Q ss_pred             ------HHHhhcCCcEEE-----eChHHHHHHHhccCccCCCccEEEechhhHhhccc----cHHHHHHHHHhCC-----
Q 022383          145 ------IRKLEHGVHVVS-----GTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----  204 (298)
Q Consensus       145 ------~~~~~~~~~ilV-----~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~----~~~~i~~i~~~~~-----  204 (298)
                            ...+....++.|     .|+..+...++........+++||||-.+.+...+    ....+..+.+.+.     
T Consensus       293 ~~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAke  372 (472)
T PRK06904        293 AKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSLKALAKE  372 (472)
T ss_pred             HHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence                  112223445666     35556655444321112358999999999885332    2233444444432     


Q ss_pred             CCccEEEEEe
Q 022383          205 PDLQVVLISA  214 (298)
Q Consensus       205 ~~~~~v~~SA  214 (298)
                      .+++++++|.
T Consensus       373 l~ipVi~lsQ  382 (472)
T PRK06904        373 LKVPVVALSQ  382 (472)
T ss_pred             hCCeEEEEEe
Confidence            2677777763

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.47  E-value=0.039  Score=48.88  Aligned_cols=27  Identities=15%  Similarity=0.398  Sum_probs=19.9

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~   96 (298)
                      .+.-++++||||||||... -.++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            5678999999999999643 34555553

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.

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

Probab=95.46  E-value=0.097  Score=48.14  Aligned_cols=83  Identities=18%  Similarity=0.181  Sum_probs=63.0

Q ss_pred             HHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHH
Q 022383           88 ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVC  163 (298)
Q Consensus        88 ~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~  163 (298)
                      +..++..+. +..+.++||.|-|+.-|+++...++..    ++++..+||+.+..+....+.    +.+.|+|+|.    
T Consensus       329 l~~lL~~~~-~~~~~KvIIFc~tkr~~~~l~~~l~~~----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATd----  399 (519)
T KOG0331|consen  329 LGKLLEDIS-SDSEGKVIIFCETKRTCDELARNLRRK----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATD----  399 (519)
T ss_pred             HHHHHHHHh-ccCCCcEEEEecchhhHHHHHHHHHhc----CcceeeecccccHHHHHHHHHhcccCCcceEEEcc----
Confidence            444555554 334568999999999999999988765    478899999998887765553    5789999996    


Q ss_pred             HHHhccCccCCCccEEEe
Q 022383          164 DMIKRKTLRTRAIKLLVL  181 (298)
Q Consensus       164 ~~~~~~~~~~~~l~~vVi  181 (298)
                        +-.+.+++.++++||-
T Consensus       400 --VAaRGLDi~dV~lVIn  415 (519)
T KOG0331|consen  400 --VAARGLDVPDVDLVIN  415 (519)
T ss_pred             --cccccCCCccccEEEe
Confidence              2235788889999884

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.43  E-value=0.19  Score=47.80  Aligned_cols=38  Identities=16%  Similarity=0.292  Sum_probs=22.1

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      ...++|||||+|.+.... ...+...+..-+....+|+.
T Consensus       119 ~~~kVvIIDEa~~L~~~a-~naLLk~LEepp~~tv~Il~  156 (585)
T PRK14950        119 ARYKVYIIDEVHMLSTAA-FNALLKTLEEPPPHAIFILA  156 (585)
T ss_pred             CCeEEEEEeChHhCCHHH-HHHHHHHHhcCCCCeEEEEE
Confidence            567899999999985433 23333444444444434443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=95.41  E-value=0.16  Score=47.81  Aligned_cols=39  Identities=10%  Similarity=0.238  Sum_probs=23.0

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...+++||||+|.|.... ...+...++.-+...-+|+++
T Consensus       118 ~~~KVIIIDEad~Lt~~A-~NaLLKtLEEPp~~tvfIL~T  156 (605)
T PRK05896        118 FKYKVYIIDEAHMLSTSA-WNALLKTLEEPPKHVVFIFAT  156 (605)
T ss_pred             CCcEEEEEechHhCCHHH-HHHHHHHHHhCCCcEEEEEEC
Confidence            356789999999985432 334444555544444444444

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.39  E-value=0.32  Score=42.09  Aligned_cols=130  Identities=16%  Similarity=0.273  Sum_probs=68.7

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--cHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHHHHHh
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDIRKL  148 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  148 (298)
                      -++++|-.|+|||....-.+.... .  .+.++++.+-  .|+=+.++   ++.+++..++.+..- .|+.+...-...+
T Consensus       141 Vil~vGVNG~GKTTTIaKLA~~l~-~--~g~~VllaA~DTFRAaAiEQ---L~~w~er~gv~vI~~~~G~DpAaVafDAi  214 (340)
T COG0552         141 VILFVGVNGVGKTTTIAKLAKYLK-Q--QGKSVLLAAGDTFRAAAIEQ---LEVWGERLGVPVISGKEGADPAAVAFDAI  214 (340)
T ss_pred             EEEEEecCCCchHhHHHHHHHHHH-H--CCCeEEEEecchHHHHHHHH---HHHHHHHhCCeEEccCCCCCcHHHHHHHH
Confidence            378889999999977543332222 2  2446666664  44544443   344555567776552 3333332222111


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCCCCc------cEEEEEeeCchhHH
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDL------QVVLISATLPHEIL  221 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~~~~------~~v~~SAT~~~~~~  221 (298)
                      .                  .  -.-+++++|++|=|-++... +....+.++.+-..+..      -++.+-||......
T Consensus       215 ~------------------~--Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqnal  274 (340)
T COG0552         215 Q------------------A--AKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNAL  274 (340)
T ss_pred             H------------------H--HHHcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhHH
Confidence            1                  0  11235566666666655433 35566666666555433      24444899876555


Q ss_pred             HHHHhc
Q 022383          222 EMTTKF  227 (298)
Q Consensus       222 ~~~~~~  227 (298)
                      ...+.+
T Consensus       275 ~QAk~F  280 (340)
T COG0552         275 SQAKIF  280 (340)
T ss_pred             HHHHHH
Confidence            544443

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=95.39  E-value=0.063  Score=45.59  Aligned_cols=50  Identities=22%  Similarity=0.373  Sum_probs=33.7

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCC-------CCccEEEEEeeCchhHHHHHH
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLP-------PDLQVVLISATLPHEILEMTT  225 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-------~~~~~v~~SAT~~~~~~~~~~  225 (298)
                      .=.++|+||+|.|. .+..+.+.-.+++.+       ...-+|++|-+-...+.+...
T Consensus       178 ~rslFIFDE~DKmp-~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~aL  234 (344)
T KOG2170|consen  178 QRSLFIFDEVDKLP-PGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIAL  234 (344)
T ss_pred             CCceEEechhhhcC-HhHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHHH
Confidence            33689999999984 456666666666654       244578899877665554433

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=95.35  E-value=0.11  Score=46.78  Aligned_cols=53  Identities=21%  Similarity=0.375  Sum_probs=28.9

Q ss_pred             ccCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           32 ITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      ..+|++++-.+...+.+.+.   .+..+..++..   .+...+.+++.||+|+|||..+
T Consensus       127 ~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~---g~~~p~gvLL~GppGtGKT~lA  182 (389)
T PRK03992        127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEV---GIEPPKGVLLYGPPGTGKTLLA  182 (389)
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCCceEEECCCCCChHHHH
Confidence            45677776444444444442   11222211111   1123468999999999999653

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=95.35  E-value=0.15  Score=46.38  Aligned_cols=144  Identities=19%  Similarity=0.212  Sum_probs=68.9

Q ss_pred             HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGED  144 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  144 (298)
                      -+..|.-+++.|++|+|||.-.+-.+.+....  .+..++|++. .--..|+..++-...  .++....+ .|.....+.
T Consensus       190 G~~~g~liviag~pg~GKT~~al~ia~~~a~~--~g~~v~~fSl-Em~~~~l~~Rl~~~~--~~v~~~~~~~~~l~~~~~  264 (421)
T TIGR03600       190 GLVKGDLIVIGARPSMGKTTLALNIAENVALR--EGKPVLFFSL-EMSAEQLGERLLASK--SGINTGNIRTGRFNDSDF  264 (421)
T ss_pred             CCCCCceEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEEC-CCCHHHHHHHHHHHH--cCCCHHHHhcCCCCHHHH
Confidence            34456778889999999995544333333212  1345677762 223444444433221  12222111 222222111


Q ss_pred             ------HHHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhcc---ccHHHHHHHHHhCC-----C
Q 022383          145 ------IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR---GFKDQIYDVYRYLP-----P  205 (298)
Q Consensus       145 ------~~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~---~~~~~i~~i~~~~~-----~  205 (298)
                            ...+. +.++.|.     |++.+...++.-......+++||||=.+.+...   .....+..+.+.+.     .
T Consensus       265 ~~~~~~~~~l~-~~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~~~~~~~~~~~~~i~~~Lk~lAke~  343 (421)
T TIGR03600       265 NRLLNAVDRLS-EKDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAPTRGRDRNEELGGISRGLKALAKEL  343 (421)
T ss_pred             HHHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence                  11222 2355553     344555444432112236899999999888531   12223333333322     2


Q ss_pred             CccEEEEEee
Q 022383          206 DLQVVLISAT  215 (298)
Q Consensus       206 ~~~~v~~SAT  215 (298)
                      ++.++++|..
T Consensus       344 ~i~Vi~lsQl  353 (421)
T TIGR03600       344 DVPVVLLAQL  353 (421)
T ss_pred             CCcEEEeccc
Confidence            5667776654

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.

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=95.35  E-value=0.073  Score=50.40  Aligned_cols=108  Identities=21%  Similarity=0.273  Sum_probs=62.7

Q ss_pred             ChHHHHHHHHHhh--------cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           56 PSAIQQRAVMPII--------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        56 ~~~~Q~~~~~~~~--------~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      +-..-.+++..+.        +|.-+.++||+|.|||..                           +..+++.+.+-   
T Consensus       328 LekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSL---------------------------gkSIA~al~Rk---  377 (782)
T COG0466         328 LEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSL---------------------------GKSIAKALGRK---  377 (782)
T ss_pred             chhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhH---------------------------HHHHHHHhCCC---
Confidence            4555555555443        356788899999999932                           33333322110   


Q ss_pred             CCceEEEEEcCCchHHHHHHhhcCCcEEEe-ChHHHHHHHhc-cCccCCCccEEEechhhHhhccccHHHHHHHHHhC
Q 022383          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSG-TPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (298)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~-Tp~~l~~~~~~-~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~  203 (298)
                         -+-...||.....+   +.+.-+=+|| -|+++..-+.. +..+.    ++++||+|.|.+...++.--.++.-+
T Consensus       378 ---fvR~sLGGvrDEAE---IRGHRRTYIGamPGrIiQ~mkka~~~NP----v~LLDEIDKm~ss~rGDPaSALLEVL  445 (782)
T COG0466         378 ---FVRISLGGVRDEAE---IRGHRRTYIGAMPGKIIQGMKKAGVKNP----VFLLDEIDKMGSSFRGDPASALLEVL  445 (782)
T ss_pred             ---EEEEecCccccHHH---hccccccccccCChHHHHHHHHhCCcCC----eEEeechhhccCCCCCChHHHHHhhc
Confidence               12223455443332   2222245555 59999988876 44444    89999999998775555444555444

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.34  E-value=0.18  Score=48.05  Aligned_cols=40  Identities=10%  Similarity=0.252  Sum_probs=23.4

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...-+++||||+|.+.... .+.+...++.-+...-+|+++
T Consensus       125 ~~~~KVvIIdEad~Lt~~a-~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        125 KGRYRVYIIDEVHMLSTAA-FNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             cCCCEEEEEeChhhcCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            3567899999999985433 233444444444444444444

>TIGR00767 rho transcription termination factor Rho

Probab=95.33  E-value=0.2  Score=44.77  Aligned_cols=31  Identities=26%  Similarity=0.344  Sum_probs=22.0

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccC
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS   98 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~   98 (298)
                      +-.|+-+.++||+|+|||.. +..+.+.+..+
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL-~~~i~~~I~~n  195 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVL-LQKIAQAITRN  195 (415)
T ss_pred             eCCCCEEEEECCCCCChhHH-HHHHHHhhccc
Confidence            34789999999999999964 33344544443

Members of this family differ in the specificity of RNA binding.

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

Probab=95.33  E-value=0.031  Score=52.37  Aligned_cols=41  Identities=22%  Similarity=0.310  Sum_probs=33.4

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhh
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTV   95 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~   95 (298)
                      .|+.+|.+.+..+.    +|+-.|+..|||+|||+..+-..+..+
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL   59 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWL   59 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHH
Confidence            48999998877654    789999999999999988766666654

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=95.32  E-value=0.14  Score=46.18  Aligned_cols=55  Identities=24%  Similarity=0.252  Sum_probs=34.6

Q ss_pred             ccccCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           30 EAITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .|..+|++++-.+..++.+++.   .+..+..++..-   +...+.+++.||+|+|||...
T Consensus       139 ~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~G---l~~pkgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        139 KPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIG---IDPPRGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             CCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcC---CCCCceEEEECCCCCCHHHHH
Confidence            4556888887666666666553   223232222211   235688999999999999653

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.32  E-value=0.11  Score=50.96  Aligned_cols=53  Identities=19%  Similarity=0.310  Sum_probs=31.0

Q ss_pred             cccCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~   86 (298)
                      +..+|++++-....++.++++   .+.++..++..   .+..++.+++.||+|+|||..
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~---gi~~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHL---GIEPPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCceEEEECCCCCChHHH
Confidence            345778876555555555543   11211111111   123568899999999999954

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=95.30  E-value=0.7  Score=36.25  Aligned_cols=17  Identities=29%  Similarity=0.425  Sum_probs=13.8

Q ss_pred             EEEEcCCCCchHHHHHH
Q 022383           73 VIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~   89 (298)
                      +++.|++|+|||.....
T Consensus         3 ~~~~G~~G~GKTt~~~~   19 (173)
T cd03115           3 ILLVGLQGVGKTTTAAK   19 (173)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            57889999999976543

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=95.28  E-value=0.32  Score=38.52  Aligned_cols=142  Identities=16%  Similarity=0.247  Sum_probs=73.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHH-HHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcC
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA-TQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~-~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (298)
                      ++|....|-|||.+++-.++..+..   +.++.|+-=.+--. .--...+.++.  ..+....+..+.....+...    
T Consensus        31 i~V~TG~GKGKTTAAlG~alRa~Gh---G~rv~vvQFiKg~~~~GE~~~~~~~~--~~v~~~~~~~g~tw~~~~~~----  101 (198)
T COG2109          31 IIVFTGNGKGKTTAALGLALRALGH---GLRVGVVQFIKGGWKYGEEAALEKFG--LGVEFHGMGEGFTWETQDRE----  101 (198)
T ss_pred             EEEEecCCCChhHHHHHHHHHHhcC---CCEEEEEEEeecCcchhHHHHHHhhc--cceeEEecCCceeCCCcCcH----
Confidence            6777889999999988888877765   44555554222110 11111222221  11221111111111100000    


Q ss_pred             CcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc--HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHh
Q 022383          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (298)
Q Consensus       152 ~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~  226 (298)
                      .++  ..+........ ..+.-..+++||+||+...+..++  .+.+..+++..|....+|+.--..|+.+.+....
T Consensus       102 ~d~--~aa~~~w~~a~-~~l~~~~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~~~~vIiTGr~ap~~lie~ADl  175 (198)
T COG2109         102 ADI--AAAKAGWEHAK-EALADGKYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGRGAPPELIELADL  175 (198)
T ss_pred             HHH--HHHHHHHHHHH-HHHhCCCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHHHHH
Confidence            011  11111111111 122234789999999998877775  4667778888777777777666667776665543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.26  E-value=0.14  Score=50.21  Aligned_cols=54  Identities=19%  Similarity=0.225  Sum_probs=31.6

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH--hhcCCcEEEEcCCCCchHHHH
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP--IIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~--~~~~~~~li~~pTG~GKT~~~   87 (298)
                      ..+|++++..+.+++.|.+. +..+..++ +.+..  +...+.+++.||+|+|||..+
T Consensus       449 ~~~~~di~g~~~~k~~l~~~-v~~~~~~~-~~~~~~g~~~~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       449 NVRWSDIGGLEEVKQELREA-VEWPLKHP-EIFEKMGIRPPKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             ccchhhcccHHHHHHHHHHH-HHhhhhCH-HHHHhcCCCCCceEEEECCCCCCHHHHH
Confidence            44777777777777777663 11111111 11211  223467999999999999653

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=95.25  E-value=0.16  Score=47.86  Aligned_cols=38  Identities=11%  Similarity=0.296  Sum_probs=22.1

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL  211 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~  211 (298)
                      ..+.+++||||+|.+.... .+.+...++.-+...-+|+
T Consensus       117 ~~~~KVvIIDEa~~Ls~~a-~naLLK~LEepp~~~vfI~  154 (563)
T PRK06647        117 SSRYRVYIIDEVHMLSNSA-FNALLKTIEEPPPYIVFIF  154 (563)
T ss_pred             cCCCEEEEEEChhhcCHHH-HHHHHHhhccCCCCEEEEE
Confidence            3577899999999985432 2333344444333343443

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

Probab=95.22  E-value=0.053  Score=49.39  Aligned_cols=41  Identities=17%  Similarity=0.340  Sum_probs=29.1

Q ss_pred             hHHHHHHHHHhhcCC--cEEEEcCCCCchHHHHHHHHHHhhccC
Q 022383           57 SAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTVCQTVDTS   98 (298)
Q Consensus        57 ~~~Q~~~~~~~~~~~--~~li~~pTG~GKT~~~~~~~~~~~~~~   98 (298)
                      .+.|...+..+.+..  =+++.||||||||.. +..+++.+...
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            567777777776553  478889999999965 44566665554

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.21  E-value=0.043  Score=51.52  Aligned_cols=20  Identities=30%  Similarity=0.546  Sum_probs=17.2

Q ss_pred             hhcCCcEEEEcCCCCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~   86 (298)
                      +..|+-+.++||+|+|||..
T Consensus       358 i~~G~~vaIvG~SGsGKSTL  377 (529)
T TIGR02868       358 LPPGERVAILGPSGSGKSTL  377 (529)
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34789999999999999963

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=95.19  E-value=0.46  Score=42.23  Aligned_cols=109  Identities=16%  Similarity=0.176  Sum_probs=59.9

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (298)
                      .+.+.+.|+.|.|||+.  +-++........+.+    ++..+...++...+.++.           ++.+.-.      
T Consensus        62 ~~GlYl~G~vG~GKT~L--md~f~~~lp~~~k~R----~HFh~Fm~~vh~~l~~~~-----------~~~~~l~------  118 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTML--MDLFYDSLPIKRKRR----VHFHEFMLDVHSRLHQLR-----------GQDDPLP------  118 (362)
T ss_pred             CceEEEECCCCCchhHH--HHHHHHhCCcccccc----ccccHHHHHHHHHHHHHh-----------CCCccHH------
Confidence            57899999999999953  223332222212212    266788888888877764           1111100      


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCC-CCccEEEEEeeCchh
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATLPHE  219 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~  219 (298)
                                 .+...+      .+...+++|||+|.- +.+-.-.+..+++.+- ...-+|+.|-+.|++
T Consensus       119 -----------~va~~l------~~~~~lLcfDEF~V~-DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~  171 (362)
T PF03969_consen  119 -----------QVADEL------AKESRLLCFDEFQVT-DIADAMILKRLFEALFKRGVVLVATSNRPPED  171 (362)
T ss_pred             -----------HHHHHH------HhcCCEEEEeeeecc-chhHHHHHHHHHHHHHHCCCEEEecCCCChHH
Confidence                       111111      235568999999863 3333444445555443 455566666666553

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PRK06620 hypothetical protein; Validated

Probab=95.15  E-value=0.081  Score=43.38  Aligned_cols=16  Identities=25%  Similarity=0.412  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSM   86 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~   86 (298)
                      +.+++.||+|+|||.-
T Consensus        45 ~~l~l~Gp~G~GKThL   60 (214)
T PRK06620         45 FTLLIKGPSSSGKTYL   60 (214)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            5689999999999953

>PRK09354 recA recombinase A; Provisional

Probab=95.13  E-value=0.073  Score=46.77  Aligned_cols=43  Identities=19%  Similarity=0.257  Sum_probs=29.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~  115 (298)
                      |+-+.+.||+|+|||.-.+..+.+....   +..++|+-.-..+-.
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~---G~~~~yId~E~s~~~  102 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDP  102 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEECCccchHH
Confidence            4678899999999996655544444332   457888886655543

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=95.13  E-value=0.43  Score=41.60  Aligned_cols=34  Identities=18%  Similarity=0.213  Sum_probs=26.0

Q ss_pred             CChHHHHHHHHHhh----cCC---cEEEEcCCCCchHHHHH
Q 022383           55 KPSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~---~~li~~pTG~GKT~~~~   88 (298)
                      .++|||...|..+.    .++   -.++.||.|.||+..+.
T Consensus         3 ~~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~   43 (319)
T PRK06090          3 NDYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVE   43 (319)
T ss_pred             cCcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHH
Confidence            36788888888765    343   58999999999995543

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=95.10  E-value=0.073  Score=50.46  Aligned_cols=41  Identities=24%  Similarity=0.324  Sum_probs=28.0

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      +++-..+|+||+..-++......+...+..+.+++.+++++
T Consensus       481 l~~~~ILILDEaTSalD~~tE~~I~~~l~~l~~~rT~iiIa  521 (567)
T COG1132         481 LRNPPILILDEATSALDTETEALIQDALKKLLKGRTTLIIA  521 (567)
T ss_pred             hcCCCEEEEeccccccCHHhHHHHHHHHHHHhcCCEEEEEe
Confidence            35668999999988777767777777776555554444443

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

Probab=95.10  E-value=0.061  Score=46.66  Aligned_cols=60  Identities=15%  Similarity=0.228  Sum_probs=39.5

Q ss_pred             CCCCChHHHHHHHHHhhcC-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHH
Q 022383           52 GFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~  115 (298)
                      .|...++-|...+-.+..+ .|++++|.||||||.. +-.+...+..   ..++|.+=-+.||-.
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~---~eRvItiEDtaELql  214 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDS---DERVITIEDTAELQL  214 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCC---cccEEEEeehhhhcc
Confidence            3556778888777666655 5999999999999953 2222222222   227788777777643

>TIGR02012 tigrfam_recA protein RecA

Probab=95.09  E-value=0.081  Score=46.03  Aligned_cols=44  Identities=16%  Similarity=0.269  Sum_probs=28.3

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~  115 (298)
                      .|+-+.+.+|+|+|||.-.+..+.+....   +..++|+-.-..+-.
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~~---g~~v~yId~E~~~~~   97 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDP   97 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEcccchhHH
Confidence            34678999999999996555444443322   456788865444333

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=95.09  E-value=0.15  Score=47.30  Aligned_cols=53  Identities=15%  Similarity=0.260  Sum_probs=29.0

Q ss_pred             cccCcccCC-CCHHHHHHHHHC--CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHH
Q 022383           31 AITSFDAMG-IKDDLLRGIYQY--GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        31 ~~~~~~~l~-l~~~i~~~l~~~--~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~   86 (298)
                      |..+|++++ +.+.+.......  .+.++..+...-   +...+.+++.||+|+|||..
T Consensus       177 p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~g---l~~p~GILLyGPPGTGKT~L  232 (512)
T TIGR03689       177 PDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYD---LKPPKGVLLYGPPGCGKTLI  232 (512)
T ss_pred             CCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhcc---CCCCcceEEECCCCCcHHHH
Confidence            345788876 444433332222  122222222211   22357899999999999964

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=95.08  E-value=0.082  Score=46.20  Aligned_cols=50  Identities=20%  Similarity=0.274  Sum_probs=31.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      .+++++||.|+|||..+-+.+-.   ......+.|=+..+.+-++++.+.+++
T Consensus       163 pSmIlWGppG~GKTtlArlia~t---sk~~SyrfvelSAt~a~t~dvR~ife~  212 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIAST---SKKHSYRFVELSATNAKTNDVRDIFEQ  212 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhh---cCCCceEEEEEeccccchHHHHHHHHH
Confidence            48999999999999644322211   112234566677777777776665554

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=95.08  E-value=0.18  Score=44.67  Aligned_cols=17  Identities=35%  Similarity=0.473  Sum_probs=14.0

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      .+++.||.|+|||....
T Consensus        38 ~~Ll~G~~G~GKt~~a~   54 (355)
T TIGR02397        38 AYLFSGPRGTGKTSIAR   54 (355)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            57899999999996543

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=95.07  E-value=0.2  Score=50.09  Aligned_cols=79  Identities=10%  Similarity=0.093  Sum_probs=62.1

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.+++|+||+++-+..+.+.++++.  .+.++..++|+.+..+....+    .+..+|+|||.      +-..++++.++
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~--p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~------iie~GIDIp~v  731 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELV--PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT------IIETGIDIPNA  731 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhC--CCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC------hhhcccccccC
Confidence            4589999999999999998888763  357899999998766554333    25689999996      23357899999


Q ss_pred             cEEEechhhHh
Q 022383          177 KLLVLDESDEM  187 (298)
Q Consensus       177 ~~vViDE~h~~  187 (298)
                      ++||++.++.+
T Consensus       732 ~~VIi~~a~~~  742 (926)
T TIGR00580       732 NTIIIERADKF  742 (926)
T ss_pred             CEEEEecCCCC
Confidence            99999999764

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.07  E-value=0.59  Score=38.77  Aligned_cols=52  Identities=12%  Similarity=0.185  Sum_probs=32.8

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .|.-+++.|++|+|||.-..--+...+..   +.+++|+.-. +-..++.+.+..+
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~~---g~~~~y~~~e-~~~~~~~~~~~~~   75 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALKQ---GKKVYVITTE-NTSKSYLKQMESV   75 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHhC---CCEEEEEEcC-CCHHHHHHHHHHC
Confidence            35678999999999995544333343332   4577777754 3345666666555

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=95.00  E-value=0.14  Score=47.72  Aligned_cols=55  Identities=18%  Similarity=0.265  Sum_probs=33.7

Q ss_pred             ccccCcccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~--~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .+..+|+++.-.+.++..+.+.-  +..+..++..-   ....+.+++.||+|+|||...
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~la  105 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLG---AKIPKGVLLVGPPGTGKTLLA  105 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcC---CCCCCcEEEECCCCCCHHHHH
Confidence            45678999876666666655421  22222222211   122367999999999999643

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK13764 ATPase; Provisional

Probab=94.97  E-value=0.059  Score=50.82  Aligned_cols=27  Identities=15%  Similarity=0.405  Sum_probs=20.3

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~   96 (298)
                      .+++++++||||||||.. +-.++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTTl-l~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTF-AQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            468899999999999954 344555554

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

Probab=94.93  E-value=0.026  Score=47.03  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      +.-++++|+|||||+....
T Consensus       127 RGLviiVGaTGSGKSTtmA  145 (375)
T COG5008         127 RGLVIIVGATGSGKSTTMA  145 (375)
T ss_pred             CceEEEECCCCCCchhhHH
Confidence            3457999999999996643

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.87  E-value=0.11  Score=49.22  Aligned_cols=40  Identities=23%  Similarity=0.289  Sum_probs=30.3

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      +++...+|+|||-.-++..-+..++..++.+..+.-++.+
T Consensus       620 lr~P~VLILDEATSALDaeSE~lVq~aL~~~~~~rTVlvI  659 (716)
T KOG0058|consen  620 LRNPRVLILDEATSALDAESEYLVQEALDRLMQGRTVLVI  659 (716)
T ss_pred             hcCCCEEEEechhhhcchhhHHHHHHHHHHhhcCCeEEEE
Confidence            4788999999998887777777888888777766434433

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=94.84  E-value=0.18  Score=44.47  Aligned_cols=50  Identities=18%  Similarity=0.177  Sum_probs=35.4

Q ss_pred             HHHhcCCCCCCCCCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCC
Q 022383            6 AMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEK   55 (298)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~   55 (298)
                      ++....+......+++.++....+..+......|+++...+.|++.||..
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~kL~~~g~~t   54 (344)
T PLN03187          5 AQADEGAQLQLVEAEEVDEEEDLFESIDKLISQGINAGDVKKLQDAGIYT   54 (344)
T ss_pred             hhhhhhhhhhhhhhhhhhhhhhcccCHHHHhhCCCCHHHHHHHHHcCCCc
Confidence            34444444555556666655555777777888899999999999999863

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.83  E-value=0.028  Score=50.52  Aligned_cols=48  Identities=21%  Similarity=0.160  Sum_probs=37.5

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      +++++||||+|||.++++|-+-..     ...+|++=|.-++........++.
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-----~~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-----PGSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-----CCCEEEEccchhHHHHHHHHHHHc
Confidence            578999999999999888766542     236788889999998877766554

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.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=94.80  E-value=0.42  Score=41.95  Aligned_cols=40  Identities=10%  Similarity=0.274  Sum_probs=26.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ...+++||||+|.+.... ...+.+.++.-|.+..+|+.|.
T Consensus       109 ~~~kvviI~~a~~~~~~a-~NaLLK~LEEPp~~~~~Il~t~  148 (329)
T PRK08058        109 SNKKVYIIEHADKMTASA-ANSLLKFLEEPSGGTTAILLTE  148 (329)
T ss_pred             cCceEEEeehHhhhCHHH-HHHHHHHhcCCCCCceEEEEeC
Confidence            467899999999985442 4555566666556666666544

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=94.80  E-value=0.19  Score=41.13  Aligned_cols=40  Identities=15%  Similarity=0.283  Sum_probs=23.2

Q ss_pred             cEEEechhhHhh-c----cccHHHHHHHHHhCCC-CccEEEEEeeC
Q 022383          177 KLLVLDESDEML-S----RGFKDQIYDVYRYLPP-DLQVVLISATL  216 (298)
Q Consensus       177 ~~vViDE~h~~~-~----~~~~~~i~~i~~~~~~-~~~~v~~SAT~  216 (298)
                      -+|||||+|.+. .    ..+...+..++..... ....++++++-
T Consensus       120 ~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~  165 (234)
T PF01637_consen  120 VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS  165 (234)
T ss_dssp             EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred             EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence            589999999998 1    2355566666666332 22234445553

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.76  E-value=0.082  Score=46.02  Aligned_cols=43  Identities=14%  Similarity=0.222  Sum_probs=28.9

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~  115 (298)
                      |+-+.+.+|+|+|||.-.+..+.+....   +..++|+..-..+-.
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~---g~~~vyId~E~~~~~   97 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKL---GGTVAFIDAEHALDP   97 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCCEEEECccccHHH
Confidence            4678899999999996554444443322   457888887555443

RecA couples ATP hydrolysis to DNA strand exchange.

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=94.76  E-value=0.4  Score=48.08  Aligned_cols=143  Identities=11%  Similarity=0.140  Sum_probs=101.8

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhc--------------
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVD--------------   96 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~--------------   96 (298)
                      ....|.+|||-  |.+.=..+|..     |++-+..+...-|++-...|--=.|+-..+.-+..+.              
T Consensus       710 kdv~FkdLGLl--IIDEEqRFGVk-----~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T  782 (1139)
T COG1197         710 KDVKFKDLGLL--IIDEEQRFGVK-----HKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKT  782 (1139)
T ss_pred             CCcEEecCCeE--EEechhhcCcc-----HHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEE
Confidence            33456666542  22222334433     7788888888888888888888888665544333320              


Q ss_pred             ----------------cCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHH----hhcCCcEEE
Q 022383           97 ----------------TSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK----LEHGVHVVS  156 (298)
Q Consensus        97 ----------------~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~ilV  156 (298)
                                      .-.++.++.||.|..+-..++.+.++.+-  ...++.+.||.....+....    +.+.+||+|
T Consensus       783 ~V~~~d~~~ireAI~REl~RgGQvfYv~NrV~~Ie~~~~~L~~LV--PEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv  860 (1139)
T COG1197         783 FVSEYDDLLIREAILRELLRGGQVFYVHNRVESIEKKAERLRELV--PEARIAVAHGQMRERELEEVMLDFYNGEYDVLV  860 (1139)
T ss_pred             EEecCChHHHHHHHHHHHhcCCEEEEEecchhhHHHHHHHHHHhC--CceEEEEeecCCCHHHHHHHHHHHHcCCCCEEE
Confidence                            01346799999999999999999999985  45789999998877654333    347899999


Q ss_pred             eChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          157 GTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       157 ~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      ||.      +-+.+++..+-..+||+-||++.
T Consensus       861 ~TT------IIEtGIDIPnANTiIIe~AD~fG  886 (1139)
T COG1197         861 CTT------IIETGIDIPNANTIIIERADKFG  886 (1139)
T ss_pred             Eee------eeecCcCCCCCceEEEecccccc
Confidence            995      34467899999999999999974

>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=94.71  E-value=0.056  Score=45.96  Aligned_cols=44  Identities=14%  Similarity=0.368  Sum_probs=29.6

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      +..+.+++++||||||||... ..++..+...  ..+++.+-...|+
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~~--~~~iv~iEd~~E~  167 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPPE--DERIVTIEDPPEL  167 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHTT--TSEEEEEESSS-S
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhcccc--ccceEEeccccce
Confidence            356789999999999999653 4555655443  2466666655554

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 ....

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.69  E-value=0.25  Score=47.24  Aligned_cols=19  Identities=32%  Similarity=0.386  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCCchHHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~   89 (298)
                      ..+++.||.|+|||..+..
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~   57 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARI   57 (620)
T ss_pred             ceEEEECCCCCChHHHHHH
Confidence            4679999999999976543

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=94.67  E-value=0.38  Score=44.68  Aligned_cols=53  Identities=21%  Similarity=0.301  Sum_probs=37.2

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      .|.-+++.+|+|+|||...+.-+.....   ++.+++|++ ..|-..|+..+++.++
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~~~---~ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENACA---NKERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            3467999999999999654444443332   245778776 6777888888887763

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.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=94.63  E-value=0.28  Score=39.88  Aligned_cols=39  Identities=13%  Similarity=0.256  Sum_probs=26.3

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      .|.-+.+.||+|+|||...+..+.+....   +.+++|+.-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~---g~~v~yi~~e   49 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQ---GKKVVYIDTE   49 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC
Confidence            45678999999999996655444443322   4467877764

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=94.58  E-value=0.18  Score=45.11  Aligned_cols=40  Identities=15%  Similarity=0.202  Sum_probs=27.4

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccC-CCCeEEEEEcC
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-SREVQALILSP  109 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-~~~~~~lil~p  109 (298)
                      ..|.++++.|+||+||++.+.  .++..... ..+|.+-|=|-
T Consensus        99 p~~~~vLi~GetGtGKel~A~--~iH~~s~r~~~~PFI~~NCa  139 (403)
T COG1221          99 PSGLPVLIIGETGTGKELFAR--LIHALSARRAEAPFIAFNCA  139 (403)
T ss_pred             CCCCcEEEecCCCccHHHHHH--HHHHhhhcccCCCEEEEEHH
Confidence            368899999999999997654  33333333 45666666553

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=94.56  E-value=0.12  Score=44.87  Aligned_cols=17  Identities=24%  Similarity=0.464  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      .++++.||+|+|||...
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            56999999999999543

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK09165 replicative DNA helicase; Provisional

Probab=94.53  E-value=0.43  Score=44.44  Aligned_cols=145  Identities=16%  Similarity=0.130  Sum_probs=70.2

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccC------------CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE-E
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS------------SREVQALILSPTRELATQTEKVILAIGDFINIQAHA-C  135 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~------------~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~-~  135 (298)
                      .|.-+++.|.+|+|||.-.+--+.+.....            ..+..++|++ ...-..|+..++-.....  +.... .
T Consensus       216 ~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fS-lEMs~~ql~~R~la~~s~--v~~~~i~  292 (497)
T PRK09165        216 PSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFS-LEMSAEQLATRILSEQSE--ISSSKIR  292 (497)
T ss_pred             CCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEe-CcCCHHHHHHHHHHHhcC--CCHHHHh
Confidence            445678889999999955443333322110            1244566664 334456666655433222  22111 1


Q ss_pred             EcCCchHHHH------HHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc------cHHHHHH
Q 022383          136 VGGKSVGEDI------RKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG------FKDQIYD  198 (298)
Q Consensus       136 ~~~~~~~~~~------~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~------~~~~i~~  198 (298)
                      .|.....+..      ..+ ...++.|-     |++.+...++.-.. -..+++||||=.+.+...+      ....+..
T Consensus       293 ~~~l~~~e~~~l~~a~~~l-~~~~l~I~d~~~~ti~~i~~~ir~l~~-~~~~~lvvIDyLqli~~~~~~~~~~r~~ev~~  370 (497)
T PRK09165        293 RGKISEEDFEKLVDASQEL-QKLPLYIDDTPALSISQLRARARRLKR-QHGLDLLVVDYLQLIRGSSKRSSDNRVQEISE  370 (497)
T ss_pred             cCCCCHHHHHHHHHHHHHH-hcCCeEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhccCCCCCCCCchHHHHHH
Confidence            2222222211      112 22345553     45555554443211 2358999999999875321      1123333


Q ss_pred             HHHhCC-----CCccEEEEEeeCchh
Q 022383          199 VYRYLP-----PDLQVVLISATLPHE  219 (298)
Q Consensus       199 i~~~~~-----~~~~~v~~SAT~~~~  219 (298)
                      +.+.+.     .++.++++|. +++.
T Consensus       371 is~~LK~lAkel~ipVi~lsQ-LnR~  395 (497)
T PRK09165        371 ITQGLKALAKELNIPVIALSQ-LSRQ  395 (497)
T ss_pred             HHHHHHHHHHHhCCeEEEeec-ccch
Confidence            433332     2566777665 4444

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=94.50  E-value=1.1  Score=38.95  Aligned_cols=57  Identities=14%  Similarity=0.313  Sum_probs=32.6

Q ss_pred             HHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhC---CCCccEEEEEeeC
Q 022383          160 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL---PPDLQVVLISATL  216 (298)
Q Consensus       160 ~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~---~~~~~~v~~SAT~  216 (298)
                      ++++..+..+....+.--.+|+||+|.+.....+..+-.+++.-   +.++-++++|..+
T Consensus       122 ~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrl  181 (408)
T KOG2228|consen  122 SKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRL  181 (408)
T ss_pred             HHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccc
Confidence            34555555544444444678999999876555454444444443   3344566666554

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

Probab=94.50  E-value=0.052  Score=50.15  Aligned_cols=50  Identities=20%  Similarity=0.261  Sum_probs=38.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      .++++.||||||||..+.+|.+-..     ...+|+.=|--++...+...+++.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~~-----~~s~iV~D~KgEl~~~t~~~r~~~G   94 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLNY-----PGSMIVTDPKGELYEKTAGYRKKRG   94 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHhc-----cCCEEEEECCCcHHHHHHHHHHHCC
Confidence            4799999999999999988876432     1257777799999888887766653

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

>PRK08840 replicative DNA helicase; Provisional

Probab=94.49  E-value=0.71  Score=42.55  Aligned_cols=144  Identities=18%  Similarity=0.133  Sum_probs=68.7

Q ss_pred             HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGED  144 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  144 (298)
                      -+..|.=+++-|.+|+|||.-.+-.+.+....  .+..++|++.- --..|+..++-....  ++....+ .|..+..+.
T Consensus       213 G~~~g~LiviaarPg~GKTafalnia~~~a~~--~~~~v~~fSlE-Ms~~ql~~Rlla~~s--~v~~~~i~~~~l~~~e~  287 (464)
T PRK08840        213 GLQGSDLIIVAARPSMGKTTFAMNLCENAAMD--QDKPVLIFSLE-MPAEQLMMRMLASLS--RVDQTKIRTGQLDDEDW  287 (464)
T ss_pred             CCCCCceEEEEeCCCCchHHHHHHHHHHHHHh--CCCeEEEEecc-CCHHHHHHHHHHhhC--CCCHHHHhcCCCCHHHH
Confidence            34455667888999999995443333332212  13356666532 224455444432211  2211111 222222222


Q ss_pred             H------HHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc----cHHHHHHHHHhCC-----
Q 022383          145 I------RKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----  204 (298)
Q Consensus       145 ~------~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~----~~~~i~~i~~~~~-----  204 (298)
                      .      ..+....++.|-     |+..+....+.-......+++||||-.|.+...+    ....+..+.+.+.     
T Consensus       288 ~~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~~~~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAke  367 (464)
T PRK08840        288 ARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMRVPALSDNRTLEIAEISRSLKALAKE  367 (464)
T ss_pred             HHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHhcCCCCCCCchHHHHHHHHHHHHHHHHH
Confidence            1      122223455553     3445544433321112358999999999885222    2233444443332     


Q ss_pred             CCccEEEEEe
Q 022383          205 PDLQVVLISA  214 (298)
Q Consensus       205 ~~~~~v~~SA  214 (298)
                      -++.++++|.
T Consensus       368 l~ipVi~LsQ  377 (464)
T PRK08840        368 LNVPVVALSQ  377 (464)
T ss_pred             hCCeEEEEEe
Confidence            2677777763

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.49  E-value=0.58  Score=44.74  Aligned_cols=40  Identities=13%  Similarity=0.179  Sum_probs=25.0

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      +...+++||||+|.+.... ...+...++..+...-+|+.+
T Consensus       119 ~~~~KVvIIdea~~Ls~~a-~naLLK~LEepp~~tifIL~t  158 (614)
T PRK14971        119 IGKYKIYIIDEVHMLSQAA-FNAFLKTLEEPPSYAIFILAT  158 (614)
T ss_pred             cCCcEEEEEECcccCCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            3567899999999985432 344555555555545444433

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=94.47  E-value=0.21  Score=41.89  Aligned_cols=30  Identities=23%  Similarity=0.370  Sum_probs=21.7

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhcc
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~   97 (298)
                      +..|+.+++.||.|+|||.. +--+++.+..
T Consensus        13 i~~Gqr~~I~G~~G~GKTTL-lr~I~n~l~~   42 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTL-LQSIANAITK   42 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHH-HHHHHhcccc
Confidence            45789999999999999953 3345554443

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK08506 replicative DNA helicase; Provisional

Probab=94.43  E-value=0.41  Score=44.26  Aligned_cols=141  Identities=20%  Similarity=0.177  Sum_probs=69.6

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHH--
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGED--  144 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--  144 (298)
                      ..|.-+++.|.+|+|||.-.+-.+.+.. .  .+..++|++. .--..|+..++-....  ++....+ .|..+..+.  
T Consensus       190 ~~G~LivIaarpg~GKT~fal~ia~~~~-~--~g~~V~~fSl-EMs~~ql~~Rlla~~s--~v~~~~i~~~~l~~~e~~~  263 (472)
T PRK08506        190 NKGDLIIIAARPSMGKTTLCLNMALKAL-N--QDKGVAFFSL-EMPAEQLMLRMLSAKT--SIPLQNLRTGDLDDDEWER  263 (472)
T ss_pred             CCCceEEEEcCCCCChHHHHHHHHHHHH-h--cCCcEEEEeC-cCCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHHHH
Confidence            3456678889999999965444444433 2  2445666653 3345555555433221  2221111 222222221  


Q ss_pred             ----HHHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc----cHHHHHHHHHhCC-----CC
Q 022383          145 ----IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----PD  206 (298)
Q Consensus       145 ----~~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~----~~~~i~~i~~~~~-----~~  206 (298)
                          ...+.+ ..+.|-     |+..+...++.-......+++||||=.+.+...+    ....+..+.+.+.     .+
T Consensus       264 ~~~a~~~l~~-~~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~~~~~~~~r~~ev~~isr~LK~lAkel~  342 (472)
T PRK08506        264 LSDACDELSK-KKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMSGSGNFKDRHLQISEISRGLKLLARELD  342 (472)
T ss_pred             HHHHHHHHHc-CCeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhccCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence                112222 345552     4555554444311112358999999999885332    1223333333321     26


Q ss_pred             ccEEEEEee
Q 022383          207 LQVVLISAT  215 (298)
Q Consensus       207 ~~~v~~SAT  215 (298)
                      +.++++|..
T Consensus       343 ipVi~lsQL  351 (472)
T PRK08506        343 IPIIALSQL  351 (472)
T ss_pred             CcEEEEeec
Confidence            777777643

>TIGR00665 DnaB replicative DNA helicase

Probab=94.42  E-value=0.44  Score=43.60  Aligned_cols=142  Identities=17%  Similarity=0.155  Sum_probs=68.5

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHH-
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGED-  144 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~-  144 (298)
                      +..|.-+++.|++|+|||.-.+--+.+....  .+..++|++. ..-..++..++.....  ++....+ .|.....+. 
T Consensus       192 ~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~--~g~~vl~~Sl-Em~~~~i~~R~~~~~~--~v~~~~~~~g~l~~~~~~  266 (434)
T TIGR00665       192 LQPSDLIILAARPSMGKTAFALNIAENAAIK--EGKPVAFFSL-EMSAEQLAMRMLSSES--RVDSQKLRTGKLSDEDWE  266 (434)
T ss_pred             CCCCeEEEEEeCCCCChHHHHHHHHHHHHHh--CCCeEEEEeC-cCCHHHHHHHHHHHhc--CCCHHHhccCCCCHHHHH
Confidence            3345668889999999995444333333222  1335666653 3334555554433322  2221111 222222211 


Q ss_pred             -----HHHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc----cHHHHHHHHHhCC-----C
Q 022383          145 -----IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----P  205 (298)
Q Consensus       145 -----~~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~----~~~~i~~i~~~~~-----~  205 (298)
                           ...+.+ ..+.|.     |++.+...++.-... ..+++||||=.+.+...+    ....+..+.+.+.     .
T Consensus       267 ~~~~a~~~l~~-~~l~i~d~~~~~~~~i~~~i~~~~~~-~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~  344 (434)
T TIGR00665       267 KLTSAAGKLSE-APLYIDDTPGLTITELRAKARRLKRE-HGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKEL  344 (434)
T ss_pred             HHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHh-cCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence                 122222 345542     445555444331111 247999999998874322    2233444433332     3


Q ss_pred             CccEEEEEee
Q 022383          206 DLQVVLISAT  215 (298)
Q Consensus       206 ~~~~v~~SAT  215 (298)
                      ++.++++|-.
T Consensus       345 ~i~vi~lsql  354 (434)
T TIGR00665       345 NVPVIALSQL  354 (434)
T ss_pred             CCeEEEEecc
Confidence            5777777653

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.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.41  E-value=1.7  Score=37.97  Aligned_cols=35  Identities=17%  Similarity=0.257  Sum_probs=21.6

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      +-+.++||+|+|||....-.+.. +..  .+.+++++.
T Consensus       115 ~vi~lvGpnGsGKTTt~~kLA~~-l~~--~g~~V~Li~  149 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIGKLAHK-YKA--QGKKVLLAA  149 (318)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH-HHh--cCCeEEEEe
Confidence            45788999999999664432222 222  244666665

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.40  E-value=0.61  Score=40.90  Aligned_cols=58  Identities=16%  Similarity=0.131  Sum_probs=36.2

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCC-hHHHHHHHHHhhcCCcEEEEcCCCCchHHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKP-SAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~-~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      ...+|.+.+=.+.+++.|++.-.-.+ +|-.-.--..+..-+.+++-+|.|+|||.++.
T Consensus        87 I~v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAK  145 (386)
T KOG0737|consen   87 IGVSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAK  145 (386)
T ss_pred             ceeehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHH
Confidence            44589998878888888877422211 11111111222345799999999999997644

>PRK07004 replicative DNA helicase; Provisional

Probab=94.38  E-value=0.39  Score=44.25  Aligned_cols=142  Identities=16%  Similarity=0.165  Sum_probs=67.3

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDI  145 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  145 (298)
                      +..|.=+++.|.+|+|||.-.+--+.+....  .+..++|++. .--..|+..++-....  ++....+ .|.....+..
T Consensus       210 ~~~g~liviaarpg~GKT~~al~ia~~~a~~--~~~~v~~fSl-EM~~~ql~~R~la~~~--~v~~~~i~~g~l~~~e~~  284 (460)
T PRK07004        210 MHGGELIIVAGRPSMGKTAFSMNIGEYVAVE--YGLPVAVFSM-EMPGTQLAMRMLGSVG--RLDQHRMRTGRLTDEDWP  284 (460)
T ss_pred             CCCCceEEEEeCCCCCccHHHHHHHHHHHHH--cCCeEEEEeC-CCCHHHHHHHHHHhhc--CCCHHHHhcCCCCHHHHH
Confidence            3345667888999999995443333322222  1335666652 2223444443321111  1211111 2222222221


Q ss_pred             ------HHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc----cHHHHHHHHHhCC-----C
Q 022383          146 ------RKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----P  205 (298)
Q Consensus       146 ------~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~----~~~~i~~i~~~~~-----~  205 (298)
                            ..+ .+.++.|.     |+..+....+.-......+++||||=.+.+...+    ....+..+.+.+.     .
T Consensus       285 ~~~~a~~~l-~~~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lAkel  363 (460)
T PRK07004        285 KLTHAVQKM-SEAQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKEL  363 (460)
T ss_pred             HHHHHHHHH-hcCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHHHHh
Confidence                  222 23456663     4445544433311122358999999999885322    2233444444442     2


Q ss_pred             CccEEEEEe
Q 022383          206 DLQVVLISA  214 (298)
Q Consensus       206 ~~~~v~~SA  214 (298)
                      +++++++|.
T Consensus       364 ~ipVi~lsQ  372 (460)
T PRK07004        364 DVPVIALSQ  372 (460)
T ss_pred             CCeEEEEec
Confidence            577777765

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=94.37  E-value=0.99  Score=43.46  Aligned_cols=181  Identities=14%  Similarity=0.091  Sum_probs=98.5

Q ss_pred             CCHHHHHHHHHC---CCCCChHHHHHHHHHhh--cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHH
Q 022383           40 IKDDLLRGIYQY---GFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (298)
Q Consensus        40 l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~--~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~  114 (298)
                      |-+.+.+.++-.   |+..++.-=.+.+....  +|-.+|+.-..|-|||+-.+- .+..+...-....+|+|+|-..|-
T Consensus       247 lapqla~v~kPHQiGGiRFlYDN~iESl~rykkSsGFGCILAHSMGLGKTlQVis-F~diflRhT~AKtVL~ivPiNTlQ  325 (1387)
T KOG1016|consen  247 LAPQLAHVLKPHQIGGIRFLYDNTIESLGRYKKSSGFGCILAHSMGLGKTLQVIS-FSDIFLRHTKAKTVLVIVPINTLQ  325 (1387)
T ss_pred             ehhhhHhhcCccccCcEEEehhhHHHHHhhccccCCcceeeeeccccCceeEEee-hhHHHhhcCccceEEEEEehHHHH
Confidence            455666666543   33334432233333222  355788999999999954221 111111112234799999977764


Q ss_pred             HHHHHHHHHhhcc----C-----CceEEEEEcCCchHHHH-HHhhc---CCcEEEeChHHHHHHHhc-------------
Q 022383          115 TQTEKVILAIGDF----I-----NIQAHACVGGKSVGEDI-RKLEH---GVHVVSGTPGRVCDMIKR-------------  168 (298)
Q Consensus       115 ~q~~~~~~~~~~~----~-----~~~~~~~~~~~~~~~~~-~~~~~---~~~ilV~Tp~~l~~~~~~-------------  168 (298)
                       .+...+..+...    .     .+.+.++..+....... +-+.+   .-.+++.--+++.-+...             
T Consensus       326 -NWlsEfnmWiP~y~sD~~vrpR~F~vf~LnD~~KT~~~Rakvi~~Wv~~GGVlLvGYemfRLL~lk~~~~~grpkkt~k  404 (1387)
T KOG1016|consen  326 -NWLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGVKTFDQRAKVIEQWVQTGGVLLVGYEMFRLLILKTLPKKGRPKKTLK  404 (1387)
T ss_pred             -HHHHHhhhhcCCCcccCCCccceeEEEEecCchhhHHHHHHHHHHHhccCCEEEehHHHHHHHHHhcccccCCcccccc
Confidence             444455554332    1     24566676665544333 22222   224555555544322211             


Q ss_pred             -----------------------cCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHH
Q 022383          169 -----------------------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMT  224 (298)
Q Consensus       169 -----------------------~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~  224 (298)
                                             ..+.-...++||.||-|++-.  -...+-..++.++..+++|+....+.+.+.+.+
T Consensus       405 r~~~~~i~~d~eD~~qe~~~li~~AL~~PGPDlVICDEGHrIKN--~~A~iS~aLk~IrtrRRiVLTGYPLQNNLlEYw  481 (1387)
T KOG1016|consen  405 RISSGFIKDDSEDQRQEAYSLIRSALLEPGPDLVICDEGHRIKN--ITAEISMALKAIRTRRRIVLTGYPLQNNLLEYW  481 (1387)
T ss_pred             ccCCcccCCchhhhHHHHHHHHHHHhcCCCCCeEEecCCceecc--chHHHHHHHHHhhhceeEEEeccccccchHHHh
Confidence                                   001114568999999999833  345555666777767778888888877655543

>TIGR00763 lon ATP-dependent protease La

Probab=94.34  E-value=0.27  Score=48.45  Aligned_cols=18  Identities=33%  Similarity=0.372  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      +..+++.||+|+|||..+
T Consensus       347 ~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            457999999999999654

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=94.33  E-value=0.49  Score=43.46  Aligned_cols=39  Identities=13%  Similarity=0.278  Sum_probs=23.7

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...++|||||+|.+.... ...+...++.-+....+|+.+
T Consensus       120 ~~~kvvIIdead~lt~~~-~n~LLk~lEep~~~~~~Il~t  158 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKEA-FNSLLKTLEEPPQHVKFFLAT  158 (451)
T ss_pred             CCCEEEEEecHHhhCHHH-HHHHHHHhhcCCCCceEEEEe
Confidence            466899999999985443 334444555544445455443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=94.31  E-value=0.26  Score=43.98  Aligned_cols=67  Identities=21%  Similarity=0.262  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHh---hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           57 SAIQQRAVMPI---IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        57 ~~~Q~~~~~~~---~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      .+.-.++++.+   -.|+-.+|.||.|+|||.. +..+.+.+....... .+|++-..+-.+++.+..+.+.
T Consensus       153 ~~~~~rvID~l~PIGkGQR~lIvgppGvGKTTL-aK~Ian~I~~nhFDv-~~~VvLIgER~~EVtdiqrsIl  222 (416)
T PRK09376        153 EDLSTRIIDLIAPIGKGQRGLIVAPPKAGKTVL-LQNIANSITTNHPEV-HLIVLLIDERPEEVTDMQRSVK  222 (416)
T ss_pred             cccceeeeeeecccccCceEEEeCCCCCChhHH-HHHHHHHHHhhcCCe-EEEEEEeCCchhHHHHHHHHhc
Confidence            34445555554   3789999999999999953 333555554432222 3343334444455555555553

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.28  E-value=0.43  Score=44.26  Aligned_cols=37  Identities=19%  Similarity=0.413  Sum_probs=21.5

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL  211 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~  211 (298)
                      ....++||||+|.+....+ ..+...+...+...-+|+
T Consensus       118 ~~~KVvIIDEad~Lt~~a~-naLLk~LEepp~~~v~Il  154 (486)
T PRK14953        118 GKYKVYIIDEAHMLTKEAF-NALLKTLEEPPPRTIFIL  154 (486)
T ss_pred             CCeeEEEEEChhhcCHHHH-HHHHHHHhcCCCCeEEEE
Confidence            5678999999998854432 333344444333433333

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.27  E-value=0.066  Score=50.70  Aligned_cols=49  Identities=12%  Similarity=-0.011  Sum_probs=40.7

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      +++++.||||||||..+++|-+-...     ..+|++=|--|+...+....++.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~~-----~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFWE-----DSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhCC-----CCEEEEeCcHHHHHHHHHHHHHC
Confidence            58999999999999999999877642     25788889999998888877765

>PRK08006 replicative DNA helicase; Provisional

Probab=94.27  E-value=1  Score=41.61  Aligned_cols=144  Identities=18%  Similarity=0.123  Sum_probs=70.4

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDI  145 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  145 (298)
                      +..|.=+++-|.+|+|||.-.+-.+.+....  .+..++|++. .--..|+..++-....  ++....+ .|..+..++.
T Consensus       221 l~~G~LiiIaarPgmGKTafalnia~~~a~~--~g~~V~~fSl-EM~~~ql~~Rlla~~~--~v~~~~i~~~~l~~~e~~  295 (471)
T PRK08006        221 LQPSDLIIVAARPSMGKTTFAMNLCENAAML--QDKPVLIFSL-EMPGEQIMMRMLASLS--RVDQTRIRTGQLDDEDWA  295 (471)
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh--cCCeEEEEec-cCCHHHHHHHHHHHhc--CCCHHHhhcCCCCHHHHH
Confidence            3344567778999999995444333333222  1335666653 2233444444432221  2222111 2222322221


Q ss_pred             ------HHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhcc----ccHHHHHHHHHhCC-----C
Q 022383          146 ------RKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR----GFKDQIYDVYRYLP-----P  205 (298)
Q Consensus       146 ------~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~----~~~~~i~~i~~~~~-----~  205 (298)
                            ..+.....+.|-     |+..+....+.-......+++||||=.+.+...    .....+..+.+.+.     .
T Consensus       296 ~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAkel  375 (471)
T PRK08006        296 RISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLKALAKEL  375 (471)
T ss_pred             HHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHccCCCCCCCcHHHHHHHHHHHHHHHHHh
Confidence                  122133456653     455555544332112236899999999988532    12333444444432     2


Q ss_pred             CccEEEEEee
Q 022383          206 DLQVVLISAT  215 (298)
Q Consensus       206 ~~~~v~~SAT  215 (298)
                      ++.++++|..
T Consensus       376 ~ipVi~LsQL  385 (471)
T PRK08006        376 QVPVVALSQL  385 (471)
T ss_pred             CCeEEEEEec
Confidence            6778887743

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

Probab=94.24  E-value=0.099  Score=41.80  Aligned_cols=32  Identities=19%  Similarity=0.363  Sum_probs=24.6

Q ss_pred             CChHHHHHHHHH-hhcCCcEEEEcCCCCchHHH
Q 022383           55 KPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        55 ~~~~~Q~~~~~~-~~~~~~~li~~pTG~GKT~~   86 (298)
                      ..++.|...+.. +..|..++++||||+|||..
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            345666666665 45788999999999999964

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.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=94.23  E-value=1  Score=38.27  Aligned_cols=16  Identities=19%  Similarity=0.345  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSM   86 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~   86 (298)
                      +++++.+|+|+|||..
T Consensus       112 ~~~~i~g~~g~GKttl  127 (270)
T TIGR02858       112 LNTLIISPPQCGKTTL  127 (270)
T ss_pred             eEEEEEcCCCCCHHHH
Confidence            6899999999999953

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.20  E-value=0.16  Score=41.77  Aligned_cols=43  Identities=16%  Similarity=0.157  Sum_probs=26.9

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccC---CCCeEEEEEcCcH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTR  111 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~  111 (298)
                      .|+-+.+.||+|+|||...+..+.......   .....++|+....
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            356789999999999975554443333221   0124678887643

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=94.19  E-value=0.32  Score=44.53  Aligned_cols=74  Identities=12%  Similarity=0.060  Sum_probs=47.5

Q ss_pred             CCCCCChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           51 YGFEKPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      +-|...+|-|.+-.-.+.    .+.+.++.+|+|+|||.+.+-.++.-...-+ ...+.|+.+-|..-.+.....++.+
T Consensus        12 FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l   90 (755)
T KOG1131|consen   12 FPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRL   90 (755)
T ss_pred             cCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHH
Confidence            346677888876655443    4678999999999999876655555433333 2336667666665555555555443

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.18  E-value=0.26  Score=43.84  Aligned_cols=16  Identities=38%  Similarity=0.648  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSM   86 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~   86 (298)
                      +|+++.||+|+|||+.
T Consensus       385 RNilfyGPPGTGKTm~  400 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMF  400 (630)
T ss_pred             hheeeeCCCCCCchHH
Confidence            7999999999999964

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=94.18  E-value=0.55  Score=45.95  Aligned_cols=19  Identities=26%  Similarity=0.454  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      ..++++.||+|+|||...-
T Consensus       207 ~~n~LLvGppGvGKT~lae  225 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAE  225 (758)
T ss_pred             CCCeEEECCCCCCHHHHHH
Confidence            4689999999999996543

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=94.17  E-value=0.19  Score=49.99  Aligned_cols=147  Identities=17%  Similarity=0.174  Sum_probs=80.1

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCC-CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEE
Q 022383           29 VEAITSFDAMGIKDDLLRGIYQYGFE-KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (298)
Q Consensus        29 ~~~~~~~~~l~l~~~i~~~l~~~~~~-~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (298)
                      ......|+++|....++.-|+++-+. -++|-+..- -.+..-+.+++++|.|+|||+.+--.+-+. ...  +.++-+ 
T Consensus       258 ~~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~-~~itpPrgvL~~GppGTGkTl~araLa~~~-s~~--~~kisf-  332 (1080)
T KOG0732|consen  258 VDSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDN-FNITPPRGVLFHGPPGTGKTLMARALAAAC-SRG--NRKISF-  332 (1080)
T ss_pred             hhcccCccccccHHHHHHHHHHHHHhHhhhhhHhhh-cccCCCcceeecCCCCCchhHHHHhhhhhh-ccc--ccccch-
Confidence            34567899999888888889887433 222211111 123455789999999999997532111111 110  001111 


Q ss_pred             cCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       108 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                                  ..++-.                        .....-|+.+++=++++.... .-.....+-+||+|-+
T Consensus       333 ------------fmrkga------------------------D~lskwvgEaERqlrllFeeA-~k~qPSIIffdeIdGl  375 (1080)
T KOG0732|consen  333 ------------FMRKGA------------------------DCLSKWVGEAERQLRLLFEEA-QKTQPSIIFFDEIDGL  375 (1080)
T ss_pred             ------------hhhcCc------------------------hhhccccCcHHHHHHHHHHHH-hccCceEEeccccccc
Confidence                        000100                        001334566666555554321 1235567889999954


Q ss_pred             hccc----------cHHHHHHHHHhCCCCccEEEEEeeCc
Q 022383          188 LSRG----------FKDQIYDVYRYLPPDLQVVLISATLP  217 (298)
Q Consensus       188 ~~~~----------~~~~i~~i~~~~~~~~~~v~~SAT~~  217 (298)
                      .-..          ....+..++.-++...|+++++||.-
T Consensus       376 apvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnR  415 (1080)
T KOG0732|consen  376 APVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNR  415 (1080)
T ss_pred             cccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCC
Confidence            3111          12333444555567899999999973

>PRK10689 transcription-repair coupling factor; Provisional

Probab=94.15  E-value=0.77  Score=47.11  Aligned_cols=79  Identities=11%  Similarity=0.104  Sum_probs=61.2

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.+++|++|+++-++.+.+.+++...  +.++..++|+.+..+....+    .+..+|+|||.     + -..++++.++
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p--~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTd-----I-ierGIDIP~v  880 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----I-IETGIDIPTA  880 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCC--CCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECc-----h-hhcccccccC
Confidence            45899999999999999988887643  46788899998776544332    26789999995     2 2347899999


Q ss_pred             cEEEechhhHh
Q 022383          177 KLLVLDESDEM  187 (298)
Q Consensus       177 ~~vViDE~h~~  187 (298)
                      ++||++.+|++
T Consensus       881 ~~VIi~~ad~f  891 (1147)
T PRK10689        881 NTIIIERADHF  891 (1147)
T ss_pred             CEEEEecCCCC
Confidence            99999998864

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.13  E-value=0.56  Score=43.21  Aligned_cols=69  Identities=23%  Similarity=0.260  Sum_probs=40.8

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHHHHHH-------hhc-C----CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEE
Q 022383           38 MGIKDDLLRGIYQYGFEKPSAIQQRAVMP-------IIK-G----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL  105 (298)
Q Consensus        38 l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-------~~~-~----~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~l  105 (298)
                      +|.+.+..+.+...|+-.-.+.=.+.+..       +.. .    .++++.||.|+|||.-++-.+     ....-|.+=
T Consensus       494 FG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA~iA-----~~S~FPFvK  568 (744)
T KOG0741|consen  494 FGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAAKIA-----LSSDFPFVK  568 (744)
T ss_pred             cCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHHHHHH-----hhcCCCeEE
Confidence            46777777777776654333333333321       111 1    379999999999995433222     233456777


Q ss_pred             EEcCcH
Q 022383          106 ILSPTR  111 (298)
Q Consensus       106 il~p~~  111 (298)
                      +++|..
T Consensus       569 iiSpe~  574 (744)
T KOG0741|consen  569 IISPED  574 (744)
T ss_pred             EeChHH
Confidence            888853

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=94.13  E-value=0.55  Score=44.80  Aligned_cols=108  Identities=24%  Similarity=0.349  Sum_probs=61.8

Q ss_pred             ChHHHHHHHHHhh--------cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           56 PSAIQQRAVMPII--------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        56 ~~~~Q~~~~~~~~--------~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      +..+-.+++..+.        +|+-+.++||+|.|||..                           +..+++.+.+-  +
T Consensus       416 m~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI---------------------------~kSIA~ALnRk--F  466 (906)
T KOG2004|consen  416 MEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSI---------------------------AKSIARALNRK--F  466 (906)
T ss_pred             hHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccH---------------------------HHHHHHHhCCc--e
Confidence            5555666666554        467888999999999943                           22223222111  0


Q ss_pred             CCceEEEEEcCCchHHHHHHhhcCCcEEEe-ChHHHHHHHhc-cCccCCCccEEEechhhHhhccccHHHHHHHHHhC
Q 022383          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSG-TPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (298)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~-Tp~~l~~~~~~-~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~  203 (298)
                          .-...||...-   ..+.+..+-+|+ -|+++...++. +.-+.    ++.|||+|.+.....++.--.++..+
T Consensus       467 ----fRfSvGG~tDv---AeIkGHRRTYVGAMPGkiIq~LK~v~t~NP----liLiDEvDKlG~g~qGDPasALLElL  533 (906)
T KOG2004|consen  467 ----FRFSVGGMTDV---AEIKGHRRTYVGAMPGKIIQCLKKVKTENP----LILIDEVDKLGSGHQGDPASALLELL  533 (906)
T ss_pred             ----EEEeccccccH---HhhcccceeeeccCChHHHHHHHhhCCCCc----eEEeehhhhhCCCCCCChHHHHHHhc
Confidence                11223443322   233333455665 59999998877 33333    78999999998443344444444444

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.09  E-value=0.46  Score=41.04  Aligned_cols=66  Identities=20%  Similarity=0.262  Sum_probs=40.0

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhc--cCCCCeEEEEE------------cCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVD--TSSREVQALIL------------SPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~--~~~~~~~~lil------------~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      +|-+++.||+|+|||. ..-++.+++.  ...+..+..++            .-+-.|+.++++.++.+.+..+.-++++
T Consensus       177 NRliLlhGPPGTGKTS-LCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvL  255 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTS-LCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVL  255 (423)
T ss_pred             eeEEEEeCCCCCChhH-HHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEE
Confidence            3568999999999993 3334445442  22222222222            2334677788888888877777666665


Q ss_pred             E
Q 022383          136 V  136 (298)
Q Consensus       136 ~  136 (298)
                      .
T Consensus       256 I  256 (423)
T KOG0744|consen  256 I  256 (423)
T ss_pred             e
Confidence            4

>PF12846 AAA_10: AAA-like domain

Probab=94.06  E-value=0.074  Score=45.67  Aligned_cols=41  Identities=17%  Similarity=0.382  Sum_probs=27.1

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~  114 (298)
                      +++++.|+||+|||......+...+..   +..++++=|..+..
T Consensus         2 ~h~~i~G~tGsGKT~~~~~l~~~~~~~---g~~~~i~D~~g~~~   42 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLKNLLEQLIRR---GPRVVIFDPKGDYS   42 (304)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHc---CCCEEEEcCCchHH
Confidence            578999999999997766444343333   34566665554433

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=94.02  E-value=0.82  Score=44.80  Aligned_cols=17  Identities=24%  Similarity=0.493  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      .|+++.||+|+|||...
T Consensus       204 ~n~lL~G~pG~GKT~l~  220 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIA  220 (731)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            58999999999999654

>PRK05748 replicative DNA helicase; Provisional

Probab=94.02  E-value=0.61  Score=42.87  Aligned_cols=143  Identities=15%  Similarity=0.169  Sum_probs=68.2

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE-EEcCCchHHH-
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA-CVGGKSVGED-  144 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-  144 (298)
                      +..|.-++|.|++|+|||.-.+-.+.+....  .+..++|++ ...-..|+..++-....  ++.... ..|.....+. 
T Consensus       200 ~~~G~livIaarpg~GKT~~al~ia~~~a~~--~g~~v~~fS-lEms~~~l~~R~l~~~~--~v~~~~i~~~~l~~~e~~  274 (448)
T PRK05748        200 LQPNDLIIVAARPSVGKTAFALNIAQNVATK--TDKNVAIFS-LEMGAESLVMRMLCAEG--NIDAQRLRTGQLTDDDWP  274 (448)
T ss_pred             CCCCceEEEEeCCCCCchHHHHHHHHHHHHh--CCCeEEEEe-CCCCHHHHHHHHHHHhc--CCCHHHhhcCCCCHHHHH
Confidence            3345668889999999995444333332222  133566654 33344555555432211  221111 1222222221 


Q ss_pred             -----HHHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc-----cHHHHHHHHHhCC-----
Q 022383          145 -----IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----FKDQIYDVYRYLP-----  204 (298)
Q Consensus       145 -----~~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-----~~~~i~~i~~~~~-----  204 (298)
                           ...+ .+.++.|.     |++.+...++.-......+++||||=.+.+...+     ....+..+.+.+.     
T Consensus       275 ~~~~a~~~l-~~~~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~~~~~~~~~r~~~i~~i~~~LK~lAke  353 (448)
T PRK05748        275 KLTIAMGSL-SDAPIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQGSGRSGENRQQEVSEISRSLKALAKE  353 (448)
T ss_pred             HHHHHHHHH-hcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcCCCCCCCcCHHHHHHHHHHHHHHHHHH
Confidence                 1122 22345553     4455554443311111268999999999884221     1233434444331     


Q ss_pred             CCccEEEEEee
Q 022383          205 PDLQVVLISAT  215 (298)
Q Consensus       205 ~~~~~v~~SAT  215 (298)
                      .++.++++|..
T Consensus       354 ~~i~vi~lsQl  364 (448)
T PRK05748        354 LKVPVIALSQL  364 (448)
T ss_pred             hCCeEEEeccc
Confidence            25667776664

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=93.99  E-value=0.11  Score=45.49  Aligned_cols=18  Identities=28%  Similarity=0.462  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      .++++.||+|+|||....
T Consensus        52 ~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             CcEEEECCCCccHHHHHH
Confidence            579999999999996544

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=93.95  E-value=0.45  Score=45.94  Aligned_cols=39  Identities=13%  Similarity=0.258  Sum_probs=23.1

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.+++||||+|.|.... ...+...+..-+....+|+++
T Consensus       117 g~~KV~IIDEa~~LT~~A-~NALLKtLEEPP~~tifILaT  155 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKSA-FNALLKTLEEPPKHVIFILAT  155 (725)
T ss_pred             CCCEEEEEEChhhCCHHH-HHHHHHHhhcCCCceEEEEEc
Confidence            577899999999985443 333344444444444444433

>CHL00176 ftsH cell division protein; Validated

Probab=93.94  E-value=0.41  Score=45.89  Aligned_cols=55  Identities=16%  Similarity=0.233  Sum_probs=30.9

Q ss_pred             ccccCcccCCCCHHHHHHHHHC-C-CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           30 EAITSFDAMGIKDDLLRGIYQY-G-FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~-~-~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +...+|+++.--+.....+.+. . +..+..++...   ....+.+++.||+|+|||..+
T Consensus       177 ~~~~~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g---~~~p~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        177 DTGITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVG---AKIPKGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             CCCCCHHhccChHHHHHHHHHHHHHHhCHHHHhhcc---CCCCceEEEECCCCCCHHHHH
Confidence            3446788876445555555553 1 11222111110   122467999999999999653

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

Probab=93.85  E-value=0.05  Score=46.59  Aligned_cols=57  Identities=14%  Similarity=0.216  Sum_probs=33.9

Q ss_pred             ccCcccCCCCHHHHHHHHHC--CCC--------CChHHHHHHHHH------hhcCCcEEEEcCCCCchHHHHH
Q 022383           32 ITSFDAMGIKDDLLRGIYQY--GFE--------KPSAIQQRAVMP------IIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~--~~~--------~~~~~Q~~~~~~------~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      ..+.++++-+.+|...|-+.  |-.        ..+.+-.+.-..      -+...|+++.||||||||+.+.
T Consensus        43 ~~~~~~lPtP~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          43 EKELSELPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             chhhccCCChHHHHHHhhhheecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHH
Confidence            34566777788888887552  211        122232322211      1233589999999999997654

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=93.84  E-value=0.55  Score=39.34  Aligned_cols=47  Identities=28%  Similarity=0.362  Sum_probs=27.7

Q ss_pred             CccEEEechhhHhh-ccccH-------HHHHHHHHhC---CCCccEEEEEeeCchhHH
Q 022383          175 AIKLLVLDESDEML-SRGFK-------DQIYDVYRYL---PPDLQVVLISATLPHEIL  221 (298)
Q Consensus       175 ~l~~vViDE~h~~~-~~~~~-------~~i~~i~~~~---~~~~~~v~~SAT~~~~~~  221 (298)
                      ....|.+||.|.+. +..|+       ..+..++..+   ..+--++.+.||-.+++.
T Consensus       210 aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~L  267 (368)
T COG1223         210 APCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELL  267 (368)
T ss_pred             CCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhc
Confidence            34678899999874 33333       2334444433   234557888899765443

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=93.80  E-value=0.52  Score=44.74  Aligned_cols=75  Identities=8%  Similarity=0.143  Sum_probs=56.9

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCC
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                      .+.++||.|+++..++++.+.+.+.    ++.+..++|+.+..+....+.    +..+|+|+|.     . -...+++.+
T Consensus       256 ~~~k~LVF~nt~~~ae~l~~~L~~~----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTd-----v-~arGIDip~  325 (572)
T PRK04537        256 EGARTMVFVNTKAFVERVARTLERH----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD-----V-AARGLHIDG  325 (572)
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHHc----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEeh-----h-hhcCCCccC
Confidence            3558999999999999999988764    678999999877665543332    5679999994     2 234688899


Q ss_pred             ccEEEechh
Q 022383          176 IKLLVLDES  184 (298)
Q Consensus       176 l~~vViDE~  184 (298)
                      +++||.-+.
T Consensus       326 V~~VInyd~  334 (572)
T PRK04537        326 VKYVYNYDL  334 (572)
T ss_pred             CCEEEEcCC
Confidence            999886554

>PRK08760 replicative DNA helicase; Provisional

Probab=93.80  E-value=0.62  Score=43.12  Aligned_cols=143  Identities=20%  Similarity=0.194  Sum_probs=69.5

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHH--
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED--  144 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  144 (298)
                      +..|.=++|.|.+|+|||.-.+-.+.+.....  +..++|++. ..-..|+..++........... ...|.....+.  
T Consensus       226 ~~~G~LivIaarPg~GKTafal~iA~~~a~~~--g~~V~~fSl-EMs~~ql~~Rl~a~~s~i~~~~-i~~g~l~~~e~~~  301 (476)
T PRK08760        226 LQPTDLIILAARPAMGKTTFALNIAEYAAIKS--KKGVAVFSM-EMSASQLAMRLISSNGRINAQR-LRTGALEDEDWAR  301 (476)
T ss_pred             CCCCceEEEEeCCCCChhHHHHHHHHHHHHhc--CCceEEEec-cCCHHHHHHHHHHhhCCCcHHH-HhcCCCCHHHHHH
Confidence            33456678889999999955443333322221  335666653 3334566655544332222111 11222222221  


Q ss_pred             ----HHHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc----cHHHHHHHHHhCC-----CC
Q 022383          145 ----IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----PD  206 (298)
Q Consensus       145 ----~~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~----~~~~i~~i~~~~~-----~~  206 (298)
                          ...+ ....+.|.     |++.+...++.-. .-..+++||||=.+.+...+    ....+..+.+.+.     .+
T Consensus       302 ~~~a~~~l-~~~~l~I~d~~~~t~~~I~~~~r~l~-~~~~~~lVvIDyLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~  379 (476)
T PRK08760        302 VTGAIKML-KETKIFIDDTPGVSPEVLRSKCRRLK-REHDLGLIVIDYLQLMSVPGNSENRATEISEISRSLKGLAKELN  379 (476)
T ss_pred             HHHHHHHH-hcCCEEEeCCCCCCHHHHHHHHHHHH-HhcCCCEEEEecHHhcCCCCCCcccHHHHHHHHHHHHHHHHHhC
Confidence                1122 22455554     4556555444311 11358999999999884222    2233444433332     25


Q ss_pred             ccEEEEEee
Q 022383          207 LQVVLISAT  215 (298)
Q Consensus       207 ~~~v~~SAT  215 (298)
                      +.++++|..
T Consensus       380 ipVi~lsQL  388 (476)
T PRK08760        380 VPVIALSQL  388 (476)
T ss_pred             CEEEEeecc
Confidence            667776643

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

Probab=93.76  E-value=0.32  Score=44.47  Aligned_cols=71  Identities=15%  Similarity=0.215  Sum_probs=56.8

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCC
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                      ..+.+||.++++.-|+-+++.+.+.    ++++..+||+.+..+....+.    +..+|+|||.      .-..+++..+
T Consensus       516 ~~ppiIIFvN~kk~~d~lAk~LeK~----g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTD------vAgRGIDIpn  585 (673)
T KOG0333|consen  516 FDPPIIIFVNTKKGADALAKILEKA----GYKVTTLHGGKSQEQRENALADFREGTGDILVATD------VAGRGIDIPN  585 (673)
T ss_pred             CCCCEEEEEechhhHHHHHHHHhhc----cceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEec------ccccCCCCCc
Confidence            4567999999999999999988876    689999999988877655543    3679999996      2235788888


Q ss_pred             ccEEE
Q 022383          176 IKLLV  180 (298)
Q Consensus       176 l~~vV  180 (298)
                      +++||
T Consensus       586 VSlVi  590 (673)
T KOG0333|consen  586 VSLVI  590 (673)
T ss_pred             cceee
Confidence            88887

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

Probab=93.73  E-value=0.21  Score=42.43  Aligned_cols=46  Identities=11%  Similarity=0.300  Sum_probs=29.1

Q ss_pred             HHHHCCCCCChHHHHHHHHHhhc--CCcEEEEcCCCCchHHHHHHHHHHhhc
Q 022383           47 GIYQYGFEKPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVD   96 (298)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~--~~~~li~~pTG~GKT~~~~~~~~~~~~   96 (298)
                      .|.+.|+   .+.|.+.+..+..  +..+++.||||||||... ..++..+.
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            4556664   4456666655443  346899999999999643 34555543

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.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=93.72  E-value=0.71  Score=37.99  Aligned_cols=52  Identities=19%  Similarity=0.215  Sum_probs=33.6

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .|..+++.|++|+|||.-.+--+...+..   +..++|+.- .+-.+++.+.+..+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~~---g~~~~y~s~-e~~~~~l~~~~~~~   66 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLKN---GEKAMYISL-EEREERILGYAKSK   66 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEEC-CCCHHHHHHHHHHc
Confidence            35678999999999985433334443332   446777754 44567777776655

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.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=93.71  E-value=0.27  Score=43.34  Aligned_cols=63  Identities=17%  Similarity=0.230  Sum_probs=38.6

Q ss_pred             HHHHHHCCCCCChHHHHHHHHHh-hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           45 LRGIYQYGFEKPSAIQQRAVMPI-IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~~~-~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      ...|.+.|+  +++.+...+..+ ..+++++++|+||+|||.. +-.++..+..   ..+.+.+-...|+
T Consensus       154 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTl-l~al~~~i~~---~~riv~iEd~~El  217 (340)
T TIGR03819       154 LDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTL-LSALLALVAP---DERIVLVEDAAEL  217 (340)
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHH-HHHHHccCCC---CCcEEEECCccee
Confidence            445555554  345566665554 4678999999999999953 3334444332   2355666666555

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.

>PRK09087 hypothetical protein; Validated

Probab=93.66  E-value=0.19  Score=41.60  Aligned_cols=40  Identities=8%  Similarity=0.120  Sum_probs=22.8

Q ss_pred             cEEEechhhHhhccccHHHHHHHHHhCCC-CccEEEEEeeCch
Q 022383          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPP-DLQVVLISATLPH  218 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~~~i~~i~~~~~~-~~~~v~~SAT~~~  218 (298)
                      +++++||+|.+.  .-...+..++..+.. ..++++.|.+.|+
T Consensus        89 ~~l~iDDi~~~~--~~~~~lf~l~n~~~~~g~~ilits~~~p~  129 (226)
T PRK09087         89 GPVLIEDIDAGG--FDETGLFHLINSVRQAGTSLLMTSRLWPS  129 (226)
T ss_pred             CeEEEECCCCCC--CCHHHHHHHHHHHHhCCCeEEEECCCChH
Confidence            389999999763  224445556655544 4444444444443

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=93.61  E-value=0.1  Score=43.20  Aligned_cols=14  Identities=21%  Similarity=0.729  Sum_probs=12.2

Q ss_pred             EEEEcCCCCchHHH
Q 022383           73 VIAQAQSGTGKTSM   86 (298)
Q Consensus        73 ~li~~pTG~GKT~~   86 (298)
                      ++|.|+.|+|||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999975

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

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

Probab=93.61  E-value=1.3  Score=41.02  Aligned_cols=97  Identities=18%  Similarity=0.164  Sum_probs=71.4

Q ss_pred             CCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHH---hh-cCCcE
Q 022383           79 SGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---LE-HGVHV  154 (298)
Q Consensus        79 TG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~i  154 (298)
                      .++||+..-++++.+.+... ..|.++|.+.+.+-+.|++..+.   ...++.+..++|..+..+....   .. +...+
T Consensus       366 vF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~---~~~~i~v~vIh~e~~~~qrde~~~~FR~g~Iwv  441 (593)
T KOG0344|consen  366 VFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELE---IYDNINVDVIHGERSQKQRDETMERFRIGKIWV  441 (593)
T ss_pred             eeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhh---hccCcceeeEecccchhHHHHHHHHHhccCeeE
Confidence            47788877666666655554 56678999999999999998776   3457889999998665544333   22 55789


Q ss_pred             EEeChHHHHHHHhccCccCCCccEEEechhh
Q 022383          155 VSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (298)
Q Consensus       155 lV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h  185 (298)
                      +|||.     ++.+ ++++..+.+||-+++-
T Consensus       442 LicTd-----ll~R-GiDf~gvn~VInyD~p  466 (593)
T KOG0344|consen  442 LICTD-----LLAR-GIDFKGVNLVINYDFP  466 (593)
T ss_pred             EEehh-----hhhc-cccccCcceEEecCCC
Confidence            99994     4444 4899999999998874

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.59  E-value=3.1  Score=35.71  Aligned_cols=154  Identities=12%  Similarity=0.130  Sum_probs=82.1

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC-----CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeE
Q 022383           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-----RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQ  103 (298)
Q Consensus        29 ~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-----~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~  103 (298)
                      .+|...|++..=-+...++|++.=+- |-     =+|++..|     +.+++-+|.|+||+..+-  +   +.... + .
T Consensus       126 EKPNVkWsDVAGLE~AKeALKEAVIL-PI-----KFPqlFtGkR~PwrgiLLyGPPGTGKSYLAK--A---VATEA-n-S  192 (439)
T KOG0739|consen  126 EKPNVKWSDVAGLEGAKEALKEAVIL-PI-----KFPQLFTGKRKPWRGILLYGPPGTGKSYLAK--A---VATEA-N-S  192 (439)
T ss_pred             cCCCCchhhhccchhHHHHHHhheee-cc-----cchhhhcCCCCcceeEEEeCCCCCcHHHHHH--H---HHhhc-C-C
Confidence            45666788775556667777764222 11     14566666     368999999999994221  1   11211 1 4


Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEech
Q 022383          104 ALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (298)
Q Consensus       104 ~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE  183 (298)
                      +.|-+.+..|+..+...-.++-                                  ..|..+.++     +..+.|.|||
T Consensus       193 TFFSvSSSDLvSKWmGESEkLV----------------------------------knLFemARe-----~kPSIIFiDE  233 (439)
T KOG0739|consen  193 TFFSVSSSDLVSKWMGESEKLV----------------------------------KNLFEMARE-----NKPSIIFIDE  233 (439)
T ss_pred             ceEEeehHHHHHHHhccHHHHH----------------------------------HHHHHHHHh-----cCCcEEEeeh
Confidence            5666677666655443222221                                  122334443     3567899999


Q ss_pred             hhHhhccc--------cHHHHHHHHHhCC---CCccEEEEEeeCchh-HHHHHHhcCCCCEEE
Q 022383          184 SDEMLSRG--------FKDQIYDVYRYLP---PDLQVVLISATLPHE-ILEMTTKFMTDPVKI  234 (298)
Q Consensus       184 ~h~~~~~~--------~~~~i~~i~~~~~---~~~~~v~~SAT~~~~-~~~~~~~~~~~~~~~  234 (298)
                      +|.+....        .+-..+.+..+..   .+--++.+.||--+. +...+++.+...+.+
T Consensus       234 iDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYI  296 (439)
T KOG0739|consen  234 IDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYI  296 (439)
T ss_pred             hhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHHHhhcceec
Confidence            99875432        1112222333332   234577888886443 333444444444433

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=93.58  E-value=0.16  Score=44.92  Aligned_cols=17  Identities=18%  Similarity=0.010  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      +-+++.||.|+|||+..
T Consensus       149 lgllL~GPPGcGKTllA  165 (413)
T PLN00020        149 LILGIWGGKGQGKSFQC  165 (413)
T ss_pred             eEEEeeCCCCCCHHHHH
Confidence            46889999999999653

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=93.53  E-value=0.86  Score=41.99  Aligned_cols=111  Identities=14%  Similarity=0.260  Sum_probs=82.4

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.+++|.+-|+-.+.++.+.+...    |+++.++|++.+.-+....+.    +.+|++||-     +++++ ++++..+
T Consensus       446 ~eRvLVTtLTKkmAEdLT~Yl~e~----gikv~YlHSdidTlER~eIirdLR~G~~DvLVGI-----NLLRE-GLDiPEV  515 (663)
T COG0556         446 NERVLVTTLTKKMAEDLTEYLKEL----GIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGI-----NLLRE-GLDLPEV  515 (663)
T ss_pred             CCeEEEEeehHHHHHHHHHHHHhc----CceEEeeeccchHHHHHHHHHHHhcCCccEEEee-----hhhhc-cCCCcce
Confidence            468999999999999998887765    899999999988877765543    568999996     35554 6889999


Q ss_pred             cEEEechhhHhhccccH----HHHHHHHHhCC-CCccEEEEEeeCchhHHHHH
Q 022383          177 KLLVLDESDEMLSRGFK----DQIYDVYRYLP-PDLQVVLISATLPHEILEMT  224 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~----~~i~~i~~~~~-~~~~~v~~SAT~~~~~~~~~  224 (298)
                      ++|.|=+||.   .||.    ..|+.+-+.-+ .+-++|+..-.++.++...+
T Consensus       516 sLVAIlDADK---eGFLRse~SLIQtIGRAARN~~GkvIlYAD~iT~sM~~Ai  565 (663)
T COG0556         516 SLVAILDADK---EGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQKAI  565 (663)
T ss_pred             eEEEEeecCc---cccccccchHHHHHHHHhhccCCeEEEEchhhhHHHHHHH
Confidence            9999999997   5543    34444433332 35678888777777665533

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=93.53  E-value=0.19  Score=46.53  Aligned_cols=47  Identities=17%  Similarity=0.316  Sum_probs=29.9

Q ss_pred             HHHHCCCCCChHHHHHHHHHhhcC-C-cEEEEcCCCCchHHHHHHHHHHhhcc
Q 022383           47 GIYQYGFEKPSAIQQRAVMPIIKG-R-DVIAQAQSGTGKTSMIALTVCQTVDT   97 (298)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~~-~-~~li~~pTG~GKT~~~~~~~~~~~~~   97 (298)
                      .|.++|+   .+.|.+.+..+... + -++++||||||||... ..++..+..
T Consensus       220 ~l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~~  268 (486)
T TIGR02533       220 DLETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLNT  268 (486)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccCC
Confidence            4455554   45666666665543 3 4789999999999653 335555543

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.

>TIGR00416 sms DNA repair protein RadA

Probab=93.49  E-value=0.93  Score=41.69  Aligned_cols=52  Identities=19%  Similarity=0.395  Sum_probs=33.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .|.-+++.|++|+|||.-.+..+.+ +...  +.+++|+.. .+-..|+..+.+++
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~-~a~~--g~kvlYvs~-EEs~~qi~~ra~rl  144 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQ-LAKN--QMKVLYVSG-EESLQQIKMRAIRL  144 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH-HHhc--CCcEEEEEC-cCCHHHHHHHHHHc
Confidence            3567899999999999654443333 2222  346888875 34556776655554

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>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=93.47  E-value=0.16  Score=44.20  Aligned_cols=53  Identities=19%  Similarity=0.208  Sum_probs=34.0

Q ss_pred             ChHHHH-HHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           56 PSAIQQ-RAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        56 ~~~~Q~-~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      +++.|. ..|-.+-.+++++++|+||||||. ++.+++..+-.   ..+.+.+=-+.+
T Consensus       128 ~~~~~~ayL~~~ie~~~siii~G~t~sGKTt-~lnall~~Ip~---~~rivtIEdt~E  181 (312)
T COG0630         128 ISPEQAAYLWLAIEARKSIIICGGTASGKTT-LLNALLDFIPP---EERIVTIEDTPE  181 (312)
T ss_pred             CCHHHHHHHHHHHHcCCcEEEECCCCCCHHH-HHHHHHHhCCc---hhcEEEEecccc
Confidence            344443 466677789999999999999994 45555555433   224555444443

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=93.45  E-value=0.26  Score=47.62  Aligned_cols=70  Identities=20%  Similarity=0.252  Sum_probs=53.9

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC-CeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR-EVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~-~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      .+++-|.+++...  ...++|.|..|||||.+..--+...+....- ...++.++=|+.-|.++.+++.++..
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            5789999998766  6788999999999998765555555544322 23688888899999999999988765

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=93.45  E-value=0.18  Score=43.81  Aligned_cols=20  Identities=30%  Similarity=0.637  Sum_probs=17.3

Q ss_pred             hhcCCcEEEEcCCCCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~   86 (298)
                      +..+.+++++||||+|||..
T Consensus       141 v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH
Confidence            44788999999999999954

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.

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=93.40  E-value=0.13  Score=49.27  Aligned_cols=157  Identities=23%  Similarity=0.194  Sum_probs=92.3

Q ss_pred             CCCChHHHHHHHHHhh--------cC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH
Q 022383           53 FEKPSAIQQRAVMPII--------KG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~--------~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~  122 (298)
                      ..+++..|.+++-...        +|  -..+|--..|.||-....-.|++...+.  ..++|+++-+..|--+..+-++
T Consensus       262 sg~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgiIfeNyLkG--RKrAlW~SVSsDLKfDAERDL~  339 (1300)
T KOG1513|consen  262 SGHLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGIIFENYLKG--RKRALWFSVSSDLKFDAERDLR  339 (1300)
T ss_pred             ccchhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEEEehhhhcc--cceeEEEEeccccccchhhchh
Confidence            3568888988886544        23  2455555566666544333355555554  3489999999999888888887


Q ss_pred             HhhccCCceEEEEEc----CCchHHHHHHhhcCCcEEEeChHHHHHHHhcc-------------CccCCCccEEEechhh
Q 022383          123 AIGDFINIQAHACVG----GKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-------------TLRTRAIKLLVLDESD  185 (298)
Q Consensus       123 ~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~-------------~~~~~~l~~vViDE~h  185 (298)
                      .++.. ++.+..+..    .++.++.   -.-.-.++++|-..|.--.+..             ..--..=.+|||||||
T Consensus       340 DigA~-~I~V~alnK~KYakIss~en---~n~krGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECH  415 (1300)
T KOG1513|consen  340 DIGAT-GIAVHALNKFKYAKISSKEN---TNTKRGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECH  415 (1300)
T ss_pred             hcCCC-Cccceehhhccccccccccc---CCccceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhh
Confidence            76532 455444321    1111110   0011268999876664322210             0001334689999999


Q ss_pred             Hhhcc---------ccHHHHHHHHHhCCCCccEEEEEeeC
Q 022383          186 EMLSR---------GFKDQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       186 ~~~~~---------~~~~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      .--.-         ..+..+..+-+.+| +.++|.-|||=
T Consensus       416 kAKNL~p~~~~k~TKtG~tVLdLQk~LP-~ARVVYASATG  454 (1300)
T KOG1513|consen  416 KAKNLVPTAGAKSTKTGKTVLDLQKKLP-NARVVYASATG  454 (1300)
T ss_pred             hhcccccccCCCcCcccHhHHHHHHhCC-CceEEEeeccC
Confidence            85321         14556667777776 68899999994

>PRK05595 replicative DNA helicase; Provisional

Probab=93.39  E-value=1.2  Score=40.89  Aligned_cols=140  Identities=14%  Similarity=0.146  Sum_probs=66.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGEDIRK  147 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  147 (298)
                      .|.-+++-|.||+|||.-.+--+.+....  .+..++|++. ..-..|+..++-....  ++....+ .|.....+. ..
T Consensus       200 ~g~liviaarpg~GKT~~al~ia~~~a~~--~g~~vl~fSl-Ems~~~l~~R~~a~~~--~v~~~~~~~~~l~~~e~-~~  273 (444)
T PRK05595        200 KGDMILIAARPSMGKTTFALNIAEYAALR--EGKSVAIFSL-EMSKEQLAYKLLCSEA--NVDMLRLRTGNLEDKDW-EN  273 (444)
T ss_pred             CCcEEEEEecCCCChHHHHHHHHHHHHHH--cCCcEEEEec-CCCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHH-HH
Confidence            44567788999999995444333322111  2445676654 2234555554433222  2221111 222222221 11


Q ss_pred             hh------cCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc----cHHHHHHHHHhCC-----CCc
Q 022383          148 LE------HGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----PDL  207 (298)
Q Consensus       148 ~~------~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~----~~~~i~~i~~~~~-----~~~  207 (298)
                      +.      ...++.|-     |++.+...++.-.. -..+++||||=.+.+...+    ....+..+.+.+.     .++
T Consensus       274 ~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~~-~~~~~~vvIDylql~~~~~~~~~r~~~v~~is~~LK~lAke~~i  352 (444)
T PRK05595        274 IARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLKI-EHGIDMILIDYLQLMSGGKGSESRQQEVSEISRSIKALAKEMEC  352 (444)
T ss_pred             HHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEeHHHhccCCCCCccHHHHHHHHHHHHHHHHHHhCC
Confidence            11      12345442     34444444433111 1358999999999985322    1233444433332     256


Q ss_pred             cEEEEEee
Q 022383          208 QVVLISAT  215 (298)
Q Consensus       208 ~~v~~SAT  215 (298)
                      .++++|..
T Consensus       353 ~vi~lsQL  360 (444)
T PRK05595        353 PVIALSQL  360 (444)
T ss_pred             eEEEeecc
Confidence            67777543

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=93.39  E-value=3.5  Score=39.83  Aligned_cols=114  Identities=13%  Similarity=0.180  Sum_probs=72.8

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCC
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                      .+.+++|.|+++..+..+.+.+.+.    ++.+..++|+....+....+    .+..+|+|||-     .+ ..++++..
T Consensus       441 ~g~~vLIf~~tk~~ae~L~~~L~~~----gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~-----~L-~rGfDiP~  510 (655)
T TIGR00631       441 RNERVLVTTLTKKMAEDLTDYLKEL----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGIN-----LL-REGLDLPE  510 (655)
T ss_pred             CCCEEEEEECCHHHHHHHHHHHhhh----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcC-----hh-cCCeeeCC
Confidence            3568999999999999999888765    67888888886655443322    25678999983     22 35788999


Q ss_pred             ccEEEechhhHhhcc-ccHHHHHHHHHhCC-CCccEEEEEeeCchhHHHH
Q 022383          176 IKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLPHEILEM  223 (298)
Q Consensus       176 l~~vViDE~h~~~~~-~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~~~~~  223 (298)
                      +++||+-|++...-. .....++.+-+--+ .....+++-...+..+...
T Consensus       511 v~lVvi~DadifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~~~~~~~a  560 (655)
T TIGR00631       511 VSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKA  560 (655)
T ss_pred             CcEEEEeCcccccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCCCHHHHHH
Confidence            999998888764322 22233333322222 2344555555555544443

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

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=93.39  E-value=0.14  Score=48.61  Aligned_cols=41  Identities=17%  Similarity=0.252  Sum_probs=27.4

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      +++-+.+++||.-.-++......+...+....++.-+|++|
T Consensus       485 l~~~~illLDEpts~LD~~~~~~i~~~L~~~~~~~tiIiit  525 (571)
T TIGR02203       485 LKDAPILILDEATSALDNESERLVQAALERLMQGRTTLVIA  525 (571)
T ss_pred             hcCCCEEEEeCccccCCHHHHHHHHHHHHHHhCCCEEEEEe
Confidence            35678999999877666666777766666654444445443

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=93.37  E-value=1.5  Score=38.32  Aligned_cols=53  Identities=13%  Similarity=0.288  Sum_probs=31.7

Q ss_pred             HHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEee
Q 022383          160 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       160 ~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      ..+...+....+. ...+++|||++|.|.... ...+.++++.-| +..++++|..
T Consensus       110 r~i~~~l~~~p~~-~~~kVvII~~ae~m~~~a-aNaLLK~LEEPp-~~~fILi~~~  162 (314)
T PRK07399        110 REIKRFLSRPPLE-APRKVVVIEDAETMNEAA-ANALLKTLEEPG-NGTLILIAPS  162 (314)
T ss_pred             HHHHHHHccCccc-CCceEEEEEchhhcCHHH-HHHHHHHHhCCC-CCeEEEEECC
Confidence            3444444443332 578999999999985443 455556666655 5555555543

>PRK12608 transcription termination factor Rho; Provisional

Probab=93.34  E-value=0.87  Score=40.45  Aligned_cols=39  Identities=23%  Similarity=0.358  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhh---cCCcEEEEcCCCCchHHHHHHHHHHhhcc
Q 022383           58 AIQQRAVMPII---KGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (298)
Q Consensus        58 ~~Q~~~~~~~~---~~~~~li~~pTG~GKT~~~~~~~~~~~~~   97 (298)
                      ..-.++++.+.   .|+..+|.||.|+|||.... -+.+.+..
T Consensus       118 ~~~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~-~la~~i~~  159 (380)
T PRK12608        118 DLSMRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQ-QIAAAVAA  159 (380)
T ss_pred             chhHhhhhheeecCCCceEEEECCCCCCHHHHHH-HHHHHHHh
Confidence            44556777765   78999999999999996533 34444433

>PRK10436 hypothetical protein; Provisional

Probab=93.33  E-value=0.22  Score=45.69  Aligned_cols=47  Identities=19%  Similarity=0.317  Sum_probs=29.4

Q ss_pred             HHHHCCCCCChHHHHHHHHHhh--cCCcEEEEcCCCCchHHHHHHHHHHhhcc
Q 022383           47 GIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (298)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~pTG~GKT~~~~~~~~~~~~~   97 (298)
                      .|.++|+   .+.|.+.+..+.  .+.-++++||||||||... ..++..+..
T Consensus       196 ~L~~LG~---~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~~  244 (462)
T PRK10436        196 DLETLGM---TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLNT  244 (462)
T ss_pred             CHHHcCc---CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhCC
Confidence            3445553   355666665544  3456899999999999653 345555533

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=93.32  E-value=0.64  Score=42.50  Aligned_cols=72  Identities=11%  Similarity=0.149  Sum_probs=55.5

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCC
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                      ...++||.|++++-+..+.+.++..    ++.+..++|+.+..+....+.    +..+|+|+|.      +-..++++.+
T Consensus       244 ~~~~~lVF~~s~~~~~~l~~~L~~~----~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd------~~~~GiDip~  313 (434)
T PRK11192        244 EVTRSIVFVRTRERVHELAGWLRKA----GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATD------VAARGIDIDD  313 (434)
T ss_pred             CCCeEEEEeCChHHHHHHHHHHHhC----CCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEcc------ccccCccCCC
Confidence            4458999999999999999988763    678889999887766544432    5678999994      2235788899


Q ss_pred             ccEEEe
Q 022383          176 IKLLVL  181 (298)
Q Consensus       176 l~~vVi  181 (298)
                      +++||.
T Consensus       314 v~~VI~  319 (434)
T PRK11192        314 VSHVIN  319 (434)
T ss_pred             CCEEEE
Confidence            999884

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=93.31  E-value=0.21  Score=46.19  Aligned_cols=39  Identities=15%  Similarity=0.341  Sum_probs=23.3

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      ..+.+..||||+|++....|-..+ +.+..=|+++.+|+.
T Consensus       117 ~~ryKVyiIDEvHMLS~~afNALL-KTLEEPP~hV~FIlA  155 (515)
T COG2812         117 EGRYKVYIIDEVHMLSKQAFNALL-KTLEEPPSHVKFILA  155 (515)
T ss_pred             cccceEEEEecHHhhhHHHHHHHh-cccccCccCeEEEEe
Confidence            468899999999998655544222 233333344444443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=93.19  E-value=1  Score=44.89  Aligned_cols=18  Identities=22%  Similarity=0.536  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      .+.++.||+|+|||...-
T Consensus       195 ~n~lL~G~pGvGKT~l~~  212 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIVE  212 (852)
T ss_pred             CceEEEcCCCCCHHHHHH
Confidence            689999999999996543

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=93.17  E-value=1.1  Score=41.46  Aligned_cols=44  Identities=20%  Similarity=0.306  Sum_probs=27.7

Q ss_pred             CCccEEEechhhHhhccc------c-HHHHHHHHHhC---CCCccEEEEEeeCc
Q 022383          174 RAIKLLVLDESDEMLSRG------F-KDQIYDVYRYL---PPDLQVVLISATLP  217 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~------~-~~~i~~i~~~~---~~~~~~v~~SAT~~  217 (298)
                      +....|.|||+|.+....      | ...+..++--+   .++--+|++.||--
T Consensus       395 ~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNf  448 (752)
T KOG0734|consen  395 RAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNF  448 (752)
T ss_pred             cCCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCC
Confidence            355788999999986542      1 12233343333   35667999999953

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=93.17  E-value=0.13  Score=49.29  Aligned_cols=49  Identities=18%  Similarity=0.135  Sum_probs=38.7

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      +++++.||||+|||..+++|-+-...     ..+||+=|--|+...+....++.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~~-----gS~VV~DpKGE~~~~Ta~~R~~~  188 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTFK-----GSVIALDVKGELFELTSRARKAS  188 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcCC-----CCEEEEeCCchHHHHHHHHHHhC
Confidence            58999999999999999998766532     25777778888888877666554

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=93.13  E-value=1  Score=37.58  Aligned_cols=30  Identities=20%  Similarity=0.369  Sum_probs=21.1

Q ss_pred             HHhhcCC-cEEEEcCCCCchHHHHHHHHHHhh
Q 022383           65 MPIIKGR-DVIAQAQSGTGKTSMIALTVCQTV   95 (298)
Q Consensus        65 ~~~~~~~-~~li~~pTG~GKT~~~~~~~~~~~   95 (298)
                      +.+.+|+ -+.++|+-|||||..-- .+...+
T Consensus        45 ~~i~d~qg~~~vtGevGsGKTv~~R-al~~s~   75 (269)
T COG3267          45 AAIADGQGILAVTGEVGSGKTVLRR-ALLASL   75 (269)
T ss_pred             HHHhcCCceEEEEecCCCchhHHHH-HHHHhc
Confidence            3455666 78899999999997655 344433

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=93.10  E-value=0.68  Score=42.17  Aligned_cols=74  Identities=14%  Similarity=0.144  Sum_probs=55.7

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      ..++||.|+++..+..+.+.+...    ++++..++|+....++...+    .+.++|+|+|.      +-..++++.++
T Consensus       255 ~~~~lVF~~t~~~~~~l~~~L~~~----g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTd------v~~rGiDip~v  324 (423)
T PRK04837        255 PDRAIIFANTKHRCEEIWGHLAAD----GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATD------VAARGLHIPAV  324 (423)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhC----CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEec------hhhcCCCcccc
Confidence            458999999999999998887654    67889999987766554333    25689999995      22357888899


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||.-+.
T Consensus       325 ~~VI~~d~  332 (423)
T PRK04837        325 THVFNYDL  332 (423)
T ss_pred             CEEEEeCC
Confidence            98875543

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=93.09  E-value=0.25  Score=47.06  Aligned_cols=32  Identities=13%  Similarity=0.219  Sum_probs=22.6

Q ss_pred             ChHHHHHHHHHhhc------CCcEEEEcCCCCchHHHH
Q 022383           56 PSAIQQRAVMPIIK------GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~------~~~~li~~pTG~GKT~~~   87 (298)
                      +.++-.+.+....+      .|-.+++||.|.|||..+
T Consensus       306 ~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGKTTLA  343 (877)
T KOG1969|consen  306 KGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGKTTLA  343 (877)
T ss_pred             cccchhhhhhcccCccCCCccceEEeecCCCCChhHHH
Confidence            44555666666552      267999999999999543

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=93.08  E-value=0.11  Score=44.04  Aligned_cols=26  Identities=31%  Similarity=0.404  Sum_probs=20.7

Q ss_pred             HHHHhhcCCcEEEEcCCCCchHHHHH
Q 022383           63 AVMPIIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        63 ~~~~~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      +...+..|+++++.||+|+|||..+.
T Consensus        14 ~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        14 ALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            34445678999999999999997654

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).

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.05  E-value=1.8  Score=38.52  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      +.+++.||.|+|||....
T Consensus        40 ~~~L~~G~~G~GKt~~a~   57 (367)
T PRK14970         40 QALLFCGPRGVGKTTCAR   57 (367)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            368899999999996544

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Probab=92.99  E-value=0.38  Score=35.35  Aligned_cols=38  Identities=18%  Similarity=0.219  Sum_probs=31.8

Q ss_pred             chHHHHHHHHhhCC--CCcEEEEecchhhHHHHHHHHhhh
Q 022383          258 WKFDTLCDLYDTLT--ITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       258 ~k~~~l~~ll~~~~--~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      .|...+..++....  .+++||||++...++.+++.|.+.
T Consensus        12 ~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~   51 (131)
T cd00079          12 EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKP   51 (131)
T ss_pred             HHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhc
Confidence            47788888887653  679999999999999999999753

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=92.94  E-value=0.2  Score=51.47  Aligned_cols=57  Identities=25%  Similarity=0.280  Sum_probs=45.8

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccC--CCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--SREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~--~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      -.+++++|.|..|||||.+..--++..+...  -.-.+.++++-|++-+.++..++..-
T Consensus        14 ~~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~   72 (1139)
T COG1074          14 PPGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDR   72 (1139)
T ss_pred             CCCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHH
Confidence            3568999999999999988777777777663  23448999999999999988887653

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=92.83  E-value=1.1  Score=41.00  Aligned_cols=80  Identities=18%  Similarity=0.194  Sum_probs=54.4

Q ss_pred             HHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH
Q 022383           43 DLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (298)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~  122 (298)
                      .+++.+++ ++-.+...|..+.-..-.|+. -+.|-.|||||...++-+-. +...+...+++|-+-|+.|+.++.+...
T Consensus       151 a~l~~ies-kIanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~-lh~knPd~~I~~Tfftk~L~s~~r~lv~  227 (660)
T COG3972         151 ALLDTIES-KIANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAE-LHSKNPDSRIAFTFFTKILASTMRTLVP  227 (660)
T ss_pred             HHHHHHHH-HHhcccchhheeeeecCCchh-hhhcccCCCchhHHHHHHHH-HhcCCCCceEEEEeehHHHHHHHHHHHH
Confidence            34444444 344566678777655666766 77899999999765443322 3333344589999999999999998887


Q ss_pred             Hhh
Q 022383          123 AIG  125 (298)
Q Consensus       123 ~~~  125 (298)
                      ++.
T Consensus       228 ~F~  230 (660)
T COG3972         228 EFF  230 (660)
T ss_pred             HHH
Confidence            764

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=92.79  E-value=0.36  Score=46.21  Aligned_cols=53  Identities=17%  Similarity=0.328  Sum_probs=37.3

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH--HHHHHHHHHHHHhhc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR--ELATQTEKVILAIGD  126 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~--~l~~q~~~~~~~~~~  126 (298)
                      ++++|.|+||+|||..+...+.+.+..   +..++++=|-.  +|...+...++..+.
T Consensus       177 ~H~lv~G~TGsGKT~l~~~l~~q~i~~---g~~viv~DpKgD~~l~~~~~~~~~~~G~  231 (634)
T TIGR03743       177 GHTLVLGTTGVGKTRLAELLITQDIRR---GDVVIVIDPKGDADLKRRMRAEAKRAGR  231 (634)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCchHHHHHHHHHHHHhCC
Confidence            689999999999998775555555543   33566666754  477777777776643

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=92.72  E-value=0.2  Score=40.50  Aligned_cols=38  Identities=16%  Similarity=0.391  Sum_probs=22.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      ++++||||||||... ..++..+... .+.+++.+-...+
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~~~-~~~~i~t~e~~~E   41 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYINKN-KTHHILTIEDPIE   41 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhhhc-CCcEEEEEcCCcc
Confidence            689999999999653 3344444332 2235555554333

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.

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=92.69  E-value=0.9  Score=41.85  Aligned_cols=73  Identities=23%  Similarity=0.252  Sum_probs=54.5

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      ..++||.|+++.-+..+.+.+.+.    ++.+..++|+.+..+....+.    +..+|+|||.     .+ ...+++..+
T Consensus       245 ~~~~lVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTd-----v~-~rGiDip~v  314 (456)
T PRK10590        245 WQQVLVFTRTKHGANHLAEQLNKD----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD-----IA-ARGLDIEEL  314 (456)
T ss_pred             CCcEEEEcCcHHHHHHHHHHHHHC----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcc-----HH-hcCCCcccC
Confidence            457999999999999999888654    678889999887665543332    4678999994     22 246888899


Q ss_pred             cEEEech
Q 022383          177 KLLVLDE  183 (298)
Q Consensus       177 ~~vViDE  183 (298)
                      ++||.=+
T Consensus       315 ~~VI~~~  321 (456)
T PRK10590        315 PHVVNYE  321 (456)
T ss_pred             CEEEEeC
Confidence            8887443

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=92.68  E-value=2.9  Score=35.94  Aligned_cols=42  Identities=21%  Similarity=0.279  Sum_probs=29.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeC
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      ...+++|||++|.|.... ...+.++++.-|.+..++++|...
T Consensus        94 ~~~kv~ii~~ad~mt~~A-aNaLLK~LEEPp~~~~fiL~~~~~  135 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDA-ISAFLKVLEDPPQHGVIILTSAKP  135 (290)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHhhcCCCCeEEEEEeCCh
Confidence            567899999999986443 566666777766666666666553

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=92.65  E-value=2.9  Score=33.47  Aligned_cols=52  Identities=13%  Similarity=0.153  Sum_probs=36.5

Q ss_pred             ccEEEechhhHhhcccc-HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhc
Q 022383          176 IKLLVLDESDEMLSRGF-KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKF  227 (298)
Q Consensus       176 l~~vViDE~h~~~~~~~-~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~  227 (298)
                      =+++||--.|....-++ ...+.+=.+..+++.+++++|+.=...+..++.+.
T Consensus       144 aDllVInK~DLa~~v~~dlevm~~da~~~np~~~ii~~n~ktg~G~~~~~~~i  196 (202)
T COG0378         144 ADLLVINKTDLAPYVGADLEVMARDAKEVNPEAPIIFTNLKTGEGLDEWLRFI  196 (202)
T ss_pred             eeEEEEehHHhHHHhCccHHHHHHHHHHhCCCCCEEEEeCCCCcCHHHHHHHH
Confidence            46677777776544443 24455556667789999999999888888877654

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=92.62  E-value=0.26  Score=43.59  Aligned_cols=43  Identities=9%  Similarity=0.255  Sum_probs=26.8

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      .+..++++||||||||... ..++..+... .+.+++.+-...+.
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~~~-~~~~i~tiEdp~E~  163 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYINKN-AAGHIITIEDPIEY  163 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhCcC-CCCEEEEEcCChhh
Confidence            4678999999999999653 3344444322 23356666554443

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.

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=92.58  E-value=0.18  Score=47.94  Aligned_cols=42  Identities=17%  Similarity=0.254  Sum_probs=25.8

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEee
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      ++.+.+++||+-.-.+......+.+.++...++.-++++|--
T Consensus       493 ~~~~ililDEpts~lD~~~~~~i~~~l~~~~~~~t~IiitH~  534 (576)
T TIGR02204       493 KDAPILLLDEATSALDAESEQLVQQALETLMKGRTTLIIAHR  534 (576)
T ss_pred             hCCCeEEEeCcccccCHHHHHHHHHHHHHHhCCCEEEEEecc
Confidence            577889999987655665555565555555444445554433

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>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=92.57  E-value=0.095  Score=44.66  Aligned_cols=20  Identities=50%  Similarity=0.747  Sum_probs=17.4

Q ss_pred             hhcCCcEEEEcCCCCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~   86 (298)
                      +..++.++++||+|+|||..
T Consensus        30 ~~~~~pvLl~G~~GtGKT~l   49 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSL   49 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHH
T ss_pred             HHcCCcEEEECCCCCchhHH
Confidence            34788999999999999965

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=92.56  E-value=0.32  Score=46.06  Aligned_cols=46  Identities=24%  Similarity=0.369  Sum_probs=29.7

Q ss_pred             HHHHCCCCCChHHHHHHHHHhhc--CCcEEEEcCCCCchHHHHHHHHHHhhc
Q 022383           47 GIYQYGFEKPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVD   96 (298)
Q Consensus        47 ~l~~~~~~~~~~~Q~~~~~~~~~--~~~~li~~pTG~GKT~~~~~~~~~~~~   96 (298)
                      .|.++|+   .+.|...+..+..  +..++++||||||||... ..++..+.
T Consensus       294 ~l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       294 DIDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             CHHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            3556664   3556666665543  356889999999999653 34555553

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

>PRK05636 replicative DNA helicase; Provisional

Probab=92.51  E-value=0.8  Score=42.69  Aligned_cols=138  Identities=17%  Similarity=0.195  Sum_probs=62.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE-EcCCchHHH----
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC-VGGKSVGED----  144 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~----  144 (298)
                      |.=+++.|.+|+|||.-.+-.+.+....  .+..++|++ ..--..|+..++-....  ++....+ .|..+..+.    
T Consensus       265 G~Liiiaarpg~GKT~~al~~a~~~a~~--~g~~v~~fS-lEMs~~ql~~R~ls~~s--~v~~~~i~~g~l~~~e~~~~~  339 (505)
T PRK05636        265 GQMIIVAARPGVGKSTLALDFMRSASIK--HNKASVIFS-LEMSKSEIVMRLLSAEA--EVRLSDMRGGKMDEDAWEKLV  339 (505)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHh--CCCeEEEEE-eeCCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHHHHHH
Confidence            4556788999999995433222222212  133566663 22223344433322211  1111111 222222221    


Q ss_pred             --HHHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc----cHHHHHHHHHhCC-----CCcc
Q 022383          145 --IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG----FKDQIYDVYRYLP-----PDLQ  208 (298)
Q Consensus       145 --~~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~----~~~~i~~i~~~~~-----~~~~  208 (298)
                        ...+ ....+.|-     |...+....+.-.. -..+++||||=.|.|....    ....+..+.+.+.     -++.
T Consensus       340 ~a~~~l-~~~~l~I~d~~~~ti~~I~~~~r~~~~-~~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ip  417 (505)
T PRK05636        340 QRLGKI-AQAPIFIDDSANLTMMEIRSKARRLKQ-KHDLKLIVVDYLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVP  417 (505)
T ss_pred             HHHHHH-hcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCe
Confidence              1112 23355553     33444443332111 1358999999999985321    1233333433332     2577


Q ss_pred             EEEEEe
Q 022383          209 VVLISA  214 (298)
Q Consensus       209 ~v~~SA  214 (298)
                      ++++|.
T Consensus       418 Vi~lsQ  423 (505)
T PRK05636        418 LIAISQ  423 (505)
T ss_pred             EEEEee
Confidence            777764

>PRK10865 protein disaggregation chaperone; Provisional

Probab=92.50  E-value=1.3  Score=44.14  Aligned_cols=18  Identities=22%  Similarity=0.536  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      .+.++.||+|+|||....
T Consensus       200 ~n~lL~G~pGvGKT~l~~  217 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIVE  217 (857)
T ss_pred             CceEEECCCCCCHHHHHH
Confidence            489999999999996543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=92.41  E-value=0.72  Score=45.92  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.4

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      .+++.||||+|||..+-
T Consensus       598 ~~lf~Gp~GvGKT~lA~  614 (852)
T TIGR03345       598 VFLLVGPSGVGKTETAL  614 (852)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            48999999999997654

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=92.35  E-value=0.44  Score=38.04  Aligned_cols=57  Identities=18%  Similarity=0.246  Sum_probs=34.4

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhcc-------CCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDT-------SSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~-------~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      .|.-+++.||+|+|||...+-.+.+....       ...+.+++|+..-.. ..++.+++..+..
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~   94 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQ   94 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhc
Confidence            56679999999999996654444443321       113457888776544 6677777777653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	298
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-122
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-122
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-122
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		1e-122
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-119
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-119
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		4e-95
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		8e-95
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-89
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-84
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		8e-71
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		8e-70
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		3e-65
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-63
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-51
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		3e-44
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		3e-44
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		4e-43
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-43
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		4e-43
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		4e-43
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		1e-37
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-37
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		3e-37
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		3e-37
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		1e-35
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-34
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		1e-33
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		7e-31
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		1e-30
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		3e-30
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		8e-30
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-29
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-29
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		3e-28
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		4e-27
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		2e-26
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		6e-25
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		2e-23
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		3e-23
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-23
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-23
3ly5_A	262	Ddx18 Dead-Domain Length = 262		4e-21
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		4e-20
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		1e-17
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		3e-16
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		4e-15
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		4e-15
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		4e-15
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		4e-13
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		5e-07
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		7e-04

>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 =  435 bits (1118), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 202/266 (75%), Positives = 239/266 (89%)
Query: 20  KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
           K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct: 25  KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 84
Query: 80  GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
           GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct: 85  GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 144
Query: 140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
           +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct: 145 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 204
Query: 200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
           YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct: 205 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 264
Query: 260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
           FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 265 FDTLCDLYDTLTITQAVIFCNTKRKV 290

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

Iteration: 1
 Score =  435 bits (1118), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 202/266 (75%), Positives = 239/266 (89%)
Query: 20  KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
           K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct: 24  KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 83
Query: 80  GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
           GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct: 84  GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 143
Query: 140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
           +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct: 144 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 203
Query: 200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
           YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct: 204 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 263
Query: 260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
           FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 264 FDTLCDLYDTLTITQAVIFCNTKRKV 289

>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 =  434 bits (1117), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 202/266 (75%), Positives = 239/266 (89%)
Query: 20  KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
           K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct: 25  KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 84
Query: 80  GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
           GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct: 85  GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 144
Query: 140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
           +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct: 145 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 204
Query: 200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
           YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct: 205 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 264
Query: 260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
           FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 265 FDTLCDLYDTLTITQAVIFCNTKRKV 290

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

Iteration: 1
 Score =  434 bits (1116), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 202/266 (75%), Positives = 239/266 (89%)
Query: 20  KMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQS 79
           K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QS
Sbjct: 3   KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 62
Query: 80  GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
           GTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG 
Sbjct: 63  GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 122
Query: 140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
           +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDV
Sbjct: 123 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 182
Query: 200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
           YRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWK
Sbjct: 183 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWK 242
Query: 260 FDTLCDLYDTLTITQAVIFCNTKRKI 285
           FDTLCDLYDTLTITQAVIFCNTKRK+
Sbjct: 243 FDTLCDLYDTLTITQAVIFCNTKRKV 268

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

Iteration: 1
 Score =  424 bits (1090), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 195/252 (77%), Positives = 231/252 (91%)
Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQ 93
           +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QSGTGKT+  +++V Q
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 94  TVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVH 153
            +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q+HAC+GG +VGEDIRKL++G H
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDYGQH 121
Query: 154 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS 213
           VV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDVYRYLPP  QVVLIS
Sbjct: 122 VVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLIS 181
Query: 214 ATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT 273
           ATLPHE+LEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT
Sbjct: 182 ATLPHEVLEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT 241
Query: 274 QAVIFCNTKRKI 285
           QAVIFCNTKRK+
Sbjct: 242 QAVIFCNTKRKV 253

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

Iteration: 1
 Score =  424 bits (1089), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 196/252 (77%), Positives = 230/252 (91%)
Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQ 93
           +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ+QSGTGKT+  +++V Q
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 94  TVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVH 153
            +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+GG +VGEDIRKL++G H
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQH 121
Query: 154 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS 213
           VV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QIYDVYRYLPP  QVVLIS
Sbjct: 122 VVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLIS 181
Query: 214 ATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT 273
           ATLPHEILEMT KFMTDP++ILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT
Sbjct: 182 ATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT 241
Query: 274 QAVIFCNTKRKI 285
           QAVIFCNTKRK+
Sbjct: 242 QAVIFCNTKRKV 253

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  344 bits (882), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 156/257 (60%), Positives = 208/257 (80%), Gaps = 1/257 (0%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           E + SFD M + + LLRGIY YGFEKPSAIQQRA++P IKG DVIAQAQSGTGKT+  A+
Sbjct: 11  EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 70
Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
           ++ Q ++   +  QAL+L+PTRELA Q +KV++A+GD++    HAC+GG +V  +++KL+
Sbjct: 71  SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 130
Query: 150 -HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
               H++ GTPGRV DM+ R+ L  + IK+ VLDE+DEMLSRGFKDQIYD+++ L  + Q
Sbjct: 131 MEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQ 190
Query: 209 VVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 268
           VVL+SAT+P ++LE+T KFM DP++ILVK++ELTLEGI+QF++ VEREEWK DTLCDLY+
Sbjct: 191 VVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYE 250
Query: 269 TLTITQAVIFCNTKRKI 285
           TLTITQAVIF NT+RK+
Sbjct: 251 TLTITQAVIFINTRRKV 267

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  343 bits (879), Expect = 8e-95,   Method: Compositional matrix adjust.
 Identities = 156/257 (60%), Positives = 208/257 (80%), Gaps = 1/257 (0%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           E + SFD M + + LLRGIY YGFEKPSAIQQRA++P IKG DVIAQAQSGTGKT+  A+
Sbjct: 37  EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 96
Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
           ++ Q ++   +  QAL+L+PTRELA Q +KV++A+GD++    HAC+GG +V  +++KL+
Sbjct: 97  SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 156
Query: 150 -HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
               H++ GTPGRV DM+ R+ L  + IK+ VLDE+DEMLSRGFKDQIYD+++ L  + Q
Sbjct: 157 MEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQ 216
Query: 209 VVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 268
           VVL+SAT+P ++LE+T KFM DP++ILVK++ELTLEGI+QF++ VEREEWK DTLCDLY+
Sbjct: 217 VVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYE 276
Query: 269 TLTITQAVIFCNTKRKI 285
           TLTITQAVIF NT+RK+
Sbjct: 277 TLTITQAVIFINTRRKV 293

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  325 bits (833), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 149/254 (58%), Positives = 201/254 (79%), Gaps = 1/254 (0%)
Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTV 91
           +  FD M + ++LLRG++ YGFE+PSAIQQRA+MPII+G DV+AQAQSGTGKT   ++  
Sbjct: 21  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 80
Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
            Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ HAC+GG S  ED   L   
Sbjct: 81  LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDA 140
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
             +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK+QIY ++  LPP  QVVL
Sbjct: 141 -QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVL 199
Query: 212 ISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT 271
           +SAT+P+++LE+TTKFM +PV+ILVK+DELTLEGIKQF+V VE EE+K++ L DLYD+++
Sbjct: 200 LSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSIS 259
Query: 272 ITQAVIFCNTKRKI 285
           +TQAVIFCNT+RK+
Sbjct: 260 VTQAVIFCNTRRKV 273

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  308 bits (790), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 191/251 (76%), Gaps = 1/251 (0%)
Query: 35  FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQT 94
           FD   + ++LLRG++ YGFE+PSAIQQRA+ PII+G DV+AQAQSGTGKT   ++   Q 
Sbjct: 23  FDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 95  VDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHV 154
           +DTS +  QAL L+PTRELA Q +KV+ A+    +I+ HAC+GG S  ED   L     +
Sbjct: 83  IDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGTSFVEDAEGLRDA-QI 141
Query: 155 VSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA 214
           V GTPGRV D I+R+  RT  IK  +LDE+DE LS GFK+QIY ++  LPP  QVVL+SA
Sbjct: 142 VVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSGFKEQIYQIFTLLPPTTQVVLLSA 201
Query: 215 TLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ 274
           T P+++LE+TTKF  +PV+ILVK+DELTLEGIKQF+V VE EE+K++ L DLYD++++TQ
Sbjct: 202 TXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQ 261
Query: 275 AVIFCNTKRKI 285
           AVIFCNT+RK+
Sbjct: 262 AVIFCNTRRKV 272

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

Iteration: 1
 Score =  263 bits (672), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 122/211 (57%), Positives = 167/211 (79%), Gaps = 1/211 (0%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           E + +FD M +K+ LLRGIY YGFEKPSAIQQRA++P IKG DVIAQAQSGTGKT+  A+
Sbjct: 27  EIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAI 86
Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
           ++ Q ++   +E QAL+L+PTRELA Q +KVILA+GD++    HAC+GG +V  +++KL+
Sbjct: 87  SILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQ 146
Query: 150 -HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
               H+V GTPGRV DM+ R+ L  + IK+ VLDE+DEMLSRGFKDQIY++++ L   +Q
Sbjct: 147 AEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQ 206
Query: 209 VVLISATLPHEILEMTTKFMTDPVKILVKRD 239
           VVL+SAT+P ++LE+T KFM DP++ILVK++
Sbjct: 207 VVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>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 =  260 bits (664), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 122/213 (57%), Positives = 164/213 (76%), Gaps = 1/213 (0%)
Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTV 91
           +  FD M + ++LLRG++ YGFE+PSAIQQRA+MPII+G DV+AQAQSGTGKT   ++  
Sbjct: 13  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 72
Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
            Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ HAC+GG S  ED   L   
Sbjct: 73  LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDA 132
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
             +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK+QIY ++  LPP  QVVL
Sbjct: 133 -QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVL 191
Query: 212 ISATLPHEILEMTTKFMTDPVKILVKRDELTLE 244
           +SAT+P+++LE+TTKFM +PV+ILVK+DELTLE
Sbjct: 192 LSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  245 bits (625), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 115/205 (56%), Positives = 155/205 (75%), Gaps = 1/205 (0%)
Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTV 91
           +  FD M + + LLRG++ YGFE+PSAIQQRA+MPII+G DV+AQAQSGTGKT   ++  
Sbjct: 20  VYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 79
Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
            Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ HAC+GG S  ED   L   
Sbjct: 80  LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDA 139
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
             +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK+QIY ++  LPP  QVVL
Sbjct: 140 -QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVL 198
Query: 212 ISATLPHEILEMTTKFMTDPVKILV 236
           +SAT+P+++LE+TTKFM +PV+ILV
Sbjct: 199 LSATMPNDVLEVTTKFMRNPVRILV 223

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  239 bits (610), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 110/208 (52%), Positives = 152/208 (73%), Gaps = 1/208 (0%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           E + SFD M + + LLRGIY YGFE PSAIQQRA++P I G DVIAQAQSGTG T+  A+
Sbjct: 12  EIVDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAI 71
Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
           ++ Q ++      QAL+L+PTRELA Q + V++A+GD++    HAC+GG +V  +++ L+
Sbjct: 72  SILQQIELDLXATQALVLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEVQXLQ 131
Query: 150 -HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
               H++ GTPGRV DM+ R+ L    I + VLDE+DEMLSRGF DQIYD+++ L  + Q
Sbjct: 132 MEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQXLNSNTQ 191
Query: 209 VVLISATLPHEILEMTTKFMTDPVKILV 236
           VVL+SAT+P ++LE+T  FM DP++ILV
Sbjct: 192 VVLLSATMPSDVLEVTXXFMRDPIRILV 219

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

Iteration: 1
 Score =  198 bits (503), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 157/273 (57%), Gaps = 12/273 (4%)
Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
            +F+   +K +LL GI++ GFEKPS IQ+ A+   I GRD++A+A++GTGKT+   +   
Sbjct: 21  NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 80
Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV 152
           + V     ++QALI+ PTRELA QT +V+  +G    I      GG ++ +DI +L   V
Sbjct: 81  EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETV 140
Query: 153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI 212
           H++ GTPGRV D+  RK        L ++DE+D+MLSR FK  I  +  +LPP  Q +L 
Sbjct: 141 HILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLF 200
Query: 213 SATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTI 272
           SAT P  + E   K +  P +I +  +ELTL+GI Q++  VE E  K   L  L+  L I
Sbjct: 201 SATFPLTVKEFMVKHLHKPYEINL-MEELTLKGITQYYAFVE-ERQKLHCLNTLFSKLQI 258
Query: 273 TQAVIFCNTKRKIY----------YSVFYFWIR 295
            QA+IFCN+  ++           YS +Y   R
Sbjct: 259 NQAIIFCNSTNRVELLAKKITDLGYSCYYSHAR 291

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  175 bits (444), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 96/253 (37%), Positives = 152/253 (60%), Gaps = 7/253 (2%)
Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTV 91
           SFD +G+  +LL+GIY   F+KPS IQ+RA+  ++    R++IAQ+QSGTGKT+  +LT+
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
              V+      QA+ L+P+RELA QT +V+  +G F  I +   V         +  +  
Sbjct: 66  LTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFE----KNKQIN 121
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQVV 210
             V+ GTPG V D+++RK ++ + IK+ VLDE+D ML  +G  DQ   V R+LP D Q+V
Sbjct: 122 AQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 181
Query: 211 LISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 270
           L SAT    + +   K + +   + ++ +E+ ++ IKQ ++  + E  KFD L +LY  +
Sbjct: 182 LFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGVM 241
Query: 271 TITQAVIFCNTKR 283
           TI  ++IF  TK+
Sbjct: 242 TIGSSIIFVATKK 254

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  175 bits (443), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 96/253 (37%), Positives = 152/253 (60%), Gaps = 7/253 (2%)
Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTV 91
           SFD +G+  +LL+GIY   F+KPS IQ+RA+  ++    R++IAQ+QSGTGKT+  +LT+
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
              V+      QA+ L+P+RELA QT +V+  +G F  I +   V         +  +  
Sbjct: 66  LTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFE----KNKQIN 121
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQVV 210
             V+ GTPG V D+++RK ++ + IK+ VLDE+D ML  +G  DQ   V R+LP D Q+V
Sbjct: 122 AQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 181
Query: 211 LISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 270
           L SAT    + +   K + +   + ++ +E+ ++ IKQ ++  + E  KFD L +LY  +
Sbjct: 182 LFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLM 241
Query: 271 TITQAVIFCNTKR 283
           TI  ++IF  TK+
Sbjct: 242 TIGSSIIFVATKK 254

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  171 bits (434), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 104/261 (39%), Positives = 158/261 (60%), Gaps = 14/261 (5%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 23  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 81
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQAHACVGGK-SVGED 144
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F      A+A  G K   G+ 
Sbjct: 82  VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 141
Query: 145 IRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRY 202
           I +      +V GTPG V D   K K +  + IK+ VLDE+D M++ +G +DQ   + R 
Sbjct: 142 ISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 196
Query: 203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT 262
           LP + Q++L SAT    + +   K + DP  I +KR+E TL+ IKQ++V     + KF  
Sbjct: 197 LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQA 256
Query: 263 LCDLYDTLTITQAVIFCNTKR 283
           LC+LY  +TI QA+IFC+T++
Sbjct: 257 LCNLYGAITIAQAMIFCHTRK 277

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

Iteration: 1
 Score =  171 bits (434), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 104/261 (39%), Positives = 158/261 (60%), Gaps = 14/261 (5%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 90  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 148
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQAHACVGGK-SVGED 144
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F      A+A  G K   G+ 
Sbjct: 149 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 208
Query: 145 IRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRY 202
           I +      +V GTPG V D   K K +  + IK+ VLDE+D M++ +G +DQ   + R 
Sbjct: 209 ISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 263
Query: 203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT 262
           LP + Q++L SAT    + +   K + DP  I +KR+E TL+ IKQ++V     + KF  
Sbjct: 264 LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQA 323
Query: 263 LCDLYDTLTITQAVIFCNTKR 283
           LC+LY  +TI QA+IFC+T++
Sbjct: 324 LCNLYGAITIAQAMIFCHTRK 344

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

Iteration: 1
 Score =  171 bits (434), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 104/261 (39%), Positives = 158/261 (60%), Gaps = 14/261 (5%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 39  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 97
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQAHACVGGK-SVGED 144
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F      A+A  G K   G+ 
Sbjct: 98  VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 157
Query: 145 IRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRY 202
           I +      +V GTPG V D   K K +  + IK+ VLDE+D M++ +G +DQ   + R 
Sbjct: 158 ISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 212
Query: 203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT 262
           LP + Q++L SAT    + +   K + DP  I +KR+E TL+ IKQ++V     + KF  
Sbjct: 213 LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQA 272
Query: 263 LCDLYDTLTITQAVIFCNTKR 283
           LC+LY  +TI QA+IFC+T++
Sbjct: 273 LCNLYGAITIAQAMIFCHTRK 293

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

Iteration: 1
 Score =  171 bits (433), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 104/261 (39%), Positives = 158/261 (60%), Gaps = 14/261 (5%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 60  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 118
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQAHACVGGK-SVGED 144
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F      A+A  G K   G+ 
Sbjct: 119 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 178
Query: 145 IRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRY 202
           I +      +V GTPG V D   K K +  + IK+ VLDE+D M++ +G +DQ   + R 
Sbjct: 179 ISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 233
Query: 203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDT 262
           LP + Q++L SAT    + +   K + DP  I +KR+E TL+ IKQ++V     + KF  
Sbjct: 234 LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQA 293
Query: 263 LCDLYDTLTITQAVIFCNTKR 283
           LC+LY  +TI QA+IFC+T++
Sbjct: 294 LCNLYGAITIAQAMIFCHTRK 314

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  153 bits (386), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 91/254 (35%), Positives = 144/254 (56%), Gaps = 5/254 (1%)
Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTV 91
           ++ F    +K +LLR I   GFE PS +Q   +   I G DV+ QA+SG GKT++  L  
Sbjct: 6   MSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT 65
Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEH 150
            Q ++  + +V  L++  TRELA Q  K       ++ N++     GG S+ +D   L+ 
Sbjct: 66  LQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK 125
Query: 151 GV-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQ 208
              H+V GTPGR+  + + K+L  + IK  +LDE+D+ML +   +  + +++R  P + Q
Sbjct: 126 NCPHIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPHEKQ 185
Query: 209 VVLISATLPHEILEMTTKFMTDPVKILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLY 267
           V++ SATL  EI  +  KFM DP++I V  + +LTL G++Q++V ++  E K   L DL 
Sbjct: 186 VMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNE-KNRKLFDLL 244
Query: 268 DTLTITQAVIFCNT 281
           D L   Q VIF  +
Sbjct: 245 DVLEFNQVVIFVKS 258

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  152 bits (383), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 142/253 (56%), Gaps = 5/253 (1%)
Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           + F    +K +LLR I   GFE PS +Q   +   I G DV+ QA+SG GKT++  L   
Sbjct: 8   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 67
Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHG 151
           Q ++  + +V  L++  TRELA Q  K       ++ N++     GG S+ +D   L+  
Sbjct: 68  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 127
Query: 152 V-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQV 209
             H+V GTPGR+  + + K+L  + IK  +LDE D+ML +   +  + +++R  P + QV
Sbjct: 128 CPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQV 187
Query: 210 VLISATLPHEILEMTTKFMTDPVKILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYD 268
           ++ SATL  EI  +  KFM DP++I V  + +LTL G++Q++V ++  E K   L DL D
Sbjct: 188 MMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNE-KNRKLFDLLD 246
Query: 269 TLTITQAVIFCNT 281
            L   Q VIF  +
Sbjct: 247 VLEFNQVVIFVKS 259

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  152 bits (383), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 142/253 (56%), Gaps = 5/253 (1%)
Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           + F    +K +LLR I   GFE PS +Q   +   I G DV+ QA+SG GKT++  L   
Sbjct: 8   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 67
Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHG 151
           Q ++  + +V  L++  TRELA Q  K       ++ N++     GG S+ +D   L+  
Sbjct: 68  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 127
Query: 152 V-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQV 209
             H+V GTPGR+  + + K+L  + IK  +LDE D+ML +   +  + +++R  P + QV
Sbjct: 128 CPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQV 187
Query: 210 VLISATLPHEILEMTTKFMTDPVKILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYD 268
           ++ SATL  EI  +  KFM DP++I V  + +LTL G++Q++V ++  E K   L DL D
Sbjct: 188 MMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNE-KNRKLFDLLD 246
Query: 269 TLTITQAVIFCNT 281
            L   Q VIF  +
Sbjct: 247 VLEFNQVVIFVKS 259

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

Iteration: 1
 Score =  146 bits (368), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 86/252 (34%), Positives = 144/252 (57%), Gaps = 11/252 (4%)
Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR--DVIAQAQSGTGKTSMIALTV 91
           +F+ + + D++L  I   GFEKP+ IQ + V+P+      +++AQA++G+GKT+  A+ +
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXK-VIPLFLNDEYNIVAQARTGSGKTASFAIPL 65
Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
            + V+ ++  ++A+IL+PTRELA Q    I ++    N++     GGK++   I+ L++ 
Sbjct: 66  IELVNENN-GIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNA 124
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
            ++V GTPGR+ D I R TL  + +K  +LDE+DE L+ GF   +  +      D +++L
Sbjct: 125 -NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKDKRILL 183
Query: 212 ISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT 271
            SAT P EIL +  K+  D   I  K +      I+Q +V V   E +F+ LC L     
Sbjct: 184 FSATXPREILNLAKKYXGDYSFIKAKIN----ANIEQSYVEVNENE-RFEALCRLLKNKE 238
Query: 272 ITQAVIFCNTKR 283
               ++FC TKR
Sbjct: 239 FY-GLVFCKTKR 249

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score =  142 bits (358), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 81/202 (40%), Positives = 122/202 (60%), Gaps = 11/202 (5%)
Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMIALT 90
           SFD +G+  +LL+GIY   F+KPS IQ+RA +P++     R++IAQ+QSGTGKT+  +LT
Sbjct: 23  SFDELGLAPELLKGIYAMKFQKPSKIQERA-LPLLLHNPPRNMIAQSQSGTGKTAAFSLT 81
Query: 91  VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH 150
           +   V+      QA+ L+P+RELA QT +V+  +G F  I +        V +   K + 
Sbjct: 82  MLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLI-----VPDSFEKNKQ 136
Query: 151 -GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQ 208
               V+ GTPG V D+++RK ++ + IK+ VLDE+D ML  +G  DQ   V R+LP D Q
Sbjct: 137 INAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQ 196
Query: 209 VVLISATLPHEILEMTTKFMTD 230
           +VL SAT    + +   K + +
Sbjct: 197 LVLFSATFADAVRQYAKKIVPN 218

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

Iteration: 1
 Score =  140 bits (352), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 68/203 (33%), Positives = 124/203 (61%), Gaps = 1/203 (0%)
Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
             F+   +K +LL GI++ G+EKPS IQ+ ++   + GRD++A+A++GTGK+    + + 
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62
Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHG 151
           + +D     +QA+++ PTRELA Q  ++ + +   +   +  A  GG ++ +DI +L+  
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
           VHVV  TPGR+ D+IK+   +   ++++VLDE+D++LS+ F   + D+   LP + Q++L
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL 182
Query: 212 ISATLPHEILEMTTKFMTDPVKI 234
            SAT P  + +     +  P +I
Sbjct: 183 YSATFPLSVQKFMNSHLEKPYEI 205

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  130 bits (328), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 73/200 (36%), Positives = 120/200 (60%), Gaps = 5/200 (2%)
Query: 35  FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQ 93
           F+++ +   +L G+   GFE+PS +Q +A+ P+ + G D+I QA+SGTGKT + +     
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAI-PLGRCGLDLIVQAKSGTGKTCVFSTIALD 84
Query: 94  TVDTSSREVQALILSPTRELATQTEKVILAIG-DFINIQAHACVGGKSVGEDIRKLEHGV 152
           ++   +   Q LIL+PTRE+A Q   VI AIG     ++ H  +GG  + +D  +L+   
Sbjct: 85  SLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK-C 143
Query: 153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYLPPDLQVVL 211
           H+  G+PGR+  +I+   L   +I+L +LDE+D++L  G F++QI  +Y  LP   Q++ 
Sbjct: 144 HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLA 203
Query: 212 ISATLPHEILEMTTKFMTDP 231
           +SAT P  +    TK+M DP
Sbjct: 204 VSATYPEFLANALTKYMRDP 223

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  130 bits (327), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 74/207 (35%), Positives = 116/207 (56%), Gaps = 3/207 (1%)
Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           + F    +K +LLR I   GFE PS +Q   +   I G DV+ QA+SG GKT++  L   
Sbjct: 14  SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 73
Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHG 151
           Q ++  + +V  L++  TRELA Q  K       ++ N++     GG S+ +D   L+  
Sbjct: 74  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 133
Query: 152 V-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQV 209
             H+V GTPGR+  + + K+L  + IK  +LDE D+ML +   +  + +++R  P + QV
Sbjct: 134 CPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQV 193
Query: 210 VLISATLPHEILEMTTKFMTDPVKILV 236
           ++ SATL  EI  +  KFM DP++I V
Sbjct: 194 MMFSATLSKEIRPVCRKFMQDPMEIFV 220

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score =  128 bits (322), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/218 (38%), Positives = 128/218 (58%), Gaps = 14/218 (6%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 23  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 81
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQAHACVGGK-SVGED 144
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F      A+A  G K   G+ 
Sbjct: 82  VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 141
Query: 145 IRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRY 202
           I +      +V GTPG V D   K K +  + IK+ VLDE+D M++ +G +DQ   + R 
Sbjct: 142 ISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 196
Query: 203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE 240
           LP + Q++L SAT    + +   K + DP  I +KR+E
Sbjct: 197 LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREE 234

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

Iteration: 1
 Score =  127 bits (319), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 71/205 (34%), Positives = 113/205 (55%), Gaps = 5/205 (2%)
Query: 35  FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQT 94
           F    +K ++L  ++  G   P+ IQ  A+   ++G+D+I QA++GTGKT   AL + + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 95  VDTS---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
           +  S    R+ +AL+L+PTRELA Q    + A+   + + A    GG   G+    L  G
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVA--VYGGTGYGKQKEALLRG 120
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
              V  TPGR  D +++  L    +++ VLDE+DEMLS GF++++  +    PP  Q +L
Sbjct: 121 ADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLL 180
Query: 212 ISATLPHEILEMTTKFMTDPVKILV 236
            SATLP     +  ++M +PV I V
Sbjct: 181 FSATLPSWAKRLAERYMKNPVLINV 205

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

Iteration: 1
 Score =  126 bits (316), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 83/217 (38%), Positives = 127/217 (58%), Gaps = 14/217 (6%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII---KGRDVIAQAQSGTGKTSMI 87
           ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A +P++     +++IAQ+QSGTGKT+  
Sbjct: 90  SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENA-LPLMLAEPPQNLIAQSQSGTGKTAAF 148
Query: 88  ALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN--IQAHACVGGK-SVGED 144
            L +   V+ +++  Q L LSPT ELA QT KVI  +G F      A+A  G K   G+ 
Sbjct: 149 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 208
Query: 145 IRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RGFKDQIYDVYRY 202
           I +      +V GTPG V D   K K +  + IK+ VLDE+D M++ +G +DQ   + R 
Sbjct: 209 ISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 263
Query: 203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD 239
           LP + Q++L SAT    + +   K + DP  I +KR+
Sbjct: 264 LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

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

Iteration: 1
 Score =  125 bits (315), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 70/205 (34%), Positives = 113/205 (55%), Gaps = 5/205 (2%)
Query: 35  FDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQT 94
           F    +K ++L  ++  G   P+ I+  A+   ++G+D+I QA++GTGKT   AL + + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 95  VDTS---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
           +  S    R+ +AL+L+PTRELA Q    + A+   + + A    GG   G+    L  G
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVA--VYGGTGYGKQKEALLRG 120
Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
              V  TPGR  D +++  L    +++ VLDE+DEMLS GF++++  +    PP  Q +L
Sbjct: 121 ADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLL 180
Query: 212 ISATLPHEILEMTTKFMTDPVKILV 236
            SATLP     +  ++M +PV I V
Sbjct: 181 FSATLPSWAKRLAERYMKNPVLINV 205

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

Iteration: 1
 Score =  122 bits (305), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 68/208 (32%), Positives = 115/208 (55%), Gaps = 1/208 (0%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           E   +F  +G+ D L     Q G+ KP+ IQ  A+   ++GRD+I  A++G+GKT   AL
Sbjct: 40  EETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFAL 99
Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
            +   +  + + + AL+L+PTRELA Q  +   A+G  I +Q+   VGG         L 
Sbjct: 100 PILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALA 159
Query: 150 HGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
              H++  TPGR+ D ++  K    RA+K LV+DE+D +L+  F+ ++  + + +P D +
Sbjct: 160 KKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRK 219
Query: 209 VVLISATLPHEILEMTTKFMTDPVKILV 236
             L SAT+  ++ ++    + +PVK  V
Sbjct: 220 TFLFSATMTKKVQKLQRAALKNPVKCAV 247

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  118 bits (296), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 104/205 (50%), Gaps = 4/205 (1%)
Query: 31  AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT 90
           A T F     +  ++  I    F KP+ IQ+R +   ++G   + Q+Q+GTGKT    L 
Sbjct: 2   AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLP 61
Query: 91  VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN----IQAHACVGGKSVGEDIR 146
           + + +     EVQA+I +PTRELATQ     L I  F      I A   +GG    + + 
Sbjct: 62  IXEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALE 121
Query: 147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPD 206
           KL    H+V GTPGR+ D I+ + L      +LV+DE+D  L  GF   +  +    P D
Sbjct: 122 KLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKD 181
Query: 207 LQVVLISATLPHEILEMTTKFMTDP 231
           LQ ++ SAT+P ++     K+  +P
Sbjct: 182 LQXLVFSATIPEKLKPFLKKYXENP 206

>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 =  115 bits (289), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 75/237 (31%), Positives = 127/237 (53%), Gaps = 19/237 (8%)
Query: 28  GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTS-- 85
               I +FD + +   +   I    +++P+ IQ+ A+  I++ RD++A AQ+G+GKT+  
Sbjct: 18  ATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAF 77
Query: 86  ---MIALTVCQTVD----TSSREVQALILSPTRELATQTEKVILAIGDF-INIQAHACV- 136
              +I   VCQ ++    + +   + LIL+PTRELA Q   ++     F +N    +CV 
Sbjct: 78  LIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQ---ILSESQKFSLNTPLRSCVV 134
Query: 137 -GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQ 195
            GG      IR+++ G H++  TPGR+ D I++  +     K +VLDE+D ML  GF+ Q
Sbjct: 135 YGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQ 194
Query: 196 IYDVYR--YLPPDL--QVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQ 248
           I  +     +P  +  Q ++ SAT P EI ++   F+ + + + V R   T + IKQ
Sbjct: 195 IRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ 251

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

Iteration: 1
 Score =  110 bits (276), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 138/280 (49%), Gaps = 34/280 (12%)
Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALT 90
           I SF  + + + ++  I    + +P+ +Q+ A+ PIIK  RD++A AQ+G+GKT+   L 
Sbjct: 14  IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAI-PIIKEKRDLMACAQTGSGKTAAFLLP 72
Query: 91  VCQTV--DTSSREVQA----------------LILSPTRELATQTEKVILAIGDFINIQA 132
           +   +  D     ++A                L+L+PTRELA Q  +          ++ 
Sbjct: 73  ILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRP 132
Query: 133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF 192
               GG  +G+ IR LE G H++  TPGR+ DM++R  +     K LVLDE+D ML  GF
Sbjct: 133 CVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGF 192
Query: 193 KDQIYDVYRY--LPPD--LQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQ 248
           + QI  +     +PP      ++ SAT P EI  +   F+ + + + V R   T E I Q
Sbjct: 193 EPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQ 252
Query: 249 FFVAVEREEWKFDTLCDLY-----DTLTITQAVIFCNTKR 283
             V VE E  K   L DL      D+LT+    +F  TK+
Sbjct: 253 KVVWVE-ESDKRSFLLDLLNATGKDSLTL----VFVETKK 287

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

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 107/217 (49%), Gaps = 5/217 (2%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           + + +F       +++  I +  F +P+AIQ +     + G D++  AQ+G+GKT    L
Sbjct: 26  KPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLL 85
Query: 90  TVCQTVDTSSREVQA-----LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED 144
                ++      +      L+L+PTRELA Q ++V         +++    GG   G  
Sbjct: 86  PAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ 145
Query: 145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP 204
           IR LE GV +   TPGR+ D ++      R    LVLDE+D ML  GF+ QI  +   + 
Sbjct: 146 IRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIR 205
Query: 205 PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDEL 241
           PD Q ++ SAT P E+ ++   F+ D + I +   EL
Sbjct: 206 PDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALEL 242

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

Iteration: 1
 Score =  105 bits (262), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 111/207 (53%), Gaps = 7/207 (3%)
Query: 36  DAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTV 95
           DA     DLL+ I + G  KP+ IQ +A   I++G D+I  AQ+GTGKT    +     +
Sbjct: 23  DAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHL 82
Query: 96  DTS--SREVQA----LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
           D+   SRE +     L+L+PTRELA   E        +  +++    GG++    I  + 
Sbjct: 83  DSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDIS 141
Query: 150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
            GV ++  TPGR+ D+    ++  R+I  LV+DE+D+ML   F+ QI  +   + PD Q 
Sbjct: 142 KGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQT 201
Query: 210 VLISATLPHEILEMTTKFMTDPVKILV 236
           V+ SAT P  + ++   ++ DP+ + V
Sbjct: 202 VMTSATWPDTVRQLALSYLKDPMIVYV 228

>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 =  105 bits (261), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 104/210 (49%), Gaps = 5/210 (2%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           + + +F       +++  I +  F +P+AIQ +     + G D++  AQ+G+GKT    L
Sbjct: 40  KPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLL 99
Query: 90  TVCQTVDTSSREVQA-----LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED 144
                ++      +      L+L+PTRELA Q ++V         +++    GG   G  
Sbjct: 100 PAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ 159
Query: 145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP 204
           IR LE GV +   TPGR+ D ++      R    LVLDE+D ML  GF+ QI  +   + 
Sbjct: 160 IRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIR 219
Query: 205 PDLQVVLISATLPHEILEMTTKFMTDPVKI 234
           PD Q ++ SAT P E+ ++   F+ D + I
Sbjct: 220 PDRQTLMWSATWPKEVRQLAEDFLKDYIHI 249

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

Iteration: 1
 Score =  104 bits (260), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 112/216 (51%), Gaps = 11/216 (5%)
Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           + I  F +  ++D ++  + + G++ P+ IQ+ ++  I  GRD++A AQ+G+GKT+   L
Sbjct: 53  QPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLL 112
Query: 90  TVCQTVDTSSREV-----QALILSPTRELATQ--TEKVILAIGDFINIQAHACVGGKSVG 142
            +   +     E+     Q +I+SPTRELA Q   E    A   ++ I      GG S  
Sbjct: 113 PILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGI--VYGGTSFR 170
Query: 143 EDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY 202
                +  G HVV  TPGR+ D + R  +     + +VLDE+D ML  GF + +  +  +
Sbjct: 171 HQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTH 230
Query: 203 --LPPDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
             + P+ Q ++ SAT P EI  M  +F+ + V + +
Sbjct: 231 VTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAI 266

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

Iteration: 1
 Score = 98.6 bits (244), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 118/219 (53%), Gaps = 21/219 (9%)
Query: 33  TSFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT 90
           TSF ++   + ++ L+ I + GF   + IQ +++ P+++GRD++A A++G+GKT    + 
Sbjct: 52  TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIP 111
Query: 91  VCQTVD----TSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA---CVGGKSVGE 143
             + +             LILSPTRELA QT  V   + + +    H     +GG +   
Sbjct: 112 AVELIVKLRFMPRNGTGVLILSPTRELAMQTFGV---LKELMTHHVHTYGLIMGGSNRSA 168
Query: 144 DIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY 202
           + +KL +G++++  TPGR+ D M        + ++ LV+DE+D +L  GF++++  + + 
Sbjct: 169 EAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKL 228
Query: 203 LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDEL 241
           LP   Q +L SAT         T+ + D  +I +K++ L
Sbjct: 229 LPTRRQTMLFSAT--------QTRKVEDLARISLKKEPL 259

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

Iteration: 1
 Score = 95.5 bits (236), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 60/209 (28%), Positives = 111/209 (53%), Gaps = 6/209 (2%)
Query: 28  GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI 87
            V  IT F    +    L+G+ +  +   + IQ++ +   ++G+DV+  A++G+GKT   
Sbjct: 20  NVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAF 79
Query: 88  ALTVCQTVD----TSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE 143
            + V + +     TS+  +  LI+SPTRELA QT +V+  +G   +  A   +GGK +  
Sbjct: 80  LVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKH 139
Query: 144 DIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY 202
           +  ++ + ++++  TPGR+   M +  +     +++LVLDE+D +L  GF D +  V   
Sbjct: 140 EAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIEN 198
Query: 203 LPPDLQVVLISATLPHEILEMTTKFMTDP 231
           LP   Q +L SAT    + ++    + +P
Sbjct: 199 LPKKRQTLLFSATQTKSVKDLARLSLKNP 227

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

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 117/220 (53%), Gaps = 11/220 (5%)
Query: 40  IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS 99
           + + + + I + GF+  + +Q + +  +++G++V+ +A++G+GKT+  A+ + +      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTP 159
             +++L+++PTREL  Q    I  IG +++ +     GG      I ++ +   +V  TP
Sbjct: 56  -GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNA-DIVVATP 113
Query: 160 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHE 219
           GR+ D+  +  +   + +++++DE+D M   GF D I  +           L SAT+P E
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEE 173
Query: 220 ILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK 259
           I ++   F+T+  +I      + L  ++  FV V +++W+
Sbjct: 174 IRKVVKDFITNYEEIEAC---IGLANVEHKFVHV-KDDWR 209

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 51/171 (29%), Positives = 94/171 (54%), Gaps = 13/171 (7%)
Query: 40  IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC-QTVDTS 98
           I   LL+ I   GF+ P+ IQ +A+  ++ GR+++A A +G+GKT   ++ +  Q    +
Sbjct: 36  INSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA 95
Query: 99  SREVQALILSPTRELATQTEKVILAIGDFINIQAH----ACVGGKSVGEDIRKLEHGVHV 154
           ++  +ALI+SPTRELA+Q  + ++ I +    + H    A V  K  G    K      +
Sbjct: 96  NKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGP---KSSKKFDI 152
Query: 155 VSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEML---SRGFKDQIYDVY 200
           +  TP R+  ++K+    +   +++ LV+DESD++      GF+DQ+  ++
Sbjct: 153 LVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIF 203

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 78.6 bits (192), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 60/206 (29%), Positives = 108/206 (52%), Gaps = 19/206 (9%)
Query: 43  DLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQ----TVD 96
           ++ + I +  F   + +QQ+ + PI+     DVIA+A++GTGKT    + + Q    T  
Sbjct: 82  EIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF 141
Query: 97  TSSREVQALILSPTRELATQTEKVILAIGDF-INIQAHAC---VGGKSVGEDIRKLEH-G 151
            S   V+A+I++PTR+LA Q E  +  I D    ++ +AC   VGG      + K+    
Sbjct: 142 DSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLR 201
Query: 152 VHVVSGTPGRVCDMIKRKTLR-TRAIKLLVLDESDEMLSRGFKDQIYDVYRYL------- 203
            ++V  TPGR+ D++++ + +  R +   VLDE+D +L  GF+D +  +   L       
Sbjct: 202 PNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKS 261
Query: 204 PPDLQVVLISATLPHEILEMTTKFMT 229
             +++ +L SATL  ++ ++    M 
Sbjct: 262 ADNIKTLLFSATLDDKVQKLANNIMN 287

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 60/206 (29%), Positives = 108/206 (52%), Gaps = 19/206 (9%)
Query: 43  DLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQ----TVD 96
           ++ + I +  F   + +QQ+ + PI+     DVIA+A++GTGKT    + + Q    T  
Sbjct: 31  EIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF 90
Query: 97  TSSREVQALILSPTRELATQTEKVILAIGDF-INIQAHAC---VGGKSVGEDIRKLEH-G 151
            S   V+A+I++PTR+LA Q E  +  I D    ++ +AC   VGG      + K+    
Sbjct: 91  DSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLR 150
Query: 152 VHVVSGTPGRVCDMIKRKTLR-TRAIKLLVLDESDEMLSRGFKDQIYDVYRYL------- 203
            ++V  TPGR+ D++++ + +  R +   VLDE+D +L  GF+D +  +   L       
Sbjct: 151 PNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKS 210
Query: 204 PPDLQVVLISATLPHEILEMTTKFMT 229
             +++ +L SATL  ++ ++    M 
Sbjct: 211 ADNIKTLLFSATLDDKVQKLANNIMN 236

>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 = 78.6 bits (192), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 60/206 (29%), Positives = 108/206 (52%), Gaps = 19/206 (9%)
Query: 43  DLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQ----TVD 96
           ++ + I +  F   + +QQ+ + PI+     DVIA+A++GTGKT    + + Q    T  
Sbjct: 31  EIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF 90
Query: 97  TSSREVQALILSPTRELATQTEKVILAIGDF-INIQAHAC---VGGKSVGEDIRKLEH-G 151
            S   V+A+I++PTR+LA Q E  +  I D    ++ +AC   VGG      + K+    
Sbjct: 91  DSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLR 150
Query: 152 VHVVSGTPGRVCDMIKRKTLR-TRAIKLLVLDESDEMLSRGFKDQIYDVYRYL------- 203
            ++V  TPGR+ D++++ + +  R +   VLDE+D +L  GF+D +  +   L       
Sbjct: 151 PNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKS 210
Query: 204 PPDLQVVLISATLPHEILEMTTKFMT 229
             +++ +L SATL  ++ ++    M 
Sbjct: 211 ADNIKTLLFSATLDDKVQKLANNIMN 236

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 72.0 bits (175), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 39/43 (90%)
Query: 243 LEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKI 285
           LEGIKQF+V VE EE+K++ L DLYD++++TQAVIFCNT+RK+
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKV 43

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 31/44 (70%)
Query: 241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
           LTL  I+Q++V  E  + K+  LC++Y ++TI QA+IFC T+R 
Sbjct: 3   LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRN 46

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 12/72 (16%)
Query: 230 DPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIY--- 286
           DP +I +  +ELTL+G+ Q++  V  E  K   L  L+  L I Q++IFCN+ +++    
Sbjct: 4   DPYEINLM-EELTLKGVTQYYAYVT-ERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLA 61
Query: 287 -------YSVFY 291
                  YS FY
Sbjct: 62  KKISQLGYSCFY 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	298
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-167
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-164
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-161
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-152
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-149
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-147
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-146
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-140
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-138
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-136
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-132
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-117
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-113
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	1e-101
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	6e-98
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	3e-81
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	2e-80
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-74
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-70
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-69
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-69
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	1e-64
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-61
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-59
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	2e-57
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	7e-56
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-55
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-55
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-55
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	1e-51
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	8e-50
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	1e-24
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	2e-23
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	7e-20
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	3e-19
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-13
3b6e_A	216	Interferon-induced helicase C domain-containing P;	2e-08
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	1e-07
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	1e-07
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	3e-07
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-07
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	2e-06
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	3e-06
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	4e-06
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	2e-05
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	2e-04
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	3e-04
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	4e-04
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	5e-04

>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 =  469 bits (1209), Expect = e-167
 Identities = 205/283 (72%), Positives = 243/283 (85%)

Query: 2   AAATAMRRRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQ 61
            A +   R+      D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQ
Sbjct: 6   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 65

Query: 62  RAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI 121
           RA+  IIKGRDVIAQ+QSGTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +
Sbjct: 66  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 125

Query: 122 LAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVL 181
           LA+GD++N+Q HAC+GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVL
Sbjct: 126 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVL 185

Query: 182 DESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDEL 241
           DE+DEML++GFK+QIYDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKRDEL
Sbjct: 186 DEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDEL 245

Query: 242 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
           TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK
Sbjct: 246 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 288

>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 =  462 bits (1192), Expect = e-164
 Identities = 158/277 (57%), Positives = 211/277 (76%), Gaps = 1/277 (0%)

Query: 9   RRGGGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII 68
           R    G    +      +   E + SFD M + + LLRGIY YGFEKPSAIQQRA++P I
Sbjct: 16  RSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCI 75

Query: 69  KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI 128
           KG DVIAQAQSGTGKT+  A+++ Q ++   +  QAL+L+PTRELA Q +KV++A+GD++
Sbjct: 76  KGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYM 135

Query: 129 NIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM 187
               HAC+GG +V  +++KL+    H++ GTPGRV DM+ R+ L  + IK+ VLDE+DEM
Sbjct: 136 GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM 195

Query: 188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIK 247
           LSRGFKDQIYD+++ L  + QVVL+SAT+P ++LE+T KFM DP++ILVK++ELTLEGI+
Sbjct: 196 LSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIR 255

Query: 248 QFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
           QF++ VEREEWK DTLCDLY+TLTITQAVIF NT+RK
Sbjct: 256 QFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRK 292

>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 =  454 bits (1170), Expect = e-161
 Identities = 152/271 (56%), Positives = 207/271 (76%), Gaps = 2/271 (0%)

Query: 14  GGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDV 73
           G  D ++   +T    + +  FD M + ++LLRG++ YGFE+PSAIQQRA+MPII+G DV
Sbjct: 3   GITDIEESQIQTNY-DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDV 61

Query: 74  IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH 133
           +AQAQSGTGKT   ++   Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ H
Sbjct: 62  LAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVH 121

Query: 134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK 193
           AC+GG S  ED   L     +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK
Sbjct: 122 ACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFK 180

Query: 194 DQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAV 253
           +QIY ++  LPP  QVVL+SAT+P+++LE+TTKFM +PV+ILVK+DELTLEGIKQF+V V
Sbjct: 181 EQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNV 240

Query: 254 EREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
           E EE+K++ L DLYD++++TQAVIFCNT+RK
Sbjct: 241 EEEEYKYECLTDLYDSISVTQAVIFCNTRRK 271

>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 =  429 bits (1106), Expect = e-152
 Identities = 105/261 (40%), Positives = 154/261 (59%), Gaps = 4/261 (1%)

Query: 26  TEGVEAI--TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGK 83
           T+ V      +F+   +K +LL GI++ GFEKPS IQ+ A+   I GRD++A+A++GTGK
Sbjct: 12  TDDVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGK 71

Query: 84  TSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE 143
           T+   +   + V     ++QALI+ PTRELA QT +V+  +G    I      GG ++ +
Sbjct: 72  TAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRD 131

Query: 144 DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL 203
           DI +L   VH++ GTPGRV D+  RK        L ++DE+D+MLSR FK  I  +  +L
Sbjct: 132 DILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFL 191

Query: 204 PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTL 263
           PP  Q +L SAT P  + E   K +  P +I +  +ELTL+GI Q++  VE E  K   L
Sbjct: 192 PPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM-EELTLKGITQYYAFVE-ERQKLHCL 249

Query: 264 CDLYDTLTITQAVIFCNTKRK 284
             L+  L I QA+IFCN+  +
Sbjct: 250 NTLFSKLQINQAIIFCNSTNR 270

>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 =  424 bits (1093), Expect = e-149
 Identities = 99/273 (36%), Positives = 158/273 (57%), Gaps = 8/273 (2%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVI 74
             + +  +    + ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A+  ++    +++I
Sbjct: 9   QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI 68

Query: 75  AQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAH 133
           AQ+QSGTGKT+   L +   V+ +++  Q L LSPT ELA QT KVI  +G F   ++  
Sbjct: 69  AQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLA 128

Query: 134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RG 191
             V G  +    +       +V GTPG V D   K K +  + IK+ VLDE+D M++ +G
Sbjct: 129 YAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQG 185

Query: 192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV 251
            +DQ   + R LP + Q++L SAT    + +   K + DP  I +KR+E TL+ IKQ++V
Sbjct: 186 HQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYV 245

Query: 252 AVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
                + KF  LC+LY  +TI QA+IFC+T++ 
Sbjct: 246 LCSSRDEKFQALCNLYGAITIAQAMIFCHTRKT 278

>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 =  420 bits (1081), Expect = e-147
 Identities = 99/273 (36%), Positives = 158/273 (57%), Gaps = 8/273 (2%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVI 74
             + +  +    + ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A+  ++    +++I
Sbjct: 76  QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI 135

Query: 75  AQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAH 133
           AQ+QSGTGKT+   L +   V+ +++  Q L LSPT ELA QT KVI  +G F   ++  
Sbjct: 136 AQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLA 195

Query: 134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RG 191
             V G  +    +       +V GTPG V D   K K +  + IK+ VLDE+D M++ +G
Sbjct: 196 YAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQG 252

Query: 192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV 251
            +DQ   + R LP + Q++L SAT    + +   K + DP  I +KR+E TL+ IKQ++V
Sbjct: 253 HQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYV 312

Query: 252 AVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
                + KF  LC+LY  +TI QA+IFC+T++ 
Sbjct: 313 LCSSRDEKFQALCNLYGAITIAQAMIFCHTRKT 345

>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 =  414 bits (1067), Expect = e-146
 Identities = 96/256 (37%), Positives = 152/256 (59%), Gaps = 7/256 (2%)

Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIAL 89
             SFD +G+  +LL+GIY   F+KPS IQ+RA+  ++    R++IAQ+QSGTGKT+  +L
Sbjct: 4   AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL 63

Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
           T+   V+      QA+ L+P+RELA QT +V+  +G F  I +   V         +  +
Sbjct: 64  TMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFE----KNKQ 119

Query: 150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQ 208
               V+ GTPG V D+++RK ++ + IK+ VLDE+D ML  +G  DQ   V R+LP D Q
Sbjct: 120 INAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQ 179

Query: 209 VVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 268
           +VL SAT    + +   K + +   + ++ +E+ ++ IKQ ++  + E  KFD L +LY 
Sbjct: 180 LVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYG 239

Query: 269 TLTITQAVIFCNTKRK 284
            +TI  ++IF  TK+ 
Sbjct: 240 LMTIGSSIIFVATKKT 255

>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 =  393 bits (1013), Expect = e-138
 Identities = 90/259 (34%), Positives = 144/259 (55%), Gaps = 5/259 (1%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
              + F    +K +LLR I   GFE PS +Q   +   I G DV+ QA+SG GKT++  L
Sbjct: 5   HMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL 64

Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKL 148
              Q ++  + +V  L++  TRELA Q  K       ++ N++     GG S+ +D   L
Sbjct: 65  ATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL 124

Query: 149 EHGV-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPD 206
           +    H+V GTPGR+  + + K+L  + IK  +LDE D+ML +   +  + +++R  P +
Sbjct: 125 KKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHE 184

Query: 207 LQVVLISATLPHEILEMTTKFMTDPVKILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCD 265
            QV++ SATL  EI  +  KFM DP++I V  + +LTL G++Q++V ++ +  K   L D
Sbjct: 185 KQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLK-DNEKNRKLFD 243

Query: 266 LYDTLTITQAVIFCNTKRK 284
           L D L   Q VIF  + ++
Sbjct: 244 LLDVLEFNQVVIFVKSVQR 262

>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 =  383 bits (985), Expect = e-136
 Identities = 123/226 (54%), Positives = 169/226 (74%), Gaps = 2/226 (0%)

Query: 19  DKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQ 78
           ++   +T    + +  FD M + ++LLRG++ YGFE+PSAIQQRA+MPII+G DV+AQAQ
Sbjct: 1   EESQIQTNY-DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQ 59

Query: 79  SGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGG 138
           SGTGKT   ++   Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ HAC+GG
Sbjct: 60  SGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGG 119

Query: 139 KSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD 198
            S  ED   L     +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK+QIY 
Sbjct: 120 TSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQ 178

Query: 199 VYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLE 244
           ++  LPP  QVVL+SAT+P+++LE+TTKFM +PV+ILVK+DELTLE
Sbjct: 179 IFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224

>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 =  372 bits (958), Expect = e-132
 Identities = 125/229 (54%), Positives = 172/229 (75%), Gaps = 2/229 (0%)

Query: 12  GGGGMDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR 71
           G   +     V E+    E + +FD M +K+ LLRGIY YGFEKPSAIQQRA++P IKG 
Sbjct: 10  GRENLYFQGGVIES-NWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 68

Query: 72  DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ 131
           DVIAQAQSGTGKT+  A+++ Q ++   +E QAL+L+PTRELA Q +KVILA+GD++   
Sbjct: 69  DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 128

Query: 132 AHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR 190
            HAC+GG +V  +++KL+    H+V GTPGRV DM+ R+ L  + IK+ VLDE+DEMLSR
Sbjct: 129 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 188

Query: 191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD 239
           GFKDQIY++++ L   +QVVL+SAT+P ++LE+T KFM DP++ILVK++
Sbjct: 189 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>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 =  334 bits (859), Expect = e-117
 Identities = 74/226 (32%), Positives = 124/226 (54%), Gaps = 4/226 (1%)

Query: 15  GMDDDKMVFETTEGV-EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDV 73
             D       T + +      F+++ +   +L G+   GFE+PS +Q +A+     G D+
Sbjct: 5   AQDLSSPRTRTGDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDL 64

Query: 74  IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQA 132
           I QA+SGTGKT + +     ++   +   Q LIL+PTRE+A Q   VI AIG  +  ++ 
Sbjct: 65  IVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLEC 124

Query: 133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG- 191
           H  +GG  + +D  +L+   H+  G+PGR+  +I+   L   +I+L +LDE+D++L  G 
Sbjct: 125 HVFIGGTPLSQDKTRLKK-CHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGS 183

Query: 192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK 237
           F++QI  +Y  LP   Q++ +SAT P  +    TK+M DP  + + 
Sbjct: 184 FQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRLN 229

>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 =  328 bits (842), Expect = e-113
 Identities = 78/228 (34%), Positives = 127/228 (55%), Gaps = 8/228 (3%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVI 74
             + +  +    + ++ SF+ + +K  LL+G+Y  GF +PS IQ+ A+  ++    +++I
Sbjct: 76  QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI 135

Query: 75  AQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAH 133
           AQ+QSGTGKT+   L +   V+ +++  Q L LSPT ELA QT KVI  +G F   ++  
Sbjct: 136 AQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLA 195

Query: 134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI-KRKTLRTRAIKLLVLDESDEMLS-RG 191
             V G  +    +       +V GTPG V D   K K +  + IK+ VLDE+D M++ +G
Sbjct: 196 YAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQG 252

Query: 192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD 239
            +DQ   + R LP + Q++L SAT    + +   K + DP  I +KR+
Sbjct: 253 HQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>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 =  294 bits (756), Expect = e-101
 Identities = 68/203 (33%), Positives = 124/203 (61%), Gaps = 1/203 (0%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
             F+   +K +LL GI++ G+EKPS IQ+ ++   + GRD++A+A++GTGK+    + + 
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHG 151
           + +D     +QA+++ PTRELA Q  ++ + +   +   +  A  GG ++ +DI +L+  
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122

Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
           VHVV  TPGR+ D+IK+   +   ++++VLDE+D++LS+ F   + D+   LP + Q++L
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL 182

Query: 212 ISATLPHEILEMTTKFMTDPVKI 234
            SAT P  + +     +  P +I
Sbjct: 183 YSATFPLSVQKFMNSHLEKPYEI 205

>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 =  286 bits (734), Expect = 6e-98
 Identities = 74/207 (35%), Positives = 116/207 (56%), Gaps = 3/207 (1%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           + F    +K +LLR I   GFE PS +Q   +   I G DV+ QA+SG GKT++  L   
Sbjct: 14  SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 73

Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHG 151
           Q ++  + +V  L++  TRELA Q  K       ++ N++     GG S+ +D   L+  
Sbjct: 74  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 133

Query: 152 V-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQV 209
             H+V GTPGR+  + + K+L  + IK  +LDE D+ML +   +  + +++R  P + QV
Sbjct: 134 CPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQV 193

Query: 210 VLISATLPHEILEMTTKFMTDPVKILV 236
           ++ SATL  EI  +  KFM DP++I V
Sbjct: 194 MMFSATLSKEIRPVCRKFMQDPMEIFV 220

>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 =  248 bits (637), Expect = 3e-81
 Identities = 86/253 (33%), Positives = 142/253 (56%), Gaps = 9/253 (3%)

Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALT 90
             +F+ + + D++L  I   GFEKP+ IQ + +   +    +++AQA++G+GKT+  A+ 
Sbjct: 5   YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIP 64

Query: 91  VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH 150
           + + V+ +   ++A+IL+PTRELA Q    I ++    N++     GGK++   I+ L+ 
Sbjct: 65  LIELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK- 122

Query: 151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV 210
             ++V GTPGR+ D I R TL  + +K  +LDE+DEML+ GF   +  +      D +++
Sbjct: 123 NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRIL 182

Query: 211 LISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 270
           L SAT+P EIL +  K+M D   I  K        I+Q +V V   E +F+ LC L    
Sbjct: 183 LFSATMPREILNLAKKYMGDYSFIKAK----INANIEQSYVEVNENE-RFEALCRLLKNK 237

Query: 271 TITQAVIFCNTKR 283
                ++FC TKR
Sbjct: 238 EF-YGLVFCKTKR 249

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  241 bits (618), Expect = 2e-80
 Identities = 71/210 (33%), Positives = 110/210 (52%), Gaps = 4/210 (1%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           T F     +  ++  I    F KP+ IQ+R +   ++G  ++ Q+Q+GTGKT    L + 
Sbjct: 4   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM 63

Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFI----NIQAHACVGGKSVGEDIRKL 148
           + +     EVQA+I +PTRELATQ     L I  F      I A   +GG    + + KL
Sbjct: 64  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL 123

Query: 149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
               H+V GTPGR+ D I+ + L      +LV+DE+D ML  GF   +  +   +P DLQ
Sbjct: 124 NVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQ 183

Query: 209 VVLISATLPHEILEMTTKFMTDPVKILVKR 238
           +++ SAT+P ++     K+M +P  + V  
Sbjct: 184 MLVFSATIPEKLKPFLKKYMENPTFVHVLE 213

>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 =  231 bits (591), Expect = 1e-74
 Identities = 55/244 (22%), Positives = 119/244 (48%), Gaps = 13/244 (5%)

Query: 40  IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS 99
           + + + + I + GF+  + +Q + +  +++G++V+ +A++G+GKT+  A+ + +      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54

Query: 100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTP 159
             +++L+++PTREL  Q    I  IG +++ +     GG      I ++     +V  TP
Sbjct: 55  LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATP 113

Query: 160 GRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHE 219
           GR+ D+  +  +   + +++++DE+D M   GF D I  +           L SAT+P E
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEE 173

Query: 220 ILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFC 279
           I ++   F+T+  +I      + L  ++  FV V+     + +             ++F 
Sbjct: 174 IRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKD---DWRSKVQALRENKDKGVIVFV 227

Query: 280 NTKR 283
            T+ 
Sbjct: 228 RTRN 231

>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 =  227 bits (579), Expect = 2e-70
 Identities = 67/288 (23%), Positives = 133/288 (46%), Gaps = 28/288 (9%)

Query: 24  ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGT 81
           + ++ V   +  +   +  ++ + I +  F   + +QQ+ + PI+  +  DVIA+A++GT
Sbjct: 12  DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 71

Query: 82  GKTSMIALTVCQTVDTSSRE----VQALILSPTRELATQTEKVILAIGDFI----NIQAH 133
           GKT    + + Q +  +  +    V+A+I++PTR+LA Q E  +  I D           
Sbjct: 72  GKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACV 131

Query: 134 ACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLR-TRAIKLLVLDESDEMLSRG 191
           + VGG      + K+     ++V  TPGR+ D++++ + +  R +   VLDE+D +L  G
Sbjct: 132 SLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG 191

Query: 192 FKDQIYDVYRYLP-------PDLQVVLISATLPHEILEMTTKFMTDPVKILV----KRDE 240
           F+D +  +   L         +++ +L SATL  ++ ++    M     + +    K + 
Sbjct: 192 FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEP 251

Query: 241 LTLEGIKQFFVAVEREEWKF-----DTLCDLYDTLTITQAVIFCNTKR 283
              E I Q  V  E+               + +  +  +A+IF  T +
Sbjct: 252 EAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVK 299

>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 =  225 bits (574), Expect = 1e-69
 Identities = 67/288 (23%), Positives = 133/288 (46%), Gaps = 28/288 (9%)

Query: 24  ETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGT 81
           + ++ V   +  +   +  ++ + I +  F   + +QQ+ + PI+  +  DVIA+A++GT
Sbjct: 63  DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 122

Query: 82  GKTSMIALTVCQTVDTSSRE----VQALILSPTRELATQTEKVILAIGDF----INIQAH 133
           GKT    + + Q +  +  +    V+A+I++PTR+LA Q E  +  I D           
Sbjct: 123 GKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACV 182

Query: 134 ACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLR-TRAIKLLVLDESDEMLSRG 191
           + VGG      + K+     ++V  TPGR+ D++++ + +  R +   VLDE+D +L  G
Sbjct: 183 SLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG 242

Query: 192 FKDQIYDVYRYLP-------PDLQVVLISATLPHEILEMTTKFMTDPVKILV----KRDE 240
           F+D +  +   L         +++ +L SATL  ++ ++    M     + +    K + 
Sbjct: 243 FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEP 302

Query: 241 LTLEGIKQFFVAVEREEWKF-----DTLCDLYDTLTITQAVIFCNTKR 283
              E I Q  V  E+               + +  +  +A+IF  T +
Sbjct: 303 EAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVK 350

>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 =  213 bits (544), Expect = 2e-69
 Identities = 71/208 (34%), Positives = 114/208 (54%), Gaps = 5/208 (2%)

Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQ 93
            F    +K ++L  ++  G   P+ IQ  A+   ++G+D+I QA++GTGKT   AL + +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 94  TVDTS---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH 150
            +  S    R+ +AL+L+PTRELA Q    + A+   + + A    GG   G+    L  
Sbjct: 62  RLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVA--VYGGTGYGKQKEALLR 119

Query: 151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV 210
           G   V  TPGR  D +++  L    +++ VLDE+DEMLS GF++++  +    PP  Q +
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTL 179

Query: 211 LISATLPHEILEMTTKFMTDPVKILVKR 238
           L SATLP     +  ++M +PV I V +
Sbjct: 180 LFSATLPSWAKRLAERYMKNPVLINVIK 207

>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 =  202 bits (516), Expect = 1e-64
 Identities = 69/222 (31%), Positives = 117/222 (52%), Gaps = 1/222 (0%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           D      +     E   +F  +G+ D L     Q G+ KP+ IQ  A+   ++GRD+I  
Sbjct: 27  DSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGL 86

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           A++G+GKT   AL +   +  + + + AL+L+PTRELA Q  +   A+G  I +Q+   V
Sbjct: 87  AETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIV 146

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFKDQ 195
           GG         L    H++  TPGR+ D ++  K    RA+K LV+DE+D +L+  F+ +
Sbjct: 147 GGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETE 206

Query: 196 IYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK 237
           +  + + +P D +  L SAT+  ++ ++    + +PVK  V 
Sbjct: 207 VDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVS 248

>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 =  199 bits (509), Expect = 2e-61
 Identities = 71/263 (26%), Positives = 125/263 (47%), Gaps = 11/263 (4%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKT---- 84
           + I  F +  ++D ++  + + G++ P+ IQ+ ++ P+I  GRD++A AQ+G+GKT    
Sbjct: 53  QPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSI-PVISSGRDLMACAQTGSGKTAAFL 111

Query: 85  -SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE 143
             +++  +    +      Q +I+SPTRELA Q             ++     GG S   
Sbjct: 112 LPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRH 171

Query: 144 DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRY- 202
               +  G HVV  TPGR+ D + R  +     + +VLDE+D ML  GF + +  +  + 
Sbjct: 172 QNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHV 231

Query: 203 -LPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFD 261
            + P+ Q ++ SAT P EI  M  +F+ + V + +         +KQ    V +   K  
Sbjct: 232 TMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYA-KRS 290

Query: 262 TLCDLYDTLTITQAVIFCNTKRK 284
            L ++         ++F  TKR 
Sbjct: 291 KLIEILSE-QADGTIVFVETKRG 312

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  194 bits (496), Expect = 1e-59
 Identities = 87/279 (31%), Positives = 134/279 (48%), Gaps = 26/279 (9%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKT---- 84
             I SF  + + + ++  I    + +P+ +Q+ A+ PII + RD++A AQ+G+GKT    
Sbjct: 12  PHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAI-PIIKEKRDLMACAQTGSGKTAAFL 70

Query: 85  -----------SMIALTVCQTVDTSSREVQ---ALILSPTRELATQTEKVILAIGDFINI 130
                         AL   +      R  Q   +L+L+PTRELA Q  +          +
Sbjct: 71  LPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRV 130

Query: 131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR 190
           +     GG  +G+ IR LE G H++  TPGR+ DM++R  +     K LVLDE+D ML  
Sbjct: 131 RPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDM 190

Query: 191 GFKDQIYDV--YRYLPPDL--QVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGI 246
           GF+ QI  +     +PP      ++ SAT P EI  +   F+ + + + V R   T E I
Sbjct: 191 GFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENI 250

Query: 247 KQFFVAVEREEWKFDTLCD-LYDTLTITQAVIFCNTKRK 284
            Q  V VE  + K   L D L  T   +  ++F  TK+ 
Sbjct: 251 TQKVVWVEESD-KRSFLLDLLNATGKDSLTLVFVETKKG 288

>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 =  183 bits (467), Expect = 2e-57
 Identities = 62/224 (27%), Positives = 114/224 (50%), Gaps = 6/224 (2%)

Query: 18  DDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQA 77
              M       V  IT F    +    L+G+ +  +   + IQ++ +   ++G+DV+  A
Sbjct: 10  SRLMQNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAA 69

Query: 78  QSGTGKTSMIALTVCQTVD----TSSREVQALILSPTRELATQTEKVILAIGDFINIQAH 133
           ++G+GKT    + V + +     TS+  +  LI+SPTRELA QT +V+  +G   +  A 
Sbjct: 70  KTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAG 129

Query: 134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTRAIKLLVLDESDEMLSRGF 192
             +GGK +  +  ++ + ++++  TPGR+   M +  +     +++LVLDE+D +L  GF
Sbjct: 130 LIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGF 188

Query: 193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
            D +  V   LP   Q +L SAT    + ++    + +P  + V
Sbjct: 189 ADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWV 232

>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 =  180 bits (458), Expect = 7e-56
 Identities = 51/219 (23%), Positives = 109/219 (49%), Gaps = 12/219 (5%)

Query: 30  EAITSFDAM----GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTS 85
           + I +F  +     I   LL+ I   GF+ P+ IQ +A+  ++ GR+++A A +G+GKT 
Sbjct: 22  DPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTL 81

Query: 86  MIALTVCQTVDTSSRE-VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED 144
             ++ +   +   + +  +ALI+SPTRELA+Q  + ++ I +    + H         + 
Sbjct: 82  AFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKK 141

Query: 145 I-RKLEHGVHVVSGTPGRVCDMIKRKTLRT--RAIKLLVLDESDEML---SRGFKDQIYD 198
              K      ++  TP R+  ++K+        +++ LV+DESD++      GF+DQ+  
Sbjct: 142 FGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLAS 201

Query: 199 VYRYL-PPDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
           ++       ++  + SAT  +++ +     + + + + +
Sbjct: 202 IFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSI 240

>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 =  178 bits (454), Expect = 1e-55
 Identities = 68/212 (32%), Positives = 107/212 (50%), Gaps = 8/212 (3%)

Query: 32  ITSF-DAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTS----- 85
              F DA     DLL+ I + G  KP+ IQ +A   I++G D+I  AQ+GTGKT      
Sbjct: 18  TCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMP 77

Query: 86  MIALTVCQTVDTSSRE-VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED 144
                  Q +    R     L+L+PTRELA   E        +  +++    GG++    
Sbjct: 78  GFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQ 136

Query: 145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP 204
           I  +  GV ++  TPGR+ D+    ++  R+I  LV+DE+D+ML   F+ QI  +   + 
Sbjct: 137 IEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVR 196

Query: 205 PDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
           PD Q V+ SAT P  + ++   ++ DP+ + V
Sbjct: 197 PDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>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 =  178 bits (455), Expect = 1e-55
 Identities = 66/211 (31%), Positives = 103/211 (48%), Gaps = 7/211 (3%)

Query: 32  ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTS----- 85
           + +F       +++  I +  F +P+AIQ +   P+   G D++  AQ+G+GKT      
Sbjct: 28  VLNFYEANFPANVMDVIARQNFTEPTAIQAQGW-PVALSGLDMVGVAQTGSGKTLSYLLP 86

Query: 86  MIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI 145
            I     Q           L+L+PTRELA Q ++V         +++    GG   G  I
Sbjct: 87  AIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQI 146

Query: 146 RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP 205
           R LE GV +   TPGR+ D ++      R    LVLDE+D ML  GF+ QI  +   + P
Sbjct: 147 RDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRP 206

Query: 206 DLQVVLISATLPHEILEMTTKFMTDPVKILV 236
           D Q ++ SAT P E+ ++   F+ D + I +
Sbjct: 207 DRQTLMWSATWPKEVRQLAEDFLKDYIHINI 237

>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 =  179 bits (456), Expect = 1e-55
 Identities = 68/233 (29%), Positives = 116/233 (49%), Gaps = 15/233 (6%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKT---- 84
             I +FD + +   +   I    +++P+ IQ+ A+ P I + RD++A AQ+G+GKT    
Sbjct: 20  NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAI-PAILEHRDIMACAQTGSGKTAAFL 78

Query: 85  -----SMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK 139
                 ++   + Q   + +   + LIL+PTRELA Q             +++    GG 
Sbjct: 79  IPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGA 138

Query: 140 SVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV 199
                IR+++ G H++  TPGR+ D I++  +     K +VLDE+D ML  GF+ QI  +
Sbjct: 139 DTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKI 198

Query: 200 YRYLPP----DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQ 248
                     + Q ++ SAT P EI ++   F+ + + + V R   T + IKQ
Sbjct: 199 IEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ 251

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  174 bits (442), Expect = 1e-51
 Identities = 38/268 (14%), Positives = 87/268 (32%), Gaps = 36/268 (13%)

Query: 42  DDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSRE 101
           +D      +   +  +  Q+     I++G+     A +G GKT+   +T    +  + + 
Sbjct: 8   EDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTA---LWLARKG 64

Query: 102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSG 157
            ++ ++ PT  L  QT + +  + D   ++           E  +  +       H++  
Sbjct: 65  KKSALVFPTVTLVKQTLERLQKLADE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVF 123

Query: 158 TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLP 217
           +   V     R+ L  +    + +D+ D +L          +   +P ++     S    
Sbjct: 124 STQFVSK--NREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQ 181

Query: 218 HEILEM---------------------TTKFMTDPVKILVKRDELTLEGIKQFFVAVERE 256
            +I E                            D +   V R       I    ++   +
Sbjct: 182 GKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSK 241

Query: 257 EWKFDTLCDLYDTLTITQAVIFCNTKRK 284
           E K   L +++    +    IF  T+ +
Sbjct: 242 E-KLVELLEIFRDGIL----IFAQTEEE 264

>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 =  164 bits (418), Expect = 8e-50
 Identities = 60/226 (26%), Positives = 114/226 (50%), Gaps = 8/226 (3%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIK--DDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVI 74
            +   +     G    TSF ++     ++ L+ I + GF   + IQ +++ P+++GRD++
Sbjct: 36  SEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLL 95

Query: 75  AQAQSGTGKTSMIALTVCQ----TVDTSSREVQALILSPTRELATQTEKVILAIGDFINI 130
           A A++G+GKT    +   +               LILSPTRELA QT  V+  +      
Sbjct: 96  AAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVH 155

Query: 131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD-MIKRKTLRTRAIKLLVLDESDEMLS 189
                +GG +   + +KL +G++++  TPGR+ D M        + ++ LV+DE+D +L 
Sbjct: 156 TYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILD 215

Query: 190 RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEM-TTKFMTDPVKI 234
            GF++++  + + LP   Q +L SAT   ++ ++       +P+ +
Sbjct: 216 VGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYV 261

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score = 96.9 bits (242), Expect = 1e-24
 Identities = 20/45 (44%), Positives = 31/45 (68%)

Query: 240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
            LTL  I+Q++V  E  + K+  LC++Y ++TI QA+IFC T+R 
Sbjct: 2   MLTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRN 46

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 93.4 bits (233), Expect = 2e-23
 Identities = 29/42 (69%), Positives = 38/42 (90%)

Query: 243 LEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
           LEGIKQF+V VE EE+K++ L DLYD++++TQAVIFCNT+RK
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRK 42

>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 Length = 172

 Score = 83.8 bits (208), Expect = 7e-20
 Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 242 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
           +L G++Q++V ++ +  K   L DL D L   Q VIF  + ++
Sbjct: 2   SLHGLQQYYVKLK-DNEKNRKLFDLLDVLEFNQVVIFVKSVQR 43

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 81.8 bits (203), Expect = 3e-19
 Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK 284
            LT   I+   + V REE KF  L D+  T      +IFC TK  
Sbjct: 4   GLTTRNIEHAVIQV-REENKFSLLKDVLMTENPDSCIIFCRTKEH 47

>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 = 69.8 bits (170), Expect = 1e-13
 Identities = 35/217 (16%), Positives = 85/217 (39%), Gaps = 4/217 (1%)

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV 120
           Q  +    K  + +    +G GKT +IA+ + +    +    + L+L+PT+ L  Q  + 
Sbjct: 14  QEVIYAKCKETNCLIVLPTGLGKT-LIAMMIAEYR-LTKYGGKVLMLAPTKPLVLQHAES 71

Query: 121 ILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV 180
              + +    +  A  G KS  E+  K      V+  TP  + + +    +    + L+V
Sbjct: 72  FRRLFNLPPEKIVALTGEKSP-EERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIV 130

Query: 181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE 240
            DE+   +       I   Y+    +  V+ ++A+      ++        ++ +  R E
Sbjct: 131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSE 190

Query: 241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI 277
            + + ++ +   +  E  + D      +   + + ++
Sbjct: 191 NSPD-VRPYVKGIRFEWVRVDLPEIYKEVRKLLREML 226

>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 = 52.5 bits (126), Expect = 2e-08
 Identities = 19/134 (14%), Positives = 46/134 (34%), Gaps = 11/134 (8%)

Query: 60  QQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC----QTVDTSSREVQALILSPTRELAT 115
           Q     P ++G+++I    +G+GKT  +A+ +          +S   + ++L     L  
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKT-RVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVE 96

Query: 116 QTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA 175
           Q  +           +     G   +     ++     ++  T   + + +        A
Sbjct: 97  QLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDA 156

Query: 176 ------IKLLVLDE 183
                   L+++DE
Sbjct: 157 GVQLSDFSLIIIDE 170

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 51.9 bits (123), Expect = 1e-07
 Identities = 32/187 (17%), Positives = 71/187 (37%), Gaps = 10/187 (5%)

Query: 55  KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTV---DTSSREVQALILSPTR 111
           KP   Q    +P +KG++ I  A +G GKT  ++L +C+         ++ + +  +   
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKT-FVSLLICEHHLKKFPQGQKGKVVFFANQI 71

Query: 112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL 171
            +  Q + V     +    +     G  +    + ++     ++  TP  + + +K+ T+
Sbjct: 72  PVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTI 131

Query: 172 -RTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTD 230
                  L++ DE      +   + I   Y     D ++   S  LP  ++ +T      
Sbjct: 132 PSLSIFTLMIFDECHNTSKQHPYNMIMFNYL----DQKLGGSSGPLPQ-VIGLTASVGVG 186

Query: 231 PVKILVK 237
             K   +
Sbjct: 187 DAKTTDE 193

>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 = 51.9 bits (123), Expect = 1e-07
 Identities = 28/188 (14%), Positives = 62/188 (32%), Gaps = 3/188 (1%)

Query: 16  MDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIA 75
             +  M +      +   S +     + + +    Y  +K  + Q     P I G++ + 
Sbjct: 209 CLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAINGKNALI 268

Query: 76  QAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPTRELATQTEKVILAIGDFINIQAH 133
            A +G+GKT +  L          + R+ + + L+    +  Q + V     +       
Sbjct: 269 CAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQ 328

Query: 134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRGF 192
              G       + K+     ++  TP  + +  +  TL       L++ DE         
Sbjct: 329 GISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHP 388

Query: 193 KDQIYDVY 200
            + +   Y
Sbjct: 389 YNVLMTRY 396

>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 = 50.6 bits (121), Expect = 3e-07
 Identities = 51/273 (18%), Positives = 99/273 (36%), Gaps = 56/273 (20%)

Query: 39  GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS 98
            I    +  + + G E+    Q  AV  +  G++++    +  GKT +  + + +     
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 99  SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE---DIRKLEHGVHVV 155
            +   +L + P R LA   EK       F   +      G S G+       L     ++
Sbjct: 69  GK---SLYVVPLRALA--GEKY----ESFKKWEKIGLRIGISTGDYESRDEHLGDC-DII 118

Query: 156 SGTPGRVCDMIKRKTLRTRAIKLLVLDE----SDE--------MLSRGFKDQIYDVYRYL 203
             T  +   +I+ +    +A+  LV+DE      E        ++++          R +
Sbjct: 119 VTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTK---------MRRM 169

Query: 204 PPDLQVVLISATLP--HEILE--MTTKFMTD--PVKILVKRDELTLEGIKQFFVAVEREE 257
              L+V+ +SAT P   EI E      +++D  PV          L         +E  +
Sbjct: 170 NKALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVP---------LVEGVLCEGTLELFD 220

Query: 258 WKFDTLCDL-YDTLTIT------QAVIFCNTKR 283
             F T   + ++ L           ++F +T+R
Sbjct: 221 GAFSTSRRVKFEELVEECVAENGGVLVFESTRR 253

>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 = 49.6 bits (117), Expect = 6e-07
 Identities = 26/182 (14%), Positives = 63/182 (34%), Gaps = 8/182 (4%)

Query: 55  KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPTRE 112
           K  + Q     P I G++ +  A +G+GKT +  L          + R+ + + L+    
Sbjct: 7   KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVP 66

Query: 113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL- 171
           +  Q + V     +          G       + K+     ++  TP  + +  +  TL 
Sbjct: 67  VYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLT 126

Query: 172 RTRAIKLLVLDES-----DEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTK 226
                 L++ DE      +   +      +   +       Q++ ++A++     +   +
Sbjct: 127 SLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEE 186

Query: 227 FM 228
            +
Sbjct: 187 TI 188

>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 = 49.1 bits (116), Expect = 9e-07
 Identities = 44/266 (16%), Positives = 95/266 (35%), Gaps = 80/266 (30%)

Query: 61  QRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQT-------------VDTSSREVQALIL 107
           ++A++ +   ++V+     G+GKT + AL VC +             ++  +      +L
Sbjct: 141 RQALLELRPAKNVLIDGVLGSGKTWV-ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199

Query: 108 SPTRELATQTEKVILAIGDF-INIQAHACVGGKSVGEDIRKL------EHGVHVVSGTPG 160
              ++L  Q +    +  D   NI+        S+  ++R+L      E+ + V+     
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRI----HSIQAELRRLLKSKPYENCLLVLLN--- 252

Query: 161 RVCDM-------IKRKTL---RTRAI------------------KLLVLDESDEMLSRGF 192
            V +        +  K L   R + +                    L  DE   +L +  
Sbjct: 253 -VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL 311

Query: 193 KDQIYDVYRYLPPD------LQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGI 246
             +  D    LP +       ++ +I+ ++   +         D  K  V  D+LT   I
Sbjct: 312 DCRPQD----LPREVLTTNPRRLSIIAESIRDGLA------TWDNWK-HVNCDKLT-TII 359

Query: 247 KQFFVAVEREEWKFDTLCDLYDTLTI 272
           +     +E  E++      ++D L++
Sbjct: 360 ESSLNVLEPAEYR-----KMFDRLSV 380

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 48.4 bits (114), Expect = 2e-06
 Identities = 30/184 (16%), Positives = 66/184 (35%), Gaps = 8/184 (4%)

Query: 60  QQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPTRELATQT 117
           Q    +P  KG++ I  A +G GKT +  L     +      ++ + +  +    +  Q 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68

Query: 118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAI 176
             V     + +     +  G  S    ++ +     ++  TP  + + +    +      
Sbjct: 69  ATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVF 128

Query: 177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
            L++ DE          +QI  ++RYL  D ++      LP  ++ +T        K   
Sbjct: 129 TLMIFDECHNTSKNHPYNQI--MFRYL--DHKLGESRDPLPQ-VVGLTASVGVGDAKTAE 183

Query: 237 KRDE 240
           +  +
Sbjct: 184 EAMQ 187

>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* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 47.3 bits (112), Expect = 3e-06
 Identities = 35/238 (14%), Positives = 70/238 (29%), Gaps = 48/238 (20%)

Query: 44  LLRGIYQYGFEKPSAIQQRAVMPII------------KGRDVIAQAQSGTGKTSMIALTV 91
             RG+ +     P    +  +   +              +     A +G+GK++ +    
Sbjct: 194 CTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAY 253

Query: 92  CQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
                   +  + L+L+P+          +          + A     ++   +R +  G
Sbjct: 254 AA------QGYKVLVLNPSVAATLGFGAYM----------SKAHGIDPNIRTGVRTITTG 297

Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-----LSRGFKDQIYDVYRYLPPD 206
             V   T G+    +        A  +++ DE         L  G    + D        
Sbjct: 298 APVTYSTYGK---FLADGGCSGGAYDIIICDECHSTDSTTILGIGT---VLDQAETAGAR 351

Query: 207 LQVVLISATL------PHEILEMTTKFMTDPVKILVKRDELTL--EGIKQFFVAVERE 256
           L VVL +AT       PH  +E      T  +    K   +     G    F   +++
Sbjct: 352 L-VVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAIRGGRHLIFCHSKKK 408

>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 = 47.3 bits (111), Expect = 4e-06
 Identities = 27/176 (15%), Positives = 59/176 (33%), Gaps = 3/176 (1%)

Query: 16  MDDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIA 75
             +  M +      +   S +     + + +    Y  +K  + Q     P I G++ + 
Sbjct: 209 CLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAINGKNALI 268

Query: 76  QAQSGTGKTSMIALTVCQTVDT--SSREVQALILSPTRELATQTEKVILAIGDFINIQAH 133
            A +G+GKT +  L          + R+ + + L+    +  Q + V     +       
Sbjct: 269 CAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQ 328

Query: 134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEML 188
              G       + K+     ++  TP  + +  +  TL       L++ DE     
Sbjct: 329 GISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTT 384

>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 = 45.2 bits (107), Expect = 2e-05
 Identities = 48/263 (18%), Positives = 104/263 (39%), Gaps = 44/263 (16%)

Query: 42  DDLLRGIYQ-YGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS 99
           D+ ++   +  G E     Q  A+   I +G++ +    + +GKT +  + +   +   +
Sbjct: 9   DERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRI--LT 66

Query: 100 REVQALILSPTRELATQTEKVILAIGDF-----INIQAHACVGGKSVGEDIRKLEHGVHV 154
           +  +A+ + P + LA   EK      +F     I ++     G     ++         +
Sbjct: 67  QGGKAVYIVPLKALAE--EKF----QEFQDWEKIGLRVAMATGDYDSKDEWLG---KYDI 117

Query: 155 VSGTPGRVCDMIKRKTLRTRAIKLLVLDE----SDEMLSRGFKDQIYDVYRYLPPDLQVV 210
           +  T  +   +++  +   + +K+LV DE          RG    +  +  ++    Q++
Sbjct: 118 IIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSR--DRG--ATLEVILAHMLGKAQII 173

Query: 211 LISATLP--HEILE--MTTKFMTD--PVKI--LVKRDELTLEGIKQFFVAVEREEWKFDT 262
            +SAT+    E+ E       ++D  PVK+   V          + F    +    +F +
Sbjct: 174 GLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVF--------YQGFVTWEDGSIDRFSS 225

Query: 263 LCDL-YDTL-TITQAVIFCNTKR 283
             +L YD +     A+IF N +R
Sbjct: 226 WEELVYDAIRKKKGALIFVNMRR 248

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

 Score = 41.7 bits (97), Expect = 2e-04
 Identities = 40/180 (22%), Positives = 65/180 (36%), Gaps = 35/180 (19%)

Query: 49  YQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA-LTVCQTVDTSSREVQALIL 107
             Y F      Q  A+  I +G  V+  A +  GKT ++A   + Q++    R    +  
Sbjct: 81  RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKT-VVAEYAIAQSLKNKQR---VIYT 135

Query: 108 SPTRELATQT--------EKVILAIGDF-INIQAHACVGGKSVGEDIRKLEHGVHVVSGT 158
           SP + L+ Q           V L  GD  IN  A   V                     T
Sbjct: 136 SPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLV--------------------MT 175

Query: 159 PGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH 218
              +  M+ R +   R +  ++ DE   M  +       +    LP  ++ V +SAT+P+
Sbjct: 176 TEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPN 235

>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 Length = 212

 Score = 40.0 bits (94), Expect = 3e-04
 Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 1/38 (2%)

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKR 283
            ++  V       + + L DL    +  +A++F  TK 
Sbjct: 6   YEEEAVPAPVRG-RLEVLSDLLYVASPDRAMVFTRTKA 42

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score = 40.5 bits (95), Expect = 4e-04
 Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 1/38 (2%)

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKR 283
            ++  V       + + L DL    +  +A++F  TK 
Sbjct: 3   YEEEAVPAPVRG-RLEVLSDLLYVASPDRAMVFTRTKA 39

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

 Score = 40.6 bits (94), Expect = 5e-04
 Identities = 40/180 (22%), Positives = 65/180 (36%), Gaps = 35/180 (19%)

Query: 49  YQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA-LTVCQTVDTSSREVQALIL 107
             Y F      Q  A+  I +G  V+  A +  GKT ++A   + Q++    R    +  
Sbjct: 179 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKT-VVAEYAIAQSLKNKQR---VIYT 233

Query: 108 SPTRELATQT--------EKVILAIGDF-INIQAHACVGGKSVGEDIRKLEHGVHVVSGT 158
           SP + L+ Q           V L  GD  IN  A   V                     T
Sbjct: 234 SPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLV--------------------MT 273

Query: 159 PGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH 218
              +  M+ R +   R +  ++ DE   M  +       +    LP  ++ V +SAT+P+
Sbjct: 274 TEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPN 333

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	298
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.98
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.97
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.97
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.97
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.97
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.97
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.97
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.97
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.97
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.96
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.96
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.96
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.95
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.95
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.95
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.94
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.94
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.94
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.93
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.92
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.92
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.92
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.92
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.92
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.91
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.9
3h1t_A	590	Type I site-specific restriction-modification syst	99.9
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.9
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.9
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.89
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.88
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.88
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.86
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.85
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.8
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.8
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.77
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.72
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.71
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.7
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.68
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.61
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.42
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.1
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	99.08
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	98.9
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.56
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.52
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.51
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.49
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.44
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.42
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	98.2
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	97.95
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.8
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	97.79
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	97.73
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	97.68
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.55
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	97.54
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.45
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.39
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.37
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.35
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.22
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.19
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.17
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.16
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.15
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.15
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.15
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.11
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.11
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.07
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.04
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.95
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.9
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.89
3co5_A	143	Putative two-component system transcriptional RES	96.83
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.79
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.74
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.69
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.68
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.63
3bos_A	242	Putative DNA replication factor; P-loop containing	96.61
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.61
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.6
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.59
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.56
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	96.52
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.48
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	96.48
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.47
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.45
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.44
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.39
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	96.39
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.33
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.29
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.27
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.27
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.23
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.23
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.21
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.19
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.16
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.14
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.06
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.02
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	95.92
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	95.91
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	95.87
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.84
2qgz_A	308	Helicase loader, putative primosome component; str	95.59
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.49
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	95.44
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.44
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	95.34
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	95.27
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	95.18
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	95.15
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	95.1
2chq_A	319	Replication factor C small subunit; DNA-binding pr	95.06
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	94.99
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	94.95
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	94.95
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.95
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.91
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	94.91
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	94.79
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	94.72
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.69
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	94.61
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	94.46
3pvs_A	447	Replication-associated recombination protein A; ma	94.43
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	94.41
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.4
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	94.28
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.13
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	93.91
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	93.9
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.82
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	93.78
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	93.76
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	93.71
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	93.61
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.49
1xp8_A	366	RECA protein, recombinase A; recombination, radior	93.46
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	93.35
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	93.35
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.18
3io5_A	333	Recombination and repair protein; storage dimer, i	93.16
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	92.97
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	92.94
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	92.65
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	92.49
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	92.41
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	92.35
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	91.77
1u94_A	356	RECA protein, recombinase A; homologous recombinat	91.76
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	91.72
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	91.55
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	91.43
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	91.43
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	91.29
2fna_A	357	Conserved hypothetical protein; structural genomic	91.22
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.07
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	91.04
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	90.95
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	90.83
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	90.74
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	90.71
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	90.65
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	90.52
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	90.44
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	90.41
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	90.39
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	90.28
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	90.26
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	90.08
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	90.03
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	89.98
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	89.94
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	89.84
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	89.78
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	89.59
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.56
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	89.47
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	89.45
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	89.28
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	89.13
1p9r_A	418	General secretion pathway protein E; bacterial typ	89.12
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	88.97
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	88.69
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	88.37
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	88.64
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	88.48
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	88.44
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	88.21
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	88.2
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	88.03
2eyu_A	261	Twitching motility protein PILT; pilus retraction	87.95
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	87.9
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	87.82
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	87.57
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	87.51
1yks_A	440	Genome polyprotein [contains: flavivirin protease	87.4
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	87.34
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	87.07
2r44_A	331	Uncharacterized protein; putative ATPase, structur	87.05
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	86.86
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	86.77
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	86.76
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	86.72
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	86.57
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	86.35
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	86.23
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	86.11
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	85.97
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	85.91
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	85.68
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	85.6
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	85.46
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	85.2
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	85.18
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	85.15
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	85.14
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	85.1
2cvh_A	220	DNA repair and recombination protein RADB; filamen	84.99
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	84.85
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	84.75
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	84.74
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	84.72
1tue_A	212	Replication protein E1; helicase, replication, E1E	84.7
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	84.61
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	84.52
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	84.41
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	84.36
2ewv_A	372	Twitching motility protein PILT; pilus retraction	84.3
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	84.27
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	84.1
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	83.86
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	83.84
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	83.79
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	83.78
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	83.72
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	83.66
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	83.55
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	83.21
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	83.17
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	83.07
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	83.03
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	83.01
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	82.96
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	82.71
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	82.5
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	82.24
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	81.94
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	81.68
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	81.48
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	81.47
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	81.43
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	81.33
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	81.24
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	81.22
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	81.21
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	81.06
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	81.05
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	81.03
4gl2_A	699	Interferon-induced helicase C domain-containing P;	80.99
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	80.94
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	80.53
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	80.43
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	80.16
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	80.13

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=100.00  E-value=3.6e-46  Score=337.43  Aligned_cols=278  Identities=26%  Similarity=0.388  Sum_probs=251.4

Q ss_pred             CCcceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc
Q 022383           18 DDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT   97 (298)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~   97 (298)
                      +.+..+.....+.++.+|+++++++.+.++|+++||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..+..
T Consensus        41 ~~~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~  120 (434)
T 2db3_A           41 NIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLE  120 (434)
T ss_dssp             GSCEEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             CceeEecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHh
Confidence            33455667777889999999999999999999999999999999999999999999999999999999999999998754


Q ss_pred             C-----CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCcc
Q 022383           98 S-----SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLR  172 (298)
Q Consensus        98 ~-----~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~  172 (298)
                      .     ..++++||++||++|+.|+.+.+++++...++++..++|+.....+...+..+++|+|+||++|..++......
T Consensus       121 ~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~  200 (434)
T 2db3_A          121 DPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFIT  200 (434)
T ss_dssp             SCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCC
T ss_pred             cccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcc
Confidence            3     23679999999999999999999999988888999999999988888888889999999999999999988888


Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhC--CCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFF  250 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~--~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~  250 (298)
                      +.+++++|+||||++.+++|...+..++..+  ++..|++++|||+++.+..+...++.++..+.+........++.+.+
T Consensus       201 l~~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~  280 (434)
T 2db3_A          201 FEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTI  280 (434)
T ss_dssp             CTTCCEEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEE
T ss_pred             cccCCeEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEE
Confidence            9999999999999999999999999999885  57899999999999999999999999999988877777778889988


Q ss_pred             EEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          251 VAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       251 ~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..+.... |...+..++..... ++||||++++.|+.+++.|++.|+
T Consensus       281 ~~~~~~~-k~~~l~~~l~~~~~-~~lVF~~t~~~a~~l~~~L~~~~~  325 (434)
T 2db3_A          281 YEVNKYA-KRSKLIEILSEQAD-GTIVFVETKRGADFLASFLSEKEF  325 (434)
T ss_dssp             EECCGGG-HHHHHHHHHHHCCT-TEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             EEeCcHH-HHHHHHHHHHhCCC-CEEEEEeCcHHHHHHHHHHHhCCC
Confidence            8888776 88888888887654 599999999999999999998765

>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=100.00  E-value=2.4e-44  Score=323.33  Aligned_cols=277  Identities=73%  Similarity=1.134  Sum_probs=252.9

Q ss_pred             ceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC
Q 022383           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR  100 (298)
Q Consensus        21 ~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~  100 (298)
                      ...+....+++..+|+++++++.+.++|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....
T Consensus        25 ~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~  104 (410)
T 2j0s_A           25 VEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVR  104 (410)
T ss_dssp             CCCCCCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSC
T ss_pred             cccCCCCCccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccC
Confidence            34455666677889999999999999999999999999999999999999999999999999999999999998876556


Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEE
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vV  180 (298)
                      +.++||++|+++|+.|+.+.+++++...++.+..+.|+.....+...+..+++|+|+||+++..++..+.+.+.++++||
T Consensus       105 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vV  184 (410)
T 2j0s_A          105 ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLV  184 (410)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEE
Confidence            77999999999999999999999998889999999999988888888888899999999999999998888889999999


Q ss_pred             echhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchH
Q 022383          181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKF  260 (298)
Q Consensus       181 iDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~  260 (298)
                      +||+|.+.++++...+..+++.+++..|++++|||+++.+..+...++.+|..+..........++.+.+..+.....+.
T Consensus       185 iDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~  264 (410)
T 2j0s_A          185 LDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKF  264 (410)
T ss_dssp             EETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHH
T ss_pred             EccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHH
Confidence            99999999999999999999999999999999999999988888888889988887766677788899999888888799


Q ss_pred             HHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          261 DTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       261 ~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..+..++.....+++||||++++.++.+++.|+..|+
T Consensus       265 ~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~  301 (410)
T 2j0s_A          265 DTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANF  301 (410)
T ss_dssp             HHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhcCCCcEEEEEcCHHHHHHHHHHHHhCCC
Confidence            9999999887778999999999999999999988764

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=1.5e-43  Score=318.69  Aligned_cols=275  Identities=29%  Similarity=0.421  Sum_probs=241.3

Q ss_pred             eeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC--
Q 022383           22 VFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS--   99 (298)
Q Consensus        22 ~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~--   99 (298)
                      ...+...++++.+|+++++++.+.++|.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+....  
T Consensus         4 ~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~   83 (417)
T 2i4i_A            4 EATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPG   83 (417)
T ss_dssp             EEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCC
T ss_pred             ccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhcccc
Confidence            445566678889999999999999999999999999999999999999999999999999999999999998764321  


Q ss_pred             ----------------CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHH
Q 022383          100 ----------------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVC  163 (298)
Q Consensus       100 ----------------~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~  163 (298)
                                      .++++||++|+++|+.|+.+.++++....++++..++|+.....+...+..+++|+|+||++|.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~  163 (417)
T 2i4i_A           84 EALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLV  163 (417)
T ss_dssp             HHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHH
T ss_pred             chhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHH
Confidence                            2368999999999999999999999888889999999999888888888888999999999999


Q ss_pred             HHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhC--CC--CccEEEEEeeCchhHHHHHHhcCCCCEEEEecCC
Q 022383          164 DMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRD  239 (298)
Q Consensus       164 ~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~--~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  239 (298)
                      .++....+.+.++++||+||+|++.+++|...+..++...  +.  ..|++++|||+++.+..+...++.++..+.....
T Consensus       164 ~~l~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  243 (417)
T 2i4i_A          164 DMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRV  243 (417)
T ss_dssp             HHHHTTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC--
T ss_pred             HHHHcCCcChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCC
Confidence            9999888889999999999999999999999999998853  32  6789999999999999999889999988877766


Q ss_pred             ccCcCCceEEEEEecCccchHHHHHHHHhhC-CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       240 ~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ......+.+.+..++... +...+..+++.. ..+++||||++++.++.+++.|+..|+
T Consensus       244 ~~~~~~i~~~~~~~~~~~-~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~  301 (417)
T 2i4i_A          244 GSTSENITQKVVWVEESD-KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGY  301 (417)
T ss_dssp             --CCSSEEEEEEECCGGG-HHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             CCCccCceEEEEEeccHh-HHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCC
Confidence            666777888888877766 888899998876 456999999999999999999988764

>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=100.00  E-value=2.9e-42  Score=309.85  Aligned_cols=270  Identities=58%  Similarity=0.971  Sum_probs=247.7

Q ss_pred             CCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEE
Q 022383           28 GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (298)
Q Consensus        28 ~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (298)
                      ......+|+++++++.+.+.|+++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....+.+++|+
T Consensus        35 ~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil  114 (414)
T 3eiq_A           35 WNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVL  114 (414)
T ss_dssp             CCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEE
T ss_pred             ccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEE
Confidence            34556799999999999999999999999999999999999999999999999999999999999998776667789999


Q ss_pred             cCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhH
Q 022383          108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (298)
Q Consensus       108 ~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~  186 (298)
                      +|+++|+.|+.+.+++++...+..+....|+.........+. .+++|+|+||++|.+.+....+.+.++++||+||+|+
T Consensus       115 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~  194 (414)
T 3eiq_A          115 APTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADE  194 (414)
T ss_dssp             CSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHH
T ss_pred             eChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHH
Confidence            999999999999999999888899999999888777666665 7789999999999999998888889999999999999


Q ss_pred             hhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHH
Q 022383          187 MLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL  266 (298)
Q Consensus       187 ~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  266 (298)
                      +.++++...+..++..++++.|++++|||+++........++.++..+...........+.+.+..+...+.+...+..+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  274 (414)
T 3eiq_A          195 MLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDL  274 (414)
T ss_dssp             HHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHH
T ss_pred             hhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999998888777777788899999888888899999999


Q ss_pred             HhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          267 YDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       267 l~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +.....+++||||++++.++.+++.|+..++
T Consensus       275 ~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~  305 (414)
T 3eiq_A          275 YETLTITQAVIFINTRRKVDWLTEKMHARDF  305 (414)
T ss_dssp             HHSSCCSSCEEECSCHHHHHHHHHHHHTTTC
T ss_pred             HHhCCCCcEEEEeCCHHHHHHHHHHHHhcCC
Confidence            9988888999999999999999999988764

>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=100.00  E-value=4.4e-42  Score=287.33  Aligned_cols=219  Identities=29%  Similarity=0.459  Sum_probs=202.5

Q ss_pred             ceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC--
Q 022383           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS--   98 (298)
Q Consensus        21 ~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~--   98 (298)
                      ..+.+...+++..+|+++++++.+.+++.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+...  
T Consensus        17 i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~   96 (242)
T 3fe2_A           17 ITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPF   96 (242)
T ss_dssp             EEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCC
T ss_pred             eEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccc
Confidence            345666778899999999999999999999999999999999999999999999999999999999999999987642  


Q ss_pred             ---CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCC
Q 022383           99 ---SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus        99 ---~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                         ..++++||++|+++|+.|+.+.++++....++++..++|+.........+..+++|+|+||+++..++......+.+
T Consensus        97 ~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~  176 (242)
T 3fe2_A           97 LERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRR  176 (242)
T ss_dssp             CCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTT
T ss_pred             cccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCccc
Confidence               34678999999999999999999999888899999999999988888888888999999999999999888888999


Q ss_pred             ccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCC
Q 022383          176 IKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD  239 (298)
Q Consensus       176 l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  239 (298)
                      ++++|+||+|++.+++|...+..+++.++++.|++++|||+++.+..+...++.+|..+.+...
T Consensus       177 ~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          177 TTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             CCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             ccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            9999999999999999999999999999999999999999999999999999999999887653

>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=100.00  E-value=5.2e-41  Score=300.55  Aligned_cols=265  Identities=38%  Similarity=0.631  Sum_probs=236.3

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      ...+|+++++++.+.++|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....+.+++|++|+
T Consensus        19 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~   98 (400)
T 1s2m_A           19 KGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPT   98 (400)
T ss_dssp             --CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCC
Confidence            45689999999999999999999999999999999999999999999999999999999999988765566789999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      ++|+.|+.+.++++....++.+....|+.........+..+++|+|+||+++...+......+.++++||+||+|++.+.
T Consensus        99 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~  178 (400)
T 1s2m_A           99 RELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSR  178 (400)
T ss_dssp             HHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSH
T ss_pred             HHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhh
Confidence            99999999999999888889999999998887777777788999999999999998887788899999999999999888


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  270 (298)
                      ++...+..++..+++..|++++|||++..+..+...++..|..+.... ......+.+.+..++... |...+..+++..
T Consensus       179 ~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-k~~~l~~~~~~~  256 (400)
T 1s2m_A          179 DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLKGITQYYAFVEERQ-KLHCLNTLFSKL  256 (400)
T ss_dssp             HHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCS-SCBCTTEEEEEEECCGGG-HHHHHHHHHHHS
T ss_pred             chHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEecc-ccccCCceeEEEEechhh-HHHHHHHHHhhc
Confidence            889999999999988999999999999999998888888887665443 344566777777776665 888899999888


Q ss_pred             CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          271 TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       271 ~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..+++||||++++.++.+++.|++.|+
T Consensus       257 ~~~~~lVf~~~~~~~~~l~~~L~~~~~  283 (400)
T 1s2m_A          257 QINQAIIFCNSTNRVELLAKKITDLGY  283 (400)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHHTC
T ss_pred             CCCcEEEEEecHHHHHHHHHHHHhcCC
Confidence            888999999999999999999988764

>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=100.00  E-value=1e-41  Score=304.33  Aligned_cols=268  Identities=56%  Similarity=0.918  Sum_probs=191.2

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        29 ~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      .+...+|+++++++.+.++|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....++++||++
T Consensus        17 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~   96 (394)
T 1fuu_A           17 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLA   96 (394)
T ss_dssp             CCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             ccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEc
Confidence            34567899999999999999999999999999999999999999999999999999999999999887766677999999


Q ss_pred             CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       109 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      |+++|+.|+.+.++++....++++..++|+.........+. +++|+|+||+++...+......+.++++||+||+|++.
T Consensus        97 P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~  175 (394)
T 1fuu_A           97 PTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEML  175 (394)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhh
Confidence            99999999999999998888899999999888766555444 57999999999999998888888999999999999999


Q ss_pred             ccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh
Q 022383          189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (298)
Q Consensus       189 ~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  268 (298)
                      ++++...+..++..+++..|++++|||+++........++..|..+..........++.+.+..+.....+...+..+++
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  255 (394)
T 1fuu_A          176 SSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYD  255 (394)
T ss_dssp             HTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC------------------------------
T ss_pred             CCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHh
Confidence            99999999999999999999999999999998888888999999888776666667777777777776667888888888


Q ss_pred             hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          269 TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       269 ~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ....+++||||++++.++.+++.|++.++
T Consensus       256 ~~~~~~~lVf~~~~~~~~~l~~~L~~~~~  284 (394)
T 1fuu_A          256 SISVTQAVIFCNTRRKVEELTTKLRNDKF  284 (394)
T ss_dssp             -----------------------------
T ss_pred             cCCCCcEEEEECCHHHHHHHHHHHHHcCC
Confidence            77778999999999999999999987654

>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=100.00  E-value=9.5e-41  Score=299.72  Aligned_cols=270  Identities=36%  Similarity=0.594  Sum_probs=237.3

Q ss_pred             cccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCe
Q 022383           25 TTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREV  102 (298)
Q Consensus        25 ~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~  102 (298)
                      ...+.....+|+++++++.+.++|.++||..|+++|.++++.+.++  +++++++|||+|||++|++|++..+.....++
T Consensus        17 ~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~   96 (412)
T 3fht_A           17 PNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYP   96 (412)
T ss_dssp             TTSTTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSC
T ss_pred             CCCCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCC
Confidence            4444556789999999999999999999999999999999999987  99999999999999999999999988777777


Q ss_pred             EEEEEcCcHHHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEE
Q 022383          103 QALILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLV  180 (298)
Q Consensus       103 ~~lil~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vV  180 (298)
                      ++||++|+++|+.|+.+.++++.... ++.+....++......   ...+++|+|+||+++...+.. ..+.+.++++||
T Consensus        97 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iV  173 (412)
T 3fht_A           97 QCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFV  173 (412)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEE
T ss_pred             CEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhcCCcChhhCcEEE
Confidence            99999999999999999999987654 5777777776554322   134579999999999998866 567788999999


Q ss_pred             echhhHhhc-cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccch
Q 022383          181 LDESDEMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK  259 (298)
Q Consensus       181 iDE~h~~~~-~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k  259 (298)
                      +||+|++.+ .++...+..+.+.+++..|++++|||+++....+...++.++..+...........+.+.+..+.....+
T Consensus       174 iDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (412)
T 3fht_A          174 LDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEK  253 (412)
T ss_dssp             EETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHH
T ss_pred             EeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHHH
Confidence            999999987 5788888999999999999999999999999999999999999888877777778888998888887778


Q ss_pred             HHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          260 FDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       260 ~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ...+..++.....+++||||++++.|+.+++.|+..++
T Consensus       254 ~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~  291 (412)
T 3fht_A          254 FQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGH  291 (412)
T ss_dssp             HHHHHHHHHHHSSSEEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhhcCCCCEEEEeCCHHHHHHHHHHHHhCCC
Confidence            99999999888888999999999999999999988764

>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=100.00  E-value=2.9e-40  Score=294.70  Aligned_cols=264  Identities=34%  Similarity=0.579  Sum_probs=232.9

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      .+|+++++++.+.++|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....+.++||++|+++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~   87 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   87 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHH
Confidence            57999999999999999999999999999999999999999999999999999999999998876666779999999999


Q ss_pred             HHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          113 LATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      |+.|+.+.++++.... ++++..++|+.........+. ..++|+|+||+++..++......+.++++||+||+|++.++
T Consensus        88 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~  167 (391)
T 1xti_A           88 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  167 (391)
T ss_dssp             HHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSS
T ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhc
Confidence            9999999999987765 788999999988766665554 44799999999999999888888999999999999999875


Q ss_pred             -ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCc-cCcCCceEEEEEecCccchHHHHHHHHh
Q 022383          191 -GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDE-LTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (298)
Q Consensus       191 -~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~~~~~~k~~~l~~ll~  268 (298)
                       ++...+..+++..++..|++++|||+++........++.+|..+...... .....+.+.+..+.... +...+..+++
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~l~  246 (391)
T 1xti_A          168 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNE-KNRKLFDLLD  246 (391)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGG-HHHHHHHHHH
T ss_pred             cchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCchh-HHHHHHHHHH
Confidence             78888889999998899999999999999999999999988887765443 33456777777776665 8889999999


Q ss_pred             hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          269 TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       269 ~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ....+++||||++++.++.+++.|+..|+
T Consensus       247 ~~~~~~~lvf~~~~~~~~~l~~~L~~~~~  275 (391)
T 1xti_A          247 VLEFNQVVIFVKSVQRCIALAQLLVEQNF  275 (391)
T ss_dssp             HSCCSEEEEECSCHHHHHHHHHHHHHTTC
T ss_pred             hcCCCcEEEEeCcHHHHHHHHHHHHhCCC
Confidence            88888999999999999999999988764

>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=100.00  E-value=2e-40  Score=295.81  Aligned_cols=263  Identities=37%  Similarity=0.580  Sum_probs=235.0

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      ...+|+++++++.+.++|.++||..|+++|.++++.+.++  +++++++|||+|||++|+++++..+.....++++||++
T Consensus         3 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~   82 (395)
T 3pey_A            3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLA   82 (395)
T ss_dssp             -CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             cccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEEC
Confidence            4579999999999999999999999999999999999988  99999999999999999999999987766677999999


Q ss_pred             CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       109 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      |+++|+.|+.+.+++++...++.+....++.....    ...+++|+|+||+++...+......+.++++||+||+|++.
T Consensus        83 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~  158 (395)
T 3pey_A           83 PSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKN----KQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNML  158 (395)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTT----SCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhh----ccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhc
Confidence            99999999999999998888888888777654322    13468999999999999998888889999999999999998


Q ss_pred             c-cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHH
Q 022383          189 S-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY  267 (298)
Q Consensus       189 ~-~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll  267 (298)
                      + .++...+..+.+.+++..|++++|||+++.+..+...++.++..+...........+.+.+..+.....+...+..++
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  238 (395)
T 3pey_A          159 DQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELY  238 (395)
T ss_dssp             HSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHH
T ss_pred             CccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHH
Confidence            7 578888999999999999999999999999999999999888888777666777788888888877777888999998


Q ss_pred             hhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          268 DTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       268 ~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .....+++||||++++.|+.+++.|+..|+
T Consensus       239 ~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~  268 (395)
T 3pey_A          239 GLMTIGSSIIFVATKKTANVLYGKLKSEGH  268 (395)
T ss_dssp             TTTTSSEEEEECSCHHHHHHHHHHHHHTTC
T ss_pred             HhccCCCEEEEeCCHHHHHHHHHHHHhcCC
Confidence            888888999999999999999999988764

>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=100.00  E-value=4.7e-41  Score=282.91  Aligned_cols=232  Identities=29%  Similarity=0.458  Sum_probs=196.3

Q ss_pred             CCcceeecccCCc--cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhh
Q 022383           18 DDKMVFETTEGVE--AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTV   95 (298)
Q Consensus        18 ~~~~~~~~~~~~~--~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~   95 (298)
                      +-+..+.+...+.  ++.+|+++++++.+.++|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+
T Consensus         6 ~~~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l   85 (253)
T 1wrb_A            6 SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHL   85 (253)
T ss_dssp             CCCCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             hCceeeeCCCCCCCCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHH
Confidence            3344444444444  77899999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccCC---------CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHH
Q 022383           96 DTSS---------REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI  166 (298)
Q Consensus        96 ~~~~---------~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~  166 (298)
                      ....         .++++||++|+++|+.|+.+.++++....++.+..++|+.....+...+..+++|+|+||+++...+
T Consensus        86 ~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l  165 (253)
T 1wrb_A           86 VCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFI  165 (253)
T ss_dssp             HTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHH
T ss_pred             HhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHH
Confidence            5432         3468999999999999999999999888888999999998888777788888999999999999999


Q ss_pred             hccCccCCCccEEEechhhHhhccccHHHHHHHHHhC--CC--CccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccC
Q 022383          167 KRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL--PP--DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELT  242 (298)
Q Consensus       167 ~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~--~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (298)
                      ......+.+++++|+||+|++.+++|...+..+++.+  +.  ..|++++|||+++.+..+...++.+|..+.+......
T Consensus       166 ~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~  245 (253)
T 1wrb_A          166 EKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGST  245 (253)
T ss_dssp             HTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC-----
T ss_pred             HcCCCChhhCCEEEEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCC
Confidence            9888889999999999999999999999999999854  33  6899999999999999999999999999988766665


Q ss_pred             cCCceEE
Q 022383          243 LEGIKQF  249 (298)
Q Consensus       243 ~~~i~~~  249 (298)
                      ..+++|.
T Consensus       246 ~~~i~q~  252 (253)
T 1wrb_A          246 SDSIKQE  252 (253)
T ss_dssp             -------
T ss_pred             cCCceec
Confidence            5555553

>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=100.00  E-value=1.9e-40  Score=274.89  Aligned_cols=211  Identities=31%  Similarity=0.482  Sum_probs=187.2

Q ss_pred             ecccCCccccCccc-CCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC----
Q 022383           24 ETTEGVEAITSFDA-MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----   98 (298)
Q Consensus        24 ~~~~~~~~~~~~~~-l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~----   98 (298)
                      +....+++..+|++ +++++.+.++|.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+...    
T Consensus        10 ~~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~   89 (228)
T 3iuy_A           10 EKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR   89 (228)
T ss_dssp             SCCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC------
T ss_pred             ccCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchh
Confidence            45556788899999 7999999999999999999999999999999999999999999999999999999877532    


Q ss_pred             --CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383           99 --SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus        99 --~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                        ..++++||++|+++|+.|+.+.++++. ..++++..++|+.........+..+++|+|+||+++..++......++++
T Consensus        90 ~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           90 EQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             ---CCCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             hccCCCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccc
Confidence              246789999999999999999999986 45788889999988877777888889999999999999998888889999


Q ss_pred             cEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEE
Q 022383          177 KLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKIL  235 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  235 (298)
                      ++||+||+|++.+++|...+..+++.++++.|++++|||+++.+..+...++.+|..+.
T Consensus       169 ~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~  227 (228)
T 3iuy_A          169 TYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVY  227 (228)
T ss_dssp             CEEEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEE
T ss_pred             eEEEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            99999999999999999999999999999999999999999999999999999998775

>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=100.00  E-value=6.7e-40  Score=267.37  Aligned_cols=202  Identities=34%  Similarity=0.640  Sum_probs=188.2

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      .+|+++++++.+.++|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....++++||++|+++
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~   82 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHH
Confidence            47999999999999999999999999999999999999999999999999999999999998876666779999999999


Q ss_pred             HHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc
Q 022383          113 LATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~  191 (298)
                      |+.|+.+.++++.... +..+..++|+.........+..+++|+|+||+++...+..+...+.+++++|+||+|++.+.+
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~  162 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhC
Confidence            9999999999988766 788899999988887777778889999999999999998888888999999999999999989


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEE
Q 022383          192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKI  234 (298)
Q Consensus       192 ~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~  234 (298)
                      +...+..+++.++++.|++++|||+++.+..++..++.+|..+
T Consensus       163 ~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          163 FVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             THHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             cHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            9999999999999899999999999999999999999988765

>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=100.00  E-value=3.2e-40  Score=273.95  Aligned_cols=211  Identities=34%  Similarity=0.561  Sum_probs=186.0

Q ss_pred             cccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEE
Q 022383           25 TTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQA  104 (298)
Q Consensus        25 ~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~  104 (298)
                      ....+.+..+|+++++++.+.++|.++||..|+++|.++++.+.+|+|+++++|||+|||++|++|++..+.....++++
T Consensus        16 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~   95 (230)
T 2oxc_A           16 GDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQI   95 (230)
T ss_dssp             --------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCE
T ss_pred             CCCCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceE
Confidence            34445667789999999999999999999999999999999999999999999999999999999999988766667799


Q ss_pred             EEEcCcHHHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEech
Q 022383          105 LILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (298)
Q Consensus       105 lil~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE  183 (298)
                      ||++|+++|+.|+.+.++++.... ++++..++|+.....+...+ .+++|+|+||+++..++..+.+.+.+++++|+||
T Consensus        96 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDE  174 (230)
T 2oxc_A           96 LILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDE  174 (230)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESS
T ss_pred             EEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhcCCcccccCCEEEeCC
Confidence            999999999999999999987655 78899999988876665554 4689999999999999988888889999999999


Q ss_pred             hhHhhccc-cHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          184 SDEMLSRG-FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       184 ~h~~~~~~-~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                      +|++.+++ |...+..+++.+++..|++++|||+++.+..++..++.+|..+.+
T Consensus       175 ah~~~~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~~  228 (230)
T 2oxc_A          175 ADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL  228 (230)
T ss_dssp             HHHHHSTTSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEECC
T ss_pred             chHhhcCcchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEEc
Confidence            99999887 999999999999989999999999999999999999999887654

>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=100.00  E-value=2.5e-40  Score=284.73  Aligned_cols=207  Identities=37%  Similarity=0.591  Sum_probs=186.1

Q ss_pred             CCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEE
Q 022383           28 GVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL  105 (298)
Q Consensus        28 ~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~l  105 (298)
                      +.....+|++++|++.+.++|.++||..|+++|.++++.++.|  +|+++++|||+|||++|++|+++.+.....++++|
T Consensus        87 p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~l  166 (300)
T 3fmo_B           87 PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCL  166 (300)
T ss_dssp             CCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEE
T ss_pred             CcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEE
Confidence            3445679999999999999999999999999999999999987  99999999999999999999999998777788999


Q ss_pred             EEcCcHHHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEEech
Q 022383          106 ILSPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDE  183 (298)
Q Consensus       106 il~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE  183 (298)
                      |++||++|+.|+.+.++.++... ++.+....|+.......   ..+++|+|+||++|..++.+ +.++++++++||+||
T Consensus       167 il~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDE  243 (300)
T 3fmo_B          167 CLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDE  243 (300)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETT
T ss_pred             EEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeC
Confidence            99999999999999999998764 67888888876543321   45679999999999999966 567889999999999


Q ss_pred             hhHhhc-cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEec
Q 022383          184 SDEMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (298)
Q Consensus       184 ~h~~~~-~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  237 (298)
                      +|++.+ .+|...+..+++.+++.+|++++|||+++.+..+...++.+|..+.+.
T Consensus       244 ad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~  298 (300)
T 3fmo_B          244 ADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLK  298 (300)
T ss_dssp             HHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEEC
T ss_pred             HHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEec
Confidence            999997 689999999999999999999999999999999999999999988764

>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=100.00  E-value=1.5e-40  Score=277.11  Aligned_cols=213  Identities=57%  Similarity=0.954  Sum_probs=181.5

Q ss_pred             cccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEE
Q 022383           25 TTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQA  104 (298)
Q Consensus        25 ~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~  104 (298)
                      .+..+++..+|+++++++.+.++|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+.....+.++
T Consensus        22 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~  101 (237)
T 3bor_A           22 ESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQA  101 (237)
T ss_dssp             -----CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCE
T ss_pred             cCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceE
Confidence            33455677899999999999999999999999999999999999999999999999999999999999998766567799


Q ss_pred             EEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcC-CcEEEeChHHHHHHHhccCccCCCccEEEech
Q 022383          105 LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (298)
Q Consensus       105 lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE  183 (298)
                      ||++|+++|+.|+.+.+++++...++.+..+.|+.....+...+..+ ++|+|+||+++..++..+...+.++++||+||
T Consensus       102 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDE  181 (237)
T 3bor_A          102 LVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDE  181 (237)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEES
T ss_pred             EEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECC
Confidence            99999999999999999999888888888888887766665556544 89999999999999988888889999999999


Q ss_pred             hhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEec
Q 022383          184 SDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (298)
Q Consensus       184 ~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  237 (298)
                      +|++.++++...+..+++.+++..|++++|||+++.+..+...++.+|..+.+.
T Consensus       182 ah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~  235 (237)
T 3bor_A          182 ADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVK  235 (237)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC--
T ss_pred             chHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEec
Confidence            999999999999999999999999999999999999999999999999887653

>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=100.00  E-value=1.1e-40  Score=305.51  Aligned_cols=265  Identities=37%  Similarity=0.603  Sum_probs=180.4

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEE
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL  107 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil  107 (298)
                      ....+|++++|++.+.++|.++||..|+++|.++++.++.+  +++++++|||+|||++|++|++..+.....++++||+
T Consensus        89 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil  168 (479)
T 3fmp_B           89 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCL  168 (479)
T ss_dssp             CCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEE
T ss_pred             cCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEE
Confidence            34668999999999999999999999999999999999987  9999999999999999999999998877777799999


Q ss_pred             cCcHHHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEEechhh
Q 022383          108 SPTRELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESD  185 (298)
Q Consensus       108 ~p~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE~h  185 (298)
                      +|+++|+.|+.+.++++.... ++.+....++......   ...+++|+|+||+++..++.+ ..+.+.++++||+||+|
T Consensus       169 ~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah  245 (479)
T 3fmp_B          169 SPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD  245 (479)
T ss_dssp             CSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHH
T ss_pred             eChHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHH
Confidence            999999999999999987654 5667777766543321   134579999999999998866 56678999999999999


Q ss_pred             Hhhc-cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHH
Q 022383          186 EMLS-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLC  264 (298)
Q Consensus       186 ~~~~-~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  264 (298)
                      .+.+ .++...+..+.+.+++.+|++++|||+++....+...++.+|..+...........+.+.+..+.....+...+.
T Consensus       246 ~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  325 (479)
T 3fmp_B          246 VMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALC  325 (479)
T ss_dssp             HHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC---------------------------
T ss_pred             HHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHH
Confidence            9987 578888999999999999999999999999999999999999988888777777788888888887777888888


Q ss_pred             HHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          265 DLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       265 ~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .++......++||||++++.|+.+++.|+..++
T Consensus       326 ~~~~~~~~~~~lvF~~s~~~~~~l~~~L~~~~~  358 (479)
T 3fmp_B          326 NLYGAITIAQAMIFCHTRKTASWLAAELSKEGH  358 (479)
T ss_dssp             ---------------------------------
T ss_pred             HHHhhccCCceEEEeCcHHHHHHHHHHHHhCCc
Confidence            888877778999999999999999999987654

>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=100.00  E-value=3.5e-40  Score=276.73  Aligned_cols=208  Identities=33%  Similarity=0.543  Sum_probs=192.8

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        29 ~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      ..+..+|+++++++.+.++|+++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....++++||++
T Consensus        39 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~  118 (249)
T 3ber_A           39 EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLT  118 (249)
T ss_dssp             HHHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEEC
T ss_pred             ccccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEe
Confidence            34567999999999999999999999999999999999999999999999999999999999999887766677899999


Q ss_pred             CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEEechhhHh
Q 022383          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       109 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE~h~~  187 (298)
                      |+++|+.|+.+.++++....++++..++|+.....+...+..+++|+|+||+++...+.. ..+.+.++++||+||+|++
T Consensus       119 Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l  198 (249)
T 3ber_A          119 PTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRI  198 (249)
T ss_dssp             SSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHH
T ss_pred             CCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhh
Confidence            999999999999999988888999999999888777777778899999999999998876 5677899999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                      .+++|...+..+++.+++..|++++|||+++.+..+...++.+|..+.+
T Consensus       199 ~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v  247 (249)
T 3ber_A          199 LNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV  247 (249)
T ss_dssp             HHTTCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             hccChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999999999999989999999999999999999999999988765

>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=100.00  E-value=5.2e-40  Score=271.50  Aligned_cols=212  Identities=55%  Similarity=0.919  Sum_probs=185.1

Q ss_pred             ccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEE
Q 022383           26 TEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQAL  105 (298)
Q Consensus        26 ~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~l  105 (298)
                      +.-++++.+|+++++++.+.+.|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....++++|
T Consensus         7 ~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~l   86 (224)
T 1qde_A            7 TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQAL   86 (224)
T ss_dssp             BSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEE
T ss_pred             cccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEE
Confidence            33456678999999999999999999999999999999999999999999999999999999999999987766678999


Q ss_pred             EEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhh
Q 022383          106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (298)
Q Consensus       106 il~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h  185 (298)
                      |++|+++|+.|+.+.++++....++++..++|+.........+.+ ++|+|+||+++...+......+.++++||+||+|
T Consensus        87 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah  165 (224)
T 1qde_A           87 MLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEAD  165 (224)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHH
T ss_pred             EEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcchhhCcEEEEcChh
Confidence            999999999999999999988888999999998776665555444 8999999999999998888888999999999999


Q ss_pred             HhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecC
Q 022383          186 EMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKR  238 (298)
Q Consensus       186 ~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~  238 (298)
                      ++.++++...+..+++.+++..|++++|||+++.+..+...++.+|..+.+..
T Consensus       166 ~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~  218 (224)
T 1qde_A          166 EMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK  218 (224)
T ss_dssp             HHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC---
T ss_pred             HHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecC
Confidence            99999999999999999999999999999999999999999999998887654

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=2e-40  Score=273.08  Aligned_cols=206  Identities=34%  Similarity=0.559  Sum_probs=188.3

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ..+|+++++++.+.++|+++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....+++++|++|++
T Consensus         3 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   82 (219)
T 1q0u_A            3 ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTR   82 (219)
T ss_dssp             -CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcH
Confidence            46799999999999999999999999999999999999999999999999999999999999987766677999999999


Q ss_pred             HHHHHHHHHHHHhhccC----CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          112 ELATQTEKVILAIGDFI----NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      +|+.|+.+.++++....    ++.+..++|+.........+..+++|+|+||+++...+..+...+.+++++|+||+|.+
T Consensus        83 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~  162 (219)
T 1q0u_A           83 ELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLM  162 (219)
T ss_dssp             HHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHH
T ss_pred             HHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHH
Confidence            99999999999988766    67888888888766655555567899999999999999888888899999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEec
Q 022383          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  237 (298)
                      .++++...+..+++.++++.|++++|||+++.+.+++..++.+|..+...
T Consensus       163 ~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~  212 (219)
T 1q0u_A          163 LDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVL  212 (219)
T ss_dssp             HHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC
T ss_pred             hhhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEee
Confidence            99999999999999999899999999999999999999999999887654

>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=100.00  E-value=1.9e-38  Score=280.32  Aligned_cols=258  Identities=33%  Similarity=0.552  Sum_probs=224.8

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcC-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      ..+|+++++++.+.++|+++||..|+++|.++++.+.++ +++++.+|||+|||++|+.|++..+... .+.+++|++|+
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P~   83 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPT   83 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSC
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEcCC
Confidence            357999999999999999999999999999999999988 7999999999999999999999887553 45689999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      ++|+.|+.+.++++....++.+....|+.........+. +++|+|+||+++...+......+.++++||+||+|.+.++
T Consensus        84 ~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~  162 (367)
T 1hv8_A           84 RELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNM  162 (367)
T ss_dssp             HHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhh
Confidence            999999999999998888888999999887766655554 6899999999999999888888899999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhC
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL  270 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  270 (298)
                      ++...+..++..+++..+++++|||+++........++.++..+....    ...+.+.+..+.... +...+..+++ .
T Consensus       163 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~-~~~~l~~~l~-~  236 (367)
T 1hv8_A          163 GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKI----NANIEQSYVEVNENE-RFEALCRLLK-N  236 (367)
T ss_dssp             TTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCS----SSSSEEEEEECCGGG-HHHHHHHHHC-S
T ss_pred             chHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecC----CCCceEEEEEeChHH-HHHHHHHHHh-c
Confidence            999999999999988999999999999998888888887766555432    235677777776665 8888888887 3


Q ss_pred             CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          271 TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       271 ~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ...++||||++++.++.+++.|+..|+
T Consensus       237 ~~~~~lvf~~~~~~~~~l~~~L~~~~~  263 (367)
T 1hv8_A          237 KEFYGLVFCKTKRDTKELASMLRDIGF  263 (367)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhcCC
Confidence            457999999999999999999988764

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=1.3e-38  Score=265.24  Aligned_cols=208  Identities=28%  Similarity=0.499  Sum_probs=185.6

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC----CCCeEE
Q 022383           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQA  104 (298)
Q Consensus        29 ~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~----~~~~~~  104 (298)
                      +++..+|+++++++.+.++|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+...    ..++++
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~  100 (236)
T 2pl3_A           21 VNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGV  100 (236)
T ss_dssp             GGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCE
T ss_pred             CcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceE
Confidence            4567789999999999999999999999999999999999999999999999999999999999886432    235689


Q ss_pred             EEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc-CccCCCccEEEech
Q 022383          105 LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDE  183 (298)
Q Consensus       105 lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~-~~~~~~l~~vViDE  183 (298)
                      ||++|+++|+.|+.+.+++++...++.+..++|+.........+ .+++|+|+||+++...+... .+.+.+++++|+||
T Consensus       101 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDE  179 (236)
T 2pl3_A          101 LIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDE  179 (236)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETT
T ss_pred             EEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEEeC
Confidence            99999999999999999999888888999999988776655555 57899999999999988764 57788999999999


Q ss_pred             hhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEec
Q 022383          184 SDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (298)
Q Consensus       184 ~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  237 (298)
                      +|++.++++...+..+++.+++..|++++|||+++.+..+.+.++.+|..+.+.
T Consensus       180 ah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~  233 (236)
T 2pl3_A          180 ADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVH  233 (236)
T ss_dssp             HHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECC
T ss_pred             hHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeC
Confidence            999999999999999999999999999999999999999999999999887654

>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=100.00  E-value=1.9e-38  Score=258.95  Aligned_cols=201  Identities=35%  Similarity=0.584  Sum_probs=184.2

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC---CCCeEEEEEcCc
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPT  110 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~  110 (298)
                      +|+++++++.+.++|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+...   ..+++++|++|+
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~   81 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPT   81 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSS
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECC
Confidence            69999999999999999999999999999999999999999999999999999999999987542   346789999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      ++|+.|+.+.++++...  +++..++|+.........+..+++|+|+||+++...+..+...+.+++++|+||+|++.++
T Consensus        82 ~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~  159 (207)
T 2gxq_A           82 RELALQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSM  159 (207)
T ss_dssp             HHHHHHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhcc
Confidence            99999999999998654  6778888988877777777778999999999999999888888999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                      ++...+..+++.+++..|++++|||+++.+..+...++.+|..+.+
T Consensus       160 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~  205 (207)
T 2gxq_A          160 GFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV  205 (207)
T ss_dssp             TCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             chHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEc
Confidence            9999999999999989999999999999999999999999987754

>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=100.00  E-value=2.1e-38  Score=261.22  Aligned_cols=205  Identities=36%  Similarity=0.602  Sum_probs=184.8

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      ...+|+++++++.+.++|.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.....+++++|++|+
T Consensus        12 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt   91 (220)
T 1t6n_A           12 HSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHT   91 (220)
T ss_dssp             --CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSC
T ss_pred             cCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCC
Confidence            34579999999999999999999999999999999999999999999999999999999999988766556789999999


Q ss_pred             HHHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          111 RELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      ++|+.|+.+.++++.... ++++..++|+.....+...+. ..++|+|+||+++..++......+.+++++|+||+|++.
T Consensus        92 ~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~  171 (220)
T 1t6n_A           92 RELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKML  171 (220)
T ss_dssp             HHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHh
Confidence            999999999999988765 788999999988776666555 457999999999999998888889999999999999998


Q ss_pred             c-cccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEE
Q 022383          189 S-RGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKIL  235 (298)
Q Consensus       189 ~-~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  235 (298)
                      + .++...+..+++.++++.|++++|||+++.+..+...++.+|..+.
T Consensus       172 ~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          172 EQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             SSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             cccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence            7 4788899999999988999999999999999999999999998764

>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=100.00  E-value=3.1e-38  Score=266.80  Aligned_cols=201  Identities=28%  Similarity=0.500  Sum_probs=179.2

Q ss_pred             ccCcccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC----CCCeEEE
Q 022383           32 ITSFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQAL  105 (298)
Q Consensus        32 ~~~~~~l~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~----~~~~~~l  105 (298)
                      ..+|++++  +++.+.++|+++||..|+++|.++++.+..|+|+++++|||+|||++|++|++..+...    ..+.++|
T Consensus        51 ~~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~l  130 (262)
T 3ly5_A           51 DTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVL  130 (262)
T ss_dssp             GGCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEE
T ss_pred             cCChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEE
Confidence            34666776  99999999999999999999999999999999999999999999999999999887542    1356899


Q ss_pred             EEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc-CccCCCccEEEechh
Q 022383          106 ILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK-TLRTRAIKLLVLDES  184 (298)
Q Consensus       106 il~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~-~~~~~~l~~vViDE~  184 (298)
                      |++|+++|+.|+.+.++++....+..+..+.|+.........+..+++|+|+||+++...+... .+.+.++++||+||+
T Consensus       131 il~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEa  210 (262)
T 3ly5_A          131 ILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEA  210 (262)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSH
T ss_pred             EEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcCh
Confidence            9999999999999999999988888999999998888887778788999999999999988764 477899999999999


Q ss_pred             hHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCE
Q 022383          185 DEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPV  232 (298)
Q Consensus       185 h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~  232 (298)
                      |++.+++|...+..+++.+++.+|++++|||+++.+..+.+.++.++.
T Consensus       211 h~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          211 DRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             HHHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             HHHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            999999999999999999999999999999999999999988876543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=9.4e-38  Score=292.07  Aligned_cols=267  Identities=25%  Similarity=0.370  Sum_probs=214.2

Q ss_pred             CccccCcccCC----CCHHHHHHHHHCCCCCChHHHHHHHHHhh--cCCcEEEEcCCCCchHHHHHHHHHHhhccCC---
Q 022383           29 VEAITSFDAMG----IKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---   99 (298)
Q Consensus        29 ~~~~~~~~~l~----l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~---   99 (298)
                      +....+|+++.    |++++.++|.++||..|+|+|.++++.++  .|+++++++|||+|||++|++|++..+....   
T Consensus        13 ~~~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~   92 (579)
T 3sqw_A           13 NSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS   92 (579)
T ss_dssp             SCCCCCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccc
Confidence            34445666654    99999999999999999999999999999  7899999999999999999999999875532   


Q ss_pred             -CCeEEEEEcCcHHHHHHHHHHHHHhhc----cCCceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhcc-Ccc
Q 022383          100 -REVQALILSPTRELATQTEKVILAIGD----FINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRK-TLR  172 (298)
Q Consensus       100 -~~~~~lil~p~~~l~~q~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~-~~~  172 (298)
                       .++++|||+|+++|+.|+.+.++++..    .....+....|+.........+. .+++|+|+||++|..++... ...
T Consensus        93 ~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~  172 (579)
T 3sqw_A           93 QYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKF  172 (579)
T ss_dssp             TTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHH
T ss_pred             cCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccc
Confidence             346899999999999999999998763    23467788888887776666653 57899999999999988764 456


Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCC-------CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCC----cc
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-------PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD----EL  241 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-------~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~----~~  241 (298)
                      +.++++||+||||++.+++|...+..++..++       ..+|++++|||+++.+..+...++..+..+.....    ..
T Consensus       173 ~~~~~~lViDEah~l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~  252 (579)
T 3sqw_A          173 FRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPE  252 (579)
T ss_dssp             CTTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCS
T ss_pred             cccCCEEEEEChHHhhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccc
Confidence            78999999999999999999999888877653       36799999999999999999888888877665432    22


Q ss_pred             CcCCceEEEEEecCccchH----HHHHHHHhh-CCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          242 TLEGIKQFFVAVEREEWKF----DTLCDLYDT-LTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       242 ~~~~i~~~~~~~~~~~~k~----~~l~~ll~~-~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ....+.+.+........+.    ..+...+.. ....++||||+|++.|+.+++.|+..
T Consensus       253 ~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~  311 (579)
T 3sqw_A          253 AHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNE  311 (579)
T ss_dssp             SCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cccccceEEEEecchhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHh
Confidence            3345666666666543232    223333333 45679999999999999999999876

>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=100.00  E-value=3.5e-38  Score=264.11  Aligned_cols=219  Identities=24%  Similarity=0.448  Sum_probs=187.5

Q ss_pred             ceeecccCCccccCcccC----CCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhc
Q 022383           21 MVFETTEGVEAITSFDAM----GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVD   96 (298)
Q Consensus        21 ~~~~~~~~~~~~~~~~~l----~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~   96 (298)
                      ..++....+.++.+|+++    ++++.+.+++.++||..|+++|.++++.+.+|+++++++|||+|||++|++|++..+.
T Consensus        13 i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~   92 (245)
T 3dkp_A           13 IHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLK   92 (245)
T ss_dssp             EEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC
T ss_pred             eEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHh
Confidence            345667778889999987    8999999999999999999999999999999999999999999999999999999886


Q ss_pred             cC-CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHH-HHhhcCCcEEEeChHHHHHHHhcc--Ccc
Q 022383           97 TS-SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI-RKLEHGVHVVSGTPGRVCDMIKRK--TLR  172 (298)
Q Consensus        97 ~~-~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ilV~Tp~~l~~~~~~~--~~~  172 (298)
                      .. ..++++||++|+++|+.|+.+.++++....++.+..++|+....... .....+++|+|+||+++..++...  .+.
T Consensus        93 ~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~  172 (245)
T 3dkp_A           93 QPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGID  172 (245)
T ss_dssp             SCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCC
T ss_pred             hcccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcc
Confidence            43 34668999999999999999999999888888887776654332221 122457899999999999999875  577


Q ss_pred             CCCccEEEechhhHhhcc---ccHHHHHHHHHhCC-CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCC
Q 022383          173 TRAIKLLVLDESDEMLSR---GFKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD  239 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~---~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  239 (298)
                      +.++++||+||+|++.++   ++...+..++..+. +..|++++|||+++.+..+...++.+|..+.+...
T Consensus       173 ~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          173 LASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             CTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             cccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            899999999999999884   68888888887764 57899999999999999999999999999887643

>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=100.00  E-value=2.6e-36  Score=263.71  Aligned_cols=241  Identities=24%  Similarity=0.443  Sum_probs=207.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      |++++.++|+++||..|+++|.++++.+.+|+++++++|||+|||++|+.|++..      +.+++|++|+++|+.|+.+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~------~~~~liv~P~~~L~~q~~~   74 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRELTRQVAS   74 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh------cCCEEEEeCCHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999874      4579999999999999999


Q ss_pred             HHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHH
Q 022383          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (298)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i  199 (298)
                      .++++....+..+..++|+.........+. .++|+|+||+++...+......+.++++||+||+|++.++++...+..+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~  153 (337)
T 2z0m_A           75 HIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKII  153 (337)
T ss_dssp             HHHHHTTTSCCCEEEECTTSCHHHHHHHHT-TCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHH
T ss_pred             HHHHHhhhcCCcEEEEECCcchHHHHhhcC-CCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHH
Confidence            999998888889999999888776655554 4899999999999998887778899999999999999999999999999


Q ss_pred             HHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEe
Q 022383          200 YRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFC  279 (298)
Q Consensus       200 ~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~  279 (298)
                      +...+...+++++|||+++........++.++..+...   .....+.+.+..+.... +  .....+.....+++||||
T Consensus       154 ~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~lvf~  227 (337)
T 2z0m_A          154 LAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDW-R--SKVQALRENKDKGVIVFV  227 (337)
T ss_dssp             HHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS---GGGGGEEEEEEECSSSS-H--HHHHHHHTCCCSSEEEEC
T ss_pred             HhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc---cccCCceEEEEEeChHH-H--HHHHHHHhCCCCcEEEEE
Confidence            99999899999999999999888888888877766432   33445666666665443 2  233556666778999999


Q ss_pred             cchhhHHHHHHHHh
Q 022383          280 NTKRKIYYSVFYFW  293 (298)
Q Consensus       280 ~s~~~~~~l~~~L~  293 (298)
                      ++++.++.+++.|+
T Consensus       228 ~~~~~~~~l~~~l~  241 (337)
T 2z0m_A          228 RTRNRVAKLVRLFD  241 (337)
T ss_dssp             SCHHHHHHHHTTCT
T ss_pred             cCHHHHHHHHHHhh
Confidence            99999999998875

>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=100.00  E-value=1.1e-36  Score=284.12  Aligned_cols=263  Identities=25%  Similarity=0.374  Sum_probs=210.2

Q ss_pred             cCcccCC----CCHHHHHHHHHCCCCCChHHHHHHHHHhh--cCCcEEEEcCCCCchHHHHHHHHHHhhccCC----CCe
Q 022383           33 TSFDAMG----IKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REV  102 (298)
Q Consensus        33 ~~~~~l~----l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~----~~~  102 (298)
                      .+|+++.    |++++.++|.++||..|+|+|.++++.++  .++|+++++|||+|||++|++|++..+....    .++
T Consensus        68 ~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~  147 (563)
T 3i5x_A           68 VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMV  147 (563)
T ss_dssp             CCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSC
T ss_pred             cCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCe
Confidence            3455553    99999999999999999999999999999  6789999999999999999999999876543    245


Q ss_pred             EEEEEcCcHHHHHHHHHHHHHhhcc----CCceEEEEEcCCchHHHHHHh-hcCCcEEEeChHHHHHHHhcc-CccCCCc
Q 022383          103 QALILSPTRELATQTEKVILAIGDF----INIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRK-TLRTRAI  176 (298)
Q Consensus       103 ~~lil~p~~~l~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~~~~~-~~~~~~l  176 (298)
                      ++|||+|+++|+.|+.+.++++...    ....+..+.|+.........+ ..+++|+|+||+++..++... ...++++
T Consensus       148 ~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~  227 (563)
T 3i5x_A          148 KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFV  227 (563)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTC
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccc
Confidence            8999999999999999999987532    245678888888776666555 457899999999999988764 4467889


Q ss_pred             cEEEechhhHhhccccHHHHHHHHHhCC-------CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCC----ccCcCC
Q 022383          177 KLLVLDESDEMLSRGFKDQIYDVYRYLP-------PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRD----ELTLEG  245 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~~~i~~i~~~~~-------~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~  245 (298)
                      ++||+||||++.+++|...+..++..++       +.+|++++|||+++.+..+...++..+..+.....    ......
T Consensus       228 ~~lViDEah~l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  307 (563)
T 3i5x_A          228 DYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHER  307 (563)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTT
T ss_pred             eEEEEeCHHHHhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCcccccc
Confidence            9999999999999999999888876653       37899999999999999998888888877665432    223345


Q ss_pred             ceEEEEEecCccchHHH----HHHHHhh-CCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          246 IKQFFVAVEREEWKFDT----LCDLYDT-LTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       246 i~~~~~~~~~~~~k~~~----l~~ll~~-~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      +.+.+........+...    +...+.. ....++||||+|++.|+.+++.|+..
T Consensus       308 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~  362 (563)
T 3i5x_A          308 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNE  362 (563)
T ss_dssp             EEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHH
T ss_pred             CceEEEECchhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            66666666554333322    2222332 45679999999999999999999876

>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=100.00  E-value=8.1e-35  Score=271.13  Aligned_cols=254  Identities=13%  Similarity=0.162  Sum_probs=193.2

Q ss_pred             cCcccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           33 TSFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ..++++++++.+.+.|++ +||..|+|+|.++++.+++|+|+++++|||+|||+||++|++..      ..++|||+|++
T Consensus        21 w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~------~g~~lVisP~~   94 (591)
T 2v1x_A           21 WNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS------DGFTLVICPLI   94 (591)
T ss_dssp             GCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS------SSEEEEECSCH
T ss_pred             cccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc------CCcEEEEeCHH
Confidence            344568899999999999 79999999999999999999999999999999999999999863      34899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHH---h---hcCCcEEEeChHHHH---HHHh--ccCccCCCccEEE
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRK---L---EHGVHVVSGTPGRVC---DMIK--RKTLRTRAIKLLV  180 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~---~~~~~ilV~Tp~~l~---~~~~--~~~~~~~~l~~vV  180 (298)
                      +|+.|+.+.++++    ++++..++|+....+....   +   ...++|+|+||++|.   .++.  .....+.++++||
T Consensus        95 ~L~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iV  170 (591)
T 2v1x_A           95 SLMEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIA  170 (591)
T ss_dssp             HHHHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEE
T ss_pred             HHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEE
Confidence            9999999999887    6788888888776544322   2   457899999999885   2222  1244577899999


Q ss_pred             echhhHhhccc--cHHHHHH--HHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecC-
Q 022383          181 LDESDEMLSRG--FKDQIYD--VYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVER-  255 (298)
Q Consensus       181 iDE~h~~~~~~--~~~~i~~--i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-  255 (298)
                      |||||++.+|+  |...+..  .+....+..+++++|||+++.+...+..++..+....+.. .....++...+..... 
T Consensus       171 iDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~-~~~r~nl~~~v~~~~~~  249 (591)
T 2v1x_A          171 VDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTA-SFNRPNLYYEVRQKPSN  249 (591)
T ss_dssp             EETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEEC-CCCCTTEEEEEEECCSS
T ss_pred             EECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEec-CCCCcccEEEEEeCCCc
Confidence            99999999887  6655544  3333345799999999999988777776665443222221 2333444443333222 


Q ss_pred             ccchHHHHHHHHhh-CCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          256 EEWKFDTLCDLYDT-LTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       256 ~~~k~~~l~~ll~~-~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ...+...+..++.. ..++++||||+|++.|+.+++.|+..|+
T Consensus       250 ~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~  292 (591)
T 2v1x_A          250 TEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGI  292 (591)
T ss_dssp             HHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCC
Confidence            12345667777754 3567999999999999999999998765

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=100.00  E-value=2.2e-35  Score=265.37  Aligned_cols=239  Identities=17%  Similarity=0.200  Sum_probs=186.6

Q ss_pred             HHHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHH
Q 022383           43 DLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        43 ~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      .+.+.+++ ++| .|+++|.++++.+++|+|+++++|||+|||++|+++++....   .++++||++|+++|+.|+.+.+
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~---~~~~~lil~Pt~~L~~q~~~~~   84 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERL   84 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc---CCCEEEEEECCHHHHHHHHHHH
Confidence            45556666 455 699999999999999999999999999999999999888763   3668999999999999999999


Q ss_pred             HHhhccCCceEEEEEcCCch---HHHHHHhhcC-CcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc--------
Q 022383          122 LAIGDFINIQAHACVGGKSV---GEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS--------  189 (298)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~--------  189 (298)
                      ++++. .++++..++|+.+.   ..+...+..+ ++|+|+||+++...+..  +.+.++++||+||+|++.+        
T Consensus        85 ~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~  161 (414)
T 3oiy_A           85 QKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTL  161 (414)
T ss_dssp             HHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHH
T ss_pred             HHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhH
Confidence            99887 78999999999887   4445555555 99999999999887764  6677999999999998764        


Q ss_pred             ---cccHHH-HHHHHHhCC-----------CCccEEEEEee-CchhHH-HHHHhcCCCCEEEEecCCccCcCCceEEEEE
Q 022383          190 ---RGFKDQ-IYDVYRYLP-----------PDLQVVLISAT-LPHEIL-EMTTKFMTDPVKILVKRDELTLEGIKQFFVA  252 (298)
Q Consensus       190 ---~~~~~~-i~~i~~~~~-----------~~~~~v~~SAT-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  252 (298)
                         .+|... +..+++.++           +..|++++||| .++.+. .+...++.    +...........+.+.+..
T Consensus       162 l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~~~~i~~~~~~  237 (414)
T 3oiy_A          162 LMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRIS  237 (414)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCCCCSEEEEEES
T ss_pred             HhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccccccchheeec
Confidence               556666 777887765           78999999999 554433 22222221    1222233444556666655


Q ss_pred             ecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          253 VEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       253 ~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +    .+...+..+++. .++++||||++++.|+.+++.|+..|+
T Consensus       238 ~----~~~~~l~~~l~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~  277 (414)
T 3oiy_A          238 S----RSKEKLVELLEI-FRDGILIFAQTEEEGKELYEYLKRFKF  277 (414)
T ss_dssp             S----CCHHHHHHHHHH-HCSSEEEEESSHHHHHHHHHHHHHTTC
T ss_pred             c----CHHHHHHHHHHH-cCCCEEEEECCHHHHHHHHHHHHHcCC
Confidence            4    266677777776 348999999999999999999998765

>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=100.00  E-value=3.7e-34  Score=263.91  Aligned_cols=248  Identities=15%  Similarity=0.233  Sum_probs=191.9

Q ss_pred             cCcccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           33 TSFDAMGIKDDLLRGIYQ-YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      .+|+++++++.+.+.|++ +||..|+++|.++++.+++|+|+++++|||+|||++|++|++..      ...+||++|++
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~------~g~~lvi~P~~   75 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLI   75 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCH
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh------CCCEEEECChH
Confidence            579999999999999999 89999999999999999999999999999999999999999854      34799999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH---H-hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---K-LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      +|+.|+.+.++++    ++.+..++++........   . ..+.++|+++||+++........+...++++|||||+|++
T Consensus        76 aL~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i  151 (523)
T 1oyw_A           76 SLMKDQVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCI  151 (523)
T ss_dssp             HHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGG
T ss_pred             HHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCcccc
Confidence            9999999998875    677888888776554332   2 2356899999999996432222344578999999999999


Q ss_pred             hccc--cHHHHHH---HHHhCCCCccEEEEEeeCchhHHHHHHhc--CCCCEEEEecCCccCcCCceEEEEEecCccchH
Q 022383          188 LSRG--FKDQIYD---VYRYLPPDLQVVLISATLPHEILEMTTKF--MTDPVKILVKRDELTLEGIKQFFVAVEREEWKF  260 (298)
Q Consensus       188 ~~~~--~~~~i~~---i~~~~~~~~~~v~~SAT~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~  260 (298)
                      .+|+  |...+..   +.+.+ ++.+++++|||+++.....+...  +.++..+.. .  ....++...  ..... .+.
T Consensus       152 ~~~g~~fr~~~~~l~~l~~~~-~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~-~--~~r~~l~~~--v~~~~-~~~  224 (523)
T 1oyw_A          152 SQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQIS-S--FDRPNIRYM--LMEKF-KPL  224 (523)
T ss_dssp             CTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEEC-C--CCCTTEEEE--EEECS-SHH
T ss_pred             CcCCCccHHHHHHHHHHHHhC-CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeC-C--CCCCceEEE--EEeCC-CHH
Confidence            9886  6555544   34445 46899999999998765544333  234443332 1  223333332  22333 377


Q ss_pred             HHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          261 DTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       261 ~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..+..++....++++||||+|++.++.+++.|+..|+
T Consensus       225 ~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~  261 (523)
T 1oyw_A          225 DQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGI  261 (523)
T ss_dssp             HHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCC
Confidence            8888888887778999999999999999999998775

>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=100.00  E-value=1.8e-33  Score=269.26  Aligned_cols=248  Identities=15%  Similarity=0.210  Sum_probs=192.4

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      +|+++++++++.+.+++.||..|+++|.++++. +.+++++++++|||+|||++|.++++..+...  +.+++|++|+++
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~~l~i~P~ra   79 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ--GGKAVYIVPLKA   79 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH--CSEEEEECSSGG
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC--CCEEEEEcCcHH
Confidence            589999999999999999999999999999998 88999999999999999999999999887632  458999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc
Q 022383          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~  192 (298)
                      |+.|+.+.++++.. .++++..++|+......   ...+++|+|+||+++..+++.....++++++||+||+|.+.++++
T Consensus        80 La~q~~~~~~~l~~-~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r  155 (720)
T 2zj8_A           80 LAEEKFQEFQDWEK-IGLRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDR  155 (720)
T ss_dssp             GHHHHHHHTGGGGG-GTCCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTT
T ss_pred             HHHHHHHHHHHHHh-cCCEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcc
Confidence            99999999975543 47899999997655432   124689999999999999888766688999999999999988888


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEE------EecC----ccchHHH
Q 022383          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV------AVER----EEWKFDT  262 (298)
Q Consensus       193 ~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~------~~~~----~~~k~~~  262 (298)
                      ...+..++..++.+.|++++|||+++. ..+.. ++..+. +..   ...+..+...+.      ....    ...+...
T Consensus       156 ~~~~~~ll~~l~~~~~ii~lSATl~n~-~~~~~-~l~~~~-~~~---~~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (720)
T 2zj8_A          156 GATLEVILAHMLGKAQIIGLSATIGNP-EELAE-WLNAEL-IVS---DWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEEL  229 (720)
T ss_dssp             HHHHHHHHHHHBTTBEEEEEECCCSCH-HHHHH-HTTEEE-EEC---CCCSSEEEEEEEETTEEEETTSCEEECSSTTHH
T ss_pred             cHHHHHHHHHhhcCCeEEEEcCCcCCH-HHHHH-HhCCcc-cCC---CCCCCcceEEEEeCCeeeccccchhhhhHHHHH
Confidence            899999988887789999999999763 44433 333211 111   111111111111      1110    1224555


Q ss_pred             HHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          263 LCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       263 l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      +...+.  .++++||||+++++|+.++..|.+.
T Consensus       230 ~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~  260 (720)
T 2zj8_A          230 VYDAIR--KKKGALIFVNMRRKAERVALELSKK  260 (720)
T ss_dssp             HHHHHH--TTCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             HHHHHh--CCCCEEEEecCHHHHHHHHHHHHHH
Confidence            555554  3489999999999999999999764

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

Probab=100.00  E-value=2.1e-32  Score=261.87  Aligned_cols=248  Identities=12%  Similarity=0.153  Sum_probs=191.0

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP-IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      .+|++++|++++.+.+++.||..|+++|.++++. +.+++++++++|||+|||+++.++++..+...  +.+++|++|++
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~il~i~P~r   85 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN--GGKAIYVTPLR   85 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS--CSEEEEECSCH
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC--CCeEEEEeCcH
Confidence            5799999999999999999999999999999999 78899999999999999999999999887643  45899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~  191 (298)
                      +|+.|+.+.++.+. ..++++...+|+......   ...+++|+|+||+++..+++.....++++++|||||+|.+.++.
T Consensus        86 ~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~  161 (715)
T 2va8_A           86 ALTNEKYLTFKDWE-LIGFKVAMTSGDYDTDDA---WLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPE  161 (715)
T ss_dssp             HHHHHHHHHHGGGG-GGTCCEEECCSCSSSCCG---GGGGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTT
T ss_pred             HHHHHHHHHHHHhh-cCCCEEEEEeCCCCCchh---hcCCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcc
Confidence            99999999996544 347889888888665432   12368999999999999998876668899999999999998778


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEE------------EEec-----
Q 022383          192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFF------------VAVE-----  254 (298)
Q Consensus       192 ~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~------------~~~~-----  254 (298)
                      +...++.++.+++ +.|++++|||+++. ..+..++ ..+. +..   ...+..+...+            ...+     
T Consensus       162 ~~~~l~~i~~~~~-~~~ii~lSATl~n~-~~~~~~l-~~~~-~~~---~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  234 (715)
T 2va8_A          162 RGPVVESVTIRAK-RRNLLALSATISNY-KQIAKWL-GAEP-VAT---NWRPVPLIEGVIYPERKKKEYNVIFKDNTTKK  234 (715)
T ss_dssp             THHHHHHHHHHHH-TSEEEEEESCCTTH-HHHHHHH-TCEE-EEC---CCCSSCEEEEEEEECSSTTEEEEEETTSCEEE
T ss_pred             cchHHHHHHHhcc-cCcEEEEcCCCCCH-HHHHHHh-CCCc-cCC---CCCCCCceEEEEecCCcccceeeecCcchhhh
Confidence            8888888887776 79999999999753 4444333 2211 111   01111111111            1111     


Q ss_pred             --CccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          255 --REEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       255 --~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                        ....+...+...+.  .++++||||+++++++.++..|++.
T Consensus       235 ~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~  275 (715)
T 2va8_A          235 VHGDDAIIAYTLDSLS--KNGQVLVFRNSRKMAESTALKIANY  275 (715)
T ss_dssp             EESSSHHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHT
T ss_pred             cccchHHHHHHHHHHh--cCCCEEEEECCHHHHHHHHHHHHHH
Confidence              01224445555543  4589999999999999999999864

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

Probab=100.00  E-value=4.5e-33  Score=274.68  Aligned_cols=249  Identities=16%  Similarity=0.186  Sum_probs=198.0

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ...|+.+++++.+...+...++..|+++|.++++.+.+|++++++||||+|||++|++|++..+..   +.+++|++|++
T Consensus       161 ~~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~---g~rvlvl~Ptr  237 (1108)
T 3l9o_A          161 PPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIK  237 (1108)
T ss_dssp             SSCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT---TCEEEEEESSH
T ss_pred             CCCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEcCcH
Confidence            346777788887777777777778999999999999999999999999999999999999998754   56899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~  191 (298)
                      +|+.|+++.+++...    .+..++|+...       ..+++|+|+||++|.+++......+.++++|||||+|++.+++
T Consensus       238 aLa~Q~~~~l~~~~~----~VglltGd~~~-------~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~  306 (1108)
T 3l9o_A          238 ALSNQKYRELLAEFG----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKE  306 (1108)
T ss_dssp             HHHHHHHHHHHHHTS----SEEEECSSCBC-------CCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHH
T ss_pred             HHHHHHHHHHHHHhC----CccEEeCcccc-------CCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccc
Confidence            999999999998754    56778887663       3458999999999999998887778899999999999999999


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCchh--HHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCc-------------
Q 022383          192 FKDQIYDVYRYLPPDLQVVLISATLPHE--ILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVERE-------------  256 (298)
Q Consensus       192 ~~~~i~~i~~~~~~~~~~v~~SAT~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-------------  256 (298)
                      +...+..++..+++..|++++|||+++.  +..++......|..+.....  .+..+.+++......             
T Consensus       307 rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~--rp~pl~~~~~~~~~~~~~~~vd~~~~~~  384 (1108)
T 3l9o_A          307 RGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF--RPTPLQHYLFPAHGDGIYLVVDEKSTFR  384 (1108)
T ss_dssp             HHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECC--CSSCEEEEEEETTSSCCEEEEETTTEEC
T ss_pred             hHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC--CcccceEEEeecCCcceeeeeccccchh
Confidence            9999999999999999999999999774  45677766767766655432  222233333221110             


Q ss_pred             -----------------------------------------cchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          257 -----------------------------------------EWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       257 -----------------------------------------~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                                                               ..+...+...+......++||||++++.|+.++..|...
T Consensus       385 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~  464 (1108)
T 3l9o_A          385 EENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKL  464 (1108)
T ss_dssp             HHHHHHHHTTC-----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSH
T ss_pred             hhhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhc
Confidence                                                     112233444444556679999999999999999998764


Q ss_pred             c
Q 022383          296 W  296 (298)
Q Consensus       296 ~  296 (298)
                      +
T Consensus       465 ~  465 (1108)
T 3l9o_A          465 D  465 (1108)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=100.00  E-value=2.4e-33  Score=267.66  Aligned_cols=247  Identities=14%  Similarity=0.155  Sum_probs=186.5

Q ss_pred             CcccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           34 SFDAMG--IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        34 ~~~~l~--l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      +|++++  +++.+.+.++++||..|+++|.++++.+.+++++++++|||+|||+++.++++..+..   +.+++|++|++
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~---~~~~l~i~P~r   78 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVPLR   78 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEESSH
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh---CCcEEEEeCcH
Confidence            588888  9999999999999999999999999999999999999999999999999999988764   45899999999


Q ss_pred             HHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc
Q 022383          112 ELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~  191 (298)
                      +|+.|+.+.++++. ..++++...+|+......   ...+++|+|+||+++..+++.....++++++||+||+|.+.+++
T Consensus        79 ~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~  154 (702)
T 2p6r_A           79 ALAGEKYESFKKWE-KIGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEK  154 (702)
T ss_dssp             HHHHHHHHHHTTTT-TTTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTT
T ss_pred             HHHHHHHHHHHHHH-hcCCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCC
Confidence            99999999996544 347889999988665432   12368999999999999998876668899999999999998877


Q ss_pred             cHHHHHHHHHhC---CCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEE------EecC------c
Q 022383          192 FKDQIYDVYRYL---PPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFV------AVER------E  256 (298)
Q Consensus       192 ~~~~i~~i~~~~---~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~------~~~~------~  256 (298)
                      +...+..++..+   +++.|++++|||+++. ..+.. ++..+. +...   ..+..+...+.      ....      .
T Consensus       155 r~~~~~~ll~~l~~~~~~~~ii~lSATl~n~-~~~~~-~l~~~~-~~~~---~r~~~l~~~~~~~~~~~~~~~~~~~~~~  228 (702)
T 2p6r_A          155 RGATLEILVTKMRRMNKALRVIGLSATAPNV-TEIAE-WLDADY-YVSD---WRPVPLVEGVLCEGTLELFDGAFSTSRR  228 (702)
T ss_dssp             THHHHHHHHHHHHHHCTTCEEEEEECCCTTH-HHHHH-HTTCEE-EECC---CCSSCEEEEEECSSEEEEEETTEEEEEE
T ss_pred             cccHHHHHHHHHHhcCcCceEEEECCCcCCH-HHHHH-HhCCCc-ccCC---CCCccceEEEeeCCeeeccCcchhhhhh
Confidence            777777766555   5789999999999862 44444 343222 1111   11111221111      1110      0


Q ss_pred             cchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          257 EWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       257 ~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ..+...+...++  .++++||||+++++++.++..|.+.
T Consensus       229 ~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~  265 (702)
T 2p6r_A          229 VKFEELVEECVA--ENGGVLVFESTRRGAEKTAVKLSAI  265 (702)
T ss_dssp             CCHHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHh--cCCCEEEEcCCHHHHHHHHHHHHHH
Confidence            114455555554  4579999999999999999999764

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=100.00  E-value=2.7e-32  Score=269.02  Aligned_cols=238  Identities=16%  Similarity=0.193  Sum_probs=188.7

Q ss_pred             HHHHHH-HCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHH
Q 022383           44 LLRGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVIL  122 (298)
Q Consensus        44 i~~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~  122 (298)
                      +.+.+. .+|| .|+++|.++++.+++|+|++++||||+|||++|+.+++..+.   .++++||++|+++|+.|+.+.++
T Consensus        67 ~~~~~~~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~---~~~~~Lil~PtreLa~Q~~~~l~  142 (1104)
T 4ddu_A           67 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERLQ  142 (1104)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh---cCCeEEEEechHHHHHHHHHHHH
Confidence            333443 3677 499999999999999999999999999999999988888773   36689999999999999999999


Q ss_pred             HhhccCCceEEEEEcCCch---HHHHHHhhcC-CcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc---------
Q 022383          123 AIGDFINIQAHACVGGKSV---GEDIRKLEHG-VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS---------  189 (298)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~---------  189 (298)
                      +++ ..++++..++|+.+.   ..+...+..+ ++|+|+||++|.+++..  +.+.++++||+||+|++..         
T Consensus       143 ~l~-~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L  219 (1104)
T 4ddu_A          143 KLA-DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLL  219 (1104)
T ss_dssp             TTS-CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHH
T ss_pred             Hhh-CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhh
Confidence            977 678899999999877   4555666655 99999999999887764  6678999999999987554         


Q ss_pred             --cccHHH-HHHHHHhCC-----------CCccEEEEEee-CchhHHH-HHHhcCCCCEEEEecCCccCcCCceEEEEEe
Q 022383          190 --RGFKDQ-IYDVYRYLP-----------PDLQVVLISAT-LPHEILE-MTTKFMTDPVKILVKRDELTLEGIKQFFVAV  253 (298)
Q Consensus       190 --~~~~~~-i~~i~~~~~-----------~~~~~v~~SAT-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~  253 (298)
                        ++|... +..+++.++           +..|++++||| .+..+.. +....+.    +.+........++.+.+..+
T Consensus       220 ~~~gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~~  295 (1104)
T 4ddu_A          220 MMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISS  295 (1104)
T ss_dssp             HTSSCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEESC
T ss_pred             HhcCCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEec
Confidence              677777 888888776           78999999999 4554332 2333322    23333344556677777655


Q ss_pred             cCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          254 EREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       254 ~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +    +...+..+++.. ++++||||++++.|+.+++.|+..|+
T Consensus       296 ~----k~~~L~~ll~~~-~~~~LVF~~s~~~a~~l~~~L~~~g~  334 (1104)
T 4ddu_A          296 R----SKEKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKF  334 (1104)
T ss_dssp             C----CHHHHHHHHHHH-CSSEEEEESSSHHHHHHHHHHHHTTC
T ss_pred             C----HHHHHHHHHHhc-CCCEEEEECcHHHHHHHHHHHHhCCC
Confidence            2    666777777763 48999999999999999999998775

>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=99.98  E-value=1.2e-32  Score=271.51  Aligned_cols=232  Identities=16%  Similarity=0.197  Sum_probs=181.5

Q ss_pred             HHHH-HCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           46 RGIY-QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        46 ~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      +.+. .+||. | ++|.++++.+++|+|+++++|||+|||+ |.+|++..+...  ++++||++||++|+.|+.+.++++
T Consensus        48 ~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~--~~~~lil~PtreLa~Q~~~~l~~l  122 (1054)
T 1gku_B           48 EFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALK--GKRCYVIFPTSLLVIQAAETIRKY  122 (1054)
T ss_dssp             HHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTT--SCCEEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhc--CCeEEEEeccHHHHHHHHHHHHHH
Confidence            4444 48999 9 9999999999999999999999999998 888888877553  568999999999999999999999


Q ss_pred             hccCCc----eEEEEEcCCchHHH---HHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHH
Q 022383          125 GDFINI----QAHACVGGKSVGED---IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (298)
Q Consensus       125 ~~~~~~----~~~~~~~~~~~~~~---~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~  197 (298)
                      +...++    ++..++|+.+...+   ...+.+ ++|+|+||++|..++..    ++++++||+||+|++.++  ...+.
T Consensus       123 ~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~~--~~~~~  195 (1054)
T 1gku_B          123 AEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKA--SKNVD  195 (1054)
T ss_dssp             HTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHTS--THHHH
T ss_pred             HhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhhc--cccHH
Confidence            988888    89999999877653   334445 99999999999987765    669999999999999874  56777


Q ss_pred             HHHHhCC-----------CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHH
Q 022383          198 DVYRYLP-----------PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL  266 (298)
Q Consensus       198 ~i~~~~~-----------~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  266 (298)
                      .++..++           ...|++++|||+++. ..+...++.++..+.+.........+.+.+.   . ..+...+..+
T Consensus       196 ~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~---~-~~k~~~L~~l  270 (1054)
T 1gku_B          196 KLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSSRITVRNVEDVAV---N-DESISTLSSI  270 (1054)
T ss_dssp             HHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCCEECCCCEEEEEE---S-CCCTTTTHHH
T ss_pred             HHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCcccCcCCceEEEe---c-hhHHHHHHHH
Confidence            7777663           468899999999876 4222222222333333333344456666665   2 3366677778


Q ss_pred             HhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          267 YDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       267 l~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      ++.. ++++||||++++.|+.+++.|+..
T Consensus       271 l~~~-~~~~LVF~~t~~~a~~l~~~L~~~  298 (1054)
T 1gku_B          271 LEKL-GTGGIIYARTGEEAEEIYESLKNK  298 (1054)
T ss_dssp             HTTS-CSCEEEEESSHHHHHHHHHTTTTS
T ss_pred             Hhhc-CCCEEEEEcCHHHHHHHHHHHhhc
Confidence            7765 478999999999999999999764

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

Probab=99.97  E-value=3.5e-30  Score=252.13  Aligned_cols=232  Identities=17%  Similarity=0.233  Sum_probs=180.7

Q ss_pred             HHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           48 IYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        48 l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      ...++|. |+++|.++++.+.+|+++++++|||+|||++|.++++..+..   +.+++|++|+++|++|+++.+++... 
T Consensus        80 ~~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~---g~rvL~l~PtkaLa~Q~~~~l~~~~~-  154 (1010)
T 2xgj_A           80 ARTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKALSNQKYRELLAEFG-  154 (1010)
T ss_dssp             SCCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT---TCEEEEEESSHHHHHHHHHHHHHHHS-
T ss_pred             HHhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc---CCeEEEECChHHHHHHHHHHHHHHhC-
Confidence            3445776 999999999999999999999999999999999999887754   56899999999999999999988754 


Q ss_pred             CCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCc
Q 022383          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDL  207 (298)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~  207 (298)
                         .+..++|+....       .+++|+|+||++|.+++......+.++++|||||+|.+.++++...+..++..++...
T Consensus       155 ---~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~  224 (1010)
T 2xgj_A          155 ---DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKV  224 (1010)
T ss_dssp             ---CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTC
T ss_pred             ---CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCC
Confidence               577788876643       3479999999999999988777889999999999999999888999999999999999


Q ss_pred             cEEEEEeeCchhH--HHHHHhcCCCCEEEEecCCccCcCCceEEEEEec---------Cc--------------------
Q 022383          208 QVVLISATLPHEI--LEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVE---------RE--------------------  256 (298)
Q Consensus       208 ~~v~~SAT~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~---------~~--------------------  256 (298)
                      |++++|||+++..  ..++......+..+.....  .+..+.+++....         ..                    
T Consensus       225 ~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~--rp~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  302 (1010)
T 2xgj_A          225 RYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF--RPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIG  302 (1010)
T ss_dssp             EEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECC--CSSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC----
T ss_pred             eEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC--CcccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhhc
Confidence            9999999998753  3444444455665554322  2223444433211         00                    


Q ss_pred             -------------------------cchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          257 -------------------------EWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       257 -------------------------~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                                               ......+...+......++||||+++..|+.++..|...+
T Consensus       303 ~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~  367 (1010)
T 2xgj_A          303 DDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLD  367 (1010)
T ss_dssp             --------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSC
T ss_pred             ccccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCC
Confidence                                     1122334444444455699999999999999999997754

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.97  E-value=9.2e-31  Score=249.91  Aligned_cols=174  Identities=16%  Similarity=0.230  Sum_probs=140.5

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC--CeEEEEEcCcHHHHHHHHHHH
Q 022383           44 LLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        44 i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~  121 (298)
                      +..+|..+||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+.....  +.++||++|+++|+.|+.+.+
T Consensus         2 ~~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~   81 (696)
T 2ykg_A            2 EVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVF   81 (696)
T ss_dssp             -----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHH
Confidence            345678899999999999999999999999999999999999999999988765432  258999999999999999999


Q ss_pred             HHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCc-cCCCccEEEechhhHhhccc-cHHHHHHH
Q 022383          122 LAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDV  199 (298)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~-~~~~l~~vViDE~h~~~~~~-~~~~i~~i  199 (298)
                      +++....++++..++|+.........+..+++|+|+||++|.+.+..+.+ .+.++++|||||||++.... +...+...
T Consensus        82 ~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~~  161 (696)
T 2ykg_A           82 SKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNY  161 (696)
T ss_dssp             HHHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHHH
T ss_pred             HHHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHHH
Confidence            99988778999999998876555556666799999999999999988766 78899999999999986553 33333333


Q ss_pred             HHh-----CCCCccEEEEEeeCc
Q 022383          200 YRY-----LPPDLQVVLISATLP  217 (298)
Q Consensus       200 ~~~-----~~~~~~~v~~SAT~~  217 (298)
                      +..     .++..+++++|||+.
T Consensus       162 l~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          162 LDQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHHHTTCCSCCCEEEEEESCCC
T ss_pred             HHHhhcccCCCCCeEEEEeCccc
Confidence            332     246789999999996

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.97  E-value=1.7e-29  Score=234.80  Aligned_cols=164  Identities=16%  Similarity=0.225  Sum_probs=139.2

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC--CeEEEEEcCcHHHHHHHHHHHHHhhccCCceE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFINIQA  132 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  132 (298)
                      .|+++|.++++.+++|+++++++|||+|||++|++|++..+.....  ++++||++|+++|+.|+.+.++++....++++
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~   83 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNI   83 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEE
Confidence            5999999999999999999999999999999999999998866432  56899999999999999999999988888999


Q ss_pred             EEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCc-cCCCccEEEechhhHhhccc-cHHHHHHHHHhC-----CC
Q 022383          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVYRYL-----PP  205 (298)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~-~~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~~-----~~  205 (298)
                      ..++|+.........+..+++|+|+||+++...+..+.+ .+.++++||+||||++...+ +...+...+...     .+
T Consensus        84 ~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (555)
T 3tbk_A           84 ASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDP  163 (555)
T ss_dssp             EEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSSCCSC
T ss_pred             EEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhccccCC
Confidence            999999877766666666789999999999999988766 78899999999999997764 333333333332     24


Q ss_pred             CccEEEEEeeCch
Q 022383          206 DLQVVLISATLPH  218 (298)
Q Consensus       206 ~~~~v~~SAT~~~  218 (298)
                      ..+++++|||++.
T Consensus       164 ~~~~l~lSAT~~~  176 (555)
T 3tbk_A          164 LPQVVGLTASVGV  176 (555)
T ss_dssp             CCEEEEEESCCCC
T ss_pred             CCeEEEEecCccc
Confidence            6799999999954

>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=99.97  E-value=7.3e-30  Score=237.41  Aligned_cols=166  Identities=15%  Similarity=0.183  Sum_probs=133.2

Q ss_pred             CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC--CeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      +...|+++|.++++.+++|+++++++|||+|||++|++|++..+.....  ++++||++|+++|+.|+.+.++++....+
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~   83 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQG   83 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccC
Confidence            4457999999999999999999999999999999999999998866432  56899999999999999999999988888


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCc-cCCCccEEEechhhHhhccccHHHH-HHHHHh----C
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRGFKDQI-YDVYRY----L  203 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~-~~~~l~~vViDE~h~~~~~~~~~~i-~~i~~~----~  203 (298)
                      +++..++|+.........+..+++|+|+||++|...+..+.+ .+.++++||+||||++.+++....+ ...+..    .
T Consensus        84 ~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~  163 (556)
T 4a2p_A           84 YSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSA  163 (556)
T ss_dssp             CCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchHHHHHHHHHHhhhccc
Confidence            999999999877666666666789999999999999988777 7899999999999999877643332 222222    1


Q ss_pred             CCCccEEEEEeeCc
Q 022383          204 PPDLQVVLISATLP  217 (298)
Q Consensus       204 ~~~~~~v~~SAT~~  217 (298)
                      .+..+++++|||++
T Consensus       164 ~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          164 SQLPQILGLTASVG  177 (556)
T ss_dssp             --CCEEEEEESCCC
T ss_pred             CCCCeEEEEeCCcc
Confidence            35689999999994

>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=99.97  E-value=4e-30  Score=261.91  Aligned_cols=249  Identities=14%  Similarity=0.224  Sum_probs=179.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhh-cCCcEEEEcCCCCchHHHHHHHHHHhhccC--------CCCeEEEEEcCc
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQTVDTS--------SREVQALILSPT  110 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~-~~~~~li~~pTG~GKT~~~~~~~~~~~~~~--------~~~~~~lil~p~  110 (298)
                      |+++...++  .||+.++++|++++|.++ .++|++++||||+|||+++.+++++.+...        ..+.++||++|+
T Consensus        66 Lp~~~~~~f--~g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~  143 (1724)
T 4f92_B           66 LPKYAQAGF--EGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPM  143 (1724)
T ss_dssp             SCGGGSTTC--TTCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSS
T ss_pred             cCHHHHHhc--CCCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCH
Confidence            455544433  279999999999999876 578999999999999999999999987531        235689999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccC--ccCCCccEEEechhhHhh
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEML  188 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~--~~~~~l~~vViDE~h~~~  188 (298)
                      ++|++|+.+.+++.....|+++..++|+......   ...+++|+|+|||++..+++...  ..++++++|||||+|.+.
T Consensus       144 kALa~e~~~~l~~~~~~~gi~V~~~tGd~~~~~~---~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~  220 (1724)
T 4f92_B          144 RSLVQEMVGSFGKRLATYGITVAELTGDHQLCKE---EISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLH  220 (1724)
T ss_dssp             HHHHHHHHHHHHHHHTTTTCCEEECCSSCSSCCT---TGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGG
T ss_pred             HHHHHHHHHHHHHHHhhCCCEEEEEECCCCCCcc---ccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcC
Confidence            9999999999998888889999999998765432   12458999999999988887643  246899999999999886


Q ss_pred             ccccHHHHHHHHH-------hCCCCccEEEEEeeCchhHHHHHHhcCCCC-EEEEecCCccCcCCceEEEEEecCcc--c
Q 022383          189 SRGFKDQIYDVYR-------YLPPDLQVVLISATLPHEILEMTTKFMTDP-VKILVKRDELTLEGIKQFFVAVEREE--W  258 (298)
Q Consensus       189 ~~~~~~~i~~i~~-------~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~i~~~~~~~~~~~--~  258 (298)
                      + ..+..++.++.       ..+++.|+|++|||+++. +++..+...++ ..+.....+..+..+.+.++......  .
T Consensus       221 d-~RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~N~-~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~  298 (1724)
T 4f92_B          221 D-DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNY-EDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIK  298 (1724)
T ss_dssp             S-TTHHHHHHHHHHHHHHHHHHTCCCEEEEEECSCTTH-HHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHH
T ss_pred             C-ccHHHHHHHHHHHHHHHHhCCCCCcEEEEecccCCH-HHHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhh
Confidence            5 45555554443       346789999999999864 44444433222 11222223344445666555554432  1


Q ss_pred             hHH----HHHHHHh-hCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          259 KFD----TLCDLYD-TLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       259 k~~----~l~~ll~-~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      +..    .+...+. ...++++||||+|++.|+.+|..|.+.
T Consensus       299 ~~~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~  340 (1724)
T 4f92_B          299 RFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDM  340 (1724)
T ss_dssp             HHHHHHHHHHHHHTTCCSSCCEEEECSSTTTTHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHHHHH
Confidence            111    2222233 234569999999999999999988654

>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=99.97  E-value=2.5e-29  Score=242.96  Aligned_cols=168  Identities=15%  Similarity=0.206  Sum_probs=135.8

Q ss_pred             HCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC--CeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      -+|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+.....  +.++|||+|+++|+.|+.+.++++...
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~  322 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGG
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhccc
Confidence            457889999999999999999999999999999999999999998876432  568999999999999999999999888


Q ss_pred             CCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCc-cCCCccEEEechhhHhhccc-cHHHHHHHHHh---
Q 022383          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVYRY---  202 (298)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~-~~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~---  202 (298)
                      .++++..++|+.........+..+++|+|+||++|...+..+.+ .+.++++|||||||++...+ +...+..++..   
T Consensus       323 ~~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~~~~~  402 (797)
T 4a2q_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFN  402 (797)
T ss_dssp             GTCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHHHHhhc
Confidence            88999999999877766667777899999999999999988766 78899999999999987664 33333333332   


Q ss_pred             -CCCCccEEEEEeeCc
Q 022383          203 -LPPDLQVVLISATLP  217 (298)
Q Consensus       203 -~~~~~~~v~~SAT~~  217 (298)
                       ..+..+++++|||+.
T Consensus       403 ~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          403 SASQLPQILGLTASVG  418 (797)
T ss_dssp             TCCCCCEEEEEESCCC
T ss_pred             cCCCCCeEEEEcCCcc
Confidence             145689999999995

>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=99.97  E-value=5.5e-29  Score=253.59  Aligned_cols=249  Identities=14%  Similarity=0.177  Sum_probs=182.1

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhc-CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIK-GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      |.+...+++...+|..++|+|+++++.+.. ++|++++||||||||++|.+|++..+...+ +.++||++|+++|++|++
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~-~~kavyi~P~raLa~q~~  989 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSS-EGRCVYITPMEALAEQVY  989 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCT-TCCEEEECSCHHHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCC-CCEEEEEcChHHHHHHHH
Confidence            556777888888899999999999999975 578999999999999999999999987643 448999999999999999


Q ss_pred             HHHHH-hhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhcc--CccCCCccEEEechhhHhhccccHHH
Q 022383          119 KVILA-IGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRK--TLRTRAIKLLVLDESDEMLSRGFKDQ  195 (298)
Q Consensus       119 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~--~~~~~~l~~vViDE~h~~~~~~~~~~  195 (298)
                      +.+++ +++..++++..++|+...+..   ...+++|+|+|||++..++++.  ...++++++||+||+|.+.+. .+..
T Consensus       990 ~~~~~~f~~~~g~~V~~ltGd~~~~~~---~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~-rg~~ 1065 (1724)
T 4f92_B          990 MDWYEKFQDRLNKKVVLLTGETSTDLK---LLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGE-NGPV 1065 (1724)
T ss_dssp             HHHHHHHTTTSCCCEEECCSCHHHHHH---HHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGST-THHH
T ss_pred             HHHHHHhchhcCCEEEEEECCCCcchh---hcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCC-CCcc
Confidence            99975 556678999999988664432   2234799999999998888763  334689999999999998764 4444


Q ss_pred             HHHHH-------HhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccch------HHH
Q 022383          196 IYDVY-------RYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWK------FDT  262 (298)
Q Consensus       196 i~~i~-------~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k------~~~  262 (298)
                      ++.++       ...+++.|+|++|||+++. .++..+....+..+.....+..+..++..+...+.....      ...
T Consensus      1066 le~il~rl~~i~~~~~~~~riI~lSATl~N~-~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~~~~~~ 1144 (1724)
T 4f92_B         1066 LEVICSRMRYISSQIERPIRIVALSSSLSNA-KDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKP 1144 (1724)
T ss_dssp             HHHHHHHHHHHHHTTSSCCEEEEEESCBTTH-HHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHHTTHHH
T ss_pred             HHHHHHHHHHHHhhcCCCceEEEEeCCCCCH-HHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhhhhcch
Confidence            44433       3456789999999999864 445544433333333333344444555555544433211      112


Q ss_pred             HHHHHh-hCCCCcEEEEecchhhHHHHHHHHhh
Q 022383          263 LCDLYD-TLTITQAVIFCNTKRKIYYSVFYFWI  294 (298)
Q Consensus       263 l~~ll~-~~~~~k~lIf~~s~~~~~~l~~~L~~  294 (298)
                      +...+. ....+++||||+|++.|+.+|..|..
T Consensus      1145 ~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~ 1177 (1724)
T 4f92_B         1145 VYHAITKHSPKKPVIVFVPSRKQTRLTAIDILT 1177 (1724)
T ss_dssp             HHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHH
Confidence            222333 34567999999999999999988754

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

Probab=99.97  E-value=8e-30  Score=249.52  Aligned_cols=157  Identities=20%  Similarity=0.287  Sum_probs=137.7

Q ss_pred             HCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .++|+ |+++|.++++.+.+|+++++++|||+|||++|++++...+..   +.+++|++|+++|+.|+++.+++...  +
T Consensus        35 ~~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~---g~~vlvl~PtraLa~Q~~~~l~~~~~--~  108 (997)
T 4a4z_A           35 SWPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN---MTKTIYTSPIKALSNQKFRDFKETFD--D  108 (997)
T ss_dssp             CCSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT---TCEEEEEESCGGGHHHHHHHHHTTC----
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc---CCeEEEEeCCHHHHHHHHHHHHHHcC--C
Confidence            34665 899999999999999999999999999999999988876544   56899999999999999999987643  5


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccE
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~  209 (298)
                      +++..++|+....       ...+|+|+||++|.+++......+.++++|||||+|++.++++...+..++..+++..|+
T Consensus       109 ~~v~~l~G~~~~~-------~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~~l~~~v~i  181 (997)
T 4a4z_A          109 VNIGLITGDVQIN-------PDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKF  181 (997)
T ss_dssp             CCEEEECSSCEEC-------TTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHHHSCTTCEE
T ss_pred             CeEEEEeCCCccC-------CCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHHhcccCCCE
Confidence            7888888887543       347999999999999998877778999999999999999999999999999999999999


Q ss_pred             EEEEeeCchh
Q 022383          210 VLISATLPHE  219 (298)
Q Consensus       210 v~~SAT~~~~  219 (298)
                      +++|||+++.
T Consensus       182 IlLSAT~~n~  191 (997)
T 4a4z_A          182 ILLSATVPNT  191 (997)
T ss_dssp             EEEECCCTTH
T ss_pred             EEEcCCCCCh
Confidence            9999999765

>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=99.96  E-value=1.6e-27  Score=217.46  Aligned_cols=160  Identities=18%  Similarity=0.180  Sum_probs=133.0

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .|+++|.++++.+.++ ++++.+|||+|||++++.++...+..  .+.++||++|+++|+.|+.+.++++....+.++..
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~--~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH--SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc--CCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEE
Confidence            5999999999999999 99999999999999999999887762  34589999999999999999999886544558888


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ++|+........ ...+++|+|+||+.+...+....+.+.++++||+||||++........+...+....+..+++++||
T Consensus        86 ~~g~~~~~~~~~-~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lTa  164 (494)
T 1wp9_A           86 LTGEKSPEERSK-AWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTA  164 (494)
T ss_dssp             ECSCSCHHHHHH-HHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEES
T ss_pred             eeCCcchhhhhh-hccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCCCeEEEEec
Confidence            888877654432 3345799999999999998887788899999999999998765444445555555566889999999


Q ss_pred             eCch
Q 022383          215 TLPH  218 (298)
Q Consensus       215 T~~~  218 (298)
                      |+..
T Consensus       165 Tp~~  168 (494)
T 1wp9_A          165 SPGS  168 (494)
T ss_dssp             CSCS
T ss_pred             CCCC
Confidence            9974

>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=99.96  E-value=3.6e-28  Score=237.66  Aligned_cols=168  Identities=15%  Similarity=0.206  Sum_probs=134.1

Q ss_pred             HCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC--CeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      -.|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+.....  +.++|||+|+++|+.|+.+.++++...
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~  322 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHT
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            346788999999999999999999999999999999999999998766432  568999999999999999999999887


Q ss_pred             CCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCc-cCCCccEEEechhhHhhccc-cHHHHHHHHHh---
Q 022383          128 INIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTL-RTRAIKLLVLDESDEMLSRG-FKDQIYDVYRY---  202 (298)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~-~~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~---  202 (298)
                      .++++..++|+.........+..+++|+|+||++|...+....+ .+.++++||+||||++...+ +...+..+...   
T Consensus       323 ~~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~~~~~~  402 (936)
T 4a2w_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFN  402 (936)
T ss_dssp             TTCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHHT
T ss_pred             cCceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHHHHhhc
Confidence            78999999999876665555556789999999999999988766 78899999999999987664 33333333332   


Q ss_pred             -CCCCccEEEEEeeCc
Q 022383          203 -LPPDLQVVLISATLP  217 (298)
Q Consensus       203 -~~~~~~~v~~SAT~~  217 (298)
                       ..+..+++++|||+.
T Consensus       403 ~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          403 SASQLPQILGLTASVG  418 (936)
T ss_dssp             TCSCCCEEEEEESCCC
T ss_pred             cCCCcCeEEEecCCcc
Confidence             145689999999994

>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=99.96  E-value=8.6e-28  Score=225.76  Aligned_cols=161  Identities=20%  Similarity=0.248  Sum_probs=135.5

Q ss_pred             HCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .+|| .|++.|..++|.+++|+  +.+++||+|||++|.+|++.....   ++.++||+||++||.|+.+.+..+...++
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~---g~~vlVltptreLA~qd~e~~~~l~~~lg  152 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGKIFEFLG  152 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            5799 89999999999999999  999999999999999999843322   45799999999999999999999999999


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhcc------CccCCCccEEEechhhHhh-ccc----------
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML-SRG----------  191 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~------~~~~~~l~~vViDE~h~~~-~~~----------  191 (298)
                      +++..++||.+...+  ....+++|+|+||++| ..+++.+      .+.++.+.++|+||||.|+ +.+          
T Consensus       153 l~v~~i~gg~~~~~r--~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~~  230 (844)
T 1tf5_A          153 LTVGLNLNSMSKDEK--REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQA  230 (844)
T ss_dssp             CCEEECCTTSCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEE
T ss_pred             CeEEEEeCCCCHHHH--HHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCCc
Confidence            999999999875443  3334689999999999 6666543      3567899999999999998 543          


Q ss_pred             -----cHHHHHHHHHhCC---------CCccEE-----------------EEEeeCch
Q 022383          192 -----FKDQIYDVYRYLP---------PDLQVV-----------------LISATLPH  218 (298)
Q Consensus       192 -----~~~~i~~i~~~~~---------~~~~~v-----------------~~SAT~~~  218 (298)
                           +...+..+++.++         +..|+.                 ++|||.+.
T Consensus       231 ~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~  288 (844)
T 1tf5_A          231 AKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVA  288 (844)
T ss_dssp             ECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHH
T ss_pred             ccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccch
Confidence                 6788899999987         367777                 88999763

>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=99.95  E-value=6.4e-28  Score=226.13  Aligned_cols=147  Identities=16%  Similarity=0.231  Sum_probs=113.5

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      +|. .|+++|..+++.++.|+  +..++||+|||++|++|++.....   ++.++|++||++||.|+.+.+..+...+++
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~---g~~vlVltPTreLA~Q~~e~~~~l~~~lgl  144 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAENNRPLFEFLGL  144 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT---SSCCEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc---CCcEEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            564 69999999999999998  999999999999999999865433   457999999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhcc------CccCCCccEEEechhhHhh-ccc-----------
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML-SRG-----------  191 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~------~~~~~~l~~vViDE~h~~~-~~~-----------  191 (298)
                      ++..++||.+...  +....+++|+||||++| ..+++.+      ...++++.++|+||+|.|+ +.+           
T Consensus       145 ~v~~i~GG~~~~~--r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~  222 (853)
T 2fsf_A          145 TVGINLPGMPAPA--KREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISGPAE  222 (853)
T ss_dssp             CEEECCTTCCHHH--HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEEC--
T ss_pred             eEEEEeCCCCHHH--HHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccCCCc
Confidence            9999999987543  33444689999999999 6777654      2567999999999999998 432           


Q ss_pred             ----cHHHHHHHHHhCCC
Q 022383          192 ----FKDQIYDVYRYLPP  205 (298)
Q Consensus       192 ----~~~~i~~i~~~~~~  205 (298)
                          +...+..+++.+++
T Consensus       223 ~~~~~y~~i~~iv~~L~~  240 (853)
T 2fsf_A          223 DSSEMYKRVNKIIPHLIR  240 (853)
T ss_dssp             ------------------
T ss_pred             cchhHHHHHHHHHHhchh
Confidence                55677777777763

>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=99.95  E-value=6.2e-26  Score=225.12  Aligned_cols=239  Identities=16%  Similarity=0.138  Sum_probs=173.0

Q ss_pred             CCCCHHHHHHHH-HCCCCCChHHHHHHHHHhhc----CC--cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           38 MGIKDDLLRGIY-QYGFEKPSAIQQRAVMPIIK----GR--DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        38 l~l~~~i~~~l~-~~~~~~~~~~Q~~~~~~~~~----~~--~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      ++.+....+.+. .++|+ ++++|.++++.+.+    |+  ++++++|||+|||++++.+++..+..   +.+++|++||
T Consensus       586 ~~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~---g~~vlvlvPt  661 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVPT  661 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECSS
T ss_pred             CCCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh---CCeEEEEech
Confidence            345666666664 46776 79999999999875    66  99999999999999999888876654   5589999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHH---HHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhH
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDI---RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~  186 (298)
                      ++|+.|+.+.+++.....++++..+++.....+..   ..+. +.++|+|+||+.+.     ..+.++++++|||||+|+
T Consensus       662 ~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIiDEaH~  736 (1151)
T 2eyq_A          662 TLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHR  736 (1151)
T ss_dssp             HHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGG
T ss_pred             HHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEEechHh
Confidence            99999999999988777788888888876654432   3333 35899999997653     346788999999999999


Q ss_pred             hhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHH
Q 022383          187 MLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL  266 (298)
Q Consensus       187 ~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  266 (298)
                      +.     ......++.++.+.+++++|||+.+....+....+.++..+...  ......+...+.....    ......+
T Consensus       737 ~g-----~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~--~~~r~~i~~~~~~~~~----~~i~~~i  805 (1151)
T 2eyq_A          737 FG-----VRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATP--PARRLAVKTFVREYDS----MVVREAI  805 (1151)
T ss_dssp             SC-----HHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCC--CCBCBCEEEEEEECCH----HHHHHHH
T ss_pred             cC-----hHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecC--CCCccccEEEEecCCH----HHHHHHH
Confidence            52     23345556666788999999999777666655555444333221  1222334444443322    2222233


Q ss_pred             Hh-hCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          267 YD-TLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       267 l~-~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      +. ...+++++||||+++.++.+++.|++..
T Consensus       806 l~~l~~g~qvlvf~~~v~~~~~l~~~L~~~~  836 (1151)
T 2eyq_A          806 LREILRGGQVYYLYNDVENIQKAAERLAELV  836 (1151)
T ss_dssp             HHHHTTTCEEEEECCCSSCHHHHHHHHHHHC
T ss_pred             HHHHhcCCeEEEEECCHHHHHHHHHHHHHhC
Confidence            32 2345799999999999999999998874

>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=99.95  E-value=6e-26  Score=213.24  Aligned_cols=161  Identities=17%  Similarity=0.230  Sum_probs=136.3

Q ss_pred             HCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           50 QYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        50 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      .+|+ .|++.|..+++.+.+|+  +.+++||+|||++|.+|++.....   +..++||+||++||.|..+.+..+...++
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~---g~~v~VvTpTreLA~Qdae~m~~l~~~lG  180 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA---GNGVHIVTVNDYLAKRDSEWMGRVHRFLG  180 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT---TSCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh---CCCeEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            3688 79999999999999998  999999999999999999754333   34799999999999999999999999999


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhcc------CccCCCccEEEechhhHhh-cc-----------
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTRAIKLLVLDESDEML-SR-----------  190 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~------~~~~~~l~~vViDE~h~~~-~~-----------  190 (298)
                      +++..++||.+....  ....+++|+++||++| ..+++.+      ...++.+.++|+||+|.|+ +.           
T Consensus       181 Lsv~~i~gg~~~~~r--~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~~  258 (922)
T 1nkt_A          181 LQVGVILATMTPDER--RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPA  258 (922)
T ss_dssp             CCEEECCTTCCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEEC
T ss_pred             CeEEEEeCCCCHHHH--HHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCCC
Confidence            999999999875433  3334589999999999 6777653      4667899999999999998 32           


Q ss_pred             ----ccHHHHHHHHHhCC---------CCccEE-----------------EEEeeCch
Q 022383          191 ----GFKDQIYDVYRYLP---------PDLQVV-----------------LISATLPH  218 (298)
Q Consensus       191 ----~~~~~i~~i~~~~~---------~~~~~v-----------------~~SAT~~~  218 (298)
                          ++...+..+++.++         +..|+.                 ++|||.+.
T Consensus       259 ~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~  316 (922)
T 1nkt_A          259 DGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSP  316 (922)
T ss_dssp             CCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCC
T ss_pred             CcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchh
Confidence                47788999999997         678888                 88999764

>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=99.94  E-value=1.2e-27  Score=228.48  Aligned_cols=163  Identities=13%  Similarity=0.179  Sum_probs=126.9

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC---CCCeEEEEEcCcHHHHHHH-HHHHHHhhccCCc
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTRELATQT-EKVILAIGDFINI  130 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~l~~q~-~~~~~~~~~~~~~  130 (298)
                      .|+++|.++++.+++|+++++.+|||+|||++|++|++..+...   ..+.++||++|+++|+.|+ .+.+++++.. ++
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~-~~   85 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-WY   85 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT-TS
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc-Cc
Confidence            59999999999999999999999999999999999999876542   1225899999999999999 9999998765 48


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHH------hccCccCCCccEEEechhhHhhccc-cHHHHHHHHHh-
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMI------KRKTLRTRAIKLLVLDESDEMLSRG-FKDQIYDVYRY-  202 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~------~~~~~~~~~l~~vViDE~h~~~~~~-~~~~i~~i~~~-  202 (298)
                      ++..++|+.........+..+++|+|+||++|...+      ....+.+.++++|||||||++...+ +...+...+.. 
T Consensus        86 ~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l~~~  165 (699)
T 4gl2_A           86 RVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQK  165 (699)
T ss_dssp             CEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHHHHH
T ss_pred             eEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHHHhh
Confidence            889999987766655666678999999999999988      4455778899999999999985543 33333222221 


Q ss_pred             ---C---------CCCccEEEEEeeCch
Q 022383          203 ---L---------PPDLQVVLISATLPH  218 (298)
Q Consensus       203 ---~---------~~~~~~v~~SAT~~~  218 (298)
                         .         .+.++++++|||+..
T Consensus       166 ~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          166 LKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             hcccccccccccCCCCCEEEEecccccc
Confidence               1         156799999999986

>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=99.94  E-value=3.2e-26  Score=218.06  Aligned_cols=233  Identities=17%  Similarity=0.176  Sum_probs=162.5

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHhhcC------CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHH
Q 022383           42 DDLLRGIYQYGFEKPSAIQQRAVMPIIKG------RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELAT  115 (298)
Q Consensus        42 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~  115 (298)
                      +.+...+..++| .|+++|.++++.+.++      .++++++|||+|||++|++|++..+..   +.+++|++|+++|+.
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~---g~qvlvlaPtr~La~  431 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILAI  431 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHH
Confidence            456666778999 7999999999998865      599999999999999999999998765   468999999999999


Q ss_pred             HHHHHHHHhhccCCceEEEEEcCCchHHHH---HHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccc
Q 022383          116 QTEKVILAIGDFINIQAHACVGGKSVGEDI---RKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG  191 (298)
Q Consensus       116 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~  191 (298)
                      |+.+.++++....++++..++|+....+..   ..+. +.++|+|+||+.+..     ...+.++++||+||+|++....
T Consensus       432 Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~~q  506 (780)
T 1gm5_A          432 QHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQ  506 (780)
T ss_dssp             HHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC----
T ss_pred             HHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhHHH
Confidence            999999999888889999999998766543   2333 358999999987743     4668899999999999863221


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh-h-
Q 022383          192 FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD-T-  269 (298)
Q Consensus       192 ~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~-~-  269 (298)
                           +..+......+++++||||+.+.......  .++...............+...+.   ... +...+...+. . 
T Consensus       507 -----r~~l~~~~~~~~vL~mSATp~p~tl~~~~--~g~~~~s~i~~~p~~r~~i~~~~~---~~~-~~~~l~~~i~~~l  575 (780)
T 1gm5_A          507 -----REALMNKGKMVDTLVMSATPIPRSMALAF--YGDLDVTVIDEMPPGRKEVQTMLV---PMD-RVNEVYEFVRQEV  575 (780)
T ss_dssp             ------CCCCSSSSCCCEEEEESSCCCHHHHHHH--TCCSSCEEECCCCSSCCCCEECCC---CSS-THHHHHHHHHHHT
T ss_pred             -----HHHHHHhCCCCCEEEEeCCCCHHHHHHHH--hCCcceeeeeccCCCCcceEEEEe---ccc-hHHHHHHHHHHHH
Confidence                 12222333578999999998765444332  222211111111111122332222   222 3333444443 2 


Q ss_pred             CCCCcEEEEecchh--------hHHHHHHHHhh
Q 022383          270 LTITQAVIFCNTKR--------KIYYSVFYFWI  294 (298)
Q Consensus       270 ~~~~k~lIf~~s~~--------~~~~l~~~L~~  294 (298)
                      ..+.+++|||++++        .++.+++.|++
T Consensus       576 ~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~  608 (780)
T 1gm5_A          576 MRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSK  608 (780)
T ss_dssp             TTSCCBCCBCCCC--------CHHHHHHHSGGG
T ss_pred             hcCCcEEEEecchhhhhhhhHHHHHHHHHHHHh
Confidence            34569999999764        47788888876

>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=99.94  E-value=1.3e-26  Score=189.74  Aligned_cols=164  Identities=14%  Similarity=0.157  Sum_probs=120.2

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC---CCCeEEEEEcCcHHHHHH-HHHHHHHhhc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTRELATQ-TEKVILAIGD  126 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~l~~q-~~~~~~~~~~  126 (298)
                      .+...|+++|.++++.+.+++++++.+|||+|||++++.++...+...   ..+.+++|++|+++|+.| +.+.++++..
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~  108 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLK  108 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHT
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhc
Confidence            345579999999999999999999999999999999999988766431   235589999999999999 7788888765


Q ss_pred             cCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccC------ccCCCccEEEechhhHhhccccHHHH-HHH
Q 022383          127 FINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKT------LRTRAIKLLVLDESDEMLSRGFKDQI-YDV  199 (298)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~------~~~~~l~~vViDE~h~~~~~~~~~~i-~~i  199 (298)
                      . ++++..+.|+.........+..+++|+|+||+++...+....      ..+.++++||+||+|++.+.++...+ ..+
T Consensus       109 ~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~  187 (216)
T 3b6e_A          109 K-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHY  187 (216)
T ss_dssp             T-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHHHHH
T ss_pred             c-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHHHHH
Confidence            4 678888888766554444444568999999999999887643      56788999999999999876544433 333


Q ss_pred             HHhC-------------CCCccEEEEEee
Q 022383          200 YRYL-------------PPDLQVVLISAT  215 (298)
Q Consensus       200 ~~~~-------------~~~~~~v~~SAT  215 (298)
                      +...             .+..+++++|||
T Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          188 LMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHhcccccccccccCCCCcceEEEeecC
Confidence            2221             157899999998

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.93  E-value=1.4e-26  Score=213.36  Aligned_cols=154  Identities=21%  Similarity=0.197  Sum_probs=128.5

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .|+++|.++++.+.+++++++++|||+|||++++.++...+...  ..++|||+|+++|+.|+.+.++++....+..+..
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~  190 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC--SSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEE
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC--CCeEEEEECcHHHHHHHHHHHHHhhcCCccceEE
Confidence            69999999999999999999999999999999999988877543  3489999999999999999999987666678888


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ++|+.....+   ...+.+|+|+||+.+..   .....+.++++|||||+|++..    ..+..+++.+++..+++++||
T Consensus       191 ~~~~~~~~~~---~~~~~~I~i~T~~~l~~---~~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~~~~~l~lSA  260 (510)
T 2oca_A          191 IGGGASKDDK---YKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLSG  260 (510)
T ss_dssp             CGGGCCTTGG---GCTTCSEEEEEHHHHTT---SCGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTTCCEEEEEES
T ss_pred             EecCCccccc---cccCCcEEEEeHHHHhh---chhhhhhcCCEEEEECCcCCCc----ccHHHHHHhcccCcEEEEEEe
Confidence            8887665443   45668999999996543   3345567899999999999854    456778888878889999999


Q ss_pred             eCchhH
Q 022383          215 TLPHEI  220 (298)
Q Consensus       215 T~~~~~  220 (298)
                      |+++..
T Consensus       261 Tp~~~~  266 (510)
T 2oca_A          261 SLRDGK  266 (510)
T ss_dssp             CGGGCS
T ss_pred             CCCCCc
Confidence            997653

>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=99.92  E-value=7e-26  Score=205.33  Aligned_cols=211  Identities=14%  Similarity=0.083  Sum_probs=142.6

Q ss_pred             CCCCChHHHHHHHHHhhcCCcE-EEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           52 GFEKPSAIQQRAVMPIIKGRDV-IAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~-li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      |+.+++|.|+ ++|.+++++++ ++++|||||||++|++|++......  +.+++|++|+++|+.|+.+.++      +.
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~------g~   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLR--RLRTLILAPTRVVAAEMEEALR------GL   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT------TS
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc--CCcEEEECCCHHHHHHHHHHhc------Cc
Confidence            6788999985 79999988877 9999999999999999998876553  5689999999999999999774      23


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHH-hCCCCccE
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR-YLPPDLQV  209 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~-~~~~~~~~  209 (298)
                      .+....+....     ....+..+.++|++.+.+.+... ..+.++++||+||+|++ +..+...+..+.. ..+++.|+
T Consensus        72 ~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~~~~~~~~~  144 (451)
T 2jlq_A           72 PIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAA  144 (451)
T ss_dssp             CEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SHHHHHHHHHHHHHHHTTSCEE
T ss_pred             eeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-CcchHHHHHHHHHhhcCCCceE
Confidence            33221111110     11234578899999988777543 55789999999999987 3333333332322 23457999


Q ss_pred             EEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHH
Q 022383          210 VLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSV  289 (298)
Q Consensus       210 v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~  289 (298)
                      +++|||++.....+   +..++..+......             +..  .+..+..++... .+++||||++++.|+.++
T Consensus       145 i~~SAT~~~~~~~~---~~~~~~~~~~~~~~-------------p~~--~~~~~~~~l~~~-~~~~lVF~~s~~~a~~l~  205 (451)
T 2jlq_A          145 IFMTATPPGSTDPF---PQSNSPIEDIEREI-------------PER--SWNTGFDWITDY-QGKTVWFVPSIKAGNDIA  205 (451)
T ss_dssp             EEECSSCTTCCCSS---CCCSSCEEEEECCC-------------CSS--CCSSSCHHHHHC-CSCEEEECSSHHHHHHHH
T ss_pred             EEEccCCCccchhh---hcCCCceEecCccC-------------Cch--hhHHHHHHHHhC-CCCEEEEcCCHHHHHHHH
Confidence            99999998754322   22333333322100             000  001112233333 469999999999999999


Q ss_pred             HHHhhhcC
Q 022383          290 FYFWIRWI  297 (298)
Q Consensus       290 ~~L~~~~~  297 (298)
                      +.|+..|+
T Consensus       206 ~~L~~~g~  213 (451)
T 2jlq_A          206 NCLRKSGK  213 (451)
T ss_dssp             HHHHTTTC
T ss_pred             HHHHHcCC
Confidence            99988764

>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=99.92  E-value=9.2e-25  Score=199.40  Aligned_cols=136  Identities=15%  Similarity=0.136  Sum_probs=113.1

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce-EE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ-AH  133 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~-~~  133 (298)
                      .|+++|.++++.+.+++++++++|||+|||++|+.++...      +.++||++|+++|+.|+.+.++++    +++ +.
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~----~~~~v~  162 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC----CCcceE
Confidence            5999999999999999999999999999999999888764      448999999999999999988773    677 77


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .++|+...         ..+|+|+|++.+......-   ..++++||+||+|++....|..    +.+.++ ..+++++|
T Consensus       163 ~~~g~~~~---------~~~Ivv~T~~~l~~~~~~~---~~~~~liIvDEaH~~~~~~~~~----~~~~~~-~~~~l~lS  225 (472)
T 2fwr_A          163 EFSGRIKE---------LKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYVQ----IAQMSI-APFRLGLT  225 (472)
T ss_dssp             EBSSSCBC---------CCSEEEEEHHHHHHTHHHH---TTTCSEEEEETGGGTTSTTTHH----HHHTCC-CSEEEEEE
T ss_pred             EECCCcCC---------cCCEEEEEcHHHHHHHHHh---cCCCCEEEEECCcCCCChHHHH----HHHhcC-CCeEEEEe
Confidence            77777543         4699999999988765421   2468999999999998777654    445553 67899999


Q ss_pred             eeCc
Q 022383          214 ATLP  217 (298)
Q Consensus       214 AT~~  217 (298)
                      ||+.
T Consensus       226 ATp~  229 (472)
T 2fwr_A          226 ATFE  229 (472)
T ss_dssp             SCCC
T ss_pred             cCcc
Confidence            9996

>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=99.92  E-value=1.4e-25  Score=208.60  Aligned_cols=202  Identities=16%  Similarity=0.125  Sum_probs=145.9

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEE
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHAC  135 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~  135 (298)
                      ++++|..+++.+.++++++++||||+|||.+|.+++++.      +.+++|++|+++|+.|+.+.+.+..   +..+...
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~------g~~vLVl~PTReLA~Qia~~l~~~~---g~~vg~~  288 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAH---GIDPNIR  288 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHH---SCCCEEE
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC------CCeEEEEcchHHHHHHHHHHHHHHh---CCCeeEE
Confidence            556677777777788999999999999999999998873      4589999999999999998776543   4455566


Q ss_pred             EcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCcc--EEEEE
Q 022383          136 VGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ--VVLIS  213 (298)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~--~v~~S  213 (298)
                      .|+..       ...+.+|+|+||++|   +....+.++++++||+||+|++ +.++...+..+++.++...+  ++++|
T Consensus       289 vG~~~-------~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~l-~~~~~~~l~~Il~~l~~~~~~llil~S  357 (666)
T 3o8b_A          289 TGVRT-------ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHST-DSTTILGIGTVLDQAETAGARLVVLAT  357 (666)
T ss_dssp             CSSCE-------ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTCC-SHHHHHHHHHHHHHTTTTTCSEEEEEE
T ss_pred             ECcEe-------ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccchhc-CccHHHHHHHHHHhhhhcCCceEEEEC
Confidence            66644       345689999999997   4566778889999999999764 56778888889999887666  77889


Q ss_pred             eeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHh
Q 022383          214 ATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFW  293 (298)
Q Consensus       214 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~  293 (298)
                      ||+++.+.      ...+....+.....  ..+ .   ...... .       ++....+++||||+++++++.+++.|+
T Consensus       358 AT~~~~i~------~~~p~i~~v~~~~~--~~i-~---~~~~~~-~-------l~~~~~~~vLVFv~Tr~~ae~la~~L~  417 (666)
T 3o8b_A          358 ATPPGSVT------VPHPNIEEVALSNT--GEI-P---FYGKAI-P-------IEAIRGGRHLIFCHSKKKCDELAAKLS  417 (666)
T ss_dssp             SSCTTCCC------CCCTTEEEEECBSC--SSE-E---ETTEEE-C-------GGGSSSSEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCcccc------cCCcceEEEeeccc--chh-H---HHHhhh-h-------hhhccCCcEEEEeCCHHHHHHHHHHHH
Confidence            99987421      11221111110000  000 0   001000 1       223356899999999999999999999


Q ss_pred             hhcC
Q 022383          294 IRWI  297 (298)
Q Consensus       294 ~~~~  297 (298)
                      +.|+
T Consensus       418 ~~g~  421 (666)
T 3o8b_A          418 GLGI  421 (666)
T ss_dssp             TTTC
T ss_pred             hCCC
Confidence            8765

>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=99.92  E-value=2.4e-26  Score=214.83  Aligned_cols=225  Identities=15%  Similarity=0.073  Sum_probs=151.9

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHH
Q 022383           38 MGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQT  117 (298)
Q Consensus        38 l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~  117 (298)
                      +++++.+.+++.+. ...++|.|+.+++.+.+|+|+++++|||||||++|++|++..+...  +.++||++||++|+.|+
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~--~~~vLvl~PtreLa~Qi  231 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR--RLRTLILAPTRVVAAEM  231 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC--CCeEEEEcChHHHHHHH
Confidence            55666666666553 4778888888899999999999999999999999999999887653  56899999999999999


Q ss_pred             HHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHH
Q 022383          118 EKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIY  197 (298)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~  197 (298)
                      .+.++.      ..+. +.+....    .....+..+.++|.+.+...+... ..++++++||+||||++ +.++...+.
T Consensus       232 ~~~l~~------~~v~-~~~~~l~----~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~  298 (618)
T 2whx_A          232 EEALRG------LPIR-YQTPAVK----SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARG  298 (618)
T ss_dssp             HHHTTT------SCEE-ECCTTSS----CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHHHHHHHH
T ss_pred             HHHhcC------Ccee-Eecccce----eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-CccHHHHHH
Confidence            987752      2232 2221100    001123356678888777655543 45789999999999998 566777777


Q ss_pred             HHHHhCC-CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEE
Q 022383          198 DVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAV  276 (298)
Q Consensus       198 ~i~~~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~l  276 (298)
                      .+.+.++ ++.|++++|||++.....+..   .++..+.+....             +..  +...+...+.. ..+++|
T Consensus       299 ~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~~~-------------~~~--~~~~ll~~l~~-~~~~~L  359 (618)
T 2whx_A          299 YISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIEREI-------------PER--SWNTGFDWITD-YQGKTV  359 (618)
T ss_dssp             HHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEECCC-------------CSS--CCSSSCHHHHH-CCSCEE
T ss_pred             HHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeeecccC-------------CHH--HHHHHHHHHHh-CCCCEE
Confidence            7777764 679999999999876443221   133333322110             111  11112222333 257999


Q ss_pred             EEecchhhHHHHHHHHhhhcC
Q 022383          277 IFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       277 If~~s~~~~~~l~~~L~~~~~  297 (298)
                      |||+|++.|+.+++.|+..|+
T Consensus       360 VF~~s~~~a~~l~~~L~~~g~  380 (618)
T 2whx_A          360 WFVPSIKAGNDIANCLRKSGK  380 (618)
T ss_dssp             EECSSHHHHHHHHHHHHHTTC
T ss_pred             EEECChhHHHHHHHHHHHcCC
Confidence            999999999999999998764

>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=99.92  E-value=1.6e-23  Score=200.36  Aligned_cols=248  Identities=15%  Similarity=0.175  Sum_probs=167.0

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhh-cCCcEEEEcCCCCchHHHHHHHHHH--hhccCCCCeEEEE
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-KGRDVIAQAQSGTGKTSMIALTVCQ--TVDTSSREVQALI  106 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~-~~~~~li~~pTG~GKT~~~~~~~~~--~~~~~~~~~~~li  106 (298)
                      .++.+|+++++++.+.+.+.+.+ ..|.+.|+++++.++ .+++++++||||+|||+.  +|++.  .......+.++++
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtl--lp~ll~~~~~~~~~g~~ilv  145 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQ--IPQFVLFDEMPHLENTQVAC  145 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHH--HHHHHHHHHCGGGGTCEEEE
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHH--HHHHHHHhccccCCCceEEe
Confidence            45678999999999999999988 679999999998876 567899999999999983  44432  2111112457999


Q ss_pred             EcCcHHHHHHHHHHHHHhh-ccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhh
Q 022383          107 LSPTRELATQTEKVILAIG-DFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (298)
Q Consensus       107 l~p~~~l~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h  185 (298)
                      ++|+++|+.|+.+.+.... ...+..+........      ....+.+|+++||+++.+.+... ..+.++++||+||+|
T Consensus       146 l~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~------~~~~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah  218 (773)
T 2xau_A          146 TQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN------KTSNKTILKYMTDGMLLREAMED-HDLSRYSCIILDEAH  218 (773)
T ss_dssp             EESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEE------ECCTTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGG
T ss_pred             cCchHHHHHHHHHHHHHHhCCchhheecceecccc------ccCCCCCEEEECHHHHHHHHhhC-ccccCCCEEEecCcc
Confidence            9999999999998775432 222222322111111      11245789999999999877654 458899999999999


Q ss_pred             H-hhccc-cHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHH--
Q 022383          186 E-MLSRG-FKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFD--  261 (298)
Q Consensus       186 ~-~~~~~-~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~--  261 (298)
                      . .++.. ....+..+.... +..|++++|||++..  .+. .++.++..+.+...   ...+.+.+...+..+....  
T Consensus       219 ~R~ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~~--~l~-~~~~~~~vi~v~gr---~~pv~~~~~~~~~~~~~~~~l  291 (773)
T 2xau_A          219 ERTLATDILMGLLKQVVKRR-PDLKIIIMSATLDAE--KFQ-RYFNDAPLLAVPGR---TYPVELYYTPEFQRDYLDSAI  291 (773)
T ss_dssp             GCCHHHHHHHHHHHHHHHHC-TTCEEEEEESCSCCH--HHH-HHTTSCCEEECCCC---CCCEEEECCSSCCSCHHHHHH
T ss_pred             ccccchHHHHHHHHHHHHhC-CCceEEEEeccccHH--HHH-HHhcCCCcccccCc---ccceEEEEecCCchhHHHHHH
Confidence            6 33332 334455555544 478999999999643  333 34444434443322   2345665554444442222  


Q ss_pred             -HHHHHHhhCCCCcEEEEecchhhHHHHHHHHhh
Q 022383          262 -TLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWI  294 (298)
Q Consensus       262 -~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~  294 (298)
                       .+..+......+++||||+++++++.+++.|++
T Consensus       292 ~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~  325 (773)
T 2xau_A          292 RTVLQIHATEEAGDILLFLTGEDEIEDAVRKISL  325 (773)
T ss_dssp             HHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHH
Confidence             233333444678999999999999999999975

>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=99.91  E-value=9.5e-24  Score=175.19  Aligned_cols=169  Identities=19%  Similarity=0.242  Sum_probs=125.4

Q ss_pred             CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC--CeEEEEEcCcHHHHHHHHHHHHHhhc-cC
Q 022383           52 GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR--EVQALILSPTRELATQTEKVILAIGD-FI  128 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~--~~~~lil~p~~~l~~q~~~~~~~~~~-~~  128 (298)
                      +...++++|.++++.+.+|++++++||||+|||.++..+++........  ..++++++|+++++.|+.+.+..... ..
T Consensus        58 ~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~  137 (235)
T 3llm_A           58 ELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEP  137 (235)
T ss_dssp             HTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCT
T ss_pred             hcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhcccc
Confidence            3345899999999999999999999999999999998888886654332  45899999999999999988865432 22


Q ss_pred             CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh-hccccH-HHHHHHHHhCCCC
Q 022383          129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-LSRGFK-DQIYDVYRYLPPD  206 (298)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~-~~~~~~-~~i~~i~~~~~~~  206 (298)
                      +..+.........     ....+++|+|+||+++.+++..   .++++++||+||+|.+ .+.++. ..++.+.... ++
T Consensus       138 ~~~~g~~~~~~~~-----~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~-~~  208 (235)
T 3llm_A          138 GKSCGYSVRFESI-----LPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PE  208 (235)
T ss_dssp             TSSEEEEETTEEE-----CCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC-TT
T ss_pred             CceEEEeechhhc-----cCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC-CC
Confidence            3333332211110     0113478999999999998876   4789999999999985 555555 4666666666 47


Q ss_pred             ccEEEEEeeCchhHHHHHHhcCCCC
Q 022383          207 LQVVLISATLPHEILEMTTKFMTDP  231 (298)
Q Consensus       207 ~~~v~~SAT~~~~~~~~~~~~~~~~  231 (298)
                      .|++++|||++...  +...+...|
T Consensus       209 ~~~il~SAT~~~~~--~~~~~~~~p  231 (235)
T 3llm_A          209 VRIVLMSATIDTSM--FCEYFFNCP  231 (235)
T ss_dssp             SEEEEEECSSCCHH--HHHHTTSCC
T ss_pred             CeEEEEecCCCHHH--HHHHcCCCC
Confidence            89999999999765  444444444

>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=99.90  E-value=4.2e-24  Score=182.15  Aligned_cols=154  Identities=21%  Similarity=0.198  Sum_probs=124.0

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .|+++|.++++.++++++.++++|||+|||.+++.++...+...  ..++||++|+++|+.|+.+.++++....+..+..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~  190 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC--CCeEEEEECCHHHHHHHHHHHHHhcccccceEEE
Confidence            69999999999999888899999999999999988877766542  3389999999999999999999987666667777


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      +.++.....   ....+.+|+|+||+.+...   ....+.++++||+||||++..    ..+..+++.+.+..+++++||
T Consensus       191 ~~~~~~~~~---~~~~~~~I~v~T~~~l~~~---~~~~~~~~~~vIiDEaH~~~~----~~~~~il~~~~~~~~~l~lSA  260 (282)
T 1rif_A          191 IGGGASKDD---KYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLSG  260 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCCH----HHHHHHTTTCTTCCEEEEECS
T ss_pred             EeCCCcchh---hhccCCcEEEEchHHHHhh---HHHHHhhCCEEEEECCccCCc----ccHHHHHHHhhcCCeEEEEeC
Confidence            777654332   2224579999999876532   234467889999999999853    467788888877899999999


Q ss_pred             eCchhH
Q 022383          215 TLPHEI  220 (298)
Q Consensus       215 T~~~~~  220 (298)
                      |+++..
T Consensus       261 Tp~~~~  266 (282)
T 1rif_A          261 SLRDGK  266 (282)
T ss_dssp             SCCTTS
T ss_pred             CCCCcc
Confidence            997653

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.90  E-value=1.7e-23  Score=196.10  Aligned_cols=151  Identities=20%  Similarity=0.266  Sum_probs=92.1

Q ss_pred             CChHHHHHHHHHhhc----C-CcEEEEcCCCCchHHHHHHHHHHhhccC------CCCeEEEEEcCcHHHHHHHH-HHHH
Q 022383           55 KPSAIQQRAVMPIIK----G-RDVIAQAQSGTGKTSMIALTVCQTVDTS------SREVQALILSPTRELATQTE-KVIL  122 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~----~-~~~li~~pTG~GKT~~~~~~~~~~~~~~------~~~~~~lil~p~~~l~~q~~-~~~~  122 (298)
                      .|+++|.++++.+.+    | +++++++|||+|||++++..+...+...      ..++++|||+|+++|+.|+. +.++
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~  257 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFT  257 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCT
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            699999999998875    4 6799999999999999665444433321      14679999999999999999 7666


Q ss_pred             HhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhc----cCccCCCccEEEechhhHhhccccHHHHHH
Q 022383          123 AIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKR----KTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (298)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~----~~~~~~~l~~vViDE~h~~~~~~~~~~i~~  198 (298)
                      .++    ..+..+.++        ....+.+|+|+||++|......    ..+...++++||+||||++.... ...+..
T Consensus       258 ~~~----~~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~~~  324 (590)
T 3h1t_A          258 PFG----DARHKIEGG--------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNWRE  324 (590)
T ss_dssp             TTC----SSEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------CHH
T ss_pred             hcc----hhhhhhhcc--------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHHHH
Confidence            543    233333322        2234679999999999887642    34556789999999999986542 245567


Q ss_pred             HHHhCCCCccEEEEEeeCchh
Q 022383          199 VYRYLPPDLQVVLISATLPHE  219 (298)
Q Consensus       199 i~~~~~~~~~~v~~SAT~~~~  219 (298)
                      +++.++ ..+++++|||+...
T Consensus       325 il~~~~-~~~~l~lTATP~~~  344 (590)
T 3h1t_A          325 ILEYFE-PAFQIGMTATPLRE  344 (590)
T ss_dssp             HHHHST-TSEEEEEESSCSCT
T ss_pred             HHHhCC-cceEEEeccccccc
Confidence            777776 47899999998743

>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=99.90  E-value=2e-25  Score=201.52  Aligned_cols=190  Identities=14%  Similarity=0.123  Sum_probs=123.0

Q ss_pred             HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (298)
                      .+.+|+|+++++|||||||++|++|++..+...  +++++|++||++|+.|+.+.++.+      .+....+...     
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~------~v~~~~~~~~-----   70 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL------DVKFHTQAFS-----   70 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS------CEEEESSCCC-----
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC------CeEEecccce-----
Confidence            467899999999999999999999999977653  568999999999999999987643      2221111100     


Q ss_pred             HHhhcCCcEEEeChHHHHHHHhc--------cCccCCCccEEEechhhHhhccccHHHHHHHHHhC-CCCccEEEEEeeC
Q 022383          146 RKLEHGVHVVSGTPGRVCDMIKR--------KTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLISATL  216 (298)
Q Consensus       146 ~~~~~~~~ilV~Tp~~l~~~~~~--------~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~-~~~~~~v~~SAT~  216 (298)
                               .|+||+++..++..        ....++++++||+||+|.+ +.++...+..+.+.. +...|+++||||+
T Consensus        71 ---------~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~  140 (440)
T 1yks_A           71 ---------AHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATP  140 (440)
T ss_dssp             ---------CCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSC
T ss_pred             ---------eccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCC
Confidence                     26666655432222        2244789999999999998 333433333333333 3579999999999


Q ss_pred             chhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          217 PHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      ++.+..+...  ..+.....              ..++... +...+ ..+... ++++||||++++.|+.+++.|+..|
T Consensus       141 ~~~~~~~~~~--~~~~~~~~--------------~~~~~~~-~~~~~-~~l~~~-~~~~lVF~~s~~~a~~l~~~L~~~~  201 (440)
T 1yks_A          141 PGTSDEFPHS--NGEIEDVQ--------------TDIPSEP-WNTGH-DWILAD-KRPTAWFLPSIRAANVMAASLRKAG  201 (440)
T ss_dssp             TTCCCSSCCC--SSCEEEEE--------------CCCCSSC-CSSSC-HHHHHC-CSCEEEECSCHHHHHHHHHHHHHTT
T ss_pred             Cchhhhhhhc--CCCeeEee--------------eccChHH-HHHHH-HHHHhc-CCCEEEEeCCHHHHHHHHHHHHHcC
Confidence            8764432211  11111111              1111111 11112 222222 5799999999999999999998876


Q ss_pred             C
Q 022383          297 I  297 (298)
Q Consensus       297 ~  297 (298)
                      +
T Consensus       202 ~  202 (440)
T 1yks_A          202 K  202 (440)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.90  E-value=3.1e-23  Score=186.84  Aligned_cols=195  Identities=12%  Similarity=0.080  Sum_probs=125.5

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      +|+++++++|||+|||++|++|++..+...  +.+++|++||++|+.|+.+.++      ++.+....++...     .-
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~--g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~~-----~~   67 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKK--RLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQS-----ER   67 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT------TSCEEEC-------------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhC--CCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCccc-----cC
Confidence            478999999999999999999999665543  5689999999999999998765      3445444443211     11


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhC-CCCccEEEEEeeCchhHHHHHHhc
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL-PPDLQVVLISATLPHEILEMTTKF  227 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~-~~~~~~v~~SAT~~~~~~~~~~~~  227 (298)
                      ..+..+.+.|.+.+.+.+.. ...++++++|||||+|++ ...+......+.... ++.+|++++|||+++.+..+... 
T Consensus        68 ~~~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~~-  144 (431)
T 2v6i_A           68 TGNEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPPS-  144 (431)
T ss_dssp             -CCCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCCC-
T ss_pred             CCCceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcCC-
Confidence            12345677788888766555 556889999999999997 333333333333332 46799999999998753221110 


Q ss_pred             CCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          228 MTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                       ..|......              ..+..  +...+..++... .+++||||+++++|+.+++.|+..++
T Consensus       145 -~~~i~~~~~--------------~~~~~--~~~~~~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~  196 (431)
T 2v6i_A          145 -NSPIIDEET--------------RIPDK--AWNSGYEWITEF-DGRTVWFVHSIKQGAEIGTCLQKAGK  196 (431)
T ss_dssp             -SSCCEEEEC--------------CCCSS--CCSSCCHHHHSC-SSCEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             -CCceeeccc--------------cCCHH--HHHHHHHHHHcC-CCCEEEEeCCHHHHHHHHHHHHHcCC
Confidence             111111100              00111  112223334443 46999999999999999999987653

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.89  E-value=1.3e-24  Score=204.44  Aligned_cols=216  Identities=15%  Similarity=0.133  Sum_probs=134.6

Q ss_pred             HHHHCCCC-----CChHHHH-----HHHHHhh------cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           47 GIYQYGFE-----KPSAIQQ-----RAVMPII------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        47 ~l~~~~~~-----~~~~~Q~-----~~~~~~~------~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      ++...||.     .|++.|+     ++++.++      +|+|+++++|||+|||++|++|++..+...  +.+++|++||
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~--~~~~lilaPT  279 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQK--RLRTAVLAPT  279 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHT--TCCEEEEESS
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC--CCcEEEEccH
Confidence            44556666     8999999     9999888      899999999999999999999999886553  5689999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                      ++|+.|+.+.++.+    ++.  ...+..      .... .+.-+-..+.+.+.+.+.. ...++++++||+||+|++ +
T Consensus       280 r~La~Q~~~~l~~~----~i~--~~~~~l------~~v~tp~~ll~~l~~~~l~~~l~~-~~~l~~l~lvViDEaH~~-~  345 (673)
T 2wv9_A          280 RVVAAEMAEALRGL----PVR--YLTPAV------QREHSGNEIVDVMCHATLTHRLMS-PLRVPNYNLFVMDEAHFT-D  345 (673)
T ss_dssp             HHHHHHHHHHTTTS----CCE--ECCC---------CCCCSCCCEEEEEHHHHHHHHHS-SSCCCCCSEEEEESTTCC-C
T ss_pred             HHHHHHHHHHHhcC----Cee--eecccc------cccCCHHHHHHHHHhhhhHHHHhc-ccccccceEEEEeCCccc-C
Confidence            99999999987644    221  100000      0000 1112233344444333333 256889999999999998 2


Q ss_pred             cccHHHHHHHHHhCC-CCccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHh
Q 022383          190 RGFKDQIYDVYRYLP-PDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD  268 (298)
Q Consensus       190 ~~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  268 (298)
                      ..+...+..+....+ ...|+++||||+++.+..+...  ..|......              ..+... ....+. .+.
T Consensus       346 ~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~i~~v~~--------------~~~~~~-~~~~l~-~l~  407 (673)
T 2wv9_A          346 PASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSPVHDVSS--------------EIPDRA-WSSGFE-WIT  407 (673)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSCEEEEEC--------------CCCSSC-CSSCCH-HHH
T ss_pred             ccHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCceEEEee--------------ecCHHH-HHHHHH-HHH
Confidence            222233333333332 5799999999998764322111  112111110              011111 111122 222


Q ss_pred             hCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          269 TLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       269 ~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      . ..+++||||+++++++.+++.|+..++
T Consensus       408 ~-~~~~~lVF~~s~~~~e~la~~L~~~g~  435 (673)
T 2wv9_A          408 D-YAGKTVWFVASVKMSNEIAQCLQRAGK  435 (673)
T ss_dssp             S-CCSCEEEECSSHHHHHHHHHHHHTTTC
T ss_pred             h-CCCCEEEEECCHHHHHHHHHHHHhCCC
Confidence            2 457999999999999999999988754

>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=99.88  E-value=8.9e-23  Score=185.27  Aligned_cols=196  Identities=13%  Similarity=0.139  Sum_probs=125.9

Q ss_pred             HHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHH
Q 022383           64 VMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE  143 (298)
Q Consensus        64 ~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  143 (298)
                      ...+.+++++++++|||+|||++|++|++..+...  +.++||++|+++|+.|+.+.++      +..+....+....  
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~------g~~v~~~~~~~~~--   84 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ--RLRTAVLAPTRVVAAEMAEALR------GLPVRYQTSAVQR--   84 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHT--TCCEEEEECSHHHHHHHHHHTT------TSCEEECC-------
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEECchHHHHHHHHHHhc------CceEeEEeccccc--
Confidence            34466789999999999999999999999877643  5689999999999999999876      2222221111110  


Q ss_pred             HHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh-----hccccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          144 DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM-----LSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       144 ~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~-----~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                         .-..+..+.++|.+.+...+... ..++++++|||||+|.+     ...++.....     .++..|++++|||++.
T Consensus        85 ---~~t~~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~-----~~~~~~~il~SAT~~~  155 (459)
T 2z83_A           85 ---EHQGNEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARGYIATKV-----ELGEAAAIFMTATPPG  155 (459)
T ss_dssp             ------CCCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHHHHHHHH-----HTTSCEEEEECSSCTT
T ss_pred             ---CCCCCcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHHHHHHHh-----ccCCccEEEEEcCCCc
Confidence               01233457778888877655543 56789999999999983     3333322211     1357999999999987


Q ss_pred             hHHHHHHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          219 EILEMTTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .+..+...  ..|.......              .+..  +...+..++... .+++||||++++.|+.+++.|+..|+
T Consensus       156 ~~~~~~~~--~~pi~~~~~~--------------~~~~--~~~~~~~~l~~~-~~~~LVF~~s~~~~~~l~~~L~~~g~  215 (459)
T 2z83_A          156 TTDPFPDS--NAPIHDLQDE--------------IPDR--AWSSGYEWITEY-AGKTVWFVASVKMGNEIAMCLQRAGK  215 (459)
T ss_dssp             CCCSSCCC--SSCEEEEECC--------------CCSS--CCSSCCHHHHHC-CSCEEEECSCHHHHHHHHHHHHHTTC
T ss_pred             chhhhccC--CCCeEEeccc--------------CCcc--hhHHHHHHHHhc-CCCEEEEeCChHHHHHHHHHHHhcCC
Confidence            64322111  2233222110              0100  111112233333 57999999999999999999988764

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.88  E-value=1.2e-20  Score=177.24  Aligned_cols=130  Identities=18%  Similarity=0.228  Sum_probs=112.2

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      +|+ .|++.|..+++.+++|+  +.+++||+|||++|.+|++.....   +..++|++||++||.|..+.+..+...+++
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~---G~qv~VvTPTreLA~Qdae~m~~l~~~lGL  149 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT---GKGVHVVTVNDYLARRDAEWMGPVYRGLGL  149 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT---CSCCEEEESSHHHHHHHHHHHHHHHHTTTC
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh---CCCEEEEeCCHHHHHHHHHHHHHHHHhcCC
Confidence            788 79999999999999998  999999999999999999644333   347999999999999999999999999999


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHH-HHHHhcc------CccCC---CccEEEechhhHhh
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRV-CDMIKRK------TLRTR---AIKLLVLDESDEML  188 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l-~~~~~~~------~~~~~---~l~~vViDE~h~~~  188 (298)
                      ++..++||.+....  ....+++|+|+||++| +.+++.+      .+.++   ++.++|+||+|.++
T Consensus       150 sv~~i~Gg~~~~~r--~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          150 SVGVIQHASTPAER--RKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             CEEECCTTCCHHHH--HHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             eEEEEeCCCCHHHH--HHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            99999999875433  3344689999999999 7777765      25567   89999999999987

>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=99.86  E-value=9.7e-22  Score=191.94  Aligned_cols=153  Identities=12%  Similarity=0.082  Sum_probs=115.1

Q ss_pred             CChHHHHHHHHHhhc--------------CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHH
Q 022383           55 KPSAIQQRAVMPIIK--------------GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKV  120 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~--------------~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~  120 (298)
                      .|+++|.++++.++.              +++.+++++||||||+++ ++++..+.......++|||+|+++|+.|+.+.
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~  349 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDYQTMKE  349 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHHHHHHH
Confidence            599999999998764              368999999999999997 55555554433446999999999999999999


Q ss_pred             HHHhhccCCceEEEEEcCCchHHHHHHhh-cCCcEEEeChHHHHHHHhccC--ccCCCccEEEechhhHhhccccHHHHH
Q 022383          121 ILAIGDFINIQAHACVGGKSVGEDIRKLE-HGVHVVSGTPGRVCDMIKRKT--LRTRAIKLLVLDESDEMLSRGFKDQIY  197 (298)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ilV~Tp~~l~~~~~~~~--~~~~~l~~vViDE~h~~~~~~~~~~i~  197 (298)
                      ++.+...      ...++.+.......+. .+.+|+|+||++|...+....  ..+....+||+||||++...   ..+.
T Consensus       350 f~~f~~~------~v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~~---~~~~  420 (1038)
T 2w00_A          350 YQRFSPD------SVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFG---EAQK  420 (1038)
T ss_dssp             HHTTSTT------CSSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHHH---HHHH
T ss_pred             HHHhccc------ccccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcch---HHHH
Confidence            9887542      1123334444444453 568999999999998876532  24567899999999997532   3455


Q ss_pred             HHHHhCCCCccEEEEEeeCch
Q 022383          198 DVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       198 ~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      .+.+.++ +.+++++|||+..
T Consensus       421 ~I~~~~p-~a~~lgfTATP~~  440 (1038)
T 2w00_A          421 NLKKKFK-RYYQFGFTGTPIF  440 (1038)
T ss_dssp             HHHHHCS-SEEEEEEESSCCC
T ss_pred             HHHHhCC-cccEEEEeCCccc
Confidence            6667775 5899999999964

>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=99.85  E-value=1.8e-20  Score=155.36  Aligned_cols=138  Identities=16%  Similarity=0.144  Sum_probs=110.1

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce-EE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ-AH  133 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~-~~  133 (298)
                      .++++|.++++.+.+++++++++|||+|||.+++.++...      +.+++|++|+++|+.|+.+.++++    ++. +.
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~----~~~~v~  162 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC----CCCeEE
Confidence            6899999999999999999999999999999988777653      347999999999999999988773    566 77


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+.|+...         ..+|+|+|++.+......   ...++++|||||+|++.+..+.    .+.+.++ ..+++++|
T Consensus       163 ~~~g~~~~---------~~~i~v~T~~~l~~~~~~---~~~~~~llIiDEaH~l~~~~~~----~i~~~~~-~~~~l~LS  225 (237)
T 2fz4_A          163 EFSGRIKE---------LKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAESYV----QIAQMSI-APFRLGLT  225 (237)
T ss_dssp             EESSSCBC---------CCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTTHH----HHHHTCC-CSEEEEEE
T ss_pred             EEeCCCCC---------cCCEEEEeHHHHHhhHHH---hcccCCEEEEECCccCCChHHH----HHHHhcc-CCEEEEEe
Confidence            77766542         469999999998765542   1246899999999999766544    4555554 67899999


Q ss_pred             eeCchh
Q 022383          214 ATLPHE  219 (298)
Q Consensus       214 AT~~~~  219 (298)
                      ||+.+.
T Consensus       226 ATp~r~  231 (237)
T 2fz4_A          226 ATFERE  231 (237)
T ss_dssp             ESCC--
T ss_pred             cCCCCC
Confidence            999754

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.80  E-value=1e-19  Score=171.02  Aligned_cols=195  Identities=17%  Similarity=0.149  Sum_probs=130.3

Q ss_pred             HHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHH
Q 022383           65 MPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED  144 (298)
Q Consensus        65 ~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (298)
                      ...++|++++++||||+|||..++    ..+...   ...+|++|+++|+.|+++.+++.    ++++..+.|+..... 
T Consensus       150 ar~l~rk~vlv~apTGSGKT~~al----~~l~~~---~~gl~l~PtR~LA~Qi~~~l~~~----g~~v~lltG~~~~iv-  217 (677)
T 3rc3_A          150 ARAMQRKIIFHSGPTNSGKTYHAI----QKYFSA---KSGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTV-  217 (677)
T ss_dssp             HHTSCCEEEEEECCTTSSHHHHHH----HHHHHS---SSEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECC-
T ss_pred             HHhcCCCEEEEEcCCCCCHHHHHH----HHHHhc---CCeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEe-
Confidence            345688999999999999998433    333232   23599999999999999998875    677888888755410 


Q ss_pred             HHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCC-CCccEEEEEeeCchhHHHH
Q 022383          145 IRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP-PDLQVVLISATLPHEILEM  223 (298)
Q Consensus       145 ~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~-~~~~~v~~SAT~~~~~~~~  223 (298)
                       ..-....+++++|++.+.        ....++++||||+|++.+.++...+..++..++ ...+++++|||.+ .+..+
T Consensus       218 -~TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~~-~i~~l  287 (677)
T 3rc3_A          218 -QPNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAID-LVMEL  287 (677)
T ss_dssp             -STTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGHH-HHHHH
T ss_pred             -cCCCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccchHH-HHHHH
Confidence             000123578888875443        246779999999999988889999999888887 7789999999953 23444


Q ss_pred             HHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          224 TTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ... .+....+.....   .....   . ...   .   + ..+... ....+|||+++++++.+++.|++.+.
T Consensus       288 ~~~-~~~~~~v~~~~r---~~~l~---~-~~~---~---l-~~l~~~-~~g~iIf~~s~~~ie~la~~L~~~g~  345 (677)
T 3rc3_A          288 MYT-TGEEVEVRDYKR---LTPIS---V-LDH---A---L-ESLDNL-RPGDCIVCFSKNDIYSVSRQIEIRGL  345 (677)
T ss_dssp             HHH-HTCCEEEEECCC---SSCEE---E-CSS---C---C-CSGGGC-CTTEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             HHh-cCCceEEEEeee---cchHH---H-HHH---H---H-HHHHhc-CCCCEEEEcCHHHHHHHHHHHHhcCC
Confidence            333 234444322111   00000   0 000   0   0 011122 24568999999999999999988654

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.80  E-value=1.7e-18  Score=159.00  Aligned_cols=149  Identities=13%  Similarity=0.139  Sum_probs=107.1

Q ss_pred             CCChHHHHHHHHHh----hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCC
Q 022383           54 EKPSAIQQRAVMPI----IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFIN  129 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~----~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~  129 (298)
                      ..|+|+|.++++.+    ..++++++..+||+|||+.++..+.. +.......++||||| ..|+.|+.+.++++..  +
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~-~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~~--~  111 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSD-AKKENELTPSLVICP-LSVLKNWEEELSKFAP--H  111 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHH-HHHTTCCSSEEEEEC-STTHHHHHHHHHHHCT--T
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHH-HHhcCCCCCEEEEcc-HHHHHHHHHHHHHHCC--C
Confidence            35999999999876    35789999999999999886554443 333333457999999 5699999999998864  4


Q ss_pred             ceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccE
Q 022383          130 IQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV  209 (298)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~  209 (298)
                      .++..++|+...     ....+++|+|+|++.+.....   +...++++||+||+|++.+..  ......+..++ ..+.
T Consensus       112 ~~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~~--~~~~~~l~~l~-~~~~  180 (500)
T 1z63_A          112 LRFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYR  180 (500)
T ss_dssp             SCEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEE
T ss_pred             ceEEEEecCchh-----ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCHh--HHHHHHHHhhc-cCcE
Confidence            566666665422     112457999999998875433   334577999999999986543  22334444553 4678


Q ss_pred             EEEEeeCc
Q 022383          210 VLISATLP  217 (298)
Q Consensus       210 v~~SAT~~  217 (298)
                      +++|||+.
T Consensus       181 l~LTaTP~  188 (500)
T 1z63_A          181 IALTGTPI  188 (500)
T ss_dssp             EEECSSCS
T ss_pred             EEEecCCC
Confidence            99999983

>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=99.77  E-value=1.3e-18  Score=170.67  Aligned_cols=159  Identities=16%  Similarity=0.094  Sum_probs=107.7

Q ss_pred             CCChHHHHHHHHHhhc--CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           54 EKPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~--~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      ..|+|+|.+++..+..  +.++++..+||+|||+.++..+...+... ...++|||||+ .|+.|+.+.+.+..   +++
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g-~~~rvLIVvP~-sLl~Qw~~E~~~~f---~l~  226 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG-AAERVLIIVPE-TLQHQWLVEMLRRF---NLR  226 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS-SCCCEEEECCT-TTHHHHHHHHHHHS---CCC
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEeCH-HHHHHHHHHHHHHh---CCC
Confidence            3699999999998775  45899999999999999877776665443 23479999999 99999999886653   566


Q ss_pred             EEEEEcCCchHHHHH--HhhcCCcEEEeChHHHHHHHhc-cCccCCCccEEEechhhHhhccccH--HHHHHHHHhCCCC
Q 022383          132 AHACVGGKSVGEDIR--KLEHGVHVVSGTPGRVCDMIKR-KTLRTRAIKLLVLDESDEMLSRGFK--DQIYDVYRYLPPD  206 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~--~~~~~~~ilV~Tp~~l~~~~~~-~~~~~~~l~~vViDE~h~~~~~~~~--~~i~~i~~~~~~~  206 (298)
                      +..+.++........  ......+|+|+|++.+...... ..+...++++||+||+|++...+..  ..+..+.......
T Consensus       227 v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~~  306 (968)
T 3dmq_A          227 FALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHV  306 (968)
T ss_dssp             CEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTTC
T ss_pred             EEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhcC
Confidence            655554332211111  1113568999999887642211 1234568899999999998654321  1222232222345


Q ss_pred             ccEEEEEeeCc
Q 022383          207 LQVVLISATLP  217 (298)
Q Consensus       207 ~~~v~~SAT~~  217 (298)
                      .+++++|||+.
T Consensus       307 ~~~L~LTATPi  317 (968)
T 3dmq_A          307 PGVLLLTATPE  317 (968)
T ss_dssp             SSEEESCSSCS
T ss_pred             CcEEEEEcCCc
Confidence            67999999983

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.72  E-value=3.8e-17  Score=151.51  Aligned_cols=129  Identities=18%  Similarity=0.062  Sum_probs=100.4

Q ss_pred             CChHHHHHHHHH----hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           55 KPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        55 ~~~~~Q~~~~~~----~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .++|+|.+++..    +..|+++++++|||+|||++|++|++..      +++++|++||++|+.|+.+.+..+.+..++
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~------~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~   76 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV------KPKVLFVVRTHNEFYPIYRDLTKIREKRNI   76 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH------CSEEEEEESSGGGHHHHHHHHTTCCCSSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC------CCeEEEEcCCHHHHHHHHHHHHHHhhhcCc
Confidence            489999997765    4578999999999999999999999982      568999999999999999999888776678


Q ss_pred             eEEEEEcCCch---------------------------------HHHH------------------HHhhcCCcEEEeCh
Q 022383          131 QAHACVGGKSV---------------------------------GEDI------------------RKLEHGVHVVSGTP  159 (298)
Q Consensus       131 ~~~~~~~~~~~---------------------------------~~~~------------------~~~~~~~~ilV~Tp  159 (298)
                      ++..+.|....                                 ....                  .....+++|+|+|+
T Consensus        77 ~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adIVV~~~  156 (551)
T 3crv_A           77 TFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALTY  156 (551)
T ss_dssp             CEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSEEEEET
T ss_pred             cEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCEEEeCc
Confidence            88777663210                                 0111                  22234689999999


Q ss_pred             HHHHHHHhccCccC-CCccEEEechhhHhhc
Q 022383          160 GRVCDMIKRKTLRT-RAIKLLVLDESDEMLS  189 (298)
Q Consensus       160 ~~l~~~~~~~~~~~-~~l~~vViDE~h~~~~  189 (298)
                      ..|........+.+ .....+||||||.+.+
T Consensus       157 ~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          157 PYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             hHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            99987653333322 4778999999999876

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.71  E-value=3e-16  Score=151.46  Aligned_cols=154  Identities=14%  Similarity=0.165  Sum_probs=109.7

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .++|+|.+++..+.    .+++.++..+||.|||+.++..+...+........+||||| ..|+.|+.+.+.++..  ++
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p--~~  312 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAP--DL  312 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHST--TC
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCC--Cc
Confidence            58999999998665    78999999999999998876555544333233446899999 7889999999998863  56


Q ss_pred             eEEEEEcCCchHHHHHHh------------hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHH
Q 022383          131 QAHACVGGKSVGEDIRKL------------EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYD  198 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~------------~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~  198 (298)
                      ++..++|+..........            ...++|+|+|++.+......  +...+.++||+||||++-...  .....
T Consensus       313 ~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn~~--s~~~~  388 (800)
T 3mwy_W          313 NCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKNAE--SSLYE  388 (800)
T ss_dssp             CEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCCSS--SHHHH
T ss_pred             eEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcCch--hHHHH
Confidence            777777766554433322            23578999999998764322  222367899999999984332  23334


Q ss_pred             HHHhCCCCccEEEEEeeC
Q 022383          199 VYRYLPPDLQVVLISATL  216 (298)
Q Consensus       199 i~~~~~~~~~~v~~SAT~  216 (298)
                      .+..++ ....+++|||+
T Consensus       389 ~l~~l~-~~~rl~LTgTP  405 (800)
T 3mwy_W          389 SLNSFK-VANRMLITGTP  405 (800)
T ss_dssp             HHTTSE-EEEEEEECSCC
T ss_pred             HHHHhh-hccEEEeeCCc
Confidence            445553 45678999998

>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=99.70  E-value=4.7e-15  Score=137.24  Aligned_cols=235  Identities=12%  Similarity=0.106  Sum_probs=162.2

Q ss_pred             CCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           51 YGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|.. |++.|....-.+..|+  +..+.||.|||+++.+|++-....   +..+.|++|+..||.|-.+.+..+...+|+
T Consensus        72 lg~r-~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~---G~~vhVvT~ndyLA~rdae~m~~l~~~Lgl  145 (822)
T 3jux_A           72 LGMR-PFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI---GKGVHLVTVNDYLARRDALWMGPVYLFLGL  145 (822)
T ss_dssp             TSCC-CCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             hCCC-CcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc---CCceEEEeccHHHHHhHHHHHHHHHHHhCC
Confidence            5655 8999998888888887  889999999999999998744333   446899999999999999999999999999


Q ss_pred             eEEEEEcC--------------------------------------------------CchHHHHHHhhcCCcEEEeChH
Q 022383          131 QAHACVGG--------------------------------------------------KSVGEDIRKLEHGVHVVSGTPG  160 (298)
Q Consensus       131 ~~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~~ilV~Tp~  160 (298)
                      ++....+.                                                  .+..+....  -.|||+.+|..
T Consensus       146 svg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~a--Y~~DItYgTn~  223 (822)
T 3jux_A          146 RVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEA--YLCDVTYGTNN  223 (822)
T ss_dssp             CEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHH--HHSSEEEEEHH
T ss_pred             EEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHH--hcCCCEEccCc
Confidence            99888872                                                  111111111  23799999998


Q ss_pred             HHH-HHHhcc------CccCCCccEEEechhhHhhccc----------------cHHHHHHHHHhC--------------
Q 022383          161 RVC-DMIKRK------TLRTRAIKLLVLDESDEMLSRG----------------FKDQIYDVYRYL--------------  203 (298)
Q Consensus       161 ~l~-~~~~~~------~~~~~~l~~vViDE~h~~~~~~----------------~~~~i~~i~~~~--------------  203 (298)
                      .|- .+++.+      ..-.+.+.+.||||+|.++=+.                ....+..+.+.+              
T Consensus       224 EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~vdek~~~  303 (822)
T 3jux_A          224 EFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKART  303 (822)
T ss_dssp             HHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEEECCSSSC
T ss_pred             chhhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEEEEcccCe
Confidence            875 344432      2234778999999999976211                001111111111              


Q ss_pred             ------------------------------------------CC------------------------------------
Q 022383          204 ------------------------------------------PP------------------------------------  205 (298)
Q Consensus       204 ------------------------------------------~~------------------------------------  205 (298)
                                                                .+                                    
T Consensus       304 v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiE  383 (822)
T 3jux_A          304 IILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAIE  383 (822)
T ss_dssp             EEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGGGHHHHHH
T ss_pred             EEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCchHHHHHHH
Confidence                                                      00                                    


Q ss_pred             -------------------------CccEEEEEeeCchhHHHHHHhcCCCCEEEEecCCccCcCCceEE-EEEecCccch
Q 022383          206 -------------------------DLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQF-FVAVEREEWK  259 (298)
Q Consensus       206 -------------------------~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~-~~~~~~~~~k  259 (298)
                                               -.++.+||+|.......+...|..+  .+.++. ......+.+. .+... ...|
T Consensus       384 aKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~~Ef~~iY~l~--vv~IPt-nkp~~R~d~~d~vy~t-~~eK  459 (822)
T 3jux_A          384 AKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGME--VVVIPT-HKPMIRKDHDDLVFRT-QKEK  459 (822)
T ss_dssp             HHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGHHHHHHHSCCC--EEECCC-SSCCCCEECCCEEESS-HHHH
T ss_pred             HHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHHHHHHHHhCCe--EEEECC-CCCcceeecCcEEEec-HHHH
Confidence                                     1359999999988877777666433  333332 2222333332 23333 3448


Q ss_pred             HHHHHHHHhhC--CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          260 FDTLCDLYDTL--TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       260 ~~~l~~ll~~~--~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ...+...+...  .+.++||||+|++.++.++..|.+.|+
T Consensus       460 ~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi  499 (822)
T 3jux_A          460 YEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGI  499 (822)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCC
Confidence            88888887653  467999999999999999999999886

>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=99.68  E-value=9e-15  Score=137.92  Aligned_cols=155  Identities=15%  Similarity=0.098  Sum_probs=107.3

Q ss_pred             CChHHHHHHHHHhh---------cCCcEEEEcCCCCchHHHHHHHHHHhhccCC----CCeEEEEEcCcHHHHHHHHHHH
Q 022383           55 KPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIALTVCQTVDTSS----REVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~---------~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~----~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      .++|+|.+++..+.         .++..++..+||.|||+.++..+...+...+    ...++|||||+ .|+.|+.+.+
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            59999999998763         4567999999999999887766655544322    23468999996 8999999999


Q ss_pred             HHhhccCCceEEEEEcCCchHH--HHHHhh------cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccH
Q 022383          122 LAIGDFINIQAHACVGGKSVGE--DIRKLE------HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (298)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~------~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~  193 (298)
                      .++... .+.+..++++.....  ......      ...+|+|+|++.+.....  .+....+++||+||+|++-... .
T Consensus       134 ~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~--~l~~~~~~~vI~DEaH~ikn~~-~  209 (644)
T 1z3i_X          134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD-N  209 (644)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC-H
T ss_pred             HHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHH--HhhcCCccEEEEECceecCChh-h
Confidence            988754 455666666644321  111211      147899999998875432  3344578999999999985432 2


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeC
Q 022383          194 DQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       194 ~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      ... ..+..+. ....+++|||+
T Consensus       210 ~~~-~al~~l~-~~~rl~LTgTP  230 (644)
T 1z3i_X          210 QTY-LALNSMN-AQRRVLISGTP  230 (644)
T ss_dssp             HHH-HHHHHHC-CSEEEEECSSC
T ss_pred             HHH-HHHHhcc-cCcEEEEecCc
Confidence            222 2333343 45789999997

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.61  E-value=8.4e-16  Score=142.06  Aligned_cols=127  Identities=17%  Similarity=0.199  Sum_probs=86.6

Q ss_pred             CCCCCChHHHHHHHHH----hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           51 YGFEKPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        51 ~~~~~~~~~Q~~~~~~----~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      .|| .++++|.+++..    +..|+++++++|||+|||++|++|++..      +.+++|++||++|+.|+.+.+.++  
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~------~~~~~~~~~t~~l~~q~~~~~~~l--   74 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL------KKKVLIFTRTHSQLDSIYKNAKLL--   74 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH------TCEEEEEESCHHHHHHHHHHHGGG--
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC------CCcEEEEcCCHHHHHHHHHHHHhc--
Confidence            366 699999998654    4588999999999999999999998764      458999999999999999887764  


Q ss_pred             cCCceEEEEEcCCc--------hH------------------------HH---------------HHHhhcCCcEEEeCh
Q 022383          127 FINIQAHACVGGKS--------VG------------------------ED---------------IRKLEHGVHVVSGTP  159 (298)
Q Consensus       127 ~~~~~~~~~~~~~~--------~~------------------------~~---------------~~~~~~~~~ilV~Tp  159 (298)
                        ++++..+.|...        ..                        ..               ......+++|+|+|+
T Consensus        75 --~~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~adiVV~n~  152 (540)
T 2vl7_A           75 --GLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDVIAMTY  152 (540)
T ss_dssp             --TCCEEEC---------------------------------------------------------CTTGGGCSEEEEET
T ss_pred             --CCcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCCEEEECh
Confidence              344444333210        00                        00               011124579999999


Q ss_pred             HHHHHHHhccCc-------cCCCccEEEechhhHhh
Q 022383          160 GRVCDMIKRKTL-------RTRAIKLLVLDESDEML  188 (298)
Q Consensus       160 ~~l~~~~~~~~~-------~~~~l~~vViDE~h~~~  188 (298)
                      ..|..-...+.+       .+....++||||||.+.
T Consensus       153 ~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          153 PYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             HHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             HHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            999864332221       24567899999999983

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.42  E-value=5.6e-13  Score=124.77  Aligned_cols=81  Identities=22%  Similarity=0.232  Sum_probs=67.3

Q ss_pred             CChHHHHHHHHH----hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           55 KPSAIQQRAVMP----IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        55 ~~~~~Q~~~~~~----~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .|++.|.+.+..    +.+|+++++++|||+|||++|++|++..+...  +.+++|++||++++.|+.+.++.+....++
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~--~~kvli~t~T~~l~~Qi~~el~~l~~~~~~   80 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER--KLKVLYLVRTNSQEEQVIKELRSLSSTMKI   80 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH--TCEEEEEESSHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc--CCeEEEECCCHHHHHHHHHHHHHHhhccCe
Confidence            489999998864    55899999999999999999999999987543  458999999999999999999988766566


Q ss_pred             eEEEEEc
Q 022383          131 QAHACVG  137 (298)
Q Consensus       131 ~~~~~~~  137 (298)
                      ++..+.|
T Consensus        81 ~~~~l~g   87 (620)
T 4a15_A           81 RAIPMQG   87 (620)
T ss_dssp             CEEECCC
T ss_pred             EEEEEEC
Confidence            6666554

>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=99.10  E-value=2.3e-09  Score=101.20  Aligned_cols=68  Identities=28%  Similarity=0.382  Sum_probs=52.3

Q ss_pred             CCCCChHHHHHHHHHhh----cCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           52 GFEKPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        52 ~~~~~~~~Q~~~~~~~~----~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      +| .|++.|..++..+.    .|. ..++.+.||+|||+++.-.+ ...     +..+|||+|+..++.|+++.++.+..
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~~-~~~-----~~~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVI-EAL-----GRPALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHH-----TCCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHHH-HHh-----CCCEEEEecCHHHHHHHHHHHHHHCC
Confidence            45 69999998888655    343 57788999999998765333 332     12489999999999999999998853

>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=99.08  E-value=3.2e-10  Score=106.05  Aligned_cols=160  Identities=15%  Similarity=0.177  Sum_probs=97.5

Q ss_pred             HHHHHHHHCC-CCCChHHHHHHHHHhhcCCcEEEEcCCCCchH--HHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           43 DLLRGIYQYG-FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKT--SMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        43 ~i~~~l~~~~-~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT--~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      .+...|.... -...++.|+.+++.++.++.+++.|++|+|||  .+++++.+..+... .+.++++++||...+.++.+
T Consensus       136 ~~~~~l~~~~~~~~~~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~-~~~~vll~APTg~AA~~L~e  214 (608)
T 1w36_D          136 LLAQTLDKLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG-ERCRIRLAAPTGKAAARLTE  214 (608)
T ss_dssp             HHHHHHHTTCCCTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS-CCCCEEEEBSSHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhc-CCCeEEEEeCChhHHHHHHH
Confidence            3444555432 12236899999999999999999999999999  56677777655322 35589999999999999998


Q ss_pred             HHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHH
Q 022383          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (298)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i  199 (298)
                      .+.......++..... .+...  ....+   ..++-.+|+.. . +........+++++||||++++ +   ...+..+
T Consensus       215 ~~~~~~~~l~l~~~~~-~~~~~--~~~Ti---h~ll~~~~~~~-~-~~~~~~~~l~~d~lIIDEAsml-~---~~~~~~L  282 (608)
T 1w36_D          215 SLGKALRQLPLTDEQK-KRIPE--DASTL---HRLLGAQPGSQ-R-LRHHAGNPLHLDVLVVDEASMI-D---LPMMSRL  282 (608)
T ss_dssp             HHTHHHHHSSCCSCCC-CSCSC--CCBTT---TSCC-------------CTTSCCSCSEEEECSGGGC-B---HHHHHHH
T ss_pred             HHHHHHhcCCCCHHHH-hccch--hhhhh---HhhhccCCCch-H-HHhccCCCCCCCEEEEechhhC-C---HHHHHHH
Confidence            8876554433221000 00000  00000   11222222211 1 1111122337899999999955 3   4567788


Q ss_pred             HHhCCCCccEEEEEee
Q 022383          200 YRYLPPDLQVVLISAT  215 (298)
Q Consensus       200 ~~~~~~~~~~v~~SAT  215 (298)
                      ++.++...|++++.-.
T Consensus       283 l~~l~~~~~liLvGD~  298 (608)
T 1w36_D          283 IDALPDHARVIFLGDR  298 (608)
T ss_dssp             HHTCCTTCEEEEEECT
T ss_pred             HHhCCCCCEEEEEcch
Confidence            8888888999888654

>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=98.90  E-value=7.5e-08  Score=90.83  Aligned_cols=66  Identities=21%  Similarity=0.317  Sum_probs=50.2

Q ss_pred             CChHHHHHHHHHhh----cCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           55 KPSAIQQRAVMPII----KGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      .|+..|..++..+.    +|. ...+.+.||+|||+...-.+ ...     +..+|||+|+..+|.|+++.++.+..
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~~~-~~~-----~~~~lvv~~~~~~A~~l~~el~~~~~   82 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLI-KEV-----NKPTLVIAHNKTLAGQLYSEFKEFFP   82 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHH-----CCCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHHHH-HHh-----CCCEEEEECCHHHHHHHHHHHHHHcC
Confidence            58899988887654    343 57788999999997654322 322     12489999999999999999999854

>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=98.56  E-value=1.1e-06  Score=82.39  Aligned_cols=69  Identities=22%  Similarity=0.186  Sum_probs=54.5

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      ..+++.|.+++..++.+...+|.||+|+|||....-.+ ..+... .+.++++++||...++++.+.+.+.
T Consensus       179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i-~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV-YHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHH-HHHHTS-SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHH-HHHHHc-CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            45899999999998888889999999999997654333 333221 3458999999999999999887654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.52  E-value=3.8e-07  Score=86.04  Aligned_cols=67  Identities=19%  Similarity=0.232  Sum_probs=54.0

Q ss_pred             CChHHHHHHHHHhhcCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           55 KPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .+++.|.+|+..++..+ -.+|+||.|+|||.+..-.+...+..   +.++|+++||..-++++.+++...
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~---~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ---GLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEcCchHHHHHHHHHHHhc
Confidence            58999999999987655 57899999999998765545444443   458999999999999999988654

>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=98.51  E-value=9.2e-07  Score=81.95  Aligned_cols=127  Identities=21%  Similarity=0.270  Sum_probs=80.9

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .+++.|.+++..+..++.+++.||.|+|||.... .++..+...  +.++++++||...+..+.+.+.       .....
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~-~l~~~l~~~--g~~Vl~~ApT~~Aa~~L~e~~~-------~~a~T  258 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTK-AVADLAESL--GLEVGLCAPTGKAARRLGEVTG-------RTAST  258 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHH-HHHHHHHHT--TCCEEEEESSHHHHHHHHHHHT-------SCEEE
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHH-HHHHHHHhc--CCeEEEecCcHHHHHHhHhhhc-------ccHHH
Confidence            4899999999999999999999999999996532 333333332  4578999999998887766431       11111


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ++          .+..   .   .|+    ............++|||||++++.    ...+..+++.++...+++++.-
T Consensus       259 ih----------~ll~---~---~~~----~~~~~~~~~~~~dvlIIDEasml~----~~~~~~Ll~~~~~~~~lilvGD  314 (574)
T 3e1s_A          259 VH----------RLLG---Y---GPQ----GFRHNHLEPAPYDLLIVDEVSMMG----DALMLSLLAAVPPGARVLLVGD  314 (574)
T ss_dssp             HH----------HHTT---E---ETT----EESCSSSSCCSCSEEEECCGGGCC----HHHHHHHHTTSCTTCEEEEEEC
T ss_pred             HH----------HHHc---C---Ccc----hhhhhhcccccCCEEEEcCccCCC----HHHHHHHHHhCcCCCEEEEEec
Confidence            10          0000   0   000    001112233467999999999863    3456677777777777777644


Q ss_pred             e
Q 022383          215 T  215 (298)
Q Consensus       215 T  215 (298)
                      .
T Consensus       315 ~  315 (574)
T 3e1s_A          315 T  315 (574)
T ss_dssp             T
T ss_pred             c
Confidence            3

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.49  E-value=1.7e-06  Score=83.18  Aligned_cols=69  Identities=19%  Similarity=0.222  Sum_probs=54.5

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      ..+++.|.+++..++.+.-++|.||.|+|||.+..-.+...+..  .+.++++++||...++++.+++.+.
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~--~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKI--HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHH--HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhC--CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            45789999999999888889999999999997654333322221  2448999999999999999988765

>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=98.44  E-value=1.4e-06  Score=78.73  Aligned_cols=136  Identities=16%  Similarity=0.213  Sum_probs=80.1

Q ss_pred             HHCCCCCChHHHHHHHHHhhc----C-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           49 YQYGFEKPSAIQQRAVMPIIK----G-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        49 ~~~~~~~~~~~Q~~~~~~~~~----~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      ..+.|..+++-|++++..+..    + ..+++.|+.|+|||... ..++..+.... ...+++++||...+..+.+.+  
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~-~~~il~~a~T~~Aa~~l~~~~--   94 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTG-ETGIILAAPTHAAKKILSKLS--   94 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTT-CCCEEEEESSHHHHHHHHHHH--
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcC-CceEEEecCcHHHHHHHHhhh--
Confidence            446788999999999997653    2 48999999999999654 34444443322 136899999998887776644  


Q ss_pred             hhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHH
Q 022383          124 IGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (298)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i  199 (298)
                           +.....+++       ...+.    .....+..          .....+...+++||||++.+.    ...+..+
T Consensus        95 -----~~~~~T~h~-------~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~iiiDE~~~~~----~~~~~~l  148 (459)
T 3upu_A           95 -----GKEASTIHS-------ILKINPVTYEENVLFEQ----------KEVPDLAKCRVLICDEVSMYD----RKLFKIL  148 (459)
T ss_dssp             -----SSCEEEHHH-------HHTEEEEECSSCEEEEE----------CSCCCCSSCSEEEESCGGGCC----HHHHHHH
T ss_pred             -----ccchhhHHH-------HhccCcccccccchhcc----------cccccccCCCEEEEECchhCC----HHHHHHH
Confidence                 111211110       00000    00000000          112345678999999999763    2344556


Q ss_pred             HHhCCCCccEEEEEe
Q 022383          200 YRYLPPDLQVVLISA  214 (298)
Q Consensus       200 ~~~~~~~~~~v~~SA  214 (298)
                      .+.++...+++++.-
T Consensus       149 ~~~~~~~~~~~~vGD  163 (459)
T 3upu_A          149 LSTIPPWCTIIGIGD  163 (459)
T ss_dssp             HHHSCTTCEEEEEEC
T ss_pred             HHhccCCCEEEEECC
Confidence            666665566666543

>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=98.42  E-value=3e-06  Score=81.39  Aligned_cols=69  Identities=20%  Similarity=0.187  Sum_probs=54.2

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      ..+++.|.+++..++.+.-.+|.||+|+|||....- ++..+... .+.++++++||..-++++.+.+.+.
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~-~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSAT-IVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHH-HHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHH-HHHHHHHc-CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            357899999999998888899999999999976443 33333321 3458999999999999999887654

>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=98.20  E-value=0.00013  Score=68.57  Aligned_cols=70  Identities=16%  Similarity=0.212  Sum_probs=55.0

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      ..+++-|.+++..  .+..++|.|+.|||||.+..--+...+.... ...+++++++|+..+.++.+++.+..
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            4689999999973  3678999999999999876555555444322 23489999999999999999998764

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=97.95  E-value=1.8e-05  Score=62.61  Aligned_cols=71  Identities=13%  Similarity=0.095  Sum_probs=46.2

Q ss_pred             HhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          225 TKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       225 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..++.+|..+.+........++.+.++.++... |...+..++.... +++||||+++..++.+++.|+..|+
T Consensus         9 ~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~~~-K~~~L~~~l~~~~-~~~lVF~~~~~~~~~l~~~L~~~g~   79 (191)
T 2p6n_A            9 SGVDLGTENLYFQSMGAASLDVIQEVEYVKEEA-KMVYLLECLQKTP-PPVLIFAEKKADVDAIHEYLLLKGV   79 (191)
T ss_dssp             -------------------CCSEEEEEECCGGG-HHHHHHHHHTTSC-SCEEEECSCHHHHHHHHHHHHHHTC
T ss_pred             ccccCCCEEEEECCCCCCCcCceEEEEEcChHH-HHHHHHHHHHhCC-CCEEEEECCHHHHHHHHHHHHHcCC
Confidence            457788888888777777889999999988776 9999999998753 6899999999999999999988765

>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=97.80  E-value=0.00015  Score=63.50  Aligned_cols=71  Identities=13%  Similarity=0.123  Sum_probs=55.9

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      .+.|+|..++..+...+-+++..+-+.|||.+....++...... .+..++++.|+..-+..+.+.++.+..
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 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS-SSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            58999999998776567799999999999987666555433332 345799999999999988888877654

>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=97.79  E-value=5.2e-05  Score=58.98  Aligned_cols=57  Identities=35%  Similarity=0.656  Sum_probs=50.7

Q ss_pred             cCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       241 ~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..+.++.|.++.++....|...+..+++....+++||||++++.|+.++..|+..|+
T Consensus         3 ~~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~   59 (175)
T 2rb4_A            3 LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGH   59 (175)
T ss_dssp             CCBCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTC
T ss_pred             CccCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCC
Confidence            345789999999998777999999999988888999999999999999999988764

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=97.73  E-value=7.1e-05  Score=57.47  Aligned_cols=56  Identities=27%  Similarity=0.261  Sum_probs=49.1

Q ss_pred             cCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       241 ~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ....++.+.++.++... |...+..+++....+++||||++++.++.+++.|+..|+
T Consensus         5 ~~~~~i~~~~~~~~~~~-K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~   60 (163)
T 2hjv_A            5 LTTRNIEHAVIQVREEN-KFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGY   60 (163)
T ss_dssp             -CCCCEEEEEEECCGGG-HHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             cCcccceEEEEECChHH-HHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCC
Confidence            45667999999988776 999999999988888999999999999999999988765

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=97.68  E-value=0.00011  Score=56.59  Aligned_cols=54  Identities=52%  Similarity=0.831  Sum_probs=47.1

Q ss_pred             CCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          244 EGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       244 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .++.|.++.++..+.|...+..+++....+++||||++++.++.++..|+..|+
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~   55 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKF   55 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTC
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCC
Confidence            357888998887777999999999988888999999999999999999988764

>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=97.55  E-value=0.0014  Score=61.05  Aligned_cols=73  Identities=12%  Similarity=0.142  Sum_probs=57.0

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccC
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI  128 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~  128 (298)
                      .++|+|..++..+...+-+++..+-|.|||.+....++..+... .+..++++.|+...+..+.+.++.+....
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~-~~~~i~~va~t~~qA~~~~~~i~~~i~~~  235 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIELL  235 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS-SSCEEEEEESSHHHHHHHHHHHHHHHTTS
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC-CCCeEEEEECCHHHHHHHHHHHHHHHHhC
Confidence            48999999998876667899999999999987665444444332 24589999999999999998888776443

>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=97.54  E-value=0.00025  Score=55.70  Aligned_cols=57  Identities=25%  Similarity=0.199  Sum_probs=48.4

Q ss_pred             ccCcCCceEEEEEecCccchHHHHHHHHhhC-CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       240 ~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .....++.+.++.++... |...+..+++.. +.+++||||++++.++.+++.|+..|+
T Consensus        14 ~~~~~~i~q~~~~v~~~~-K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~   71 (185)
T 2jgn_A           14 GSTSENITQKVVWVEESD-KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGY   71 (185)
T ss_dssp             --CCTTEEEEEEECCGGG-HHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCceEEEEEeCcHH-HHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCC
Confidence            345678999999998776 999999999876 467999999999999999999988765

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.45  E-value=0.00052  Score=60.94  Aligned_cols=85  Identities=24%  Similarity=0.185  Sum_probs=52.3

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH  150 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (298)
                      +-.++.|+.|+|||....    +.+..    ...+|++||+++++++.+.+.+.+..                      .
T Consensus       162 ~v~~I~G~aGsGKTt~I~----~~~~~----~~~lVlTpT~~aa~~l~~kl~~~~~~----------------------~  211 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEIL----SRVNF----EEDLILVPGRQAAEMIRRRANASGII----------------------V  211 (446)
T ss_dssp             EEEEEEECTTSCHHHHHH----HHCCT----TTCEEEESCHHHHHHHHHHHTTTSCC----------------------C
T ss_pred             cEEEEEcCCCCCHHHHHH----HHhcc----CCeEEEeCCHHHHHHHHHHhhhcCcc----------------------c
Confidence            357889999999997642    22221    24699999999999988866432100                      0


Q ss_pred             CCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       151 ~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      ....-|.|-++++.  +.........+.+||||+-++
T Consensus       212 ~~~~~V~T~dsfL~--~~~~~~~~~~d~liiDE~sm~  246 (446)
T 3vkw_A          212 ATKDNVRTVDSFLM--NYGKGARCQFKRLFIDEGLML  246 (446)
T ss_dssp             CCTTTEEEHHHHHH--TTTSSCCCCCSEEEEETGGGS
T ss_pred             cccceEEEeHHhhc--CCCCCCCCcCCEEEEeCcccC
Confidence            01223556655442  222222235799999999754

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.39  E-value=0.00092  Score=52.36  Aligned_cols=40  Identities=15%  Similarity=0.114  Sum_probs=26.9

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      .|+-.++.||+|+|||...+-.+......   +.+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~~~~~---g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEIYKLG---KKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHT---TCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEeecc
Confidence            35667899999999997755444333322   34788888874

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.37  E-value=0.00073  Score=52.52  Aligned_cols=19  Identities=26%  Similarity=0.524  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|+.+++.||+|+|||...
T Consensus        37 ~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4789999999999999543

>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=97.35  E-value=0.00032  Score=66.42  Aligned_cols=80  Identities=15%  Similarity=0.093  Sum_probs=58.9

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc-CCCCeEEEEEcCcHHHHHHHHHHHHHhhccC---Cc
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIGDFI---NI  130 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~---~~  130 (298)
                      .+++-|.+++..  .+.+++|.|+.|||||.+..--+...+.. .-...++++|+.|+..+.++.+++.+.....   ++
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~~~~~~~~   79 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGL   79 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSCTTTTTTS
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcCcccccCC
Confidence            478999999975  36789999999999998765545444433 2234589999999999999999998764322   35


Q ss_pred             eEEEEE
Q 022383          131 QAHACV  136 (298)
Q Consensus       131 ~~~~~~  136 (298)
                      .+.+++
T Consensus        80 ~v~Tfh   85 (673)
T 1uaa_A           80 MISTFH   85 (673)
T ss_dssp             EEEEHH
T ss_pred             EEEeHH
Confidence            555544

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.22  E-value=0.002  Score=48.23  Aligned_cols=21  Identities=19%  Similarity=0.139  Sum_probs=17.5

Q ss_pred             hcCCcEEEEcCCCCchHHHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~   88 (298)
                      ..+.++++.||+|+|||..+-
T Consensus        22 ~~~~~vll~G~~GtGKt~lA~   42 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGAR   42 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHHH
Confidence            466899999999999996543

>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=97.19  E-value=0.00085  Score=64.00  Aligned_cols=81  Identities=15%  Similarity=0.134  Sum_probs=59.4

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHhhcc--CCc
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAIGDF--INI  130 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~~~~--~~~  130 (298)
                      ..+++-|.+++.+  .+.+++|.|+.|||||.+..--+...+.... ...++++++.|+..+.++.+++.++...  .++
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~~~~~~   87 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDV   87 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGGGGTTS
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhcccccCc
Confidence            4689999999876  3578999999999999876555555444322 3347999999999999999998876422  245


Q ss_pred             eEEEEE
Q 022383          131 QAHACV  136 (298)
Q Consensus       131 ~~~~~~  136 (298)
                      .+.+++
T Consensus        88 ~v~Tfh   93 (724)
T 1pjr_A           88 WISTFH   93 (724)
T ss_dssp             EEEEHH
T ss_pred             EEeeHH
Confidence            555543

>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=97.17  E-value=0.0012  Score=52.08  Aligned_cols=40  Identities=10%  Similarity=0.121  Sum_probs=27.7

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      .|+-.++.||+|+|||.+.+-.+.+....   +.+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~~~~---g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRAKIA---KQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEecc
Confidence            45667889999999997765444443322   45788888874

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.16  E-value=0.00032  Score=53.01  Aligned_cols=18  Identities=22%  Similarity=0.510  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCCchHHH
Q 022383           69 KGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~   86 (298)
                      .|+.+++.||+|+|||..
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            688999999999999954

>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=97.15  E-value=0.00049  Score=55.60  Aligned_cols=113  Identities=13%  Similarity=0.095  Sum_probs=59.7

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      .|.-+++.||+|+|||.+.+-.+......   +.+++++.|...-  . .  ...+....++..                
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~---g~kVli~~~~~d~--r-~--~~~i~srlG~~~----------------   66 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYA---DVKYLVFKPKIDT--R-S--IRNIQSRTGTSL----------------   66 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEEECCCG--G-G--CSSCCCCCCCSS----------------
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhc---CCEEEEEEeccCc--h-H--HHHHHHhcCCCc----------------
Confidence            45668889999999997755444443322   4478888765421  0 0  001111112110                


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                         ..+-+.+.+.+...+... ..-...++|||||++.+.. .....+..+.+   .+.++++..
T Consensus        67 ---~~~~~~~~~~i~~~i~~~-~~~~~~dvViIDEaQ~l~~-~~ve~l~~L~~---~gi~Vil~G  123 (223)
T 2b8t_A           67 ---PSVEVESAPEILNYIMSN-SFNDETKVIGIDEVQFFDD-RICEVANILAE---NGFVVIISG  123 (223)
T ss_dssp             ---CCEEESSTHHHHHHHHST-TSCTTCCEEEECSGGGSCT-HHHHHHHHHHH---TTCEEEEEC
T ss_pred             ---cccccCCHHHHHHHHHHH-hhCCCCCEEEEecCccCcH-HHHHHHHHHHh---CCCeEEEEe
Confidence               123345566666666543 2234689999999987532 22333433333   245555443

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.15  E-value=0.0017  Score=55.86  Aligned_cols=33  Identities=21%  Similarity=0.313  Sum_probs=24.6

Q ss_pred             ChHHHHHHHHHhh----cCC---cEEEEcCCCCchHHHHH
Q 022383           56 PSAIQQRAVMPII----KGR---DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        56 ~~~~Q~~~~~~~~----~~~---~~li~~pTG~GKT~~~~   88 (298)
                      ++|||.+++..+.    +|+   .+++.||.|+|||....
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~   42 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIY   42 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHH
Confidence            4678888876654    443   48999999999996654

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.15  E-value=0.0027  Score=53.09  Aligned_cols=55  Identities=18%  Similarity=0.253  Sum_probs=34.3

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH--hhcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP--IIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~--~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+..++.+.+.- ..+. ...+.+..  +..++.+++.||+|+|||...
T Consensus        12 ~~~~~~~i~G~~~~~~~l~~~~-~~~~-~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           12 PNVRYEDIGGLEKQMQEIREVV-ELPL-KHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHT-HHHH-HCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHH-HHHh-hCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            3467899877777777776631 1111 11122222  235678999999999999653

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.11  E-value=0.0032  Score=53.62  Aligned_cols=41  Identities=10%  Similarity=0.280  Sum_probs=25.0

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHh---CCCCccEEEEEeeCc
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRY---LPPDLQVVLISATLP  217 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~---~~~~~~~v~~SAT~~  217 (298)
                      ...-+|++||+|.+.+   .+.+..+++.   -....-+|++++|+.
T Consensus       131 ~~~~ii~lDE~d~l~~---q~~L~~l~~~~~~~~s~~~vI~i~n~~d  174 (318)
T 3te6_A          131 KRKTLILIQNPENLLS---EKILQYFEKWISSKNSKLSIICVGGHNV  174 (318)
T ss_dssp             SCEEEEEEECCSSSCC---THHHHHHHHHHHCSSCCEEEEEECCSSC
T ss_pred             CCceEEEEecHHHhhc---chHHHHHHhcccccCCcEEEEEEecCcc
Confidence            3456899999999872   3334444432   122445667787763

>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=97.11  E-value=0.0053  Score=48.68  Aligned_cols=40  Identities=15%  Similarity=0.292  Sum_probs=26.0

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ..-.++|+||+|.+... ....+..+++..+.+..+++.|.
T Consensus       101 ~~~~vliiDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~~~  140 (226)
T 2chg_A          101 APFKIIFLDEADALTAD-AQAALRRTMEMYSKSCRFILSCN  140 (226)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             cCceEEEEeChhhcCHH-HHHHHHHHHHhcCCCCeEEEEeC
Confidence            45679999999987433 34455666666655565555443

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.07  E-value=0.0014  Score=52.34  Aligned_cols=40  Identities=18%  Similarity=0.189  Sum_probs=27.6

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      |+-.++.||.|+|||.+.+-.+.+....   +.+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~---g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFA---KQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEeccC
Confidence            4556789999999998766555554433   457899988753

>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=97.04  E-value=0.0013  Score=66.41  Aligned_cols=67  Identities=19%  Similarity=0.300  Sum_probs=54.8

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC---CCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS---REVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~---~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      .+++-|.+++..-  +++++|.|+.|||||.+.+--++..+....   ...+++++++|++.+.++.+++..
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~   79 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAE   79 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHH
Confidence            4899999998754  889999999999999887666666655532   334899999999999999988876

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.95  E-value=0.0037  Score=54.44  Aligned_cols=29  Identities=34%  Similarity=0.441  Sum_probs=19.6

Q ss_pred             CccEEEechhhHhhccc-cHHHHHHHHHhC
Q 022383          175 AIKLLVLDESDEMLSRG-FKDQIYDVYRYL  203 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~-~~~~i~~i~~~~  203 (298)
                      ...+||+||+|.+.... ....+..+++..
T Consensus       130 ~~~vlilDEi~~l~~~~~~~~~l~~l~~~~  159 (387)
T 2v1u_A          130 GIYIIVLDEIDFLPKRPGGQDLLYRITRIN  159 (387)
T ss_dssp             SEEEEEEETTTHHHHSTTHHHHHHHHHHGG
T ss_pred             CeEEEEEccHhhhcccCCCChHHHhHhhch
Confidence            45689999999986542 345555666544

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=96.90  E-value=0.0083  Score=49.77  Aligned_cols=18  Identities=28%  Similarity=0.442  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      +.+++.||+|+|||..+.
T Consensus        65 ~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            579999999999996543

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=96.89  E-value=0.0058  Score=52.13  Aligned_cols=18  Identities=28%  Similarity=0.440  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      +..+++.||+|+|||...
T Consensus        37 ~~~lll~G~~GtGKT~la   54 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLL   54 (324)
T ss_dssp             CSSEEEECSSSSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            468999999999999653

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.83  E-value=0.003  Score=47.12  Aligned_cols=20  Identities=10%  Similarity=0.177  Sum_probs=16.7

Q ss_pred             hhcCCcEEEEcCCCCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~   86 (298)
                      ...+.++++.||+|+|||..
T Consensus        24 ~~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHH
T ss_pred             hCCCCcEEEECCCCccHHHH
Confidence            34568999999999999953

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=96.79  E-value=0.0042  Score=50.12  Aligned_cols=40  Identities=13%  Similarity=0.173  Sum_probs=29.0

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      .|+-.++.|+.|+|||.+.+-.+.+....   +.+++++-|.+
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~~---g~kvli~kp~~   57 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYAK   57 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEEEETT
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHC---CCeEEEEeecC
Confidence            46678889999999998766555554433   45788888765

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=96.74  E-value=0.0072  Score=54.05  Aligned_cols=41  Identities=17%  Similarity=0.504  Sum_probs=24.0

Q ss_pred             CccEEEechhhHhhcc-ccHHHHHHHHHhC-CCCccEEEEEee
Q 022383          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYL-PPDLQVVLISAT  215 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~-~~~~~i~~i~~~~-~~~~~~v~~SAT  215 (298)
                      ..+++++||+|.+... .....+..++..+ ....++|+.|..
T Consensus       194 ~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             TCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             CCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            5679999999998653 2334444444433 334555554433

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.69  E-value=0.0041  Score=54.21  Aligned_cols=37  Identities=30%  Similarity=0.524  Sum_probs=22.3

Q ss_pred             EEEechhhHhhccccHHH-HHHHHHhCCCCccEEEEEee
Q 022383          178 LLVLDESDEMLSRGFKDQ-IYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       178 ~vViDE~h~~~~~~~~~~-i~~i~~~~~~~~~~v~~SAT  215 (298)
                      +||+||+|.+........ +..+.+.. .+..+|+.|..
T Consensus       136 vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~~  173 (384)
T 2qby_B          136 IIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISND  173 (384)
T ss_dssp             EEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECSS
T ss_pred             EEEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEECC
Confidence            999999999865432344 55555544 34445544433

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.68  E-value=0.013  Score=52.04  Aligned_cols=54  Identities=15%  Similarity=0.302  Sum_probs=37.3

Q ss_pred             ccccCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHH
Q 022383           30 EAITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~   86 (298)
                      +|..+|++++-.+..++.|++.   .+.+|..++..-   +...+.+++.||+|+|||+.
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g---~~~prGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMG---IRAPKGALMYGPPGTGKTLL  231 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHC---CCCCCEEEEESCTTSSHHHH
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeeEEECcCCCCHHHH
Confidence            4667999998888888888763   122333333322   22357899999999999964

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=96.63  E-value=0.015  Score=49.48  Aligned_cols=41  Identities=12%  Similarity=0.180  Sum_probs=25.9

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ....++++||+|.+........+..+++..+.+.++|+.+.
T Consensus       104 ~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n  144 (324)
T 3u61_B          104 GRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITAN  144 (324)
T ss_dssp             SCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEES
T ss_pred             CCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeC
Confidence            36789999999998622234555555665555566665433

>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=96.61  E-value=0.0043  Score=50.12  Aligned_cols=19  Identities=16%  Similarity=0.237  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .++.+++.||+|+|||...
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4678999999999999653

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=96.61  E-value=0.0072  Score=51.61  Aligned_cols=51  Identities=8%  Similarity=0.083  Sum_probs=33.0

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhh-----cCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII-----KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~-----~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+..++.|.+.- .  .|   ...+.+.     ..+.+++.||+|+|||..+
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i-~--~~---~~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAV-I--LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHT-H--HH---HHCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCCHHHhcChHHHHHHHHHHH-H--HH---HhCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            3457999987778888777641 1  11   1112221     2367999999999999654

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=96.60  E-value=0.009  Score=50.68  Aligned_cols=39  Identities=15%  Similarity=0.380  Sum_probs=25.7

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      .+-.++|+||+|.+... ....+..++...+.+..+++.+
T Consensus       109 ~~~~vliiDe~~~l~~~-~~~~L~~~le~~~~~~~~i~~~  147 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD-AQQALRRTMEMFSSNVRFILSC  147 (327)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCCeEEEEeCCCcCCHH-HHHHHHHHHHhcCCCCeEEEEe
Confidence            45689999999997433 3445556666665566665544

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.59  E-value=0.01  Score=52.09  Aligned_cols=54  Identities=22%  Similarity=0.334  Sum_probs=35.4

Q ss_pred             cccCcccCCCCHHHHHHHHHCC---CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~---~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      |..+|++.+=-+..++.|++.=   +.+|..++..-   +...+.+++.||+|+|||+.+
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~g---i~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLG---IAQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCCCEEEESCSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCceEEeCCCCCCHHHHH
Confidence            5579999987777888777641   11222222211   233588999999999999653

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.56  E-value=0.014  Score=49.27  Aligned_cols=17  Identities=29%  Similarity=0.413  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      .++++.||+|+|||...
T Consensus        68 ~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            57999999999999654

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.52  E-value=0.027  Score=48.49  Aligned_cols=43  Identities=5%  Similarity=0.344  Sum_probs=29.7

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCc
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLP  217 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~  217 (298)
                      .+.+++|+||+|.+ +......+..+++..+.+..+|+.|-.+.
T Consensus       133 ~~~~vlilDE~~~L-~~~~~~~L~~~le~~~~~~~~Il~t~~~~  175 (354)
T 1sxj_E          133 HRYKCVIINEANSL-TKDAQAALRRTMEKYSKNIRLIMVCDSMS  175 (354)
T ss_dssp             -CCEEEEEECTTSS-CHHHHHHHHHHHHHSTTTEEEEEEESCSC
T ss_pred             CCCeEEEEeCcccc-CHHHHHHHHHHHHhhcCCCEEEEEeCCHH
Confidence            46789999999994 44456667777777766666666665543

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.48  E-value=0.0079  Score=47.19  Aligned_cols=39  Identities=13%  Similarity=0.154  Sum_probs=27.3

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      .|+=.++.||+|+|||.-.+-.+-+....   +.+++++.|.
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~---~~kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHT---TCCEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEccc
Confidence            46778999999999996544444443333   3578888876

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=96.48  E-value=0.0055  Score=52.37  Aligned_cols=51  Identities=12%  Similarity=0.117  Sum_probs=32.3

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHh-----hcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPI-----IKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~-----~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|++++-.+.+++.|++.- .  .|.+   .+.+     ...+.+++.||+|+|||..+
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v-~--~p~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAV-I--LPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHH-H--HHHH---CGGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHH-H--HHHh---CHHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            3468999987777777776531 0  0110   1112     12368999999999999654

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=96.47  E-value=0.005  Score=53.69  Aligned_cols=16  Identities=31%  Similarity=0.447  Sum_probs=14.2

Q ss_pred             cEEEEcCCCCchHHHH
Q 022383           72 DVIAQAQSGTGKTSMI   87 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~   87 (298)
                      .+++.||+|+|||...
T Consensus        46 ~~li~G~~G~GKTtl~   61 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL   61 (389)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999654

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.45  E-value=0.013  Score=54.68  Aligned_cols=113  Identities=14%  Similarity=0.215  Sum_probs=71.9

Q ss_pred             CChHHHHHHHHHhhc--CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceE
Q 022383           55 KPSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQA  132 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~--~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~  132 (298)
                      .++.-|.+++..+..  ....++.|+-|.|||.+.-+ ++..+..     +++|.+|+.+-+..+.+...+         
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~-~~a~~~~-----~~~vtAP~~~a~~~l~~~~~~---------  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQ-LISRIAG-----RAIVTAPAKASTDVLAQFAGE---------  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHH-HHHHSSS-----CEEEECSSCCSCHHHHHHHGG---------
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHH-HHHHHHh-----CcEEECCCHHHHHHHHHHhhC---------
Confidence            688999999988775  34579999999999954433 3333322     368889998877655543211         


Q ss_pred             EEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          133 HACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                                          .+-...|+.+.   .    .....+++|||||=.+    -.+.+..++...    ..+++
T Consensus       240 --------------------~i~~~~Pd~~~---~----~~~~~dlliVDEAAaI----p~pll~~ll~~~----~~v~~  284 (671)
T 2zpa_A          240 --------------------KFRFIAPDALL---A----SDEQADWLVVDEAAAI----PAPLLHQLVSRF----PRTLL  284 (671)
T ss_dssp             --------------------GCCBCCHHHHH---H----SCCCCSEEEEETGGGS----CHHHHHHHHTTS----SEEEE
T ss_pred             --------------------CeEEeCchhhh---h----CcccCCEEEEEchhcC----CHHHHHHHHhhC----CeEEE
Confidence                                02223454432   1    1235899999999665    245555555533    36888


Q ss_pred             EeeCc
Q 022383          213 SATLP  217 (298)
Q Consensus       213 SAT~~  217 (298)
                      |.|+.
T Consensus       285 ~tTv~  289 (671)
T 2zpa_A          285 TTTVQ  289 (671)
T ss_dssp             EEEBS
T ss_pred             EecCC
Confidence            88873

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.44  E-value=0.075  Score=41.65  Aligned_cols=141  Identities=14%  Similarity=0.175  Sum_probs=72.2

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH-HHHHHHHHHHHhhccCCceEEEEEcCCch-HHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE-LATQTEKVILAIGDFINIQAHACVGGKSV-GEDIRK  147 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~  147 (298)
                      ...+++..++|.|||.+++-.++..+..   +.+|+|+.-.+. .-..-.+.++++    ++.......+-.. ......
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~---G~rV~~vQF~Kg~~~~gE~~~l~~L----~v~~~~~g~gf~~~~~~~~~  100 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGH---GKNVGVVQFIKGTWPNGERNLLEPH----GVEFQVMATGFTWETQNREA  100 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHT---TCCEEEEESSCCSSCCHHHHHHGGG----TCEEEECCTTCCCCGGGHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEEeeCCCCCccHHHHHHhC----CcEEEEcccccccCCCCcHH
Confidence            4589999999999999887777776655   557888743321 000001112222    2222211111100 000000


Q ss_pred             hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc--HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHH
Q 022383          148 LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (298)
Q Consensus       148 ~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~  225 (298)
                      -.       ........... ..+.-..+++||+||+-.....++  .+.+..++...+....+|+.+--.++.+.+...
T Consensus       101 ~~-------~~a~~~l~~a~-~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e~AD  172 (196)
T 1g5t_A          101 DT-------AACMAVWQHGK-RMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLAD  172 (196)
T ss_dssp             HH-------HHHHHHHHHHH-HHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHCS
T ss_pred             HH-------HHHHHHHHHHH-HHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHHhCc
Confidence            00       00011111111 123336789999999977655543  456667777777666666665556666665543

>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=96.39  E-value=0.0086  Score=50.59  Aligned_cols=56  Identities=16%  Similarity=0.290  Sum_probs=33.3

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHH-HhhcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVM-PIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~-~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+..++.|.+.- ..+..+...... .+..++.+++.||+|+|||...
T Consensus        10 ~~~~~~di~G~~~~~~~l~~~v-~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           10 PQVTWEDIGGLEDVKRELQELV-QYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHH-HHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHH-HHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            3468899876777777776531 101101111111 1235678999999999999654

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=96.39  E-value=0.028  Score=47.53  Aligned_cols=39  Identities=13%  Similarity=0.234  Sum_probs=25.4

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...+++||||+|.|.... .+.+...++.-+++..+|+.+
T Consensus        81 ~~~kvviIdead~lt~~a-~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           81 YTRKYVIVHDCERMTQQA-ANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             SSSEEEEETTGGGBCHHH-HHHTHHHHHSCCTTEEEEEEE
T ss_pred             CCceEEEeccHHHhCHHH-HHHHHHHHhCCCCCeEEEEEE
Confidence            467899999999985443 344555666555555555554

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.33  E-value=0.016  Score=51.43  Aligned_cols=129  Identities=15%  Similarity=0.274  Sum_probs=65.6

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc--CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~--p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      +-++++||+|+|||......+.. +..  .+.+++++.  +.+.-+.   +.+..++...++.+.....+..        
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~-l~~--~G~kVllv~~D~~r~~a~---eqL~~~~~~~gv~~~~~~~~~d--------  163 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYF-YKK--RGYKVGLVAADVYRPAAY---DQLLQLGNQIGVQVYGEPNNQN--------  163 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHH-HHH--TTCCEEEEEECCSCHHHH---HHHHHHHHTTTCCEECCTTCSC--------
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH-HHH--cCCeEEEEecCccchhHH---HHHHHHHHhcCCceeeccccCC--------
Confidence            35788899999999765433322 222  244666655  3333332   2333344444544332211111        


Q ss_pred             hcCCcEEEeChHHHH-HHHhccCccCCCccEEEechhhHhh---ccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHH
Q 022383          149 EHGVHVVSGTPGRVC-DMIKRKTLRTRAIKLLVLDESDEML---SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMT  224 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~-~~~~~~~~~~~~l~~vViDE~h~~~---~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~  224 (298)
                                |..+. ..+..  ......+++|||++-...   +..+...+..+.+...+..-++.++|+.........
T Consensus       164 ----------p~~i~~~al~~--a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a  231 (433)
T 3kl4_A          164 ----------PIEIAKKGVDI--FVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLA  231 (433)
T ss_dssp             ----------HHHHHHHHHHH--TTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHH
T ss_pred             ----------HHHHHHHHHHH--HHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHH
Confidence                      21111 11111  122467888888886543   223455666666666556666777887655444444


Q ss_pred             H
Q 022383          225 T  225 (298)
Q Consensus       225 ~  225 (298)
                      .
T Consensus       232 ~  232 (433)
T 3kl4_A          232 S  232 (433)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.29  E-value=0.02  Score=43.95  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      .+++++.||+|+|||...
T Consensus        43 ~~~vll~G~~G~GKT~la   60 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIV   60 (187)
T ss_dssp             SCEEEEESCGGGCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            468999999999999654

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.27  E-value=0.043  Score=48.64  Aligned_cols=55  Identities=22%  Similarity=0.230  Sum_probs=34.6

Q ss_pred             ccccCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           30 EAITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .|..+|++.+--+..++.|.+.   .+.+|..++..   -+...+.+++.||+|+|||+.+
T Consensus       166 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~---g~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQI---GIDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCceEEEECCCCCCHHHHH
Confidence            3456899998777777777663   11222222221   1234578999999999999653

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.27  E-value=0.0059  Score=48.69  Aligned_cols=40  Identities=10%  Similarity=0.098  Sum_probs=27.2

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      .|.-.++.||.|+|||...+-.+ ......  +.+++++.|..
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~~-~r~~~~--g~kvli~kp~~   66 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRRL-RRGIYA--KQKVVVFKPAI   66 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH-HHHHHT--TCCEEEEEEC-
T ss_pred             CceEEEEECCCCCCHHHHHHHHH-HHHHHc--CCceEEEEecc
Confidence            46667899999999997655444 333332  44788888865

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.23  E-value=0.038  Score=43.39  Aligned_cols=17  Identities=24%  Similarity=0.479  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      +++++.||+|+|||...
T Consensus        55 ~~~~l~G~~GtGKT~la   71 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL   71 (202)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            78999999999999653

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.23  E-value=0.026  Score=48.40  Aligned_cols=39  Identities=21%  Similarity=0.425  Sum_probs=26.7

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...+++|+||+|.+... -...+..+++..+....+++.+
T Consensus       109 ~~~~viiiDe~~~l~~~-~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADAMTNA-AQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCHH-HHHHHHHHHhcCCCCeEEEEEe
Confidence            35789999999998543 3455666777766666665544

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.21  E-value=0.042  Score=46.94  Aligned_cols=17  Identities=24%  Similarity=0.518  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      .++++.||+|+|||..+
T Consensus        56 ~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            58999999999999654

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=96.19  E-value=0.093  Score=41.83  Aligned_cols=39  Identities=13%  Similarity=0.239  Sum_probs=22.6

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ..-.+||+||+|.+... ....+...+...+....+|+.|
T Consensus       125 ~~~~vlviDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~t  163 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLAT  163 (250)
T ss_dssp             SSSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEE
T ss_pred             CCceEEEEECcccccHH-HHHHHHHHHhcCCCceEEEEEe
Confidence            34579999999986332 2344444555444445455444

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.16  E-value=0.0095  Score=51.72  Aligned_cols=18  Identities=28%  Similarity=0.558  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      ++.+++.||+|+|||...
T Consensus        45 ~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            568999999999999653

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.14  E-value=0.017  Score=49.57  Aligned_cols=40  Identities=20%  Similarity=0.295  Sum_probs=26.1

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ....++++||+|.+... ....+..+++..+....+++.+.
T Consensus       132 ~~~~vliiDE~~~l~~~-~~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          132 PPYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             CSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCceEEEEECCCccCHH-HHHHHHHHHHhcCCCceEEEEeC
Confidence            35579999999987533 34555666666665665665443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.06  E-value=0.052  Score=48.39  Aligned_cols=56  Identities=18%  Similarity=0.243  Sum_probs=36.4

Q ss_pred             ccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH--hhcCCcEEEEcCCCCchHHHH
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMP--IIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~--~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .|..+|++.+-.+..++.|++.= ..|. ..-+.+..  +...+.+++.||+|+|||+.+
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V-~~pl-~~pe~f~~~Gi~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVV-ELPL-LSPERFATLGIDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHT-HHHH-HCHHHHHHHTCCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHH-HHHh-cCHHHHHHCCCCCCCceEeeCCCCCcHHHHH
Confidence            45578999988888888887741 1111 11122222  234589999999999999643

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.02  E-value=0.014  Score=51.91  Aligned_cols=55  Identities=24%  Similarity=0.380  Sum_probs=35.0

Q ss_pred             ccccCcccCCCCHHHHHHHHHCC---CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           30 EAITSFDAMGIKDDLLRGIYQYG---FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~~---~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .|..+|++.+-.+..++.|++.=   +.+|..++..-   +...+.+++.||+|+|||+.+
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g---~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVG---IKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeEEEECCCCCcHHHHH
Confidence            45568999987777777776631   12222222111   234589999999999999653

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=95.92  E-value=0.038  Score=49.98  Aligned_cols=43  Identities=19%  Similarity=0.289  Sum_probs=27.9

Q ss_pred             ccEEEechhhHhhccc----------cHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          176 IKLLVLDESDEMLSRG----------FKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       176 l~~vViDE~h~~~~~~----------~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      ...+++||+|.+....          ....+..++........++++.||-.+
T Consensus       298 p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~  350 (489)
T 3hu3_A          298 PAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP  350 (489)
T ss_dssp             SEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCG
T ss_pred             CcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCc
Confidence            4689999999986431          223444555555556667777787544

>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=95.91  E-value=0.048  Score=44.58  Aligned_cols=52  Identities=15%  Similarity=0.205  Sum_probs=29.4

Q ss_pred             cCcccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~--~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .+|+++.-.+..++.++++-  +..+..+...   .+...+.+++.||+|+|||...
T Consensus         3 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---g~~~~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A            3 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQL---GAKVPKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCCC---------CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHc---CCCCCceEEEECCCCCCHHHHH
Confidence            46777766666666665521  1111111111   1123578999999999999654

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=95.87  E-value=0.041  Score=46.05  Aligned_cols=54  Identities=11%  Similarity=0.115  Sum_probs=32.0

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHH-HHHHHHh-hcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQ-QRAVMPI-IKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q-~~~~~~~-~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+...+.+.+.- .  .+.. .+.+..+ ..++.+++.||+|+|||..+
T Consensus        16 ~~~~~~~i~G~~~~~~~l~~~i-~--~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           16 AKVEWTDIAGQDVAKQALQEMV-I--LPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             SCCCGGGSCCCHHHHHHHHHHT-H--HHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHH-H--hhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHH
Confidence            3457888876777777776531 1  0000 0011111 13578999999999999654

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.84  E-value=0.048  Score=48.17  Aligned_cols=55  Identities=22%  Similarity=0.332  Sum_probs=35.9

Q ss_pred             ccccCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           30 EAITSFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        30 ~~~~~~~~l~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .+..+|++++=-+..++.|++.   .+.+|..++..-   +...+.+++.||+|+|||+.+
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~G---i~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMG---IKPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHT---CCCCSEEEEESSTTTTHHHHH
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCCCceECCCCchHHHHH
Confidence            4567999998666777777663   123343333222   223578999999999999643

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.59  E-value=0.0086  Score=50.83  Aligned_cols=18  Identities=17%  Similarity=0.390  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      ++++++.||+|+|||...
T Consensus       152 ~~~lll~G~~GtGKT~La  169 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLL  169 (308)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            589999999999999654

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=95.49  E-value=0.17  Score=44.95  Aligned_cols=58  Identities=17%  Similarity=0.145  Sum_probs=32.9

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc--CcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS--PTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~--p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .-++++|++|+|||....-.+. .+..  .+.+++++.  |.+.-+   .+.++.++...++.+..
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA~-~l~~--~G~kVllv~~D~~R~aa---~eqL~~~~~~~gvpv~~  160 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLAR-YFQK--RGYKVGVVCSDTWRPGA---YHQLRQLLDRYHIEVFG  160 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH-HHHT--TTCCEEEEECCCSSTHH---HHHHHHHHGGGTCEEEC
T ss_pred             eEEEEECcCCCCHHHHHHHHHH-HHHH--CCCeEEEEeCCCcchhH---HHHHHHHHHhcCCcEEe
Confidence            3578899999999976543332 2222  244566665  444433   23444555555665543

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=95.44  E-value=0.032  Score=49.84  Aligned_cols=54  Identities=11%  Similarity=0.095  Sum_probs=31.7

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHH-HHHH-HhhcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQ-RAVM-PIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~-~~~~-~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+.+.+.|...-.   .|... +.+. .....+.+++.||+|+|||..+
T Consensus       129 ~~~~~~di~G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          129 PNVKWSDVAGLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHT---HHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHH---HHhhCHHHhhccCCCCceEEEECCCCCCHHHHH
Confidence            45678888766677777665310   01000 0000 1123478999999999999654

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.44  E-value=0.053  Score=45.74  Aligned_cols=39  Identities=15%  Similarity=0.298  Sum_probs=25.0

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      +-.++||||+|.+.... ...+..+++..+.+..+++.|.
T Consensus       107 ~~~viiiDe~~~l~~~~-~~~L~~~le~~~~~~~~il~~~  145 (323)
T 1sxj_B          107 KHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFACN  145 (323)
T ss_dssp             CCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEES
T ss_pred             CceEEEEECcccCCHHH-HHHHHHHHhccCCCceEEEEeC
Confidence            46899999999975432 3344555566555566666543

>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=95.34  E-value=0.13  Score=39.35  Aligned_cols=73  Identities=16%  Similarity=0.139  Sum_probs=55.3

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++..+..+...+++.    ++.+..++|+.+..+....+    .+..+|+|+|.      .-..++++..+
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~------~~~~Gid~~~~  103 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN------VCARGIDVKQV  103 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC------SCCTTTCCTTE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec------chhcCCCcccC
Confidence            458999999999999999888764    67888999988766554333    25678999994      12356888899


Q ss_pred             cEEEech
Q 022383          177 KLLVLDE  183 (298)
Q Consensus       177 ~~vViDE  183 (298)
                      ++||.-+
T Consensus       104 ~~Vi~~d  110 (175)
T 2rb4_A          104 TIVVNFD  110 (175)
T ss_dssp             EEEEESS
T ss_pred             CEEEEeC
Confidence            9988543

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=95.27  E-value=0.081  Score=45.72  Aligned_cols=51  Identities=8%  Similarity=0.062  Sum_probs=29.0

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHh-----hcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPI-----IKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~-----~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+..++.|...- .  .+   .-.+.+     ...+.+++.||+|+|||..+
T Consensus        46 ~~~~~~di~G~~~~~~~l~~~v-~--~~---~~~~~~~~~~~~~~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           46 PNVKWEDVAGLEGAKEALKEAV-I--LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             -CCCGGGSCCGGGHHHHHHHHT-H--HH---HHCGGGGCSSCCCCCCEEEECSTTSCHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHH-H--HH---HhCHHHHhcCCCCCceEEEECCCCCcHHHHH
Confidence            3457777765555666655421 0  00   001111     12367999999999999654

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=95.18  E-value=0.56  Score=35.21  Aligned_cols=74  Identities=12%  Similarity=0.164  Sum_probs=55.7

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++..+..+.+.++..    ++.+..++|+.+..+....+    .+..+|+|+|.      .-..++++..+
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gld~~~~  104 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD------VAARGIDIENI  104 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG------GGTTTCCCSCC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC------hhhcCCchhcC
Confidence            347999999999999999988775    67888999987766554333    24678999994      12346788889


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||.-+.
T Consensus       105 ~~Vi~~~~  112 (163)
T 2hjv_A          105 SLVINYDL  112 (163)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEeCC
Confidence            99887544

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=95.15  E-value=0.16  Score=43.83  Aligned_cols=39  Identities=13%  Similarity=0.239  Sum_probs=23.8

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ....++||||+|.+... ....+...++..+.+..+|+.+
T Consensus       118 ~~~~vliiDe~~~l~~~-~~~~Ll~~le~~~~~~~~Il~~  156 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLAT  156 (373)
T ss_dssp             SSSEEEEEECGGGSCHH-HHHHHHHHHHSCCSSEEEEEEE
T ss_pred             CCeEEEEEECcchhcHH-HHHHHHHHHhcCCCceEEEEEe
Confidence            45679999999997433 2344455555554444444444

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=95.10  E-value=0.11  Score=45.33  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      .+++++.||+|+|||..+
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999654

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=95.06  E-value=0.033  Score=46.90  Aligned_cols=41  Identities=22%  Similarity=0.391  Sum_probs=25.5

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +|+++--.+...+.+.+. +..            ....++++.||+|+|||...
T Consensus        15 ~~~~~~g~~~~~~~l~~~-l~~------------~~~~~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           15 TLDEVVGQDEVIQRLKGY-VER------------KNIPHLLFSGPPGTGKTATA   55 (319)
T ss_dssp             SGGGSCSCHHHHHHHHTT-TTT------------TCCCCEEEESSSSSSHHHHH
T ss_pred             CHHHHhCCHHHHHHHHHH-HhC------------CCCCeEEEECcCCcCHHHHH
Confidence            456655555666665543 110            12236999999999999654

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=94.99  E-value=0.14  Score=44.27  Aligned_cols=19  Identities=26%  Similarity=0.368  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      .+.+++.||+|+|||..+-
T Consensus       117 ~~~vLl~GppGtGKT~la~  135 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIGK  135 (357)
T ss_dssp             CSEEEEESSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4789999999999996543

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=94.95  E-value=0.18  Score=38.11  Aligned_cols=74  Identities=12%  Similarity=0.118  Sum_probs=55.3

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++.-+..+...+++.    ++.+..++|+.+..+....+    .+..+|+|+|.      .-..++++..+
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~G~d~~~~   99 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD------LLARGIDVQQV   99 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG------GGTTTCCCCSC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC------hhhcCCCcccC
Confidence            347999999999999999988764    67888899987766554333    25678999994      12346788888


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||.-+.
T Consensus       100 ~~Vi~~~~  107 (165)
T 1fuk_A          100 SLVINYDL  107 (165)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEeCC
Confidence            98887543

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=94.95  E-value=0.16  Score=40.40  Aligned_cols=52  Identities=12%  Similarity=0.103  Sum_probs=28.2

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      ..|.-+++.||+|+|||......+......   +..++++.... ...++...+..
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~---~~~v~~~~~~~-~~~~~~~~~~~   72 (235)
T 2w0m_A           21 PQGFFIALTGEPGTGKTIFSLHFIAKGLRD---GDPCIYVTTEE-SRDSIIRQAKQ   72 (235)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHHHHHHH---TCCEEEEESSS-CHHHHHHHHHH
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHHHHHHHC---CCeEEEEEccc-CHHHHHHHHHH
Confidence            356789999999999995433222122211   23566665322 23444444443

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.95  E-value=0.097  Score=46.85  Aligned_cols=142  Identities=16%  Similarity=0.186  Sum_probs=65.7

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHH--
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED--  144 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  144 (298)
                      +..|.-+++.|++|+|||.-.+-.+.+.....  +..++|+..-.. ..++..++..........- ...|.....+.  
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~--g~~Vl~~s~E~s-~~~l~~r~~~~~~~~~~~~-l~~g~l~~~~~~~  275 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATKT--NENVAIFSLEMS-AQQLVMRMLCAEGNINAQN-LRTGKLTPEDWGK  275 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHHS--SCCEEEEESSSC-HHHHHHHHHHHHHTCCHHH-HHTSCCCHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEEECCCC-HHHHHHHHHHHHcCCCHHH-HhcCCCCHHHHHH
Confidence            34567789999999999955443333332221  335777764321 2344444321100101000 00111121111  


Q ss_pred             ----HHHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhccc-----cHHHHHHHHHhCC-----C
Q 022383          145 ----IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRG-----FKDQIYDVYRYLP-----P  205 (298)
Q Consensus       145 ----~~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~-----~~~~i~~i~~~~~-----~  205 (298)
                          ...+. ..++.+.     |.+.+...++.- ..-..+++||||+.+.+....     ....+..+.+.+.     .
T Consensus       276 ~~~a~~~l~-~~~l~i~d~~~~s~~~i~~~~~~l-~~~~~~~livID~l~~~~~~~~~~~~~~~~i~~i~~~Lk~lAke~  353 (454)
T 2r6a_A          276 LTMAMGSLS-NAGIYIDDTPSIRVSDIRAKCRRL-KQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALAREL  353 (454)
T ss_dssp             HHHHHHHHH-SSCEEEECCTTCCHHHHHHHHHHH-HTTTCCCEEEEECGGGSCCSCC----CHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHH-HHHcCCCEEEEccHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence                11122 2345553     344444433321 111368999999999986432     2233333333321     2


Q ss_pred             CccEEEEEe
Q 022383          206 DLQVVLISA  214 (298)
Q Consensus       206 ~~~~v~~SA  214 (298)
                      ++.++++|-
T Consensus       354 ~i~vi~~sq  362 (454)
T 2r6a_A          354 EVPVIALSQ  362 (454)
T ss_dssp             TCCEEEEEC
T ss_pred             CCeEEEEec
Confidence            566777765

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.91  E-value=0.035  Score=58.04  Aligned_cols=41  Identities=15%  Similarity=0.200  Sum_probs=28.4

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      .++++++.+|+|+|||....-.+.+...   .+.+++|+.....
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~---~G~~v~Fi~~e~~ 1466 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHA 1466 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHT---TTCCEEEECTTSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEEEcccc
Confidence            3689999999999999665444433332   2557888876543

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=94.91  E-value=0.11  Score=45.57  Aligned_cols=18  Identities=28%  Similarity=0.457  Sum_probs=14.4

Q ss_pred             CCcEEE--EcCCCCchHHHH
Q 022383           70 GRDVIA--QAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li--~~pTG~GKT~~~   87 (298)
                      +..+++  .||.|+|||...
T Consensus        50 ~~~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           50 DVNMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             CEEEEEECTTCCSSSHHHHH
T ss_pred             CCEEEEeCcCcCCCCHHHHH
Confidence            346888  899999999653

>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=94.79  E-value=0.15  Score=40.43  Aligned_cols=71  Identities=24%  Similarity=0.315  Sum_probs=54.8

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++.-+..+.+.+.+.    ++.+..++|+.+..++...+    .+..+|+|+|.      +-..++++..+
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~------~~~~Gidi~~v  100 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD------VAARGLDIPQV  100 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT------TTTCSSSCCCB
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC------hhhcCCCCccC
Confidence            347999999999999999988775    67888999998776554333    25678999994      23357888899


Q ss_pred             cEEEe
Q 022383          177 KLLVL  181 (298)
Q Consensus       177 ~~vVi  181 (298)
                      ++||.
T Consensus       101 ~~Vi~  105 (212)
T 3eaq_A          101 DLVVH  105 (212)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            98884

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=94.72  E-value=0.033  Score=47.17  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      ...+++.||+|+|||...
T Consensus        38 ~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCCEEECCTTCCCHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            378999999999999654

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.69  E-value=0.086  Score=47.04  Aligned_cols=115  Identities=17%  Similarity=0.113  Sum_probs=54.9

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHH----
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGED----  144 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  144 (298)
                      .|.-+++.|++|+|||.-.+-.+.+.....  +..++|++.- .-..|+..++.......+..- ...|.....+.    
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~~--g~~vl~~slE-~~~~~l~~R~~~~~~~i~~~~-l~~g~l~~~~~~~~~  274 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALKE--GVGVGIYSLE-MPAAQLTLRMMCSEARIDMNR-VRLGQLTDRDFSRLV  274 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTT--CCCEEEEESS-SCHHHHHHHHHHHHTTCCTTT-CCGGGCCHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEECC-CCHHHHHHHHHHHHcCCCHHH-HhCCCCCHHHHHHHH
Confidence            456789999999999954443333333221  3357776642 223444444332211111100 00122222211    


Q ss_pred             --HHHhhcCCcEEEe-----ChHHHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          145 --IRKLEHGVHVVSG-----TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       145 --~~~~~~~~~ilV~-----Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                        ...+. ...+.+-     |++.+...++.-. .-..+++||||..+.+..
T Consensus       275 ~a~~~l~-~~~l~i~d~~~~s~~~l~~~~~~l~-~~~~~~lIvID~l~~~~~  324 (444)
T 2q6t_A          275 DVASRLS-EAPIYIDDTPDLTLMEVRARARRLV-SQNQVGLIIIDYLQLMSG  324 (444)
T ss_dssp             HHHHHHH-TSCEEEECCTTCBHHHHHHHHHHHH-HHSCCCEEEEECGGGCBC
T ss_pred             HHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHH-HHcCCCEEEEcChhhcCC
Confidence              11122 2355553     3445544333210 012589999999999864

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=94.61  E-value=0.28  Score=38.22  Aligned_cols=72  Identities=22%  Similarity=0.259  Sum_probs=54.6

Q ss_pred             eEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCcc
Q 022383          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (298)
Q Consensus       102 ~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~  177 (298)
                      .++||.|+++.-+..+.+.++..    ++.+..++|+.+..+....+    .+..+|+|+|.     .+ ..++++..++
T Consensus        55 ~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----~~-~~Gldi~~v~  124 (191)
T 2p6n_A           55 PPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD-----VA-SKGLDFPAIQ  124 (191)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH-----HH-HTTCCCCCCS
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC-----ch-hcCCCcccCC
Confidence            47999999999999999988775    67888999987766554333    25679999993     22 2467888899


Q ss_pred             EEEech
Q 022383          178 LLVLDE  183 (298)
Q Consensus       178 ~vViDE  183 (298)
                      +||.-+
T Consensus       125 ~VI~~d  130 (191)
T 2p6n_A          125 HVINYD  130 (191)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            888644

>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=94.46  E-value=0.55  Score=43.00  Aligned_cols=111  Identities=7%  Similarity=0.060  Sum_probs=73.2

Q ss_pred             chHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEe
Q 022383           82 GKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSG  157 (298)
Q Consensus        82 GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~  157 (298)
                      .+....+-.+...+.....+.++||.|+++.-+..+.+.+++... .++.+..++|+....+....+    .+..+|+|+
T Consensus       320 ~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~-~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLva  398 (563)
T 3i5x_A          320 NSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVC  398 (563)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEE
T ss_pred             hhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEE
Confidence            333333444444444434456899999999999999999987643 267888899988766554333    256899999


Q ss_pred             ChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhC
Q 022383          158 TPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYL  203 (298)
Q Consensus       158 Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~  203 (298)
                      |.      .-..++++.++++||.-..-    .+....++.+-+--
T Consensus       399 T~------~~~~GiDip~v~~VI~~~~p----~s~~~y~Qr~GRag  434 (563)
T 3i5x_A          399 TD------VGARGMDFPNVHEVLQIGVP----SELANYIHRIGRTA  434 (563)
T ss_dssp             CG------GGTSSCCCTTCCEEEEESCC----SSTTHHHHHHTTSS
T ss_pred             cc------hhhcCCCcccCCEEEEECCC----CchhhhhhhcCccc
Confidence            96      23357889999998865542    23344445444433

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=94.43  E-value=0.07  Score=47.69  Aligned_cols=18  Identities=33%  Similarity=0.527  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      .++++.||+|+|||...-
T Consensus        51 ~~vLL~GppGtGKTtlAr   68 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAE   68 (447)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            479999999999996543

>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=94.41  E-value=0.18  Score=38.56  Aligned_cols=74  Identities=11%  Similarity=0.107  Sum_probs=55.6

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++..+..+.+.++..    ++.+..++|+.+..+....+    .+..+|+|+|.-      -..++++..+
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~------~~~Gldi~~~  100 (172)
T 1t5i_A           31 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FGRGMDIERV  100 (172)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CSTTCCGGGC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc------hhcCcchhhC
Confidence            347999999999999999988775    67888899987766554333    256789999951      2346778888


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||.-+.
T Consensus       101 ~~Vi~~d~  108 (172)
T 1t5i_A          101 NIAFNYDM  108 (172)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEECC
Confidence            88886544

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.40  E-value=0.07  Score=45.75  Aligned_cols=51  Identities=25%  Similarity=0.221  Sum_probs=30.2

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      +..|.-+++.|++|+|||.-.+-.+.+...   .+..++|++.- .-..|+..++
T Consensus        43 l~~G~LiiIaG~pG~GKTt~al~ia~~~a~---~g~~Vl~fSlE-ms~~ql~~Rl   93 (338)
T 4a1f_A           43 FNKGSLVIIGARPSMGKTSLMMNMVLSALN---DDRGVAVFSLE-MSAEQLALRA   93 (338)
T ss_dssp             BCTTCEEEEEECTTSCHHHHHHHHHHHHHH---TTCEEEEEESS-SCHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEEeCC-CCHHHHHHHH
Confidence            345567899999999999544433333322   24467777642 2244554444

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.28  E-value=0.095  Score=47.74  Aligned_cols=41  Identities=20%  Similarity=0.199  Sum_probs=26.2

Q ss_pred             CCccEEEechhhHhhccc--cHHHHHHHHHhCCCCccEEEEEeeC
Q 022383          174 RAIKLLVLDESDEMLSRG--FKDQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~--~~~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      ....+++|||+|.+....  ....+..+++..  ..++|+++++.
T Consensus       147 ~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~--~~~iIli~~~~  189 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNER  189 (516)
T ss_dssp             TTSEEEEECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESCT
T ss_pred             CCCeEEEEECCCccchhhHHHHHHHHHHHHhc--CCCEEEEEcCC
Confidence            455799999999986532  224444555443  45677777764

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.13  E-value=0.19  Score=42.60  Aligned_cols=53  Identities=15%  Similarity=0.080  Sum_probs=31.6

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      +..|.-+++.|++|+|||.-.+-.+.+....   +..++|++-- .-..|+..++..
T Consensus        65 l~~G~l~li~G~pG~GKTtl~l~ia~~~a~~---g~~vl~~slE-~s~~~l~~R~~~  117 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSLE-MGKKENIKRLIV  117 (315)
T ss_dssp             BCTTCEEEEECCTTSSHHHHHHHHHHHHHTT---TCEEEEEESS-SCHHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEECC-CCHHHHHHHHHH
Confidence            4456779999999999995444333333322   2467777643 334555555443

>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=93.91  E-value=0.49  Score=39.40  Aligned_cols=22  Identities=23%  Similarity=0.466  Sum_probs=17.6

Q ss_pred             hhcCCcEEEEcCCCCchHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      +..|.-+++.||+|+|||....
T Consensus        32 l~~G~~~~i~G~~G~GKTTl~~   53 (296)
T 1cr0_A           32 ARGGEVIMVTSGSGMGKSTFVR   53 (296)
T ss_dssp             BCTTCEEEEEESTTSSHHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHHHHH
Confidence            4467889999999999995443

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=93.90  E-value=0.83  Score=42.06  Aligned_cols=88  Identities=7%  Similarity=0.092  Sum_probs=63.3

Q ss_pred             HHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHH
Q 022383           90 TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDM  165 (298)
Q Consensus        90 ~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~  165 (298)
                      .+...+.....+.++||.|+++.-+..+.+.+++... .++.+..++|+....+....+    .+..+|+|+|.      
T Consensus       277 ~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~-~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~------  349 (579)
T 3sqw_A          277 HIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD------  349 (579)
T ss_dssp             HHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG------
T ss_pred             HHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhc-CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc------
Confidence            3444444333456899999999999999999987643 267888899998766554333    25678999996      


Q ss_pred             HhccCccCCCccEEEechh
Q 022383          166 IKRKTLRTRAIKLLVLDES  184 (298)
Q Consensus       166 ~~~~~~~~~~l~~vViDE~  184 (298)
                      .-..++++.++++||.-..
T Consensus       350 ~~~~GiDip~v~~VI~~~~  368 (579)
T 3sqw_A          350 VGARGMDFPNVHEVLQIGV  368 (579)
T ss_dssp             GGTSSCCCTTCCEEEEESC
T ss_pred             hhhcCCCcccCCEEEEcCC
Confidence            2335788999999887654

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=93.82  E-value=0.16  Score=48.76  Aligned_cols=54  Identities=17%  Similarity=0.332  Sum_probs=34.7

Q ss_pred             cccCcccCCCCHHHHHHHHHCC-CC--CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYG-FE--KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~-~~--~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|++++..+..++.|++.- +.  .|..++..   .+...+.+++.||.|+|||+.+
T Consensus       472 p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~---g~~~~~gvLl~GPPGtGKT~lA  528 (806)
T 3cf2_A          472 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKF---GMTPSKGVLFYGPPGCGKTLLA  528 (806)
T ss_dssp             CCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSS---CCCCCSCCEEESSTTSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCceEEEecCCCCCchHHH
Confidence            4568999988888888887742 11  11111100   0123468999999999999643

>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=93.78  E-value=0.23  Score=38.39  Aligned_cols=90  Identities=13%  Similarity=0.183  Sum_probs=52.6

Q ss_pred             CCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH---Hh-hcCCcEE
Q 022383           80 GTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR---KL-EHGVHVV  155 (298)
Q Consensus        80 G~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~~il  155 (298)
                      ...|-. .+.-++...   ..+.++||.|+++.-+..+.+.++..    ++.+..++|+.+..+...   .. .+..+|+
T Consensus        29 ~~~K~~-~L~~ll~~~---~~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vL  100 (185)
T 2jgn_A           29 ESDKRS-FLLDLLNAT---GKDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPIL  100 (185)
T ss_dssp             GGGHHH-HHHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSEE
T ss_pred             cHHHHH-HHHHHHHhc---CCCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEE
Confidence            456654 333444432   23457999999999999999988764    678888888766544322   22 2567899


Q ss_pred             EeChHHHHHHHhccCccCCCccEEEech
Q 022383          156 SGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (298)
Q Consensus       156 V~Tp~~l~~~~~~~~~~~~~l~~vViDE  183 (298)
                      |+|. .+     ..++++..+++||.-+
T Consensus       101 vaT~-~~-----~~Gldi~~~~~VI~~d  122 (185)
T 2jgn_A          101 VATA-VA-----ARGLDISNVKHVINFD  122 (185)
T ss_dssp             EEEC------------CCCSBSEEEESS
T ss_pred             EEcC-hh-----hcCCCcccCCEEEEeC
Confidence            9994 22     2356778888887643

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=93.76  E-value=0.31  Score=39.06  Aligned_cols=42  Identities=17%  Similarity=0.057  Sum_probs=25.2

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccC---CCCeEEEEEcC
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSP  109 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~---~~~~~~lil~p  109 (298)
                      ..|.-+.+.||+|+|||......+...+...   ..+..++++.-
T Consensus        22 ~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           22 ETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             cCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEEC
Confidence            3567899999999999965544333322211   01235677654

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=93.71  E-value=0.48  Score=41.33  Aligned_cols=73  Identities=14%  Similarity=0.174  Sum_probs=55.7

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCC
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                      .+.++||.|++++-+..+.+.+++.    ++.+..++|+.+..+....+    .+..+|+|+|.     . -..++++..
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~-----~-~~~Gidip~  344 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----V-AARGLDISN  344 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH-----H-HHTTSCCCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----h-hhcCCCccc
Confidence            4568999999999999999988764    67888999988766554333    25678999995     2 234688889


Q ss_pred             ccEEEec
Q 022383          176 IKLLVLD  182 (298)
Q Consensus       176 l~~vViD  182 (298)
                      +++||.-
T Consensus       345 v~~Vi~~  351 (417)
T 2i4i_A          345 VKHVINF  351 (417)
T ss_dssp             EEEEEES
T ss_pred             CCEEEEE
Confidence            9988853

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=93.49  E-value=1.4  Score=42.20  Aligned_cols=16  Identities=38%  Similarity=0.632  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSM   86 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~   86 (298)
                      +.+++.||.|+|||+.
T Consensus       239 ~GILL~GPPGTGKT~L  254 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLI  254 (806)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6899999999999964

>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=93.46  E-value=0.19  Score=43.62  Aligned_cols=40  Identities=18%  Similarity=0.208  Sum_probs=25.3

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      .|.-+++.+|+|+|||...+-.+.+....   +..++|+..-.
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~~~---g~~vlyi~~E~  112 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEH  112 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSC
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHHHC---CCeEEEEECCC
Confidence            34678999999999996544333333222   33677777543

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=93.35  E-value=0.11  Score=44.87  Aligned_cols=41  Identities=20%  Similarity=0.213  Sum_probs=25.5

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      .|.-+++.||+|+|||...+ .+...+..  .+..++|+..-..
T Consensus        60 ~G~i~~I~GppGsGKSTLal-~la~~~~~--~gg~VlyId~E~s  100 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLAL-HAIAEAQK--MGGVAAFIDAEHA  100 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHH-HHHHHHHH--TTCCEEEEESSCC
T ss_pred             CCcEEEEECCCCCCHHHHHH-HHHHHHHh--cCCeEEEEecccc
Confidence            35678999999999995433 33333322  2346788875443

>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=93.35  E-value=2.7  Score=35.93  Aligned_cols=76  Identities=13%  Similarity=0.089  Sum_probs=57.9

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCC
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                      .+.++||.|+++.-+..+.+.+++.    +..+..++|+.+..++...+    .+..+|+|+|.      .-..++++.+
T Consensus       242 ~~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidip~  311 (395)
T 3pey_A          242 TIGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN------VLARGIDIPT  311 (395)
T ss_dssp             TSSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG------GGSSSCCCTT
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC------hhhcCCCccc
Confidence            3458999999999999999988765    57788899987766554333    24678999995      2345788999


Q ss_pred             ccEEEechhh
Q 022383          176 IKLLVLDESD  185 (298)
Q Consensus       176 l~~vViDE~h  185 (298)
                      +++||.-+..
T Consensus       312 ~~~Vi~~~~p  321 (395)
T 3pey_A          312 VSMVVNYDLP  321 (395)
T ss_dssp             EEEEEESSCC
T ss_pred             CCEEEEcCCC
Confidence            9999876553

>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=93.18  E-value=0.67  Score=39.27  Aligned_cols=55  Identities=13%  Similarity=0.067  Sum_probs=31.4

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhcc---CCCCeEEEEEcCcHHH-HHHHHHHHHHh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDT---SSREVQALILSPTREL-ATQTEKVILAI  124 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~---~~~~~~~lil~p~~~l-~~q~~~~~~~~  124 (298)
                      |.-+++.||+|+|||...+..+.+....   ...+..++|+.-...+ ..++...++++
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~  165 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKAL  165 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            4678999999999996544434332211   0113478888754332 34444444443

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=93.16  E-value=0.11  Score=43.92  Aligned_cols=90  Identities=9%  Similarity=0.094  Sum_probs=50.2

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcC
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG  151 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (298)
                      -+.+.+|+|+|||...+-.+.+.... ..+.+++|+..-..+...   ++++++-..                       
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~-g~g~~vlyId~E~s~~~~---ra~~lGvd~-----------------------   82 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQ-YPDAVCLFYDSEFGITPA---YLRSMGVDP-----------------------   82 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHH-CTTCEEEEEESSCCCCHH---HHHHTTCCG-----------------------
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEeccchhhHH---HHHHhCCCH-----------------------
Confidence            57899999999996655444443322 124478888865554322   244443211                       


Q ss_pred             CcEEEeChHHHHHH----Hhc-cCccCCCccEEEechhhHhh
Q 022383          152 VHVVSGTPGRVCDM----IKR-KTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       152 ~~ilV~Tp~~l~~~----~~~-~~~~~~~l~~vViDE~h~~~  188 (298)
                      .++++..|..+...    +.. ..+.-..+++||||-+..+.
T Consensus        83 d~llv~~~~~~E~~~l~i~~~l~~i~~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A           83 ERVIHTPVQSLEQLRIDMVNQLDAIERGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             GGEEEEECSBHHHHHHHHHHHHHTCCTTCCEEEEEECSTTCB
T ss_pred             HHeEEEcCCCHHHHHHHHHHHHHHhhccCceEEEEecccccc
Confidence            13444443333222    211 11334578999999988875

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=92.97  E-value=0.14  Score=47.00  Aligned_cols=19  Identities=37%  Similarity=0.496  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|..+++.||+|+|||..+
T Consensus       107 ~g~~vll~Gp~GtGKTtla  125 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLA  125 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999654

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=92.94  E-value=0.4  Score=43.08  Aligned_cols=52  Identities=19%  Similarity=0.325  Sum_probs=31.2

Q ss_pred             cccCcccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHh--hcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPI--IKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~--~~~~~~~Q~~~~~~~--~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+..++.+++.-  +..+.     .+..+  .-.+.+++.||+|+|||...
T Consensus        11 ~~~~f~di~G~~~~~~~l~e~v~~l~~~~-----~~~~~g~~~p~gvLL~GppGtGKT~La   66 (476)
T 2ce7_A           11 KRVTFKDVGGAEEAIEELKEVVEFLKDPS-----KFNRIGARMPKGILLVGPPGTGKTLLA   66 (476)
T ss_dssp             CCCCGGGCCSCHHHHHHHHHHHHHHHCTH-----HHHTTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHhhChH-----HHhhcCCCCCCeEEEECCCCCCHHHHH
Confidence            3458888876666666665531  11111     12221  12367999999999999654

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=92.65  E-value=0.19  Score=44.76  Aligned_cols=51  Identities=16%  Similarity=0.064  Sum_probs=30.5

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      +..|.-+++.|++|+|||.-.+-.+.+....   +..++|++-- .-..|+..++
T Consensus       194 l~~G~liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSlE-ms~~ql~~R~  244 (444)
T 3bgw_A          194 YKRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSLE-MGKKENIKRL  244 (444)
T ss_dssp             BCSSCEEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECSS-SCTTHHHHHH
T ss_pred             CCCCcEEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEECC-CCHHHHHHHH
Confidence            3355679999999999996544444443333   4467777643 2233444443

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=92.49  E-value=0.42  Score=40.18  Aligned_cols=73  Identities=22%  Similarity=0.293  Sum_probs=54.7

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++.-++.+.+.+...    ++.+..++|+.+..++...+    .+..+|+|+|.      +-..++++..+
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~------va~~Gidi~~v   97 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD------VAARGLDIPQV   97 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTT----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS------TTTCSTTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec------hhhcCccccce
Confidence            447999999999999988877654    67889999997766554333    25678999994      23357888889


Q ss_pred             cEEEech
Q 022383          177 KLLVLDE  183 (298)
Q Consensus       177 ~~vViDE  183 (298)
                      ++||.=+
T Consensus        98 ~~VI~~d  104 (300)
T 3i32_A           98 DLVVHYR  104 (300)
T ss_dssp             SEEEESS
T ss_pred             eEEEEcC
Confidence            9887533

>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=92.41  E-value=1.3  Score=40.97  Aligned_cols=74  Identities=11%  Similarity=0.126  Sum_probs=56.5

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCC
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                      .+..+||.|+++.-+.++.+.+++.    ++.+..++++.+..+....+    .+..+|+|+|.      .-..+++..+
T Consensus       266 ~~~~~IVf~~sr~~~e~la~~L~~~----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~------a~~~GID~p~  335 (591)
T 2v1x_A          266 KGQSGIIYCFSQKDSEQVTVSLQNL----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV------AFGMGIDKPD  335 (591)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECT------TSCTTCCCSC
T ss_pred             cCCCeEEEeCcHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec------hhhcCCCccc
Confidence            4568999999999999999988775    67889999998776554333    25678999995      2235678888


Q ss_pred             ccEEEech
Q 022383          176 IKLLVLDE  183 (298)
Q Consensus       176 l~~vViDE  183 (298)
                      +++||.-.
T Consensus       336 V~~VI~~~  343 (591)
T 2v1x_A          336 VRFVIHHS  343 (591)
T ss_dssp             EEEEEESS
T ss_pred             ccEEEEeC
Confidence            88888543

>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=92.35  E-value=0.14  Score=44.03  Aligned_cols=39  Identities=18%  Similarity=0.234  Sum_probs=25.5

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      .|+-+++.||+|+|||...+..+......   +..++|+.-.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~---g~~vlyi~~E   98 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA---GGIAAFIDAE   98 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC
Confidence            45779999999999996544433333222   3467777643

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=91.77  E-value=0.63  Score=44.48  Aligned_cols=17  Identities=29%  Similarity=0.452  Sum_probs=14.6

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      ++++.||||+|||..+-
T Consensus       523 ~~Ll~Gp~GtGKT~lA~  539 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELAR  539 (758)
T ss_dssp             EEEEESCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            59999999999996543

>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=91.76  E-value=0.14  Score=44.19  Aligned_cols=39  Identities=15%  Similarity=0.201  Sum_probs=25.9

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      .|+-+++.|++|+|||...+-.+......   +..++|+...
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~---g~~vlyid~E  100 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAE  100 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEeCC
Confidence            45779999999999996554444333322   3367887753

>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=91.72  E-value=5.7  Score=37.19  Aligned_cols=91  Identities=16%  Similarity=0.200  Sum_probs=65.4

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh---h-cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++..+..+.+.++..    ++++..++|+.+..+....+   . +..+|+|+|.      +-..++++..+
T Consensus       445 ~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~------~l~~GlDip~v  514 (661)
T 2d7d_A          445 NERVLVTTLTKKMSEDLTDYLKEI----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN------LLREGLDIPEV  514 (661)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESC------CCSTTCCCTTE
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhc----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecc------hhhCCcccCCC
Confidence            458999999999999999988775    67888889887765554432   2 5689999995      23457889999


Q ss_pred             cEEEechhhHhhc-cccHHHHHHHHH
Q 022383          177 KLLVLDESDEMLS-RGFKDQIYDVYR  201 (298)
Q Consensus       177 ~~vViDE~h~~~~-~~~~~~i~~i~~  201 (298)
                      ++||+-|++...- ......++.+-+
T Consensus       515 ~lVi~~d~d~~G~p~s~~~~iQr~GR  540 (661)
T 2d7d_A          515 SLVAILDADKEGFLRSERSLIQTIGR  540 (661)
T ss_dssp             EEEEETTTTCCTTTTSHHHHHHHHHT
T ss_pred             CEEEEeCcccccCCCCHHHHHHHhCc
Confidence            9999999876432 122344444443

>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=91.55  E-value=1.2  Score=39.26  Aligned_cols=70  Identities=13%  Similarity=0.178  Sum_probs=54.7

Q ss_pred             EEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCccE
Q 022383          103 QALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (298)
Q Consensus       103 ~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~  178 (298)
                      .+||.|+++.-+..+.+.+++.    ++.+..++|+....++...+.    +..+|+|+|.      +-..++++.++++
T Consensus       302 ~~lVF~~t~~~a~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~------v~~rGlDi~~v~~  371 (434)
T 2db3_A          302 GTIVFVETKRGADFLASFLSEK----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS------VASRGLDIKNIKH  371 (434)
T ss_dssp             TEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG------GGTSSCCCTTCCE
T ss_pred             CEEEEEeCcHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch------hhhCCCCcccCCE
Confidence            3999999999999999988765    678889999987665544332    5678999996      3345788999999


Q ss_pred             EEec
Q 022383          179 LVLD  182 (298)
Q Consensus       179 vViD  182 (298)
                      ||.-
T Consensus       372 VI~~  375 (434)
T 2db3_A          372 VINY  375 (434)
T ss_dssp             EEES
T ss_pred             EEEE
Confidence            8853

>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=91.43  E-value=0.96  Score=39.12  Aligned_cols=73  Identities=11%  Similarity=0.102  Sum_probs=55.2

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++.-+..+.+.+++.    ++.+..++|+.+..+....+    .+..+|+|+|.      .-..++++..+
T Consensus       258 ~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~------~~~~Gidip~~  327 (400)
T 1s2m_A          258 INQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD------LLTRGIDIQAV  327 (400)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS------CSSSSCCCTTE
T ss_pred             CCcEEEEEecHHHHHHHHHHHHhc----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC------ccccCCCccCC
Confidence            348999999999999999988876    57788889987765544332    24578999995      23357888899


Q ss_pred             cEEEech
Q 022383          177 KLLVLDE  183 (298)
Q Consensus       177 ~~vViDE  183 (298)
                      ++||.-+
T Consensus       328 ~~Vi~~~  334 (400)
T 1s2m_A          328 NVVINFD  334 (400)
T ss_dssp             EEEEESS
T ss_pred             CEEEEeC
Confidence            9888643

>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=91.29  E-value=0.79  Score=39.75  Aligned_cols=73  Identities=16%  Similarity=0.136  Sum_probs=56.1

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++.-+..+.+.+++.    +..+..++|+.+..+....+    .+..+|+|+|.      .-..++++.++
T Consensus       266 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidip~~  335 (412)
T 3fht_A          266 IAQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN------VCARGIDVEQV  335 (412)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG------GGTSSCCCTTE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhC----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC------ccccCCCccCC
Confidence            348999999999999999988875    57788899988766554333    25678999995      23457889999


Q ss_pred             cEEEech
Q 022383          177 KLLVLDE  183 (298)
Q Consensus       177 ~~vViDE  183 (298)
                      ++||.-+
T Consensus       336 ~~Vi~~~  342 (412)
T 3fht_A          336 SVVINFD  342 (412)
T ss_dssp             EEEEESS
T ss_pred             CEEEEEC
Confidence            9988543

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=91.22  E-value=6  Score=33.21  Aligned_cols=37  Identities=19%  Similarity=0.366  Sum_probs=23.3

Q ss_pred             ccEEEechhhHhhc---cccHHHHHHHHHhCCCCccEEEEE
Q 022383          176 IKLLVLDESDEMLS---RGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       176 l~~vViDE~h~~~~---~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      --+|||||+|.+..   ..+...+..+....+ +..+|+.+
T Consensus       138 ~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~-~~~~i~~g  177 (357)
T 2fna_A          138 NVIIVLDEAQELVKLRGVNLLPALAYAYDNLK-RIKFIMSG  177 (357)
T ss_dssp             CEEEEEETGGGGGGCTTCCCHHHHHHHHHHCT-TEEEEEEE
T ss_pred             CeEEEEECHHHhhccCchhHHHHHHHHHHcCC-CeEEEEEc
Confidence            45899999999864   345566666666542 44444433

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=91.07  E-value=0.44  Score=46.26  Aligned_cols=18  Identities=22%  Similarity=0.516  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      ..+++++||+|+|||...
T Consensus       191 ~~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          191 KNNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             CCCCEEEECTTSCHHHHH
T ss_pred             CCceEEEcCCCCCHHHHH
Confidence            358999999999999643

>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=91.04  E-value=3.5  Score=35.30  Aligned_cols=74  Identities=11%  Similarity=0.139  Sum_probs=56.4

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++.-+..+.+.+++.    ++.+..++|+.+..+....+    .+..+|+|+|.      .-..++++..+
T Consensus       250 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~------~~~~Gidi~~~  319 (391)
T 1xti_A          250 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN------LFGRGMDIERV  319 (391)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESC------CCSSCBCCTTE
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECC------hhhcCCCcccC
Confidence            458999999999999999988765    67788899987765544333    24678999994      22357888999


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||..+.
T Consensus       320 ~~Vi~~~~  327 (391)
T 1xti_A          320 NIAFNYDM  327 (391)
T ss_dssp             EEEEESSC
T ss_pred             CEEEEeCC
Confidence            99987654

>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=90.95  E-value=1.7  Score=39.05  Aligned_cols=52  Identities=13%  Similarity=0.219  Sum_probs=39.4

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      .|....+.+-||+|||+...-.+ ...     +..+|||+|+...+.++++.++.+..
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~l~-~~~-----~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAEIA-ERH-----AGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHHHH-HHS-----SSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHHHHHHH-HHh-----CCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            45678999999999997543222 211     22589999999999999999988754

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=90.83  E-value=0.23  Score=39.91  Aligned_cols=52  Identities=15%  Similarity=0.151  Sum_probs=31.3

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      ..|.-+++.||+|+|||...+-.+......   +..++|+.-. ....++.+.+..
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~---~~~v~~~~~e-~~~~~~~~~~~~   72 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIFSQQFLWNGLKM---GEPGIYVALE-EHPVQVRQNMAQ   72 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHHHT---TCCEEEEESS-SCHHHHHHHHHT
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEcc-CCHHHHHHHHHH
Confidence            356789999999999996544333333222   3357777643 234555555543

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=90.74  E-value=0.36  Score=48.53  Aligned_cols=40  Identities=20%  Similarity=0.311  Sum_probs=29.8

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      -+|.|+.|||||.+.+--+...+.....+.++++|+|...
T Consensus         4 ~lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~   43 (1166)
T 3u4q_B            4 EFLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQM   43 (1166)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGG
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCcc
Confidence            3789999999998766656555555444568999999764

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=90.71  E-value=0.26  Score=50.96  Aligned_cols=90  Identities=16%  Similarity=0.265  Sum_probs=54.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (298)
                      |+.+.+.+|.|+|||...+..+-+....   +..++|+.+-.+|-...   +++++-+++                    
T Consensus      1431 g~~iei~g~~~sGkttl~~~~~a~~~~~---g~~~~~i~~e~~~~~~~---~~~~Gv~~~-------------------- 1484 (1706)
T 3cmw_A         1431 GRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIY---ARKLGVDID-------------------- 1484 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEECTTSCCCHHH---HHHTTCCGG--------------------
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhc---CCeEEEEecCCCCCHHH---HHHcCCCHH--------------------
Confidence            4779999999999997755544333222   55789998877665554   445532221                    


Q ss_pred             cCCcEEEeChH---HHHHHHhccCccCCCccEEEechhhHhhc
Q 022383          150 HGVHVVSGTPG---RVCDMIKRKTLRTRAIKLLVLDESDEMLS  189 (298)
Q Consensus       150 ~~~~ilV~Tp~---~l~~~~~~~~~~~~~l~~vViDE~h~~~~  189 (298)
                         +++|.-|+   +.+..... .+.-..+++||||.+..+..
T Consensus      1485 ---~l~~~~p~~~e~~l~~~~~-~~~s~~~~~vvvDsv~al~~ 1523 (1706)
T 3cmw_A         1485 ---NLLCSQPDTGEQALEICDA-LARSGAVDVIVVDSVAALTP 1523 (1706)
T ss_dssp             ---GCEEECCSSHHHHHHHHHH-HHHHTCCSEEEESCSTTCCC
T ss_pred             ---HeEEeCCCcHHHHHHHHHH-HHHcCCCCEEEEccHHhCCc
Confidence               35555552   22222221 22234678999999877653

>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=90.65  E-value=1.1  Score=38.93  Aligned_cols=72  Identities=15%  Similarity=0.166  Sum_probs=55.0

Q ss_pred             eEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCcc
Q 022383          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIK  177 (298)
Q Consensus       102 ~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~  177 (298)
                      .++||.|+++.-+..+.+.+++.    ++.+..++|+.+..+....+    .+..+|+|+|.      .-..++++..++
T Consensus       277 ~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidi~~v~  346 (410)
T 2j0s_A          277 TQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD------VWARGLDVPQVS  346 (410)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG------GGSSSCCCTTEE
T ss_pred             CcEEEEEcCHHHHHHHHHHHHhC----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC------hhhCcCCcccCC
Confidence            48999999999999999988765    57788899987765544333    25678999995      234578899999


Q ss_pred             EEEech
Q 022383          178 LLVLDE  183 (298)
Q Consensus       178 ~vViDE  183 (298)
                      +||.-+
T Consensus       347 ~Vi~~~  352 (410)
T 2j0s_A          347 LIINYD  352 (410)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            988643

>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=90.52  E-value=0.42  Score=41.17  Aligned_cols=20  Identities=20%  Similarity=0.413  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCCchHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~   88 (298)
                      .+.++++.||+|+|||..+-
T Consensus        50 ~~~~vll~GppGtGKT~la~   69 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAE   69 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            35789999999999997543

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=90.44  E-value=0.59  Score=50.69  Aligned_cols=74  Identities=15%  Similarity=0.115  Sum_probs=44.3

Q ss_pred             CCHHHHHHHHHCCCCCChHHH-HHH---HHHhhcCCcEEEEcCCCCchHHHHHHHH--HHhhccCCCCeEEEEEcCcHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQ-QRA---VMPIIKGRDVIAQAQSGTGKTSMIALTV--CQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q-~~~---~~~~~~~~~~li~~pTG~GKT~~~~~~~--~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      +...+.+.+.+.++. +.+.+ ..+   +..+..++.++++||||+|||.++-..+  +..+..  ....+.++-|..--
T Consensus       890 l~~~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~~La~al~~l~~--~~~~~~~inpk~~t  966 (2695)
T 4akg_A          890 IVQCLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFDG--HANVVYVIDTKVLT  966 (2695)
T ss_dssp             HHHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHHHHHHHHHHHTC--CEEEEEEECTTTSC
T ss_pred             HHHHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHHHHHHHHHHhcC--CCceEEEeCCCCCC
Confidence            345677777888876 45544 333   3345567899999999999998865332  233322  23345556564333


Q ss_pred             HHH
Q 022383          114 ATQ  116 (298)
Q Consensus       114 ~~q  116 (298)
                      ..|
T Consensus       967 ~~e  969 (2695)
T 4akg_A          967 KES  969 (2695)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            333

>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=90.41  E-value=9.1  Score=35.86  Aligned_cols=77  Identities=13%  Similarity=0.133  Sum_probs=59.3

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh---h-cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E-HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++..+..+.+.+.+.    ++.+..++|+.+..+....+   . +..+|+|+|.      +-..++++..+
T Consensus       439 ~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~------~l~~GlDip~v  508 (664)
T 1c4o_A          439 GERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN------LLREGLDIPEV  508 (664)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC------CCCTTCCCTTE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhc----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccC------hhhcCccCCCC
Confidence            458999999999999999988775    57788888887766554432   2 4679999995      12457888999


Q ss_pred             cEEEechhhHh
Q 022383          177 KLLVLDESDEM  187 (298)
Q Consensus       177 ~~vViDE~h~~  187 (298)
                      ++||+=+++..
T Consensus       509 ~lVI~~d~d~~  519 (664)
T 1c4o_A          509 SLVAILDADKE  519 (664)
T ss_dssp             EEEEETTTTSC
T ss_pred             CEEEEeCCccc
Confidence            99998888654

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=90.39  E-value=0.88  Score=41.27  Aligned_cols=40  Identities=15%  Similarity=0.099  Sum_probs=26.0

Q ss_pred             HHHHHHCCCCCChHHHHHHHH-HhhcCCcEEEEcCCCCchHHH
Q 022383           45 LRGIYQYGFEKPSAIQQRAVM-PIIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        45 ~~~l~~~~~~~~~~~Q~~~~~-~~~~~~~~li~~pTG~GKT~~   86 (298)
                      ...|.+.|.  +++.+...+. .+..|..++++||||||||..
T Consensus       236 ~~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          236 PIDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHH
T ss_pred             hhhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            344556553  2233333333 356788999999999999954

>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=90.28  E-value=1.2  Score=40.57  Aligned_cols=73  Identities=14%  Similarity=0.124  Sum_probs=55.7

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +..+||.|+++.-++.+.+.+++.    ++.+..++|+.+..+.....    .+..+|+|+|.      .-..++++.++
T Consensus       236 ~~~~IVf~~sr~~~e~l~~~L~~~----g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~------a~~~GiD~p~v  305 (523)
T 1oyw_A          236 GKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV------AFGMGINKPNV  305 (523)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT------TSCTTTCCTTC
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec------hhhCCCCccCc
Confidence            457899999999999999988875    67888999998765544332    25679999996      22356788889


Q ss_pred             cEEEech
Q 022383          177 KLLVLDE  183 (298)
Q Consensus       177 ~~vViDE  183 (298)
                      ++||.-.
T Consensus       306 ~~VI~~~  312 (523)
T 1oyw_A          306 RFVVHFD  312 (523)
T ss_dssp             CEEEESS
T ss_pred             cEEEEEC
Confidence            9888643

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=90.26  E-value=2.8  Score=34.94  Aligned_cols=19  Identities=26%  Similarity=0.230  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      ++-+.+++++|+|||....
T Consensus        98 ~~~i~i~g~~G~GKTT~~~  116 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAA  116 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4467788999999996543

>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=90.08  E-value=1.7  Score=43.62  Aligned_cols=78  Identities=13%  Similarity=0.097  Sum_probs=60.5

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.+++|+|++++-+..+.+.+++..  .+.++..++|+.+..+....+    .+..+|+|||.      +-..++++.++
T Consensus       812 g~qvlvf~~~v~~~~~l~~~L~~~~--p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~------v~e~GiDip~v  883 (1151)
T 2eyq_A          812 GGQVYYLYNDVENIQKAAERLAELV--PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIETGIDIPTA  883 (1151)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHC--TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS------TTGGGSCCTTE
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhC--CCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECC------cceeeecccCC
Confidence            4689999999999999999888763  357788899988766543332    25689999996      33457899999


Q ss_pred             cEEEechhhH
Q 022383          177 KLLVLDESDE  186 (298)
Q Consensus       177 ~~vViDE~h~  186 (298)
                      ++||+..++.
T Consensus       884 ~~VIi~~~~~  893 (1151)
T 2eyq_A          884 NTIIIERADH  893 (1151)
T ss_dssp             EEEEETTTTS
T ss_pred             cEEEEeCCCC
Confidence            9999887764

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=90.03  E-value=0.64  Score=35.81  Aligned_cols=62  Identities=13%  Similarity=0.098  Sum_probs=43.2

Q ss_pred             ChHHHHHHHHHhhc--CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           56 PSAIQQRAVMPIIK--GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~--~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      ..+-|..++..++.  .+-.++.++-|++|+...+-.++..-..  .|.++.+|+|+..-...+.+
T Consensus        35 ~~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~--~Gr~V~vLAp~~~s~~~l~~   98 (189)
T 2l8b_A           35 RTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMARE--QGREVQIIAADRRSQMNMKQ   98 (189)
T ss_dssp             CHHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHH--TTCCEEEECSTTHHHHHHSC
T ss_pred             cCccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHh--cCeEEEEEcCchHHHHHHHh
Confidence            44678888888763  3457788999999997754444443333  36689999999876555444

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=89.98  E-value=0.3  Score=43.32  Aligned_cols=43  Identities=19%  Similarity=0.354  Sum_probs=26.2

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELA  114 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~  114 (298)
                      ...++++.|+||+|||... ..++..+...  +..++|+=|..++.
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~~--g~~viv~Dpkge~~   94 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLLR--GDRMVIVDPNGDML   94 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHHT--TCEEEEEEETTHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHHC--CCcEEEEeCCCchh
Confidence            4579999999999999874 3333333221  23455555554443

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=89.94  E-value=0.067  Score=44.44  Aligned_cols=54  Identities=13%  Similarity=0.186  Sum_probs=29.1

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHH-HHHHHHHhh--cCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAI-QQRAVMPII--KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~-Q~~~~~~~~--~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|++++-.+.+++.|++.- .  .|+ ...++..+.  -.+.+++.||+|+|||...
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i-~--~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAI-L--APVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             -------CCHHHHHHHHHHHHH-T--HHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHH-H--HHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHH
Confidence            4568999987778888877631 1  121 123333321  2345999999999999643

>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=89.84  E-value=1.2  Score=37.79  Aligned_cols=73  Identities=12%  Similarity=0.215  Sum_probs=54.1

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|++++-+..+.+.+++.    +..+..++|+.+..+....+    .+..+|+|+|. .+     ..++++.++
T Consensus       238 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-~~-----~~Gid~~~~  307 (367)
T 1hv8_A          238 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-VM-----SRGIDVNDL  307 (367)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-TH-----HHHCCCSCC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC-hh-----hcCCCcccC
Confidence            457999999999999999988775    67788899987766544332    24678999994 22     235778888


Q ss_pred             cEEEech
Q 022383          177 KLLVLDE  183 (298)
Q Consensus       177 ~~vViDE  183 (298)
                      ++||.-+
T Consensus       308 ~~Vi~~~  314 (367)
T 1hv8_A          308 NCVINYH  314 (367)
T ss_dssp             SEEEESS
T ss_pred             CEEEEec
Confidence            8888644

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=89.78  E-value=0.45  Score=37.60  Aligned_cols=32  Identities=25%  Similarity=0.214  Sum_probs=26.2

Q ss_pred             ChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           56 PSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      -+.-|..++..+..|.-+.+.||+|+|||...
T Consensus         8 k~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            8 KTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             CCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            34456778888889999999999999999643

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=89.59  E-value=2.6  Score=35.73  Aligned_cols=52  Identities=21%  Similarity=0.394  Sum_probs=28.5

Q ss_pred             ccEEEechhhHhh-ccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhc
Q 022383          176 IKLLVLDESDEML-SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKF  227 (298)
Q Consensus       176 l~~vViDE~h~~~-~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~  227 (298)
                      .+++++|.+-... ...+...+..+.+.+.+...++.+.++-.......+..+
T Consensus       212 ~d~vliDtaG~~~~~~~l~~eL~~i~ral~~de~llvLDa~t~~~~~~~~~~~  264 (328)
T 3e70_C          212 IDVVLIDTAGRSETNRNLMDEMKKIARVTKPNLVIFVGDALAGNAIVEQARQF  264 (328)
T ss_dssp             CSEEEEEECCSCCTTTCHHHHHHHHHHHHCCSEEEEEEEGGGTTHHHHHHHHH
T ss_pred             chhhHHhhccchhHHHHHHHHHHHHHHHhcCCCCEEEEecHHHHHHHHHHHHH
Confidence            4566677664432 123344455555555556667777777665555555443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.56  E-value=0.49  Score=49.76  Aligned_cols=48  Identities=13%  Similarity=0.133  Sum_probs=32.0

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTE  118 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~  118 (298)
                      +..|+++++.+|+|+|||......+.+....   +.+++|+. ..++.+++.
T Consensus      1078 i~~g~~vll~G~~GtGKT~la~~~~~ea~k~---Ge~~~Fit-~ee~~~~L~ 1125 (2050)
T 3cmu_A         1078 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFID-AEHALDPIY 1125 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEEC-TTSCCCHHH
T ss_pred             cCCCcEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEE-ccccHHHHH
Confidence            3356899999999999997655555554433   45677776 344444544

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=89.47  E-value=0.92  Score=49.88  Aligned_cols=77  Identities=16%  Similarity=0.163  Sum_probs=46.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHH---HhhcCCcEEEEcCCCCchHHHHHHHH--HHhhccCCCCeEEEEEcCcHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVM---PIIKGRDVIAQAQSGTGKTSMIALTV--CQTVDTSSREVQALILSPTRELA  114 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~---~~~~~~~~li~~pTG~GKT~~~~~~~--~~~~~~~~~~~~~lil~p~~~l~  114 (298)
                      +...+.+.+.++|+..-..+-..++.   .+.-+..++++||||+|||.++-...  +..+..  .....-++-|----.
T Consensus       873 l~~ai~~~~~~~~L~~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~~L~~al~~l~~--~~~~~~~iNPKait~  950 (3245)
T 3vkg_A          873 LRKKIQEIAKQRHLVTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDN--IKSEAHVMDPKAITK  950 (3245)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHHHHHHHHTTTTT--CEEEEEEECTTTSCH
T ss_pred             HHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHHHHHHHHHHhhC--CCceEEEECCCCCch
Confidence            44567777888888744334344443   34467789999999999999875322  222211  223455666755445


Q ss_pred             HHHH
Q 022383          115 TQTE  118 (298)
Q Consensus       115 ~q~~  118 (298)
                      .|++
T Consensus       951 ~eLy  954 (3245)
T 3vkg_A          951 DQLF  954 (3245)
T ss_dssp             HHHH
T ss_pred             hhhc
Confidence            5544

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=89.45  E-value=0.23  Score=50.54  Aligned_cols=40  Identities=20%  Similarity=0.292  Sum_probs=26.0

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ++-+.+|+||+=.-++..-...+...++...+++-++.++
T Consensus      1234 r~~~ILiLDEaTSaLD~~tE~~Iq~~l~~~~~~~TvI~IA 1273 (1321)
T 4f4c_A         1234 RNPKILLLDEATSALDTESEKVVQEALDRAREGRTCIVIA 1273 (1321)
T ss_dssp             SCCSEEEEESCCCSTTSHHHHHHHHHHTTTSSSSEEEEEC
T ss_pred             hCCCEEEEeCccccCCHHHHHHHHHHHHHHcCCCEEEEec
Confidence            4567888888865555555666777777666555555543

>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=89.28  E-value=0.91  Score=37.00  Aligned_cols=19  Identities=26%  Similarity=0.420  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .+.++++.||+|+|||...
T Consensus        28 ~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHH
Confidence            5679999999999999654

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=89.13  E-value=0.32  Score=37.05  Aligned_cols=18  Identities=22%  Similarity=0.516  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      ++.+++.||+|+|||...
T Consensus        43 ~~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            468999999999999653

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=89.12  E-value=0.73  Score=40.67  Aligned_cols=27  Identities=15%  Similarity=0.334  Sum_probs=18.7

Q ss_pred             HHHHHHHhh--cCCcEEEEcCCCCchHHH
Q 022383           60 QQRAVMPII--KGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        60 Q~~~~~~~~--~~~~~li~~pTG~GKT~~   86 (298)
                      +..++..+.  .|.-+++.||||||||..
T Consensus       155 ~~~~L~~l~~~~ggii~I~GpnGSGKTTl  183 (418)
T 1p9r_A          155 NHDNFRRLIKRPHGIILVTGPTGSGKSTT  183 (418)
T ss_dssp             HHHHHHHHHTSSSEEEEEECSTTSCHHHH
T ss_pred             HHHHHHHHHHhcCCeEEEECCCCCCHHHH
Confidence            444444433  345689999999999954

>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=88.97  E-value=0.78  Score=46.19  Aligned_cols=54  Identities=20%  Similarity=0.143  Sum_probs=41.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccC---------CCCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTS---------SREVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~---------~~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      ...+|.|+.|||||.+..--++..+...         -...++|+|+=|++-+.++.+++++.
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~   79 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHH
Confidence            3459999999999988766666666432         12348999999999999999888764

>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=88.69  E-value=1.9  Score=37.87  Aligned_cols=96  Identities=18%  Similarity=0.196  Sum_probs=60.6

Q ss_pred             CCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEc--------CCchHHHHHH---
Q 022383           79 SGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG--------GKSVGEDIRK---  147 (298)
Q Consensus        79 TG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~---  147 (298)
                      ..++|... +.-++........+.++||.|+++.-+..+.+.++..    ++.+..++|        +.+..++...   
T Consensus       340 ~~~~k~~~-l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~  414 (494)
T 1wp9_A          340 LDHPKMDK-LKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDE  414 (494)
T ss_dssp             CSCHHHHH-HHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHH
T ss_pred             CCChHHHH-HHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHc----CCCcEEEeccccccccccCCHHHHHHHHHH
Confidence            44555543 3333333321123558999999999999999988875    678888888        5444333222   


Q ss_pred             h-hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhh
Q 022383          148 L-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (298)
Q Consensus       148 ~-~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h  185 (298)
                      . .+.++|+|+|.      .-..++++..+++||+-+..
T Consensus       415 F~~~~~~vLv~T~------~~~~Gldl~~~~~Vi~~d~~  447 (494)
T 1wp9_A          415 FARGEFNVLVATS------VGEEGLDVPEVDLVVFYEPV  447 (494)
T ss_dssp             HHHTSCSEEEECG------GGGGGGGSTTCCEEEESSCC
T ss_pred             HhcCCceEEEECC------ccccCCCchhCCEEEEeCCC
Confidence            2 25578999994      12346888889998876553

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=88.37  E-value=0.083  Score=40.28  Aligned_cols=74  Identities=12%  Similarity=0.135  Sum_probs=51.0

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++..+..+.+.++..    ++.+..++|+.+..+....+    .+..+|+|+|. .+     ..++++..+
T Consensus        30 ~~~~iVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~-~~-----~~Gid~~~~   99 (170)
T 2yjt_D           30 ATRSIVFVRKRERVHELANWLREA----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATD-VA-----ARGIDIPDV   99 (170)
Confidence            457999999999999998887764    56777888876654443322    24567999993 22     235667777


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||.-+.
T Consensus       100 ~~Vi~~~~  107 (170)
T 2yjt_D          100 SHVFNFDM  107 (170)
Confidence            77776443

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=88.64  E-value=0.66  Score=41.97  Aligned_cols=44  Identities=14%  Similarity=0.192  Sum_probs=28.6

Q ss_pred             HHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           43 DLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .+...+.+. +..-...-..+...+..+.++++.||+|+|||..+
T Consensus        15 ~l~~~l~~~-ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           15 RLSSSLEKG-LYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HHHHHHHTT-CSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             HHHHHHHhh-hHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            344444443 33333334455556678899999999999999643

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=88.48  E-value=0.34  Score=37.18  Aligned_cols=19  Identities=11%  Similarity=0.324  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|+-++++||+|+|||...
T Consensus         4 ~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5678899999999999643

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=88.44  E-value=4  Score=36.64  Aligned_cols=74  Identities=8%  Similarity=0.004  Sum_probs=50.8

Q ss_pred             EEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCccE
Q 022383          103 QALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKL  178 (298)
Q Consensus       103 ~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~  178 (298)
                      ..++++....-+..+.+.+.+.    +.++..++|+.+..+....+    .+..+|+|+|+..+..     ++++.++++
T Consensus       349 ~~~ivf~~~~~~~~l~~~L~~~----~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~-----GiDip~v~~  419 (510)
T 2oca_A          349 NAFVMFKHVSHGKAIFDLIKNE----YDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFST-----GISVKNLHH  419 (510)
T ss_dssp             EEEEEESSHHHHHHHHHHHHTT----CSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHH-----SCCCCSEEE
T ss_pred             CeEEEEecHHHHHHHHHHHHHc----CCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhc-----ccccccCcE
Confidence            4555555566666677666553    34788889987765443322    3567899999755543     678899999


Q ss_pred             EEechhh
Q 022383          179 LVLDESD  185 (298)
Q Consensus       179 vViDE~h  185 (298)
                      ||+.+..
T Consensus       420 vi~~~~~  426 (510)
T 2oca_A          420 VVLAHGV  426 (510)
T ss_dssp             EEESSCC
T ss_pred             EEEeCCC
Confidence            9998876

>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=88.21  E-value=1.2  Score=37.00  Aligned_cols=18  Identities=22%  Similarity=0.542  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      ..++++.||+|+|||...
T Consensus        50 ~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            578999999999999654

>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=88.20  E-value=0.55  Score=40.94  Aligned_cols=44  Identities=18%  Similarity=0.213  Sum_probs=28.1

Q ss_pred             CCccEEEechhhHhhcc---ccHHHHHHHHHhCCC-CccEEEEEeeCc
Q 022383          174 RAIKLLVLDESDEMLSR---GFKDQIYDVYRYLPP-DLQVVLISATLP  217 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~---~~~~~i~~i~~~~~~-~~~~v~~SAT~~  217 (298)
                      ..-.++|+||+|.+...   .....+..+++..++ +.-+++.|-.+.
T Consensus       261 ~~~~~i~iDEa~~~~~~~~~~~~~~l~~~~~~~Rk~g~~~~~~tQ~~~  308 (392)
T 4ag6_A          261 RERTVLVVDEAWMLVDPQTPQAIAFLRDTSKRIRKYNGSLIVISQNVI  308 (392)
T ss_dssp             CTTCEEEETTGGGGCCTTCTHHHHHHHHHHHHGGGGTCEEEEEESCGG
T ss_pred             CccEEEEEecHHHHhCcCchHHHHHHHHHHHHhhhhCeEEEEEcCCHH
Confidence            34678999999999852   245556666666553 455566555553

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=88.03  E-value=0.52  Score=40.46  Aligned_cols=19  Identities=47%  Similarity=0.760  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      ++.+++.||+|+|||....
T Consensus        70 ~~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            4689999999999996543

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=87.95  E-value=0.28  Score=40.35  Aligned_cols=20  Identities=20%  Similarity=0.305  Sum_probs=17.1

Q ss_pred             hhcCCcEEEEcCCCCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~   86 (298)
                      +..|.-+.++||||+|||..
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            45678899999999999964

>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=87.90  E-value=0.23  Score=38.61  Aligned_cols=16  Identities=38%  Similarity=0.767  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSM   86 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~   86 (298)
                      |-++++||+|+|||..
T Consensus         2 RpIVi~GPSG~GK~Tl   17 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            5689999999999964

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=87.82  E-value=0.36  Score=41.70  Aligned_cols=20  Identities=25%  Similarity=0.577  Sum_probs=17.6

Q ss_pred             hhcCCcEEEEcCCCCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~   86 (298)
                      +..|..+.++||||+|||..
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            45789999999999999964

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=87.57  E-value=0.19  Score=40.93  Aligned_cols=54  Identities=11%  Similarity=0.078  Sum_probs=32.4

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhh--cCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+.....+++.-..  . -....+..+.  -.+.+++.||+|+|||...
T Consensus        11 ~~~~~~~i~g~~~~~~~l~~l~~~--~-~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A           11 PKVTFKDVAGAEEAKEELKEIVEF--L-KNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHH--H-HCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHH--H-HCHHHHHHcCCCCCCeEEEECCCCCCHHHHH
Confidence            456888887777777766653211  0 0112333221  1345999999999999643

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=87.51  E-value=0.94  Score=38.01  Aligned_cols=19  Identities=32%  Similarity=0.480  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .+.++++.||+|+|||..+
T Consensus        24 ~~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHH
T ss_pred             CCCcEEEECCCCchHHHHH
Confidence            4678999999999999654

>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=87.40  E-value=1.2  Score=39.49  Aligned_cols=68  Identities=6%  Similarity=-0.008  Sum_probs=47.8

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh-hcCCcEEEeChHHHHHHHhccCccCCCccEE
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~v  179 (298)
                      +.+++|.||+++-+..+.+.+++.    ++++..++|+... ...... .+..+|+|+|.      +-..++++. +++|
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~----~~~v~~lhg~~R~-~~~~~F~~g~~~vLVaT~------v~e~GiDip-v~~V  244 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFE-REYPTIKQKKPDFILATD------IAEMGANLC-VERV  244 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC---------CCCSEEEESS------STTCCTTCC-CSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCCEEEecchhHH-HHHhhhcCCCceEEEECC------hhheeeccC-ceEE
Confidence            357999999999999999988875    5788888884332 222333 35679999995      233567888 8887


Q ss_pred             E
Q 022383          180 V  180 (298)
Q Consensus       180 V  180 (298)
                      |
T Consensus       245 I  245 (440)
T 1yks_A          245 L  245 (440)
T ss_dssp             E
T ss_pred             E
Confidence            7

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=87.34  E-value=0.7  Score=38.15  Aligned_cols=41  Identities=7%  Similarity=-0.170  Sum_probs=34.6

Q ss_pred             cchHHHHHHHHhhC--CCCcEEEEecchhhHHHHHHHHhhh-cC
Q 022383          257 EWKFDTLCDLYDTL--TITQAVIFCNTKRKIYYSVFYFWIR-WI  297 (298)
Q Consensus       257 ~~k~~~l~~ll~~~--~~~k~lIf~~s~~~~~~l~~~L~~~-~~  297 (298)
                      ..|...+..++...  .+.|+||||++...++.+...|... |+
T Consensus        95 s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~  138 (271)
T 1z5z_A           95 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNT  138 (271)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCS
T ss_pred             CHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCC
Confidence            34899998888765  6689999999999999999999874 53

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=87.07  E-value=0.44  Score=37.46  Aligned_cols=19  Identities=26%  Similarity=0.471  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|+-++++||+|+|||...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            5677899999999999653

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=87.05  E-value=0.33  Score=41.19  Aligned_cols=26  Identities=23%  Similarity=0.413  Sum_probs=20.1

Q ss_pred             HHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           62 RAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        62 ~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .+...+..++++++.||+|+|||...
T Consensus        38 ~l~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           38 RLLIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHHHcCCeEEEECCCCCcHHHHH
Confidence            33444557899999999999999643

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=86.86  E-value=0.32  Score=38.08  Aligned_cols=22  Identities=23%  Similarity=0.394  Sum_probs=17.7

Q ss_pred             HhhcCCcEEEEcCCCCchHHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +...|+-++++||+|+|||...
T Consensus         8 ~~~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A            8 HMARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             -CCCCCCEEEECCTTSCHHHHH
T ss_pred             ccccCCEEEEECCCCCCHHHHH
Confidence            3457889999999999999643

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=86.77  E-value=0.48  Score=36.91  Aligned_cols=21  Identities=19%  Similarity=0.164  Sum_probs=17.0

Q ss_pred             hcCCcEEEEcCCCCchHHHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~   88 (298)
                      ..++.++++|++|+|||...-
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~   43 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGK   43 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHH
Confidence            357889999999999996543

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=86.76  E-value=0.46  Score=37.10  Aligned_cols=19  Identities=32%  Similarity=0.613  Sum_probs=15.0

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|+-+.++||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999653

>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=86.72  E-value=0.39  Score=37.69  Aligned_cols=19  Identities=32%  Similarity=0.494  Sum_probs=15.6

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|+-+++.||||+|||...
T Consensus        33 ~g~~ilI~GpsGsGKStLA   51 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETA   51 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            4567999999999999543

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=86.57  E-value=0.86  Score=38.48  Aligned_cols=55  Identities=11%  Similarity=0.126  Sum_probs=32.2

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccC---------CCC----eEEEEEcCcHHH-HHHHHHHHHHh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTS---------SRE----VQALILSPTREL-ATQTEKVILAI  124 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~---------~~~----~~~lil~p~~~l-~~q~~~~~~~~  124 (298)
                      |.-+++.||+|+|||...+-.+.+.....         ..+    ..++|+.-...+ ..++...++++
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~~  166 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHA  166 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHHc
Confidence            35689999999999965444444322110         112    578888754432 45555555444

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=86.35  E-value=0.39  Score=40.97  Aligned_cols=19  Identities=21%  Similarity=0.401  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      ++-++|+||||+|||....
T Consensus        40 ~~lIvI~GPTgsGKTtLa~   58 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSI   58 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            3568999999999996543

>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=86.23  E-value=0.35  Score=41.22  Aligned_cols=19  Identities=42%  Similarity=0.712  Sum_probs=17.0

Q ss_pred             hhcCCcEEEEcCCCCchHH
Q 022383           67 IIKGRDVIAQAQSGTGKTS   85 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~   85 (298)
                      +..|+.+.++||||+|||.
T Consensus       168 i~~g~~v~i~G~~GsGKTT  186 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTT  186 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHH
T ss_pred             ccCCCEEEEECCCCCCHHH
Confidence            4578999999999999996

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=86.11  E-value=1.6  Score=35.78  Aligned_cols=45  Identities=13%  Similarity=0.257  Sum_probs=30.4

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHhhcCC-----cEEEEcCCCCchHHHHH
Q 022383           42 DDLLRGIYQYGFEKPSAIQQRAVMPIIKGR-----DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        42 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~-----~~li~~pTG~GKT~~~~   88 (298)
                      ..|.+.|+-.|++ |-.+- .++..+++++     .+++.||.|+|||..+.
T Consensus        73 n~i~~~l~~qg~~-~~~~~-~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           73 NRIYKILELNGYD-PQYAA-SVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             CHHHHHHHHTTCC-HHHHH-HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHcCCC-HHHHH-HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            3788888888877 33222 2344455443     49999999999996554

>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=85.97  E-value=1.1  Score=40.65  Aligned_cols=24  Identities=13%  Similarity=0.274  Sum_probs=18.2

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVC   92 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~   92 (298)
                      ++.+++|.|+||||||.+.-..+.
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~  189 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMIL  189 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHH
T ss_pred             cCceEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999976443333

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=85.91  E-value=0.46  Score=38.17  Aligned_cols=52  Identities=19%  Similarity=0.308  Sum_probs=29.7

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILA  123 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~  123 (298)
                      .|.-+++.|++|+|||.-.+-.+.+.....  +..++|++-. .-..++..++..
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~--~~~v~~~s~E-~~~~~~~~~~~~   80 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEEY--GEPGVFVTLE-ERARDLRREMAS   80 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHHH--CCCEEEEESS-SCHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCCceeeccc-CCHHHHHHHHHH
Confidence            356799999999999954433333332221  2246666532 334555555543

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=85.68  E-value=0.43  Score=36.53  Aligned_cols=19  Identities=26%  Similarity=0.253  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      ++.++++|++|+|||...-
T Consensus         5 ~~~i~l~G~~GsGKst~a~   23 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGS   23 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            5679999999999997544

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=85.60  E-value=0.9  Score=40.54  Aligned_cols=20  Identities=40%  Similarity=0.657  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCCchHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~   88 (298)
                      .++++++.||+|+|||..+.
T Consensus        62 ~~~~iLl~GppGtGKT~la~   81 (456)
T 2c9o_A           62 AGRAVLLAGPPGTGKTALAL   81 (456)
T ss_dssp             TTCEEEEECCTTSSHHHHHH
T ss_pred             CCCeEEEECCCcCCHHHHHH
Confidence            34689999999999996543

>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=85.46  E-value=0.38  Score=36.73  Aligned_cols=21  Identities=19%  Similarity=0.338  Sum_probs=17.2

Q ss_pred             hcCCcEEEEcCCCCchHHHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~   88 (298)
                      ..++.+++.|++|+|||...-
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~   29 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGK   29 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHH
Confidence            356789999999999997543

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=85.20  E-value=0.14  Score=42.10  Aligned_cols=18  Identities=33%  Similarity=0.495  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      .+.+++.||+|+|||...
T Consensus        44 ~~~vll~G~~GtGKT~la   61 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLA   61 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            467999999999999654

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=85.18  E-value=0.3  Score=40.39  Aligned_cols=54  Identities=11%  Similarity=0.088  Sum_probs=32.9

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhh--cCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPII--KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~pTG~GKT~~~   87 (298)
                      +..+|+++.-.+.+...+++.-..  .. ....+..+.  -.+.+++.||+|+|||...
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~--~~-~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEF--LK-NPSRFHEMGARIPKGVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHH--HH-CHHHHHHTTCCCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHH--HH-CHHHHHHcCCCCCCeEEEECCCcChHHHHH
Confidence            456888987777777777654211  00 112232221  1345999999999999643

>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=85.15  E-value=0.66  Score=36.32  Aligned_cols=18  Identities=17%  Similarity=0.457  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCCchHHH
Q 022383           69 KGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~   86 (298)
                      .|+-++++||+|+|||..
T Consensus        18 ~g~~ivl~GPSGaGKsTL   35 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHI   35 (197)
T ss_dssp             SCCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEECcCCCCHHHH
Confidence            678899999999999964

>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=85.14  E-value=0.31  Score=37.48  Aligned_cols=20  Identities=20%  Similarity=0.503  Sum_probs=16.7

Q ss_pred             hhcCCcEEEEcCCCCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~   86 (298)
                      +..|.-+++.||+|+|||..
T Consensus         6 i~~g~~i~l~G~~GsGKSTl   25 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTI   25 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHH
Confidence            44677899999999999964

>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=85.10  E-value=0.5  Score=35.81  Aligned_cols=18  Identities=28%  Similarity=0.505  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      ++-++++|++|+|||...
T Consensus         3 ~~~i~l~G~~GsGKST~a   20 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            456899999999999654

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=84.99  E-value=0.6  Score=36.67  Aligned_cols=35  Identities=14%  Similarity=0.031  Sum_probs=23.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      .|.-+++.||+|+|||......+.   .   .+..++++.-
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~---~---~~~~v~~i~~   53 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL---L---SGKKVAYVDT   53 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH---H---HCSEEEEEES
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH---H---cCCcEEEEEC
Confidence            467789999999999965443332   1   1336777663

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=84.85  E-value=0.67  Score=35.98  Aligned_cols=19  Identities=47%  Similarity=0.623  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|.-+.+.||+|+|||...
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~   24 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLV   24 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            5777899999999999653

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=84.75  E-value=0.7  Score=36.66  Aligned_cols=21  Identities=24%  Similarity=0.339  Sum_probs=16.5

Q ss_pred             hhcCCcEEEEcCCCCchHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +..|+-+.++||+|+|||...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            346888999999999999643

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=84.74  E-value=0.58  Score=39.54  Aligned_cols=18  Identities=22%  Similarity=0.213  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      +-++|.||||+|||....
T Consensus         4 ~~i~i~GptgsGKt~la~   21 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSV   21 (322)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCcCCHHHHHH
Confidence            457889999999996543

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=84.72  E-value=0.65  Score=38.91  Aligned_cols=19  Identities=26%  Similarity=0.536  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      ++.++++||+|+|||....
T Consensus       105 g~vi~lvG~~GsGKTTl~~  123 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLA  123 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5678999999999997654

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=84.70  E-value=1.5  Score=34.55  Aligned_cols=45  Identities=16%  Similarity=0.120  Sum_probs=28.0

Q ss_pred             CHHHHHHHHHCCCCCChHHHHHHHHHhhcC----CcEEEEcCCCCchHHHH
Q 022383           41 KDDLLRGIYQYGFEKPSAIQQRAVMPIIKG----RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        41 ~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~----~~~li~~pTG~GKT~~~   87 (298)
                      ...|.+.|+-.|++ +..+ ...+..+.++    +.+++.||.|+|||..+
T Consensus        27 w~~I~~~l~yq~~~-~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a   75 (212)
T 1tue_A           27 WRPIVQFLRYQQIE-FITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG   75 (212)
T ss_dssp             SHHHHHHHHHTTCC-HHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH
T ss_pred             HHHHHHHHHHcCcC-HHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH
Confidence            34566666655544 4444 3444444444    35999999999999543

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=84.61  E-value=0.63  Score=36.18  Aligned_cols=20  Identities=30%  Similarity=0.411  Sum_probs=16.6

Q ss_pred             hcCCcEEEEcCCCCchHHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~   87 (298)
                      ..|.-+.++||+|||||...
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            45778999999999999654

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=84.52  E-value=0.48  Score=38.52  Aligned_cols=53  Identities=23%  Similarity=0.246  Sum_probs=29.9

Q ss_pred             ccCcccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           32 ITSFDAMGIKDDLLRGIYQYG--FEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~--~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      ..+|+++.-.+...+.+.+.-  +..+..++..   .....+.+++.||+|+|||...
T Consensus         8 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A            8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHc---CCCCCCeEEEECcCCCCHHHHH
Confidence            457888876777766665420  0011100000   0112457999999999999654

>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=84.41  E-value=1  Score=39.16  Aligned_cols=73  Identities=16%  Similarity=0.142  Sum_probs=47.0

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      ..++||.|+++.-+..+.+.+++.    ++.+..++|+.+..++...+.    +..+|+|+|.      .-..++++..+
T Consensus       280 ~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidip~v  349 (414)
T 3eiq_A          280 ITQAVIFINTRRKVDWLTEKMHAR----DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTD------LLARGIDVQQV  349 (414)
T ss_dssp             CSSCEEECSCHHHHHHHHHHHHTT----TCCCEEC---CHHHHHHHHHHHHSCC---CEEECS------SCC--CCGGGC
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHhc----CCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECC------ccccCCCccCC
Confidence            347899999999999998887654    677888898877655443332    4568999995      22346777888


Q ss_pred             cEEEech
Q 022383          177 KLLVLDE  183 (298)
Q Consensus       177 ~~vViDE  183 (298)
                      ++||.-+
T Consensus       350 ~~Vi~~~  356 (414)
T 3eiq_A          350 SLVINYD  356 (414)
T ss_dssp             SCEEESS
T ss_pred             CEEEEeC
Confidence            8887543

>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=84.36  E-value=0.61  Score=39.29  Aligned_cols=17  Identities=18%  Similarity=0.393  Sum_probs=13.8

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      -++|+||||+|||....
T Consensus        12 ~i~i~GptgsGKt~la~   28 (316)
T 3foz_A           12 AIFLMGPTASGKTALAI   28 (316)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCccCHHHHHH
Confidence            47889999999996543

>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=84.30  E-value=0.49  Score=41.06  Aligned_cols=20  Identities=20%  Similarity=0.305  Sum_probs=16.7

Q ss_pred             hhcCCcEEEEcCCCCchHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~   86 (298)
                      +..|..++++||||+|||..
T Consensus       133 ~~~g~~i~ivG~~GsGKTTl  152 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTT  152 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHH
Confidence            34677899999999999954

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=84.10  E-value=0.52  Score=35.36  Aligned_cols=17  Identities=18%  Similarity=0.434  Sum_probs=13.9

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      -++++||+|||||...-
T Consensus         3 ~I~l~G~~GsGKsT~a~   19 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAK   19 (179)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999997543

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=83.86  E-value=0.84  Score=46.51  Aligned_cols=39  Identities=18%  Similarity=0.245  Sum_probs=25.1

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEE
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL  211 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~  211 (298)
                      +++-+.+|+||+=.-++..-...+...++.+.+++-+|+
T Consensus       570 ~~~~~IliLDE~tSaLD~~te~~i~~~l~~~~~~~T~ii  608 (1321)
T 4f4c_A          570 VRNPKILLLDEATSALDAESEGIVQQALDKAAKGRTTII  608 (1321)
T ss_dssp             TTCCSEEEEESTTTTSCTTTHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCCCEEEEecccccCCHHHHHHHHHHHHHHhCCCEEEE
Confidence            367789999999776666556666666655543333333

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=83.84  E-value=0.5  Score=35.89  Aligned_cols=20  Identities=25%  Similarity=0.338  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCCchHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~   88 (298)
                      .|.-+.++||+|||||..+-
T Consensus         8 ~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            56678999999999996543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=83.79  E-value=0.63  Score=35.04  Aligned_cols=18  Identities=22%  Similarity=0.447  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      +..+.+.||.|||||...
T Consensus         4 ~~~i~l~G~~GsGKSTl~   21 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIG   21 (173)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            567899999999999653

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=83.78  E-value=2.7  Score=37.93  Aligned_cols=96  Identities=16%  Similarity=0.151  Sum_probs=54.6

Q ss_pred             CchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEc--------CCchHHHHH---Hhh
Q 022383           81 TGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVG--------GKSVGEDIR---KLE  149 (298)
Q Consensus        81 ~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~---~~~  149 (298)
                      ++|... +.-++........+.++||.|+++..+..+.+.++..+...++.+..++|        +.+..++..   ...
T Consensus       370 ~~k~~~-l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~  448 (555)
T 3tbk_A          370 NPKLRD-LYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR  448 (555)
T ss_dssp             CHHHHH-HHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-----------------------
T ss_pred             CHHHHH-HHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHh
Confidence            455543 23333333222234589999999999999999998865433344444444        443333322   222


Q ss_pred             --cCCcEEEeChHHHHHHHhccCccCCCccEEEech
Q 022383          150 --HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDE  183 (298)
Q Consensus       150 --~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE  183 (298)
                        +..+|+|+|.      .-..++++..+++||.=+
T Consensus       449 ~~g~~~vLvaT~------~~~~GlDlp~v~~VI~~d  478 (555)
T 3tbk_A          449 ASGDNNILIATS------VADEGIDIAECNLVILYE  478 (555)
T ss_dssp             ---CCSEEEECC------CTTCCEETTSCSEEEEES
T ss_pred             cCCCeeEEEEcc------hhhcCCccccCCEEEEeC
Confidence              3578999995      223578889999988644

>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=83.72  E-value=0.6  Score=35.82  Aligned_cols=20  Identities=45%  Similarity=0.712  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCCchHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~   88 (298)
                      .+..++++|++|+|||...-
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~   28 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAE   28 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            46789999999999997543

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=83.66  E-value=0.62  Score=37.12  Aligned_cols=22  Identities=41%  Similarity=0.600  Sum_probs=16.6

Q ss_pred             HhhcCCcEEEEcCCCCchHHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      +...|+-+.++||+|+|||...
T Consensus        12 ~~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           12 HMAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             ---CCCEEEEECCTTSCHHHHH
T ss_pred             cCCCCcEEEEECCCCCCHHHHH
Confidence            3457888999999999999643

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=83.55  E-value=2.4  Score=36.48  Aligned_cols=19  Identities=26%  Similarity=0.476  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      ..++++.||+|+|||..+-
T Consensus        72 ~~~ill~Gp~GtGKT~la~   90 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQ   90 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHH
Confidence            4689999999999996543

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=83.21  E-value=1.7  Score=37.11  Aligned_cols=54  Identities=9%  Similarity=0.018  Sum_probs=30.5

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccC---CCCeEEEEEcCcHHH-HHHHHHHHHHh
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTREL-ATQTEKVILAI  124 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~l-~~q~~~~~~~~  124 (298)
                      .-+++.||+|+|||...+-.+.+.....   ..+..++|+.-...+ ..++...++++
T Consensus       123 ~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~~  180 (343)
T 1v5w_A          123 AITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRF  180 (343)
T ss_dssp             EEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHc
Confidence            5689999999999965444343322211   024478888754421 33444444443

>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=83.17  E-value=0.86  Score=35.70  Aligned_cols=22  Identities=32%  Similarity=0.587  Sum_probs=16.8

Q ss_pred             HhhcCCcEEEEcCCCCchHHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      .+..|+-+.+.||+|+|||...
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl   37 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVV   37 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHH
Confidence            5677889999999999999643

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=83.07  E-value=0.68  Score=36.03  Aligned_cols=19  Identities=37%  Similarity=0.594  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|.-+.+.||.|+|||...
T Consensus        28 ~g~~i~l~G~~GsGKSTl~   46 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIA   46 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            5678999999999999654

>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=83.03  E-value=0.66  Score=40.00  Aligned_cols=19  Identities=21%  Similarity=0.438  Sum_probs=15.6

Q ss_pred             hcCCcEEEEcCCCCchHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~   86 (298)
                      ..+..++++||||||||..
T Consensus       121 ~~~g~i~I~GptGSGKTTl  139 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTT  139 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3456799999999999954

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=83.01  E-value=0.76  Score=37.44  Aligned_cols=17  Identities=24%  Similarity=0.219  Sum_probs=13.7

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      -++++||+|||||....
T Consensus         3 li~I~G~~GSGKSTla~   19 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAI   19 (253)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCcCHHHHHH
Confidence            36899999999996543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=82.96  E-value=2.2  Score=37.69  Aligned_cols=68  Identities=6%  Similarity=-0.076  Sum_probs=47.4

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEE
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~v  179 (298)
                      +.+++|+||+++-++.+.+.+++.    +.++..++|+........-..+..+|+|+|.      +-..++++. +..|
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~v~~lhg~~r~~~~~~f~~g~~~vLVaT~------v~e~GiDip-~~~V  238 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKA----GKKVLYLNRKTFESEYPKCKSEKWDFVITTD------ISEMGANFK-ADRV  238 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTTHHHHTTHHHHSCCSEEEECG------GGGTSCCCC-CSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCeEEEeCCccHHHHHHhhcCCCCeEEEECc------hHHcCcccC-CcEE
Confidence            347999999999999999988876    6788889987332211122235689999996      223456776 5555

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=82.71  E-value=0.86  Score=38.52  Aligned_cols=37  Identities=8%  Similarity=0.125  Sum_probs=21.5

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ..+.+|++..|.+. ..  ..+...++.+.+...++..|-
T Consensus       151 ~ad~ill~k~dl~d-e~--~~l~~~l~~l~~~~~ii~~sh  187 (318)
T 1nij_A          151 YADRILLTKTDVAG-EA--EKLHERLARINARAPVYTVTH  187 (318)
T ss_dssp             TCSEEEEECTTTCS-CT--HHHHHHHHHHCSSSCEEECCS
T ss_pred             hCCEEEEECcccCC-HH--HHHHHHHHHhCCCCeEEEecc
Confidence            45778888887662 22  455555555555555555443

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=82.50  E-value=0.57  Score=39.08  Aligned_cols=17  Identities=18%  Similarity=0.010  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      +.+++.||+|+|||...
T Consensus        37 ~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             SEEEEEECTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            57899999999999643

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=82.24  E-value=3  Score=39.18  Aligned_cols=68  Identities=6%  Similarity=0.003  Sum_probs=48.3

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh-hcCCcEEEeChHHHHHHHhccCccCCCccEE
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLL  179 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~v  179 (298)
                      +.++||.||+++-++.+.+.+++.    ++++..++|... ....... .+..+|+|+|.      +-..++++. +++|
T Consensus       410 ~~~~lVF~~s~~~~e~la~~L~~~----g~~v~~lHg~eR-~~v~~~F~~g~~~VLVaTd------v~e~GIDip-v~~V  477 (673)
T 2wv9_A          410 AGKTVWFVASVKMSNEIAQCLQRA----GKRVIQLNRKSY-DTEYPKCKNGDWDFVITTD------ISEMGANFG-ASRV  477 (673)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSSH-HHHGGGGGTCCCSEEEECG------GGGTTCCCC-CSEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCeEEEeChHHH-HHHHHHHHCCCceEEEECc------hhhcceeeC-CcEE
Confidence            457999999999999999888764    678888998422 2222222 25678999995      233467777 8777


Q ss_pred             E
Q 022383          180 V  180 (298)
Q Consensus       180 V  180 (298)
                      |
T Consensus       478 I  478 (673)
T 2wv9_A          478 I  478 (673)
T ss_dssp             E
T ss_pred             E
Confidence            6

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=81.94  E-value=1.1  Score=38.63  Aligned_cols=23  Identities=26%  Similarity=0.530  Sum_probs=17.3

Q ss_pred             HHhhcCCc--EEEEcCCCCchHHHH
Q 022383           65 MPIIKGRD--VIAQAQSGTGKTSMI   87 (298)
Q Consensus        65 ~~~~~~~~--~li~~pTG~GKT~~~   87 (298)
                      +.+++|.|  ++.-|+||||||...
T Consensus        98 ~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           98 SQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHhCCCCEEEEEeCCCCCCccEEe
Confidence            44557876  566799999999764

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=81.68  E-value=0.65  Score=35.10  Aligned_cols=19  Identities=21%  Similarity=0.321  Sum_probs=15.6

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|..+.++||.|+|||...
T Consensus         7 ~g~~i~l~G~~GsGKSTl~   25 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVA   25 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            3567899999999999654

>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=81.48  E-value=3.4  Score=34.45  Aligned_cols=71  Identities=11%  Similarity=0.142  Sum_probs=49.9

Q ss_pred             CCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCC
Q 022383          100 REVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRA  175 (298)
Q Consensus       100 ~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~  175 (298)
                      .+.++||.+++++-+..+.+.++        .+..++|+.+..+....+    .+..+|+|+|.     . -..++++..
T Consensus       219 ~~~~~lvf~~~~~~~~~l~~~l~--------~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~-~~~Gid~~~  284 (337)
T 2z0m_A          219 KDKGVIVFVRTRNRVAKLVRLFD--------NAIELRGDLPQSVRNRNIDAFREGEYDMLITTD-----V-ASRGLDIPL  284 (337)
T ss_dssp             CCSSEEEECSCHHHHHHHHTTCT--------TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECH-----H-HHTTCCCCC
T ss_pred             CCCcEEEEEcCHHHHHHHHHHhh--------hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcC-----c-cccCCCccC
Confidence            34579999999998888776543        456778887765554333    24678999995     2 234788889


Q ss_pred             ccEEEechh
Q 022383          176 IKLLVLDES  184 (298)
Q Consensus       176 l~~vViDE~  184 (298)
                      +++||.-+.
T Consensus       285 ~~~Vi~~~~  293 (337)
T 2z0m_A          285 VEKVINFDA  293 (337)
T ss_dssp             BSEEEESSC
T ss_pred             CCEEEEecC
Confidence            999887543

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=81.47  E-value=0.63  Score=42.97  Aligned_cols=39  Identities=26%  Similarity=0.340  Sum_probs=26.8

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEE
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI  212 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~  212 (298)
                      .+.+++++||.-.-++......+...++.+..+.-+++.
T Consensus       497 ~~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~i  535 (582)
T 3b5x_A          497 RDAPVLILDEATSALDTESERAIQAALDELQKNKTVLVI  535 (582)
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            678899999997766666666777777666544434443

>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=81.43  E-value=2.1  Score=39.18  Aligned_cols=41  Identities=12%  Similarity=0.308  Sum_probs=25.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhcc-CCCCeEEEEEcCc
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPT  110 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~  110 (298)
                      ..+++|.|.||||||.+.-..+...+.. .+...+.+++=|-
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpK  255 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPK  255 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSS
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCC
Confidence            3689999999999997654444444332 2233344444444

>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=81.33  E-value=1.3  Score=37.59  Aligned_cols=24  Identities=29%  Similarity=0.567  Sum_probs=17.9

Q ss_pred             HHHhhcCCc--EEEEcCCCCchHHHH
Q 022383           64 VMPIIKGRD--VIAQAQSGTGKTSMI   87 (298)
Q Consensus        64 ~~~~~~~~~--~li~~pTG~GKT~~~   87 (298)
                      ++.+++|.|  ++.-|+||+|||...
T Consensus        70 v~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           70 VKDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCeEEEEEECCCCCCCceEe
Confidence            344567876  566799999999764

>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=81.24  E-value=3.7  Score=36.38  Aligned_cols=67  Identities=10%  Similarity=0.012  Sum_probs=48.2

Q ss_pred             eEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh-hcCCcEEEeChHHHHHHHhccCccCCCccEEE
Q 022383          102 VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (298)
Q Consensus       102 ~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vV  180 (298)
                      .++||.||++.-++++.+.+++.    ++.+..++++.... ..... .+..+|+|+|.      +-..++++.. ++||
T Consensus       189 ~~~lVF~~s~~~a~~l~~~L~~~----g~~~~~lh~~~~~~-~~~~f~~g~~~vLVaT~------v~~~GiDip~-~~VI  256 (451)
T 2jlq_A          189 GKTVWFVPSIKAGNDIANCLRKS----GKRVIQLSRKTFDT-EYPKTKLTDWDFVVTTD------ISEMGANFRA-GRVI  256 (451)
T ss_dssp             SCEEEECSSHHHHHHHHHHHHTT----TCCEEEECTTTHHH-HGGGGGSSCCSEEEECG------GGGSSCCCCC-SEEE
T ss_pred             CCEEEEcCCHHHHHHHHHHHHHc----CCeEEECCHHHHHH-HHHhhccCCceEEEECC------HHHhCcCCCC-CEEE
Confidence            47999999999999999988764    67788888865532 22222 35679999995      2345677877 6666

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=81.22  E-value=0.77  Score=34.68  Aligned_cols=16  Identities=19%  Similarity=0.385  Sum_probs=13.5

Q ss_pred             cEEEEcCCCCchHHHH
Q 022383           72 DVIAQAQSGTGKTSMI   87 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~   87 (298)
                      -++++|++|||||...
T Consensus         4 ~I~i~G~~GsGKST~a   19 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWA   19 (181)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEecCCCCCHHHHH
Confidence            4789999999999754

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=81.21  E-value=0.95  Score=38.38  Aligned_cols=18  Identities=17%  Similarity=0.329  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      +.++++||||+|||....
T Consensus         6 ~~i~i~GptGsGKTtla~   23 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAM   23 (323)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            358899999999996543

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=81.06  E-value=0.76  Score=34.42  Aligned_cols=17  Identities=18%  Similarity=0.122  Sum_probs=13.9

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      .+++.|+.|+|||...-
T Consensus         3 ~i~l~G~~GsGKsT~~~   19 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAA   19 (173)
T ss_dssp             EEEEECSSSSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999996543

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=81.05  E-value=0.86  Score=34.79  Aligned_cols=18  Identities=22%  Similarity=0.377  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      +.-+++.|+.|+|||...
T Consensus         3 ~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            567899999999999654

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=81.03  E-value=0.71  Score=38.51  Aligned_cols=18  Identities=22%  Similarity=0.390  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      ..+++.||+|+|||..+-
T Consensus        48 ~~~ll~G~~GtGKt~la~   65 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAK   65 (311)
T ss_dssp             EEEEEESCSSSSHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHH
Confidence            379999999999996543

>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=80.99  E-value=1.9  Score=40.51  Aligned_cols=105  Identities=13%  Similarity=0.157  Sum_probs=64.0

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHh--hccCCceEEEEEcC--------CchHHHHHHhh----cCCcEEEeChHHHHHHH
Q 022383          101 EVQALILSPTRELATQTEKVILAI--GDFINIQAHACVGG--------KSVGEDIRKLE----HGVHVVSGTPGRVCDMI  166 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~--~~~~~~~~~~~~~~--------~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~  166 (298)
                      +.++||.|+++..+..+.+.++..  ....++++..++|+        .+..++...+.    +..+|+|+|.      .
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~------~  473 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATT------V  473 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEEC------S
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEcc------c
Confidence            458999999999999999988764  12236788888888        66555443332    4578999995      2


Q ss_pred             hccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEee
Q 022383          167 KRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       167 ~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      -..++++.++++||.=+.    .++....++.+-+--.....+++++..
T Consensus       474 ~~~GIDip~v~~VI~~d~----p~s~~~~~Qr~GRArr~g~~~~l~~~~  518 (699)
T 4gl2_A          474 AEEGLDIKECNIVIRYGL----VTNEIAMVQARGRARADESTYVLVAHS  518 (699)
T ss_dssp             CCTTSCCCSCCCCEEESC----CCCHHHHHHHHTTSCSSSCEEEEEEES
T ss_pred             cccCCccccCCEEEEeCC----CCCHHHHHHHcCCCCCCCceEEEEEeC
Confidence            335788889988874332    234445555555533334455555553

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=80.94  E-value=13  Score=33.12  Aligned_cols=23  Identities=39%  Similarity=0.582  Sum_probs=18.6

Q ss_pred             HhhcCCcEEEEcCCCCchHHHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      .+.+|+..++.+|.|+|||....
T Consensus       147 pi~kGq~~~i~G~sGvGKTtL~~  169 (473)
T 1sky_E          147 PYIKGGKIGLFGGAGVGKTVLIQ  169 (473)
T ss_dssp             CEETTCEEEEECCSSSCHHHHHH
T ss_pred             hhccCCEEEEECCCCCCccHHHH
Confidence            34578999999999999996543

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=80.53  E-value=1.2  Score=38.01  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=17.1

Q ss_pred             HHhhcCCc--EEEEcCCCCchHHHH
Q 022383           65 MPIIKGRD--VIAQAQSGTGKTSMI   87 (298)
Q Consensus        65 ~~~~~~~~--~li~~pTG~GKT~~~   87 (298)
                      ..+++|.|  ++.-|+||||||...
T Consensus        88 ~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           88 DKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hHhhCCCceEEEEecCCCCCCCeEE
Confidence            34457876  566799999999764

>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=80.43  E-value=2.6  Score=34.59  Aligned_cols=24  Identities=17%  Similarity=0.260  Sum_probs=19.2

Q ss_pred             HhhcCCcEEEEcCCCCchHHHHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMIAL   89 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~~~   89 (298)
                      -+..|.-+++.||+|+|||.....
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~   49 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQ   49 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHH
Confidence            456788999999999999965443

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=80.16  E-value=1.5  Score=37.68  Aligned_cols=26  Identities=31%  Similarity=0.498  Sum_probs=19.8

Q ss_pred             HHHHhhcCCc--EEEEcCCCCchHHHHH
Q 022383           63 AVMPIIKGRD--VIAQAQSGTGKTSMIA   88 (298)
Q Consensus        63 ~~~~~~~~~~--~li~~pTG~GKT~~~~   88 (298)
                      .+..+++|.|  ++.-|+||+|||....
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm~  104 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTML  104 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEeC
Confidence            5566778887  4667999999997753

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=80.13  E-value=1.4  Score=38.62  Aligned_cols=26  Identities=31%  Similarity=0.487  Sum_probs=19.8

Q ss_pred             HHHHhhcCCc--EEEEcCCCCchHHHHH
Q 022383           63 AVMPIIKGRD--VIAQAQSGTGKTSMIA   88 (298)
Q Consensus        63 ~~~~~~~~~~--~li~~pTG~GKT~~~~   88 (298)
                      .+..+++|.|  ++.-|+||||||....
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM~  159 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTML  159 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEeC
Confidence            4566678877  5667999999997753

---

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	298
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	5e-59
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	7e-52
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	9e-52
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	1e-49
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	6e-43
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	2e-42
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	8e-42
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	1e-38
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	1e-33
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	8e-22
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	7e-21
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	9e-21
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-17
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	2e-13
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	3e-13
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	5e-11
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	6e-10
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-08
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	4e-08
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	1e-05
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	0.003

>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 =  186 bits (472), Expect = 5e-59
 Identities = 157/222 (70%), Positives = 193/222 (86%)

Query: 17  DDDKMVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQ 76
           D  K+ FET+E V+   +FD MG+++DLLRGIY YGFEKPSAIQQRA+  IIKGRDVIAQ
Sbjct: 1   DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQ 60

Query: 77  AQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACV 136
           +QSGTGKT+  +++V Q +D   RE QALIL+PTRELA Q +K +LA+GD++N+Q HAC+
Sbjct: 61  SQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACI 120

Query: 137 GGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQI 196
           GG +VGEDIRKL++G HVV+GTPGRV DMI+R++LRTRAIK+LVLDE+DEML++GFK+QI
Sbjct: 121 GGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQI 180

Query: 197 YDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKR 238
           YDVYRYLPP  QVVLISATLPHEILEMT KFMTDP++ILVKR
Sbjct: 181 YDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKR 222

>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 =  167 bits (424), Expect = 7e-52
 Identities = 119/210 (56%), Positives = 164/210 (78%), Gaps = 1/210 (0%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           E + SFD M + + LLRGIY YGFEKPSAIQQRA++P IKG DVIAQAQSGTGKT+  A+
Sbjct: 9   EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 68

Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
           ++ Q ++   +  QAL+L+PTRELA Q +KV++A+GD++    HAC+GG +V  +++KL+
Sbjct: 69  SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 128

Query: 150 HGV-HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
               H++ GTPGRV DM+ R+ L  + IK+ VLDE+DEMLSRGFKDQIYD+++ L  + Q
Sbjct: 129 MEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQ 188

Query: 209 VVLISATLPHEILEMTTKFMTDPVKILVKR 238
           VVL+SAT+P ++LE+T KFM DP++ILVK+
Sbjct: 189 VVLLSATMPSDVLEVTKKFMRDPIRILVKK 218

>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 =  167 bits (423), Expect = 9e-52
 Identities = 115/207 (55%), Positives = 157/207 (75%), Gaps = 1/207 (0%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
           + +  FD M + ++LLRG++ YGFE+PSAIQQRA+MPII+G DV+AQAQSGTGKT   ++
Sbjct: 7   KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 66

Query: 90  TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE 149
              Q +DTS +  QAL+L+PTRELA Q +KV++A+   ++I+ HAC+GG S  ED   L 
Sbjct: 67  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL- 125

Query: 150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQV 209
               +V GTPGRV D I+R+  RT  IK+ +LDE+DEMLS GFK+QIY ++  LPP  QV
Sbjct: 126 RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQV 185

Query: 210 VLISATLPHEILEMTTKFMTDPVKILV 236
           VL+SAT+P+++LE+TTKFM +PV+ILV
Sbjct: 186 VLLSATMPNDVLEVTTKFMRNPVRILV 212

>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 =  161 bits (409), Expect = 1e-49
 Identities = 71/205 (34%), Positives = 120/205 (58%), Gaps = 3/205 (1%)

Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVC 92
           +F+ + + D++L  I   GFEKP+ IQ + +   +    +++AQA++G+GKT+  A+ + 
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV 152
           + V+ ++     +IL+PTRELA Q    I ++    N++     GGK++   I+ L+   
Sbjct: 65  ELVNENNGIEA-IILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 122

Query: 153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLI 212
           ++V GTPGR+ D I R TL  + +K  +LDE+DEML+ GF   +  +      D +++L 
Sbjct: 123 NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLF 182

Query: 213 SATLPHEILEMTTKFMTDPVKILVK 237
           SAT+P EIL +  K+M D   I  K
Sbjct: 183 SATMPREILNLAKKYMGDYSFIKAK 207

>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 =  144 bits (363), Expect = 6e-43
 Identities = 73/207 (35%), Positives = 114/207 (55%), Gaps = 3/207 (1%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           + F    +K +LLR I   GFE PS +Q   +   I G DV+ QA+SG GKT++  L   
Sbjct: 1   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 60

Query: 93  QTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGK-SVGEDIRKL-EH 150
           Q ++  + +V  L++  TRELA Q  K       ++     A   G  S+ +D   L ++
Sbjct: 61  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 120

Query: 151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQV 209
             H+V GTPGR+  + + K+L  + IK  +LDE D+ML +   +  + +++R  P + QV
Sbjct: 121 CPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQV 180

Query: 210 VLISATLPHEILEMTTKFMTDPVKILV 236
           ++ SATL  EI  +  KFM DP++I V
Sbjct: 181 MMFSATLSKEIRPVCRKFMQDPMEIFV 207

>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 =  142 bits (359), Expect = 2e-42
 Identities = 67/203 (33%), Positives = 120/203 (59%), Gaps = 1/203 (0%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
             F+   +K +LL GI++ G+EKPS IQ+ ++   + GRD++A+A++GTGK+    + + 
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 93  QTVDTSSREVQALILSPTREL-ATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHG 151
           + +D     +QA+++ PTREL    ++  I         +  A  GG ++ +DI +L+  
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122

Query: 152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVL 211
           VHVV  TPGR+ D+IK+   +   ++++VLDE+D++LS+ F   + D+   LP + Q++L
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL 182

Query: 212 ISATLPHEILEMTTKFMTDPVKI 234
            SAT P  + +     +  P +I
Sbjct: 183 YSATFPLSVQKFMNSHLEKPYEI 205

>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 =  142 bits (358), Expect = 8e-42
 Identities = 61/220 (27%), Positives = 110/220 (50%), Gaps = 13/220 (5%)

Query: 30  EAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL 89
             I +FD + +   +   I    +++P+ IQ+ A+  I++ RD++A AQ+G+GKT+   +
Sbjct: 18  NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLI 77

Query: 90  TVCQTV---------DTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKS 140
            +   +          + +   + LIL+PTRELA Q             +++    GG  
Sbjct: 78  PIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGAD 137

Query: 141 VGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVY 200
               IR+++ G H++  TPGR+ D I++  +     K +VLDE+D ML  GF+ QI  + 
Sbjct: 138 THSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKII 197

Query: 201 RYL----PPDLQVVLISATLPHEILEMTTKFMTDPVKILV 236
                    + Q ++ SAT P EI ++   F+ + + + V
Sbjct: 198 EESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV 237

>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 =  133 bits (335), Expect = 1e-38
 Identities = 82/201 (40%), Positives = 121/201 (60%)

Query: 34  SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQ 93
           +F+   +K +LL GI++ GFEKPS IQ+ A+   I GRD++A+A++GTGKT+   +   +
Sbjct: 2   TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 61

Query: 94  TVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVH 153
            V     ++QALI+ PTRELA QT +V+  +G    I      GG ++ +DI +L   VH
Sbjct: 62  KVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVH 121

Query: 154 VVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS 213
           ++ GTPGRV D+  RK        L ++DE+D+MLSR FK  I  +  +LPP  Q +L S
Sbjct: 122 ILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFS 181

Query: 214 ATLPHEILEMTTKFMTDPVKI 234
           AT P  + E   K +  P +I
Sbjct: 182 ATFPLTVKEFMVKHLHKPYEI 202

>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 =  120 bits (301), Expect = 1e-33
 Identities = 59/208 (28%), Positives = 101/208 (48%), Gaps = 4/208 (1%)

Query: 33  TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVC 92
           T F     +  ++  I    F KP+ IQ+R +   ++G  ++ Q+Q+GTGKT    L + 
Sbjct: 1   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM 60

Query: 93  QTVDTSSRE----VQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL 148
           + +     E    + A       ++  +T K+         I A   +GG    + + KL
Sbjct: 61  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL 120

Query: 149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQ 208
               H+V GTPGR+ D I+ + L      +LV+DE+D ML  GF   +  +   +P DLQ
Sbjct: 121 NVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQ 180

Query: 209 VVLISATLPHEILEMTTKFMTDPVKILV 236
           +++ SAT+P ++     K+M +P  + V
Sbjct: 181 MLVFSATIPEKLKPFLKKYMENPTFVHV 208

>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 = 88.9 bits (219), Expect = 8e-22
 Identities = 28/208 (13%), Positives = 69/208 (33%), Gaps = 13/208 (6%)

Query: 32  ITSFDAMGIKDDLLRGIYQY-GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALT 90
           +   + + ++    + + +  G+++    Q+  +  ++ GRD +    +G GK+    + 
Sbjct: 1   MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIP 60

Query: 91  VCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEH 150
                         +++SP   L       + A G             + +         
Sbjct: 61  ALL------LNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTG 114

Query: 151 GVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQ----IYDVYRYLPPD 206
            + ++   P R+      + L      LL +DE+  +   G   +         R   P 
Sbjct: 115 QIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPT 174

Query: 207 LQVVLISATLPHEILEMTTKF--MTDPV 232
           L  + ++AT      +   +   + DP+
Sbjct: 175 LPFMALTATADDTTRQDIVRLLGLNDPL 202

>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 = 87.3 bits (215), Expect = 7e-21
 Identities = 27/193 (13%), Positives = 55/193 (28%), Gaps = 24/193 (12%)

Query: 45  LRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQA 104
               ++    +P AIQ+     I++     A A +G GKTS                 + 
Sbjct: 33  FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK---RC 89

Query: 105 LILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGE------DIRKLEHGVHVVSGT 158
            ++ PT  L  Q  + I    +   +     +G            +  +      +V  T
Sbjct: 90  YVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITT 149

Query: 159 PGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-----------GFKDQIYDVYRYLPPDL 207
              +    +           + +D+ D +L             GF   +           
Sbjct: 150 TQFLSKHYR----ELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARG 205

Query: 208 QVVLISATLPHEI 220
            +++ +AT     
Sbjct: 206 CLMVSTATAKKGK 218

>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 = 85.8 bits (211), Expect = 9e-21
 Identities = 32/183 (17%), Positives = 69/183 (37%), Gaps = 10/183 (5%)

Query: 39  GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS 98
            I    +  + + G E+    Q  AV  +  G++++    +  GKT +  + + +     
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 99  SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGT 158
            + +    + P R LA +  +              +    +S  E +   +  V     T
Sbjct: 69  GKSLY---VVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHLGDCDIIVT----T 121

Query: 159 PGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQ---IYDVYRYLPPDLQVVLISAT 215
             +   +I+ +    +A+  LV+DE   + S         +    R +   L+V+ +SAT
Sbjct: 122 SEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSAT 181

Query: 216 LPH 218
            P+
Sbjct: 182 APN 184

>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 = 79.6 bits (195), Expect = 1e-17
 Identities = 36/219 (16%), Positives = 66/219 (30%), Gaps = 33/219 (15%)

Query: 69  KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI 128
           K R  I     G GKT      + +  +   R ++ LIL+PTR +A + E+ +       
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVR--EAIKRGLRTLILAPTRVVAAEMEEAL------- 58

Query: 129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML 188
                  +  +     IR    G  +V         M     +R     L+++DE+    
Sbjct: 59  -----RGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTD 113

Query: 189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVKRDELTLEGIKQ 248
                 + Y   R    +   + ++AT P         F      I+ +  E+       
Sbjct: 114 PASIAARGYISTRVEMGEAAGIFMTATPPGSRDP----FPQSNAPIMDEEREIPERSWNS 169

Query: 249 FFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYY 287
               V   +                + V F  + +    
Sbjct: 170 GHEWVTDFKG---------------KTVWFVPSIKAGND 193

>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 = 65.6 bits (158), Expect = 2e-13
 Identities = 31/203 (15%), Positives = 76/203 (37%), Gaps = 5/203 (2%)

Query: 48  IYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALIL 107
           + +    +P   Q+       K  + +    +G GKT +  +     +     +V   +L
Sbjct: 2   VLRRDLIQPRIYQEVIY-AKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVL--ML 58

Query: 108 SPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIK 167
           +PT+ L  Q  +    + +    +  A  G KS  E  +       +V+ TP  + + + 
Sbjct: 59  APTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVA-TPQTIENDLL 117

Query: 168 RKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKF 227
              +    + L+V DE+   +       I   Y+    +  V+ ++A+      ++    
Sbjct: 118 AGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVI 177

Query: 228 MTDPVKILVKRDELTLEGIKQFF 250
               ++ +  R E + + ++ + 
Sbjct: 178 NNLGIEHIEYRSENSPD-VRPYV 199

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 64.6 bits (156), Expect = 3e-13
 Identities = 46/58 (79%), Positives = 48/58 (82%)

Query: 239 DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW 296
           DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRK+ +         
Sbjct: 1   DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREAN 58

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

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 = 54.9 bits (131), Expect = 6e-10
 Identities = 26/50 (52%), Positives = 36/50 (72%)

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR 295
           IKQF+V VE EE+K++ L DLYD++++TQAVIFCNT+RK+          
Sbjct: 1   IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRND 50

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 51.2 bits (121), Expect = 1e-08
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 245 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFW 293
           G++Q++V ++ +  K   L DL D L   Q VIF  + ++         
Sbjct: 1   GLQQYYVKLK-DNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLV 48

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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 = 50.0 bits (118), Expect = 4e-08
 Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFW 293
           ELTL+GI Q++  VE E  K   L  L+  L I QA+IFCN+  ++        
Sbjct: 1   ELTLKGITQYYAFVE-ERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKIT 53

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

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 = 42.3 bits (98), Expect = 1e-05
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 2/51 (3%)

Query: 246 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW 296
           I+Q +V V   E +F+ LC L         ++FC TKR             
Sbjct: 4   IEQSYVEVNENE-RFEALCRLLKNKEF-YGLVFCKTKRDTKELASMLRDIG 52

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

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]

 Score = 35.0 bits (79), Expect = 0.003
 Identities = 21/149 (14%), Positives = 51/149 (34%), Gaps = 14/149 (9%)

Query: 69  KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFI 128
           KG   +     G GKT      +              +L+PTR + ++ ++    +    
Sbjct: 6   KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTL--VLAPTRVVLSEMKEAFHGLDVKF 63

Query: 129 NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML 188
           + QA +  G                + +     +   +   T      +++++DE+  + 
Sbjct: 64  HTQAFSAHGSGRE-----------VIDAMCHATLTYRMLEPTRVVN-WEVIIMDEAHFLD 111

Query: 189 SRGFKDQIYDVYRYLPPDLQVVLISATLP 217
                 + +  +R    +   +L++AT P
Sbjct: 112 PASIAARGWAAHRARANESATILMTATPP 140

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	298
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.97
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.96
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.96
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.95
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.9
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.85
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.84
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.81
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.79
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.79
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.72
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.27
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.19
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.91
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.79
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.42
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.22
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	98.2
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	98.05
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.01
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	97.92
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.81
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.79
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.51
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.51
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.34
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.3
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.2
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.19
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.13
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.07
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.01
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.0
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.96
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	96.95
d1okkd2	207	GTPase domain of the signal recognition particle r	96.94
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.92
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.76
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	96.73
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.71
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.65
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	96.47
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.37
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.19
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.14
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	96.0
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.9
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	95.89
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.76
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.45
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	95.19
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	95.18
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	95.14
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	95.07
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	94.98
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	94.94
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	94.9
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	94.81
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.52
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	94.51
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.43
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.41
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	94.17
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.9
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.84
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	93.22
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.18
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	92.96
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	92.91
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	92.73
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	92.71
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	92.09
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	91.9
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	91.88
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	91.25
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	90.48
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	90.39
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	90.2
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	89.97
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	89.94
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	89.86
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	89.86
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	89.83
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	89.62
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	89.52
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	89.15
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	88.91
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	88.72
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	88.6
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	88.06
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	88.01
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	87.72
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	87.62
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	87.42
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	87.26
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	87.17
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	87.0
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	86.66
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	86.22
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	86.03
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	85.82
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	85.54
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	85.46
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	85.29
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	85.05
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	85.04
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	85.04
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	84.98
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	83.8
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	83.79
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	83.73
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	83.72
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	83.68
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	83.51
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	83.21
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	82.57
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	82.52
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	82.47
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	82.28
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	82.2
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	81.99
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	81.9
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	81.64
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	81.43
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	81.28
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	81.14
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	81.08
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	80.74
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	80.68
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	80.62
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	80.54
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	80.54
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	80.46
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	80.18

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.9e-48  Score=314.60  Aligned_cols=216  Identities=71%  Similarity=1.134  Sum_probs=204.3

Q ss_pred             ceeecccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCC
Q 022383           21 MVFETTEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSR  100 (298)
Q Consensus        21 ~~~~~~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~  100 (298)
                      .+.+.++..+...+|++|+|++.+.++|+++||..|+++|..++|.+++|+|+++.||||||||+||++|+++.+.....
T Consensus         5 ~~~~~~~~~~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~   84 (222)
T d2j0sa1           5 VEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVR   84 (222)
T ss_dssp             CCCCCCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSC
T ss_pred             cccccCCCCCCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccccccccccccc
Confidence            44455666777889999999999999999999999999999999999999999999999999999999999999988878


Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEE
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vV  180 (298)
                      .++++|++||++|+.|+.+.++++++..++++..+.|+.....+...+..+++|+|+||+++.++++.+..++++++++|
T Consensus        85 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lV  164 (222)
T d2j0sa1          85 ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLV  164 (222)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             CceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeee
Confidence            88999999999999999999999999999999999999998888888888999999999999999999999999999999


Q ss_pred             echhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          181 LDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       181 iDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                      +||||.+++.+|...+..+++.+++.+|++++|||+++.+.++.+.++.+|..+.+
T Consensus       165 lDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V  220 (222)
T d2j0sa1         165 LDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV  220 (222)
T ss_dssp             EETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECC
T ss_pred             ecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEE
Confidence            99999999999999999999999999999999999999999999999999988765

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4e-45  Score=295.50  Aligned_cols=203  Identities=33%  Similarity=0.630  Sum_probs=190.9

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      ..+|++++|+++++++|.++||+.|+++|++++|.+++|+|++++||||+|||+||++|+++++.....+++++|++|++
T Consensus         2 ~~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~   81 (206)
T d1veca_           2 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTR   81 (206)
T ss_dssp             CSSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCH
T ss_pred             CCChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecc
Confidence            36899999999999999999999999999999999999999999999999999999999999998888889999999999


Q ss_pred             HHHHHHHHHHHHhhccC-CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          112 ELATQTEKVILAIGDFI-NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       112 ~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      +|+.|+.+.++++.+.. +.......|+.........+..+++|+|+||+++..++..+...+++++++|+||||.|++.
T Consensus        82 el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~  161 (206)
T d1veca_          82 ELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQ  161 (206)
T ss_dssp             HHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTST
T ss_pred             hhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEecccccccc
Confidence            99999999999887654 46777788888888888888899999999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEE
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKI  234 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~  234 (298)
                      +|...+..+++.+++++|++++|||+++.+.++.+.++.+|..+
T Consensus       162 ~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         162 DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             TTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             chHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            99999999999999999999999999999999999999999765

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=8.6e-45  Score=294.50  Aligned_cols=208  Identities=55%  Similarity=0.918  Sum_probs=188.1

Q ss_pred             cCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEE
Q 022383           27 EGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALI  106 (298)
Q Consensus        27 ~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~li  106 (298)
                      ..++++.+|++|+|++++.++|+++||+.|+++|.++||++++|+|+++++|||+|||++|++|+++++.....+++++|
T Consensus         4 ~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~li   83 (212)
T d1qdea_           4 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALM   83 (212)
T ss_dssp             SCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEE
T ss_pred             CCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEE
Confidence            45677899999999999999999999999999999999999999999999999999999999999999988888999999


Q ss_pred             EcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhH
Q 022383          107 LSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (298)
Q Consensus       107 l~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~  186 (298)
                      ++|+++++.|+...+..+.....+......++....++...+ ++++|+|+||+++..++..+.+++.+++++|+||||.
T Consensus        84 l~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~  162 (212)
T d1qdea_          84 LAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADE  162 (212)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C-TTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHH
T ss_pred             EcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHh-cCCcEEEECCCccccccccCceecCcceEEeehhhhh
Confidence            999999999999999999888888888888877666555544 4689999999999999999999999999999999999


Q ss_pred             hhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEE
Q 022383          187 MLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKIL  235 (298)
Q Consensus       187 ~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  235 (298)
                      +.+.+|...+..+++.+++++|++++|||+++.+.++.+.++.+|..+.
T Consensus       163 lld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         163 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             HHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC
T ss_pred             hcccchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            9999999999999999999999999999999999999999999998764

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.3e-45  Score=296.85  Aligned_cols=209  Identities=56%  Similarity=0.948  Sum_probs=191.9

Q ss_pred             CccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           29 VEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        29 ~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      ++++.+|++++|++.+.++|.++||..|+++|+++||.+++|+|++++||||||||++|++|+++++.....+++++|++
T Consensus         8 ~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~   87 (218)
T d2g9na1           8 NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLA   87 (218)
T ss_dssp             CCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             CCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEc
Confidence            46788999999999999999999999999999999999999999999999999999999999999998888889999999


Q ss_pred             CcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH-HhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          109 PTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR-KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       109 p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      ||++|+.|+.+.++++....+.....+.++........ ...+.++|+|+||+++..++.++...+++++++|+||||.+
T Consensus        88 Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~l  167 (218)
T d2g9na1          88 PTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM  167 (218)
T ss_dssp             SSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHH
T ss_pred             ccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchh
Confidence            99999999999999999998888888777655444332 33467899999999999999998899999999999999999


Q ss_pred             hccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEec
Q 022383          188 LSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILVK  237 (298)
Q Consensus       188 ~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  237 (298)
                      .+.+|...+..+++.++++.|++++|||+++.+..+.+.++.+|..+.+.
T Consensus       168 l~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         168 LSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             HHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             hcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            99999999999999999999999999999999999999999999988764

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2e-44  Score=291.59  Aligned_cols=204  Identities=36%  Similarity=0.613  Sum_probs=188.7

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      ..|++|+|++++.++|+++||+.|+|+|.++||.+++|+|++++||||||||+||++|+++.+.....+++++|++|+++
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~Ptre   80 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   80 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccch
Confidence            37999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHhhccCC-ceEEEEEcCCchHHHHHHh-hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          113 LATQTEKVILAIGDFIN-IQAHACVGGKSVGEDIRKL-EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      |+.|+.+.++.+....+ +....+.|+.....+...+ ..+++|+|+||+++..+++++.++++++.++|+||||.+++.
T Consensus        81 L~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~  160 (207)
T d1t6na_          81 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  160 (207)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSS
T ss_pred             hhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhc
Confidence            99999999999987764 5677888888877666655 467899999999999999999999999999999999999975


Q ss_pred             -ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          191 -GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       191 -~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                       +|...+..+++.+++.+|++++|||+++.++++.+.++.+|..+.+
T Consensus       161 ~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         161 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             CCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence             8999999999999999999999999999999999999999987753

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=100.00  E-value=3.4e-43  Score=290.04  Aligned_cols=211  Identities=29%  Similarity=0.485  Sum_probs=194.2

Q ss_pred             ccCCccccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccC-------
Q 022383           26 TEGVEAITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTS-------   98 (298)
Q Consensus        26 ~~~~~~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~-------   98 (298)
                      ...++++.+|++++|++++.++|.++||..|+++|..+||.+++|+|++++||||+|||+||++|+++++...       
T Consensus        14 ~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~   93 (238)
T d1wrba1          14 YSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRY   93 (238)
T ss_dssp             SSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC-----
T ss_pred             CCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccc
Confidence            3456678999999999999999999999999999999999999999999999999999999999999987432       


Q ss_pred             --CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383           99 --SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus        99 --~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                        ..+++++|++|+++|+.|+.+.+..++...++++..+.|+.....+......+++|+|+||++|..++..+...+.++
T Consensus        94 ~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v  173 (238)
T d1wrba1          94 SKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFC  173 (238)
T ss_dssp             -CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             cCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceecccc
Confidence              345789999999999999999999999998999999999988888877888899999999999999999999999999


Q ss_pred             cEEEechhhHhhccccHHHHHHHHHhCC----CCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          177 KLLVLDESDEMLSRGFKDQIYDVYRYLP----PDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~~~i~~i~~~~~----~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                      +++|+||+|.+++.+|..++..+++.+.    .++|++++|||+++.++.+.+.++.+|..+.+
T Consensus       174 ~~lViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~v  237 (238)
T d1wrba1         174 KYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV  237 (238)
T ss_dssp             CEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEE
T ss_pred             ceeeeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999999999999999999998764    25799999999999999999999999988765

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.2e-42  Score=281.32  Aligned_cols=204  Identities=40%  Similarity=0.681  Sum_probs=195.5

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      .+|++|+|++.+.++|+++||..|+|+|+++||.+++|+|+++.||||+|||++|++|+++.+.....+.++++++|+.+
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~   80 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE   80 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchh
Confidence            48999999999999999999999999999999999999999999999999999999999999988888889999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc
Q 022383          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~  192 (298)
                      ++.+....+..+....++++...+|+.........+..+++|+|+||+++.++++.+.+++.+++++|+||||.|.+.+|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~f  160 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDF  160 (206)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHH
T ss_pred             hhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhhh
Confidence            99999999999999999999999999998888888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       193 ~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                      ...+..+++.+++.+|++++|||+++.+..+...++.+|..+.+
T Consensus       161 ~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~  204 (206)
T d1s2ma1         161 KTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL  204 (206)
T ss_dssp             HHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESC
T ss_pred             HHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999999999999999999999987754

>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=100.00  E-value=1.5e-42  Score=281.04  Aligned_cols=203  Identities=35%  Similarity=0.604  Sum_probs=187.6

Q ss_pred             ccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc
Q 022383           32 ITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT  110 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~  110 (298)
                      ..+|++++|++++.++|.++||..|+|+|+++||.+++|+ |+++++|||+|||++|++|+++.... ..+++++|++|+
T Consensus         3 ~msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~-~~~~~~lil~pt   81 (208)
T d1hv8a1           3 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE-NNGIEAIILTPT   81 (208)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS-SSSCCEEEECSC
T ss_pred             ccCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc-ccCcceEEEeec
Confidence            3589999999999999999999999999999999998875 99999999999999999999987654 457799999999


Q ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc
Q 022383          111 RELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR  190 (298)
Q Consensus       111 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~  190 (298)
                      ++|+.|+.+.++++....+.++...+|+.+...+...+ .+++|+|+||+++.++++.+.+++++++++|+||+|.+.+.
T Consensus        82 ~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~  160 (208)
T d1hv8a1          82 RELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNM  160 (208)
T ss_dssp             HHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTT
T ss_pred             cccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc-CCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcC
Confidence            99999999999999999999999999998877776655 46899999999999999999899999999999999999999


Q ss_pred             ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          191 GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       191 ~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                      ++...+..+++.+++++|++++|||+++.+.++.+.++.+|..+..
T Consensus       161 ~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         161 GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             TTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEEC
T ss_pred             CChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEE
Confidence            9999999999999999999999999999999999999999877754

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=1.8e-40  Score=269.49  Aligned_cols=204  Identities=35%  Similarity=0.572  Sum_probs=184.6

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      ++|+++||++++.++|++.||+.|+++|+++||.+++|+|++++||||||||+||++|+++.+.........++++|+..
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~   80 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   80 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccc
Confidence            47999999999999999999999999999999999999999999999999999999999999988877889999999999


Q ss_pred             HHHHHHHHHHHhhccC----CceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          113 LATQTEKVILAIGDFI----NIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      ++.+....+.......    ........++.+...+......+++|+|+||+++..++.+....+.+++++|+||+|.+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll  160 (209)
T d1q0ua_          81 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLML  160 (209)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHH
T ss_pred             hhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeeccccc
Confidence            9999998887765443    345556666666655555566789999999999999999988889999999999999999


Q ss_pred             ccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcCCCCEEEEe
Q 022383          189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFMTDPVKILV  236 (298)
Q Consensus       189 ~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  236 (298)
                      +++|...+..+++.++++.|++++|||+++++..+++.++.+|..+.+
T Consensus       161 ~~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         161 DMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             HTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             ccccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            999999999999999999999999999999999999999999988764

>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=99.97  E-value=3.7e-31  Score=213.70  Aligned_cols=188  Identities=15%  Similarity=0.190  Sum_probs=145.3

Q ss_pred             CcccCCCCHHHHHHHHHC-CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           34 SFDAMGIKDDLLRGIYQY-GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~-~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      ..+.++|++.+.+.|++. ||+.++|+|.++++++.+|+|+++++|||+|||++|.+|++..      ..++++++|+++
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~------~~~~~~v~P~~~   76 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLIS   76 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCHH
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc------cCceEEeccchh
Confidence            567889999999999986 9999999999999999999999999999999999999998864      447999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchHH----HHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          113 LATQTEKVILAIGDFINIQAHACVGGKSVGE----DIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      |++|..+.++..+.    ......+......    .........+++++||+.+............+++++|+||+|.+.
T Consensus        77 L~~q~~~~l~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~  152 (206)
T d1oywa2          77 LMKDQVDQLQANGV----AAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCIS  152 (206)
T ss_dssp             HHHHHHHHHHHTTC----CEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGC
T ss_pred             hhhhHHHHHHhhcc----cccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeee
Confidence            99999999987743    2333333322221    122334668999999998876555555667889999999999998


Q ss_pred             cccc--HH---HHHHHHHhCCCCccEEEEEeeCchhHHH-HHHh-cCCCCE
Q 022383          189 SRGF--KD---QIYDVYRYLPPDLQVVLISATLPHEILE-MTTK-FMTDPV  232 (298)
Q Consensus       189 ~~~~--~~---~i~~i~~~~~~~~~~v~~SAT~~~~~~~-~~~~-~~~~~~  232 (298)
                      ++++  ..   .+..+...+ +++|++++|||+++.+.+ .... .+.+|.
T Consensus       153 ~~~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         153 QWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             TTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             ccccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            7753  22   233444555 478999999999998765 4444 367774

>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=99.96  E-value=1.9e-30  Score=208.82  Aligned_cols=181  Identities=18%  Similarity=0.242  Sum_probs=143.2

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHH
Q 022383           40 IKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEK  119 (298)
Q Consensus        40 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~  119 (298)
                      +++++...|++.||..|+|+|.++++++.+|+|+++++|||+|||+++.++++..+..   +.++|+++|+++|+.|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~---~~~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc---cCcceeecccHHHHHHHHH
Confidence            6788999999999999999999999999999999999999999999999999887755   4479999999999999999


Q ss_pred             HHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHH
Q 022383          120 VILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (298)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i  199 (298)
                      .++++... ...+....++.....   .....++++++||..+..++......+.++++||+||+|.+.++.+...+..+
T Consensus        87 ~~~~~~~~-~~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~  162 (202)
T d2p6ra3          87 SFKKWEKI-GLRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEIL  162 (202)
T ss_dssp             HHTTTTTT-TCCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHH
T ss_pred             HHHHHhhc-cccceeeccCccccc---ccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHH
Confidence            99887654 345555555544322   22346799999999999999888778889999999999999877655444444


Q ss_pred             ---HHhCCCCccEEEEEeeCchhHHHHHHhcCC
Q 022383          200 ---YRYLPPDLQVVLISATLPHEILEMTTKFMT  229 (298)
Q Consensus       200 ---~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~  229 (298)
                         ++..+++.|++++|||+++. .++. .++.
T Consensus       163 l~~i~~~~~~~~~l~lSATl~n~-~~~~-~~l~  193 (202)
T d2p6ra3         163 VTKMRRMNKALRVIGLSATAPNV-TEIA-EWLD  193 (202)
T ss_dssp             HHHHHHHCTTCEEEEEECCCTTH-HHHH-HHTT
T ss_pred             HHHHHhcCCCCcEEEEcCCCCcH-HHHH-HHcC
Confidence               44456789999999999763 5544 4444

>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=99.96  E-value=1.2e-29  Score=209.22  Aligned_cols=180  Identities=15%  Similarity=0.100  Sum_probs=132.6

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      ..|.+..+.+.+.+.+ +.++..|+++|+++++.+++|+|+++++|||+|||++++++++.....   +.+++|++|+++
T Consensus        22 ~~~~~~~~~~~~~~~~-~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~---~~rvliv~Pt~~   97 (237)
T d1gkub1          22 CLFPEDFLLKEFVEFF-RKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK---GKRCYVIFPTSL   97 (237)
T ss_dssp             SCCTTHHHHHHHHHHH-HTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT---SCCEEEEESCHH
T ss_pred             ccCccchhHHHHHHHH-HhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh---cCeEEEEeccHH
Confidence            3455544555565554 447789999999999999999999999999999999999998876654   458999999999


Q ss_pred             HHHHHHHHHHHhhccCCce----EEEEEcCCchHHHHHH--hhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhH
Q 022383          113 LATQTEKVILAIGDFINIQ----AHACVGGKSVGEDIRK--LEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~--~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~  186 (298)
                      |+.|+.+.++++.+..++.    .....++.........  ...+++|+|+||+++.+    ....++++++|||||+|.
T Consensus        98 La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~----~~~~~~~~~~vVvDE~d~  173 (237)
T d1gkub1          98 LVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSK----HYRELGHFDFIFVDDVDA  173 (237)
T ss_dssp             HHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHH----CSTTSCCCSEEEESCHHH
T ss_pred             HHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHH----hhhhcCCCCEEEEEChhh
Confidence            9999999999988776553    3334444443333322  23567999999987654    334567899999999999


Q ss_pred             hhccccHHHHHHHHHh-------------CCCCccEEEEEeeCchhHHH
Q 022383          187 MLSRGFKDQIYDVYRY-------------LPPDLQVVLISATLPHEILE  222 (298)
Q Consensus       187 ~~~~~~~~~i~~i~~~-------------~~~~~~~v~~SAT~~~~~~~  222 (298)
                      +++.+..  +..++..             .+...|++++|||+++....
T Consensus       174 ~l~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~  220 (237)
T d1gkub1         174 ILKASKN--VDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKA  220 (237)
T ss_dssp             HHTSTHH--HHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTH
T ss_pred             hhhcccc--hhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHH
Confidence            9766422  2222222             23567899999999876443

>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=99.95  E-value=1.7e-26  Score=185.13  Aligned_cols=165  Identities=17%  Similarity=0.169  Sum_probs=132.8

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEE
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAH  133 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~  133 (298)
                      -.|+++|.++++.+. ++|+++++|||+|||+++++++...+...  +.+++|++|+++|++|+.+.++++....+.++.
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~--~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~   84 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY--GGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIV   84 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS--CSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEE
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc--CCcEEEEcCchHHHHHHHHHHHHhhccccccee
Confidence            359999999998875 56899999999999999988877766543  347999999999999999999999887788888


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ...++........... .++++++||+.+...+....+.++++++||+||+|++........+...+.....+.+++++|
T Consensus        85 ~~~~~~~~~~~~~~~~-~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~~S  163 (200)
T d1wp9a1          85 ALTGEKSPEERSKAWA-RAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLT  163 (200)
T ss_dssp             EECSCSCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEE
T ss_pred             eeecccchhHHHHhhh-cccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCCCCcEEEEE
Confidence            8888777665544433 458999999999999888888899999999999999866554444444444445678999999


Q ss_pred             eeCchhHHH
Q 022383          214 ATLPHEILE  222 (298)
Q Consensus       214 AT~~~~~~~  222 (298)
                      ||++.....
T Consensus       164 ATp~~~~~~  172 (200)
T d1wp9a1         164 ASPGSTPEK  172 (200)
T ss_dssp             SCSCSSHHH
T ss_pred             ecCCCcHHH
Confidence            998654443

>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=99.90  E-value=7.4e-25  Score=186.65  Aligned_cols=197  Identities=14%  Similarity=0.035  Sum_probs=125.8

Q ss_pred             HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHH
Q 022383           66 PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDI  145 (298)
Q Consensus        66 ~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (298)
                      .+.+|+++++.||||+|||++|+.+++......  +.++||++|+++|+.|+.+.++.+....    ....       ..
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~--~~~~lvi~Ptr~La~q~~~~l~~~~~~~----~~~~-------~~   71 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALRGLPIRY----QTPA-------IR   71 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHTTTSCCBC----CC-----------
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc--CCEEEEEccHHHHHHHHHHHHhcCCcce----eeeE-------Ee
Confidence            356889999999999999999988888765443  4589999999999999998876543211    1100       01


Q ss_pred             HHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccH--HHHHHHHHhCCCCccEEEEEeeCchhHHHH
Q 022383          146 RKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK--DQIYDVYRYLPPDLQVVLISATLPHEILEM  223 (298)
Q Consensus       146 ~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~--~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~  223 (298)
                      ........++++|++.+...... ...+.++++|||||+|++..+++.  ..+..+..  ....+++++|||++......
T Consensus        72 ~~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~~--~~~~~~v~~SAT~~~~~~~~  148 (305)
T d2bmfa2          72 AEHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASIAARGYISTRVE--MGEAAGIFMTATPPGSRDPF  148 (305)
T ss_dssp             ----CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHH--HTSCEEEEECSSCTTCCCSS
T ss_pred             ecccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhHHHHHHHHHhhc--cccceEEEeecCCCcceeee
Confidence            12224568999999988776654 455789999999999998665422  22222221  24688999999997542211


Q ss_pred             HHhcCCCCEEEEecCCccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          224 TTKFMTDPVKILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ..  ...+.....              ....... +...... + ....++++|||+++++++.+++.|++.|+
T Consensus       149 ~~--~~~~~~~~~--------------~~~~~~~-~~~~~~~-~-~~~~~~~lvf~~~~~~~~~l~~~L~~~~~  203 (305)
T d2bmfa2         149 PQ--SNAPIMDEE--------------REIPERS-WNSGHEW-V-TDFKGKTVWFVPSIKAGNDIAACLRKNGK  203 (305)
T ss_dssp             CC--CSSCEEEEE--------------CCCCCSC-CSSCCHH-H-HSSCSCEEEECSCHHHHHHHHHHHHHHTC
T ss_pred             cc--cCCcceEEE--------------EeccHHH-HHHHHHH-H-HhhCCCEEEEeccHHHHHHHHHHHHhCCC
Confidence            00  001111111              0011111 1111111 1 22457999999999999999999998875

>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=99.85  E-value=5.2e-20  Score=148.24  Aligned_cols=174  Identities=18%  Similarity=0.193  Sum_probs=133.4

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHHHHHHhhc----C--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           39 GIKDDLLRGIYQYGFEKPSAIQQRAVMPIIK----G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        39 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~----~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      ..+....+.+.+..-..+++-|..++..+.+    +  .+.+++|.||||||.+|+..+...+..   +.++++++|+..
T Consensus        39 ~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~---g~qv~~l~Pt~~  115 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVPTTL  115 (233)
T ss_dssp             CCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECSSHH
T ss_pred             CCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc---CCceEEEccHHH
Confidence            3455666666554444599999999988752    3  378999999999999999999888865   669999999999


Q ss_pred             HHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhh
Q 022383          113 LATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEML  188 (298)
Q Consensus       113 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~  188 (298)
                      |+.|.++.++++....++.+..++|.....+....+    .+..+|+|||-..+.     ..+.++++.+|||||-|.. 
T Consensus       116 La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~LgLiIiDEeH~f-  189 (233)
T d2eyqa3         116 LAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRF-  189 (233)
T ss_dssp             HHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGS-
T ss_pred             hHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccccceeeechhhh-
Confidence            999999999999888899999999988766554332    356899999974443     3466789999999999974 


Q ss_pred             ccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHH
Q 022383          189 SRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (298)
Q Consensus       189 ~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~  225 (298)
                        ++..  +..++....++.++.+|||+.+....+..
T Consensus       190 --g~kQ--~~~l~~~~~~~~~l~~SATPiprtl~~~~  222 (233)
T d2eyqa3         190 --GVRH--KERIKAMRANVDILTLTATPIPRTLNMAM  222 (233)
T ss_dssp             --CHHH--HHHHHHHHTTSEEEEEESSCCCHHHHHHH
T ss_pred             --hhHH--HHHHHhhCCCCCEEEEecchhHHHHHHHH
Confidence              3222  22334444578899999999776554443

>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=99.84  E-value=3.2e-20  Score=152.24  Aligned_cols=169  Identities=19%  Similarity=0.207  Sum_probs=129.5

Q ss_pred             HHHHHHHHCCCCCChHHHHHHHHHhhc----C--CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHH
Q 022383           43 DLLRGIYQYGFEKPSAIQQRAVMPIIK----G--RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQ  116 (298)
Q Consensus        43 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~----~--~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q  116 (298)
                      .+.....++.|+ +|.-|.+++..+..    +  .+.+++|.||||||.+|+..++..+..   +.++++++||..|+.|
T Consensus        72 l~~~f~~~LPFe-LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~---g~q~~~m~Pt~~La~Q  147 (264)
T d1gm5a3          72 LAEEFIKSLPFK-LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILAIQ  147 (264)
T ss_dssp             HHHHHHHHSSSC-CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHHHH
T ss_pred             HHHHHHhhcccc-CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc---ccceeEEeehHhhhHH
Confidence            344445556776 99999999998763    3  378999999999999999999888876   5689999999999999


Q ss_pred             HHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc
Q 022383          117 TEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF  192 (298)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~  192 (298)
                      .++.++++....++.+..++|+....+....+    .+.++|+|||..-+.     ..+.++++++|||||-|.+.-.. 
T Consensus       148 h~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~-----~~~~f~~LglviiDEqH~fgv~Q-  221 (264)
T d1gm5a3         148 HYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQ-----EDVHFKNLGLVIIDEQHRFGVKQ-  221 (264)
T ss_dssp             HHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHH-----HCCCCSCCCEEEEESCCCC-----
T ss_pred             HHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhc-----CCCCccccceeeeccccccchhh-
Confidence            99999999988899999999998776554333    357899999984443     24557899999999999863221 


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCchhHHHHHH
Q 022383          193 KDQIYDVYRYLPPDLQVVLISATLPHEILEMTT  225 (298)
Q Consensus       193 ~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~  225 (298)
                          +..+.+...++.++++|||+.+....+..
T Consensus       222 ----r~~l~~~~~~~~~l~~SATPiprtl~~~~  250 (264)
T d1gm5a3         222 ----REALMNKGKMVDTLVMSATPIPRSMALAF  250 (264)
T ss_dssp             -----CCCCSSSSCCCEEEEESSCCCHHHHHHH
T ss_pred             ----HHHHHHhCcCCCEEEEECCCCHHHHHHHH
Confidence                12233334578899999998765554443

>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=99.81  E-value=5.5e-20  Score=153.98  Aligned_cols=153  Identities=22%  Similarity=0.196  Sum_probs=112.3

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .|+++|.+++..+++++..++.+|||+|||+.....+.......  ..++|||+|+++|+.|+.+.+.+++......+..
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~--~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~  190 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcc--cceEEEEEcCchhHHHHHHHHHHhhcccccccee
Confidence            59999999999999999999999999999987654443333332  3489999999999999999999887555455555


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ..++.....   ......+++|+|++.+....   ...+.++++||+||||++.    ...+..++..+.+....+++||
T Consensus       191 ~~~g~~~~~---~~~~~~~i~i~t~qs~~~~~---~~~~~~f~~VIvDEaH~~~----a~~~~~il~~~~~~~~rlGlTa  260 (282)
T d1rifa_         191 IGGGASKDD---KYKNDAPVVVGTWQTVVKQP---KEWFSQFGMMMNDECHLAT----GKSISSIISGLNNCMFKFGLSG  260 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTTSC---GGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTTCCEEEEECS
T ss_pred             ecceecccc---cccccceEEEEeeehhhhhc---ccccCCCCEEEEECCCCCC----chhHHHHHHhccCCCeEEEEEe
Confidence            555543221   12234689999997765432   2345688999999999874    3455667777755555799999


Q ss_pred             eCchh
Q 022383          215 TLPHE  219 (298)
Q Consensus       215 T~~~~  219 (298)
                      |++..
T Consensus       261 T~~~~  265 (282)
T d1rifa_         261 SLRDG  265 (282)
T ss_dssp             SCCTT
T ss_pred             ecCCC
Confidence            98643

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.79  E-value=5.7e-20  Score=137.75  Aligned_cols=136  Identities=14%  Similarity=0.193  Sum_probs=91.2

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIR  146 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (298)
                      +.+|+++++++|||+|||.+++..++......  +.++++++|++++++|..+.+...    ...+....+...      
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~--~~~vli~~p~~~l~~q~~~~~~~~----~~~~~~~~~~~~------   71 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAFSAH------   71 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS----CEEEESSCCCCC------
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhc--CceeeeeecchhHHHHHHHHhhhh----hhhhcccccccc------
Confidence            45789999999999999988876766665554  458999999999999998865432    222211111111      


Q ss_pred             HhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccH-HHHHHHHHhCCCCccEEEEEeeCc
Q 022383          147 KLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK-DQIYDVYRYLPPDLQVVLISATLP  217 (298)
Q Consensus       147 ~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~-~~i~~i~~~~~~~~~~v~~SAT~~  217 (298)
                       ......+.+.|...+..... ....+.++++||+||+|++...++. ..+...+.. .++.++++||||+|
T Consensus        72 -~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          72 -GSGREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             -CCSSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             -cccccchhhhhHHHHHHHHh-ccccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence             01234677788777766443 3456789999999999987444322 112222222 35789999999987

>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=99.79  E-value=3.7e-19  Score=142.40  Aligned_cols=136  Identities=16%  Similarity=0.150  Sum_probs=101.1

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .|+++|.+++..+.++++.++.+|||+|||++++..+ ..+     +.++||+||+++|++|+.+.+++++..   .+..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~~-----~~~~Liv~p~~~L~~q~~~~~~~~~~~---~~~~  140 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NEL-----STPTLIVVPTLALAEQWKERLGIFGEE---YVGE  140 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HHS-----CSCEEEEESSHHHHHHHHHHHGGGCGG---GEEE
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HHh-----cCceeEEEcccchHHHHHHHHHhhccc---chhh
Confidence            5999999999999999999999999999998765444 332     337899999999999999988776432   3334


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ..|+..         ...+++|+|.+.+......   ...++++||+||+|++....    +..++..++ ....+++||
T Consensus       141 ~~~~~~---------~~~~i~i~t~~~~~~~~~~---~~~~~~lvIiDEaH~~~a~~----~~~i~~~~~-~~~~lgLTA  203 (206)
T d2fz4a1         141 FSGRIK---------ELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAES----YVQIAQMSI-APFRLGLTA  203 (206)
T ss_dssp             ESSSCB---------CCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTT----HHHHHHTCC-CSEEEEEEE
T ss_pred             cccccc---------cccccccceehhhhhhhHh---hCCcCCEEEEECCeeCCcHH----HHHHHhccC-CCcEEEEec
Confidence            444322         2357999999887765443   23578899999999985443    345555553 456789999


Q ss_pred             eC
Q 022383          215 TL  216 (298)
Q Consensus       215 T~  216 (298)
                      |+
T Consensus       204 Tl  205 (206)
T d2fz4a1         204 TF  205 (206)
T ss_dssp             SC
T ss_pred             CC
Confidence            97

>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=99.72  E-value=1.5e-17  Score=124.14  Aligned_cols=128  Identities=16%  Similarity=0.140  Sum_probs=86.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL  148 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (298)
                      ..+..++.+|||+|||..+...+..      .+.+++|++|+++|++|+.+.+.+....   ......++....      
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~------~~~~vli~~P~~~l~~q~~~~~~~~~~~---~~~~~~~~~~~~------   71 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAHGV---DPNIRTGVRTIT------   71 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHT------TTCCEEEEESCHHHHHHHHHHHHHHHSC---CCEEECSSCEEC------
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH------cCCcEEEEcChHHHHHHHHHHHHHHhhc---cccccccccccc------
Confidence            3467899999999999765433321      2558999999999999999998876432   222333332211      


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCC--CCccEEEEEeeC
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLP--PDLQVVLISATL  216 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~--~~~~~v~~SAT~  216 (298)
                       ....+.++|.+.+...   ....+.++++||+||+|++... ....+..+++.+.  +..+++++|||+
T Consensus        72 -~~~~~~~~~~~~~~~~---~~~~~~~~~~vIiDE~H~~~~~-~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          72 -TGSPITYSTYGKFLAD---GGCSGGAYDIIICDECHSTDAT-SILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             -CCCSEEEEEHHHHHHT---TGGGGCCCSEEEEETTTCCSHH-HHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             -cccceEEEeeeeeccc---cchhhhcCCEEEEecccccCHH-HHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence             2346888888766543   3345778999999999986333 2233445555443  456789999995

>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=99.27  E-value=7.7e-11  Score=98.68  Aligned_cols=155  Identities=16%  Similarity=0.115  Sum_probs=97.4

Q ss_pred             CChHHHHHHHHHhh---------cCCcEEEEcCCCCchHHHHHHHHHHhhccC----CCCeEEEEEcCcHHHHHHHHHHH
Q 022383           55 KPSAIQQRAVMPII---------KGRDVIAQAQSGTGKTSMIALTVCQTVDTS----SREVQALILSPTRELATQTEKVI  121 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~---------~~~~~li~~pTG~GKT~~~~~~~~~~~~~~----~~~~~~lil~p~~~l~~q~~~~~  121 (298)
                      .+.|+|.+++..+.         .+...++.=.+|.|||+..+-.+...+...    +....+|||||.. |+.|+.+.+
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHHH
Confidence            58999999997542         345789999999999975433222222221    1234699999975 889999999


Q ss_pred             HHhhccCCceEEEEEcCCchHHHHH--Hhh------cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccH
Q 022383          122 LAIGDFINIQAHACVGGKSVGEDIR--KLE------HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFK  193 (298)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~------~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~  193 (298)
                      .++... .......+++........  ...      ...+++|+|.+.+.....  .+...+.++||+||+|.+-... .
T Consensus       134 ~k~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn~~-s  209 (298)
T d1z3ix2         134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD-N  209 (298)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC-H
T ss_pred             HhhcCC-ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeeccccccccccc-c
Confidence            887654 234455555543322211  111      235689999887765433  2233467899999999985443 2


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeC
Q 022383          194 DQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       194 ~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      .... .+..+ +....+++|||+
T Consensus       210 ~~~~-a~~~l-~~~~rllLTGTP  230 (298)
T d1z3ix2         210 QTYL-ALNSM-NAQRRVLISGTP  230 (298)
T ss_dssp             HHHH-HHHHH-CCSEEEEECSSC
T ss_pred             hhhh-hhhcc-ccceeeeecchH
Confidence            2222 22333 245679999998

>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=99.19  E-value=4.5e-11  Score=96.29  Aligned_cols=147  Identities=12%  Similarity=0.121  Sum_probs=94.1

Q ss_pred             CChHHHHHHHHHhh----cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCc
Q 022383           55 KPSAIQQRAVMPII----KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINI  130 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~----~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~  130 (298)
                      .+.|+|.+++..+.    .+..+++.-++|.|||...+.. +..+.......+++|+|| ..+..|+.+.+.++...  .
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~-~~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~--~   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAV-FSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPH--L   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHH-HHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTT--S
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHh-hhhhhhcccccccceecc-hhhhhHHHHHHHhhccc--c
Confidence            58999999987543    4567899999999999876443 343333333347899999 66778888888887543  2


Q ss_pred             eEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEE
Q 022383          131 QAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVV  210 (298)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v  210 (298)
                      .+....+......     ..+.+++++|.+.+.....   +.--+.++||+||+|.+-...- .. ......+. ....+
T Consensus        88 ~~~~~~~~~~~~~-----~~~~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~~s-~~-~~~~~~l~-a~~r~  156 (230)
T d1z63a1          88 RFAVFHEDRSKIK-----LEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQT-KI-FKAVKELK-SKYRI  156 (230)
T ss_dssp             CEEECSSSTTSCC-----GGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTTS-HH-HHHHHTSC-EEEEE
T ss_pred             cceeeccccchhh-----ccCcCEEEeeHHHHHhHHH---HhcccceEEEEEhhhcccccch-hh-hhhhhhhc-cceEE
Confidence            3333222211111     1346899999987754322   1223568899999999855432 22 23333443 45578


Q ss_pred             EEEeeC
Q 022383          211 LISATL  216 (298)
Q Consensus       211 ~~SAT~  216 (298)
                      ++|||+
T Consensus       157 ~LTgTP  162 (230)
T d1z63a1         157 ALTGTP  162 (230)
T ss_dssp             EECSSC
T ss_pred             EEecch
Confidence            999998

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=98.91  E-value=4.4e-08  Score=78.27  Aligned_cols=164  Identities=18%  Similarity=0.236  Sum_probs=118.3

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEE
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHA  134 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~  134 (298)
                      .+++.|.-.--.+..|+  +....||-|||++..+|+.-....   +..+=+++.+--||..=.+++..+...+|+.+..
T Consensus        80 RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~---g~~vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~  154 (273)
T d1tf5a3          80 FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGL  154 (273)
T ss_dssp             CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhc---CCCceEEecCccccchhhhHHhHHHHHcCCCccc
Confidence            37777776665666664  889999999999988877665444   3357888999999999999999999999999998


Q ss_pred             EEcCCchHHHHHHhhcCCcEEEeChHHHH-HHHhcc------CccCCCccEEEechhhHhhcc-cc------------H-
Q 022383          135 CVGGKSVGEDIRKLEHGVHVVSGTPGRVC-DMIKRK------TLRTRAIKLLVLDESDEMLSR-GF------------K-  193 (298)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~-~~~~~~------~~~~~~l~~vViDE~h~~~~~-~~------------~-  193 (298)
                      ...+....+.....  .+||+.+|...+. .+++.+      ....+.+.+.||||+|.++=+ ..            . 
T Consensus       155 ~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg~~~~~a~  232 (273)
T d1tf5a3         155 NLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQSMTLAT  232 (273)
T ss_dssp             CCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEEEEEE
T ss_pred             cccccCHHHHHHHh--hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEeccCccchhh
Confidence            87776665554444  4799999998875 345442      223578999999999998632 10            0 


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeCchhHHHHHHhcC
Q 022383          194 DQIYDVYRYLPPDLQVVLISATLPHEILEMTTKFM  228 (298)
Q Consensus       194 ~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~~~  228 (298)
                      -.++..++..   .++.+||.|...+..++..-|.
T Consensus       233 it~q~~f~~y---~~l~gmtgta~~~~~e~~~iy~  264 (273)
T d1tf5a3         233 ITFQNYFRMY---EKLAGMTGTAKTEEEEFRNIYN  264 (273)
T ss_dssp             EEHHHHHTTS---SEEEEEESCCGGGHHHHHHHHC
T ss_pred             hhHHHHHHHH---HHHhCCccccHHHHHHHHhccC
Confidence            0133444444   4688999998777677766654

>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=98.42  E-value=5.3e-07  Score=76.53  Aligned_cols=143  Identities=15%  Similarity=0.165  Sum_probs=86.2

Q ss_pred             CCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHH--HHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCce
Q 022383           54 EKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIAL--TVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQ  131 (298)
Q Consensus        54 ~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~--~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~  131 (298)
                      .....+|..++..++.++-++|.||.|+|||.....  ..+..... ..+.++++.+||..-+..+.+.+..........
T Consensus       147 ~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~-~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~  225 (359)
T d1w36d1         147 SDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGKALRQLPLT  225 (359)
T ss_dssp             TTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCC
T ss_pred             cccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHh-ccCCeEEEecCcHHHHHHHHHHHHHHHhhcCch
Confidence            346779999999999999999999999999976432  22222222 235589999999998888887765433222110


Q ss_pred             EEEEEcCCchHHHHHHhhcCCcEEEeChHHHHH------HHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCC
Q 022383          132 AHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCD------MIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPP  205 (298)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~------~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~  205 (298)
                      ......              ...-..|..++..      .+.....+....+++||||+-++.    ...+..++..++.
T Consensus       226 ~~~~~~--------------~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~----~~l~~~ll~~~~~  287 (359)
T d1w36d1         226 DEQKKR--------------IPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID----LPMMSRLIDALPD  287 (359)
T ss_dssp             SCCCCS--------------CSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB----HHHHHHHHHTCCT
T ss_pred             hhhhhh--------------hhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC----HHHHHHHHHHhcC
Confidence            000000              0000011111111      112223345578999999997652    3456678888888


Q ss_pred             CccEEEEEee
Q 022383          206 DLQVVLISAT  215 (298)
Q Consensus       206 ~~~~v~~SAT  215 (298)
                      ..++|++--.
T Consensus       288 ~~~lILvGD~  297 (359)
T d1w36d1         288 HARVIFLGDR  297 (359)
T ss_dssp             TCEEEEEECT
T ss_pred             CCEEEEECCh
Confidence            8888877544

>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=98.22  E-value=1.5e-06  Score=65.74  Aligned_cols=56  Identities=34%  Similarity=0.519  Sum_probs=51.0

Q ss_pred             cCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          241 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       241 ~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .++.++.|+|+.++..+ |...+..+++..+.+++||||++++.|+.++..|+..|+
T Consensus         2 ~tl~~i~q~yi~v~~~~-K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~   57 (171)
T d1s2ma2           2 LTLKGITQYYAFVEERQ-KLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGY   57 (171)
T ss_dssp             CBCTTEEEEEEECCGGG-HHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTC
T ss_pred             CCccceEEEEEEcCHHH-HHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccc
Confidence            35678999999998766 999999999999889999999999999999999998875

>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=98.20  E-value=1.4e-06  Score=65.74  Aligned_cols=58  Identities=78%  Similarity=1.122  Sum_probs=53.1

Q ss_pred             ccCcCCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          240 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       240 ~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +.++.++.|+|+.++.+++|+..+..+++.....++||||+++..|+.+++.|+..|+
T Consensus         2 ~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~   59 (168)
T d2j0sa2           2 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANF   59 (168)
T ss_dssp             GCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhccc
Confidence            4567899999999999888999999999988889999999999999999999998875

>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=98.01  E-value=6.3e-06  Score=67.92  Aligned_cols=69  Identities=17%  Similarity=0.137  Sum_probs=51.6

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc-CCCCeEEEEEcCcHHHHHHHHHHHHHhh
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRELATQTEKVILAIG  125 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~~~l~~q~~~~~~~~~  125 (298)
                      +++|-|++++..  ...+++|.|+.|||||.+.+--+...+.. .....+++++++|+++++.+.+.+.+..
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~   70 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTL   70 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhc
Confidence            478999999965  34679999999999997755433333322 1223479999999999999999887764

>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=97.92  E-value=1.2e-05  Score=59.61  Aligned_cols=52  Identities=27%  Similarity=0.412  Sum_probs=46.1

Q ss_pred             CCceEEEEEecCccchHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          244 EGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       244 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      ++++|.|+.++..+ |++.+..+++.. ..++||||++++.|+.++..|+..|+
T Consensus         2 ~nI~~~~i~v~~~~-K~~~L~~ll~~~-~~k~IIF~~s~~~~~~l~~~L~~~g~   53 (155)
T d1hv8a2           2 ANIEQSYVEVNENE-RFEALCRLLKNK-EFYGLVFCKTKRDTKELASMLRDIGF   53 (155)
T ss_dssp             SSSEEEEEECCGGG-HHHHHHHHHCST-TCCEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             CCeEEEEEEeChHH-HHHHHHHHHccC-CCCEEEEECchHHHHHHHhhhccccc
Confidence            57899999998766 999999999864 46899999999999999999998875

>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=97.81  E-value=3e-05  Score=64.24  Aligned_cols=68  Identities=18%  Similarity=0.218  Sum_probs=52.1

Q ss_pred             CChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCC-CCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           55 KPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSS-REVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        55 ~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~-~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      .+++-|.+++.+.  +..++|.|+.|||||.+.+--+...+.... ...+++++++++..+.++...+...
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~   79 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhh
Confidence            4889999999753  457999999999999876554444443322 2347999999999999999888654

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.79  E-value=3.3e-05  Score=60.00  Aligned_cols=42  Identities=7%  Similarity=0.108  Sum_probs=29.7

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeC
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATL  216 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~  216 (298)
                      ...+++||||+|.|... -...+..+++.-+++..+++.+-.+
T Consensus       107 ~~~kviIide~d~l~~~-a~n~Llk~lEep~~~~~fIl~t~~~  148 (207)
T d1a5ta2         107 GGAKVVWVTDAALLTDA-AANALLKTLEEPPAETWFFLATREP  148 (207)
T ss_dssp             SSCEEEEESCGGGBCHH-HHHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             CccceEEechhhhhhhh-hhHHHHHHHHhhcccceeeeeecCh
Confidence            46789999999998544 3566667777766666666655444

>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=97.51  E-value=0.00013  Score=56.28  Aligned_cols=130  Identities=17%  Similarity=0.215  Sum_probs=64.2

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--cHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE  149 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (298)
                      -++++||||+|||....-.+.... ..  +.++.+++.  .|.-+.++.   +.+++..++.+................ 
T Consensus        12 vi~lvGp~GvGKTTTiaKLA~~~~-~~--g~kV~lit~Dt~R~gA~eQL---~~~a~~l~v~~~~~~~~~~~~~~~~~~-   84 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTAAKLALYYK-GK--GRRPLLVAADTQRPAAREQL---RLLGEKVGVPVLEVMDGESPESIRRRV-   84 (207)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHH-HT--TCCEEEEECCSSCHHHHHHH---HHHHHHHTCCEEECCTTCCHHHHHHHH-
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HC--CCcEEEEecccccchHHHHH---HHHHHhcCCccccccccchhhHHHHHH-
Confidence            356799999999977655443332 22  335566664  444443333   333434456655544433322211100 


Q ss_pred             cCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcc-ccHHHHHHHHHhCCCCccEEEEEeeCchhHHHHHHh
Q 022383          150 HGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSR-GFKDQIYDVYRYLPPDLQVVLISATLPHEILEMTTK  226 (298)
Q Consensus       150 ~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~~~  226 (298)
                                   ..+     ....+.++|+||=+-+...+ .....+..+.+...+..-++.++|+......+....
T Consensus        85 -------------~~~-----~~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~~~~  144 (207)
T d1ls1a2          85 -------------EEK-----ARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARA  144 (207)
T ss_dssp             -------------HHH-----HHHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHHHHH
T ss_pred             -------------HHH-----HhhccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHHHHH
Confidence                         000     01123455555544332211 233455555555665566777888877665555544

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.34  E-value=0.00089  Score=51.17  Aligned_cols=113  Identities=12%  Similarity=0.175  Sum_probs=65.1

Q ss_pred             HHHHHHHhhc---CCcEEEEcCCCCchHHHHHHHHHHhhcc-CCCCeEEEEEcCcHH--HHHHHHHHHHHhhccCCceEE
Q 022383           60 QQRAVMPIIK---GRDVIAQAQSGTGKTSMIALTVCQTVDT-SSREVQALILSPTRE--LATQTEKVILAIGDFINIQAH  133 (298)
Q Consensus        60 Q~~~~~~~~~---~~~~li~~pTG~GKT~~~~~~~~~~~~~-~~~~~~~lil~p~~~--l~~q~~~~~~~~~~~~~~~~~  133 (298)
                      |.+.+..+.+   +.++++.||.|+|||..+...+ +.+.. ....+-++++.|...  -++|+.+.             
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~-~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i-------------   67 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELP-EYVEKFPPKASDVLEIDPEGENIGIDDIRTI-------------   67 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHH-HHHHTSCCCTTTEEEECCSSSCBCHHHHHHH-------------
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH-HHHhccccCCCCEEEEeCCcCCCCHHHHHHH-------------
Confidence            4555555443   4589999999999996654322 22221 122334666666421  12222221             


Q ss_pred             EEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEE
Q 022383          134 ACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                                                   ...+.... .....+++|+||+|.|... -+..+..+++--|++..++++|
T Consensus        68 -----------------------------~~~~~~~~-~~~~~KviIId~ad~l~~~-aqNaLLK~LEEPp~~t~fiLit  116 (198)
T d2gnoa2          68 -----------------------------KDFLNYSP-ELYTRKYVIVHDCERMTQQ-AANAFLKALEEPPEYAVIVLNT  116 (198)
T ss_dssp             -----------------------------HHHHTSCC-SSSSSEEEEETTGGGBCHH-HHHHTHHHHHSCCTTEEEEEEE
T ss_pred             -----------------------------HHHHhhCc-ccCCCEEEEEeCccccchh-hhhHHHHHHhCCCCCceeeecc
Confidence                                         12222211 1245689999999998544 3566777777777778777776


Q ss_pred             eeCc
Q 022383          214 ATLP  217 (298)
Q Consensus       214 AT~~  217 (298)
                      ..+.
T Consensus       117 ~~~~  120 (198)
T d2gnoa2         117 RRWH  120 (198)
T ss_dssp             SCGG
T ss_pred             CChh
Confidence            6654

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.30  E-value=0.0027  Score=49.84  Aligned_cols=41  Identities=12%  Similarity=0.233  Sum_probs=27.1

Q ss_pred             CCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEee
Q 022383          174 RAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISAT  215 (298)
Q Consensus       174 ~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT  215 (298)
                      ....++||||+|.|... ....+...++..+.+..+++.+-.
T Consensus       114 ~~~kviiIde~d~l~~~-~q~~Llk~lE~~~~~~~~il~tn~  154 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLATTD  154 (239)
T ss_dssp             SSSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEESC
T ss_pred             CCCEEEEEECcccCCHH-HHHHHHHHHhcCCCCeEEEEEcCC
Confidence            45679999999998543 345566667666666666655433

>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=97.20  E-value=0.0014  Score=50.92  Aligned_cols=43  Identities=19%  Similarity=0.392  Sum_probs=27.8

Q ss_pred             ccCCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          171 LRTRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       171 ~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ........+|+||+|.+... ....+..++...++...+++.+-
T Consensus        95 ~~~~~~kiiiiDe~d~~~~~-~~~~Ll~~le~~~~~~~~~~~~~  137 (227)
T d1sxjc2          95 IFSKGFKLIILDEADAMTNA-AQNALRRVIERYTKNTRFCVLAN  137 (227)
T ss_dssp             SSSCSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             ccCCCeEEEEEeccccchhh-HHHHHHHHhhhcccceeeccccC
Confidence            34455679999999998544 35556666777665555555443

>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=97.19  E-value=0.0015  Score=50.12  Aligned_cols=62  Identities=21%  Similarity=0.246  Sum_probs=34.8

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCc--HHHHHHHHHHHHHhhccCCceEEEEEcCCc
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPT--RELATQTEKVILAIGDFINIQAHACVGGKS  140 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~  140 (298)
                      ++++||||+|||.+..-.+.. +...  +.++.+++-.  |.=+.   ++++.+++..++.+.....+..
T Consensus        12 i~lvGptGvGKTTTiAKLA~~-~~~~--g~kV~lit~Dt~R~gA~---eQL~~~a~~l~v~~~~~~~~~d   75 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQ-FEQQ--GKSVMLAAGDTFRAAAV---EQLQVWGQRNNIPVIAQHTGAD   75 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH-HHTT--TCCEEEECCCTTCHHHH---HHHHHHHHHTTCCEECCSTTCC
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHC--CCcEEEEecccccccch---hhhhhhhhhcCCcccccccCCC
Confidence            567999999999876655433 3332  3355555542  33333   3344455555666655444433

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=97.13  E-value=0.0023  Score=50.54  Aligned_cols=54  Identities=13%  Similarity=0.164  Sum_probs=33.3

Q ss_pred             cccCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHh--hcCCcEEEEcCCCCchHHHH
Q 022383           31 AITSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPI--IKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        31 ~~~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~--~~~~~~li~~pTG~GKT~~~   87 (298)
                      |..+|++++-.+..++.|.+. +. + ..+.+.+..+  ...+.+++.||.|+|||...
T Consensus         4 p~~~~~di~G~~~~k~~l~~~-i~-~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEI-VE-F-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHH-HH-H-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHH-HH-H-HHCHHHHHHcCCCCCceEEEecCCCCChhHHH
Confidence            447899998777777777552 11 1 0111223222  12357999999999999654

>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=97.07  E-value=0.001  Score=51.74  Aligned_cols=45  Identities=13%  Similarity=0.214  Sum_probs=30.5

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCch
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPH  218 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~  218 (298)
                      ..+..++|+||+|.+... ....+...+...+....+++.+.....
T Consensus        99 ~~~~kviiiDe~d~~~~~-~~~~ll~~~e~~~~~~~~i~~~~~~~~  143 (224)
T d1sxjb2          99 PGKHKIVILDEADSMTAG-AQQALRRTMELYSNSTRFAFACNQSNK  143 (224)
T ss_dssp             TTCCEEEEEESGGGSCHH-HHHTTHHHHHHTTTTEEEEEEESCGGG
T ss_pred             CcceEEEEEecccccchh-HHHHHhhhccccccceeeeeccCchhh
Confidence            355679999999998554 344555666666666777776665543

>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=97.01  E-value=0.0022  Score=49.46  Aligned_cols=42  Identities=17%  Similarity=0.366  Sum_probs=25.3

Q ss_pred             CccEEEechhhHhhcc-ccHHHHHHHHHhCC-CCccEEEEEeeCc
Q 022383          175 AIKLLVLDESDEMLSR-GFKDQIYDVYRYLP-PDLQVVLISATLP  217 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~-~~~~~i~~i~~~~~-~~~~~v~~SAT~~  217 (298)
                      ..+++++|++|.+... ..+..+-.++..+. .+.++++ |+..+
T Consensus        97 ~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iii-ts~~~  140 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIIL-ASDRH  140 (213)
T ss_dssp             TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEE-EESSC
T ss_pred             hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEE-ecCCc
Confidence            6689999999998543 23444445555543 4455555 55543

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.00  E-value=0.00067  Score=53.63  Aligned_cols=44  Identities=18%  Similarity=0.252  Sum_probs=30.9

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      .+|+++-.++.+.+.|+.+--. .           ....++++.||.|+|||..+.
T Consensus         8 ~~~~diig~~~~~~~L~~~~~~-~-----------~~~~~lll~Gp~G~GKTt~~~   51 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSLSDQ-P-----------RDLPHLLLYGPNGTGKKTRCM   51 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTC-T-----------TCCCCEEEECSTTSSHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHc-C-----------CCCCeEEEECCCCCCHHHHHH
Confidence            3688888888888888764211 0           112369999999999996543

>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=96.96  E-value=0.0023  Score=49.20  Aligned_cols=60  Identities=15%  Similarity=0.144  Sum_probs=31.7

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc-C-cHHHHHHHHHHHHHhhccCCceEEEEEc
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS-P-TRELATQTEKVILAIGDFINIQAHACVG  137 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~-p-~~~l~~q~~~~~~~~~~~~~~~~~~~~~  137 (298)
                      -++++||||+|||.+..-.+.... ..  +.++.+++ . .|.=+.++   ++.+++..++.+.....
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~~-~~--~~kV~lit~Dt~R~gA~eQ---L~~~a~~l~i~~~~~~~   74 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMFV-DE--GKSVVLAAADTFRAAAIEQ---LKIWGERVGATVISHSE   74 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH-HT--TCCEEEEEECTTCHHHHHH---HHHHHHHHTCEEECCST
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HC--CCceEEEeecccccchhHH---HHHHhhhcCccccccCC
Confidence            367799999999977655443332 22  22344444 3 34333333   33344444666554333

>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=96.95  E-value=0.01  Score=43.83  Aligned_cols=112  Identities=13%  Similarity=0.099  Sum_probs=77.8

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++.-++.+...+++.    |+++..++|+.+..+....+.    +..+|+|+|.      +-..+++..++
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~------v~~~GiDip~V  100 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN------LLREGLDIPEV  100 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC------CCCTTCCCTTE
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeee------eeeeeccCCCC
Confidence            568999999999999999988875    789999999988776655443    6789999996      33457899999


Q ss_pred             cEEEechhhHhhc-cccHHHHHHHHHhCCC-CccEEEEEeeCchhHHH
Q 022383          177 KLLVLDESDEMLS-RGFKDQIYDVYRYLPP-DLQVVLISATLPHEILE  222 (298)
Q Consensus       177 ~~vViDE~h~~~~-~~~~~~i~~i~~~~~~-~~~~v~~SAT~~~~~~~  222 (298)
                      ++||+=.++...- ......+..+-+-.+. ....+++.......+..
T Consensus       101 ~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~  148 (174)
T d1c4oa2         101 SLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQR  148 (174)
T ss_dssp             EEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHH
T ss_pred             cEEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHH
Confidence            9999877765321 1223445555555443 23344444444444443

>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=96.94  E-value=0.0026  Score=48.72  Aligned_cols=63  Identities=21%  Similarity=0.188  Sum_probs=34.7

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--cHHHHHHHHHHHHHhhccCCceEEEEEcC
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACVGG  138 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~  138 (298)
                      ++-++++||||+|||.+..-.+.. +...  +.++.+++-  .|.=+.++.+   .+++..++.+.....+
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~-~~~~--g~kV~lit~Dt~R~gA~eQL~---~~a~~l~i~~~~~~~~   70 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRY-YQNL--GKKVMFCAGDTFRAAGGTQLS---EWGKRLSIPVIQGPEG   70 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHH-HHTT--TCCEEEECCCCSSTTHHHHHH---HHHHHHTCCEECCCTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH-HHHC--CCcEEEEEeccccccchhhHh---hcccccCceEEeccCC
Confidence            456788999999999876554432 2222  335555553  3454444333   2333335655444433

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.92  E-value=0.0013  Score=50.35  Aligned_cols=92  Identities=13%  Similarity=0.109  Sum_probs=70.5

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----hcCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----EHGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++.||||..+-...+.+.++++.  .+.++..+||..+..+....+    .+..+|+|||.      +-+.+++..+.
T Consensus        31 GgQvy~V~p~I~~~e~~~~~l~~~~--p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt------vIEvGiDvpnA  102 (211)
T d2eyqa5          31 GGQVYYLYNDVENIQKAAERLAELV--PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIETGIDIPTA  102 (211)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHC--TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS------TTGGGSCCTTE
T ss_pred             CCeEEEEEcCccchhhHHHHHHHhC--CceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh------hhhhccCCCCC
Confidence            6699999999999999999988874  467899999988766554333    36689999996      23346889999


Q ss_pred             cEEEechhhHhhccccHHHHHHHHHhCC
Q 022383          177 KLLVLDESDEMLSRGFKDQIYDVYRYLP  204 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~~~i~~i~~~~~  204 (298)
                      .++||.++|++   | ..++..+..+..
T Consensus       103 ~~iiI~~a~rf---G-LaQLhQLRGRVG  126 (211)
T d2eyqa5         103 NTIIIERADHF---G-LAQLHQLRGRVG  126 (211)
T ss_dssp             EEEEETTTTSS---C-HHHHHHHHTTCC
T ss_pred             cEEEEecchhc---c-ccccccccceee
Confidence            99999999875   2 344556655554

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.76  E-value=0.011  Score=45.72  Aligned_cols=42  Identities=14%  Similarity=0.249  Sum_probs=27.7

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHHH
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      +|+++-.++.+.+.|+.+-       +      -.+..++++.||+|+|||..+-
T Consensus        22 ~~~diig~~~~~~~l~~~i-------~------~~~~~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHYV-------K------TGSMPHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             STTTCCSCHHHHHHHHHHH-------H------HTCCCEEEEESCTTSSHHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHH-------H------cCCCCeEEEECCCCCcHHHHHH
Confidence            6777766666666665530       0      0122579999999999996643

>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=96.73  E-value=0.00012  Score=52.64  Aligned_cols=30  Identities=20%  Similarity=0.226  Sum_probs=26.3

Q ss_pred             hhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          268 DTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       268 ~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +....+++||||+|++.|+.+++.|+..|+
T Consensus        31 ~~~~~~k~IVFc~t~~~ae~la~~L~~~G~   60 (138)
T d1jr6a_          31 EVIKGGRHLIFCHSKKKCDELAAKLVALGI   60 (138)
T ss_dssp             HHHTTSCEEEECSCHHHHHHHHHHHHHHTC
T ss_pred             hhcCCCCEEEEeCcHHHHHHHHHHHhcccc
Confidence            444568999999999999999999998875

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=96.71  E-value=0.0073  Score=47.83  Aligned_cols=53  Identities=23%  Similarity=0.241  Sum_probs=32.3

Q ss_pred             ccCcccCCCCHHHHHHHHHC--CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHHH
Q 022383           32 ITSFDAMGIKDDLLRGIYQY--GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        32 ~~~~~~l~l~~~i~~~l~~~--~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~~   87 (298)
                      -.+|++.+-.+..++.|.+.  .+..+..+|..   .+...+.+++.||+|+|||...
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~---g~~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHc---CCCCCCeEEeeCCCCCCccHHH
Confidence            35899998888777777652  01111112211   1122467999999999999653

>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=96.65  E-value=0.0015  Score=50.16  Aligned_cols=58  Identities=14%  Similarity=0.170  Sum_probs=26.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC--cHHHHHHHHHHHHHhhccCCceEEEEE
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP--TRELATQTEKVILAIGDFINIQAHACV  136 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p--~~~l~~q~~~~~~~~~~~~~~~~~~~~  136 (298)
                      ++++||||+|||.+.+-.+.. +...  +.++.+++-  .|.=+.+   +++.+++..++.+....
T Consensus        15 i~lvGptGvGKTTTiAKLA~~-~~~~--g~kV~lit~Dt~R~ga~e---QL~~~a~~l~v~~~~~~   74 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYF-YKKK--GFKVGLVGADVYRPAALE---QLQQLGQQIGVPVYGEP   74 (211)
T ss_dssp             EEEECSCCC----HHHHHHHH-HHHT--TCCEEEEECCCSSHHHHH---HHHHHHHHHTCCEECCT
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHC--CCceEEEEeeccccchhH---HHHHhccccCcceeecc
Confidence            667899999999776554432 3332  224444443  3333332   33334444455554433

>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=96.47  E-value=0.018  Score=42.82  Aligned_cols=103  Identities=16%  Similarity=0.145  Sum_probs=74.4

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+++.-+..+...+++.    |+.+..++|+.+..+....+.    +..+|+|+|.      +-..+++..++
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd------v~~rGiDip~v  100 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEA----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN------LLREGLDIPEV  100 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC------CCSSSCCCTTE
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhC----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh------HHHccCCCCCC
Confidence            458999999999999988887754    789999999988876655443    6789999995      33467899999


Q ss_pred             cEEEechhhHhhc-cccHHHHHHHHHhCCCCccEEEEE
Q 022383          177 KLLVLDESDEMLS-RGFKDQIYDVYRYLPPDLQVVLIS  213 (298)
Q Consensus       177 ~~vViDE~h~~~~-~~~~~~i~~i~~~~~~~~~~v~~S  213 (298)
                      ++||.-++..... ..+...+.++-+--+...-.+++.
T Consensus       101 ~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~~~~  138 (181)
T d1t5la2         101 SLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMY  138 (181)
T ss_dssp             EEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEE
T ss_pred             CEEEEecCCcccccccHHHHHHHHHhhccccCceeEee
Confidence            9999988875321 234555666666554433333333

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=96.37  E-value=0.0054  Score=48.29  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      +.+++.||+|+|||...
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46999999999999654

>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=96.19  E-value=0.0046  Score=52.48  Aligned_cols=65  Identities=25%  Similarity=0.348  Sum_probs=47.5

Q ss_pred             ChHHHHHHHHHhh----cC-CcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           56 PSAIQQRAVMPII----KG-RDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        56 ~~~~Q~~~~~~~~----~~-~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      |+--|=+++..+.    +| ++.++.|-||||||+... .++...     +..+|||+|+..+|.|+++.++.+..
T Consensus        12 p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~-----~rp~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          12 PQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV-----NKPTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             CCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHHcC
Confidence            5555666665544    44 678999999999997543 223332     22589999999999999999998864

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.14  E-value=0.012  Score=46.56  Aligned_cols=50  Identities=22%  Similarity=0.345  Sum_probs=28.8

Q ss_pred             CcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHhhcCCcEEEEcCCCCchHHH
Q 022383           34 SFDAMGIKDDLLRGIYQY---GFEKPSAIQQRAVMPIIKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~---~~~~~~~~Q~~~~~~~~~~~~~li~~pTG~GKT~~   86 (298)
                      +|++++-.+..++.|++.   .+..+..++..   .+...+.+++.||.|+|||..
T Consensus         2 ~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~---g~~~~~giLL~GppGtGKT~l   54 (258)
T d1e32a2           2 GYDDVGGCRKQLAQIKEMVELPLRHPALFKAI---GVKPPRGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHC---CCCCCCEEEEECCTTSSHHHH
T ss_pred             ChhhhccHHHHHHHHHHHHHHHhcCHHHHHhC---CCCCCceeEEecCCCCCchHH
Confidence            577876555666666552   11111111111   111246899999999999964

>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=96.00  E-value=0.021  Score=41.66  Aligned_cols=74  Identities=12%  Similarity=0.122  Sum_probs=57.9

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      ..++||.|.++..++++.+.+...    ++.+..++|+.+..+....+.    +...|+|+|.      +-..++++.++
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td------v~~rGiDi~~v   96 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD------LLARGIDVQQV   96 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG------GGTTTCCCCSC
T ss_pred             CCcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc------cccccccCCCc
Confidence            347999999999999999887665    678899999988776654432    5678999996      23467889999


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||.=+.
T Consensus        97 ~~VI~~d~  104 (162)
T d1fuka_          97 SLVINYDL  104 (162)
T ss_dssp             SEEEESSC
T ss_pred             eEEEEecc
Confidence            99987554

>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=95.90  E-value=0.0071  Score=49.64  Aligned_cols=65  Identities=22%  Similarity=0.301  Sum_probs=40.0

Q ss_pred             HHHHHHCCCCC---ChHHHHHHHH-HhhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           45 LRGIYQYGFEK---PSAIQQRAVM-PIIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        45 ~~~l~~~~~~~---~~~~Q~~~~~-~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      ...+.+.|+-.   ..+.+...+. .+..+++++|+||||||||.. +-.++..+..   ..+++.+--+.|+
T Consensus       137 l~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~~---~~rivtiEd~~El  205 (323)
T d1g6oa_         137 HSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIPK---EERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSCT---TCCEEEEESSCCC
T ss_pred             hHHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhccc---ccceeeccchhhh
Confidence            34455555433   2344444443 456789999999999999964 4455555433   3467777666665

>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=95.89  E-value=0.0081  Score=46.56  Aligned_cols=48  Identities=19%  Similarity=0.273  Sum_probs=28.4

Q ss_pred             CccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEeeCchhHHHH
Q 022383          175 AIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISATLPHEILEM  223 (298)
Q Consensus       175 ~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~  223 (298)
                      ....+|+||+|.+.... ...+..++...+....+++.+.....-...+
T Consensus       108 ~~~viiiDe~d~l~~~~-~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l  155 (237)
T d1sxjd2         108 PYKIIILDEADSMTADA-QSALRRTMETYSGVTRFCLICNYVTRIIDPL  155 (237)
T ss_dssp             SCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEESCGGGSCHHH
T ss_pred             CceEEEEecccccCHHH-HHHHhhccccccccccccccccccccccccc
Confidence            45689999999985543 3445555555555555555544444433333

>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=95.76  E-value=0.032  Score=40.98  Aligned_cols=85  Identities=9%  Similarity=0.049  Sum_probs=62.7

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      ..++||.|+++.-++.+...++..    ++.+..++|+.+..+....+.    +..+++|||.-      -..++++.++
T Consensus        32 ~~k~iVF~~~~~~~~~l~~~L~~~----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~------~~~Gid~~~v  101 (171)
T d1s2ma2          32 INQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL------LTRGIDIQAV  101 (171)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC------SSSSCCCTTE
T ss_pred             CCceEEEEeeeehhhHhHHhhhcc----cccccccccccchhhhhhhhhhcccCccccccchhH------hhhcccccee
Confidence            448999999999999999888775    688888999888765544432    56889999972      3457889999


Q ss_pred             cEEEechhhHhhccccHHHHHHH
Q 022383          177 KLLVLDESDEMLSRGFKDQIYDV  199 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~~~i~~i  199 (298)
                      ++||.-++.    +.....+.++
T Consensus       102 ~~VI~~d~p----~~~~~y~qr~  120 (171)
T d1s2ma2         102 NVVINFDFP----KTAETYLHRI  120 (171)
T ss_dssp             EEEEESSCC----SSHHHHHHHH
T ss_pred             EEEEecCCc----chHHHHHHHh
Confidence            999866553    3334444444

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=95.45  E-value=0.018  Score=40.88  Aligned_cols=87  Identities=15%  Similarity=0.169  Sum_probs=48.9

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCC
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGV  152 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (298)
                      -++.||..||||.-.+ -.+++....  +.+++++-|...-         +...    .+ ..+.|..          -.
T Consensus         5 ~~i~GpMfsGKTteLi-~~~~~~~~~--~~kv~~ikp~~D~---------R~~~----~i-~s~~g~~----------~~   57 (139)
T d2b8ta1           5 EFITGPMFAGKTAELI-RRLHRLEYA--DVKYLVFKPKIDT---------RSIR----NI-QSRTGTS----------LP   57 (139)
T ss_dssp             EEEECSTTSCHHHHHH-HHHHHHHHT--TCCEEEEEECCCG---------GGCS----SC-CCCCCCS----------SC
T ss_pred             EEEEccccCHHHHHHH-HHHHHHHHC--CCcEEEEEEcccc---------cccc----eE-EcccCce----------ee
Confidence            4789999999996533 333443332  4478888886431         0000    11 1111111          12


Q ss_pred             cEEEeChHHHHHHHhccCccCCCccEEEechhhHh
Q 022383          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       153 ~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~  187 (298)
                      .+.+.....+...+..... ..+.++|.|||++.+
T Consensus        58 ~~~~~~~~~~~~~~~~~~~-~~~~dvI~IDE~QFf   91 (139)
T d2b8ta1          58 SVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFF   91 (139)
T ss_dssp             CEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGS
T ss_pred             eEEeccchhhHHHHHhhcc-ccCcCEEEechhhhc
Confidence            3555555566665554332 357899999999986

>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=95.19  E-value=0.041  Score=40.27  Aligned_cols=74  Identities=11%  Similarity=0.102  Sum_probs=56.3

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      ..++||.|+++.-++.+.+.+++.    +..+..++|+.+..+....+.    +.++++|+|.-      -..++++..+
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~------~~~Gid~~~~   96 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FGRGMDIERV   96 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CSTTCCGGGC
T ss_pred             CCeEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeecccc------ccchhhcccc
Confidence            347999999999999988887765    678889999988776654443    56789999952      2356788888


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||.-+.
T Consensus        97 ~~vi~~~~  104 (168)
T d1t5ia_          97 NIAFNYDM  104 (168)
T ss_dssp             SEEEESSC
T ss_pred             hhhhhhhc
Confidence            88876654

>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=95.18  E-value=0.058  Score=40.67  Aligned_cols=89  Identities=15%  Similarity=0.111  Sum_probs=62.7

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|+|+.-++.+...++..    ++.+..++|+.+..+....+.    +..+|+|+|.      .-..++++.++
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd------~~~~GiD~p~v   99 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV------AFGMGINKPNV   99 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT------TSCTTTCCTTC
T ss_pred             CCCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc------hhhhccCCCCC
Confidence            447999999999999999887765    678889999987765544332    5678999996      23357888999


Q ss_pred             cEEEechhhHhhccccHHHHHHHHHhC
Q 022383          177 KLLVLDESDEMLSRGFKDQIYDVYRYL  203 (298)
Q Consensus       177 ~~vViDE~h~~~~~~~~~~i~~i~~~~  203 (298)
                      ++||.=+.    .......+..+-+--
T Consensus       100 ~~VI~~~~----P~~~~~y~qr~GR~g  122 (200)
T d1oywa3         100 RFVVHFDI----PRNIESYYQETGRAG  122 (200)
T ss_dssp             CEEEESSC----CSSHHHHHHHHTTSC
T ss_pred             CEEEECCC----ccchHHHHHHhhhhh
Confidence            99874433    233344444444433

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

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: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.14  E-value=0.072  Score=38.34  Aligned_cols=138  Identities=15%  Similarity=0.179  Sum_probs=74.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCch-HHHHHHhhcC
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSV-GEDIRKLEHG  151 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  151 (298)
                      +.|-...|-|||.|++--++..+..   +.+|+++-=.+--...=..   .+....++.......+... ......... 
T Consensus         5 i~vytG~GKGKTTAAlG~alRA~G~---G~rV~ivQFlKg~~~~ge~---~~~~~~~~~~~~~~~~~~~~~~~~e~~~~-   77 (157)
T d1g5ta_           5 IIVFTGNGKGKTTAAFGTAARAVGH---GKNVGVVQFIKGTWPNGER---NLLEPHGVEFQVMATGFTWETQNREADTA-   77 (157)
T ss_dssp             EEEEESSSSCHHHHHHHHHHHHHHT---TCCEEEEESSCCSSCCHHH---HHHGGGTCEEEECCTTCCCCGGGHHHHHH-
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHhcC---CCEEEEEEEecCCcccchh---hhhcccCcEEEEecCCCcccCCChHHHHH-
Confidence            5566779999999988888887765   4567766533211100001   1111223333222111110 000000000 


Q ss_pred             CcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhcccc--HHHHHHHHHhCCCCccEEEEEeeCchhHHHHH
Q 022383          152 VHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGF--KDQIYDVYRYLPPDLQVVLISATLPHEILEMT  224 (298)
Q Consensus       152 ~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~--~~~i~~i~~~~~~~~~~v~~SAT~~~~~~~~~  224 (298)
                            ..+......+ ..+.-..+++||+||+-.....++  ...+..+++..|....+|+.--..|+++.+..
T Consensus        78 ------~a~~~~~~a~-~~~~~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~A  145 (157)
T d1g5ta_          78 ------ACMAVWQHGK-RMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  145 (157)
T ss_dssp             ------HHHHHHHHHH-HHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             ------HHHHHHHHHH-HHhhcCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhc
Confidence                  0011111111 223446789999999998877764  56777888888888877776666777766543

>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=95.07  E-value=0.19  Score=36.48  Aligned_cols=108  Identities=13%  Similarity=0.097  Sum_probs=73.1

Q ss_pred             EEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh----
Q 022383           73 VIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL----  148 (298)
Q Consensus        73 ~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  148 (298)
                      ..+..+....|.. ++..++...    .+.++||.|+++.-++.+...++..    ++.+..++|+.+..+....+    
T Consensus        11 ~~v~v~~~~~K~~-~L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~fk   81 (168)
T d2j0sa2          11 FFVAVEREEWKFD-TLCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFR   81 (168)
T ss_dssp             EEEEESSTTHHHH-HHHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEecChHHHHH-HHHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHHh
Confidence            3444455556653 344444443    2348999999999999999888765    57788899998877664443    


Q ss_pred             hcCCcEEEeChHHHHHHHhccCccCCCccEEEechhhHhhccccHHHHHHH
Q 022383          149 EHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDV  199 (298)
Q Consensus       149 ~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i  199 (298)
                      .+..+++|+|-      +-..++++.++++||.=++    .+.....+.++
T Consensus        82 ~g~~~iLv~Td------~~~rGiDi~~v~~VIn~d~----P~~~~~yihR~  122 (168)
T d2j0sa2          82 SGASRVLISTD------VWARGLDVPQVSLIINYDL----PNNRELYIHRI  122 (168)
T ss_dssp             HTSSCEEEECG------GGSSSCCCTTEEEEEESSC----CSSHHHHHHHH
T ss_pred             cCCccEEeccc------hhcccccccCcceEEEecC----CcCHHHHHhhh
Confidence            25679999996      2345889999999886544    23344444444

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=94.98  E-value=0.036  Score=39.29  Aligned_cols=40  Identities=10%  Similarity=0.164  Sum_probs=25.9

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRE  112 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~  112 (298)
                      |.=-++.||..||||.- ++-.+++....  +.+++++-|...
T Consensus         7 G~l~lI~GpMfSGKTte-Li~~~~~~~~~--g~~vl~i~~~~D   46 (141)
T d1xx6a1           7 GWVEVIVGPMYSGKSEE-LIRRIRRAKIA--KQKIQVFKPEID   46 (141)
T ss_dssp             CEEEEEECSTTSSHHHH-HHHHHHHHHHT--TCCEEEEEEC--
T ss_pred             eeEEEEEeccccHHHHH-HHHHHHHhhhc--CCcEEEEEeccc
Confidence            44568899999999965 33344444332  447899988753

>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=94.90  E-value=0.0052  Score=49.19  Aligned_cols=27  Identities=22%  Similarity=0.183  Sum_probs=24.8

Q ss_pred             CCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          271 TITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       271 ~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      +++|+||||+|++.|+.++..|+++|+
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi   61 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGI   61 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCC
Confidence            357999999999999999999999876

>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=94.81  E-value=0.016  Score=48.22  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      .++++.||||+|||..+-
T Consensus        69 ~niLfiGPTGvGKTElAk   86 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMAQ   86 (364)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             cceeeeCCCCccHHHHHH
Confidence            689999999999997653

>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=94.52  E-value=0.067  Score=41.18  Aligned_cols=38  Identities=24%  Similarity=0.370  Sum_probs=26.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      .|.-+++.|++|+|||...+-.+.+....   +..+++++-
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~~---~~~~~~is~   62 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACAN---KERAILFAY   62 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTT---TCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh---ccccceeec
Confidence            34679999999999997655555554433   445677764

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.51  E-value=0.055  Score=37.87  Aligned_cols=39  Identities=10%  Similarity=0.211  Sum_probs=25.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTR  111 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~  111 (298)
                      |.=-++.||..||||.- ++-.++.....  +.+++++-|..
T Consensus         2 G~L~li~GpMfsGKTt~-Li~~~~~~~~~--g~~v~~ikp~~   40 (133)
T d1xbta1           2 GQIQVILGPMFSGKSTE-LMRRVRRFQIA--QYKCLVIKYAK   40 (133)
T ss_dssp             CEEEEEECCTTSCHHHH-HHHHHHHHHTT--TCCEEEEEETT
T ss_pred             cEEEEEEecccCHHHHH-HHHHHHHHHHc--CCcEEEEeccc
Confidence            33457899999999964 44444444333  44688888864

>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=94.43  E-value=0.017  Score=42.38  Aligned_cols=27  Identities=26%  Similarity=0.464  Sum_probs=19.7

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccC
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTS   98 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~   98 (298)
                      |++++.||+|+|||.. +..++..+...
T Consensus         2 k~v~ItG~~GtGKTtl-~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTL-IHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHH-HHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHH-HHHHHHHHHHC
Confidence            6899999999999963 34455555443

>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=94.41  E-value=0.038  Score=46.57  Aligned_cols=41  Identities=17%  Similarity=0.285  Sum_probs=26.9

Q ss_pred             ChHHHHHHHHHhhcC--CcEEEEcCCCCchHHHHHHHHHHhhcc
Q 022383           56 PSAIQQRAVMPIIKG--RDVIAQAQSGTGKTSMIALTVCQTVDT   97 (298)
Q Consensus        56 ~~~~Q~~~~~~~~~~--~~~li~~pTG~GKT~~~~~~~~~~~~~   97 (298)
                      +.+.|.+.+..+...  .-+++.||||||||.... .+++.+..
T Consensus       142 ~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~-~~l~~~~~  184 (401)
T d1p9ra_         142 MTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLY-AGLQELNS  184 (401)
T ss_dssp             CCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHH-HHHHHHCC
T ss_pred             ccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHH-HHhhhhcC
Confidence            346666666666644  348899999999996533 34555533

>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=94.17  E-value=0.18  Score=35.97  Aligned_cols=74  Identities=12%  Similarity=0.196  Sum_probs=55.2

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhh----cCCcEEEeChHHHHHHHhccCccCCCc
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLE----HGVHVVSGTPGRVCDMIKRKTLRTRAI  176 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~ilV~Tp~~l~~~~~~~~~~~~~l  176 (298)
                      +.++||.|++++-+.++...+++.    ++.+..++++.+..+....+.    +..+++|+|. .+     ..++++..+
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~-~~-----~~Gid~~~v   97 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-VM-----SRGIDVNDL   97 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-TH-----HHHCCCSCC
T ss_pred             CCCEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehh-HH-----hhhhhhccC
Confidence            347999999999999999888765    678888999887766544432    5678999995 22     135778888


Q ss_pred             cEEEechh
Q 022383          177 KLLVLDES  184 (298)
Q Consensus       177 ~~vViDE~  184 (298)
                      ++||.=++
T Consensus        98 ~~Vi~~d~  105 (155)
T d1hv8a2          98 NCVINYHL  105 (155)
T ss_dssp             SEEEESSC
T ss_pred             cEEEEecC
Confidence            88885443

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.90  E-value=0.017  Score=46.93  Aligned_cols=20  Identities=20%  Similarity=0.479  Sum_probs=16.7

Q ss_pred             cCCcEEEEcCCCCchHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~   88 (298)
                      ..++++++||||+|||+.+-
T Consensus        48 ~~~~iLl~GPpG~GKT~lAk   67 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIAR   67 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            35799999999999997543

>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=93.84  E-value=0.013  Score=50.23  Aligned_cols=19  Identities=21%  Similarity=0.503  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      .+|++++||||+|||+.+-
T Consensus        49 ksNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             cccEEEECCCCCCHHHHHH
Confidence            3699999999999997543

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=93.22  E-value=0.23  Score=36.97  Aligned_cols=113  Identities=13%  Similarity=0.196  Sum_probs=59.5

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhccC-----CCCeEEEEEcCcHHHH------HHHHHHHHHhhccC---CceEEEEE
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDTS-----SREVQALILSPTRELA------TQTEKVILAIGDFI---NIQAHACV  136 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~~-----~~~~~~lil~p~~~l~------~q~~~~~~~~~~~~---~~~~~~~~  136 (298)
                      .|++++||.|.|||...--.+ ..+...     -.+ +-+|-.....|+      -+..++++.+....   .-++.++.
T Consensus        44 ~n~lLvG~pGVGKTalv~~LA-~ri~~~~vp~~L~~-~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfI  121 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVEGLA-QRIINGEVPEGLKG-RRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFI  121 (195)
T ss_dssp             CEEEEECCTTSCHHHHHHHHH-HHHHHTCSCGGGTT-CEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEE
T ss_pred             CCeEEEecCCcccHHHHHHHH-HHHHhCCCCHHHcC-ceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEc
Confidence            589999999999995543222 222211     123 335555544444      24555554433211   11233332


Q ss_pred             c-------------CCchHHHHHH-hh-cCCcEE-EeChHHHHHHHhccCccCCCccEEEechhh
Q 022383          137 G-------------GKSVGEDIRK-LE-HGVHVV-SGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (298)
Q Consensus       137 ~-------------~~~~~~~~~~-~~-~~~~il-V~Tp~~l~~~~~~~~~~~~~l~~vViDE~h  185 (298)
                      +             +.+.....+. +. +...+| -+||+.+..++....-..+++..|-++|-+
T Consensus       122 Deih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         122 DELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPS  186 (195)
T ss_dssp             ETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCC
T ss_pred             chHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCC
Confidence            2             1122222221 22 334444 478899888877755555778888888864

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=93.18  E-value=0.1  Score=40.56  Aligned_cols=26  Identities=19%  Similarity=0.245  Sum_probs=18.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHhhcc
Q 022383           71 RDVIAQAQSGTGKTSMIALTVCQTVDT   97 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~~~~~~~~~~   97 (298)
                      .++++.||+|+|||.+. -.+...+..
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l~~   69 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELYKD   69 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHHTT
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHHhc
Confidence            68999999999999654 334444433

>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=92.96  E-value=0.11  Score=44.29  Aligned_cols=55  Identities=20%  Similarity=0.150  Sum_probs=39.1

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCC---------CCeEEEEEcCcHHHHHHHHHHHHHh
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSS---------REVQALILSPTRELATQTEKVILAI  124 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~---------~~~~~lil~p~~~l~~q~~~~~~~~  124 (298)
                      ...++|.|+.|||||.+..--++..+....         ....+|+|+=|+.-+.++.+++.+.
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~   79 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHH
Confidence            356899999999999776555555543211         1136899999998888888877543

>d1yksa2 c.37.1.14 (A:325-623) 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=92.91  E-value=0.11  Score=41.66  Aligned_cols=69  Identities=7%  Similarity=-0.050  Sum_probs=46.4

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEE
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vV  180 (298)
                      +.+++|.||+..-++++.+.+++.    +.++..++|.....+..+...+..+|+|+|.      +-+..+++ ++.+||
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~------~~~~~~~~-~~~~vi  104 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILATD------IAEMGANL-CVERVL  104 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEESS------STTCCTTC-CCSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhc----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEec------hhhhceec-CceEEE
Confidence            347999999999999999998875    5678889998776665554456778999996      22344555 455554

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=92.73  E-value=0.04  Score=39.34  Aligned_cols=19  Identities=21%  Similarity=0.414  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      .|++++.||+|+|||...-
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4789999999999997654

>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=92.71  E-value=0.042  Score=46.56  Aligned_cols=43  Identities=16%  Similarity=0.353  Sum_probs=27.0

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      ...++++|.|+||+|||..+...+.+.+..   +..++|+=|.-++
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l~~li~~~~~~---g~~~iiiD~kge~   90 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLLRELAYTGLLR---GDRMVIVDPNGDM   90 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHHHHHHHHHHHT---TCEEEEEEETTHH
T ss_pred             cccceEEEEeCCCCcHHHHHHHHHHHHHhC---CCCEEEEeCChhH
Confidence            445789999999999997653334333322   3345555555443

>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=92.09  E-value=0.032  Score=43.49  Aligned_cols=55  Identities=11%  Similarity=0.081  Sum_probs=32.2

Q ss_pred             cCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHh-----hcCCcEEEEcCCCCchHHHHH
Q 022383           33 TSFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVMPI-----IKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        33 ~~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~-----~~~~~~li~~pTG~GKT~~~~   88 (298)
                      .+|+++-..+...+.|+++ +..........++..     ...+.+++.||+|+|||.+.-
T Consensus        11 ~~~~dlig~~~~~~~L~~~-l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          11 TNLQQVCGNKGSVMKLKNW-LANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SSGGGCCSCHHHHHHHHHH-HHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHH-HHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHH
Confidence            3689998888888887763 110000011111111     112579999999999996543

>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=91.90  E-value=0.27  Score=41.12  Aligned_cols=66  Identities=29%  Similarity=0.359  Sum_probs=45.6

Q ss_pred             CChHHHHHHHHH----hhcCC-cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhc
Q 022383           55 KPSAIQQRAVMP----IIKGR-DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGD  126 (298)
Q Consensus        55 ~~~~~Q~~~~~~----~~~~~-~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~  126 (298)
                      .|+--|-+++..    +.+|+ ...+.|.+||+|++... .++...     +..+|||+|+...|.++++.++.+..
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~-----~rp~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEAL-----GRPALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHhcC
Confidence            344455555554    44554 47889999999996433 122222     22579999999999999999998854

>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=91.88  E-value=0.048  Score=42.02  Aligned_cols=43  Identities=16%  Similarity=0.242  Sum_probs=27.1

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHH-Hhhc---CCcEEEEcCCCCchHHHHH
Q 022383           34 SFDAMGIKDDLLRGIYQYGFEKPSAIQQRAVM-PIIK---GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        34 ~~~~l~l~~~i~~~l~~~~~~~~~~~Q~~~~~-~~~~---~~~~li~~pTG~GKT~~~~   88 (298)
                      +|+++--.+.+.+.|+..            +. ....   ..++++.||+|+|||..+-
T Consensus         7 ~~~divGqe~~~~~l~~~------------i~~~~~~~~~~~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2           7 SLDEFIGQENVKKKLSLA------------LEAAKMRGEVLDHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             SGGGCCSCHHHHHHHHHH------------HHHHHHHTCCCCCEEEESSTTSSHHHHHH
T ss_pred             cHHHcCChHHHHHHHHHH------------HHHHHhcCCCCCeEEEECCCCCcHHHHHH
Confidence            677775566665555432            11 1111   2579999999999997543

>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=91.25  E-value=0.063  Score=41.40  Aligned_cols=18  Identities=22%  Similarity=0.420  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      +++++.||+|+|||..+-
T Consensus        36 ~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            589999999999996543

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=90.48  E-value=0.078  Score=41.42  Aligned_cols=17  Identities=35%  Similarity=0.526  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      +.+++.||+|+|||..+
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            35999999999999654

>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=90.39  E-value=0.063  Score=37.94  Aligned_cols=15  Identities=20%  Similarity=0.428  Sum_probs=12.8

Q ss_pred             cEEEEcCCCCchHHH
Q 022383           72 DVIAQAQSGTGKTSM   86 (298)
Q Consensus        72 ~~li~~pTG~GKT~~   86 (298)
                      -++++||+|||||..
T Consensus         4 lIii~G~pGsGKTTl   18 (152)
T d1ly1a_           4 IILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            368899999999964

>d1wp9a2 c.37.1.19 (A:201-486) 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=90.20  E-value=0.17  Score=40.06  Aligned_cols=39  Identities=18%  Similarity=0.166  Sum_probs=31.3

Q ss_pred             hHHHHHHHH----hhCCCCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          259 KFDTLCDLY----DTLTITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       259 k~~~l~~ll----~~~~~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      |...+.+++    ......++||||+++..++.+++.|.+.|+
T Consensus       144 K~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~  186 (286)
T d1wp9a2         144 KMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGI  186 (286)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCC
Confidence            666555554    456677999999999999999999988765

>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=89.97  E-value=0.054  Score=39.23  Aligned_cols=19  Identities=21%  Similarity=0.532  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .|+-+++.||+|||||...
T Consensus         3 ~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4677899999999999753

>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=89.94  E-value=0.27  Score=34.32  Aligned_cols=66  Identities=18%  Similarity=0.197  Sum_probs=49.5

Q ss_pred             CeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHhhcCCcEEEeChHHHHHHHhccCccCCCccEEE
Q 022383          101 EVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKLEHGVHVVSGTPGRVCDMIKRKTLRTRAIKLLV  180 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilV~Tp~~l~~~~~~~~~~~~~l~~vV  180 (298)
                      +.++||.|+|+.-|+++.+.+++.    ++++..++++....+.   ..+..+++|+|.     .+ ...++ .+++.||
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~---~~~~~~vlvaTd-----~~-~~GiD-~~v~~Vi  100 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVI---PTNGDVVVVATD-----AL-MTGFT-GDFDSVI  100 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCC---TTSSCEEEEESS-----SS-CSSSC-CCBSEEE
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhh---hhhhcceeehhH-----HH-Hhccc-cccceEE
Confidence            347899999999999999998876    6888889988765432   235679999995     22 23466 5777775

>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=89.86  E-value=0.08  Score=38.21  Aligned_cols=18  Identities=44%  Similarity=0.732  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      +.++++.||+|+|||...
T Consensus         5 ~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           5 GINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHH
Confidence            457999999999999754

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=89.86  E-value=0.2  Score=39.45  Aligned_cols=42  Identities=19%  Similarity=0.257  Sum_probs=27.7

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      .|+-+.+.+|.|+|||...+..+.+....   +..++||---..+
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q~~---g~~~vyIDtE~~~  100 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQAA---GGVAAFIDAEHAL  100 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHHHT---TCEEEEEESSCCC
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHhcC---CCEEEEEECCccC
Confidence            45789999999999997655544443332   4467776544433

>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=89.83  E-value=0.18  Score=37.79  Aligned_cols=34  Identities=9%  Similarity=-0.004  Sum_probs=26.5

Q ss_pred             HHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhh
Q 022383          260 FDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIR  295 (298)
Q Consensus       260 ~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~  295 (298)
                      .+.+.+.++.  ++++||||+|++.|+.+|..|...
T Consensus        30 ~~l~~~~i~~--~~~~LVF~~sRk~~~~~A~~L~~~   63 (201)
T d2p6ra4          30 EELVEECVAE--NGGVLVFESTRRGAEKTAVKLSAI   63 (201)
T ss_dssp             HHHHHHHHHT--TCCEEEECSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCcEEEEeCCHHHHHHHHHHHHHH
Confidence            4455555554  479999999999999999988653

>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=89.62  E-value=0.06  Score=39.26  Aligned_cols=16  Identities=19%  Similarity=0.368  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSM   86 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~   86 (298)
                      |.+++.||+|+|||..
T Consensus         8 K~I~i~G~~GsGKTTl   23 (192)
T d1lw7a2           8 KTVAILGGESSGKSVL   23 (192)
T ss_dssp             EEEEEECCTTSHHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            6799999999999964

>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=89.52  E-value=0.078  Score=38.09  Aligned_cols=17  Identities=24%  Similarity=0.391  Sum_probs=14.0

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      +-+++.||+|+|||..+
T Consensus         3 klI~i~G~~GsGKTTva   19 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            34789999999999754

>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=89.15  E-value=0.12  Score=37.12  Aligned_cols=17  Identities=24%  Similarity=0.503  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      .+++++||.|||||...
T Consensus         5 ~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46899999999999644

>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=88.91  E-value=0.14  Score=36.80  Aligned_cols=18  Identities=17%  Similarity=0.477  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      |+++++|+.|+|||...-
T Consensus         1 k~I~liG~~GsGKsTi~k   18 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLAR   18 (161)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            578999999999997644

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.72  E-value=0.018  Score=45.64  Aligned_cols=18  Identities=28%  Similarity=0.457  Sum_probs=15.4

Q ss_pred             cCCcEEEEcCCCCchHHH
Q 022383           69 KGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~   86 (298)
                      ..+.+++.||+|+|||..
T Consensus        40 ~~~giLL~Gp~GtGKT~l   57 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLL   57 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHH
T ss_pred             CCCeEEEECCCCCcchhH
Confidence            347899999999999964

>d2fwra1 c.37.1.19 (A:257-456) 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=88.60  E-value=0.11  Score=38.83  Aligned_cols=39  Identities=18%  Similarity=0.233  Sum_probs=33.9

Q ss_pred             chHHHHHHHHhhCCCCcEEEEecchhhHHHHHHHHhhhc
Q 022383          258 WKFDTLCDLYDTLTITQAVIFCNTKRKIYYSVFYFWIRW  296 (298)
Q Consensus       258 ~k~~~l~~ll~~~~~~k~lIf~~s~~~~~~l~~~L~~~~  296 (298)
                      .|+..+..+++...+.++||||++...++.+++.|...+
T Consensus        79 ~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~~~~  117 (200)
T d2fwra1          79 NKIRKLREILERHRKDKIIIFTRHNELVYRISKVFLIPA  117 (200)
T ss_dssp             HHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTTCCB
T ss_pred             HHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcCcce
Confidence            388899999999888899999999999999998875443

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

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: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=88.06  E-value=0.34  Score=38.02  Aligned_cols=41  Identities=20%  Similarity=0.213  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSPTREL  113 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l  113 (298)
                      |+-+.+.+|.|+|||...+..+.+....   +..++|+---..+
T Consensus        57 g~itei~G~~~sGKT~l~l~~~~~aqk~---g~~v~yiDtE~~~   97 (268)
T d1xp8a1          57 GRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEHAL   97 (268)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCC
T ss_pred             ceEEEEecCCccchHHHHHHHHHHHHhC---CCEEEEEECCccC
Confidence            4678999999999997554444333322   3467777644333

>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=88.01  E-value=0.088  Score=38.08  Aligned_cols=20  Identities=15%  Similarity=0.320  Sum_probs=16.5

Q ss_pred             hcCCcEEEEcCCCCchHHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~   87 (298)
                      .+|.-++++|++|+|||...
T Consensus         4 ~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            45667889999999999764

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=87.72  E-value=0.69  Score=35.64  Aligned_cols=40  Identities=18%  Similarity=0.221  Sum_probs=25.6

Q ss_pred             hcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           68 IKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      ..+..+++.|++|+|||..+-  .++........+.+.+-|.
T Consensus        21 ~~~~pvlI~Ge~GtGK~~~A~--~ih~~s~~~~~~~~~~~~~   60 (247)
T d1ny5a2          21 CAECPVLITGESGVGKEVVAR--LIHKLSDRSKEPFVALNVA   60 (247)
T ss_dssp             TCCSCEEEECSTTSSHHHHHH--HHHHHSTTTTSCEEEEETT
T ss_pred             CCCCCEEEECCCCcCHHHHHH--HHHHhcCCcccccccchhh
Confidence            356789999999999996543  3444444444444555443

>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=87.62  E-value=0.26  Score=38.54  Aligned_cols=41  Identities=15%  Similarity=0.125  Sum_probs=26.7

Q ss_pred             hhcCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      +..|.=+++.|+||+|||...+-.+.+....  .+.+++|++.
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~--~g~~v~~~s~   72 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTA--MGKKVGLAML   72 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHHHHHHHHHHHT--SCCCEEEEES
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHhhhhh--cccceeEeee
Confidence            4567788999999999995444334333222  2446788774

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.42  E-value=0.2  Score=38.08  Aligned_cols=41  Identities=15%  Similarity=0.084  Sum_probs=24.7

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhcc---CCCCeEEEEEcC
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDT---SSREVQALILSP  109 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~---~~~~~~~lil~p  109 (298)
                      .|+-+++.||+|+|||...+-.+.+....   ...+..++++.-
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~   76 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDT   76 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEES
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEee
Confidence            45789999999999996544333332211   122446676653

>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=87.26  E-value=0.15  Score=37.60  Aligned_cols=16  Identities=38%  Similarity=0.767  Sum_probs=14.0

Q ss_pred             CcEEEEcCCCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSM   86 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~   86 (298)
                      |.++++||+|+|||..
T Consensus         2 rpIvl~GpsG~GK~tl   17 (186)
T d1gkya_           2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5689999999999963

>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=87.17  E-value=0.27  Score=34.93  Aligned_cols=34  Identities=21%  Similarity=0.241  Sum_probs=19.8

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEc
Q 022383           72 DVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILS  108 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~  108 (298)
                      -+.++|+.|||||.- +-.++..+...  +.++.++.
T Consensus         4 vi~itG~~GSGKTTL-~~~L~~~l~~~--g~~v~v~~   37 (170)
T d1np6a_           4 LLAFAAWSGTGKTTL-LKKLIPALCAR--GIRPGLIK   37 (170)
T ss_dssp             EEEEECCTTSCHHHH-HHHHHHHHHHT--TCCEEEEE
T ss_pred             EEEEEcCCCCCHHHH-HHHHHHHHHHC--CCeEEEec
Confidence            367899999999952 33343433332  33444444

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=87.00  E-value=0.17  Score=36.37  Aligned_cols=18  Identities=28%  Similarity=0.505  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~   87 (298)
                      .+-+++.|++|||||...
T Consensus         3 ~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            466889999999999654

>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=86.66  E-value=0.14  Score=36.75  Aligned_cols=19  Identities=21%  Similarity=0.331  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      ++-++++||+|||||...-
T Consensus         6 ~~iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3457889999999996543

>d1gm5a4 c.37.1.19 (A:550-755) 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=86.22  E-value=0.046  Score=41.42  Aligned_cols=81  Identities=15%  Similarity=0.175  Sum_probs=50.1

Q ss_pred             CeEEEEEcCcHHHHHH-----HHHHHHHhhcc--CCceEEEEEcCCchHHHHH---Hh-hcCCcEEEeChHHHHHHHhcc
Q 022383          101 EVQALILSPTRELATQ-----TEKVILAIGDF--INIQAHACVGGKSVGEDIR---KL-EHGVHVVSGTPGRVCDMIKRK  169 (298)
Q Consensus       101 ~~~~lil~p~~~l~~q-----~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~---~~-~~~~~ilV~Tp~~l~~~~~~~  169 (298)
                      +.++.||||..+-.+.     ..+....+.+.  .+.++..+||..+..+...   .. .+..+|+|||.      +-+.
T Consensus        29 g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTt------ViE~  102 (206)
T d1gm5a4          29 GGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTT------VIEV  102 (206)
T ss_dssp             SCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSS------CCCS
T ss_pred             CCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEeh------hhhc
Confidence            5588899998754332     22233333322  2667888999866544332   33 35689999995      2345


Q ss_pred             CccCCCccEEEechhhHh
Q 022383          170 TLRTRAIKLLVLDESDEM  187 (298)
Q Consensus       170 ~~~~~~l~~vViDE~h~~  187 (298)
                      +++..+..++|+.+++.+
T Consensus       103 GIDip~a~~iii~~a~~f  120 (206)
T d1gm5a4         103 GIDVPRANVMVIENPERF  120 (206)
T ss_dssp             CSCCTTCCEEEBCSCSSS
T ss_pred             cccccCCcEEEEEccCCc
Confidence            789999999999999864

>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=86.03  E-value=0.24  Score=36.73  Aligned_cols=26  Identities=19%  Similarity=0.101  Sum_probs=19.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQT   94 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~   94 (298)
                      .|+-+++.||+|+|||...+-.+.+.
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            35789999999999996554444443

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=85.82  E-value=0.46  Score=34.12  Aligned_cols=17  Identities=24%  Similarity=0.392  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCCchHHHH
Q 022383           71 RDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~   87 (298)
                      |-+++.|++|+|||...
T Consensus         2 kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            56889999999999643

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=85.54  E-value=0.21  Score=36.56  Aligned_cols=17  Identities=35%  Similarity=0.614  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCCchHHH
Q 022383           70 GRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~   86 (298)
                      |+-++++||+|+|||..
T Consensus         2 G~iivl~GpsG~GK~tl   18 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTV   18 (182)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            66789999999999964

>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=85.46  E-value=0.22  Score=37.43  Aligned_cols=18  Identities=44%  Similarity=0.648  Sum_probs=15.5

Q ss_pred             cCCcEEEEcCCCCchHHH
Q 022383           69 KGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~   86 (298)
                      +|+-++++||+|+|||..
T Consensus         1 ~G~livi~GPSG~GK~tl   18 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSL   18 (205)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            467789999999999964

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=85.29  E-value=0.29  Score=35.23  Aligned_cols=18  Identities=17%  Similarity=0.252  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      +.+++.|+.|+|||...-
T Consensus         3 ~~Iil~G~~GsGKSTia~   20 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGR   20 (170)
T ss_dssp             CCEEEESCTTSSHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHH
Confidence            578899999999997654

>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=85.05  E-value=0.27  Score=35.37  Aligned_cols=41  Identities=17%  Similarity=0.067  Sum_probs=22.9

Q ss_pred             CCCccEEEechhhHhhccccHHHHHHHHHhCCCCccEEEEEe
Q 022383          173 TRAIKLLVLDESDEMLSRGFKDQIYDVYRYLPPDLQVVLISA  214 (298)
Q Consensus       173 ~~~l~~vViDE~h~~~~~~~~~~i~~i~~~~~~~~~~v~~SA  214 (298)
                      ..+.+++++||++...... ......+.+.+......++++.
T Consensus        97 ~~~~~vlllDE~~~~~~~~-~~~~~~l~~~l~~~~~~il~~~  137 (178)
T d1ye8a1          97 KDRRKVIIIDEIGKMELFS-KKFRDLVRQIMHDPNVNVVATI  137 (178)
T ss_dssp             HCTTCEEEECCCSTTGGGC-HHHHHHHHHHHTCTTSEEEEEC
T ss_pred             hcCCCceeecCCCccchhh-HHHHHHHHHHhccCCCEEEEEE
Confidence            3677999999987653332 3334444444443334455443

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.04  E-value=0.21  Score=36.32  Aligned_cols=15  Identities=33%  Similarity=0.543  Sum_probs=12.9

Q ss_pred             cEEEEcCCCCchHHH
Q 022383           72 DVIAQAQSGTGKTSM   86 (298)
Q Consensus        72 ~~li~~pTG~GKT~~   86 (298)
                      =++++|++|||||..
T Consensus        16 liil~G~pGsGKST~   30 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTF   30 (172)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999964

>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=85.04  E-value=0.23  Score=36.73  Aligned_cols=16  Identities=38%  Similarity=0.725  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCCchHHH
Q 022383           71 RDVIAQAQSGTGKTSM   86 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~   86 (298)
                      |.++++||+|+|||..
T Consensus         1 rpIvl~GPsGsGK~tl   16 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTL   16 (190)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4589999999999964

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=84.98  E-value=4  Score=33.44  Aligned_cols=35  Identities=14%  Similarity=0.242  Sum_probs=24.4

Q ss_pred             CCcEE-EeChHHHHHHHhccCccCCCccEEEechhhH
Q 022383          151 GVHVV-SGTPGRVCDMIKRKTLRTRAIKLLVLDESDE  186 (298)
Q Consensus       151 ~~~il-V~Tp~~l~~~~~~~~~~~~~l~~vViDE~h~  186 (298)
                      ...+| -+||+.+.. +....-..+++..|-|+|-+.
T Consensus       151 ~~~~I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~~  186 (387)
T d1qvra2         151 ELRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPTV  186 (387)
T ss_dssp             CCCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCCH
T ss_pred             CcceeeecCHHHHHH-hcccHHHHHhcccccCCCCcH
Confidence            34544 578888876 454444568889999999765

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=83.80  E-value=0.38  Score=35.21  Aligned_cols=19  Identities=21%  Similarity=0.375  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      |-.+++.||+|||||...-
T Consensus         3 ~~riil~G~pGSGKsT~a~   21 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAP   21 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHH
Confidence            4567889999999997654

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.79  E-value=0.28  Score=35.82  Aligned_cols=17  Identities=12%  Similarity=0.431  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCCchHHH
Q 022383           70 GRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~   86 (298)
                      .+-++++||+|+||+..
T Consensus         3 ~k~ivl~Gpsg~GK~tl   19 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHI   19 (178)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CCcEEEECCCCCCHHHH
Confidence            46789999999999964

>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=83.73  E-value=0.32  Score=36.66  Aligned_cols=39  Identities=21%  Similarity=0.264  Sum_probs=24.1

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccCCCCeEEEEEcC
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTSSREVQALILSP  109 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p  109 (298)
                      .|.-+++.|++|+|||.-.+-.+.+.....  +..++++..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~--~~~~~~~s~   63 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEF--DEPGVFVTF   63 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH--CCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCCcccccc
Confidence            457899999999999955433333332222  224666654

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=83.72  E-value=0.61  Score=35.49  Aligned_cols=40  Identities=10%  Similarity=0.024  Sum_probs=24.4

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhcc---CCCCeEEEEEc
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDT---SSREVQALILS  108 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~---~~~~~~~lil~  108 (298)
                      .|+-++|.||+|+|||.-.+-.+.+....   ...+..++++.
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~   77 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID   77 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEe
Confidence            34679999999999996555444443321   12234555554

>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=83.68  E-value=0.15  Score=39.82  Aligned_cols=15  Identities=27%  Similarity=0.366  Sum_probs=12.1

Q ss_pred             EEEEcCCCCchHHHH
Q 022383           73 VIAQAQSGTGKTSMI   87 (298)
Q Consensus        73 ~li~~pTG~GKT~~~   87 (298)
                      +++.||+|+|||...
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            456799999999654

>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=83.51  E-value=0.44  Score=38.39  Aligned_cols=24  Identities=29%  Similarity=0.567  Sum_probs=18.3

Q ss_pred             HHHhhcCCc--EEEEcCCCCchHHHH
Q 022383           64 VMPIIKGRD--VIAQAQSGTGKTSMI   87 (298)
Q Consensus        64 ~~~~~~~~~--~li~~pTG~GKT~~~   87 (298)
                      ++.+++|.+  ++..|+||||||...
T Consensus        68 v~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          68 VKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHcCCCcceeeecccCCCCceec
Confidence            445667876  677799999999763

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=83.21  E-value=0.21  Score=40.50  Aligned_cols=19  Identities=26%  Similarity=0.400  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCCchHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMI   87 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~   87 (298)
                      .+.++++.||+|+|||..+
T Consensus        27 ~~h~vLl~G~pG~GKT~la   45 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAV   45 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCCeEEEECCCCccHHHHH
Confidence            4578999999999999653

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=82.57  E-value=0.38  Score=34.74  Aligned_cols=17  Identities=18%  Similarity=0.389  Sum_probs=14.2

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      .+++.||+|||||....
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAE   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999997654

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.52  E-value=0.15  Score=37.44  Aligned_cols=19  Identities=37%  Similarity=0.457  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 022383           70 GRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        70 ~~~~li~~pTG~GKT~~~~   88 (298)
                      |.-++++|++|||||..+-
T Consensus        19 g~vI~L~G~pGSGKTTiAk   37 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSM   37 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3457788999999997543

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=82.47  E-value=0.59  Score=35.28  Aligned_cols=27  Identities=15%  Similarity=0.121  Sum_probs=20.3

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhh
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTV   95 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~   95 (298)
                      .|.-+++.|++|+|||...+-.+.+..
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            356789999999999976655555543

>d1wp9a2 c.37.1.19 (A:201-486) 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=82.28  E-value=8.9  Score=29.40  Aligned_cols=89  Identities=19%  Similarity=0.239  Sum_probs=57.3

Q ss_pred             CCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchH--------HH---HHHhh-cCCcEEEeChHHHHHHH
Q 022383           99 SREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVG--------ED---IRKLE-HGVHVVSGTPGRVCDMI  166 (298)
Q Consensus        99 ~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~---~~~~~-~~~~ilV~Tp~~l~~~~  166 (298)
                      ..+.++||.|++++-+..+.+.+.+.    ++++..++|.....        ++   ..... +.++|+|+|-      .
T Consensus       159 ~~~~k~iiF~~~~~~~~~~~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~------~  228 (286)
T d1wp9a2         159 KQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS------V  228 (286)
T ss_dssp             CTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG------G
T ss_pred             CCCCcEEEEeCcHHhHHHHHHHHHHc----CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEcc------c
Confidence            34558999999999999999887764    56666666643221        11   22222 4678999994      1


Q ss_pred             hccCccCCCccEEEechhhHhhccccHHHHHHHHH
Q 022383          167 KRKTLRTRAIKLLVLDESDEMLSRGFKDQIYDVYR  201 (298)
Q Consensus       167 ~~~~~~~~~l~~vViDE~h~~~~~~~~~~i~~i~~  201 (298)
                      -..++++..+++||.=+.+    ++....++.+-+
T Consensus       229 ~~~Gld~~~~~~Vi~~d~~----~~~~~~~Qr~GR  259 (286)
T d1wp9a2         229 GEEGLDVPEVDLVVFYEPV----PSAIRSIQRRGR  259 (286)
T ss_dssp             GGGGGGSTTCCEEEESSCC----HHHHHHHHHHTT
T ss_pred             eeccccCCCCCEEEEeCCC----CCHHHHHHHHHh
Confidence            3347889999999875554    333444444444

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=82.20  E-value=0.29  Score=39.43  Aligned_cols=17  Identities=24%  Similarity=0.450  Sum_probs=14.5

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      +++++||||+|||..+-
T Consensus        54 ~~lf~Gp~GvGKT~lak   70 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTV   70 (315)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCcchhHHHHH
Confidence            68999999999996544

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=81.99  E-value=0.72  Score=37.76  Aligned_cols=34  Identities=15%  Similarity=0.187  Sum_probs=21.4

Q ss_pred             CCCChHHHHHHHHHhhc----CCcEEEEcCCCCchHHH
Q 022383           53 FEKPSAIQQRAVMPIIK----GRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        53 ~~~~~~~Q~~~~~~~~~----~~~~li~~pTG~GKT~~   86 (298)
                      +......-.+++..++.    ++.+++.||+|+|||..
T Consensus       133 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~  170 (362)
T d1svma_         133 LPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTL  170 (362)
T ss_dssp             STTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHH
T ss_pred             ccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHH
Confidence            44333333344444443    36799999999999954

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=81.90  E-value=0.48  Score=34.78  Aligned_cols=22  Identities=18%  Similarity=0.335  Sum_probs=17.5

Q ss_pred             hhcCCcEEEEcCCCCchHHHHH
Q 022383           67 IIKGRDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        67 ~~~~~~~li~~pTG~GKT~~~~   88 (298)
                      +.+.+-+++.||+|||||....
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~a~   26 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQCE   26 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHH
Confidence            4456778999999999997544

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=81.64  E-value=0.44  Score=34.56  Aligned_cols=17  Identities=18%  Similarity=0.409  Sum_probs=14.0

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      .+++.||+|||||....
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQAD   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37899999999997654

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=81.43  E-value=0.41  Score=34.98  Aligned_cols=17  Identities=18%  Similarity=0.327  Sum_probs=14.1

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      .+++.||+|||||....
T Consensus         5 ~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           5 KVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            48899999999997544

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.28  E-value=0.46  Score=34.38  Aligned_cols=17  Identities=24%  Similarity=0.384  Sum_probs=14.2

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      ++++.||.|||||...-
T Consensus         2 ~I~i~G~pGsGKsT~a~   18 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAV   18 (181)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999997654

>d1yksa2 c.37.1.14 (A:325-623) 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=81.14  E-value=0.55  Score=37.39  Aligned_cols=26  Identities=8%  Similarity=-0.157  Sum_probs=24.0

Q ss_pred             CCcEEEEecchhhHHHHHHHHhhhcC
Q 022383          272 ITQAVIFCNTKRKIYYSVFYFWIRWI  297 (298)
Q Consensus       272 ~~k~lIf~~s~~~~~~l~~~L~~~~~  297 (298)
                      .++++|||+++.+++.+++.|++.|.
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~   61 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGK   61 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCC
Confidence            47999999999999999999998875

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=81.08  E-value=0.43  Score=34.99  Aligned_cols=17  Identities=29%  Similarity=0.364  Sum_probs=13.9

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      -+++.||+|||||....
T Consensus         8 iI~i~G~pGSGKsT~a~   24 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCA   24 (194)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999997543

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=80.74  E-value=0.45  Score=34.41  Aligned_cols=17  Identities=18%  Similarity=0.202  Sum_probs=14.0

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      .+++.||+|||||...-
T Consensus         2 ~I~i~G~pGSGKsT~~~   18 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQ   18 (179)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999997653

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.68  E-value=0.47  Score=36.17  Aligned_cols=48  Identities=10%  Similarity=-0.002  Sum_probs=28.3

Q ss_pred             cCCcEEEEcCCCCchHHHHHHHHHHhhccC---CCCeEEEEEcCcHHHHHH
Q 022383           69 KGRDVIAQAQSGTGKTSMIALTVCQTVDTS---SREVQALILSPTRELATQ  116 (298)
Q Consensus        69 ~~~~~li~~pTG~GKT~~~~~~~~~~~~~~---~~~~~~lil~p~~~l~~q  116 (298)
                      .|+-+++.||+|+|||...+-.+.+.....   .....++++.........
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH
Confidence            456799999999999966554444433221   123356666654443333

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.62  E-value=0.5  Score=34.71  Aligned_cols=17  Identities=18%  Similarity=0.294  Sum_probs=13.7

Q ss_pred             cEEEEcCCCCchHHHHH
Q 022383           72 DVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        72 ~~li~~pTG~GKT~~~~   88 (298)
                      -+++.||+|||||...-
T Consensus        10 iI~i~GppGSGKsT~a~   26 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCE   26 (196)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47888999999996544

>d1z5za1 c.37.1.19 (A:663-906) 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=80.54  E-value=6.4  Score=29.53  Aligned_cols=97  Identities=9%  Similarity=0.030  Sum_probs=60.6

Q ss_pred             CCCCchHHHHHHHHHHhhccCCCCeEEEEEcCcHHHHHHHHHHHHHhhccCCceEEEEEcCCchHHHHHHh---h--cCC
Q 022383           78 QSGTGKTSMIALTVCQTVDTSSREVQALILSPTRELATQTEKVILAIGDFINIQAHACVGGKSVGEDIRKL---E--HGV  152 (298)
Q Consensus        78 pTG~GKT~~~~~~~~~~~~~~~~~~~~lil~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~--~~~  152 (298)
                      ...|||... +.-++..+...  +.++||.|....-.+-+...+.+.   .+..+..++|+.+..+....+   .  .++
T Consensus        65 ~~~S~K~~~-l~~~l~~~~~~--g~kviIFs~~~~~~~~l~~~l~~~---~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~  138 (244)
T d1z5za1          65 VRRSGKMIR-TMEIIEEALDE--GDKIAIFTQFVDMGKIIRNIIEKE---LNTEVPFLYGELSKKERDDIISKFQNNPSV  138 (244)
T ss_dssp             STTCHHHHH-HHHHHHHHHHT--TCCEEEEESCHHHHHHHHHHHHHH---HCSCCCEECTTSCHHHHHHHHHHHHHCTTC
T ss_pred             hhhhhHHHH-HHHHHHhhccc--ccceEEEeeceehHHHHHHHHHhh---ccceEEEEecccchhccchhhhhhhccccc
Confidence            456788754 34444443332  457999999998777766666543   256667788988766543332   2  346


Q ss_pred             cEEEeChHHHHHHHhccCccCCCccEEEechhh
Q 022383          153 HVVSGTPGRVCDMIKRKTLRTRAIKLLVLDESD  185 (298)
Q Consensus       153 ~ilV~Tp~~l~~~~~~~~~~~~~l~~vViDE~h  185 (298)
                      .++++|+..     -..++++...+.+|+=+.+
T Consensus       139 ~vll~~~~~-----~g~Glnl~~a~~vi~~~~~  166 (244)
T d1z5za1         139 KFIVLSVKA-----GGFGINLTSANRVIHFDRW  166 (244)
T ss_dssp             CEEEEECCT-----TCCCCCCTTCSEEEECSCC
T ss_pred             hhccccccc-----cccccccchhhhhhhcCch
Confidence            788888733     2235677777777765543

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=80.54  E-value=0.57  Score=33.36  Aligned_cols=18  Identities=17%  Similarity=0.329  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 022383           71 RDVIAQAQSGTGKTSMIA   88 (298)
Q Consensus        71 ~~~li~~pTG~GKT~~~~   88 (298)
                      ..+++.|+.|+|||...-
T Consensus         2 p~IvliG~~G~GKSTig~   19 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGR   19 (165)
T ss_dssp             CSEEEECSTTSSHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            357888999999997654

>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=80.46  E-value=0.61  Score=36.16  Aligned_cols=63  Identities=14%  Similarity=0.177  Sum_probs=36.6

Q ss_pred             HHHhhcCCcEEEEcCCCCchHHHHHHHHHHhhcc-------CCCCeEEEEEcCcHHHHHHHHHHHHHhhcc
Q 022383           64 VMPIIKGRDVIAQAQSGTGKTSMIALTVCQTVDT-------SSREVQALILSPTRELATQTEKVILAIGDF  127 (298)
Q Consensus        64 ~~~~~~~~~~li~~pTG~GKT~~~~~~~~~~~~~-------~~~~~~~lil~p~~~l~~q~~~~~~~~~~~  127 (298)
                      ++-+..|.-+++.|++|+|||...+-.+.+....       ...+.+++|+.- ..-..++..++..+...
T Consensus        23 i~G~~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~-E~~~~~~~~Rl~~~~~~   92 (274)
T d1nlfa_          23 LPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPA-EDPPTAIHHRLHALGAH   92 (274)
T ss_dssp             ETTEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEES-SSCHHHHHHHHHHHHTT
T ss_pred             hCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEec-cchHHHHHHHHHHHhhc
Confidence            4445567889999999999996544433332111       112335676653 33345666666666543

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=80.18  E-value=0.4  Score=35.73  Aligned_cols=19  Identities=37%  Similarity=0.489  Sum_probs=16.3

Q ss_pred             hcCCcEEEEcCCCCchHHH
Q 022383           68 IKGRDVIAQAQSGTGKTSM   86 (298)
Q Consensus        68 ~~~~~~li~~pTG~GKT~~   86 (298)
                      .+|+-+.+.||.|+|||..
T Consensus        25 ~~Gei~~l~G~NGsGKSTL   43 (200)
T d1sgwa_          25 EKGNVVNFHGPNGIGKTTL   43 (200)
T ss_dssp             ETTCCEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCChHHHH
Confidence            3678899999999999964